app: create migration scripts, #TASK-6445

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v4/v4_0_0/catalog/IndexesTask6445.java

@@ -0,0 +1,16 @@
+package org.opencb.opencga.app.migrations.v4.v4_0_0.catalog;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "new_indexes_6445",
+        description = "New indexes from #TASK-6445", version = "4.0.0",
+        language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20241113)
+public class IndexesTask6445 extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+        catalogManager.installIndexes(organizationId, token);
+    }
+
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v4/v4_0_0/catalog/JobModelChangesMigrationTask6445.java

@@ -0,0 +1,34 @@
+package org.opencb.opencga.app.migrations.v4.v4_0_0.catalog;
+
+
+import com.mongodb.client.model.Filters;
+import com.mongodb.client.model.Updates;
+import org.bson.Document;
+import org.bson.conversions.Bson;
+import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+import java.util.Arrays;
+import java.util.Collections;
+
+@Migration(id = "job_model_changes_6445",
+        description = "Job data model changes #TASK-6445", version = "4.0.0",
+        language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20241113)
+public class JobModelChangesMigrationTask6445 extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+        Bson query = Filters.exists("type", false);
+        Bson update = Updates.combine(
+                Updates.set("type", "NATIVE"),
+                Updates.set("tool.minimumRequirements", new Document()),
+                Updates.set("execution.dependencies", Collections.emptyList())
+        );
+        for (String collection : Arrays.asList(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION,
+                OrganizationMongoDBAdaptorFactory.DELETED_JOB_COLLECTION)) {
+            getMongoCollection(collection).updateMany(query, update);
+        }
+    }
+
+}

opencga-catalog/src/main/resources/catalog-indexes.txt

@@ -20,7 +20,6 @@
 {"collections": ["job"], "fields": {"id": 1, "studyUid": 1}, "options": {"unique": true}}
 {"collections": ["job"], "fields": {"tool.id": 1, "studyUid": 1}, "options": {}}
 {"collections": ["job"], "fields": {"tool.type": 1, "studyUid": 1}, "options": {}}
-{"collections": ["job"], "fields": {"tool.externalExecutor.id": 1, "studyUid": 1}, "options": {}}
 {"collections": ["job"], "fields": {"userId": 1, "studyUid": 1}, "options": {}}
 {"collections": ["job"], "fields": {"parentId": 1, "studyUid": 1}, "options": {}}
 {"collections": ["job"], "fields": {"outDir.uid": 1, "studyUid": 1}, "options": {}}