Prepare new release 5.2.2

opencb · Aug 2, 2022 · f1282b1 · f1282b1
2 parents 0a81a33 + a99d0f9
commit f1282b1
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Showing 11 changed files with 18 additions and 15 deletions.
diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.2.1</version>
+        <version>5.2.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.2.1</version>
+        <version>5.2.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.2.1</version>
+        <version>5.2.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.2.1</version>
+        <version>5.2.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AbstractManager.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/AbstractManager.java
@@ -30,7 +30,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-public class AbstractManager {
+public class AbstractManager implements AutoCloseable {
 
     protected String species;
     protected String assembly;
@@ -89,4 +89,9 @@ protected List<Query> createQueries(Query query, String csvField, String queryKe
         }
         return queries;
     }
+
+    @Override
+    public void close()  {
+        mongoDBManager.close();
+    }
 }
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.2.1</version>
+        <version>5.2.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java
@@ -177,7 +177,7 @@ private void initQuery() throws CellBaseException {
                         assembly = SpeciesUtils.getSpecies(cellBaseConfiguration, species, assembly).getAssembly();
                     }
                     if (StringUtils.isNotEmpty(assembly)) {
-                        DataReleaseManager releaseManager = new DataReleaseManager(species, assembly, cellBaseConfiguration);
+                        DataReleaseManager releaseManager = cellBaseManagerFactory.getDataReleaseManager(species, assembly);
                         DataRelease dr = releaseManager.getDefault();
                         if (dr != null) {
                             defaultDataRelease = dr.getRelease();

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java
@@ -131,7 +131,7 @@ public Response getDataRelease(@PathParam("species")
                 return createErrorResponse("getVersion", "Invalid species: '" + species + "' or assembly: '"
                         + assembly + "'");
             }
-            DataReleaseManager dataReleaseManager = new DataReleaseManager(species, assembly, cellBaseConfiguration);
+            DataReleaseManager dataReleaseManager = cellBaseManagerFactory.getDataReleaseManager(species, assembly);
             CellBaseDataResult<DataRelease> result = dataReleaseManager.getReleases();
             if (onlyActive) {
                 for (DataRelease release : result.getResults()) {

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java
@@ -61,7 +61,6 @@ public class GeneWSServer extends GenericRestWSServer {
     private TranscriptManager transcriptManager;
     private VariantManager variantManager;
     private ProteinManager proteinManager;
-    private TfbsManager tfbsManager;
 
     public GeneWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", value = VERSION_DESCRIPTION,
             defaultValue = DEFAULT_VERSION) String apiVersion,
@@ -82,10 +81,9 @@ public GeneWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", valu
         }
 
         geneManager = cellBaseManagerFactory.getGeneManager(species, assembly);
-//        transcriptManager = cellBaseManagerFactory.getTranscriptManager(species, assembly);
-//        variantManager = cellBaseManagerFactory.getVariantManager(species, assembly);
-//        proteinManager = cellBaseManagerFactory.getProteinManager(species, assembly);
-//        tfbsManager = cellBaseManagerFactory.getTFManager(species, assembly);
+        transcriptManager = cellBaseManagerFactory.getTranscriptManager(species, assembly);
+        variantManager = cellBaseManagerFactory.getVariantManager(species, assembly);
+        proteinManager = cellBaseManagerFactory.getProteinManager(species, assembly);
     }
 
     @GET

diff --git a/cellbase-test/pom.xml b/cellbase-test/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase-test</artifactId>
-    <version>5.2.1</version>
+    <version>5.2.2</version>
     <packaging>pom</packaging>
 
     <dependencies>

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>5.2.1</version>
+    <version>5.2.2</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>