Merge branch 'develop' into TASK-2095

opencb · Nov 15, 2023 · ebaff42 · ebaff42
2 parents 768606f + baa3631
commit ebaff42
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Showing 6 changed files with 35 additions and 23 deletions.
diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml
@@ -11,7 +11,7 @@ jobs:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -DCELLBASE.WAR.NAME=cellbase -P default-config-test
-
+      
   test:
     uses: ./.github/workflows/test-analysis.yml
     needs: build

diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -20,11 +20,12 @@ jobs:
           distribution: 'temurin'
           java-version: '11'
           cache: 'maven'
-      - name: Start MongoDB v6.0
-        uses: supercharge/[email protected]
-        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 27017:27017 --kubeconfig ./admin.conf &
       - name: Install dependencies branches
         run: |
           if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then

diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java
@@ -159,10 +159,13 @@ public class ApiKeyCommandOptions {
         @ParametersDelegate
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
-        @Parameter(names = {"--create-api-key"}, description = "Create an API key with the licensed data sources indicated separated by"
-                + " commas and optionally the expiration date: source[:dd/mm/yyyy]. e.g.: cosmic:31/01/2025,hgmd. In addition the"
-                + " 'organization' has to be specified", arity = 1)
-        public String createWithDataSources;
+        @Parameter(names = {"--create-api-key"}, description = "Create an API key", arity = 0)
+        public boolean createApiKey;
+
+        @Parameter(names = {"--licensed-data-sources"}, description = "Use this parameter in conjunction with --create-api-key to specify the"
+                + " licensed data sources separated by commas and optionally the expiration date: source[:dd/mm/yyyy]. e.g.:"
+                + " cosmic:31/01/2025,hgmd", arity = 1)
+        public String dataSources;
 
         @Parameter(names = {"--expiration"}, description = "Use this parameter in conjunction with --create-api-key to specify the"
                 + " expiration date in format dd/mm/yyyy, e.g.: 03/09/2030", arity = 1)

diff --git a/...-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/ApiKeyCommandExecutor.java b/...-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/ApiKeyCommandExecutor.java
@@ -48,7 +48,6 @@ public ApiKeyCommandExecutor(AdminCliOptionsParser.ApiKeyCommandOptions apiKeyCo
         this.apiKeyCommandOptions = apiKeyCommandOptions;
     }
 
-
     /**
      * Execute one of the selected actions according to the input parameters.
      */
@@ -60,7 +59,7 @@ public void execute() {
         ApiKeyManager apiKeyManager = new ApiKeyManager(SignatureAlgorithm.HS256.getValue(), key);
 
         try {
-            if (StringUtils.isNotEmpty(apiKeyCommandOptions.createWithDataSources)) {
+            if (apiKeyCommandOptions.createApiKey) {
                 // Create the API key JWT payload
                 ApiKeyJwtPayload payload = new ApiKeyJwtPayload();
                 payload.setSubject(apiKeyCommandOptions.organization);
@@ -69,7 +68,7 @@ public void execute() {
                 if (apiKeyCommandOptions.expiration != null) {
                     payload.setExpiration(parseDate(apiKeyCommandOptions.expiration));
                 }
-                payload.setSources(parseSources(apiKeyCommandOptions.createWithDataSources));
+                payload.setSources(parseSources(apiKeyCommandOptions.dataSources));
                 payload.setQuota(new ApiKeyQuota(apiKeyCommandOptions.maxNumQueries));
 
                 // Create API key
@@ -86,20 +85,23 @@ public void execute() {
     }
 
     private void checkParameters() {
-        if (StringUtils.isNotEmpty(apiKeyCommandOptions.createWithDataSources)
-                && StringUtils.isNotEmpty(apiKeyCommandOptions.apiKeyToView)) {
-            throw new IllegalArgumentException("Please, select only one of these input parameters: create or view");
+        if (apiKeyCommandOptions.createApiKey && StringUtils.isNotEmpty(apiKeyCommandOptions.apiKeyToView)) {
+            throw new IllegalArgumentException("Please, select only one of these input parameters: create-api-key or view-api-key");
         }
-        if (StringUtils.isEmpty(apiKeyCommandOptions.createWithDataSources)
-                && StringUtils.isEmpty(apiKeyCommandOptions.apiKeyToView)) {
-            throw new IllegalArgumentException("Please, it is mandatory to select one of these input parameters: create or view");
+        if (!apiKeyCommandOptions.createApiKey && StringUtils.isEmpty(apiKeyCommandOptions.apiKeyToView)) {
+            throw new IllegalArgumentException("Please, it is mandatory to select one of these input parameters: create-api-key or"
+                    + " view-api-key");
         }
 
         // Check create parameters
-        if (StringUtils.isNotEmpty(apiKeyCommandOptions.createWithDataSources)) {
+        if (apiKeyCommandOptions.createApiKey) {
             if (StringUtils.isEmpty(apiKeyCommandOptions.organization)) {
                 throw new IllegalArgumentException("Missing organization");
             }
+            if (StringUtils.isEmpty(apiKeyCommandOptions.dataSources) && apiKeyCommandOptions.maxNumQueries <= 0) {
+                throw new IllegalArgumentException("Please, it is mandatory to specify either the licensed data sources, the maximum number"
+                        + " of queries, or both");
+            }
         }
 
         if (StringUtils.isEmpty(configuration.getSecretKey())) {

diff --git a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/VariantClientTest.java b/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/VariantClientTest.java
@@ -17,6 +17,7 @@
 package org.opencb.cellbase.client.rest;
 
 import org.apache.avro.specific.SpecificRecordBase;
+import org.apache.commons.collections4.CollectionUtils;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.TestInstance;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -105,6 +106,10 @@ private void orderVariantAnnotation(VariantAnnotation va) {
                 c.getProteinVariantAnnotation().getFeatures().sort(Comparator.comparing(SpecificRecordBase::hashCode));
             }
         });
+
+        if (CollectionUtils.isNotEmpty(va.getFunctionalScore())) {
+            va.getFunctionalScore().sort(Comparator.comparing(SpecificRecordBase::hashCode));
+        }
     }
 
 //    @Test

diff --git a/cellbase-lib/src/test/resources/configuration.test.yaml b/cellbase-lib/src/test/resources/configuration.test.yaml
@@ -8,10 +8,11 @@ secretKey: "xPacig89igHSieEnveJEi4KCfdEslhmssC3vui1JJQGgDQ0y8v"
 databases:
   mongodb:
     host: localhost:27017
-    user: ''
-    password: ''
+    user: 'cellbase'
+    password: 'cellbase'
     options:
-      authenticationDatabase: ''
+      authenticationDatabase: 'admin'
+      authenticationMechanism: 'SCRAM-SHA-256'
       readPreference: ''
       replicaSet: ''
       connectionsPerHost: 20