Merge pull request #659 from opencb/TASK-4225

TASK-4225
opencb · Jul 13, 2023 · 4c9946c · 4c9946c
2 parents 4374d16 + a33d59a
commit 4c9946c
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diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -11,22 +11,22 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -DCELLBASE.WAR.NAME=cellbase
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase -P default-config-test
 
   test:
     uses: ./.github/workflows/test-analysis.yml
     needs: build
     secrets: inherit
 
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,27 +13,27 @@ jobs:
       maven_opts: -DCELLBASE.WAR.NAME=cellbase
 
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base
     secrets: inherit
 
   deploy-python:
-    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
     needs: test
     with:
       cli: bash ./clients/python/python-build.sh push
       artifact: build-folder
     secrets: inherit
 
   release:
-    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
     needs: [deploy-maven, deploy-docker, deploy-python]
diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml
@@ -10,15 +10,15 @@ jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
-      maven_opts: -DCELLBASE.WAR.NAME=cellbase
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase -P default-config-test
 
   test:
     uses: ./.github/workflows/test-analysis.yml
     needs: build
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.6.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base --tag ${{ github.ref_name }}

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
@@ -36,6 +36,7 @@ public class AdminCliOptionsParser extends CliOptionsParser {
     private DataReleaseCommandOptions dataReleaseCommandOptions;
     private DataTokenCommandOptions dataTokenCommandOptions;
     private LoadCommandOptions loadCommandOptions;
+    private ExportCommandOptions exportCommandOptions;
     private CustomiseCommandOptions customiseCommandOptions;
     private IndexCommandOptions indexCommandOptions;
     private InstallCommandOptions installCommandOptions;
@@ -52,6 +53,7 @@ public AdminCliOptionsParser() {
         dataReleaseCommandOptions = new DataReleaseCommandOptions();
         dataTokenCommandOptions = new DataTokenCommandOptions();
         loadCommandOptions = new LoadCommandOptions();
+        exportCommandOptions = new ExportCommandOptions();
         customiseCommandOptions = new CustomiseCommandOptions();
         indexCommandOptions = new IndexCommandOptions();
         installCommandOptions = new InstallCommandOptions();
@@ -63,6 +65,7 @@ public AdminCliOptionsParser() {
         jCommander.addCommand("data-release", dataReleaseCommandOptions);
         jCommander.addCommand("data-token", dataTokenCommandOptions);
         jCommander.addCommand("load", loadCommandOptions);
+        jCommander.addCommand("export", exportCommandOptions);
         jCommander.addCommand("customise", customiseCommandOptions);
         jCommander.addCommand("index", indexCommandOptions);
         jCommander.addCommand("install", installCommandOptions);
@@ -212,6 +215,40 @@ public class LoadCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"export"}, commandDescription = "Export data into JSON files")
+    public class ExportCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"-d", "--data"}, description = "Data model type to be loaded: genome, gene, variation, "
+                + "conservation, regulation, protein, clinical_variants, repeats, regulatory_pfm, splice_score, pubmed. 'all' "
+                + " loads everything", required = true, arity = 1)
+        public String data;
+
+        @Parameter(names = {"--db", "--database"}, description = "Database name, e.g., cellbase_hsapiens_grch38_v5", required = true,
+                arity = 1)
+        public String database;
+
+        @Parameter(names = {"--data-release"}, description = "Data release for exporting data.", required = true, arity = 1)
+        public int dataRelease;
+
+        @Parameter(names = {"--token"}, description = "Data token to export licensed data.", arity = 1)
+        public String token;
+
+        @Parameter(names = {"--gene"}, description = "List of genes (separated by commas). Exported data will be related to these genes"
+                + " (gene coordinates will be taken into account).", required = true, arity = 1)
+        public String gene;
+
+        @Parameter(names = {"--region"}, description = "List of regions (separated by commas). Exported data will be related to these"
+                + " regions taking into account their coordinates.", arity = 1)
+        public String region;
+
+        @Parameter(names = {"-o", "--output"}, required = true, arity = 1,
+                description = "Output directory where to save the JSON data models.")
+        public String output;
+    }
+
     @Parameters(commandNames = {"load"}, commandDescription = "Load the built data models into the database")
     public class CustomiseCommandOptions {
 
@@ -360,9 +397,9 @@ public DataTokenCommandOptions getDataTokenCommandOptions() {
         return dataTokenCommandOptions;
     }
 
-    public LoadCommandOptions getLoadCommandOptions() {
-        return loadCommandOptions;
-    }
+    public LoadCommandOptions getLoadCommandOptions() { return loadCommandOptions; }
+
+    public ExportCommandOptions getExportCommandOptions() { return exportCommandOptions; }
 
     public IndexCommandOptions getIndexCommandOptions() {
         return indexCommandOptions;

diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminMain.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminMain.java
@@ -72,6 +72,9 @@ public static void main(String[] args) {
                     case "load":
                         commandExecutor = new LoadCommandExecutor(cliOptionsParser.getLoadCommandOptions());
                         break;
+                    case "export":
+                        commandExecutor = new ExportCommandExecutor(cliOptionsParser.getExportCommandOptions());
+                        break;
                     case "index":
                         commandExecutor = new IndexCommandExecutor(cliOptionsParser.getIndexCommandOptions());
                         break;