Merge branch 'release/1.0-SNAPSHOT'

goksel · goksel · commit 94371ec5b57c · 2020-09-20T20:13:08.000+01:00
diff --git a/README.md b/README.md
@@ -1,30 +1,42 @@
-# libSBOLj
-XML
-```
-<rdf:RDF
-    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:sbol="http://sbols.org/v3#">
-   <sbol:Sequence rdf:about="http://myseq.org/seqabc">
-      <sbol:encoding rdf:resource="http://sbols.org/v3#iupacNucleicAcid"/>
-      <sbol:elements>aaaatttggg</sbol:elements>
-      <sbol:description>pTetR promoter</sbol:description>
-      <sbol:name>pTetR</sbol:name>
-      <sbol:displayId>pTetR</sbol:displayId>
-   </sbol:Sequence>
-</rdf:RDF>
-```
+# libSBOLj3 - A Java library for the Synthetic Biology Open Language 3
+The libSBOLj Java library has been developed for the [Synthetic Biology Open Language 3.0](https://sbolstandard.org/data-model-specification). The library is  under development and is currently available as an alpha release. 
 
-Turtle:
-```
+SBOL represents data using RDF graphs, which can be serialised in different formats. The libSBOLj3 library supports the following RDF formats.
+* RDF/XML
+* Turtle
+* N3
+* JSON-LD
+* RDF/JSON
 
-@base          <http://testbase.org> .
-@prefix sbol:  <http://sbols.org/v3#> .
+## How to use libSBOLj3
 
-<http://myseq.org/seqabc>
-        a                 sbol:Sequence ;
-        sbol:description  "pTetR promoter" ;
-        sbol:displayId    "pTetR" ;
-        sbol:elements     "aaaatttggg" ;
-        sbol:encoding     sbol:iupacNucleicAcid ;
-        sbol:name         "pTetR" .
+### As a Maven dependency in a Maven project
+Use this option if you are developing a Java application using [Maven](https://maven.apache.org/). Add the following libSBOLj3 dependency to your Maven applications's POM file (pom.xml). Please also make sure that you include the Nexus' Snapshots repository URL in the POM file. 
+``` 
+</dependencies>
+	...
+   <dependency>
+		<groupId>org.sbolstandard</groupId>
+		<artifactId>libSBOLj3</artifactId>
+		<version>1.0-SNAPSHOT</version>
+	</dependency>
+   ...
+</dependencies>
+
+<repositories>
+   <repository>
+      <id>oss-sonatype</id>
+      <name>oss-sonatype</name>
+      <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
+      <snapshots>
+         <enabled>true</enabled>
+      </snapshots>
+   </repository>
+</repositories>
 ```
+
+### As a Java dependency in a non-Maven project
+The libSBOLj3 library is available as a JAR file. Please download the file from the [releases page](https://github.com/goksel/libSBOLj3/tags). A single JAR file (with the "withDepencencies" suffix), which includes all the required libSBOLj3 related dependencies, is also available.
+
+## SBOL Examples
+[Several SBOL3 examples](https://github.com/goksel/libSBOLj3/tree/master/libSBOLj3/output) are available as part of the libSBOLj3 library. These examples have also been made available as part of the [SBOLTestSuite](https://github.com/SynBioDex/SBOLTestSuite/tree/master/SBOL3). Some of these examples have beeen explained in the recent SBOL3 paper, titled "[The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering]"(https://doi.org/10.3389/fbioe.2020.01009).
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld
@@ -1,5 +1,5 @@
 {
-  "@id" : "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122",
+  "@id" : "urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122",
   "@type" : "sbol:Component",
   "name" : "TetR",
   "type" : "SBO:0000252",
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt
@@ -1,3 +1,3 @@
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://sbols.org/v3#name> "TetR" .
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122> <http://sbols.org/v3#name> "TetR" .
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf
@@ -10,7 +10,7 @@
     xmlns="https://sbolstandard.org/examples/"
     xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
    xml:base="https://sbolstandard.org/examples/">
-   <sbol:Component rdf:about="urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122">
+   <sbol:Component rdf:about="urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122">
       <sbol:name>TetR</sbol:name>
       <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
    </sbol:Component>
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj
@@ -1,5 +1,5 @@
 { 
-  "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122" : { 
+  "urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122" : { 
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
       "type" : "uri" ,
       "value" : "http://sbols.org/v3#Component"
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl
@@ -9,7 +9,7 @@
 @prefix prov:  <http://www.w3.org/ns/prov#> .
 @prefix om:    <http://www.ontology-of-units-of-measure.org/resource/om-2/> .
 
-<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122>
+<urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122>
         a          sbol:Component ;
         sbol:name  "TetR" ;
         sbol:type  SBO:0000252 .
