Merge pull request #2464 from opencb/TASK-6281

TASK-6281 - Port Patch 2.0.0.1 -> 2.2.0

opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java

@@ -6,7 +6,7 @@
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.opencga.app.cli.admin.options.MigrationCommandOptions;
 import org.opencb.opencga.app.cli.main.io.Table;
-import org.opencb.opencga.app.migrations.v3_0_0.OrganizationMigration;
+import org.opencb.opencga.app.migrations.v3.v3_0_0.OrganizationMigration;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.managers.CatalogManager;
 import org.opencb.opencga.catalog.migration.Migration;

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java

@@ -0,0 +1,14 @@
+package org.opencb.opencga.app.migrations.v2.v2_0_3.catalog.java;
+
+import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "recalculate_roles", description = "Recalculate roles from Family #1763", version = "2.0.3", date = 20210528,
+    deprecatedSince = "3.0.0")
+public class Migration1 extends MigrationTool {
+
+    @Override
+    protected void run() throws CatalogException {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java

@@ -0,0 +1,15 @@
+package org.opencb.opencga.app.migrations.v2.v2_0_5.catalog.java;
+
+
+import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "initialise_groups", description = "Initialise userIds list from groups #1791", version = "2.0.5", date = 20210621,
+        deprecatedSince = "3.0.0")
+public class initialiseGroups extends MigrationTool {
+
+    @Override
+    protected void run() throws CatalogException {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java

@@ -0,0 +1,16 @@
+package org.opencb.opencga.app.migrations.v2.v2_0_6.catalog;
+
+
+import org.opencb.opencga.catalog.exceptions.CatalogException;
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "remove_file_references_from_sample", description = "Remove deleted file references from samples #1815", version = "2.0.6",
+        date = 20210901, deprecatedSince = "3.0.0")
+public class removeDeletedFileReferencesFromSample extends MigrationTool {
+
+    @Override
+    protected void run() throws CatalogException {
+    }
+
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java

@@ -0,0 +1,20 @@
+package org.opencb.opencga.app.migrations.v2.v2_12_0.catalog;
+
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "add_annotation_sets_to_clinical_analysis" ,
+        description = "Add private annotation fields to ClinicalAnalysis documents #TASK-5198",
+        version = "2.12.0",
+        domain = Migration.MigrationDomain.CATALOG,
+        language = Migration.MigrationLanguage.JAVA,
+        date = 20231116,
+        deprecatedSince = "3.0.0"
+)
+public class AddAnnotationSetsInClinicalAnalysisMigration extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java

@@ -0,0 +1,19 @@
+package org.opencb.opencga.app.migrations.v2.v2_12_0.catalog;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "complete_clinical_report_data_model" ,
+        description = "Complete Clinical Report data model #TASK-5198",
+        version = "2.12.0",
+        domain = Migration.MigrationDomain.CATALOG,
+        language = Migration.MigrationLanguage.JAVA,
+        date = 20231128,
+        deprecatedSince = "3.0.0"
+)
+public class CompleteClinicalReportDataModelMigration extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "add_missing_indexes",
+        description = "Add missing indexes", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        patch = 1,
+        date = 20210928,
+        deprecatedSince = "3.0.0")
+public class AddMissingIndexes extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java

@@ -0,0 +1,17 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "add_panels_to_interpretations",
+        description = "Add panels to Interpretations #1802", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        date = 20210713,
+        deprecatedSince = "3.0.0")
+public class AddPanelsToInterpretations extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java

@@ -0,0 +1,19 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "create_audit_indexes", description = "Create Audit indexes", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        patch = 1,
+        date = 20210622,
+        deprecatedSince = "3.0.0")
+public class CreateAuditIndexes extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+
+}
+

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "add_panel_lock",
+        description = "Add new panelLock to ClinicalAnalysis #1802", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        patch = 1,
+        date = 20210713,
+        deprecatedSince = "3.0.0")
+public class PanelLock extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "remove_rc_version_from_migration_runs",
+        description = "Remove RC versions from migration runs stored in catalog", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        patch = 1,
+        date = 20210723,
+        deprecatedSince = "3.0.0")
+public class RemoveRCVersionsFromMigrationRuns extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "rename_datastore_configuration_to_options", description = "Rename project.internal.datastores.variant.configuration to options", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        patch = 1,
+        date = 20210617,
+        deprecatedSince = "3.0.0")
+public class RenameDatastoreConfigurationToOptions extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java

