From 789b4227a059e1b8776f978495b222de91008d98 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 26 Aug 2023 20:29:21 +0200 Subject: [PATCH 01/64] Updated BridgeDb Datasources from https://github.com/bridgedb/datasources/pull/43 --- org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv | 4 ++-- .../src/main/resources/org/bridgedb/bio/datasources.tsv | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index d3c029c9f..d8c7d7b47 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -123,7 +123,7 @@ SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/prote SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein -SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids swisslipid metabolite +SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene @@ -133,7 +133,7 @@ TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway -Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein +UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index d3c029c9f..d8c7d7b47 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -123,7 +123,7 @@ SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/prote SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein -SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids swisslipid metabolite +SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene @@ -133,7 +133,7 @@ TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway -Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein +UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene From e9665b7e276134e8f4e4b1e57743946e36fc2993 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 8 Oct 2023 21:49:45 +0200 Subject: [PATCH 02/64] Match the new BridgeDb Datasources --- org.bridgedb.rdf/resources/BioDataSource.ttl | 2 +- org.bridgedb.rdf/resources/DataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 996f91d0c..33127c1de 100644 --- a/org.bridgedb.rdf/resources/BioDataSource.ttl +++ b/org.bridgedb.rdf/resources/BioDataSource.ttl @@ -1263,7 +1263,7 @@ bridgeDB:DataSource_Uniprot_SwissProt a bridgeDB:DataSource ; dcterms:alternative "UniProtKB/Swiss-Prot" . bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ; - bridgeDB:fullName "Uniprot-TrEMBL" ; + bridgeDB:fullName "UniProtKB" ; bridgeDB:systemCode "S" ; bridgeDB:mainUrl "http://www.uniprot.org/" ; bridgeDB:idExample "P62158" ; diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index a786321d8..9b881fdf5 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -1135,7 +1135,7 @@ bridgeDB:DataSource_Uniprot_Enzyme a bridgeDB:DataSource ; bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ; - bridgeDB:fullName "Uniprot-TrEMBL" ; + bridgeDB:fullName "UniProtKB" ; bridgeDB:alternativeFullName "Uniprot/TrEMBL" ; bridgeDB:systemCode "S" ; bridgeDB:mainUrl "http://www.uniprot.org/" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index ab3092e11..eb1ca8d2a 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -6202,7 +6202,7 @@ bridgeDB:DataSource_Uniprot_SwissProt a bridgeDB:DataSource ; bridgeDB:hasUriPattern . bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ; - bridgeDB:fullName "Uniprot-TrEMBL" ; + bridgeDB:fullName "UniProtKB" ; bridgeDB:systemCode "S" ; bridgeDB:mainUrl "http://www.uniprot.org/" ; bridgeDB:idExample "P62158" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index 3b35ab01a..ac92510e3 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -540,7 +540,7 @@ Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.gr Uniprot Enzyme Enzyme http://purl.uniprot.org/enzyme/$id unknown 1 UniProt Isoform uniprot.isoform http://www.uniprot.org/uniprot/$id Q5BJF6-3 unknown 1 urn:miriam:uniprot.isoform ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$ Uniprot-SwissProt Sp http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id CALM_HUMAN protein 1 ^[A-Z0-9]+_[A-Z]+$ UniProtKB/Swiss-Prot -Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ UniProtKB/TrEMBL +UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ UniProtKB/TrEMBL UniSTS unists http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$id 456789 unknown 1 urn:miriam:unists ^\d+$ Unit Ontology unit http://purl.bioontology.org/ontology/UO/$id UO:0000080 unknown 1 urn:miriam:unit ^UO:\d{7}? Unite unite http://unite.ut.ee/bl_forw.php?nimi=$id UDB000691 unknown 1 urn:miriam:unite ^UDB\d{6}$ From d78f7e6382f9e2789c1c217442d8de8f5e7ca8d0 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 8 Oct 2023 21:55:59 +0200 Subject: [PATCH 03/64] Implemented the expectations as tests --- .../java/org/bridgedb/bio/UniProtKBTest.java | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java new file mode 100644 index 000000000..67cec09d7 --- /dev/null +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java @@ -0,0 +1,58 @@ +/* Copyright (c) 2023 Egon Willighagen + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and limitations under the License. + */ +package org.bridgedb.bio; + +import static org.junit.Assert.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import org.bridgedb.DataSource; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class UniProtKBTest { + + @BeforeAll + public static void setUpSources() { + DataSourceTxt.init(); + } + + @Test + public void getBySystemCode() { + DataSource ds1 = DataSource.getExistingBySystemCode("S"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } + + @Test + public void getByFullName_TrEMBL() { + DataSource ds1 = DataSource.getExistingByFullName("Uniprot-TrEMBL"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } + + @Test + public void getByFullName_SwissProt() { + DataSource ds1 = DataSource.getExistingByFullName("Uniprot-SwissProt"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } + + @Test + public void getByFullName_UniProtKB() { + DataSource ds1 = DataSource.getExistingByFullName("UniProtKB"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } +} From 3d602daa9275e88fb2f78ae04c9ceb038d171337 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 8 Oct 2023 21:56:41 +0200 Subject: [PATCH 04/64] Added the backwards compatability --- org.bridgedb/src/main/java/org/bridgedb/DataSource.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java index 355c6cc06..2c8712d5a 100644 --- a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java +++ b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java @@ -807,6 +807,10 @@ public static DataSource getExistingByFullName(String fullName) { if (byFullName.containsKey(fullName)){ return byFullName.get(fullName); + // the following lines are added on 2023-10 for backwards compatibility + } else if ("Uniprot-TrEMBL".equals(fullName) || + "Uniprot-SwissProt".equals(fullName)) { + return byFullName.get("UniProtKB"); } throw new IllegalArgumentException ("No DataSource known for " + fullName); } From 729f5e61dfd52eb99c3dad8672d6d5d4ca951a72 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 8 Oct 2023 22:14:33 +0200 Subject: [PATCH 05/64] Removed needless initialization --- .../org/bridgedb/bio/DataSourceTxtTest.java | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java index ca9794406..df989ca7a 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java @@ -14,6 +14,13 @@ */ package org.bridgedb.bio; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNotSame; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.io.BufferedWriter; import java.io.File; import java.io.FileInputStream; @@ -24,14 +31,8 @@ import java.lang.reflect.Method; import java.util.HashSet; import java.util.Set; -import java.util.regex.Pattern; import org.bridgedb.DataSource; -import org.bridgedb.DataSourcePatterns; -import org.junit.BeforeClass; -import org.junit.jupiter.api.BeforeAll; - -import static org.junit.jupiter.api.Assertions.*; /** @@ -40,11 +41,6 @@ */ public class DataSourceTxtTest { - @BeforeAll - public static void setUpSources() { - DataSourceTxt.init(); - } - @org.junit.jupiter.api.Test public void testUniqueSystemCodes() { Set codes = new HashSet(); From 22533214a0bec4a6d97d0fa2ab6bf7fa826892e4 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 5 Nov 2023 12:40:43 +0100 Subject: [PATCH 06/64] Use the global variable --- org.bridgedb.ws.core/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 3dde85a80..f0c8fc790 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -80,7 +80,7 @@ org.junit.platform junit-platform-surefire-provider - 1.2.0 + ${junit-platform-surefire-provider} test From 8feed636c4059cbed5cd615169a92f464d9d3266 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 5 Nov 2023 12:47:28 +0100 Subject: [PATCH 07/64] Bumped the release version --- CITATION.cff | 4 ++-- README.md | 14 +++++++------- org.bridgedb/src/main/resources/version.props | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 76ec07fb0..4bfe1388e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.0.23 -date-released: '2023-08-07' +version: 3.1.0 +date-released: '2023-11-05' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 49786071c..5fced022b 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.23`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.0`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.0.23 + 3.1.0 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.23' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.0' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.0.23' +'org.bridgedb:org.bridgedb.bio:jar:3.1.0' ``` @@ -133,7 +133,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.0.23 +mvn versions:set -DnewVersion=3.1.0 mvn clean deploy ``` @@ -143,7 +143,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.0.23-SNAPSHOT +mvn versions:set -DnewVersion=3.1.1-SNAPSHOT mvn clean deploy ``` diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 645ae3a65..fff58826a 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.0.23 +bridgedb.version=3.1.0 From 3e7aab49e38dbef68185c09cf5dae54836bcc57f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 5 Nov 2023 12:51:41 +0100 Subject: [PATCH 08/64] Release 3.1.0 --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 1e6f5ed1b..2df95159c 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index d46207678..7c89938f5 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 95be40a64..a87896961 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 216267721..475cfddc4 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index b1d6bd0d7..6824871e6 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 8b75100f7..ccec29938 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 40f505e81..8aa5cfba7 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 111270a52..e6e134ebe 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 89bcf8fac..9756a1224 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.0.23 + 3.1.0 compile org.bridgedb org.bridgedb.bio - 3.0.23 + 3.1.0 compile org.bridgedb org.bridgedb.rdb - 3.0.23 + 3.1.0 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 96afc0d73..dfa510219 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index c61438b76..efe2541fe 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index d20732b63..b6287f1f5 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index dea13dc22..674408375 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 635bb5794..67a890ef6 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index ce6767b3b..cc24df3e0 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 50abcd29a..7b6e68550 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index fc54d5fd5..934a95b68 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index e5ab5c25f..4ade2d960 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 910e813f4..a486e30a5 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 60376e71d..b2243e70e 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 4ddcc92e8..c674b05ee 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index fd1978afb..26193f525 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index f0c8fc790..816863fbf 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index a7558a2d8..f1f119ebe 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index abba6a136..9f65fa0de 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.0 diff --git a/pom.xml b/pom.xml index 8f7867726..470a6524a 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.0.23 + 3.1.0 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From f98a0f21d2f389204b5afcf8277fae7b01345d8e Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 5 Nov 2023 13:15:25 +0100 Subject: [PATCH 09/64] Guava minimal version update --- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index efe2541fe..a48cb34e5 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -90,7 +90,7 @@ com.google.guava guava - [32.0.1-jre,) + [32.0.0-jre,) org.apache.derby diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index b6287f1f5..49900d9db 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -90,7 +90,7 @@ com.google.guava guava - [30.0-jre,) + [32.0-jre,) org.apache.derby From f2d2165924a991b16ac39f23fdca183751fcfad9 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 5 Nov 2023 14:41:26 +0100 Subject: [PATCH 10/64] Compile the main branch --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index fe1cbc680..e3b06d4c2 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,9 +2,9 @@ name: build on: push: - branches: [ master ] + branches: [ main ] pull_request: - branches: [ master ] + branches: [ main ] jobs: build: From 107dd906484c1f0f882196dc489311f43369eeeb Mon Sep 17 00:00:00 2001 From: Alexander Pico Date: Wed, 15 Nov 2023 10:47:28 -0800 Subject: [PATCH 11/64] https and 443 for bridgedb webservice --- .../src/org/bridgedb/gui/BridgeRestParameterModel.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java b/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java index 4fea80c82..adad8e088 100644 --- a/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java +++ b/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java @@ -15,8 +15,8 @@ public class BridgeRestParameterModel extends AbstractParameterModel implements { static final int PARAMETER_NUM = 3; - private Object[] metadata = new Object[] {"http://webservice.bridgedb.org", "80", Collections.emptyList()}; - private Object[] values = new Object[] {"http://webservice.bridgedb.org", "80", null}; + private Object[] metadata = new Object[] {"https://webservice.bridgedb.org", "443", Collections.emptyList()}; + private Object[] values = new Object[] {"https://webservice.bridgedb.org", "443", null}; private String[] labels = new String[] {"Base URL", "Port", "Species"}; /** @@ -68,7 +68,7 @@ public String getHelpHtml() "in advance, and no cross-species mapping is possible. Mapping data is derived from " + "Ensembl and HMDB." + "

maintainer:Gladstone Institute / UCSF and BiGCaT / Maastricht University" + - "

more info:http://webservice.bridgedb.org"; + "

more info:https://webservice.bridgedb.org"; } @Override From 3dde020a6e2af693337d2761fa4aac5f4b9f2ca8 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 21 Nov 2023 17:42:31 +0100 Subject: [PATCH 12/64] Use HTTPS by default --- .../src/org/bridgedb/benchmarking/ComparisonScript.java | 2 +- benchmarking/test/org/bridgedb/benchmarking/TestAll.java | 2 +- examples/src/org/bridgedb/examples/ChebiPubchemExample.java | 2 +- examples/src/org/bridgedb/examples/ExHello.java | 2 +- examples/src/org/bridgedb/examples/ExIDSearch.java | 2 +- .../src/org/bridgedb/webservice/bridgerest/BridgeRest.java | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java b/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java index 2744b8743..1c9c7a97b 100644 --- a/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java +++ b/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java @@ -300,7 +300,7 @@ enum Connector PICR ("picr", "idmapper-picr:"), SYNERGIZER_ENSEMBL ("synergizer(ensembl)", "idmapper-synergizer:authority=ensembl&species=Homo sapiens"), - BRIDGEWEBSERVICE ("BridgeWebservice", "idmapper-bridgerest:http://webservice.bridgedb.org/Human"), + BRIDGEWEBSERVICE ("BridgeWebservice", "idmapper-bridgerest:https://webservice.bridgedb.org/Human"), BRIDGEWEBSERVICE_LOCAL ("BridgeWebservice(local)", "idmapper-bridgerest:http://localhost:8183/Human"), BIOMART ("biomart", "idmapper-biomart:http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl"), CRONOS ("cronos", "idmapper-cronos:hsa"), diff --git a/benchmarking/test/org/bridgedb/benchmarking/TestAll.java b/benchmarking/test/org/bridgedb/benchmarking/TestAll.java index 5be513373..f1cc3d2e1 100644 --- a/benchmarking/test/org/bridgedb/benchmarking/TestAll.java +++ b/benchmarking/test/org/bridgedb/benchmarking/TestAll.java @@ -74,7 +74,7 @@ public void testBridgeWebservice() throws IDMapperException, ClassNotFoundExcept Class.forName("org.bridgedb.webservice.bridgerest.BridgeRest"); Xref insr1 = new Xref ("ENSG00000171105", DataSource.getBySystemCode("EnHs")); Xref insr2 = new Xref ("3643", DataSource.getBySystemCode("L")); - basicMapperTest (measure, "bridgerest", "idmapper-bridgerest:http://webservice.bridgedb.org/Human", insr1, insr2); + basicMapperTest (measure, "bridgerest", "idmapper-bridgerest:https://webservice.bridgedb.org/Human", insr1, insr2); } public void testFile() throws IDMapperException, ClassNotFoundException diff --git a/examples/src/org/bridgedb/examples/ChebiPubchemExample.java b/examples/src/org/bridgedb/examples/ChebiPubchemExample.java index eadc6a5df..6b507827e 100644 --- a/examples/src/org/bridgedb/examples/ChebiPubchemExample.java +++ b/examples/src/org/bridgedb/examples/ChebiPubchemExample.java @@ -15,7 +15,7 @@ public static void main (String[] args) throws ClassNotFoundException, IDMapperE // We'll use the BridgeRest webservice in this case, as it does compound mapping fairly well. // We'll use the human database, but it doesn't really matter which species we pick. Class.forName ("org.bridgedb.webservice.bridgerest.BridgeRest"); - IDMapper mapper = BridgeDb.connect("idmapper-bridgerest:http://webservice.bridgedb.org/Human"); + IDMapper mapper = BridgeDb.connect("idmapper-bridgerest:https://webservice.bridgedb.org/Human"); DataSourceTxt.init(); // Start with defining the Chebi identifier for diff --git a/examples/src/org/bridgedb/examples/ExHello.java b/examples/src/org/bridgedb/examples/ExHello.java index baf811d6c..35efbd6e2 100644 --- a/examples/src/org/bridgedb/examples/ExHello.java +++ b/examples/src/org/bridgedb/examples/ExHello.java @@ -23,7 +23,7 @@ public static void main(String args[]) throws ClassNotFoundException, IDMapperEx DataSourceTxt.init(); // now we connect to the driver and create a IDMapper instance. - IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human"); + IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:https://webservice.bridgedb.org/Human"); // We create an Xref instance for the identifier that we want to look up. // In this case we want to look up Entrez gene 3643. diff --git a/examples/src/org/bridgedb/examples/ExIDSearch.java b/examples/src/org/bridgedb/examples/ExIDSearch.java index f309b89db..60029a480 100644 --- a/examples/src/org/bridgedb/examples/ExIDSearch.java +++ b/examples/src/org/bridgedb/examples/ExIDSearch.java @@ -20,7 +20,7 @@ public static void main(String args[]) throws ClassNotFoundException, IDMapperEx DataSourceTxt.init(); // now we connect to the driver and create a IDMapper instance. - IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human"); + IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:https://webservice.bridgedb.org/Human"); String query = "3643"; diff --git a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java b/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java index 6062dcdc0..8adf39eae 100644 --- a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java +++ b/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java @@ -276,7 +276,7 @@ private BufferedReader openReader() throws IOException } /** - * @param baseUrl base Url, e.g. http://webservice.bridgedb.org/Human or + * @param baseUrl base Url, e.g. https://webservice.bridgedb.org/Human or * http://localhost:8182 * @throws IDMapperException when service is unavailable */ From b4b53e3fab47190db776ae800ff5f6009e38a7bf Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 21 Nov 2023 18:30:37 +0100 Subject: [PATCH 13/64] Compile the series/3.1.0 branch --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e3b06d4c2..417ccb74d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,9 +2,9 @@ name: build on: push: - branches: [ main ] + branches: [ series/3.1.0 ] pull_request: - branches: [ main ] + branches: [ series/3.1.0 ] jobs: build: From aaab562cb6593697c59b7fdd79d0468c3df14aa8 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 21 Nov 2023 18:53:46 +0100 Subject: [PATCH 14/64] Newer Maven War plugin --- org.bridgedb.uri.ws.server/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 4ade2d960..d7544240d 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -21,7 +21,7 @@ org.apache.maven.plugins maven-war-plugin - 2.4 + 3.4.0 BridgeDb From b031932b2fd1778349f8f8c4faf247c902e19e35 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 20:34:13 +0100 Subject: [PATCH 15/64] Open for development --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 2df95159c..0d846839d 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 7c89938f5..d27fe4cb8 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index a87896961..6cf3c0747 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 475cfddc4..a04609afb 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 6824871e6..a4ebb736a 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index ccec29938..b49633bab 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 8aa5cfba7..86cc48316 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index e6e134ebe..906378f1d 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 9756a1224..97dac4e30 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.0 + 3.1.1-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.0 + 3.1.1-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index dfa510219..06fcfd984 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index a48cb34e5..14e8a177d 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 49900d9db..508a522df 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 674408375..5e98f4024 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 67a890ef6..3a10ac109 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index cc24df3e0..efc09f859 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 7b6e68550..3f746819b 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 934a95b68..093873e9a 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index d7544240d..8d15232f0 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index a486e30a5..0b3b58fa1 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index b2243e70e..069cbc011 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index c674b05ee..b20768f56 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 26193f525..2019f425f 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 816863fbf..328f127eb 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index f1f119ebe..d535b5f68 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 9f65fa0de..f1ea89d80 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.0 + 3.1.1-SNAPSHOT diff --git a/pom.xml b/pom.xml index 470a6524a..2c4b74299 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.0 + 3.1.1-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 4ac23f94980d51b613c9e63d96c4d59622439a45 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 16:11:34 +0100 Subject: [PATCH 16/64] slf4j 2.0.9 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 2c4b74299..32eba4c2d 100644 --- a/pom.xml +++ b/pom.xml @@ -54,7 +54,7 @@ 3.4 3.7.7 2.5 - 1.6.4 + 2.0.9 10.15.2.0 1.3.2 5.10.0 From 665f89fc866ebd3c26874bc47ea67dc002511a30 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 18:14:18 +0100 Subject: [PATCH 17/64] Updated RDF4J to 4.0.0 --- .../org/bridgedb/rdf/BridgeDBRdfHandler.java | 44 ++--- .../src/org/bridgedb/rdf/OrganismRdf.java | 18 +- .../src/org/bridgedb/rdf/RdfBase.java | 19 +- .../src/org/bridgedb/rdf/UriPattern.java | 19 +- .../rdf/constants/BridgeDBConstants.java | 89 +++++----- .../bridgedb/rdf/constants/CitoConstants.java | 6 +- .../rdf/constants/DCTermsConstants.java | 20 ++- .../bridgedb/rdf/constants/DCatConstants.java | 24 +-- .../bridgedb/rdf/constants/DulConstants.java | 6 +- .../bridgedb/rdf/constants/FoafConstants.java | 10 +- .../constants/IdenitifiersOrgConstants.java | 12 +- .../bridgedb/rdf/constants/OWLConstants.java | 6 +- .../bridgedb/rdf/constants/PavConstants.java | 49 +++--- .../bridgedb/rdf/constants/RdfConstants.java | 6 +- .../bridgedb/rdf/constants/VoidConstants.java | 35 ++-- .../rdf/constants/XMLSchemaConstants.java | 53 +++--- .../bridgedb/rdf/create/FormatConvertor.java | 2 +- .../bridgedb/rdf/create/LinkSetCombiner.java | 4 +- .../identifiers/org/IdentifersOrgReader.java | 9 +- .../rdf/DataSourceComparatorTest.java | 19 +- .../org/bridgedb/uri/loader/LinkHandler.java | 19 +- .../bridgedb/uri/loader/LinksetHandler.java | 14 +- .../bridgedb/uri/loader/LinksetListener.java | 14 +- .../org/bridgedb/uri/loader/RdfParser.java | 20 +-- .../uri/loader/SetupWithTestData.java | 7 +- .../loader/transative/TransativeCreator.java | 18 +- .../bridgedb/loader/LinksetListenerTest.java | 14 +- .../transative/TransativeCreatorTest.java | 8 +- .../src/org/bridgedb/uri/lens/LensTools.java | 21 ++- .../uri/tools/DirectStatementMaker.java | 94 +++++----- .../bridgedb/mysql/UriMapperRecoverTest.java | 12 +- .../mysql/transative/TransitiveTest.java | 64 +++---- .../org/bridgedb/uri/UriListenerTest.java | 22 +-- .../org/bridgedb/uri/UriMapperRdfTest.java | 163 +++++++++--------- pom.xml | 2 +- 35 files changed, 472 insertions(+), 470 deletions(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java index 3ee58896f..72fa651dd 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java @@ -47,9 +47,7 @@ import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; import org.eclipse.rdf4j.model.Value; -import org.eclipse.rdf4j.model.impl.BooleanLiteralImpl; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.Repository; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -86,7 +84,7 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); repositoryConnection.add(stream, DEFAULT_BASE_URI, DEFAULT_FILE_FORMAT); readAllDataSources(repositoryConnection); @@ -216,7 +214,7 @@ public DataSource readDataSource(RepositoryConnection repositoryConnection, Reso private void readCodeMapper(RepositoryConnection repositoryConnection, String systemCode, Pattern regex) throws RepositoryException, BridgeDBException { RepositoryResult statements = - repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(systemCode), true); + repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(systemCode), true); // String xrefPrefix = null; Resource codeMapperReseource = null; while (statements.hasNext()) { @@ -321,7 +319,7 @@ public static void writeRdfToFile(File file, SortedSet dataSources) RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); for (DataSource dataSource: dataSources){ writeDataSource(repositoryConnection, dataSource); @@ -341,29 +339,25 @@ private static void writeDataSource(RepositoryConnection repositoryConnection, D repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.DATA_SOURCE_URI); if (dataSource.getFullName() != null){ - repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, new LiteralImpl(dataSource.getFullName())); + repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getFullName())); } if (dataSource.getSystemCode() != null && (!dataSource.getSystemCode().trim().isEmpty())){ - repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode())); + repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode())); } if (dataSource.getMainUrl() != null){ - repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, new LiteralImpl(dataSource.getMainUrl())); + repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getMainUrl())); } if (dataSource.getExample() != null && dataSource.getExample().getId() != null){ - repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, new LiteralImpl(dataSource.getExample().getId())); + repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getExample().getId())); } - if (dataSource.isPrimary()){ - repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.TRUE); - } else { - repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.FALSE); - } + repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.isPrimary())); if (dataSource.getType() != null){ - repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, new LiteralImpl(dataSource.getType())); + repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getType())); } Pattern regex = DataSourcePatterns.getPatterns().get(dataSource); @@ -391,16 +385,16 @@ private static void writeDataSource(RepositoryConnection repositoryConnection, D Pattern pattern = DataSourcePatterns.getPatterns().get(dataSource); if (pattern != null && !pattern.toString().isEmpty()){ - Value patternValue = new LiteralImpl(pattern.toString()); + Value patternValue = SimpleValueFactory.getInstance().createLiteral(pattern.toString()); repositoryConnection.add(id, BridgeDBConstants.HAS_REGEX_PATTERN_URI, patternValue); } if (dataSource.getAlternative() != null){ - repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, new LiteralImpl(dataSource.getAlternative())); + repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getAlternative())); } if (dataSource.getDescription() != null){ - repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, new LiteralImpl(dataSource.getDescription())); + repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getDescription())); } SortedSet sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.dataSourceUriPattern); @@ -421,8 +415,8 @@ private static void writeCodeMapper(RepositoryConnection repositoryConnection, D } Resource id = asCodeMapperResource(dataSource); repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.CODE_MAPPER_URI); - repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode())); - Value prefixValue = new LiteralImpl(xrefPrefix); + repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode())); + Value prefixValue = SimpleValueFactory.getInstance().createLiteral(xrefPrefix); repositoryConnection.add(id, BridgeDBConstants.XREF_PREFIX_URI, prefixValue); SortedSet sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.codeMapperPattern); @@ -476,17 +470,17 @@ private static RDFFormat getFormat(File file){ protected static Resource asResource(DataSource dataSource) { if (dataSource.getFullName() == null){ - return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); } else { - return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName())); } } protected static Resource asCodeMapperResource(DataSource dataSource) { if (dataSource.getFullName() == null){ - return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); } else { - return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName())); } } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java index 36407e02b..a25752ffa 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java @@ -22,16 +22,16 @@ import java.io.IOException; import java.util.HashMap; import java.util.Set; + import org.bridgedb.bio.Organism; import org.bridgedb.rdf.constants.BridgeDBConstants; import org.bridgedb.rdf.constants.RdfConstants; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; import org.eclipse.rdf4j.rio.RDFHandler; @@ -64,8 +64,8 @@ public static final String getRdfLabel(Organism organism) { return scrub(organism.code()); } - public static final URI getResourceId(Organism organism){ - return new URIImpl(BridgeDBConstants.ORGANISM1 + "_" + getRdfLabel(organism)); + public static final IRI getResourceId(Organism organism){ + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.ORGANISM1 + "_" + getRdfLabel(organism)); } public static void addAll(RepositoryConnection repositoryConnection) throws IOException, RepositoryException { @@ -82,11 +82,11 @@ public void addComments(RDFHandler handler) throws RDFHandlerException{ public static void add(RepositoryConnection repositoryConnection, Organism organism) throws IOException, RepositoryException { - URI id = getResourceId(organism); + IRI id = getResourceId(organism); repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.ORGANISM_URI); - repositoryConnection.add(id, BridgeDBConstants.CODE_URI, new LiteralImpl(organism.code())); - repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, new LiteralImpl(organism.shortName())); - repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, new LiteralImpl(organism.latinName())); + repositoryConnection.add(id, BridgeDBConstants.CODE_URI, SimpleValueFactory.getInstance().createLiteral(organism.code())); + repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.shortName())); + repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.latinName())); } public static Object readRdf(Resource organismId, Set allStatements) throws BridgeDBException { diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java index 3c2999eda..11847b3d9 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java @@ -21,13 +21,14 @@ import java.util.HashSet; import java.util.Set; + import org.apache.log4j.Logger; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.Repository; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -61,7 +62,7 @@ static String convertToShortName(Value value) { return id; } - public static String getSingletonString(RepositoryConnection repositoryConnection, Resource id, URI predicate) + public static String getSingletonString(RepositoryConnection repositoryConnection, Resource id, IRI predicate) throws BridgeDBException, RepositoryException { String result = getPossibleSingletonString(repositoryConnection, id, predicate); if (result == null){ @@ -71,7 +72,7 @@ public static String getSingletonString(RepositoryConnection repositoryConnectio } public static String getPossibleSingletonString(RepositoryConnection repositoryConnection, Resource id, - URI predicate) throws RepositoryException, BridgeDBException { + IRI predicate) throws RepositoryException, BridgeDBException { Value result = getPossibleSingleton(repositoryConnection, id, predicate); if (result == null) { return null; @@ -81,7 +82,7 @@ public static String getPossibleSingletonString(RepositoryConnection repositoryC } static Resource getPossibleSingletonResource(RepositoryConnection repositoryConnection, Resource id, - URI predicate) throws RepositoryException, BridgeDBException { + IRI predicate) throws RepositoryException, BridgeDBException { Value value = getPossibleSingleton(repositoryConnection, id, predicate); return toResource(value); } @@ -92,11 +93,11 @@ private static Resource toResource(Value value){ } else if (value instanceof Resource){ return (Resource)value; } - return new URIImpl(value.stringValue()); + return SimpleValueFactory.getInstance().createIRI(value.stringValue()); } static Value getPossibleSingleton(RepositoryConnection repositoryConnection, Resource id, - URI predicate) throws RepositoryException, BridgeDBException { + IRI predicate) throws RepositoryException, BridgeDBException { RepositoryResult statements = repositoryConnection.getStatements(id, predicate, null, true); if (statements.hasNext()) { @@ -111,7 +112,7 @@ static Value getPossibleSingleton(RepositoryConnection repositoryConnection, Res return null; } - static Set getAllStrings(RepositoryConnection repositoryConnection, Resource id, URI predicate) + static Set getAllStrings(RepositoryConnection repositoryConnection, Resource id, IRI predicate) throws RepositoryException { HashSet results = new HashSet(); RepositoryResult statements = @@ -123,7 +124,7 @@ static Set getAllStrings(RepositoryConnection repositoryConnection, Reso return results; } - static Set getAllResources(RepositoryConnection repositoryConnection, Resource id, URI predicate) + static Set getAllResources(RepositoryConnection repositoryConnection, Resource id, IRI predicate) throws RepositoryException { HashSet results = new HashSet(); RepositoryResult statements = diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index af615b6c4..362e8b4ad 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java @@ -27,18 +27,17 @@ import java.util.SortedSet; import java.util.TreeSet; import java.util.regex.Pattern; + import org.bridgedb.DataSource; import org.bridgedb.DataSourcePatterns; import org.bridgedb.bio.DataSourceTxt; import org.bridgedb.rdf.constants.BridgeDBConstants; -import org.bridgedb.rdf.constants.IdenitifiersOrgConstants; import org.bridgedb.rdf.constants.RdfConstants; import org.bridgedb.rdf.identifiers.org.IdentifersOrgReader; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -59,7 +58,7 @@ public class UriPattern extends RdfBase implements Comparable{ private static HashMap> byCode = new HashMap>(); static boolean initialized = false; - private static HashSet expectedPredicates = new HashSet(Arrays.asList(new URI[] { + private static HashSet expectedPredicates = new HashSet(Arrays.asList(new IRI[] { BridgeDBConstants.HAS_POSTFIX_URI, BridgeDBConstants.HAS_PREFIX_URI, RdfConstants.TYPE_URI, @@ -201,8 +200,8 @@ public static UriPattern existingByPrefixAndPostfix(String prefix, String postfi return existingByPattern(prefix + "$id" + postfix); } - public final URI getResourceId(){ - return new URIImpl(getUriPattern()); + public final IRI getResourceId(){ + return SimpleValueFactory.getInstance().createIRI(getUriPattern()); } public String getUriPattern() { @@ -221,11 +220,11 @@ public static void addAll(RepositoryConnection repositoryConnection) } public void add(RepositoryConnection repositoryConnection) throws RepositoryException{ - URI id = getResourceId(); + IRI id = getResourceId(); repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.URI_PATTERN_URI); - repositoryConnection.add(id, BridgeDBConstants.HAS_PREFIX_URI, new LiteralImpl(prefix)); + repositoryConnection.add(id, BridgeDBConstants.HAS_PREFIX_URI, SimpleValueFactory.getInstance().createLiteral(prefix)); if (!postfix.isEmpty()){ - repositoryConnection.add(id, BridgeDBConstants.HAS_POSTFIX_URI, new LiteralImpl(postfix)); + repositoryConnection.add(id, BridgeDBConstants.HAS_POSTFIX_URI, SimpleValueFactory.getInstance().createLiteral(postfix)); } } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java index b88c61eb1..d0546c091 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java @@ -19,14 +19,15 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class BridgeDBConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); public static final String OLD_PREFIX = "http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl#"; public static final String OLD_PREFIX_NAME = "bridgeDB"; @@ -36,92 +37,92 @@ public class BridgeDBConstants { //Types public static final String DATA_SOURCE_LABEL = "DataSource"; public static final String DATA_SOURCE1 = PREFIX + DATA_SOURCE_LABEL; - public static final URI DATA_SOURCE_URI = new URIImpl(PREFIX + DATA_SOURCE_LABEL); + public static final IRI DATA_SOURCE_URI = factory.createIRI(PREFIX + DATA_SOURCE_LABEL); //public static final String URI_MAPPING = "UriMapping"; - //public static final URI URI_MAPPING_URI = new URIImpl(PREFIX + URI_MAPPING); + //public static final IRI URI_MAPPING_URI = factory.createIRI(PREFIX + URI_MAPPING); public static final String URI_PATTERN_LABEL = "UriPattern"; public static final String URI_PATTERN1 = PREFIX + URI_PATTERN_LABEL; - public static final URI URI_PATTERN_URI = new URIImpl(URI_PATTERN1); + public static final IRI URI_PATTERN_URI = factory.createIRI(URI_PATTERN1); //DataSource fields private static final String FULL_NAME = "fullName"; - public static final URI FULL_NAME_URI = new URIImpl(PREFIX + FULL_NAME); + public static final IRI FULL_NAME_URI = factory.createIRI(PREFIX + FULL_NAME); private static final String ID_EXAMPLE = "idExample"; - public static final URI ID_EXAMPLE_URI = new URIImpl(PREFIX + ID_EXAMPLE); + public static final IRI ID_EXAMPLE_URI = factory.createIRI(PREFIX + ID_EXAMPLE); private static final String MAIN_URL = "mainUrl"; - public static final URI MAIN_URL_URI = new URIImpl(PREFIX + MAIN_URL); + public static final IRI MAIN_URL_URI = factory.createIRI(PREFIX + MAIN_URL); public static final String ORGANISM_LABEL = "Organism"; public static final String ORGANISM1 = PREFIX + ORGANISM_LABEL; - public static final URI ORGANISM_URI = new URIImpl(ORGANISM1); + public static final IRI ORGANISM_URI = factory.createIRI(ORGANISM1); public static final String ABOUT_ORGANISM_LABEL = "aboutOrganism"; public static final String ABOUT_ORGANISM1 = PREFIX + ORGANISM_LABEL; - public static final URI ABOUT_ORGANISM_URI = new URIImpl(ORGANISM1); + public static final IRI ABOUT_ORGANISM_URI = factory.createIRI(ORGANISM1); private static final String PRIMARY = "primary"; - public static final URI PRIMARY_URI = new URIImpl(PREFIX + PRIMARY); + public static final IRI PRIMARY_URI = factory.createIRI(PREFIX + PRIMARY); private static final String SYSTEM_CODE = "systemCode"; - public static final URI SYSTEM_CODE_URI = new URIImpl(PREFIX + SYSTEM_CODE); + public static final IRI SYSTEM_CODE_URI = factory.createIRI(PREFIX + SYSTEM_CODE); private static final String TYPE = "type"; - public static final URI TYPE_URI = new URIImpl(PREFIX + TYPE); - public static final URI HAS_DATA_TYPE_URI = new URIImpl(PREFIX + "hasDataType"); + public static final IRI TYPE_URI = factory.createIRI(PREFIX + TYPE); + public static final IRI HAS_DATA_TYPE_URI = factory.createIRI(PREFIX + "hasDataType"); - public static final URI HAS_REGEX_PATTERN_URI = new URIImpl(PREFIX + "hasRegexPattern"); - public static final URI HAS_REGEX_URL_PATTERN_URI = new URIImpl(PREFIX + "hasRegexUrlPattern"); - public static final URI HAS_PRIMARY_URI_PATTERN_URI = new URIImpl(PREFIX + "hasPrimaryUriPattern"); - public static final URI HAS_URI_PATTERN_URI = new URIImpl(PREFIX + "hasUriPattern"); - public static final URI HAS_REGEX_URI_PATTERN_URI = new URIImpl(PREFIX + "hasRegexUriPattern"); - public static final URI IS_DEPRICATED_BY_URI = new URIImpl(PREFIX + "isDepricatedBy"); + public static final IRI HAS_REGEX_PATTERN_URI = factory.createIRI(PREFIX + "hasRegexPattern"); + public static final IRI HAS_REGEX_URL_PATTERN_URI = factory.createIRI(PREFIX + "hasRegexUrlPattern"); + public static final IRI HAS_PRIMARY_URI_PATTERN_URI = factory.createIRI(PREFIX + "hasPrimaryUriPattern"); + public static final IRI HAS_URI_PATTERN_URI = factory.createIRI(PREFIX + "hasUriPattern"); + public static final IRI HAS_REGEX_URI_PATTERN_URI = factory.createIRI(PREFIX + "hasRegexUriPattern"); + public static final IRI IS_DEPRICATED_BY_URI = factory.createIRI(PREFIX + "isDepricatedBy"); public static final String VARIOUS = PREFIX + "various"; //old verions private static final String URN_BASE = "urnBase"; - public static final URI URN_BASE_URI = new URIImpl(PREFIX + URN_BASE); + public static final IRI URN_BASE_URI = factory.createIRI(PREFIX + URN_BASE); //Organism Fields private static final String CODE = "code"; - public static final URI CODE_URI = new URIImpl(PREFIX + CODE); + public static final IRI CODE_URI = factory.createIRI(PREFIX + CODE); private static final String SHORT_NAME = "shortName"; - public static final URI SHORT_NAME_URI = new URIImpl(PREFIX + SHORT_NAME); + public static final IRI SHORT_NAME_URI = factory.createIRI(PREFIX + SHORT_NAME); private static final String LATIN_NAME = "latinName"; - public static final URI LATIN_NAME_URI = new URIImpl(PREFIX + LATIN_NAME); + public static final IRI LATIN_NAME_URI = factory.createIRI(PREFIX + LATIN_NAME); //UriPatternFields private static final String HAS_PREFIX = "hasPrefix"; - public static final URI HAS_PREFIX_URI = new URIImpl(PREFIX + HAS_PREFIX); + public static final IRI HAS_PREFIX_URI = factory.createIRI(PREFIX + HAS_PREFIX); private static final String HAS_POSTFIX = "hasPostfix"; - public static final URI HAS_POSTFIX_URI = new URIImpl(PREFIX + HAS_POSTFIX); + public static final IRI HAS_POSTFIX_URI = factory.createIRI(PREFIX + HAS_POSTFIX); private static final String IDENTIFERS_ORG_PATTERN = "IdentifiersOrgPattern"; - public static final URI HAS_IDENTIFERS_ORG_PATTERN_URI = new URIImpl(PREFIX + "has" + IDENTIFERS_ORG_PATTERN); + public static final IRI HAS_IDENTIFERS_ORG_PATTERN_URI = factory.createIRI(PREFIX + "has" + IDENTIFERS_ORG_PATTERN); private static final String IDENTIFERS_ORG_INFO_PATTERN = "IdentifiersOrgInfoPattern"; - public static final URI HAS_IDENTIFERS_ORG_INFO_PATTERN_URI = new URIImpl(PREFIX + "has" + IDENTIFERS_ORG_INFO_PATTERN); + public static final IRI HAS_IDENTIFERS_ORG_INFO_PATTERN_URI = factory.createIRI(PREFIX + "has" + IDENTIFERS_ORG_INFO_PATTERN); //CodeMapper feilds private static final String CODE_MAPPER = "CodeMapper"; public static final String CODE_MAPPER1 = PREFIX + CODE_MAPPER; - public static final URI CODE_MAPPER_URI = new URIImpl(CODE_MAPPER1); + public static final IRI CODE_MAPPER_URI = factory.createIRI(CODE_MAPPER1); private static final String XREF_PREFIX = "xrefPrefix"; - public static final URI XREF_PREFIX_URI = new URIImpl(PREFIX + XREF_PREFIX); + public static final IRI XREF_PREFIX_URI = factory.createIRI(PREFIX + XREF_PREFIX); - public static final URI HAS_DATA_SOURCE = new URIImpl(PREFIX + "hasDataSource"); - public static final URI IS_URI_PATTERN_OF = new URIImpl(PREFIX + "isUriPatternOf"); + public static final IRI HAS_DATA_SOURCE = factory.createIRI(PREFIX + "hasDataSource"); + public static final IRI IS_URI_PATTERN_OF = factory.createIRI(PREFIX + "isUriPatternOf"); private static final String bdb = "http://www.bridgedb.org/test#"; - public static final URI TEST_PREDICATE = new URIImpl(bdb + "testPredicate"); + public static final IRI TEST_PREDICATE = factory.createIRI(bdb + "testPredicate"); - public static final URI ASSERTION_METHOD = new URIImpl(PREFIX + "assertionMethod "); - public static final URI VIA_URI = new URIImpl(PREFIX + "isTransativeVia"); - public static final URI IS_SYMETRIC = new URIImpl(PREFIX + "isSymetric"); - public static final URI LINKSET_JUSTIFICATION = new URIImpl(PREFIX + "linksetJustification"); - public static final URI SUBJECTS_DATATYPE = new URIImpl(PREFIX + "subjectsDatatype"); - public static final URI OBJECTS_DATATYPE = new URIImpl(PREFIX + "objectsDatatype"); - public static final URI SUBJECTS_SPECIES = new URIImpl(PREFIX + "subjectsSpecies"); - public static final URI OBJECTS_SPECIES = new URIImpl(PREFIX + "objectsSpecies"); - public static final URI FULFILLS_LENS = new URIImpl(PREFIX + "fulfillsLens"); + public static final IRI ASSERTION_METHOD = factory.createIRI(PREFIX + "assertionMethod "); + public static final IRI VIA_URI = factory.createIRI(PREFIX + "isTransativeVia"); + public static final IRI IS_SYMETRIC = factory.createIRI(PREFIX + "isSymetric"); + public static final IRI LINKSET_JUSTIFICATION = factory.createIRI(PREFIX + "linksetJustification"); + public static final IRI SUBJECTS_DATATYPE = factory.createIRI(PREFIX + "subjectsDatatype"); + public static final IRI OBJECTS_DATATYPE = factory.createIRI(PREFIX + "objectsDatatype"); + public static final IRI SUBJECTS_SPECIES = factory.createIRI(PREFIX + "subjectsSpecies"); + public static final IRI OBJECTS_SPECIES = factory.createIRI(PREFIX + "objectsSpecies"); + public static final IRI FULFILLS_LENS = factory.createIRI(PREFIX + "fulfillsLens"); - public static final URI LENS_URI = new URIImpl(PREFIX + "lens"); + public static final IRI LENS_URI = factory.createIRI(PREFIX + "lens"); public static final String TRANSITIVE = PREFIX + "Transitive"; - public static final URI TRANSITIVE_URI = new URIImpl(TRANSITIVE); + public static final IRI TRANSITIVE_URI = factory.createIRI(TRANSITIVE); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java index 43b69f2cf..0d036730a 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java @@ -4,8 +4,8 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -16,6 +16,6 @@ public class CitoConstants { public static final String PREFIX_NAME = "cito"; public static final String CITE_AS_AUTHORITY = "citeAsAuthority"; - public static final URI CITE_AS_AUTHORITY_URI = new URIImpl(voidns + CITE_AS_AUTHORITY); + public static final IRI CITE_AS_AUTHORITY_URI = SimpleValueFactory.getInstance().createIRI(voidns + CITE_AS_AUTHORITY); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java index 27be81a10..0da39f63d 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java @@ -4,35 +4,37 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class DCTermsConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://purl.org/dc/terms/"; public static final String PREFIX_NAME = "dcterms"; public static final String ACCRUAL_PERIODICITY = "accrualPeriodicity"; - public static final URI ACCRUAL_PERIODICITY_URI = new URIImpl(voidns + ACCRUAL_PERIODICITY); + public static final IRI ACCRUAL_PERIODICITY_URI = factory.createIRI(voidns + ACCRUAL_PERIODICITY); public static final String ALTERNATIVE = "alternative"; - public static final URI ALTERNATIVE_URI = new URIImpl(voidns + ALTERNATIVE); + public static final IRI ALTERNATIVE_URI = factory.createIRI(voidns + ALTERNATIVE); public static final String DESCRIPTION = "description"; - public static final URI DESCRIPTION_URI = new URIImpl(voidns + DESCRIPTION); + public static final IRI DESCRIPTION_URI = factory.createIRI(voidns + DESCRIPTION); public static final String ISSUED = "issued"; - public static final URI ISSUED_URI = new URIImpl(voidns + ISSUED); + public static final IRI ISSUED_URI = factory.createIRI(voidns + ISSUED); public static final String LICENSE = "license"; - public static final URI LICENSE_URI = new URIImpl(voidns + LICENSE); + public static final IRI LICENSE_URI = factory.createIRI(voidns + LICENSE); public static final String PUBLISHER = "publisher"; - public static final URI PUBLISHER_URI = new URIImpl(voidns + PUBLISHER); + public static final IRI PUBLISHER_URI = factory.createIRI(voidns + PUBLISHER); public static final String TITLE = "title"; - public static final URI TITLE_URI = new URIImpl(voidns + TITLE); + public static final IRI TITLE_URI = factory.createIRI(voidns + TITLE); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java index 2e7ee9b89..443f80700 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java @@ -4,35 +4,37 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class DCatConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://www.w3.org/ns/dcat#"; public static final String PREFIX_NAME = "dcat"; public static final String ACCESS_URL = "accessURL"; - public static final URI ACCESS_URL_URI = new URIImpl(voidns + ACCESS_URL); + public static final IRI ACCESS_URL_URI = factory.createIRI(voidns + ACCESS_URL); public static final String BYTE_SIZE = "byteSize"; - public static final URI BYTE_SIZE_URI = new URIImpl(voidns + BYTE_SIZE); + public static final IRI BYTE_SIZE_URI = factory.createIRI(voidns + BYTE_SIZE); public static final String DESCRIPTION = "description"; - public static final URI DESCRIPTION_URI = new URIImpl(voidns + DESCRIPTION); + public static final IRI DESCRIPTION_URI = factory.createIRI(voidns + DESCRIPTION); public static final String DISTRIBUTION = "distribution"; - public static final URI DISTRIBUTION_URI = new URIImpl(voidns + DISTRIBUTION); + public static final IRI DISTRIBUTION_URI = factory.createIRI(voidns + DISTRIBUTION); public static final String DOWNLOAD = "downloadURL"; - public static final URI DOWNLOAD_URI = new URIImpl(voidns + DOWNLOAD); + public static final IRI DOWNLOAD_URI = factory.createIRI(voidns + DOWNLOAD); public static final String LANDING_PAGE = "landingPage"; - public static final URI LANDING_PAGE_URI = new URIImpl(voidns + LANDING_PAGE); + public static final IRI LANDING_PAGE_URI = factory.createIRI(voidns + LANDING_PAGE); public static final String MEDIA_TYPE = "mediaType "; - public static final URI MEDIA_TYPE_URI = new URIImpl(voidns + MEDIA_TYPE); + public static final IRI MEDIA_TYPE_URI = factory.createIRI(voidns + MEDIA_TYPE); public static final String THEME = "theme"; - public static final URI THEME_URI = new URIImpl(voidns + THEME); + public static final IRI THEME_URI = factory.createIRI(voidns + THEME); public static final String TITLE = "title"; - public static final URI TITLE_URI = new URIImpl(voidns + TITLE); + public static final IRI TITLE_URI = factory.createIRI(voidns + TITLE); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java index 7d78296fb..ba92aab66 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java @@ -19,13 +19,13 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; public class DulConstants { public static final String dulns = "http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#"; - public static final URI EXPRESSES = new URIImpl(dulns + "expresses"); + public static final IRI EXPRESSES = SimpleValueFactory.getInstance().createIRI(dulns + "expresses"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java index 0bd87ca78..17a5be926 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java @@ -4,21 +4,23 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class FoafConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://xmlns.com/foaf/0.1/"; public static final String PREFIX_NAME = "foaf"; public static final