TASK-4913 - Unable to update cellbase-token

.github/workflows/develop.yml

@@ -15,7 +15,7 @@ jobs:
 
   test:
     uses: ./.github/workflows/test-analysis.yml
-    needs: deploy-docker-ext-tools
+    needs: build
     with:
       test_profile: runShortTests,runMediumTests
     secrets: inherit

.github/workflows/docker-ext-tools.yml

@@ -8,7 +8,6 @@ on:
       - TASK-*
     paths:
       - opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile
-  workflow_dispatch:
 
 jobs:
   build:
@@ -19,5 +18,4 @@ jobs:
     needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
-    secrets: inherit
-
+    secrets: inherit

.github/workflows/long-test-analysis.yml

@@ -5,13 +5,13 @@ name: Long test for run only on weekend
 on:
   schedule:
     - cron: '10 1 * * 6'
+  workflow_dispatch:
 
 jobs:
   test:
     uses: ./.github/workflows/test-analysis.yml
     secrets: inherit
     with:
-      test_profile: runLongTests,runMediumTests,runShortTests
-      report_context: development
+      test_profile: runShortTests,runMediumTests,runLongTests,
 
 

.github/workflows/manual-deploy-docker.yml

@@ -0,0 +1,50 @@
+name: Manual deploy Docker base
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: "The branch, tag or SHA of the source code to build docker."
+        type: string
+        required: true
+      tag:
+        description: "The tag for the new docker."
+        type: string
+        required: true
+
+jobs:
+  build:
+    name: Build Java app
+    runs-on: ubuntu-22.04
+    outputs:
+      version: ${{ steps.get_project_version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: '10'
+          ref: "${{ inputs.branch }}"
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
+      - name: Install dependencies branches
+        run: |
+          if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
+            chmod +x ./.github/workflows/scripts/get_same_branch.sh
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+          fi
+      - name: Maven Build (skip tests)
+        run: mvn -T 2 clean install -DskipTests
+      - uses: actions/upload-artifact@v3
+        with:
+          name: build-folder
+          path: build
+
+
+  deploy-docker:
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    needs: build
+    with:
+      cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ inputs.tag }}
+    secrets: inherit

.github/workflows/manual-deploy-ext-tools.yml

@@ -0,0 +1,50 @@
+name: Manual deploy Docker Ext-Tools
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: "The branch, tag or SHA of the source code to build docker."
+        type: string
+        required: true
+      tag:
+        description: "The tag for the new docker."
+        type: string
+        required: true
+
+jobs:
+  build:
+    name: Build Java app
+    runs-on: ubuntu-22.04
+    outputs:
+      version: ${{ steps.get_project_version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: '10'
+          ref: "${{ inputs.branch }}"
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
+      - name: Install dependencies branches
+        run: |
+          if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
+            chmod +x ./.github/workflows/scripts/get_same_branch.sh
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+          fi
+      - name: Maven Build (skip tests)
+        run: mvn -T 2 clean install -DskipTests
+      - uses: actions/upload-artifact@v3
+        with:
+          name: build-folder
+          path: build
+
+
+  deploy-docker-ext-tools:
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    needs: build
+    with:
+      cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ inputs.tag }}
+    secrets: inherit

.github/workflows/release.yml

@@ -42,3 +42,4 @@ jobs:
       file: |
         opencga-client-${{ needs.build.outputs.version }}.tar.gz
         clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz
+

opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java

@@ -1,20 +1,24 @@
 package org.opencb.opencga.core.cellbase;
 
+import io.jsonwebtoken.JwtException;
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.biodata.models.variant.avro.VariantAnnotation;
 import org.opencb.cellbase.client.rest.CellBaseClient;
 import org.opencb.cellbase.core.config.SpeciesConfiguration;
 import org.opencb.cellbase.core.config.SpeciesProperties;
 import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.cellbase.core.result.CellBaseDataResponse;
 import org.opencb.cellbase.core.token.DataAccessTokenManager;
 import org.opencb.cellbase.core.token.DataAccessTokenSources;
+import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.core.common.VersionUtils;
 import org.opencb.opencga.core.config.storage.CellBaseConfiguration;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -46,6 +50,7 @@ private CellBaseClient newCellBaseClient(CellBaseConfiguration cellBaseConfigura
                 toCellBaseSpeciesName(species),
                 assembly,
                 cellBaseConfiguration.getDataRelease(),
+                cellBaseConfiguration.getToken(),
                 cellBaseConfiguration.toClientConfiguration());
     }
 
@@ -136,7 +141,7 @@ public void validate() throws IOException {
         validate(false);
     }
 