@@ -0,0 +1,19 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "move_study_clinical_config_to_internal",
+        description = "Move Study ClinicalConfiguration to internal.configuration", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        patch = 1,
+        date = 20210708,
+        deprecatedSince = "3.0.0")
+public class StudyClinicalConfigurationRelocation extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "move_variant_file_stats_to_qc", description = "Move opencga_file_variant_stats annotation set from variable sets to " +
+        "FileQualityControl", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.STORAGE,
+        patch = 1,
+        date = 20210614,
+        deprecatedSince = "3.0.0")
+public class VariantFileStatsRelocation extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java

@@ -0,0 +1,14 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationException;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "build_rga_indexes", description = "Create index for sample RGA status #1693", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0")
+public class Migration1 extends MigrationTool {
+
+    @Override
+    protected void run() throws MigrationException {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java

@@ -0,0 +1,14 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationException;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "init_userId_group_arrays", description = "Initialise all userIds arrays from groups #1735", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0")
+public class Migration2 extends MigrationTool {
+
+    @Override
+    protected void run() throws MigrationException {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java

@@ -0,0 +1,14 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationException;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "init_ca_panel_arrays", description = "Initialise panels array in Clinical Analysis #1759", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0")
+public class Migration3 extends MigrationTool {
+
+    @Override
+    protected void run() throws MigrationException {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java

@@ -0,0 +1,14 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationException;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "update_qc_file_sample_fields", description = "Update QC fields from Sample and File #1730", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "3.0.0")
+public class Migration4 extends MigrationTool {
+
+    @Override
+    protected void run() throws MigrationException {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.storage;
+
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "add_cellbase_configuration_to_project", description = "Add cellbase configuration from storage-configuration.yml to project.internal.cellbase", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.STORAGE,
+        patch = 3,
+        date = 20210616,
+        deprecatedSince = "3.0.0")
+public class AddCellbaseConfigurationToProject extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.storage;
+
+
+import org.opencb.opencga.app.migrations.StorageMigrationTool;
+import org.opencb.opencga.catalog.migration.Migration;
+
+@Migration(id = "default_sample_index_configuration", description = "Add a default backward compatible sample index configuration", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.STORAGE,
+        patch = 7,
+        date = 20210721,
+        deprecatedSince = "3.0.0") // Needs to run after StudyClinicalConfigurationRelocation
+public class DefaultSampleIndexConfiguration extends StorageMigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java

@@ -0,0 +1,18 @@
+package org.opencb.opencga.app.migrations.v2.v2_1_0.storage;
+
+import org.opencb.opencga.app.migrations.StorageMigrationTool;
+import org.opencb.opencga.catalog.migration.Migration;
+
+
+@Migration(id = "new_clinical_significance_fields", description = "Add new clinical significance fields and combinations for variant storage and solr", version = "2.1.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.STORAGE,
+        patch = 1,
+        date = 20210708,
+        deprecatedSince = "3.0.0")
+public class NewClinicalSignificanceFields extends StorageMigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+}

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java

@@ -0,0 +1,17 @@
+package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog;
+
+import org.opencb.opencga.catalog.migration.Migration;
+import org.opencb.opencga.catalog.migration.MigrationTool;
+
+@Migration(id = "add_missing_create_interpretation_in_clinical_audit",
+        description = "Add missing CREATE_INTERPRETATION audits in ClinicalAnalysis", version = "2.2.0",
+        language = Migration.MigrationLanguage.JAVA,
+        domain = Migration.MigrationDomain.CATALOG,
+        date = 20211227, deprecatedSince = "3.0.0")
+public class AddMissingClinicalAudit extends MigrationTool {
+
+    @Override
+    protected void run() throws Exception {
+    }
+
+}