String PAGE = "citeAsAuthority"; - public static final URI PAGE_URI = new URIImpl(voidns + PAGE); + public static final IRI PAGE_URI = factory.createIRI(voidns + PAGE); public static final String PRIMARY_TOPIC = "primaryTopic"; - public static final URI PRIMARY_TOPIC_URI = new URIImpl(voidns + PRIMARY_TOPIC); + public static final IRI PRIMARY_TOPIC_URI = factory.createIRI(voidns + PRIMARY_TOPIC); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java index 7bc37e1c6..c1dec6384 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java @@ -4,22 +4,22 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class IdenitifiersOrgConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://identifiers.org/terms#"; public static final String PREFIX_NAME = "idot:"; public static final String NAMESPACE = "namespace"; - public static final URI NAMESPACE_URI = new URIImpl(voidns + NAMESPACE); + public static final IRI NAMESPACE_URI = factory.createIRI(voidns + NAMESPACE); public static final String REGEX = "idRegexPattern"; - public static final URI REGEX_URI = new URIImpl(voidns + REGEX); - - + public static final IRI REGEX_URI = factory.createIRI(voidns + REGEX); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java index a6dcb8ed3..7ba7bb6a2 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java @@ -19,8 +19,8 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -31,7 +31,7 @@ public class OWLConstants { public static final String EQUIVALENT_CLASS = xmlschemans + "equivalentClass"; public static final String SAME_AS = xmlschemans + "sameAs"; - public static final URI SAMEAS_URI = new URIImpl(SAME_AS); + public static final IRI SAMEAS_URI = SimpleValueFactory.getInstance().createIRI(SAME_AS); public static final String THING = "owl:Thing"; } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java index 7fb0909cc..abd85435c 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java @@ -19,37 +19,38 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * */ public class PavConstants { - + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + private static final String pavTermns = "http://purl.org/pav/"; - public static final URI SOURCE_ACCESSED_BY = new URIImpl(pavTermns + "sourceAccessedBy"); - public static final URI SOURCE_ACCESSED_FROM = new URIImpl(pavTermns + "sourceAccessedAt"); - public static final URI SOURCE_ACCESSED_ON = new URIImpl(pavTermns + "sourceAccessedOn"); - public static final URI AUTHORED_BY = new URIImpl(pavTermns + "authoredBy"); - public static final URI AUTHORED_ON = new URIImpl(pavTermns + "authoredOn"); - public static final URI CREATED_BY = new URIImpl(pavTermns + "createdBy"); - public static final URI CREATED_ON = new URIImpl(pavTermns + "createdOn"); - public static final URI CREATED_WITH = new URIImpl(pavTermns + "createdWith"); - public static final URI DERIVED_BY = new URIImpl(pavTermns + "derivedBy"); - public static final URI DERIVED_FROM = new URIImpl(pavTermns + "derivedFrom"); - public static final URI DERIVED_ON = new URIImpl(pavTermns + "derivedOn"); - public static final URI IMPORTED_BY = new URIImpl(pavTermns + "importedBy"); - public static final URI IMPORTED_FROM = new URIImpl(pavTermns + "importedFrom"); - public static final URI IMPORTED_ON = new URIImpl(pavTermns + "importedOn"); - public static final URI LAST_REFERSHED_ON = new URIImpl(pavTermns + "lastRefreshedOn"); - public static final URI MODIFIED_ON = new URIImpl(pavTermns + "modified"); - public static final URI PREVIOUS_VERSION = new URIImpl(pavTermns + "previousVersion"); - public static final URI RETRIEVED_BY = new URIImpl(pavTermns + "retrievedBy"); - public static final URI RETRIEVED_ON = new URIImpl(pavTermns + "retrievedOn"); - public static final URI RETRIEVED_FROM = new URIImpl(pavTermns + "retrievedFrom"); - public static final URI VERSION = new URIImpl(pavTermns + "version"); + public static final IRI SOURCE_ACCESSED_BY = factory.createIRI(pavTermns + "sourceAccessedBy"); + public static final IRI SOURCE_ACCESSED_FROM = factory.createIRI(pavTermns + "sourceAccessedAt"); + public static final IRI SOURCE_ACCESSED_ON = factory.createIRI(pavTermns + "sourceAccessedOn"); + public static final IRI AUTHORED_BY = factory.createIRI(pavTermns + "authoredBy"); + public static final IRI AUTHORED_ON = factory.createIRI(pavTermns + "authoredOn"); + public static final IRI CREATED_BY = factory.createIRI(pavTermns + "createdBy"); + public static final IRI CREATED_ON = factory.createIRI(pavTermns + "createdOn"); + public static final IRI CREATED_WITH = factory.createIRI(pavTermns + "createdWith"); + public static final IRI DERIVED_BY = factory.createIRI(pavTermns + "derivedBy"); + public static final IRI DERIVED_FROM = factory.createIRI(pavTermns + "derivedFrom"); + public static final IRI DERIVED_ON = factory.createIRI(pavTermns + "derivedOn"); + public static final IRI IMPORTED_BY = factory.createIRI(pavTermns + "importedBy"); + public static final IRI IMPORTED_FROM = factory.createIRI(pavTermns + "importedFrom"); + public static final IRI IMPORTED_ON = factory.createIRI(pavTermns + "importedOn"); + public static final IRI LAST_REFERSHED_ON = factory.createIRI(pavTermns + "lastRefreshedOn"); + public static final IRI MODIFIED_ON = factory.createIRI(pavTermns + "modified"); + public static final IRI PREVIOUS_VERSION = factory.createIRI(pavTermns + "previousVersion"); + public static final IRI RETRIEVED_BY = factory.createIRI(pavTermns + "retrievedBy"); + public static final IRI RETRIEVED_ON = factory.createIRI(pavTermns + "retrievedOn"); + public static final IRI RETRIEVED_FROM = factory.createIRI(pavTermns + "retrievedFrom"); + public static final IRI VERSION = factory.createIRI(pavTermns + "version"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java index edab7a489..34de791ed 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java @@ -19,8 +19,8 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -29,5 +29,5 @@ public class RdfConstants { static final String TYPE = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"; - public static final URI TYPE_URI = new URIImpl(TYPE); + public static final IRI TYPE_URI = SimpleValueFactory.getInstance().createIRI(TYPE); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java index b250e2925..336663915 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java @@ -19,33 +19,34 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * */ public class VoidConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); public static final String voidns = "http://rdfs.org/ns/void#"; public static final String PREFIX_NAME = "void:"; - public static final URI DATA_DUMP = new URIImpl(voidns + "dataDump"); - public static final URI DATASET = new URIImpl(voidns + "Dataset"); - public static final URI DATASET_DESCRIPTION = new URIImpl(voidns + "DatasetDescription"); - public static final URI EXAMPLE_RESOURCE = new URIImpl(voidns + "exampleResource"); - public static final URI LINK_PREDICATE = new URIImpl(voidns + "linkPredicate"); - public static final URI IN_DATASET = new URIImpl(voidns + "inDataset"); - public static final URI LINKSET = new URIImpl(voidns + "Linkset"); - public static final URI TARGET = new URIImpl(voidns + "target"); - public static final URI TRIPLES = new URIImpl(voidns + "triples"); - public static final URI SUBJECTSTARGET = new URIImpl(voidns + "subjectsTarget"); - public static final URI OBJECTSTARGET = new URIImpl(voidns + "objectsTarget"); - public static final URI SUBSET = new URIImpl(voidns + "subset"); - public static final URI SPARQL_ENDPOINT = new URIImpl(voidns + "sparqlEndpoint"); + public static final IRI DATA_DUMP = factory.createIRI(voidns + "dataDump"); + public static final IRI DATASET = factory.createIRI(voidns + "Dataset"); + public static final IRI DATASET_DESCRIPTION = factory.createIRI(voidns + "DatasetDescription"); + public static final IRI EXAMPLE_RESOURCE = factory.createIRI(voidns + "exampleResource"); + public static final IRI LINK_PREDICATE = factory.createIRI(voidns + "linkPredicate"); + public static final IRI IN_DATASET = factory.createIRI(voidns + "inDataset"); + public static final IRI LINKSET = factory.createIRI(voidns + "Linkset"); + public static final IRI TARGET = factory.createIRI(voidns + "target"); + public static final IRI TRIPLES = factory.createIRI(voidns + "triples"); + public static final IRI SUBJECTSTARGET = factory.createIRI(voidns + "subjectsTarget"); + public static final IRI OBJECTSTARGET = factory.createIRI(voidns + "objectsTarget"); + public static final IRI SUBSET = factory.createIRI(voidns + "subset"); + public static final IRI SPARQL_ENDPOINT = factory.createIRI(voidns + "sparqlEndpoint"); private static final String URI_SPACE = "uriSpace"; public static final String URI_SPACE_SHORT = PREFIX_NAME + URI_SPACE; - public static final URI URI_SPACE_URI = new URIImpl(voidns + URI_SPACE); - public static final URI VOCABULARY = new URIImpl(voidns + "vocabulary"); + public static final IRI URI_SPACE_URI = factory.createIRI(voidns + URI_SPACE); + public static final IRI VOCABULARY = factory.createIRI(voidns + "vocabulary"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java index 2a4103b4e..2b0394c0b 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java @@ -19,37 +19,34 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; -/** - * - */ public class XMLSchemaConstants { - + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); public static final String PREFIX = "http://www.w3.org/2001/XMLSchema#"; - public static final URI STRING = new URIImpl(PREFIX + "string"); - public static final URI BOOLEAN = new URIImpl(PREFIX + "boolean"); - public static final URI DECIMAL = new URIImpl(PREFIX + "decimal"); - public static final URI FLOAT = new URIImpl(PREFIX + "float"); - public static final URI DOUBLE = new URIImpl(PREFIX + "double"); - public static final URI DURATION = new URIImpl(PREFIX + "duration"); - public static final URI DATE_TIME = new URIImpl(PREFIX + "dateTime"); - public static final URI TIME = new URIImpl(PREFIX + "time"); - public static final URI DATE = new URIImpl(PREFIX + "date"); - public static final URI G_YEAR_MONTH = new URIImpl(PREFIX + "gYearMonth"); - public static final URI G_YEAR = new URIImpl(PREFIX + "gYear"); - public static final URI G_MONTH_DAY = new URIImpl(PREFIX + "gMonthDay"); - public static final URI G_DAY = new URIImpl(PREFIX + "gDay"); - public static final URI G_MONTH = new URIImpl(PREFIX + "gMonth"); - public static final URI HEX_BINARY = new URIImpl(PREFIX + "hexBinary"); - public static final URI BASE_64_BINARY = new URIImpl(PREFIX + "base64Binary"); - public static final URI ANY_URI = new URIImpl(PREFIX + "anyURI"); - public static final URI QNAME = new URIImpl(PREFIX + "QName"); - public static final URI NOTATION = new URIImpl(PREFIX + "NOTATION"); - public static final URI INTEGER = new URIImpl(PREFIX + "integer"); - public static final URI NON_NEGATIVE_INTEGER = new URIImpl(PREFIX + "nonNegativeInteger"); - public static final URI UNISGNED_BYTE = new URIImpl(PREFIX + "unsignedByte"); + public static final IRI STRING = factory.createIRI(PREFIX + "string"); + public static final IRI BOOLEAN = factory.createIRI(PREFIX + "boolean"); + public static final IRI DECIMAL = factory.createIRI(PREFIX + "decimal"); + public static final IRI FLOAT = factory.createIRI(PREFIX + "float"); + public static final IRI DOUBLE = factory.createIRI(PREFIX + "double"); + public static final IRI DURATION = factory.createIRI(PREFIX + "duration"); + public static final IRI DATE_TIME = factory.createIRI(PREFIX + "dateTime"); + public static final IRI TIME = factory.createIRI(PREFIX + "time"); + public static final IRI DATE = factory.createIRI(PREFIX + "date"); + public static final IRI G_YEAR_MONTH = factory.createIRI(PREFIX + "gYearMonth"); + public static final IRI G_YEAR = factory.createIRI(PREFIX + "gYear"); + public static final IRI G_MONTH_DAY = factory.createIRI(PREFIX + "gMonthDay"); + public static final IRI G_DAY = factory.createIRI(PREFIX + "gDay"); + public static final IRI G_MONTH = factory.createIRI(PREFIX + "gMonth"); + public static final IRI HEX_BINARY = factory.createIRI(PREFIX + "hexBinary"); + public static final IRI BASE_64_BINARY = factory.createIRI(PREFIX + "base64Binary"); + public static final IRI ANY_URI = factory.createIRI(PREFIX + "anyURI"); + public static final IRI QNAME = factory.createIRI(PREFIX + "QName"); + public static final IRI NOTATION = factory.createIRI(PREFIX + "NOTATION"); + public static final IRI INTEGER = factory.createIRI(PREFIX + "integer"); + public static final IRI NON_NEGATIVE_INTEGER = factory.createIRI(PREFIX + "nonNegativeInteger"); + public static final IRI UNISGNED_BYTE = factory.createIRI(PREFIX + "unsignedByte"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java index 4fb1e9434..415644f16 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java @@ -76,7 +76,7 @@ public static void convert(File inputFile, File outputFile) throws Exception { RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); repositoryConnection.add(inputFile, DEFAULT_BASE_URI, getFormat(inputFile.getName())); writeRDF(repositoryConnection, outputFile); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java index b9d25a2cb..29fb8b077 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java @@ -77,7 +77,7 @@ public static void convert(Collection inputFiles, File outputFile) throws RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); for (File inputFile:inputFiles){ Reporter.println("Parsing " + inputFile.getAbsolutePath()); @@ -96,7 +96,7 @@ public static long count(File inputFile) throws Exception { RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); Reporter.println("Parsing (to count)" + inputFile.getAbsolutePath()); repositoryConnection.add(inputFile, DEFAULT_BASE_URI, getFormat(inputFile.getName())); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java index 777b7cdc4..32bd0d745 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java @@ -33,6 +33,7 @@ import java.util.HashSet; import java.util.Set; import java.util.regex.Pattern; + import org.apache.log4j.Logger; import org.bridgedb.DataSource; import org.bridgedb.DataSourcePatterns; @@ -48,10 +49,10 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.Repository; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -85,7 +86,7 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); repositoryConnection.add(stream, DEFAULT_BASE_URI, DEFAULT_FILE_FORMAT); // for (String multiple:multiples){ @@ -283,7 +284,7 @@ private void loadUriPatterns(RepositoryConnection repositoryConnection, Resource } private void checkMultiple(RepositoryConnection repositoryConnection, String multiple) throws Exception{ - URI uri = new URIImpl(multiple); + IRI uri = SimpleValueFactory.getInstance().createIRI(multiple); RepositoryResult accessStatements = repositoryConnection.getStatements(null, null, uri, true); while(accessStatements.hasNext()) { diff --git a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java index 35d3e49c9..5e084af37 100644 --- a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java +++ b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java @@ -16,19 +16,24 @@ package org.bridgedb.rdf; +import static org.hamcrest.Matchers.greaterThan; +import static org.hamcrest.Matchers.hasItem; +import static org.hamcrest.Matchers.lessThan; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertThat; + import java.io.InputStream; import java.util.Set; + import org.bridgedb.DataSource; import org.bridgedb.bio.DataSourceComparator; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; -import static org.hamcrest.Matchers.*; - -import static org.junit.Assert.*; -import org.junit.jupiter.api.*; - import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; +import org.junit.jupiter.api.Test; /** * @@ -46,7 +51,7 @@ public class DataSourceComparatorTest { public void testGetResourceId() { Reporter.println("getResourceId"); DataSource dataSource = DataSource.register("DataSourceUrisTest_testGetResourceId", "DataSourceUrisTest_testGetResourceId").asDataSource(); - Resource expResult = new URIImpl("http://vocabularies.bridgedb.org/ops#DataSource_DataSourceUrisTest_testGetResourceId"); + Resource expResult = SimpleValueFactory.getInstance().createIRI("http://vocabularies.bridgedb.org/ops#DataSource_DataSourceUrisTest_testGetResourceId"); Resource result = BridgeDBRdfHandler.asResource(dataSource); assertEquals(expResult, result); } diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java index 1b6c5f380..f799087f0 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java @@ -19,16 +19,17 @@ // package org.bridgedb.uri.loader; +import java.net.URI; + import org.apache.log4j.Logger; -import org.bridgedb.uri.tools.RegexUriPattern; import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; import org.eclipse.rdf4j.rio.RDFHandlerException; -import org.eclipse.rdf4j.rio.helpers.RDFHandlerBase; +import org.eclipse.rdf4j.rio.helpers.AbstractRDFHandler; /** * Reads an RDF linkset file and passes the information on to a RdfLoader. @@ -39,9 +40,9 @@ * * @author Christian */ -public class LinkHandler extends RDFHandlerBase{ +public class LinkHandler extends AbstractRDFHandler { - protected final URI linkPredicate; + protected final IRI linkPredicate; private boolean symetric; protected final UriListener uriListener; @@ -49,13 +50,13 @@ public class LinkHandler extends RDFHandlerBase{ static final Logger logger = Logger.getLogger(LinkHandler.class); - public LinkHandler(UriListener uriListener, URI linkPredicate, boolean symetric){ + public LinkHandler(UriListener uriListener, IRI linkPredicate, boolean symetric){ this.uriListener = uriListener; this.linkPredicate = linkPredicate; this.symetric = symetric; } - public LinkHandler(UriListener uriListener, URI linkPredicate){ + public LinkHandler(UriListener uriListener, IRI linkPredicate){ this (uriListener, linkPredicate, true); } @@ -87,10 +88,10 @@ public void endRDF() throws RDFHandlerException{ private void insertUriMapping(Statement st) throws RDFHandlerException { Resource subject = st.getSubject(); Value object = st.getObject(); - if (!(subject instanceof URI)){ + if (!(subject instanceof IRI)){ throw new RDFHandlerException ("None URI subject in " + st); } - if (!(object instanceof URI)){ + if (!(object instanceof IRI)){ throw new RDFHandlerException ("None URI object in " + st); } String sourceUri = subject.stringValue(); diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java index 5049c2b92..41709c78b 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java @@ -25,9 +25,9 @@ import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; import org.eclipse.rdf4j.rio.RDFHandlerException; @@ -46,12 +46,12 @@ public class LinksetHandler extends LinkHandler{ protected final String justification; protected final String backwardJustification; - protected final URI mappingSource; + protected final IRI mappingSource; private int noneLinkStatements; static final Logger logger = Logger.getLogger(LinksetHandler.class); - public LinksetHandler(UriListener uriListener, URI linkPredicate, String justification, URI mappingSource){ + public LinksetHandler(UriListener uriListener, IRI linkPredicate, String justification, IRI mappingSource){ super(uriListener, linkPredicate); this.justification = justification; this.mappingSource = mappingSource; @@ -66,7 +66,7 @@ public LinksetHandler(UriListener uriListener, URI linkPredicate, String justifi * @param mappingSource * @param ignore */ - public LinksetHandler(UriListener uriListener, URI linkPredicate, String justification, URI mappingSource, boolean ignore){ + public LinksetHandler(UriListener uriListener, IRI linkPredicate, String justification, IRI mappingSource, boolean ignore){ this(uriListener, linkPredicate, justification, mappingSource); } @@ -91,17 +91,17 @@ public void handleStatement(Statement st) throws RDFHandlerException { * @throws RDFHandlerException */ private void processFirstStatement(Statement st) throws RDFHandlerException{ - final URI predicate = st.getPredicate(); + final IRI predicate = st.getPredicate(); if (predicate.equals(linkPredicate)) { Resource subject = st.getSubject(); Value object = st.getObject(); try { processingFirstStatement = false; - if (!(subject instanceof URI)){ + if (!(subject instanceof IRI)){ Reporter.error("None URI subject in " + st); return; } - if (!(object instanceof URI)){ + if (!(object instanceof IRI)){ Reporter.error("None URI object in " + st); return; } diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java index 783f7110c..7b29d2f59 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java @@ -20,12 +20,12 @@ package org.bridgedb.uri.loader; import java.io.File; -import java.util.Set; +import java.net.URI; + import org.apache.log4j.Logger; import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; -import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.URI; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.rio.RDFHandler; public class LinksetListener { @@ -39,15 +39,15 @@ public LinksetListener(UriListener uriListener){ static final Logger logger = Logger.getLogger(LinksetListener.class); - public int parse(File file, URI linkPredicate, String justification, boolean symetric) throws BridgeDBException{ - URI mappingUri = RdfParser.fileToURL(file); + public int parse(File file, IRI linkPredicate, String justification, boolean symetric) throws BridgeDBException{ + IRI mappingUri = RdfParser.fileToURL(file); LinksetHandler handler = new LinksetHandler(uriListener, linkPredicate, justification, mappingUri, symetric); RdfParser parser = getParser(handler); parser.parse(mappingUri.stringValue(), file); return handler.getMappingsetId(); } - public int parse(File file, URI mappingSource, URI linkPredicate, String justification, + public int parse(File file, IRI mappingSource, IRI linkPredicate, String justification, Boolean symetric) throws BridgeDBException{ LinksetHandler handler = new LinksetHandler(uriListener, linkPredicate, justification, mappingSource, symetric); RdfParser parser = getParser(handler); @@ -55,7 +55,7 @@ public int parse(File file, URI mappingSource, URI linkPredicate, String justifi return handler.getMappingsetId(); } - public int parse(String uri, URI mappingSource, URI linkPredicate, String justification, boolean symetric) + public int parse(String uri, IRI mappingSource, IRI linkPredicate, String justification, boolean symetric) throws BridgeDBException{ LinksetHandler handler = new LinksetHandler(uriListener, linkPredicate, justification, mappingSource, symetric); RdfParser parser = getParser(handler); diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java index d441a645b..679d8f92b 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java @@ -32,9 +32,9 @@ import org.apache.log4j.Logger; import org.bridgedb.uri.loader.transative.TransativeConfig; import org.bridgedb.utils.BridgeDBException; -import org.eclipse.rdf4j.OpenRDFException; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.common.exception.RDF4JException; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.rio.RDFFormat; import org.eclipse.rdf4j.rio.RDFHandler; import org.eclipse.rdf4j.rio.RDFParser; @@ -66,11 +66,10 @@ public void parse(String baseURI, File file, String rdfFormatName) throws Bridge RDFParser parser = getParser(file.getName(), rdfFormatName); parser.setRDFHandler(handler); parser.setParseErrorListener(new LinksetParserErrorListener()); - parser.setVerifyData(true); parser.parse (reader, baseURI); } catch (IOException ex) { throw new BridgeDBException("Error reading " + file.getAbsolutePath() + " " + ex.getMessage(), ex); - } catch (OpenRDFException ex) { + } catch (RDF4JException ex) { throw new BridgeDBException("Error parsing " + file.getAbsolutePath() + " " + ex.getMessage(), ex); } finally { try { @@ -98,11 +97,10 @@ public void parse(InputStream stream, String mappingSource, String rdfFormatName RDFParser parser = getParser(mappingSource, rdfFormatName); parser.setRDFHandler(handler); parser.setParseErrorListener(new LinksetParserErrorListener()); - parser.setVerifyData(true); parser.parse (stream, mappingSource); } catch (IOException ex) { throw new BridgeDBException("Error reading " + mappingSource + " " + ex.getMessage(), ex); - } catch (OpenRDFException ex) { + } catch (RDF4JException ex) { throw new BridgeDBException("Error parsing " + mappingSource + " " + ex.getMessage(), ex); } finally { try { @@ -128,22 +126,22 @@ public InputStream getInputStream(String uri) throws BridgeDBException { } } - public static URI fileToURL(File file) throws BridgeDBException{ + public static IRI fileToURL(File file) throws BridgeDBException{ String baseURI = TransativeConfig.getTransitiveBaseUri(); if (baseURI == null || baseURI.isEmpty()){ return fileToURI(file); } if (file.getParent().equals(TransativeConfig.getTransativeDirectory())){ - return new URIImpl(baseURI + file.getName()); + return SimpleValueFactory.getInstance().createIRI(baseURI + file.getName()); } else { return RdfParser.fileToURI(file); } } - private static URI fileToURI(File file) throws BridgeDBException{ + private static IRI fileToURI(File file) throws BridgeDBException{ try { String uri = file.toURI().toURL().toExternalForm(); - return new URIImpl(uri); + return SimpleValueFactory.getInstance().createIRI(uri); } catch (MalformedURLException ex) { throw new BridgeDBException("Unable to convert file to URI", ex); } diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java index be84bea78..7382bcf63 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java @@ -5,12 +5,13 @@ package org.bridgedb.uri.loader; import java.io.File; + import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.uri.lens.Lens; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -20,7 +21,7 @@ public class SetupWithTestData { static final String MAIN_JUSTIFCATION = "http://semanticscience.org/resource/CHEMINF_000059"; static final String LENS_JUSTIFCATION = "http://www.bridgedb.org/test#testJustification"; - static final URI linkPredicate = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + static final IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); private SQLUriMapper uriListener; private LinksetListener instance; diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java index e76d8743b..c25150890 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java @@ -10,6 +10,7 @@ import java.sql.Connection; import java.sql.ResultSet; import java.sql.SQLException; + import org.apache.log4j.Logger; import org.bridgedb.DataSource; import org.bridgedb.rdf.UriPattern; @@ -24,10 +25,9 @@ import org.bridgedb.uri.tools.RegexUriPattern; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.StatementImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.rio.RDFHandlerException; import org.eclipse.rdf4j.rio.RDFWriter; import org.eclipse.rdf4j.rio.turtle.TurtleWriter; @@ -42,13 +42,13 @@ public class TransativeCreator { private final UriMapper mapper; protected final MappingSetInfo leftInfo; protected final MappingSetInfo rightInfo; - protected final URI predicate; + protected final IRI predicate; protected final String justification; private final RegexUriPattern sourceRegexUriPattern; private final RegexUriPattern targetRegexUriPattern; private final boolean reflexive; - private static URI GENERATE_PREDICATE = null; + private static IRI GENERATE_PREDICATE = null; static final Logger logger = Logger.getLogger(TransativeCreator.class); @@ -73,7 +73,7 @@ protected TransativeCreator(MappingSetInfo left, MappingSetInfo right) mapper = SQLUriMapper.getExisting(); leftInfo = left; rightInfo = right; - predicate = new URIImpl(LoosePredicateMaker.getInstance().combine(left.getPredicate(), right.getPredicate())); + predicate = SimpleValueFactory.getInstance().createIRI(LoosePredicateMaker.getInstance().combine(left.getPredicate(), right.getPredicate())); justification = OpsJustificationMaker.getInstance().combine(left.getJustification(), right.getJustification()); reflexive = left.getSource().getSysCode().equals(right.getTarget().getSysCode()); UriPattern sourceUriPattern = getUriPattern(left.getSource()); @@ -145,10 +145,10 @@ private boolean getSQL(RDFWriter rdfwriter) throws BridgeDBException, IOExceptio //do nothing as same uri; } else { String sourceUri = sourceRegexUriPattern.getUri(sourceId); - URI sourceURI = new URIImpl(sourceUri); + IRI sourceURI = SimpleValueFactory.getInstance().createIRI(sourceUri); String targetUri = targetRegexUriPattern.getUri(targetId); - URI targetURI = new URIImpl(targetUri); - Statement statment = new StatementImpl(sourceURI, predicate, targetURI); + IRI targetURI = SimpleValueFactory.getInstance().createIRI(targetUri); + Statement statment = SimpleValueFactory.getInstance().createStatement(sourceURI, predicate, targetURI); rdfwriter.handleStatement(statment); found = true; } diff --git a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java index 14181297c..429a4f9ee 100644 --- a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java +++ b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java @@ -4,12 +4,14 @@ */ package org.bridgedb.loader; +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.greaterThanOrEqualTo; + import java.io.File; import java.io.FileOutputStream; import java.io.InputStream; import org.apache.commons.io.IOUtils; -import org.bridgedb.loader.transative.TransativeCreatorTest; import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.sql.TestSqlFactory; import org.bridgedb.statistics.MappingSetInfo; @@ -18,22 +20,18 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; - +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import static org.hamcrest.MatcherAssert.assertThat; -import static org.hamcrest.Matchers.