Merge branch 'release-6.2.x'

opencb · Jul 17, 2024 · 6039f5d · 6039f5d
2 parents 8b1829b + 8b754fc
commit 6039f5d
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Showing 10 changed files with 67 additions and 25 deletions.
diff --git a/.github/workflows/manual-test.yml b/.github/workflows/manual-test.yml
@@ -18,12 +18,12 @@ jobs:
     name: JUnit Test
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.inputs.branch }}
           fetch-depth: '0'
       - name: Set up JDK 11
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '11'

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
@@ -0,0 +1,15 @@
+name: Pull request approve workflow
+
+on:
+  pull_request_review:
+    types: [ submitted ]
+
+jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
+  test:
+    name: "Test analysis"
+    uses: ./.github/workflows/test-analysis.yml
+    needs: build
+    secrets: inherit
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -11,11 +11,11 @@ jobs:
     name: Test and push Sonar analysis
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
       - name: Set up JDK 11
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '11'

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>6.1.0</version>
+        <version>6.2.0</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>6.1.0</version>
+        <version>6.2.0</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>6.1.0</version>
+        <version>6.2.0</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>6.1.0</version>
+        <version>6.2.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -187,4 +187,22 @@
         </dependency>
 
     </dependencies>
+
+    <build>
+        <testResources>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <excludes>
+                    <exclude>configuration.test.yaml</exclude>
+                </excludes>
+            </testResource>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <includes>
+                    <include>configuration.test.yaml</include>
+                </includes>
+                <filtering>true</filtering>
+            </testResource>
+        </testResources>
+    </build>
 </project>
diff --git a/cellbase-lib/src/test/resources/configuration.test.yaml b/cellbase-lib/src/test/resources/configuration.test.yaml
@@ -7,40 +7,40 @@ maintainerContact: [email protected]
 secretKey: "xPacig89igHSieEnveJEi4KCfdEslhmssC3vui1JJQGgDQ0y8v"
 databases:
   mongodb:
-    host: localhost:27017
-    user: 'cellbase'
-    password: 'cellbase'
+    host: "${JUNIT.CELLBASE.DB.MONGODB.HOST}"
+    user: "${JUNIT.CELLBASE.DB.USER}"
+    password: "${JUNIT.CELLBASE.DB.PASSWORD}"
     options:
-      authenticationDatabase: 'admin'
-      authenticationMechanism: 'SCRAM-SHA-256'
+      authenticationDatabase: "${JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE}"
+      authenticationMechanism: "${JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATION_MECHANISM}"
       readPreference: ''
       replicaSet: ''
       connectionsPerHost: 20
   neo4j:
     hsapiens:
-      host: "${CELLBASE.DB.NEO4J.HOST}"
-      user: "${CELLBASE.DB.USER}"
-      password: "${CELLBASE.DB.PASSWORD}"
+      host: "${JUNIT.CELLBASE.DB.NEO4J.HOST}"
+      user: "${JUNIT.CELLBASE.DB.USER}"
+      password: "${JUNIT.CELLBASE.DB.PASSWORD}"
     mmusculus:
-      host: "${CELLBASE.DB.NEO4J.HOST}"
-      user: "${CELLBASE.DB.USER}"
-      password: "${CELLBASE.DB.PASSWORD}"
+      host: "${JUNIT.CELLBASE.DB.NEO4J.HOST}"
+      user: "${JUNIT.CELLBASE.DB.USER}"
+      password: "${JUNIT.CELLBASE.DB.PASSWORD}"
 defaultOutdir: "/tmp"
 download:
   ensembl:
     database:
       host: ensembldb.ensembl.org:3306
       user: anonymous
       password: ''
-    libs: "${CELLBASE.ENSEMBL.LIBS}"
+    libs: "${JUNIT.CELLBASE.ENSEMBL.LIBS}"
     url:
       host: ftp://ftp.ensembl.org/pub
   ensemblGenomes:
     database:
       host: mysql-eg-publicsql.ebi.ac.uk:4157
       user: anonymous
       password: ''
-    libs: "${CELLBASE.ENSEMBL.LIBS}"
+    libs: "${JUNIT.CELLBASE.ENSEMBL.LIBS}"
     url:
       host: ftp://ftp.ensemblgenomes.org/pub
   geneUniprotXref:

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>6.1.0</version>
+        <version>6.2.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>6.1.0</version>
+    <version>6.2.0</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>
@@ -23,8 +23,8 @@
 
     <properties>
         <pycellbase.version>${project.version}</pycellbase.version>
-        <java-common-libs.version>5.1.0</java-common-libs.version>
-        <biodata.version>3.1.0</biodata.version>
+        <java-common-libs.version>5.2.0</java-common-libs.version>
+        <biodata.version>3.2.0</biodata.version>
         <bionetdb.version>0.1.0</bionetdb.version>
         <jackson.version>2.11.4</jackson.version>
         <jackson-asl.version>1.9.13</jackson-asl.version>
@@ -614,6 +614,15 @@
                 <CELLBASE.DB.MONGODB.READPREFERENCE>secondaryPreferred</CELLBASE.DB.MONGODB.READPREFERENCE>
                 <CELLBASE.SERVER.REST.PORT>9090</CELLBASE.SERVER.REST.PORT>
                 <CELLBASE.MONITOR.AGENT></CELLBASE.MONITOR.AGENT>
+
+                <!--
+                Configuration for JUnit tets (using the file configuration.test.yaml)
+                -->
+                <JUNIT.CELLBASE.DB.MONGODB.HOST>localhost:27017</JUNIT.CELLBASE.DB.MONGODB.HOST>
+                <JUNIT.CELLBASE.DB.USER>cellbase</JUNIT.CELLBASE.DB.USER>
+                <JUNIT.CELLBASE.DB.PASSWORD>cellbase</JUNIT.CELLBASE.DB.PASSWORD>
+                <JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE>admin</JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATIONDATABASE>
+                <JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATION_MECHANISM>SCRAM-SHA-256</JUNIT.CELLBASE.DB.MONGODB.AUTHENTICATION_MECHANISM>
             </properties>
         </profile>