Merge branch 'release-3.2.x' into TASK-6708

opencb · Sep 3, 2024 · 55167e9 · 55167e9
2 parents ded97e0 + 867865d
commit 55167e9
Show file tree

Hide file tree

Showing 16 changed files with 166 additions and 75 deletions.
diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
@@ -0,0 +1,34 @@
+name: Pull request approve workflow
+run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}'
+
+on:
+  pull_request_review:
+    types: [ submitted ]
+
+jobs:
+  calculate-xetabase-branch:
+    name: Calculate Xetabase branch
+    runs-on: ubuntu-22.04
+    outputs:
+      xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
+    steps:
+      - name: Clone java-common-libs
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '10'
+      - id: get_xetabase_branch
+        name: "Get current branch for Xetabase from target branch"
+        run: |
+          chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }})
+          echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
+          echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
+
+  test:
+    name: "Run all tests before merging"
+    needs: calculate-xetabase-branch
+    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
+    with:
+      branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
+      task: ${{ github.event.pull_request.head.ref }}
+    secrets: inherit
diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# Function to calculate the corresponding branch of Xetabase project
+get_xetabase_branch() {
+  # Input parameter (branch name)
+  input_branch="$1"
+
+  # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it
+  if [[ $input_branch == TASK* ]]; then
+    if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then
+      echo "$GIT_BRANCH";
+      exit 0;
+    fi
+  fi
+
+  # Check if the branch name is "develop" in that case return the same branch name
+  if [[ "$input_branch" == "develop" ]]; then
+    echo "develop"
+    return 0
+  fi
+
+  # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x"
+  if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then
+    # Extract the MAJOR part of the branch name
+    MAJOR=${BASH_REMATCH[1]}
+    # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR
+    XETABASE_MAJOR=$((MAJOR - 1))
+    # Check if the XETABASE_MAJOR is negative
+    if (( XETABASE_MAJOR < 0 )); then
+      echo "Error: 'MAJOR' digit after subtraction results in a negative number."
+      return 1
+    fi
+    # Construct and echo the new branch name
+    echo "release-$XETABASE_MAJOR.${input_branch#release-$MAJOR.}"
+    return 0
+  fi
+
+  # If the branch name does not match any of the expected patterns
+  echo "Error: The branch name is not correct."
+  return 1
+}
+
+# Check if the script receives exactly one argument
+if [ "$#" -ne 1 ]; then
+  echo "Usage: $0 <branch-name>"
+  exit 1
+fi
+
+# Call the function with the input branch name
+get_xetabase_branch "$1"
diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml
@@ -88,11 +88,11 @@
             <groupId>org.apache.avro</groupId>
             <artifactId>avro</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
             <scope>test</scope>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java b/...s/src/test/java/org/opencb/biodata/formats/variant/annotation/io/VepFormatWriterTest.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.formats.variant.annotation.io;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAvro;

diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml
@@ -74,10 +74,10 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java b/biodata-models/src/main/java/org/opencb/biodata/models/alignment/RegionCoverage.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.models.alignment;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import org.opencb.biodata.models.core.Region;
 
 import java.io.IOException;

diff --git a/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java b/...dels/src/main/java/org/opencb/biodata/models/clinical/interpretation/ClinicalVariant.java
@@ -115,19 +115,7 @@ public ClinicalVariant(VariantAvro avro, List<ClinicalVariantEvidence> evidences
 
     @Override
     public String toString() {
-        final StringBuilder sb = new StringBuilder("ClinicalVariant{");
-        sb.append("evidences=").append(evidences);
-        sb.append(", comments=").append(comments);
-        sb.append(", filters=").append(filters);
-        sb.append(", recommendation='").append(recommendation).append('\'');
-        sb.append(", references=").append(references);
-        sb.append(", discussion=").append(discussion);
-        sb.append(", confidence=").append(confidence);
-        sb.append(", tags=").append(tags);
-        sb.append(", status=").append(status);
-        sb.append(", attributes=").append(attributes);
-        sb.append('}');
-        return sb.toString();
+        return super.toString();
     }
 
     public List<ClinicalVariantEvidence> getEvidences() {

diff --git a/...odels/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java b/...odels/src/main/java/org/opencb/biodata/models/clinical/interpretation/Interpretation.java
@@ -28,29 +28,29 @@
 
 public class Interpretation {
 
-    private String id;
-    private String uuid;
-    private String description;
-    private String clinicalAnalysisId;
+    protected String id;
+    protected String uuid;
+    protected String name;
+    protected String description;
+    protected String clinicalAnalysisId;
 
     /**
      * Interpretation algorithm tool used to generate this interpretation.
      */
-    private ClinicalAnalyst analyst;
-    private InterpretationMethod method;
+    protected ClinicalAnalyst analyst;
+    protected InterpretationMethod method;
 
-    private List<ClinicalVariant> primaryFindings;
-    private List<ClinicalVariant> secondaryFindings;
+    protected List<ClinicalVariant> primaryFindings;
+    protected List<ClinicalVariant> secondaryFindings;
 
-    private List<ClinicalComment> comments;
+    protected List<ClinicalComment> comments;
 
-    private InterpretationStats stats;
+    protected InterpretationStats stats;
 
-    private boolean locked;
-    private Status status;
-    private String creationDate;
-    private String modificationDate;
-    private int version;
+    protected boolean locked;
+    protected String creationDate;
+    protected String modificationDate;
+    protected int version;
 
     /**
      * Users can add custom information in this field.
@@ -61,12 +61,23 @@ public class Interpretation {
     public Interpretation() {
     }
 