*; - /** * * @author Christian */ public class LinksetListenerTest { - static final URI linkPredicate = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + static final IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); static SQLUriMapper uriListener; static LinksetListener instance; diff --git a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java index 36841348f..bfaea772c 100644 --- a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java +++ b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java @@ -20,7 +20,7 @@ package org.bridgedb.loader.transative; import static org.hamcrest.MatcherAssert.assertThat; -import static org.hamcrest.Matchers.*; +import static org.hamcrest.Matchers.greaterThanOrEqualTo; import java.io.File; import java.io.FileOutputStream; @@ -37,10 +37,10 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; /** * @@ -48,7 +48,7 @@ */ public class TransativeCreatorTest { - static final URI linkPredicate = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + static final IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); static SQLUriMapper uriListener; static LinksetListener instance; diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java b/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java index 746c4d7ec..216873956 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java @@ -26,6 +26,7 @@ import java.util.List; import java.util.Properties; import java.util.Set; + import org.apache.log4j.Logger; import org.bridgedb.rdf.BridgeDBRdfHandler; import org.bridgedb.rdf.constants.BridgeDBConstants; @@ -35,11 +36,9 @@ import org.bridgedb.uri.api.UriMapper; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.StatementImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.sail.memory.model.CalendarMemLiteral; /** @@ -291,15 +290,15 @@ public static Set getLensAsRdf(String baseUri, String group) throws B public static Set asRdf(Lens lens, String baseUri) { HashSet results = new HashSet(); - URI subject = new URIImpl(lens.toUri(baseUri)); - results.add(new StatementImpl(subject, RdfConstants.TYPE_URI, BridgeDBConstants.LENS_URI)); - results.add(new StatementImpl(subject, DCTermsConstants.TITLE_URI, new LiteralImpl(lens.getName()))); - results.add(new StatementImpl(subject, DCTermsConstants.DESCRIPTION_URI, new LiteralImpl(lens.getDescription()))); - results.add(new StatementImpl(subject, PavConstants.CREATED_BY, new LiteralImpl(lens.getCreatedBy()))); + IRI subject = SimpleValueFactory.getInstance().createIRI(lens.toUri(baseUri)); + results.add(SimpleValueFactory.getInstance().createStatement(subject, RdfConstants.TYPE_URI, BridgeDBConstants.LENS_URI)); + results.add(SimpleValueFactory.getInstance().createStatement(subject, DCTermsConstants.TITLE_URI, SimpleValueFactory.getInstance().createLiteral(lens.getName()))); + results.add(SimpleValueFactory.getInstance().createStatement(subject, DCTermsConstants.DESCRIPTION_URI, SimpleValueFactory.getInstance().createLiteral(lens.getDescription()))); + results.add(SimpleValueFactory.getInstance().createStatement(subject, PavConstants.CREATED_BY, SimpleValueFactory.getInstance().createLiteral(lens.getCreatedBy()))); CalendarMemLiteral createdOnLiteral = new CalendarMemLiteral(lens, lens.getCreatedOn()); - results.add(new StatementImpl(subject, PavConstants.CREATED_ON, createdOnLiteral)); + results.add(SimpleValueFactory.getInstance().createStatement(subject, PavConstants.CREATED_ON, createdOnLiteral)); for (String justification:lens.getJustifications()){ - results.add(new StatementImpl(subject, BridgeDBConstants.LINKSET_JUSTIFICATION, new URIImpl(justification))); + results.add(SimpleValueFactory.getInstance().createStatement(subject, BridgeDBConstants.LINKSET_JUSTIFICATION, SimpleValueFactory.getInstance().createIRI(justification))); } return results; } diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java b/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java index 4e1b00c7a..d05e438c3 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java @@ -26,11 +26,9 @@ import org.bridgedb.uri.lens.Lens; import org.bridgedb.uri.lens.LensTools; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.ContextStatementImpl; -import org.eclipse.rdf4j.model.impl.StatementImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -38,41 +36,41 @@ */ public class DirectStatementMaker implements StatementMaker{ - protected final URI toURI(String text){ + protected final IRI toURI(String text){ try { - return new URIImpl(text); + return SimpleValueFactory.getInstance().createIRI(text); } catch (IllegalArgumentException ex){ - return new URIImpl("<" + text + ">"); + return SimpleValueFactory.getInstance().createIRI("<" + text + ">"); } } private Set asRDF(SetMappings setMappings, String lens, String baseUri, String methodName) throws BridgeDBException { HashSet statements = new HashSet(); - URI setUri; - setUri = new URIImpl(baseUri + methodName + "/" + setMappings.getId()); - URI predicateURI = toURI(setMappings.getPredicate()); - Statement statement = new StatementImpl(setUri, VoidConstants.LINK_PREDICATE, predicateURI); + IRI setUri; + setUri = SimpleValueFactory.getInstance().createIRI(baseUri + methodName + "/" + setMappings.getId()); + IRI predicateURI = toURI(setMappings.getPredicate()); + Statement statement = SimpleValueFactory.getInstance().createStatement(setUri, VoidConstants.LINK_PREDICATE, predicateURI); statements.add(statement); - URI justifcationURI = toURI(setMappings.getJustification()); - statement = new StatementImpl(setUri, DulConstants.EXPRESSES, justifcationURI); + IRI justifcationURI = toURI(setMappings.getJustification()); + statement = SimpleValueFactory.getInstance().createStatement(setUri, DulConstants.EXPRESSES, justifcationURI); statements.add(statement); String source = setMappings.getMappingSource(); if (source != null && !source.isEmpty()){ - URI mappingSourceURI = toURI(setMappings.getMappingSource()); - statement = new StatementImpl(setUri, VoidConstants.DATA_DUMP, mappingSourceURI); + IRI mappingSourceURI = toURI(setMappings.getMappingSource()); + statement = SimpleValueFactory.getInstance().createStatement(setUri, VoidConstants.DATA_DUMP, mappingSourceURI); statements.add(statement); } if (lens != null){ Lens theLens = LensTools.byId(lens); - URI lensUri = new URIImpl(theLens.toUri(baseUri)); - URI hasLensUri = BridgeDBConstants.FULFILLS_LENS; - statement = new StatementImpl(setUri, hasLensUri, lensUri); + IRI lensUri = SimpleValueFactory.getInstance().createIRI(theLens.toUri(baseUri)); + IRI hasLensUri = BridgeDBConstants.FULFILLS_LENS; + statement = SimpleValueFactory.getInstance().createStatement(setUri, hasLensUri, lensUri); statements.add(statement); } for (UriMapping mapping:setMappings.getMappings()){ - URI sourceURI = toURI(mapping.getSourceUri()); - URI targetURI = toURI(mapping.getTargetUri()); - statement = new ContextStatementImpl(sourceURI, predicateURI, targetURI, setUri); + IRI sourceURI = toURI(mapping.getSourceUri()); + IRI targetURI = toURI(mapping.getTargetUri()); + statement = SimpleValueFactory.getInstance().createStatement(sourceURI, predicateURI, targetURI, setUri); statements.add(statement); } return statements; @@ -95,9 +93,9 @@ public Set asRDF(MappingsBySet mappingsBySet, String baseUri, String for (UriMapping mapping:mappingsBySet.getMappings()){ //Inclusion of mapping to self at Antonis request April 2014 //if (!mapping.getSourceUri().equals(mapping.getTargetUri())){ - URI sourceURI = toURI(mapping.getSourceUri()); - URI targetURI = toURI(mapping.getTargetUri()); - Statement statement = new StatementImpl(sourceURI, OWLConstants.SAMEAS_URI, targetURI); + IRI sourceURI = toURI(mapping.getSourceUri()); + IRI targetURI = toURI(mapping.getTargetUri()); + Statement statement = SimpleValueFactory.getInstance().createStatement(sourceURI, OWLConstants.SAMEAS_URI, targetURI); statements.add(statement); //} } @@ -105,7 +103,7 @@ public Set asRDF(MappingsBySet mappingsBySet, String baseUri, String return statements; } - protected URI mappingSetURI(String id, String baseUri, String predicateURI){ + protected IRI mappingSetURI(String id, String baseUri, String predicateURI){ String uriStr = baseUri + UriConstants.MAPPING_SET + UriConstants.RDF + "/" + id; if (predicateURI != null) { String p; @@ -129,28 +127,28 @@ private String encodeWithinQuery(String str) { @Override public Set asRDF(MappingSetInfo info, String baseUri, String contextString) throws BridgeDBException{ HashSet results = new HashSet(); - URI linksetId = mappingSetURI(info.getStringId(), baseUri, null); - URI source = toURI(info.getMappingSource()); - URI context = new URIImpl(contextString); - results.add(new ContextStatementImpl(linksetId, PavConstants.IMPORTED_FROM, source, context)); - URI predicate = toURI(info.getPredicate()); - results.add(new ContextStatementImpl(linksetId, VoidConstants.LINK_PREDICATE, predicate, context)); - URI justification = toURI(info.getJustification()); - results.add(new ContextStatementImpl(linksetId, BridgeDBConstants.LINKSET_JUSTIFICATION, justification, context)); + IRI linksetId = mappingSetURI(info.getStringId(), baseUri, null); + IRI source = toURI(info.getMappingSource()); + IRI context = SimpleValueFactory.getInstance().createIRI(contextString); + results.add(SimpleValueFactory.getInstance().createStatement(linksetId, PavConstants.IMPORTED_FROM, source, context)); + IRI predicate = toURI(info.getPredicate()); + results.add(SimpleValueFactory.getInstance().createStatement(linksetId, VoidConstants.LINK_PREDICATE, predicate, context)); + IRI justification = toURI(info.getJustification()); + results.add(SimpleValueFactory.getInstance().createStatement(linksetId, BridgeDBConstants.LINKSET_JUSTIFICATION, justification, context)); return results; } - private void addMappingsRDF(Set statements, Mapping mapping, URI predicateUri, URI mappingSet) throws BridgeDBException{ + private void addMappingsRDF(Set statements, Mapping mapping, IRI predicateUri, IRI mappingSet) throws BridgeDBException{ for (String source:mapping.getSourceUri()){ - URI sourceUri = new URIImpl(source); + IRI sourceUri = SimpleValueFactory.getInstance().createIRI(source); for (String target: mapping.getTargetUri()){ - URI targetUri = new URIImpl(target); - statements.add(new ContextStatementImpl(sourceUri, predicateUri, targetUri, mappingSet)); + IRI targetUri = SimpleValueFactory.getInstance().createIRI(target); + statements.add(SimpleValueFactory.getInstance().createStatement(sourceUri, predicateUri, targetUri, mappingSet)); } } } - protected void addLinksetInfo(Set statements, Mapping mapping, URI mappingSet) throws BridgeDBException{ + protected void addLinksetInfo(Set statements, Mapping mapping, IRI mappingSet) throws BridgeDBException{ if (mapping.isMappingToSelf()){ //No void for mapping to self at the moment. } else if (mapping.isTransitive()){ @@ -162,26 +160,26 @@ protected void addLinksetInfo(Set statements, Mapping mapping, URI ma } } - protected void addMappingVoid(Set statements, Mapping mapping, URI mappingSet) + protected void addMappingVoid(Set statements, Mapping mapping, IRI mappingSet) throws BridgeDBException { - URI sourceUri = toURI(mapping.getMappingSource()); - statements.add(new ContextStatementImpl(mappingSet, PavConstants.DERIVED_FROM, sourceUri, mappingSet)); + IRI sourceUri = toURI(mapping.getMappingSource()); + statements.add(SimpleValueFactory.getInstance().createStatement(mappingSet, PavConstants.DERIVED_FROM, sourceUri, mappingSet)); } private void addSelfMappingsRDF(Set statements, Mapping mapping, String selfMappingPredicateURI) throws BridgeDBException{ - URI predicate; + IRI predicate; if (selfMappingPredicateURI == null || selfMappingPredicateURI.isEmpty()) { predicate = OWLConstants.SAMEAS_URI; } else { - predicate = new URIImpl(selfMappingPredicateURI); + predicate = SimpleValueFactory.getInstance().createIRI(selfMappingPredicateURI); } for (String source:mapping.getSourceUri()){ - URI sourceUri = new URIImpl(source); + IRI sourceUri = SimpleValueFactory.getInstance().createIRI(source); for (String target: mapping.getTargetUri()){ if (!source.equals(target)){ - URI targetUri = new URIImpl(target); - statements.add(new StatementImpl(sourceUri, predicate, targetUri)); + IRI targetUri = SimpleValueFactory.getInstance().createIRI(target); + statements.add(SimpleValueFactory.getInstance().createStatement(sourceUri, predicate, targetUri)); } } } @@ -200,8 +198,8 @@ public Set asRDF(Set mappings, String baseUri, boolean links } if (predicate != null){ String id = mapping.getMappingSetId(); - URI mappingSet = mappingSetURI(id, baseUri, overridePredicateURI); - URI predicateUri = new URIImpl(predicate); + IRI mappingSet = mappingSetURI(id, baseUri, overridePredicateURI); + IRI predicateUri = SimpleValueFactory.getInstance().createIRI(predicate); addMappingsRDF(statements, mapping, predicateUri, mappingSet); if (linksetInfo){ addLinksetInfo(statements, mapping, mappingSet); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java index 4738159c3..d1eee6396 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java @@ -21,7 +21,10 @@ package org.bridgedb.mysql; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.util.Date; + import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.sql.TestSqlFactory; import org.bridgedb.statistics.OverallStatistics; @@ -29,13 +32,10 @@ import org.bridgedb.uri.lens.Lens; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; - -import org.junit.jupiter.api.Test; import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.impl.URIImpl; - -import static org.junit.jupiter.api.Assertions.assertEquals; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; /** @@ -68,7 +68,7 @@ public void testRecover()throws BridgeDBException{ stats = uriMapper.getOverallStatistics(Lens.ALL_LENS_NAME); assertEquals(12, stats.getNumberOfMappings()); assertEquals(4, stats.getNumberOfMappingSets()); - Resource resource = new URIImpl("http://example.com/1to2Another"); + Resource resource = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2Another"); int mappingSet = listener.registerMappingSet(regexUriPattern1, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern2, resource); assertEquals(5, mappingSet); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java index 557742e5f..b158346fd 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java @@ -20,7 +20,11 @@ package org.bridgedb.mysql.transative; +import static org.bridgedb.uri.UriListenerTest.SYMETRIC; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.util.Set; + import org.bridgedb.DataSource; import org.bridgedb.pairs.IdSysCodePair; import org.bridgedb.rdf.UriPattern; @@ -28,9 +32,6 @@ import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.sql.TestSqlFactory; import org.bridgedb.sql.transative.DirectMapping; -import static org.bridgedb.uri.UriListenerTest.SYMETRIC; -import static org.junit.jupiter.api.Assertions.assertEquals; - import org.bridgedb.uri.api.Mapping; import org.bridgedb.uri.lens.Lens; import org.bridgedb.uri.lens.LensTools; @@ -38,11 +39,10 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; - +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Tag; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; /** * Tests the UriMapper interface (and by loading the UriListener interface) @@ -162,107 +162,107 @@ public static void setupIDMapper() throws BridgeDBException{ public static void loadData() throws BridgeDBException{ - URI source = new URIImpl("http://example.com/TransitiveTest/AtoB"); + IRI source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoB"); mappingSetAB = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternB, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoB2"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoB2"); mappingSetAB2 = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE2, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternB, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoC"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoC"); mappingSetAC = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoD"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoD"); mappingSetAD = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoE"); mappingSetAE = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoF"); mappingSetAF = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoC"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoC"); mappingSetBC = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoC2"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoC2"); mappingSetBC2 = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE2, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoC9"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoC9"); mappingSetBC9 = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, TEST_JUSTIFICATION9, TEST_JUSTIFICATION9, regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoD"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoD"); mappingSetBD = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoE"); mappingSetBE = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoF"); mappingSetBF = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoD"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoD"); mappingSetCD = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoD2"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoD2"); mappingSetCD2 = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE2, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoD9"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoD9"); mappingSetCD9 = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, TEST_JUSTIFICATION9, TEST_JUSTIFICATION9, regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoE"); mappingSetCE = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoF"); mappingSetCF = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/DtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/DtoE"); mappingSetDE = sqlUriMapper.registerMappingSet(regexUriPatternD, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/DtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/DtoF"); mappingSetDF = sqlUriMapper.registerMappingSet(regexUriPatternD, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/EtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/EtoE"); mappingSetEE = sqlUriMapper.registerMappingSet(regexUriPatternE, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/EtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/EtoF"); mappingSetEF = sqlUriMapper.registerMappingSet(regexUriPatternE, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/FtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/FtoF"); mappingSetFF = sqlUriMapper.registerMappingSet(regexUriPatternF, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoX"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoX"); mappingSetAX = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternX, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoX"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoX"); mappingSetCX = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternX, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoY"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoY"); mappingSetAY = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternY, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoY"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoY"); mappingSetCY = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternY, source); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java index 441cc3c36..8d12943bd 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java @@ -21,8 +21,11 @@ package org.bridgedb.uri; +import static org.junit.jupiter.api.Assertions.assertFalse; + import java.util.Set; import java.util.regex.Pattern; + import org.bridgedb.DataSourcePatterns; import org.bridgedb.Xref; import org.bridgedb.rdf.UriPattern; @@ -33,13 +36,10 @@ import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.IDMapperTestBase; - +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Tag; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; - -import static org.junit.jupiter.api.Assertions.assertFalse; /** * Base class of all Test using Uris @@ -215,14 +215,14 @@ public static void setupUriPatterns() throws BridgeDBException{ */ public static void loadDataPart1() throws BridgeDBException{ - URI source = new URIImpl("http://example.com/1to2"); + IRI source = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2"); mappingSet1to2 = listener.registerMappingSet(regexUriPattern1, TEST_PREDICATE, Lens.getDefaultJustifictaionString(), Lens.getDefaultJustifictaionString(), regexUriPattern2, source); listener.insertUriMapping(map1Uri1, map1Uri2, mappingSet1to2, SYMETRIC); listener.insertUriMapping(map2Uri1, map2Uri2, mappingSet1to2, SYMETRIC); listener.insertUriMapping(map3Uri1, map3Uri2, mappingSet1to2, SYMETRIC); - source = new URIImpl("http://example.com/2to3"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3"); mappingSet2to3 = listener.registerMappingSet(regexUriPattern2, TEST_PREDICATE, Lens.getDefaultJustifictaionString(), Lens.getDefaultJustifictaionString(), regexUriPattern3, source); listener.insertUriMapping(map1Uri2, map1Uri3, mappingSet2to3, SYMETRIC); @@ -232,21 +232,21 @@ public static void loadDataPart1() throws BridgeDBException{ //Close here to test recover listener.closeInput(); - source = new URIImpl("http://example.com/3to3Lensed"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/3to3Lensed"); mappingSet3to3Lensed = listener.registerMappingSet(regexUriPattern3, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern3, source); listener.insertUriMapping(map1Uri3, map1AUri3, mappingSet3to3Lensed, SYMETRIC); listener.insertUriMapping(map2Uri3, map2AUri3, mappingSet3to3Lensed, SYMETRIC); listener.insertUriMapping(map3Uri3, map3AUri3, mappingSet3to3Lensed, SYMETRIC); - source = new URIImpl("http://example.com/1to2lensed"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2lensed"); mappingSet1to2Lensed = listener.registerMappingSet(regexUriPattern1, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern2, source); listener.insertUriMapping(map1AUri1, map1AUri2, mappingSet1to2Lensed, SYMETRIC); listener.insertUriMapping(map2AUri1, map2AUri2, mappingSet1to2Lensed, SYMETRIC); listener.insertUriMapping(map3AUri1, map3AUri2, mappingSet1to2Lensed, SYMETRIC); - source = new URIImpl("http://example.com/2to3"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3"); mappingSet2to3Lensed = listener.registerMappingSet(regexUriPattern2, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern3, source); listener.insertUriMapping(map1AUri2, map1AUri3, mappingSet2to3Lensed, SYMETRIC); @@ -267,7 +267,7 @@ public static void loadData() throws BridgeDBException{ * @throws BridgeDBException */ public static void loadData2Way() throws BridgeDBException{ - URI source = new URIImpl("http://example.com/2to3Lensed"); + IRI source = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3Lensed"); int mappingSet = listener.registerMappingSet(regexUriPattern2, TEST_PREDICATE, Lens.getTestJustifictaion() +"Forward", Lens.getTestJustifictaion() +"BackWard", regexUriPattern3, source); listener.insertUriMapping(map1Uri2, map1AUri3, mappingSet, SYMETRIC); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java index fd7540036..d7662147a 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java @@ -19,6 +19,9 @@ */ package org.bridgedb.uri; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.util.Set; import org.bridgedb.DataSource; @@ -26,18 +29,16 @@ import org.bridgedb.statistics.MappingSetInfo; import org.bridgedb.uri.api.Mapping; import org.bridgedb.uri.tools.StatementMaker; -import org.junit.jupiter.api.*; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Model; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.model.impl.TreeModel; -import org.eclipse.rdf4j.model.impl.URIImpl; import org.eclipse.rdf4j.rio.RDFFormat; import org.eclipse.rdf4j.rio.RDFHandlerException; import org.eclipse.rdf4j.rio.Rio; - -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertTrue; +import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; /** * Tests the UriMapper interface (and by loading the UriListener interface) @@ -57,20 +58,20 @@ public abstract class UriMapperRdfTest extends UriListenerTest{ public static StatementMaker statementMaker; - URI mappingSet1 = new URIImpl("http://example.com/testBasemappingSetRDF/1"); - URI linksetJustification = new URIImpl("http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl#linksetJustification"); - URI inChlKey = new URIImpl("http://semanticscience.org/resource/CHEMINF_000059"); + IRI mappingSet1 = SimpleValueFactory.getInstance().createIRI("http://example.com/testBasemappingSetRDF/1"); + IRI linksetJustification = SimpleValueFactory.getInstance().createIRI("http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl#linksetJustification"); + IRI inChlKey = SimpleValueFactory.getInstance().createIRI("http://semanticscience.org/resource/CHEMINF_000059"); - URI importedFrom = new URIImpl("http://purl.org/pav/importedFrom"); - URI derivedFrom = new URIImpl("http://purl.org/pav/derivedFrom"); - URI example1to2 = new URIImpl("http://example.com/1to2"); - URI linkPredicate = new URIImpl("http://rdfs.org/ns/void#linkPredicate"); - URI exactMatch = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + IRI importedFrom = SimpleValueFactory.getInstance().createIRI("http://purl.org/pav/importedFrom"); + IRI derivedFrom = SimpleValueFactory.getInstance().createIRI("http://purl.org/pav/derivedFrom"); + IRI example1to2 = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2"); + IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://rdfs.org/ns/void#linkPredicate"); + IRI exactMatch = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); - URI sameAs = new URIImpl("http://www.w3.org/2002/07/owl#sameAs"); - URI concept = new URIImpl("http://www.conceptwiki.org/concept/f25a234e-df03-419f-8504-cde8689a4d1f"); + IRI sameAs = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2002/07/owl#sameAs"); + IRI concept = SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/f25a234e-df03-419f-8504-cde8689a4d1f"); - URI override = new URIImpl("http://example.com/override"); + IRI override = SimpleValueFactory.getInstance().createIRI("http://example.com/override"); public void checkMapping(Mapping mapping){ if (!mapping.isMappingToSelf()){ @@ -116,22 +117,22 @@ public void testMappingNoLink() throws Exception { Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", false, null); Model m = asModel(rdf); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @@ -143,34 +144,34 @@ public void testMappingNoLinkFixedPredicate() throws Exception { Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", true, "http://example.com/override"); Model m = asModel(rdf); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, override, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); - assertTrue(m.contains(concept, override, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); - URI mapSet1Override = new URIImpl("http://example.com/testContextmappingSetRDF/1?predicate=http%3A%2F%2Fexample.com%2Foverride"); - URI mapSet1_3Override = new URIImpl("http://example.com/testContextmappingSetRDF/1_3?predicate=http%3A%2F%2Fexample.com%2Foverride"); - URI example1to2 = new URIImpl("http://example.com/1to2"); - URI example2to3 = new URIImpl("http://example.com/2to3"); + IRI mapSet1Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1?predicate=http%3A%2F%2Fexample.com%2Foverride"); + IRI mapSet1_3Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1_3?predicate=http%3A%2F%2Fexample.com%2Foverride"); + IRI example1to2 = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2"); + IRI example2to3 = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3"); // FIXME: Exactly how should the provenance chains go here? -// URIImpl mapset1 = new URIImpl("http://example.com/testContextmappingSetRDF/1"); +// URIImpl mapset1 = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1"); // assertTrue(m.contains(mapSet1Override, derivedFrom, mapset1)); // assertTrue(m.contains(mapset1, derivedFrom, example1to2)); // -// URIImpl mapset1_3 = new URIImpl("http://example.com/testContextmappingSetRDF/1_3"); +// URIImpl mapset1_3 = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1_3"); // assertTrue(m.contains(mapSet1_3Override, derivedFrom, mapset1_3)); // assertTrue(m.contains(mapset1_3, derivedFrom, example1to2)); // assertTrue(m.contains(mapset1_3, derivedFrom, example2to3)); @@ -183,22 +184,22 @@ public void testMappingWithLink() throws Exception { Set mappings = uriMapper.mapFull(map1Uri1, null, true, null, null); Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", false, "http://example.com/override"); Model m = asModel(rdf); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - - assertTrue(m.contains(concept, override, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); - - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); - - assertTrue(m.contains(concept, override, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); + + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); + + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @Test @@ -207,22 +208,22 @@ public void testMappingWithLinkOverride() throws Exception { Set mappings = uriMapper.mapFull(map1Uri1, null, true, null, null); Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", false, null); Model m = asModel(rdf); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); - - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); - - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); + + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); + + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } } diff --git a/pom.xml b/pom.xml index 32eba4c2d..559693c52 100644 --- a/pom.xml +++ b/pom.xml @@ -52,7 +52,7 @@ 8.0.33 Tomcat 3.4 - 3.7.7 + 4.0.0 2.5 2.0.9 10.15.2.0 From 32b6d3363d33dfbcbbc5d02ff7937f15c3f8488b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 18:35:07 +0100 Subject: [PATCH 18/64] Updated RDF4J to 4.3.8 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 559693c52..be0f298ff 100644 --- a/pom.xml +++ b/pom.xml @@ -52,7 +52,7 @@ 8.0.33 Tomcat 3.4 - 4.0.0 + 4.3.8 2.5 2.0.9 10.15.2.0 From 6cd348ee8905f8029c2142ddf106ca554d1c5e13 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 18:52:01 +0100 Subject: [PATCH 19/64] BridgeDb Datasources 20231202 --- org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv | 2 +- .../src/main/resources/org/bridgedb/bio/datasources.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index d8c7d7b47..1c4891254 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -54,7 +54,7 @@ ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapie Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction -InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein +InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index d8c7d7b47..1c4891254 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -54,7 +54,7 @@ ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapie Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction -InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein +InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication From 2ab0822ee40c9fc1afb7b0a3d580bba0bb8854f0 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 19:19:21 +0100 Subject: [PATCH 20/64] Updated to match the new BridgeDb Datasources --- org.bridgedb.rdf/resources/DataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 9b881fdf5..950b8ac7a 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -646,7 +646,7 @@ bridgeDB:DataSource_InterPro a bridgeDB:DataSource ; bridgeDB:idExample "IPR000100" ; bridgeDB:primary "true"^^ ; bridgeDB:type "protein" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index eb1ca8d2a..e97443446 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -1,4 +1,4 @@ - @prefix bridgeDB: . +@prefix bridgeDB: . @prefix dcat: . @prefix dcterms: . @@ -3101,7 +3101,7 @@ bridgeDB:DataSource_InterPro a bridgeDB:DataSource ; bridgeDB:idExample "IPR000100" ; bridgeDB:primary "true"^^ ; bridgeDB:type "protein" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^IPR\\d{6}$" ; @@ -11427,8 +11427,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/interpro/entry/InterPro/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/interpro/entry/" . From 13a62d719f0d3e90f696eea0c396e0bf1f5b9287 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 2 Dec 2023 20:03:15 +0100 Subject: [PATCH 21/64] Two further updates for JUnit --- org.bridgedb.rdb/pom.xml | 2 +- pom.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index b49633bab..3cd3a306c 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -108,7 +108,7 @@ org.junit.platform junit-platform-launcher - 1.9.3 + 1.10.1 test diff --git a/pom.xml b/pom.xml index be0f298ff..368363eb0 100644 --- a/pom.xml +++ b/pom.xml @@ -57,7 +57,7 @@ 2.0.9 10.15.2.0 1.3.2 - 5.10.0 + 5.10.1 mysql From 58f42e000a35662f323b3188e20df2aed7ed8c18 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 18 Dec 2023 11:49:22 +0100 Subject: [PATCH 22/64] Log4j 2.22 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 368363eb0..7d960b9b8 100644 --- a/pom.xml +++ b/pom.xml @@ -48,7 +48,7 @@ 3.2.14 2.2 1.10 - 2.20.0 + 2.22.0 8.0.33 Tomcat 3.4 From 8af1e7907df304e0d608a5f60f1917bb54710534 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 18 Dec 2023 12:31:19 +0100 Subject: [PATCH 23/64] Release 3.1.1 --- CITATION.cff | 4 ++-- README.md | 12 ++++++------ examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- org.bridgedb/src/main/resources/version.props | 2 +- pom.xml | 2 +- 29 files changed, 38 insertions(+), 38 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 4bfe1388e..716c1c9a7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.1.0 -date-released: '2023-11-05' +version: 3.1.1 +date-released: '2023-12-18' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 5fced022b..dbeb70269 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.0`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.1`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.0 + 3.1.1 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.0' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.1' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.0' +'org.bridgedb:org.bridgedb.bio:jar:3.1.1' ``` @@ -133,7 +133,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.0 +mvn versions:set -DnewVersion=3.1.2-SNAPSHOT mvn clean deploy ``` diff --git a/examples/pom.xml b/examples/pom.xml index 0d846839d..8f520b6c3 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index d27fe4cb8..5edbf57bb 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 6cf3c0747..b5c3a3c96 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index a04609afb..e2e49b203 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index a4ebb736a..d73e02894 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 3cd3a306c..282d4c103 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 86cc48316..af50b8cc1 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 906378f1d..37893c4cc 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 97dac4e30..7152afd91 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 compile org.bridgedb org.bridgedb.bio - 3.1.1-SNAPSHOT + 3.1.1 compile org.bridgedb org.bridgedb.rdb - 3.1.1-SNAPSHOT + 3.1.1 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 06fcfd984..299b5d02a 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 14e8a177d..4daabcfc8 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 508a522df..51f1d0627 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 5e98f4024..5e8c6f957 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 3a10ac109..9a3d64760 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index efc09f859..ea4e50116 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 3f746819b..9d1369447 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 093873e9a..06ba63833 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 8d15232f0..d6b6ee1fa 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 0b3b58fa1..badebf1ce 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 069cbc011..5245abf57 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index b20768f56..a3d85fcba 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 2019f425f..272b44eec 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 328f127eb..22a1b841b 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index d535b5f68..4ccb52e5f 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index f1ea89d80..51dace4ed 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.1-SNAPSHOT + 3.1.1 diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index fff58826a..3d10b72ab 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.1.0 +bridgedb.version=3.1.1 diff --git a/pom.xml b/pom.xml index 7d960b9b8..9ba7bc0b1 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.1-SNAPSHOT + 3.1.1 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 91b9a9e5e7834c5e26737f029f77b648d6a7af25 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Fri, 26 Jul 2024 07:51:27 +0200 Subject: [PATCH 24/64] Open for development --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 8f520b6c3..fcebe7a70 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 5edbf57bb..b63dda2b2 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index b5c3a3c96..194f6548e 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index e2e49b203..1655d6b1a 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index d73e02894..d45ad5df8 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 282d4c103..61d780844 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index af50b8cc1..83ca9b27a 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 37893c4cc..c0555e252 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 7152afd91..9889d24d9 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.1 + 3.1.2-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.1 + 3.1.2-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 299b5d02a..2a6fdd71a 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 4daabcfc8..ecb265353 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 51f1d0627..37768a064 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 5e8c6f957..8bce22c78 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 9a3d64760..cb9f80dbe 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index ea4e50116..379b9ba3d 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 9d1369447..69919c820 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 06ba63833..a350d9c72 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index d6b6ee1fa..30c55a733 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index badebf1ce..3aaaeeb59 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 5245abf57..c30eb03a2 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index a3d85fcba..eea6d5376 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 272b44eec..308d74fc9 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 22a1b841b..68d3bdfe9 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 4ccb52e5f..fba9a3dd9 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 51dace4ed..e3881be63 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.1 + 3.1.2-SNAPSHOT diff --git a/pom.xml b/pom.xml index 9ba7bc0b1..d2dbb521c 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.1 + 3.1.2-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 88e5bbca0d15ca5d3c3589a77c6a61ce6de5bec1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:37:18 +0200 Subject: [PATCH 25/64] Added a line on how to compile with Java 8 (e.g. for PathVisio) --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index dbeb70269..847361b70 100644 --- a/README.md +++ b/README.md @@ -58,6 +58,8 @@ able to compile with a simple: mvn clean install -Dgpg.skip ``` +When compiling the Java8-compatible components, use the `pom-java8.xml` file instead, with `mvn -f pom-java8.xml`. + You can find the libraries in the folder called "target", in each sublibrary folder (used to be called "dist" in ant). If you want to ignore failing tests, e.g. because you are not online, From 3414c198bbb8c7c394df348c13699487340c31bd Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:51:30 +0200 Subject: [PATCH 26/64] Added some syntax highlighting --- UPGRADE_NOTES.md | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/UPGRADE_NOTES.md b/UPGRADE_NOTES.md index f6b3f5dab..53aa00618 100644 --- a/UPGRADE_NOTES.md +++ b/UPGRADE_NOTES.md @@ -1,35 +1,49 @@ -Upgrade notes to BridgeDb 2.0 +# Upgrade notes to BridgeDb 2.0 -1. Initialing data sources +## 1. Initialing data sources Replace +```java BioDataSource.init(); +``` with +```java DataSourceTxt.init(); +``` -2. Getting DataSource's +## 2. Getting DataSource's Replace +```java DataSource ds = DataSource.getBySystemCode("Ck"); +``` with +```java DataSource ds = DataSource.getExistingBySystemCode("Ck"); +``` Similarly, and more important: +```java DataSource ds = DataSource.getByFullName("PubChem-compound"); +``` with +```java DataSource ds = DataSource.getExistingByFullName("PubChem-compound"); +``` -The latter two new methods throw an IllegalArgumentException if the DataSource does not exist. +The latter two new methods throw an `IllegalArgumentException` if the `DataSource` does not exist. Use one of the following two methods to check first: +```java DataSource.systemCodeExists("Ck"); DataSource.fullNameExists("PubChem-compound"); +``` From 4bea7ea599363f1336c1d05a68a75c764675f50b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:52:58 +0200 Subject: [PATCH 27/64] BridgeDb Datasources 202407252 --- .../org/bridgedb/bio/datasources.tsv | 34 +++++++++---------- .../resources/org/bridgedb/bio/organisms.tsv | 1 + .../org/bridgedb/bio/datasources.tsv | 32 ++++++++--------- .../resources/org/bridgedb/bio/organisms.tsv | 1 + 4 files changed, 35 insertions(+), 33 deletions(-) diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 1c4891254..770e6c833 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe -Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe +Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe +Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene -BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction -BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway -BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway -BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein -BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite +BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene +BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction +BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway +BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway +BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein +BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite -CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene +CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite -ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite +ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction @@ -35,9 +35,9 @@ GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nucco Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene -Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene +Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene -Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene @@ -77,7 +77,7 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction -miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material @@ -85,7 +85,7 @@ NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana NCBI Protein Np http://www.ncbi.nlm.nih.gov/protein http://www.ncbi.nlm.nih.gov/protein/$id CAA71118.1 protein 1 urn:miriam:ncbiprotein ^\w+\d+(\.\d+)?$ NCBI Protein ncbiprotein protein NCI Pathway Interaction Database Pid http://pid.nci.nih.gov/ http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id pi3kcipathway pathway 1 urn:miriam:pid.pathway ^\w+$ NCI Pathway Interaction Database pid.pathway pathway OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:mim ^[*#+%^]?\d{6}$ OMIM P492 omim gene,disease -OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ ensembl gene +OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ gene ORCID orcid https://orcid.org https://orcid.org/$id 0000-0002-5355-2576 other Homo sapiens 1 urn:miriam:orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID P496 orcid other,author Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orphanet other Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene @@ -110,7 +110,7 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene -RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene +RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene @@ -125,7 +125,7 @@ SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/s SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology -TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene +TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv index f20b733ea..560d65f42 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv @@ -43,6 +43,7 @@ Rattus norvegicus Rat Rn 10116 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index 1c4891254..bb0f7d8cb 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe -Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe +Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe +Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene -BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction -BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway -BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway -BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein -BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite +BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene +BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction +BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway +BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway +BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein +BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite -CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene +CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite -ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite +ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction @@ -35,9 +35,9 @@ GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nucco Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene -Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene +Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene -Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene @@ -77,7 +77,7 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction -miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material @@ -110,7 +110,7 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene -RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene +RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene @@ -125,7 +125,7 @@ SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/s SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology -TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene +TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv index f20b733ea..560d65f42 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv @@ -43,6 +43,7 @@ Rattus norvegicus Rat Rn 10116 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 From f330b5cc4bf27ccff8e1b98ed6b712e8d82278c2 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:09:24 +0200 Subject: [PATCH 28/64] Use https for ChemSpider --- org.bridgedb.rdf/resources/BioDataSource.ttl | 2 +- org.bridgedb.rdf/resources/DataSource.ttl | 10 +++--- .../resources/IdentifiersOrgDataSource.ttl | 32 +++++++++---------- .../resources/IdentifiersOrgDataSource.txt | 4 +-- org.bridgedb.rdf/resources/MiriamRegistry.ttl | 12 +++---- org.bridgedb.rdf/test-data/DataSourceMin.ttl | 8 ++--- .../rdf/DataSourceComparatorTest.java | 2 +- .../src/test/resources/test-data/cs-ops.ttl | 4 +-- .../resources/test-data/cs-ops_lensed.ttl | 4 +-- .../src/test/resources/test-data/cw-cs.ttl | 2 +- .../test/resources/test-data/cw-cs_lensed.ttl | 2 +- .../resources/test-data/ops-ops_lensed.ttl | 2 +- .../org/bridgedb/uri/UriListenerTest.java | 2 +- .../org/bridgedb/uri/UriMapperRdfTest.java | 32 +++++++++---------- .../java/org/bridgedb/IDMapperTestBase.java | 2 +- 15 files changed, 60 insertions(+), 60 deletions(-) diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 33127c1de..52ef12bcb 100644 --- a/org.bridgedb.rdf/resources/BioDataSource.ttl +++ b/org.bridgedb.rdf/resources/BioDataSource.ttl @@ -115,7 +115,7 @@ bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 950b8ac7a..91f9b7d43 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -286,16 +286,16 @@ bridgeDB:DataSource_ChEMBL_target_component a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index e97443446..cb04c8a2a 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -1055,16 +1055,16 @@ bridgeDB:DataSource_ChemIDplus a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; dcterms:alternative "ChemSpider" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; @@ -3029,11 +3029,11 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ; bridgeDB:idExample "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:fullName "InChIKey" ; @@ -3045,7 +3045,7 @@ bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-N])?" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_IntAct a bridgeDB:DataSource ; bridgeDB:fullName "IntAct" ; @@ -11292,22 +11292,22 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; bridgeDB:hasPrefix "http://www.cellsignal.com/reference/pathway/" ; bridgeDB:hasPostfix ".html" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".html" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".rdf" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/inchi-resolver/Resolver.aspx?q=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/inchi-resolver/Resolver.aspx?q=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.conceptwiki.org/concept/" . diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index ac92510e3..917d59c9e 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -94,7 +94,7 @@ LinkedChemistry ChEMBL target linkedchemistry.chembl.target http://l ChemDB chemdb http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id 3966782 unknown 1 urn:miriam:chemdb ^\d+$ Chemical Component Dictionary pdb-ccd http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id AB0 unknown 1 urn:miriam:pdb-ccd ^\w{3}$ ChemIDplus chemidplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 000057272 metabolite 1 urn:miriam:chemidplus ^\d+$ -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider Cint C probe 0 CLDB cldb http://bioinformatics.istge.it/hypercldb/$id.html cl3603 unknown 1 urn:miriam:cldb ^cl\d+$ ClinicalTrials.gov clinicaltrials http://clinicaltrials.gov/ct2/show/$id NCT00222573 unknown 1 urn:miriam:clinicaltrials ^NCT\d{8}$ @@ -266,7 +266,7 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 ILMN_\d+ Illumina IMEx imex http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id IM-12080-80 unknown 1 urn:miriam:imex ^IM-\d+(-?)(\d+?)$ IMGT HLA imgt.hla http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$id A*01:01:01:01 unknown 1 urn:miriam:imgt.hla ^[A-Z0-9*:]+$ IMGT LIGM imgt.ligm http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+%5BIMGT%3A%27$id%27%5D M94112 unknown 1 urn:miriam:imgt.ligm ^M\d+$ -InChI inchi http://www.chemspider.com/$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 unknown 1 urn:miriam:inchi ^InChI\=1S\/[A-Za-z0-9]+(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,]+)+$ +InChI inchi https://www.chemspider.com/$id InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 unknown 1 urn:miriam:inchi ^InChI\=1S\/[A-Za-z0-9]+(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,]+)+$ InChIKey inchikey http://cactus.nci.nih.gov/chemical/structure/$id/names RYYVLZVUVIJVGH-UHFFFAOYSA-N unknown 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-N])? IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct IntAct Molecule intact.molecule http://www.ebi.ac.uk/intact/molecule/$id EBI-366083 unknown 1 urn:miriam:intact.molecule ^EBI\-[0-9]+$ diff --git a/org.bridgedb.rdf/resources/MiriamRegistry.ttl b/org.bridgedb.rdf/resources/MiriamRegistry.ttl index 4bed0d74c..10dc666bf 100644 --- a/org.bridgedb.rdf/resources/MiriamRegistry.ttl +++ b/org.bridgedb.rdf/resources/MiriamRegistry.ttl @@ -1313,7 +1313,7 @@ Each page contains information about a particular group, with pages linked one t a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5126,7 +5126,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -9518,7 +9518,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -10534,7 +10534,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "98"^^ ; @@ -12015,7 +12015,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -14554,7 +14554,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . diff --git a/org.bridgedb.rdf/test-data/DataSourceMin.ttl b/org.bridgedb.rdf/test-data/DataSourceMin.ttl index 8902f8567..c69676afd 100644 --- a/org.bridgedb.rdf/test-data/DataSourceMin.ttl +++ b/org.bridgedb.rdf/test-data/DataSourceMin.ttl @@ -3,19 +3,19 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . a bridgeDB:uriPattern ; bridgeDB:hasPrefix "http://identifiers.org/chemspider/" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . - a bridgeDB:uriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:uriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".html" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . diff --git a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java index 5e084af37..edfe9769d 100644 --- a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java +++ b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java @@ -100,7 +100,7 @@ public void testGetUriPatterns() throws BridgeDBException{ BridgeDBRdfHandler.parseRdfInputStream(dataSourceStream); Set result = UriPattern.byCodeAndType("Cs", UriPatternType.mainUrlPattern); assertFalse("Could not find main URL pattern for Cs", result.isEmpty()); - UriPattern pattern = UriPattern.existingByPattern("http://www.chemspider.com/Chemical-Structure.$id.html"); + UriPattern pattern = UriPattern.existingByPattern("https://www.chemspider.com/Chemical-Structure.$id.html"); assertThat (result, hasItem(pattern)); // pattern = UriPattern.existingOrCreateByPattern("http://identifiers.org/chemspider/$id"); // assertThat (result, hasItem(pattern)); diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl index 8b7f06aa8..b83034c73 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl @@ -30,11 +30,11 @@ pav:createdOn "2014-11-03"^^xsd:date . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl index 43a8723fe..402a2dbae 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl @@ -25,11 +25,11 @@ dcterms:created "2014-11-21"^^xsd:date . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl index 6b66cd9e9..09c540d2a 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl @@ -29,7 +29,7 @@ void:uriSpace . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl index c5e22fc58..47e9e5701 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl @@ -29,7 +29,7 @@ void:uriSpace . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl index 8fde9b3ba..57e7f7dfa 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl @@ -25,7 +25,7 @@ dcterms:created "2014-11-21"^^xsd:date . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java index 8d12943bd..38040182b 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java @@ -192,7 +192,7 @@ public static void setupUriPatterns() throws BridgeDBException{ DataSourcePatterns.registerPattern(DataSource2, Pattern.compile("^\\d+$")); uriPattern1 = UriPattern.register(uriSpace1, dataSource1Code, UriPatternType.dataSourceUriPattern); uriPattern2 = UriPattern.register(uriSpace2, dataSource2Code, UriPatternType.dataSourceUriPattern); - uriPattern2 = UriPattern.register("http://www.chemspider.com/Chemical-Structure.$id.html", dataSource2Code, UriPatternType.dataSourceUriPattern); + uriPattern2 = UriPattern.register("https://www.chemspider.com/Chemical-Structure.$id.html", dataSource2Code, UriPatternType.dataSourceUriPattern); UriPattern.register(uriSpace2a + "$id", dataSource2Code, UriPatternType.dataSourceUriPattern); uriPattern3 = UriPattern.register(uriSpace3, dataSource3Code, UriPatternType.dataSourceUriPattern); UriPattern.register(uriSpace3a + "$id", dataSource3Code, UriPatternType.dataSourceUriPattern); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java index d7662147a..e1cca43a5 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java @@ -129,10 +129,10 @@ public void testMappingNoLink() throws Exception { assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @@ -156,10 +156,10 @@ public void testMappingNoLinkFixedPredicate() throws Exception { assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); IRI mapSet1Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1?predicate=http%3A%2F%2Fexample.com%2Foverride"); IRI mapSet1_3Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1_3?predicate=http%3A%2F%2Fexample.com%2Foverride"); @@ -196,10 +196,10 @@ public void testMappingWithLink() throws Exception { assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @Test @@ -220,10 +220,10 @@ public void testMappingWithLinkOverride() throws Exception { assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } } diff --git a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java index 7b1c83849..bf17d16b4 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java +++ b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java @@ -71,7 +71,7 @@ public abstract class IDMapperTestBase { protected static String badKey; protected static final String uriSpace1 = "http://www.conceptwiki.org/concept/$id"; - protected static final String uriSpace2 = "http://www.chemspider.com/Chemical-Structure.$id.html"; + protected static final String uriSpace2 = "https://www.chemspider.com/Chemical-Structure.$id.html"; protected static final String uriSpace3 = "http://chemistry.openphacts.org/OPS$id"; @BeforeAll From eef95263cbf7c2f352b1712631de46dc57e0f318 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:48:16 +0200 Subject: [PATCH 29/64] Only initialize if not done already --- org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index 362e8b4ad..d178a5196 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java @@ -95,7 +95,7 @@ public static void refreshUriPatterns() throws BridgeDBException{ if (initialized){ return; } - DataSourceTxt.init(); + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); DataSourceMetaDataProvidor.assumeUnknownsAreBio(); BridgeDBRdfHandler.init(); IdentifersOrgReader.init(); From 96bdb86683992bfa0e767a092d075618a4db8d9c Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:48:44 +0200 Subject: [PATCH 30/64] Fixed a minor typo --- .../org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java index 32bd0d745..85ab7b114 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java @@ -134,7 +134,7 @@ public static void init() throws BridgeDBException{ public static void saveRegister() throws BridgeDBException { try { URL url = new URL(MIRAM_REGISTRY_URI); - Reporter.println("Readng " + url); + Reporter.println("Reading " + url); InputStream inputStream = url.openStream(); InputStreamReader inputReader = new InputStreamReader(inputStream); BufferedReader inputBuffer = new BufferedReader(inputReader); From d05ee7f1d27ec72e57022b2452b024824fdfaf46 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:49:18 +0200 Subject: [PATCH 31/64] Mock new datasources, to not cause URL overwrite errors --- .../src/test/java/org/bridgedb/IDMapperTestBase.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java index bf17d16b4..2d5a4d312 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java +++ b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java @@ -87,16 +87,16 @@ public abstract class IDMapperTestBase { public static void setupXref() throws IDMapperException{ //If the actual source to be tested does not contain these please overwrite with ones that do exist. dataSource1Code = "ConceptWiki"; - DataSource1 = DataSource.register(dataSource1Code, "ConceptWiki"). urlPattern(uriSpace1) + DataSource1 = DataSource.mock(dataSource1Code, "ConceptWiki"). urlPattern(uriSpace1) .idExample("33a28bb2-35ed-4d94-adfd-3c96053cbaaf").asDataSource(); dataSource2Code = "Cs"; - DataSource2 = DataSource.register(dataSource2Code, "Chemspider").urlPattern(uriSpace2) + DataSource2 = DataSource.mock(dataSource2Code, "Chemspider").urlPattern(uriSpace2) .idExample("56586").asDataSource(); dataSource3Code = "OPS-CRS"; - DataSource3 = DataSource.register(dataSource3Code, "OPS Chemical Registry Service").urlPattern(uriSpace3) + DataSource3 = DataSource.mock(dataSource3Code, "OPS Chemical Registry Service").urlPattern(uriSpace3) .idExample("8").asDataSource(); //This DataSource MUST not be supported - DataSourceBad = DataSource.register("TestDSBad", "TestDSBad") + DataSourceBad = DataSource.mock("TestDSBad", "TestDSBad") .urlPattern("http://www.NotInTheURlMapper.com#$id").asDataSource(); //Set of Xrefs that are expected to map together. From 194aba640dd4b4a048aa757b291ad35a48d327ae Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 14:49:40 +0200 Subject: [PATCH 32/64] Updated to match the new BridgeDb Datasources version --- org.bridgedb.rdf/resources/DataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl | 2 +- org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt | 2 +- org.bridgedb.rdf/resources/MiriamRegistry.ttl | 2 +- org.bridgedb.rdf/test-data/DataSourceMin.ttl | 6 +++++- .../test/org/bridgedb/rdf/DataSourceComparatorTest.java | 2 +- 6 files changed, 10 insertions(+), 6 deletions(-) diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 91f9b7d43..231929112 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -290,7 +290,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index cb04c8a2a..f8a350259 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -1059,7 +1059,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index 917d59c9e..924e51b36 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -94,7 +94,7 @@ LinkedChemistry ChEMBL target linkedchemistry.chembl.target http://l ChemDB chemdb http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id 3966782 unknown 1 urn:miriam:chemdb ^\d+$ Chemical Component Dictionary pdb-ccd http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id AB0 unknown 1 urn:miriam:pdb-ccd ^\w{3}$ ChemIDplus chemidplus http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id 000057272 metabolite 1 urn:miriam:chemidplus ^\d+$ -Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider Cint C probe 0 CLDB cldb http://bioinformatics.istge.it/hypercldb/$id.html cl3603 unknown 1 urn:miriam:cldb ^cl\d+$ ClinicalTrials.gov clinicaltrials http://clinicaltrials.gov/ct2/show/$id NCT00222573 unknown 1 urn:miriam:clinicaltrials ^NCT\d{8}$ diff --git a/org.bridgedb.rdf/resources/MiriamRegistry.ttl b/org.bridgedb.rdf/resources/MiriamRegistry.ttl index 10dc666bf..711baf3de 100644 --- a/org.bridgedb.rdf/resources/MiriamRegistry.ttl +++ b/org.bridgedb.rdf/resources/MiriamRegistry.ttl @@ -14554,7 +14554,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . diff --git a/org.bridgedb.rdf/test-data/DataSourceMin.ttl b/org.bridgedb.rdf/test-data/DataSourceMin.ttl index c69676afd..29f328e3c 100644 --- a/org.bridgedb.rdf/test-data/DataSourceMin.ttl +++ b/org.bridgedb.rdf/test-data/DataSourceMin.ttl @@ -7,7 +7,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . a bridgeDB:uriPattern ; @@ -19,3 +19,7 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:hasPostfix ".html" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . + a bridgeDB:uriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/" ; + bridgeDB:hasPostfix "" ; + bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . diff --git a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java index edfe9769d..2b4e8fa58 100644 --- a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java +++ b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java @@ -100,7 +100,7 @@ public void testGetUriPatterns() throws BridgeDBException{ BridgeDBRdfHandler.parseRdfInputStream(dataSourceStream); Set result = UriPattern.byCodeAndType("Cs", UriPatternType.mainUrlPattern); assertFalse("Could not find main URL pattern for Cs", result.isEmpty()); - UriPattern pattern = UriPattern.existingByPattern("https://www.chemspider.com/Chemical-Structure.$id.html"); + UriPattern pattern = UriPattern.existingByPattern("https://www.chemspider.com/$id"); assertThat (result, hasItem(pattern)); // pattern = UriPattern.existingOrCreateByPattern("http://identifiers.org/chemspider/$id"); // assertThat (result, hasItem(pattern)); From e876e3d639b627cd4abe89ee01287051336a5fdb Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 15:04:32 +0200 Subject: [PATCH 33/64] Added the missing regexp --- org.bridgedb.rdf/resources/DataSource.ttl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 231929112..2d2bbb9d6 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -366,7 +366,7 @@ bridgeDB:DataSource_drugbankv4Target a bridgeDB:DataSource ; bridgeDB:fullName "Drugbank Target v4" ; bridgeDB:systemCode "drugbankv4.target" ; bridgeDB:idExample "BE0000938" ; - bridgeDB:hasRegexPattern "^BE\\d{7}$" ; + bridgeDB:hasRegexPattern "^BE\\d{7}$" ; bridgeDB:mainUrl "http://www.drugbank.ca/" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; @@ -379,6 +379,7 @@ bridgeDB:DataSource_drugbankDrugs a bridgeDB:DataSource ; bridgeDB:systemCode "Dr" ; bridgeDB:mainUrl "http://www.drugbank.ca/" ; bridgeDB:idExample "DB00001" ; + bridgeDB:hasRegexPattern "^DB\\d{5,7}$" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; bridgeDB:hasPrimaryUriPattern ; From 0c68c3309b50d80977d1db2f8690853b8abcbf3f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:46:15 +0200 Subject: [PATCH 34/64] Added another test --- .../test/java/org/bridgedb/bio/DataSourceTxtTest.java | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java index df989ca7a..67f06fba0 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java @@ -127,6 +127,15 @@ public void testMIRIAMFeatures() throws Exception { assertEquals("chebi", chebi.getCompactIdentifierPrefix()); } + @org.junit.jupiter.api.Test + public void testEcoGene() throws Exception { + DataSource ecogene = DataSource.getExistingByFullName("EcoGene"); + assertNotNull(ecogene); + assertEquals("urn:miriam:ecogene:EG10173", ecogene.getMiriamURN("EG10173")); + assertNotNull(DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/")); + assertNotNull(DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/")); + } + @org.junit.jupiter.api.Test public void testPrefix() throws Exception { DataSource ds = DataSource.getExistingBySystemCode("L"); From da202ed9ef772685e67ce43e6ad32ddd571ab212 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:54:06 +0200 Subject: [PATCH 35/64] Tests may have registered things, so do a more realistic check --- org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index d178a5196..f7a62083e 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java @@ -95,7 +95,7 @@ public static void refreshUriPatterns() throws BridgeDBException{ if (initialized){ return; } - if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); DataSourceMetaDataProvidor.assumeUnknownsAreBio(); BridgeDBRdfHandler.init(); IdentifersOrgReader.init(); From 5386289a1df7f33462fd3b6011d7adc87d1c3a80 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:54:57 +0200 Subject: [PATCH 36/64] More precise status message --- .../org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java index 85ab7b114..5b7182e60 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java @@ -92,7 +92,7 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException // for (String multiple:multiples){ // checkMultiple(repositoryConnection, multiple); // } - Reporter.println("Registry read in. Now loading DataSources"); + Reporter.println("Registry read in. Now loading DataSources from the in memory store"); loadData(repositoryConnection); } catch (Exception ex) { throw new BridgeDBException ("Error parsing RDF inputStream: " + ex.getMessage(), ex); @@ -204,7 +204,7 @@ private DataSource readDataSource(RepositoryConnection repositoryConnection, Res UriPattern.register(identiferOrgBase + "$id", sysCode, UriPatternType.identifiersOrgPatternSimple); String identifersOrgInfoBase = identiferOrgBase.replace("identifiers.org","info.identifiers.org"); UriPattern.register(identifersOrgInfoBase + "$id", sysCode, UriPatternType.identifiersOrgPatternInfo); - + DataSource ds = DataSource.register(sysCode, fullName) .identifiersOrgBase(identiferOrgBase) .asDataSource(); From c8b657ea30abcc319990c2c9de737946b027299f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:56:58 +0200 Subject: [PATCH 37/64] Support also https --- org.bridgedb/src/main/java/org/bridgedb/DataSource.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java index 2c8712d5a..1487399ae 100644 --- a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java +++ b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java @@ -973,10 +973,10 @@ public static DataSource getByMiriamBase(String base) * @return the DataSource for a given base, or null if the base is invalid or unknown. */ public static DataSource getByIdentiferOrgBase(String base) { - if (base == null || !base.startsWith (IDENTIFIERS_ORG_PREFIX)) - { - return null; - } + if (base == null) return null; + // support the HTTPS variant too + base = base.replace("https://identifiers.org", "http://identifiers.org"); + if (!base.startsWith (IDENTIFIERS_ORG_PREFIX)) return null; String key = base.substring(IDENTIFIERS_ORG_PREFIX.length()); if (key.endsWith("/")){ From 88194686249154bd93d07fdb177bd6a7a140a48a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 16:57:16 +0200 Subject: [PATCH 38/64] More testing --- org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java index 4eab3aa5c..c782b6a30 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java +++ b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java @@ -375,7 +375,9 @@ public void testBuilders() { .alternative("MetaboLoci Alternative") .asDataSource(); assertEquals("Ecogene",DataSource.getByMiriamBase("urn:miriam:ecogene").toString()); - assertEquals("urn:miriam:ecogene:urn%3Amiriam%3Aecogene",source3.getMiriamURN("urn:miriam:ecogene").toString()); + assertEquals("Ecogene",DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/").toString()); + assertEquals("Ecogene",DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/").toString()); + assertEquals("urn:miriam:ecogene:EG10173",source3.getMiriamURN("EG10173").toString()); DataSource source4 = DataSource.register("Ect", "EPA CompTox") .urnBase("urn:miriam:Ect") From b3cdc2a8e976f4ddc8cf8fd64e49e96bab7164e6 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 20:26:58 +0200 Subject: [PATCH 39/64] More updates for the new BridgeDb Datasources release --- .../extract/Ensembl_ETL_Device_v18_local.pl | 12 +- .../org/bridgedb/bio/datasources.tsv | 12 +- .../org/bridgedb/bio/datasources.tsv | 12 +- org.bridgedb.rdf/resources/BioDataSource.ttl | 28 +-- org.bridgedb.rdf/resources/DataSource.ttl | 60 +++--- .../resources/IdentifiersOrgDataSource.ttl | 184 +++++++++--------- .../resources/IdentifiersOrgDataSource.txt | 46 ++--- org.bridgedb.rdf/resources/MiriamRegistry.ttl | 74 +++---- .../resources/graph.properties | 4 +- .../src/org/bridgedb/sql/SQLUriMapper.java | 2 +- .../src/org/bridgedb/pairs/IdSysCodePair.java | 2 +- 11 files changed, 218 insertions(+), 218 deletions(-) diff --git a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl index 42d8576ad..ffbb03311 100755 --- a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl +++ b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl @@ -743,7 +743,7 @@ %{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'], 'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'", "\'ID\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", + "\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", "\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'PRIMARY KEY (ID)' @@ -863,7 +863,7 @@ %{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'], 'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", + "\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", "\'ftp://rgd.mcw.edu/pub/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', @@ -916,8 +916,8 @@ %{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'], 'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", - "\'http://www.gramene.org\'"], + "\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", + "\'https://www.gramene.org\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', @@ -926,8 +926,8 @@ %{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'], 'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'", "\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/pathway\'", "\'\'", - "\'http://www.gramene.org/pathway\'"], + "\'https://www.gramene.org/pathway\'", "\'\'", + "\'https://www.gramene.org/pathway\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', 'PRIMARY KEY (ID)' diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 770e6c833..289fb0957 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology -Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene -Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway -Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene @@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz? Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene +Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index bb0f7d8cb..66cb63176 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology -Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene -Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway -Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -78,7 +78,7 @@ MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NI MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene @@ -112,7 +112,7 @@ RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz? Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene +Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 52ef12bcb..5b3bc8747 100644 --- a/org.bridgedb.rdf/resources/BioDataSource.ttl +++ b/org.bridgedb.rdf/resources/BioDataSource.ttl @@ -35,7 +35,7 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -45,7 +45,7 @@ bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:fullName "BioGrid" ; bridgeDB:systemCode "Bg" ; - bridgeDB:mainUrl "http://thebiogrid.org/" ; + bridgeDB:mainUrl "https://thebiogrid.org/" ; bridgeDB:idExample "31623" ; bridgeDB:primary "true"^^ ; bridgeDB:type "interaction" ; @@ -55,7 +55,7 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; @@ -105,7 +105,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; @@ -473,7 +473,7 @@ bridgeDB:DataSource_GeneOntology a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -484,7 +484,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -494,7 +494,7 @@ bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; @@ -503,7 +503,7 @@ bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -512,7 +512,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; @@ -521,7 +521,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -780,7 +780,7 @@ bridgeDB:DataSource_MINT a bridgeDB:DataSource ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1032,7 +1032,7 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1053,7 +1053,7 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1175,7 +1175,7 @@ bridgeDB:DataSource_Systems_Biology_Ontology a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index 2d2bbb9d6..cd15ae023 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -38,32 +38,32 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:fullName "BioGrid" ; bridgeDB:systemCode "Bg" ; - bridgeDB:mainUrl "http://thebiogrid.org/" ; + bridgeDB:mainUrl "https://thebiogrid.org/" ; bridgeDB:idExample "31623" ; bridgeDB:primary "true"^^ ; bridgeDB:type "interaction" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . @@ -134,16 +134,16 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:idExample "CCDS43989" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasUriPattern ; #Deprecated bridgeDB:hasIdentifiersOrgPattern . @@ -519,45 +519,45 @@ bridgeDB:DataSource_GOA a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_At . bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "false"^^ ; bridgeDB:type "pathway" . @@ -565,7 +565,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -807,11 +807,11 @@ bridgeDB:CodeMapper_MGI a bridgeDB:CodeMapper ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; @@ -822,7 +822,7 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; bridgeDB:idExample "MI0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_NASC_Gene a bridgeDB:DataSource ; @@ -915,7 +915,7 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ; bridgeDB:systemCode "PW" ; bridgeDB:xrefPrefix "PW:"; - bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; @@ -1037,24 +1037,24 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; - bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:Organism bridgeDB:Organism_Rn . bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_Os ; bridgeDB:hasRegexUriPattern . @@ -1072,11 +1072,11 @@ bridgeDB:DataSource_SGD a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_TIGR a bridgeDB:DataSource ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index f8a350259..0b72ed5d4 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -504,11 +504,11 @@ bridgeDB:DataSource_BioCatalogue a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^[A-Z-0-9]+(? ; bridgeDB:type "interaction" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; @@ -531,11 +531,11 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$" ; @@ -832,7 +832,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:idExample "CCDS43989" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CCDS\\d+(\\.