Portpatch 6.1.0 -> 7.0.0-SNAPSHOT

.github/workflows/deploy-maven-repository-workflow.yml

@@ -33,7 +33,7 @@
           gpg-private-key: ${{ secrets.MAVEN_GPG_PRIVATE_KEY }}   # Value of the GPG private key to import
           gpg-passphrase: MAVEN_GPG_PASSPHRASE                    # env variable for GPG private key passphrase
       - name: Deploy to Maven Central repository
-        run: mvn clean deploy -DskipTests -P deploy-maven ${{ inputs.maven_opts }} --no-transfer-progress
+        run: mvn clean deploy -DskipTests -Pdeploy-maven ${{ inputs.maven_opts }} --no-transfer-progress
         env:
           MAVEN_NEXUS_USER: ${{ secrets.MAVEN_USER_TOKEN }}
           MAVEN_NEXUS_PASSWORD: ${{ secrets.MAVEN_PASSWORD_TOKEN }}
@@ -44,6 +44,6 @@
           distribution: 'temurin'
           java-version: '8'
       - name: Deploy to GitHub Packages repository
-        run: mvn clean deploy -DskipTests -P deploy-github ${{ inputs.maven_opts }} --no-transfer-progress
+        run: mvn clean deploy -DskipTests -Pdeploy-github ${{ inputs.maven_opts }} --no-transfer-progress
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pull-request-approved.yml

@@ -35,7 +35,7 @@ jobs:
   test:
     name: "Run all tests before merging"
     needs: calculate-xetabase-branch
-    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop
+    uses: ./.github/workflows/test-xetabase-workflow.yml
     with:
       branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
       task: ${{ github.event.pull_request.head.ref }}

.github/workflows/test-analysis.yml

@@ -39,4 +39,4 @@ jobs:
           check_name: "Surefire tests report"
           report_paths: './**/surefire-reports/TEST-*.xml'
           commit: '${{ github.sha }}'
-          fail_on_test_failures: true
+          fail_on_test_failures: true

.github/workflows/test-xetabase-workflow.yml

@@ -77,17 +77,6 @@
         with:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
-      - name: K8s Tunnel MongoDB
-        run: |
-          wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
-          chmod +x ./kubectl
-          echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf
-          ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf &
-      - name: DockerHub login
-        uses: docker/login-action@v3
-        with:
-          username: ${{ env.DOCKER_HUB_USER }}
-          password: ${{ env.DOCKER_HUB_PASSWORD }}
       - name: Install sshpass
         run: sudo apt-get install sshpass
       - name: Add SSH Host to known_hosts
@@ -97,11 +86,11 @@
         env:
           SSH_HOST: ${{ env.SSH_HOST }}
           SSH_PORT: ${{ env.SSH_PORT }}
-      - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
+      - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise
         run: |
           cd opencga-enterprise
           ln -s ../opencga opencga-home
-          ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1
+          ./build.sh -t -l runShortTests -b -s -T ${{ inputs.task }}
       - name: Upload reports results to Github
         uses: actions/upload-artifact@v4
         with:

commons-datastore/commons-datastore-core/pom.xml

@@ -13,6 +13,10 @@
     <artifactId>commons-datastore-core</artifactId>
     <packaging>jar</packaging>
 
+    <name>OpenCB commons-datastore-core project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
     <dependencies>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>

commons-datastore/commons-datastore-core/src/main/java/org/opencb/commons/datastore/core/ObjectMap.java

@@ -38,7 +38,6 @@ public class ObjectMap implements Map<String, Object>, Serializable {
 
     private static final Pattern KEY_SPLIT_PATTERN = Pattern.compile("(^[^\\[\\].]+(?:\\[[^\\]]+\\])?)(?:\\.(.*))*");
     private static final Pattern LIST_FILTER_PATTERN = Pattern.compile("([^\\[\\]]+)\\[([^=]*?)(?:[=]?)([^=]+)\\]$");
-    public static final Pattern COMMA_SEPARATED_LIST_SPLIT_PATTERN = Pattern.compile("((?:(?!,\\S).)+)+");
 
     public ObjectMap() {
         objectMap = new LinkedHashMap<>();

commons-datastore/commons-datastore-core/src/test/java/org/opencb/commons/datastore/core/ObjectMapTest.java