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.jsonld b/libSBOLj3/output/provenance_entity/activity/activity.jsonld
@@ -26,10 +26,10 @@
     "displayId" : "codon_optimization_activity",
     "name" : "Codon optimization activity",
     "type" : "sbol:design",
-    "endedAtTime" : "2020-08-30T17:16:29.495Z",
+    "endedAtTime" : "2020-08-30T17:48:04.765Z",
     "qualifiedAssociation" : "codon_optimization_activity/association",
     "qualifiedUsage" : [ "codon_optimization_activity/optimised_usage", "codon_optimization_activity/source_usage" ],
-    "startedAtTime" : "2019-07-29T17:16:29.495Z"
+    "startedAtTime" : "2019-07-29T17:48:04.765Z"
   }, {
     "@id" : "codon_optimization_activity/association",
     "@type" : "prov:Association",
@@ -112,15 +112,15 @@
       "@id" : "http://www.w3.org/ns/prov#qualifiedAssociation",
       "@type" : "@id"
     },
-    "endedAtTime" : {
-      "@id" : "http://www.w3.org/ns/prov#endedAtTime"
+    "startedAtTime" : {
+      "@id" : "http://www.w3.org/ns/prov#startedAtTime"
     },
     "qualifiedUsage" : {
       "@id" : "http://www.w3.org/ns/prov#qualifiedUsage",
       "@type" : "@id"
     },
-    "startedAtTime" : {
-      "@id" : "http://www.w3.org/ns/prov#startedAtTime"
+    "endedAtTime" : {
+      "@id" : "http://www.w3.org/ns/prov#endedAtTime"
     },
     "@vocab" : "https://sbolstandard.org/examples/",
     "SBO" : "https://identifiers.org/SBO:",
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.nt b/libSBOLj3/output/provenance_entity/activity/activity.nt
@@ -39,11 +39,11 @@
 <https://sbolstandard.org/examples/CodonOptimisationProtocol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Plan> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#type> <http://sbols.org/v3#design> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedAssociation> <https://sbolstandard.org/examples/codon_optimization_activity/association> .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#endedAtTime> "2020-08-30T17:16:29.495Z" .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#startedAtTime> "2019-07-29T17:48:04.765Z" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedUsage> <https://sbolstandard.org/examples/codon_optimization_activity/optimised_usage> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#name> "Codon optimization activity" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#description> "An activity that is used to optimise codons" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://sbols.org/v3#displayId> "codon_optimization_activity" .
-<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#startedAtTime> "2019-07-29T17:16:29.495Z" .
+<https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#endedAtTime> "2020-08-30T17:48:04.765Z" .
 <https://sbolstandard.org/examples/codon_optimization_activity> <http://www.w3.org/ns/prov#qualifiedUsage> <https://sbolstandard.org/examples/codon_optimization_activity/source_usage> .
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.rdf b/libSBOLj3/output/provenance_entity/activity/activity.rdf
@@ -55,7 +55,7 @@
             <sbol:displayId>association</sbol:displayId>
          </prov:Association>
       </prov:qualifiedAssociation>
-      <prov:endedAtTime>2020-08-30T17:16:29.495Z</prov:endedAtTime>
+      <prov:startedAtTime>2019-07-29T17:48:04.765Z</prov:startedAtTime>
       <prov:qualifiedUsage>
          <prov:Usage rdf:about="codon_optimization_activity/optimised_usage">
             <prov:hadRole rdf:resource="https://identifiers.org/SBO:0000011"/>
@@ -66,7 +66,7 @@
       <sbol:name>Codon optimization activity</sbol:name>
       <sbol:description>An activity that is used to optimise codons</sbol:description>
       <sbol:displayId>codon_optimization_activity</sbol:displayId>
-      <prov:startedAtTime>2019-07-29T17:16:29.495Z</prov:startedAtTime>
+      <prov:endedAtTime>2020-08-30T17:48:04.765Z</prov:endedAtTime>
       <prov:qualifiedUsage>
          <prov:Usage rdf:about="codon_optimization_activity/source_usage">
             <prov:hadRole rdf:resource="https://identifiers.org/SBO:0000645"/>
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.rj b/libSBOLj3/output/provenance_entity/activity/activity.rj
@@ -165,19 +165,19 @@
      ] ,
     "http://www.w3.org/ns/prov#endedAtTime" : [ { 
       "type" : "literal" ,
-      "value" : "2020-08-30T17:16:29.495Z"
+      "value" : "2020-08-30T17:48:04.765Z"
+    }
+     ] ,
+    "http://www.w3.org/ns/prov#startedAtTime" : [ { 
+      "type" : "literal" ,
+      "value" : "2019-07-29T17:48:04.765Z"
     }
      ] ,
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
       "type" : "uri" ,
       "value" : "http://www.w3.org/ns/prov#Activity"
     }
      ] ,
-    "http://www.w3.org/ns/prov#startedAtTime" : [ { 
-      "type" : "literal" ,
-      "value" : "2019-07-29T17:16:29.495Z"
-    }
-     ] ,
     "http://sbols.org/v3#name" : [ { 
       "type" : "literal" ,
       "value" : "Codon optimization activity"
diff --git a/libSBOLj3/output/provenance_entity/activity/activity.ttl b/libSBOLj3/output/provenance_entity/activity/activity.ttl
@@ -69,7 +69,7 @@
         sbol:displayId             "codon_optimization_activity" ;
         sbol:name                  "Codon optimization activity" ;
         sbol:type                  sbol:design ;
-        prov:endedAtTime           "2020-08-30T17:16:29.495Z" ;
+        prov:endedAtTime           "2020-08-30T17:48:04.765Z" ;
         prov:qualifiedAssociation  <codon_optimization_activity/association> ;
         prov:qualifiedUsage        <codon_optimization_activity/optimised_usage> , <codon_optimization_activity/source_usage> ;
-        prov:startedAtTime         "2019-07-29T17:16:29.495Z" .