-    public CellBaseConfiguration validate(boolean autoComplete) throws IOException {
+    private CellBaseConfiguration validate(boolean autoComplete) throws IOException {
         CellBaseConfiguration cellBaseConfiguration = getCellBaseConfiguration();
         String inputVersion = getVersion();
         CellBaseDataResponse<SpeciesProperties> species;
@@ -189,6 +194,38 @@ public CellBaseConfiguration validate(boolean autoComplete) throws IOException {
                 }
             }
         }
+        if (getToken() != null) {
+            // Check it's supported
+            if (!supportsToken(serverVersion)) {
+                throw new IllegalArgumentException("Token not supported for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion + "'");
+            }
+
+            // Check it's an actual token
+            DataAccessTokenManager tokenManager = new DataAccessTokenManager();
+            try {
+                tokenManager.decode(getToken());
+            } catch (JwtException e) {
+                throw new IllegalArgumentException("Malformed token for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion
+                        + "', species: '" + getSpecies()
+                        + "', assembly: '" + getAssembly() + "'");
+            }
+
+            // Check it's a valid token
+            CellBaseDataResponse<VariantAnnotation> response = cellBaseClient.getVariantClient()
+                    .getAnnotationByVariantIds(Collections.singletonList("1:1:N:C"), new QueryOptions(), true);
+            if (response.firstResult() == null) {
+                throw new IllegalArgumentException("Invalid token for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion
+                        + "', species: '" + getSpecies()
+                        + "', assembly: '" + getAssembly() + "'");
+            }
+        }
+
         return cellBaseConfiguration;
     }
 
@@ -231,6 +268,11 @@ public static boolean supportsDataReleaseActiveByDefaultIn(String serverVersion)
         return VersionUtils.isMinVersion("5.5.0", serverVersion, true);
     }
 
+    public static boolean supportsToken(String serverVersion) {
+        // Tokens support starts at version 5.4.0
+        return VersionUtils.isMinVersion("5.4.0", serverVersion);
+    }
+
     public String getVersionFromServerMajor() throws IOException {
         return major(getVersionFromServer());
     }

opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java

@@ -1,6 +1,8 @@
 package org.opencb.opencga.core.cellbase;
 
+import org.apache.commons.lang3.StringUtils;
 import org.junit.Assert;
+import org.junit.Assume;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
@@ -70,4 +72,37 @@ public void testNoActiveReleases() throws IOException {
         thrown.expectMessage("No active data releases found on cellbase");
         CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, null), "mmusculus", "GRCm38", true);
     }
+
+    @Test
+    public void testToken() throws IOException {
+        String token = System.getenv("CELLBASE_HGMD_TOKEN");
+        Assume.assumeTrue(StringUtils.isNotEmpty(token));
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testTokenNotSupported() throws IOException {
+        String token = System.getenv("CELLBASE_HGMD_TOKEN");
+        Assume.assumeTrue(StringUtils.isNotEmpty(token));
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testMalformedToken() throws IOException {
+        thrown.expectMessage("Malformed token for cellbase");
+        String token = "MALFORMED_TOKEN";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testUnsignedToken() throws IOException {
+        thrown.expectMessage("Invalid token for cellbase");
+        String token = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2OTMyMTY5MDd9.invalidsignature";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
 }

opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java

@@ -71,6 +71,7 @@ public enum VariantField {
     ANNOTATION_CONSERVATION(ANNOTATION, "annotation.conservation"),
     ANNOTATION_CANCER_HOTSPOTS(ANNOTATION, "annotation.cancerHotspots"),
     ANNOTATION_GENE_EXPRESSION(ANNOTATION, "annotation.geneExpression"),
+    ANNOTATION_PHARMACOGENOMICS(ANNOTATION, "annotation.pharmacogenomics"),
     ANNOTATION_GENE_TRAIT_ASSOCIATION(ANNOTATION, "annotation.geneTraitAssociation"),
     ANNOTATION_GENE_DRUG_INTERACTION(ANNOTATION, "annotation.geneDrugInteraction"),
     ANNOTATION_GENE_CANCER_ASSOCIATIONS(ANNOTATION, "annotation.geneCancerAssociations"),

opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java

@@ -59,7 +59,7 @@ public List<VariantAnnotation> annotate(List<Variant> variants) throws VariantAn
     public ProjectMetadata.VariantAnnotationMetadata getVariantAnnotationMetadata() throws VariantAnnotatorException {
         return new ProjectMetadata.VariantAnnotationMetadata(-1, null, null,
                 new ProjectMetadata.VariantAnnotatorProgram("MyAnnotator", key, null),
-                Collections.singletonList(new ObjectMap("data", "genes")), null);
+                Collections.singletonList(new ObjectMap("data", "genes")), null,null);
     }
 
 }