Version 0.9.1 using OpenCGA 0.4.0 final

Author: Cristina Yenyxe Gonzalez Garcia

eva-lib/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>uk.ac.ebi.variation.eva</groupId>
         <artifactId>eva</artifactId>
-        <version>0.3.1</version>
+        <version>0.9.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

eva-lib/src/main/java/uk/ac/ebi/variation/eva/lib/storage/metadata/ArchiveDgvaDBAdaptor.java

@@ -90,9 +90,9 @@ public QueryResult countStudiesPerType(QueryOptions options) {
         StringBuilder query = new StringBuilder("select study_type, count(*) as COUNT from dgva_study_browser ");
         if (options.containsKey("species")) {
             query.append("where ");
-            query.append(EvaproUtils.getInClause("common_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("common_name", options.getAsStringList("species")));
             query.append(" or ");
-            query.append(EvaproUtils.getInClause("scientific_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("scientific_name", options.getAsStringList("species")));
         }
         query.append(" group by study_type order by COUNT desc");
 

eva-lib/src/main/java/uk/ac/ebi/variation/eva/lib/storage/metadata/ArchiveEvaproDBAdaptor.java

@@ -50,9 +50,9 @@ public QueryResult countStudiesPerSpecies(QueryOptions options) {
         StringBuilder query = new StringBuilder("select common_name, count(*) as COUNT from study_browser ");
         if (options.containsKey("species")) {
             query.append("where ");
-            query.append(EvaproUtils.getInClause("common_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("common_name", options.getAsStringList("species")));
             query.append(" or ");
-            query.append(EvaproUtils.getInClause("scientific_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("scientific_name", options.getAsStringList("species")));
         }
         query.append(" group by common_name order by COUNT desc");
 
@@ -96,9 +96,9 @@ public QueryResult countStudiesPerType(QueryOptions options) {
         StringBuilder query = new StringBuilder("select experiment_type, count(*) as COUNT from study_browser ");
         if (options.containsKey("species")) {
             query.append("where ");
-            query.append(EvaproUtils.getInClause("common_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("common_name", options.getAsStringList("species")));
             query.append(" or ");
-            query.append(EvaproUtils.getInClause("scientific_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("scientific_name", options.getAsStringList("species")));
         }
         query.append(" group by experiment_type order by COUNT desc");
 

eva-lib/src/main/java/uk/ac/ebi/variation/eva/lib/storage/metadata/StudyDgvaDBAdaptor.java

@@ -42,16 +42,16 @@ public QueryResult getAllStudies(QueryOptions options) {
         }
         if (hasSpecies) {
             query.append("(");
-            query.append(EvaproUtils.getInClause("common_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("common_name", options.getAsStringList("species")));
             query.append(" or ");
-            query.append(EvaproUtils.getInClause("scientific_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("scientific_name", options.getAsStringList("species")));
             query.append(")");
         }
         if (hasType) {
             if (hasSpecies) {
                 query.append(" and ");
             }
-            query.append(EvaproUtils.getInClause("study_type", options.getListAs("type", String.class)));
+            query.append(EvaproUtils.getInClause("study_type", options.getAsStringList("species")));
         }
 
         Connection conn = null;

eva-lib/src/main/java/uk/ac/ebi/variation/eva/lib/storage/metadata/StudyEvaproDBAdaptor.java

@@ -42,17 +42,17 @@ public QueryResult getAllStudies(QueryOptions options) {
         }
         if (hasSpecies) {
             query.append("(");
-            query.append(EvaproUtils.getInClause("common_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("common_name", options.getAsStringList("species")));
             query.append(" or ");
-            query.append(EvaproUtils.getInClause("scientific_name", options.getListAs("species", String.class)));
+            query.append(EvaproUtils.getInClause("scientific_name", options.getAsStringList("species")));
             query.append(")");
         }
         if (hasType) {
             if (hasSpecies) {
                 query.append(" and ");
             }
-            query.append(EvaproUtils.getInClause("experiment_type", options.getListAs("type", String.class)));
-            for (String t : options.getListAs("type", String.class)) {
+            query.append(EvaproUtils.getInClause("experiment_type", options.getAsStringList("type")));
+            for (String t : options.getAsStringList("type")) {
                 query.append(" or experiment_type like '%").append(t).append("%'");
             }
         }

eva-lib/src/main/java/uk/ac/ebi/variation/eva/lib/storage/metadata/VariantSourceEvaproDBAdaptor.java

@@ -14,6 +14,7 @@
 import javax.naming.InitialContext;
 import javax.naming.NamingException;
 import javax.sql.DataSource;
+import org.opencb.biodata.models.variant.stats.VariantSourceStats;
 import org.opencb.datastore.core.QueryOptions;
 import org.opencb.datastore.core.QueryResult;
 import org.opencb.opencga.storage.core.variant.adaptors.VariantSourceDBAdaptor;
@@ -89,6 +90,11 @@ public QueryResult getSamplesBySources(List<String> fileIds, QueryOptions option
         throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
     }
 
+    @Override
+    public QueryResult getSourceDownloadUrlById(String fileId, String studyId) {
+        throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+    }
+
     @Override
     public QueryResult getSourceDownloadUrlByName(String filename) {
         Connection conn = null;
@@ -213,7 +219,7 @@ public List<QueryResult> getSourceDownloadUrlByName(List<String> filenames) {
     }
 
     @Override
-    public QueryResult getSourceDownloadUrlById(String fileId, String studyId) {
+    public QueryResult updateSourceStats(VariantSourceStats variantSourceStats, QueryOptions queryOptions) {
         throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
     }
 

eva-server/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>eva</artifactId>
         <groupId>uk.ac.ebi.variation.eva</groupId>
-        <version>0.3.1</version>
+        <version>0.9.1</version>
         <relativePath>..</relativePath>
     </parent>
 

pom.xml

@@ -7,7 +7,7 @@
     <groupId>uk.ac.ebi.variation.eva</groupId>
     <artifactId>eva</artifactId>
     <packaging>pom</packaging>
-    <version>0.3.1</version>
+    <version>0.9.1</version>
 
     <modules>
         <module>eva-lib</module>