+    @Deprecated
     public Interpretation(String id, String uuid, String description, String clinicalAnalysisId, ClinicalAnalyst analyst,
                           InterpretationMethod method, List<ClinicalVariant> primaryFindings, List<ClinicalVariant> secondaryFindings,
                           List<ClinicalComment> comments, InterpretationStats stats, Status status, String creationDate,
                           String modificationDate, boolean locked, int version, Map<String, Object> attributes) {
+        this(id, uuid, id, description, clinicalAnalysisId, analyst, method, primaryFindings, secondaryFindings,
+                comments, stats, locked, creationDate, modificationDate, version, attributes);
+    }
+
+    public Interpretation(String id, String uuid, String name, String description, String clinicalAnalysisId,
+                          ClinicalAnalyst analyst, InterpretationMethod method, List<ClinicalVariant> primaryFindings,
+                          List<ClinicalVariant> secondaryFindings, List<ClinicalComment> comments,
+                          InterpretationStats stats, boolean locked, String creationDate, String modificationDate,
+                          int version, Map<String, Object> attributes) {
         this.id = id;
         this.uuid = uuid;
+        this.name = name;
         this.description = description;
         this.clinicalAnalysisId = clinicalAnalysisId;
         this.analyst = analyst;
@@ -75,10 +86,9 @@ public Interpretation(String id, String uuid, String description, String clinica
         this.secondaryFindings = secondaryFindings;
         this.comments = comments;
         this.stats = stats;
-        this.status = status;
+        this.locked = locked;
         this.creationDate = creationDate;
         this.modificationDate = modificationDate;
-        this.locked = locked;
         this.version = version;
         this.attributes = attributes;
     }
@@ -88,6 +98,7 @@ public String toString() {
         final StringBuilder sb = new StringBuilder("Interpretation{");
         sb.append("id='").append(id).append('\'');
         sb.append(", uuid='").append(uuid).append('\'');
+        sb.append(", name='").append(name).append('\'');
         sb.append(", description='").append(description).append('\'');
         sb.append(", clinicalAnalysisId='").append(clinicalAnalysisId).append('\'');
         sb.append(", analyst=").append(analyst);
@@ -96,7 +107,6 @@ public String toString() {
         sb.append(", secondaryFindings=").append(secondaryFindings);
         sb.append(", comments=").append(comments);
         sb.append(", stats=").append(stats);
-        sb.append(", status=").append(status);
         sb.append(", creationDate='").append(creationDate).append('\'');
         sb.append(", modificationDate='").append(modificationDate).append('\'');
         sb.append(", locked='").append(locked).append('\'');
@@ -124,6 +134,15 @@ public Interpretation setUuid(String uuid) {
         return this;
     }
 
+    public String getName() {
+        return name;
+    }
+
+    public Interpretation setName(String name) {
+        this.name = name;
+        return this;
+    }
+
     public String getDescription() {
         return description;
     }
@@ -196,15 +215,6 @@ public Interpretation setStats(InterpretationStats stats) {
         return this;
     }
 
-    public Status getStatus() {
-        return status;
-    }
-
-    public Interpretation setStatus(Status status) {
-        this.status = status;
-        return this;
-    }
-
     public String getCreationDate() {
         return creationDate;
     }

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java b/biodata-models/src/main/java/org/opencb/biodata/models/clinical/pedigree/Pedigree.java
@@ -19,7 +19,7 @@
 
 package org.opencb.biodata.models.clinical.pedigree;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.opencb.biodata.models.clinical.Disorder;
 import org.opencb.biodata.models.clinical.Phenotype;
 

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java b/biodata-models/src/main/java/org/opencb/biodata/models/common/Status.java
@@ -19,17 +19,22 @@
 public class Status {
 
     protected String id;
-    protected String name;
     protected String description;
     protected String date;
 
     public Status() {
-        this("", "", "", "");
+        this("", "", "");
     }
 
+    public Status(String id, String description, String date) {
+        this.id = id;
+        this.description = description;
+        this.date = date;
+    }
+
+    @Deprecated
     public Status(String id, String name, String description, String date) {
         this.id = id;
-        this.name = name;
         this.description = description;
         this.date = date;
     }
@@ -38,7 +43,6 @@ public Status(String id, String name, String description, String date) {
     public String toString() {
         final StringBuilder sb = new StringBuilder("Status{");
         sb.append("id='").append(id).append('\'');
-        sb.append(", name='").append(name).append('\'');
         sb.append(", description='").append(description).append('\'');
         sb.append(", date='").append(date).append('\'');
         sb.append('}');
@@ -53,15 +57,13 @@ public boolean equals(Object o) {
         Status status = (Status) o;
 
         if (!id.equals(status.id)) return false;
-        if (name != null ? !name.equals(status.name) : status.name != null) return false;
         if (description != null ? !description.equals(status.description) : status.description != null) return false;
         return date != null ? date.equals(status.date) : status.date == null;
     }
 
     @Override
     public int hashCode() {
         int result = id.hashCode();
-        result = 31 * result + (name != null ? name.hashCode() : 0);
         result = 31 * result + (description != null ? description.hashCode() : 0);
         result = 31 * result + (date != null ? date.hashCode() : 0);
         return result;
@@ -76,12 +78,13 @@ public Status setId(String id) {
         return this;
     }
 
+    @Deprecated
     public String getName() {
-        return name;
+        return id;
     }
 
+    @Deprecated
     public Status setName(String name) {
-        this.name = name;
         return this;
     }
 

diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -96,10 +96,10 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
         </dependency>
-        <dependency>
+<!--        <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
+        </dependency>-->
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>

diff --git a/...ta-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java b/...ta-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceKmers.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/stats/SequenceKmers.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.alignment.stats;
 
-import org.codehaus.jackson.map.ObjectMapper;
-import org.codehaus.jackson.map.ObjectWriter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 
 import java.io.IOException;
 import java.util.HashMap;