Merge branch 'develop' into TASK-6322

opencga-app/app/misc/clients/copyright.txt

@@ -0,0 +1,13 @@
+Copyright 2015-2024 OpenCB
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

opencga-app/app/misc/clients/java_client_generator.py

@@ -36,19 +36,7 @@ def get_imports(self):
 
         headers = []
         headers.append('/*')
-        headers.append('* Copyright 2015-' + str(date.today().year) + ' OpenCB')
-        headers.append('*')
-        headers.append('* Licensed under the Apache License, Version 2.0 (the "License");')
-        headers.append('* you may not use this file except in compliance with the License.')
-        headers.append('* You may obtain a copy of the License at')
-        headers.append('*')
-        headers.append('*     http://www.apache.org/licenses/LICENSE-2.0')
-        headers.append('*')
-        headers.append('* Unless required by applicable law or agreed to in writing, software')
-        headers.append('* distributed under the License is distributed on an "AS IS" BASIS,')
-        headers.append('* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.')
-        headers.append('* See the License for the specific language governing permissions and')
-        headers.append('* limitations under the License.')
+        headers.append(self.get_copyright_message(prefix='* '))
         headers.append('*/')
         headers.append('')
         # We need to calculate the Java package and no use: headers.append('package org.opencb.opencga.client.rest.clients;')
@@ -99,7 +87,6 @@ def get_class_definition(self, category):
         text.append('/**')
         text.append(' * This class contains methods for the {} webservices.'.format(
             self.categories[self.get_category_name(category)]))
-        text.append(' *{}Client version: {}'.format(' ' * 4, self.version))
         text.append(' *{}PATH: {}'.format(' ' * 4, self.get_category_path(category)))
         text.append(' */')
         text.append('public class {}Client extends {} {{'.format(self.categories[self.get_category_name(category)], parentClientClass))

opencga-app/app/misc/clients/javascript_client_generator.py

@@ -28,18 +28,10 @@ def __init__(self, server_url, output_dir):
         }
 
     def get_imports(self):
+        copyright = self.get_copyright_message(prefix=' * ')
         auto_msg = "\n * ".join(self.get_autogenerated_message())
         return (f'/**\n'
-                f' * Copyright 2015-2020 OpenCB\n'
-                f' * Licensed under the Apache License, Version 2.0 (the "License");\n'
-                f' * you may not use this file except in compliance with the License.\n'
-                f' * You may obtain a copy of the License at\n'
-                f' * http://www.apache.org/licenses/LICENSE-2.0\n'
-                f' * Unless required by applicable law or agreed to in writing, software\n'
-                f' * distributed under the License is distributed on an "AS IS" BASIS,\n'
-                f' * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n'
-                f' * See the License for the specific language governing permissions and\n'
-                f' * limitations under the License.\n'
+                f'{copyright}\n'
                 f' * {auto_msg}'
                 f' \n *\n**/\n\n'
                 f'import OpenCGAParentClass from "./../opencga-parent-class.js";\n\n')

opencga-app/app/misc/clients/python_client_generator.py

@@ -70,7 +70,6 @@ def get_class_definition(self, category):
         text.append('{}"""'.format(' ' * 4))
         text.append('{}This class contains methods for the \'{}\' webservices'.format(' ' * 4,
                                                                                       self.get_category_name(category)))
-        text.append('{}Client version: {}'.format(' ' * 4, self.version))
         text.append('{}PATH: {}'.format(' ' * 4, category['path']))
         text.append('{}"""'.format(' ' * 4))
         text.append('')

opencga-app/app/misc/clients/r_client_generator.py

@@ -75,6 +75,7 @@ def get_class_definition(self, category):
                                                        myEndpoint['path'],
                                                        ", ".join(endpoint_params)))
         path_params = set(class_path_params)
+        path_params = sorted(list(path_params))
         text.append("#'\n#' @md")
         text.append("#' @seealso \\url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation")
         text.append("#' \\url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}")

opencga-app/app/misc/clients/rest_client_generator.py

@@ -56,14 +56,39 @@ def __init__(self, rest_api_file, output_dir):
             'Admin': 'Admin'
         }
 
+    @staticmethod
+    def get_copyright_message(prefix=""):
+        # copyright = [
+        #     'Copyright 2015-2024 OpenCB',
+        #     '',
+        #     'Licensed under the Apache License, Version 2.0 (the "License");',
+        #     'you may not use this file except in compliance with the License.',
+        #     'You may obtain a copy of the License at',
+        #     '',
+        #     '    http://www.apache.org/licenses/LICENSE-2.0',
+        #     '',
+        #     'Unless required by applicable law or agreed to in writing, software',
+        #     'distributed under the License is distributed on an "AS IS" BASIS,',
+        #     'WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.',
+        #     'See the License for the specific language governing permissions and',
+        #     'limitations under the License.'
+        # ]
+        copyright_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'copyright.txt')
+        print("Reading from file: ", copyright_file)
+        with open(copyright_file, 'r') as file:
+            copyright = file.read().splitlines()
+        ## Add prefix to each line
+        if prefix:
+            for line in range(len(copyright)):
+                copyright[line] = (prefix + copyright[line]).rstrip()
+        return "\n".join(copyright)
+
     @staticmethod
     def get_autogenerated_message():
-        date_ = datetime.now().strftime("%Y-%m-%d")
         return [
             'WARNING: AUTOGENERATED CODE',
             '',
             'This code was generated by a tool.',
-            'Autogenerated on: ' + date_,
             '',
             'Manual changes to this file may cause unexpected behavior in your application.',
             'Manual changes to this file will be overwritten if the code is regenerated.'

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/cli/main/OpenCgaCompleter.java

@@ -1,19 +1,3 @@
-/*
-* Copyright 2015-2024-04-29 OpenCB
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
-
 package org.opencb.opencga.app.cli.main;
 
 import org.jline.reader.Candidate;

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,19 +1,3 @@
-/*
-* Copyright 2015-2024-04-29 OpenCB
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
-
 package org.opencb.opencga.app.cli.main;
 
 import com.beust.jcommander.JCommander;

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 {
+    }
+}