+        prov:startedAtTime         "2019-07-29T17:48:04.765Z" .
diff --git a/libSBOLj3/pom.xml b/libSBOLj3/pom.xml
@@ -1,20 +1,25 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>org.sbolstandard</groupId>
-  <artifactId>libSBOLj3</artifactId>
-  <packaging>jar</packaging>
-  <version>1.0-SNAPSHOT</version>
-  <name>libSBOLj3</name>
-  <url>http://maven.apache.org</url>
-  <dependencies>
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13</version>
-      <scope>test</scope>
-    </dependency>
-    		<dependency>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>org.sbolstandard</groupId>
+	<artifactId>libSBOLj3</artifactId>
+	<packaging>jar</packaging>
+	<version>1.0-SNAPSHOT</version>
+	<name>libSBOLj3</name>
+	<url>https://github.com/goksel/libSBOLj3</url>
+	<issueManagement>
+		<system>GitHub Issues</system>
+		<url>https://github.com/goksel/libSBOLj3/issues</url>
+	</issueManagement>
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.13</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-base</artifactId>
 			<version>3.14.0</version>
@@ -23,25 +28,67 @@
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-arq</artifactId>
 			<version>3.14.0</version>
-		</dependency>  
+		</dependency>
 		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
-<dependency>
-    <groupId>commons-io</groupId>
-    <artifactId>commons-io</artifactId>
-    <version>2.6</version>
-</dependency>
-		
-  </dependencies>
-<build>
-  <plugins>
-    <plugin>
-      <groupId>org.apache.maven.plugins</groupId>
-      <artifactId>maven-compiler-plugin</artifactId>
-      <version>3.3</version>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.6</version>
+		</dependency>
+
+	</dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.3</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+			
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>3.2.4</version>
+				<configuration>
+					<shadedArtifactAttached>true</shadedArtifactAttached>
+					<shadedClassifierName>withDependencies</shadedClassifierName>
+				</configuration>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+
+				
+				    <plugin>
+      <groupId>org.sonatype.plugins</groupId>
+      <artifactId>nexus-staging-maven-plugin</artifactId>
+      <version>1.6.7</version>
+      <extensions>true</extensions>
       <configuration>
-        <source>1.8</source>
-        <target>1.8</target>
+        <serverId>ossrh</serverId>
+        <nexusUrl>https://oss.sonatype.org/</nexusUrl>
+        <autoReleaseAfterClose>false</autoReleaseAfterClose>
       </configuration>
     </plugin>
-  </plugins>
-</build></project>
+    
+
+		</plugins>
+	</build>
+	
+		<distributionManagement>
+		<snapshotRepository>
+			<id>ossrh</id>
+			<url>https://oss.sonatype.org/content/repositories/snapshots</url>
+		</snapshotRepository>
+	</distributionManagement>
+	
+</project>

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "@id" : "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122",`
	`2`	`+ "@id" : "urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122",`
`3`	`3`	`"@type" : "sbol:Component",`
`4`	`4`	`"name" : "TetR",`
`5`	`5`	`"type" : "SBO:0000252",`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122" : {`
	`2`	`+ "urn:uuid:d1ce016f-2c60-11b2-80b5-acde48001122" : {`
`3`	`3`	`"http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ {`
`4`	`4`	`"type" : "uri" ,`
`5`	`5`	`"value" : "http://sbols.org/v3#Component"`