@@ -263,35 +263,4 @@ public void testGetWithFilterFromList() {
         assertEquals("CGHI", objectMap.get("nestedList[nested.value=G].nested.list[id=Cghi].name"));
     }
 
-    @Test
-    public void testPatternListSplit() {
-        List<String> originalValues = Arrays.asList("disorder1", "disorder2, blabla", "disorder3");
-        objectMap.put("key", StringUtils.join(originalValues, ","));
-        objectMap.put("key1", "");
-        objectMap.put("key2", "my value");
-        objectMap.put("key3", Arrays.asList("1", "2"));
-        objectMap.put("key4", Arrays.asList(1, 2));
-
-        List<String> values = objectMap.getAsStringList("key", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(originalValues.size(), values.size());
-        assertTrue(originalValues.containsAll(values));
-
-        values = objectMap.getAsStringList("key1", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(1, values.size());
-        assertEquals("", values.get(0));
-
-        values = objectMap.getAsStringList("key2", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(1, values.size());
-        assertEquals("my value", values.get(0));
-
-        values = objectMap.getAsStringList("key3", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(2, values.size());
-        assertEquals("1", values.get(0));
-        assertEquals("2", values.get(1));
-
-        values = objectMap.getAsStringList("key4", ObjectMap.COMMA_SEPARATED_LIST_SPLIT_PATTERN);
-        assertEquals(2, values.size());
-        assertEquals("1", values.get(0));
-        assertEquals("2", values.get(1));
-    }
 }

commons-datastore/commons-datastore-mongodb/pom.xml

@@ -13,6 +13,10 @@
     <artifactId>commons-datastore-mongodb</artifactId>
     <packaging>jar</packaging>
 
+    <name>OpenCB commons-datastore-mongodb project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
     <dependencies>
         <dependency>
             <groupId>org.opencb.commons</groupId>

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBQueryUtils.java

@@ -36,9 +36,9 @@
 
 import static com.mongodb.client.model.Aggregates.*;
 import static com.mongodb.client.model.Projections.*;
+import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.*;
 import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.bucket;
 import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.count;
-import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.*;
 
 /**
  * Created by imedina on 17/01/16.
@@ -178,6 +178,53 @@ public static Bson createFilter(String mongoDbField, String queryParam, Query qu
         return filter;
     }
 
+    /**
+     * Splits a string by the given separator, handling quoted values properly.
+     * Quoted values can contain the separator character without being split.
+     * Removes surrounding quotes and trims whitespace from each value.
+     *
+     * @param input the input string to split
+     * @param separator the separator to split by ("," or ";")
+     * @return list of trimmed, unquoted values
+     */
+    public static List<String> smartSplit(String input, String separator) {
+        List<String> result = new ArrayList<>();
+        if (input == null || input.isEmpty()) {
+            return result;
+        }
+
+        boolean inQuotes = false;
+        StringBuilder currentValue = new StringBuilder();
+
+        for (int i = 0; i < input.length(); i++) {
+            char c = input.charAt(i);
+
+            if (c == '"') {
+                inQuotes = !inQuotes;
+            } else if (!inQuotes && input.substring(i).startsWith(separator)) {
+                // Found separator outside quotes
+                String value = currentValue.toString().trim();
+                if (value.startsWith("\"") && value.endsWith("\"") && value.length() > 1) {
+                    value = value.substring(1, value.length() - 1);
+                }
+                result.add(value.trim());
+                currentValue = new StringBuilder();
+                i += separator.length() - 1; // Skip the separator
+            } else {
+                currentValue.append(c);
+            }
+        }
+
+        // Add the last value
+        String value = currentValue.toString().trim();
+        if (value.startsWith("\"") && value.endsWith("\"") && value.length() > 1) {
+            value = value.substring(1, value.length() - 1);
+        }
+        result.add(value.trim());
+
+        return result;
+    }
+
     private static String getLogicalSeparator(LogicalOperator operator) {
         return (operator != null && operator.equals(LogicalOperator.AND)) ? AND : OR;
     }
@@ -258,8 +305,13 @@ protected static String getOp2(String op, String value) {
 