\\d+)?$" ; @@ -921,11 +921,11 @@ bridgeDB:DataSource_CharProt a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CHEBI:\\d+$" ; @@ -2515,11 +2515,11 @@ bridgeDB:DataSource_GPCRDB a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_At ; bridgeDB:hasRegexPattern "AT[\\dCM]G\\d{5}\\-TAIR\\-G" ; dcterms:alternative "Grameen Arabidopsis" . @@ -2527,11 +2527,11 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GR\\:\\d+$" ; @@ -2543,36 +2543,36 @@ bridgeDB:DataSource_Gramene_Growth_Stage_Ontology a bridgeDB:DataSource ; bridgeDB:idExample "GRO:0007133" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GRO\\:\\d+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Literature" . bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Maize" . bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "false"^^ ; bridgeDB:type "pathway" ; @@ -2584,7 +2584,7 @@ bridgeDB:DataSource_Gramene_protein a bridgeDB:DataSource ; bridgeDB:idExample "78073" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -2595,7 +2595,7 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ; bridgeDB:idExample "CQG5" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\w+$" . @@ -2603,11 +2603,11 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Rice" . bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ; @@ -2616,11 +2616,11 @@ bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ; bridgeDB:idExample "GR_tax:013681" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GR\\_tax\\:\\d+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_GreenGenes a bridgeDB:DataSource ; bridgeDB:fullName "GreenGenes" ; @@ -3033,7 +3033,7 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:fullName "InChIKey" ; @@ -3799,11 +3799,11 @@ bridgeDB:DataSource_MIPModDB a bridgeDB:DataSource ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "MIMAT\\d{7}" ; @@ -3816,12 +3816,12 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; bridgeDB:idExample "MI0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "MI\\d{7}" ; dcterms:alternative "miRBase Sequence" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_mirEX a bridgeDB:DataSource ; bridgeDB:fullName "mirEX" ; @@ -4608,7 +4608,7 @@ bridgeDB:DataSource_Pathway_Commons a bridgeDB:DataSource ; bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:fullName "Pathway Ontology" ; bridgeDB:systemCode "PW" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/rgdweb/ontology/search.html" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/rgdweb/ontology/search.html" ; bridgeDB:idExample "PW:0000208" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; @@ -4616,12 +4616,12 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^PW:\\d{7}$" ; - bridgeDB:hasUriPattern , . + bridgeDB:hasUriPattern , . bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ; bridgeDB:systemCode "PW" ; bridgeDB:xrefPrefix "PW:" ; - bridgeDB:hasUriPattern , , , , . + bridgeDB:hasUriPattern , , , , . bridgeDB:DataSource_PATO a bridgeDB:DataSource ; bridgeDB:fullName "PATO" ; @@ -5195,7 +5195,7 @@ bridgeDB:DataSource_Rat_Genome_Database_qTL a bridgeDB:DataSource ; bridgeDB:idExample "1354581" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -5206,7 +5206,7 @@ bridgeDB:DataSource_Rat_Genome_Database_strain a bridgeDB:DataSource ; bridgeDB:idExample "5688061" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -5290,17 +5290,17 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:Organism bridgeDB:Organism_Rn ; bridgeDB:hasRegexPattern "^\\d{4,7}$" ; dcterms:alternative "Rat Genome Database" ; - bridgeDB:hasUriPattern , . + bridgeDB:hasUriPattern , . bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:fullName "Rhea" ; @@ -5318,11 +5318,11 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_Os ; dcterms:alternative "Rice Ensembl Gene" . @@ -5770,11 +5770,11 @@ bridgeDB:DataSource_T3DB a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^AT[1-5]G\\d{5}$" ; @@ -6875,8 +6875,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?accession=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?type=locus&name=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://arxiv.org/abs/" . @@ -7007,8 +7007,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://bio2rdf.org/uniprot:" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://biocyc.org/getid?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://biocyc.org/getid?id=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=" . @@ -10557,8 +10557,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://mi.caspur.it/PMDB/user/search.php?idsearch=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=" . @@ -10953,23 +10953,23 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://rfam.sanger.ac.uk/family/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=" . @@ -11076,8 +11076,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://tgr.pharma.openphacts.com/target/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://thebiogrid.org/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://thebiogrid.org/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://tolweb.org/" . @@ -11347,8 +11347,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/arrayexpress/experiments/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/biomodels-main/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/biomodels/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/biosamples/browse.html?keywords=" . @@ -11363,11 +11363,11 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "https://www.ebi.ac.uk/chembl/target/inspect/" . @@ -11610,29 +11610,29 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.gpcr.org/7tm/proteins/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/genes/search_gene?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/genes/search_gene?acc=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/literature/pub_search?ref_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/literature/pub_search?ref_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/ontology/search?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/ontology/search?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/protein/protein_search?protein_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/protein/protein_search?protein_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Oryza_sativa/geneview?gene=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Oryza_sativa/geneview?gene=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" . @@ -11722,7 +11722,7 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=" . - a bridgeDB:UriPattern ; + a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.maizesequence.org/Zea_mays/Gene/Summary?g=" . a bridgeDB:UriPattern ; @@ -11734,11 +11734,11 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://mirbase.org/mature/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=" . @@ -11764,8 +11764,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/biosystems/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&%3BDATA=" . diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index 924e51b36..6b85d16d7 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -47,9 +47,9 @@ BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch BindingDB bindingDB http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$id 22360 unknown 1 urn:miriam:bindingDB ^\d+$ BioCarta Pathway biocarta.pathway http://www.biocarta.com/pathfiles/$id.asp h_aktPathway unknown 1 urn:miriam:biocarta.pathway ^([hm]\_)?\w+Pathway$ BioCatalogue biocatalogue.service https://www.biocatalogue.org/services/$id 614 unknown 1 urn:miriam:biocatalogue.service ^\d+$ -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^[A-Z-0-9]+(? ; "Medical College of Wisconsin, Milwaukee, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -1003,7 +1003,7 @@ Each page contains information about a particular group, with pages linked one t "USA"^^ ; "Medical College of Wisconsin, Milwaukee, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -1329,7 +1329,7 @@ Each page contains information about a particular group, with pages linked one t a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -2236,7 +2236,7 @@ The interactions include direct (physical) and indirect (functional) association a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -3203,7 +3203,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3368,7 +3368,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3781,7 +3781,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3904,7 +3904,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4134,7 +4134,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -4274,7 +4274,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4461,7 +4461,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "United Kingdom"^^ ; "European Bioinformatics Institute"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4551,7 +4551,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "United Kingdom"^^ ; "European Bioinformatics Institute"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4945,7 +4945,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Medical College of Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -5431,7 +5431,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Bioinformatics Research Group, SRI International, California"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "100"^^ ; @@ -5451,7 +5451,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5510,7 +5510,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5875,7 +5875,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -6485,7 +6485,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -6555,7 +6555,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7041,7 +7041,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7093,7 +7093,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7265,7 +7265,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -8447,7 +8447,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Faculty of Life Sciences, University of Manchester"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -8545,7 +8545,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -9346,7 +9346,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "Canada"^^ ; "Ontario Cancer Institute"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -9925,7 +9925,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -12342,7 +12342,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "UK"^^ ; "European Bioinformatics Institute, Hinxton, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -12408,7 +12408,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "USA"^^ ; "Medical College of Wisconsin, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -13094,7 +13094,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -13327,7 +13327,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14443,7 +14443,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14554,7 +14554,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14576,7 +14576,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from "UK"^^ ; "Faculty of Life Sciences, University of Manchester"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -14618,7 +14618,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "100"^^ ; @@ -16492,7 +16492,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -17403,7 +17403,7 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -18125,7 +18125,7 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; diff --git a/org.bridgedb.uri.sql/resources/graph.properties b/org.bridgedb.uri.sql/resources/graph.properties index c77029660..ab351ded6 100644 --- a/org.bridgedb.uri.sql/resources/graph.properties +++ b/org.bridgedb.uri.sql/resources/graph.properties @@ -80,10 +80,10 @@ context.chebi1.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id context.chebi1.graph http://www.ebi.ac.uk/chebi context.chebi2.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id -context.chebi2.graph http://www.ebi.ac.uk/chebi/direct +context.chebi2.graph https://www.ebi.ac.uk/chebi/direct context.chebi3.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id -context.chebi3.graph http://www.ebi.ac.uk/chebi/inference +context.chebi3.graph https://www.ebi.ac.uk/chebi/inference context.enzyme1.pattern.1 http://purl.uniprot.org/enzyme/$id context.enzyme1.graph http://purl.uniprot.org/enzyme diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java b/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java index f3c442a60..76065ee22 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java @@ -449,7 +449,7 @@ public IdSysCodePair toIdSysCodePair(String uri) throws BridgeDBException { //Know dulicate prefixes of this type include //http://www.kegg.jp/entry/ //http://www.ebi.ac.uk/ontology-lookup/?termId= - //http://www.gramene.org/db/ontology/search?id= + //https://www.gramene.org/db/ontology/search?id= //http://stke.sciencemag.org/cgi/cm/stkecm; //http://purl.uniprot.org/uniprot/ //http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name= diff --git a/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java b/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java index 45d680a78..9646affe0 100644 --- a/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java +++ b/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java @@ -28,7 +28,7 @@ * This is required for xrefs like "ChEBI" * These refs contain "CHEBI:" as part of the id. Such as CHEBI:36927 * Which is fine for URIs like: - * http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36927 or + * https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36927 or * http://identifiers.org/obo.chebi/CHEBI:36927 * but does not work for others like: * http://purl.org/obo/owl/CHEBI#CHEBI_36927 or From af89100e846c43d0fcb946b63f71c927185467e2 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Fri, 26 Jul 2024 07:14:14 +0200 Subject: [PATCH 40/64] Different server id, to address a local ID conflict --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index d2dbb521c..89e5e6559 100644 --- a/pom.xml +++ b/pom.xml @@ -150,7 +150,7 @@ 1.6.8 true - ossrh + sso https://oss.sonatype.org/ true @@ -192,11 +192,11 @@ - ossrh + sso https://oss.sonatype.org/service/local/staging/deploy/maven2/ - ossrh + sso https://oss.sonatype.org/content/repositories/snapshots From f6d831f4764bb1178873d3e9dbeb9617ae3d12a1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 30 Jul 2024 10:37:39 +0200 Subject: [PATCH 41/64] Release 3.1.2 --- CITATION.cff | 4 ++-- README.md | 14 +++++++------- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- org.bridgedb/src/main/resources/version.props | 2 +- pom.xml | 2 +- 29 files changed, 39 insertions(+), 39 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 716c1c9a7..cdd95bc91 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.1.1 -date-released: '2023-12-18' +version: 3.1.2 +date-released: '2024-07-30' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 847361b70..833a6e7f8 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.1`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.1 + 3.1.2 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.1' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.1' +'org.bridgedb:org.bridgedb.bio:jar:3.1.2' ``` @@ -135,7 +135,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.2-SNAPSHOT +mvn versions:set -DnewVersion=3.1.2 mvn clean deploy ``` @@ -145,7 +145,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.1.1-SNAPSHOT +mvn versions:set -DnewVersion=3.1.3-SNAPSHOT mvn clean deploy ``` diff --git a/examples/pom.xml b/examples/pom.xml index fcebe7a70..0c490e85b 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index b63dda2b2..d92cfc8fe 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 194f6548e..2cd2f9413 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 1655d6b1a..a2e97b835 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index d45ad5df8..feb7e76d3 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 61d780844..88c3a389e 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 83ca9b27a..50eec5bc7 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index c0555e252..763f300fe 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 9889d24d9..4d26f9632 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 compile org.bridgedb org.bridgedb.bio - 3.1.2-SNAPSHOT + 3.1.2 compile org.bridgedb org.bridgedb.rdb - 3.1.2-SNAPSHOT + 3.1.2 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 2a6fdd71a..dcd850997 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index ecb265353..9dd9273a2 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 37768a064..32b8fdd5a 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 8bce22c78..7203717ab 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index cb9f80dbe..99572ef6c 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 379b9ba3d..c1ea354c8 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 69919c820..dc097d6e5 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index a350d9c72..6b615cf78 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 30c55a733..4638f2530 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 3aaaeeb59..6d769698e 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index c30eb03a2..eaf9b5248 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index eea6d5376..afb7fe1aa 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 308d74fc9..ccd78fba1 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 68d3bdfe9..9aed75286 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index fba9a3dd9..3ac9a6a9b 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index e3881be63..d641b271f 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.2-SNAPSHOT + 3.1.2 diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 3d10b72ab..6cc9da92d 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.1.1 +bridgedb.version=3.1.2 diff --git a/pom.xml b/pom.xml index 89e5e6559..e8c9507fc 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.2-SNAPSHOT + 3.1.2 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 64287d2c1e88e39a4ebb90bca5d4c9b49d808675 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:09:38 +0200 Subject: [PATCH 42/64] Added Java8 build step --- .github/workflows/build.yml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 417ccb74d..d97e8d99b 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -7,8 +7,21 @@ on: branches: [ series/3.1.0 ] jobs: - build: + java8: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Java + uses: actions/setup-java@v4 + with: + distribution: 'temurin' + java-version: 8 + cache: maven + - name: Build with Maven + run: mvn -f pom-java8.xml clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql + + build: runs-on: ubuntu-latest steps: From 1bab9d743c1e142e7fc2293634426410dd95dca8 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:11:15 +0200 Subject: [PATCH 43/64] Only do the second step if compiling with Java8 worked --- .github/workflows/build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d97e8d99b..0d38b3f7e 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -22,6 +22,7 @@ jobs: run: mvn -f pom-java8.xml clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql build: + needs: java8 runs-on: ubuntu-latest steps: From 4f36020147b58e8196a2354831afc37da585e70b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 25 Jul 2024 13:29:49 +0200 Subject: [PATCH 44/64] Do not run when not having Java 11 or higher --- org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java index f9cf6b643..59ae298e6 100644 --- a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java +++ b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java @@ -61,6 +61,14 @@ public static void setup() { @org.junit.jupiter.api.Test public void testGdbProvider() throws ClassNotFoundException, IDMapperException, IOException{ + // only for Java 11 and higher + String specVersion = System.getProperty("java.specification.version"); + if (specVersion.contains(".")) specVersion = specVersion.substring(0, specVersion.indexOf('.')); + if (Integer.valueOf(specVersion) < 11) { + System.out.print("Only running testGdbProvider() for Java 11 or higher"); + return; + } + Class.forName("org.bridgedb.file.IDMapperText"); ClassLoader classLoader = this.getClass().getClassLoader(); From f83387458d16c0d5e9f657f96394e97ad1f12366 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 30 Jul 2024 11:04:06 +0200 Subject: [PATCH 45/64] Bumped the PathVisio bundle too --- README.md | 2 +- pom-java8.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 833a6e7f8..555e3e9a8 100644 --- a/README.md +++ b/README.md @@ -129,7 +129,7 @@ Making releases --------------- If it is time for a release, first, update `org.bridgedb/src/main/resources/version.props` (for BridgeDb), -this `README.md` and `CITATION.cff` (for Zenodo). +this `README.md` and `CITATION.cff` (for Zenodo), as well as the `pom-java8.xml`. To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: diff --git a/pom-java8.xml b/pom-java8.xml index 107aa4116..4b568673d 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.0.22 + 3.1.2 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database From 1b6f47e6404ff84d080936d1f5c0169f928cf785 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 21 Sep 2024 09:10:48 +0200 Subject: [PATCH 46/64] Open for development --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 0c490e85b..a2c683fc1 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index d92cfc8fe..211fb58f8 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 2cd2f9413..88b5d884f 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index a2e97b835..a3e041099 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index feb7e76d3..fe55c4414 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 88c3a389e..fdeffdc43 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 50eec5bc7..14e4863d9 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 763f300fe..5ccd3e6d0 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 4d26f9632..4a489cede 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.2 + 3.1.3-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.2 + 3.1.3-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index dcd850997..b5ecac8a0 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 9dd9273a2..d9145e1d0 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 32b8fdd5a..96e160566 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 7203717ab..8b74b4eea 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 99572ef6c..4fc3d983e 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index c1ea354c8..f671bda7d 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index dc097d6e5..2beeba819 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 6b615cf78..a1349048c 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 4638f2530..f3672d4e3 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 6d769698e..f8ac233e2 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index eaf9b5248..c5ac195d8 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index afb7fe1aa..394f3fd18 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index ccd78fba1..ea57e2096 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 9aed75286..d39248962 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 3ac9a6a9b..ebbe3b200 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index d641b271f..a4f99bee8 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/pom.xml b/pom.xml index e8c9507fc..d19e892e8 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.2 + 3.1.3-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From a76888fb91f52296d58a54c135ded3b9de079de3 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 21 Sep 2024 10:23:01 +0200 Subject: [PATCH 47/64] Newer MySQL driver --- org.bridgedb.rdb.construct/pom.xml | 4 ++-- org.bridgedb.rdb/pom.xml | 4 ++-- org.bridgedb.sql/pom.xml | 4 ++-- org.bridgedb.tools.qc/pom.xml | 8 ++++---- org.bridgedb.tools.voidtool/pom.xml | 8 ++++---- org.bridgedb.uri.sql/pom.xml | 4 ++-- pom.xml | 9 ++++++++- 7 files changed, 24 insertions(+), 17 deletions(-) diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index fe55c4414..dc64e183c 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -80,8 +80,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index fdeffdc43..bb546516b 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -79,8 +79,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 5ccd3e6d0..e33449052 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -47,8 +47,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index d9145e1d0..04e125150 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,8 +82,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 96e160566..e592e3388 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,8 +82,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index f671bda7d..00a76920c 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -64,8 +64,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/pom.xml b/pom.xml index d19e892e8..e3887cf7b 100644 --- a/pom.xml +++ b/pom.xml @@ -49,7 +49,7 @@ 2.2 1.10 2.22.0 - 8.0.33 + 9.0.0 Tomcat 3.4 4.3.8 @@ -317,4 +317,11 @@ https://github.com/bridgedb/BridgeDb/issues + + + mvnrepository + https://mvnrepository.com/artifact/ + + + From 