     public static Bson createAutoFilter(String mongoDbField, String queryParam, Query query, QueryParam.Type type, LogicalOperator operator)
             throws NumberFormatException {
-
-        List<String> queryParamList = query.getAsStringList(queryParam, getLogicalSeparator(operator));
+        List<String> queryParamList;
+        String value = query.getString(queryParam);
+        if (StringUtils.isNotEmpty(value) && value.contains("\"")) {
+            queryParamList = smartSplit(value, getLogicalSeparator(operator));
+        } else {
+            queryParamList = query.getAsStringList(queryParam, getLogicalSeparator(operator));
+        }
         return createAutoFilter(mongoDbField, queryParam, type, operator, queryParamList);
     }
 

commons-datastore/commons-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/SmartSplitTest.java

@@ -0,0 +1,63 @@
+package org.opencb.commons.datastore.mongodb;
+
+import org.junit.Test;
+import java.util.List;
+import static org.junit.Assert.assertEquals;
+
+public class SmartSplitTest {
+
+    @Test
+    public void testSmartSplitWithQuotedCommaValues() {
+        String input = "\"a \",\" b\",\" c \"";
+        List<String> result = MongoDBQueryUtils.smartSplit(input, ",");
+
+        assertEquals(3, result.size());
+        assertEquals("a", result.get(0));
+        assertEquals("b", result.get(1));
+        assertEquals("c", result.get(2));
+    }
+
+    @Test
+    public void testSmartSplitWithQuotedSemicolonValues() {
+        String input = "\"a \";\" b\";\" c \"";
+        List<String> result = MongoDBQueryUtils.smartSplit(input, ";");
+
+        assertEquals(3, result.size());
+        assertEquals("a", result.get(0));
+        assertEquals("b", result.get(1));
+        assertEquals("c", result.get(2));
+    }
+
+    @Test
+    public void testSmartSplitWithNonQuotedValues() {
+        String input = "a,b,c";
+        List<String> result = MongoDBQueryUtils.smartSplit(input, ",");
+
+        assertEquals(3, result.size());
+        assertEquals("a", result.get(0));
+        assertEquals("b", result.get(1));
+        assertEquals("c", result.get(2));
+    }
+
+    @Test
+    public void testSmartSplitWithNonQuotedValuesAndSpaces() {
+        String input = "a, b,c ";
+        List<String> result = MongoDBQueryUtils.smartSplit(input, ",");
+
+        assertEquals(3, result.size());
+        assertEquals("a", result.get(0));
+        assertEquals("b", result.get(1));
+        assertEquals("c", result.get(2));
+    }
+
+    @Test
+    public void testSmartSplitWithMixedValues() {
+        String input = "\"a, with comma\",b,\"c\"";
+        List<String> result = MongoDBQueryUtils.smartSplit(input, ",");
+
+        assertEquals(3, result.size());
+        assertEquals("a, with comma", result.get(0));
+        assertEquals("b", result.get(1));
+        assertEquals("c", result.get(2));
+    }
+}

commons-datastore/commons-datastore-solr/pom.xml

@@ -29,6 +29,11 @@
     <artifactId>commons-datastore-solr</artifactId>
     <packaging>jar</packaging>
 
+    <name>OpenCB commons-datastore-solr project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
+
     <dependencies>
         <dependency>
             <groupId>org.opencb.commons</groupId>

commons-datastore/pom.xml

@@ -13,6 +13,11 @@
     <artifactId>commons-datastore</artifactId>
     <packaging>pom</packaging>
 
+    <name>OpenCB commons-datastore project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
+
     <modules>
         <module>commons-datastore-core</module>
         <module>commons-datastore-mongodb</module>

commons-lib/pom.xml

@@ -13,6 +13,10 @@
     <artifactId>commons-lib</artifactId>
     <packaging>jar</packaging>
 
+    <name>OpenCB commons-lib project</name>
+    <description>OpenCB commons project contains several Java libs for Bioinformatics</description>
+    <url>http://www.opencb.org</url>
+
     <dependencies>
         <dependency>
             <groupId>org.opencb.commons</groupId>