3c1f57a9748e590735d96b0dc1db7bc0f73b7d89 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 09:10:32 +0200 Subject: [PATCH 48/64] Removed an unused dependency --- examples/pom.xml | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index a2c683fc1..477368ef7 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -69,18 +69,6 @@ jar runtime - - org.apache.axis - axis - 1.4 - jar - - - org.apache.axis - axis-jaxrpc - 1.4 - jar - From b78a5a52c2eb0537f12249f14dc8227471da06ef Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 09:18:49 +0200 Subject: [PATCH 49/64] Newer Apache CFX version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e3887cf7b..de58ae97d 100644 --- a/pom.xml +++ b/pom.xml @@ -45,7 +45,7 @@ UTF-8 UTF-8 1.2 - 3.2.14 + 3.6.4 2.2 1.10 2.22.0 From 1ae2751f1b64a5cf2ec8a7a20d6c5e7b2bbdd167 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 09:36:50 +0200 Subject: [PATCH 50/64] Maven style --- org.bridgedb.webservice.bridgerest/pom.xml | 8 ++++---- .../org/bridgedb/webservice/bridgerest/BridgeRest.java | 0 2 files changed, 4 insertions(+), 4 deletions(-) rename org.bridgedb.webservice.bridgerest/src/{ => main/java}/org/bridgedb/webservice/bridgerest/BridgeRest.java (100%) diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 394f3fd18..b8cd705a4 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -16,17 +16,17 @@ target/classes ${project.artifactId}-${project.version} target/test-classes - src + src/main/java scripts - test + src/test/main - resources + src/main/resources - test-resources + src/test/resources diff --git a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java b/org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java similarity index 100% rename from org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java rename to org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java From d250241c2c44e2cd5ef6c5b7eaab068342e0ba82 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:01:24 +0200 Subject: [PATCH 51/64] Added a simple test --- org.bridgedb.webservice.bridgerest/pom.xml | 26 +++++++++++++- .../webservice/bridgerest/BridgeRestTest.java | 35 +++++++++++++++++++ 2 files changed, 60 insertions(+), 1 deletion(-) create mode 100644 org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index b8cd705a4..25f704fa9 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -18,7 +18,7 @@ target/test-classes src/main/java scripts - src/test/main + src/test/java src/main/resources @@ -80,5 +80,29 @@ ${project.parent.version} compile + + org.junit.platform + junit-platform-surefire-provider + 1.3.2 + test + + + org.junit.jupiter + junit-jupiter-engine + ${junit5.jupiter.version} + test + + + org.junit.vintage + junit-vintage-engine + ${junit5.jupiter.version} + test + + + org.junit.jupiter + junit-jupiter-api + ${junit5.jupiter.version} + test + diff --git a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java new file mode 100644 index 000000000..610b00f88 --- /dev/null +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -0,0 +1,35 @@ +// Copyright 2024 Egon Willighagen +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. +// +package org.bridgedb.webservice.bridgerest; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.bridgedb.IDMapperException; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class BridgeRestTest { + + @BeforeAll + public static void init() { + + } + + @Test + public void test() throws IDMapperException { + BridgeRest service = new BridgeRest("https://webservice.bridgedb.org/Human"); + assertNotNull(service); + } +} From 07d37b082965b655e2970b09c3143f5dd0014f07 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:14:42 +0200 Subject: [PATCH 52/64] Restructured and added a mapping test --- org.bridgedb.webservice.bridgerest/pom.xml | 6 +++++ .../webservice/bridgerest/BridgeRestTest.java | 22 +++++++++++++++---- 2 files changed, 24 insertions(+), 4 deletions(-) diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 25f704fa9..d5bc08fef 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -80,6 +80,12 @@ ${project.parent.version} compile + + org.bridgedb + org.bridgedb.bio + ${project.parent.version} + test + org.junit.platform junit-platform-surefire-provider diff --git a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java index 610b00f88..645f2e75d 100644 --- a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -14,22 +14,36 @@ // package org.bridgedb.webservice.bridgerest; +import static org.junit.Assert.assertNotSame; +import static org.junit.Assert.assertTrue; import static org.junit.jupiter.api.Assertions.assertNotNull; +import java.util.Set; + +import org.bridgedb.DataSource; import org.bridgedb.IDMapperException; +import org.bridgedb.Xref; +import org.bridgedb.bio.DataSourceTxt; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; public class BridgeRestTest { + private static BridgeRest service; + @BeforeAll - public static void init() { - + public static void init() throws IDMapperException { + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + BridgeRestTest.service = new BridgeRest("https://webservice.bridgedb.org/Human"); + assertNotNull(service); + assertTrue(service.isConnected()); } @Test - public void test() throws IDMapperException { - BridgeRest service = new BridgeRest("https://webservice.bridgedb.org/Human"); + public void testMap() throws IDMapperException { assertNotNull(service); + assertTrue(service.isConnected()); + Set mappings = service.mapID(new Xref("CHEBI:123", DataSource.getExistingBySystemCode("Ce"))); + assertNotSame(0, mappings.size()); } } From e86b179f3f4760be60926ef7e4054c0732276806 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:34:47 +0200 Subject: [PATCH 53/64] Updated Maven Jar plugin --- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index d5bc08fef..1546e20f2 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -57,7 +57,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index a4f99bee8..f363b121d 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -81,7 +81,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF From 3a054e32c76bd693efb33840674e3b2ab2ee741d Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:52:15 +0200 Subject: [PATCH 54/64] Central, updated Felix maven plugin --- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 1 + 7 files changed, 7 insertions(+), 6 deletions(-) diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 211fb58f8..cbcc44086 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index a3e041099..22a091701 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index dc64e183c..2fdee3665 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index bb546516b..94b5cd35b 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 1546e20f2..6726e0633 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -33,7 +33,7 @@ org.apache.felix maven-bundle-plugin - 5.1.1 + ${felix.version} true diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index f363b121d..7b96e71fb 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -57,7 +57,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/pom.xml b/pom.xml index de58ae97d..5bdf16cd2 100644 --- a/pom.xml +++ b/pom.xml @@ -46,6 +46,7 @@ UTF-8 1.2 3.6.4 + 5.1.9 2.2 1.10 2.22.0 From b8184a06fd4650c2572708acd3da3a174bb4de7a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 11:32:08 +0200 Subject: [PATCH 55/64] Updated more dependencies: Hamcrest 3.0, JUnit 5.11, and WSDL4J 1.6.3 --- examples/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- pom.xml | 5 +++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 477368ef7..3fe355949 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -65,7 +65,7 @@ wsdl4j wsdl4j - 1.6.2 + 1.6.3 jar runtime diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 94b5cd35b..75ea6d092 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -108,7 +108,7 @@ org.junit.platform junit-platform-launcher - 1.10.1 + ${junit5.platform.launcher.version} test diff --git a/pom.xml b/pom.xml index 5bdf16cd2..502cb7f58 100644 --- a/pom.xml +++ b/pom.xml @@ -47,7 +47,7 @@ 1.2 3.6.4 5.1.9 - 2.2 + 3.0 1.10 2.22.0 9.0.0 @@ -58,7 +58,8 @@ 2.0.9 10.15.2.0 1.3.2 - 5.10.1 + 1.11.0 + 5.11.0 mysql From 5b2a6d8960fdca5dc3d5d4ee2c9bbe73069cc001 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 26 Sep 2024 04:42:57 +0200 Subject: [PATCH 56/64] BridgeDb Datasources 20240925 --- org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv | 1 - org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv | 3 ++- .../src/main/resources/org/bridgedb/bio/datasources.tsv | 1 - .../src/main/resources/org/bridgedb/bio/organisms.tsv | 3 ++- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 289fb0957..655878bd4 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -55,7 +55,6 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina i InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein -IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv index 560d65f42..940d8117d 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv @@ -40,10 +40,11 @@ Plasmodium falciparum Malaria parasite Pf 5833 Prymnesium parvum Pp 97485 Populus trichocarpa Western Balsam Poplar Pi 3694 Rattus norvegicus Rat Rn 10116 +Rosmarinus officinalis Rosemary Ro 39367 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 -Solanum tuberosum St 4113 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index 66cb63176..4b50c0d78 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -55,7 +55,6 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina i InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein -IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv index 560d65f42..940d8117d 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv @@ -40,10 +40,11 @@ Plasmodium falciparum Malaria parasite Pf 5833 Prymnesium parvum Pp 97485 Populus trichocarpa Western Balsam Poplar Pi 3694 Rattus norvegicus Rat Rn 10116 +Rosmarinus officinalis Rosemary Ro 39367 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 -Solanum tuberosum St 4113 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 From fc5c436f22cb82bc1b1519309120dff21e8ef616 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 07:41:49 +0200 Subject: [PATCH 57/64] Release 3.1.3 --- CITATION.cff | 4 ++-- README.md | 14 +++++++------- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- org.bridgedb/src/main/resources/version.props | 2 +- pom-java8.xml | 2 +- pom.xml | 2 +- 30 files changed, 40 insertions(+), 40 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index cdd95bc91..1c035e2b9 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.1.2 -date-released: '2024-07-30' +version: 3.1.3 +date-released: '2024-10-01' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 555e3e9a8..83fbdba8e 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.3`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.2 + 3.1.3 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.3' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.2' +'org.bridgedb:org.bridgedb.bio:jar:3.1.3' ``` @@ -135,7 +135,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.2 +mvn versions:set -DnewVersion=3.1.3 mvn clean deploy ``` @@ -145,7 +145,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.1.3-SNAPSHOT +mvn versions:set -DnewVersion=3.1.4-SNAPSHOT mvn clean deploy ``` diff --git a/examples/pom.xml b/examples/pom.xml index 3fe355949..046535746 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index cbcc44086..32af86677 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 88b5d884f..609362c96 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 22a091701..e4e9c498a 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 2fdee3665..1ee0d0da8 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 75ea6d092..169b5be78 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 14e4863d9..d7a497f28 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index e33449052..22fec0bd2 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 4a489cede..be079f4b8 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 compile org.bridgedb org.bridgedb.bio - 3.1.3-SNAPSHOT + 3.1.3 compile org.bridgedb org.bridgedb.rdb - 3.1.3-SNAPSHOT + 3.1.3 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index b5ecac8a0..26c9f2308 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 04e125150..3fafb090e 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index e592e3388..a7e5b5a3b 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 8b74b4eea..f8d17ca80 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 4fc3d983e..3fe0993f3 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 00a76920c..523efff03 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 2beeba819..5f0f5b744 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index a1349048c..2027b7914 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index f3672d4e3..f6ae18627 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index f8ac233e2..468fcf5cb 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index c5ac195d8..0ad3609ea 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 6726e0633..820d4039a 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index ea57e2096..05d56cc59 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index d39248962..6494251c5 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index ebbe3b200..378d6371a 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 7b96e71fb..29cd03789 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 6cc9da92d..0da9c3ac6 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.1.2 +bridgedb.version=3.1.3 diff --git a/pom-java8.xml b/pom-java8.xml index 4b568673d..e994adb9a 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.1.2 + 3.1.3-java8 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database diff --git a/pom.xml b/pom.xml index 502cb7f58..d95abc4a0 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.3-SNAPSHOT + 3.1.3 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From dddd78f035f14331b9e424b344d78044ade51521 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 08:13:10 +0200 Subject: [PATCH 58/64] Use Derby 10.4 --- pom-java8.xml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/pom-java8.xml b/pom-java8.xml index e994adb9a..6728dfff4 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.1.3-java8 + 3.1.3 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database @@ -36,7 +36,7 @@ 3.7.7 2.5 1.6.4 - 10.15.2.0 + 10.4.2.0 1.3.2 5.10.0 mysql @@ -110,4 +110,12 @@ + + + mvnrepository + MVN Repository + https://mvnrepository.com/artifact/ + + + From 336dab4bd844d23a67c762afa1a353eca7b427ae Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 08:30:10 +0200 Subject: [PATCH 59/64] Make sure we have data sources defined --- .../src/test/java/org/bridgedb/bio/DataSourceTxtTest.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java index 67f06fba0..6825e1a4f 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java @@ -33,6 +33,7 @@ import java.util.Set; import org.bridgedb.DataSource; +import org.junit.jupiter.api.BeforeAll; /** @@ -41,6 +42,11 @@ */ public class DataSourceTxtTest { + @BeforeAll + public static void setUpSources() { + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); + } + @org.junit.jupiter.api.Test public void testUniqueSystemCodes() { Set codes = new HashSet(); From 73e1115969565ab5955fc61cd08fcf391e97c319 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 08:40:44 +0200 Subject: [PATCH 60/64] Make sure we don't define data source twice --- .../src/test/java/org/bridgedb/bio/UniProtKBTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java index 67cec09d7..1e639458b 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java @@ -21,7 +21,7 @@ public class UniProtKBTest { @BeforeAll public static void setUpSources() { - DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); } @Test From 90bf94734f51f81e687c27075bbd7d18ff6454f5 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 09:12:47 +0200 Subject: [PATCH 61/64] Synched the versions with the main pom.xml --- pom-java8.xml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/pom-java8.xml b/pom-java8.xml index 6728dfff4..59e8db953 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -26,19 +26,20 @@ UTF-8 UTF-8 1.2 - 3.2.14 - 2.2 + 3.6.4 + 3.0 1.10 - 2.20.0 - 8.0.33 + 2.22.0 + 9.0.0 Tomcat 3.4 - 3.7.7 + 4.3.8 2.5 - 1.6.4 + 2.0.9 10.4.2.0 1.3.2 - 5.10.0 + 1.11.0 + 5.11.0 mysql From f797159b81ad7098768313fe073bf0dc50dbfc38 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 3 Oct 2024 12:13:50 +0200 Subject: [PATCH 62/64] Open for development --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 046535746..e61a2f13d 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 32af86677..bd8806470 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 609362c96..cddd5add9 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index e4e9c498a..7d155a927 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 1ee0d0da8..6d15c284b 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 169b5be78..887749e4a 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index d7a497f28..db39cd26e 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 22fec0bd2..f6592f1dd 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index be079f4b8..c00e69f35 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.3 + 3.1.4-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.3 + 3.1.4-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 26c9f2308..665a81e98 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 3fafb090e..620e0f064 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index a7e5b5a3b..f554bfe3c 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index f8d17ca80..65da76e5f 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 3fe0993f3..104dd3af5 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 523efff03..92f713da2 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 5f0f5b744..62741b9f5 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 2027b7914..7eaab1571 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index f6ae18627..14811e538 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 468fcf5cb..741d3d77d 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 0ad3609ea..edf6c8470 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 820d4039a..d9597712c 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 05d56cc59..5db82a505 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 6494251c5..e3d89f9a1 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 378d6371a..fb0a78813 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 29cd03789..bbaa7a341 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.3 + 3.1.4-SNAPSHOT diff --git a/pom.xml b/pom.xml index d95abc4a0..9029d6d6a 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.3 + 3.1.4-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 684513f64e78b71e380e3d0e56b797965d4ec3f7 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 3 Oct 2024 12:04:00 +0200 Subject: [PATCH 63/64] A dual world: Derby 10.4 and 10.14+ --- .../rdb/construct/DBConnectorDerbyServer.java | 11 ++++++----- .../src/org/bridgedb/rdb/construct/DataDerby.java | 11 ++++++----- .../src/org/bridgedb/rdb/IDMapperRdb.java | 13 +++++++------ org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java | 10 +++++++--- 4 files changed, 26 insertions(+), 19 deletions(-) diff --git a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java index 0d60c7728..3576277d7 100644 --- a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java +++ b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java @@ -65,11 +65,12 @@ public Connection createConnection(String dbName) throws IDMapperException try { sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString()); - Class.forName("org.apache.derby.jdbc.ClientDriver"); - } - catch (ClassNotFoundException e) - { - throw new IDMapperException (e); + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } } catch (IOException f) { diff --git a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java index 64b7b6788..46b172eb4 100644 --- a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java +++ b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java @@ -123,11 +123,12 @@ public Connection createConnection(String dbName, int props) throws IDMapperExce { sysprop.setProperty("derby.storage.tempDirectory", System.getProperty("java.io.tmpdir")); sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString()); - Class.forName("org.apache.derby.jdbc.ClientDriver"); - } - catch (ClassNotFoundException e) - { - throw new IDMapperException (e); + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } } catch (IOException f) { diff --git a/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java b/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java index ad128adfa..7fb4e2dfd 100644 --- a/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java +++ b/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java @@ -89,8 +89,13 @@ public IDMapper connect(String location) throws IDMapperException String host = args.containsKey("host") ? args.get("host") : "wikipathways.org"; String port = args.containsKey("port") ? args.get("port") : "1527"; - - Class.forName("org.apache.derby.jdbc.ClientDriver"); + + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } Properties sysprop = System.getProperties(); sysprop.setProperty("derby.storage.tempDirectory", System.getProperty("java.io.tmpdir")); sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString()); @@ -102,10 +107,6 @@ public IDMapper connect(String location) throws IDMapperException { throw new IDMapperException (e); } - catch (ClassNotFoundException e) - { - throw new IDMapperException (e); - } } } diff --git a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java index 59ae298e6..c72f48bf0 100644 --- a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java +++ b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java @@ -151,7 +151,6 @@ public void testSimpleGdb() throws ClassNotFoundException, IDMapperException, IO Class.forName("org.bridgedb.file.IDMapperText"); Class.forName("org.bridgedb.rdb.IDMapperRdb"); Class.forName("com.mysql.jdbc.Driver"); - // no longer needed?? Class.forName("org.apache.derby.jdbc.ClientDriver"); String fileName = "yeast_id_mapping"; String fullName = fileName + ".txt"; @@ -181,8 +180,13 @@ public void testDerbyClient() throws IDMapperException, ClassNotFoundException { long start, end, delta; start = System.currentTimeMillis(); Class.forName ("org.bridgedb.rdb.IDMapperRdb"); - Class.forName ("org.apache.derby.jdbc.ClientDriver"); - + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } + IDMapper mapper = BridgeDb.connect ("idmapper-derbyclient:Homo sapiens?host=www.wikipathways.org"); end = System.currentTimeMillis(); delta = end - start; From a8f0264728bae5d09f8b982027fa4a1482914161 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 19 Dec 2024 15:18:08 +0100 Subject: [PATCH 64/64] Release 3.1.4 --- CITATION.cff | 4 ++-- README.md | 14 +++++++------- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom-java8.xml | 2 +- pom.xml | 2 +- 29 files changed, 39 insertions(+), 39 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 1c035e2b9..9c9192b3b 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.1.3 -date-released: '2024-10-01' +version: 3.1.4 +date-released: '2024-12-19' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 83fbdba8e..fee8fd1b2 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.3`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.4`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.3 + 3.1.4 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.3' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.4' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.3' +'org.bridgedb:org.bridgedb.bio:jar:3.1.4' ``` @@ -135,7 +135,7 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.3 +mvn versions:set -DnewVersion=3.1.4 mvn clean deploy ``` @@ -145,7 +145,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.1.4-SNAPSHOT +mvn versions:set -DnewVersion=3.1.5-SNAPSHOT mvn clean deploy ``` diff --git a/examples/pom.xml b/examples/pom.xml index e61a2f13d..d2a705db1 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index bd8806470..c0f0be58d 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index cddd5add9..3433845a9 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 7d155a927..6b21739b9 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 6d15c284b..026adc09b 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 887749e4a..fdc996246 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index db39cd26e..e56013aa6 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index f6592f1dd..d8ed5f761 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index c00e69f35..d65a4d9a3 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 compile org.bridgedb org.bridgedb.bio - 3.1.4-SNAPSHOT + 3.1.4 compile org.bridgedb org.bridgedb.rdb - 3.1.4-SNAPSHOT + 3.1.4 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 665a81e98..91adf6d8c 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 620e0f064..327225eab 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index f554bfe3c..f195a05c2 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 65da76e5f..6f74e8c71 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 104dd3af5..867d93212 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 92f713da2..8a83fe0c9 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 62741b9f5..fcaa82428 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 7eaab1571..b39522c77 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 14811e538..f20a40911 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 741d3d77d..2d4066439 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index edf6c8470..d6b1d7ca5 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index d9597712c..d00d424d7 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index 5db82a505..e98637f25 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index e3d89f9a1..a4f29eb99 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index fb0a78813..bda968c58 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index bbaa7a341..15c9a5641 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.4-SNAPSHOT + 3.1.4 diff --git a/pom-java8.xml b/pom-java8.xml index 59e8db953..f0bd47b1a 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.1.3 + 3.1.4 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database diff --git a/pom.xml b/pom.xml index 9029d6d6a..d7ab84f33 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.4-SNAPSHOT + 3.1.4 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database