diff --git a/opencga-app/app/misc/clients/copyright.txt b/opencga-app/app/misc/clients/copyright.txt new file mode 100644 index 00000000000..5c551251867 --- /dev/null +++ b/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. \ No newline at end of file diff --git a/opencga-app/app/misc/clients/java_client_generator.py b/opencga-app/app/misc/clients/java_client_generator.py index 9555f4fe4b1..f65a89983e9 100755 --- a/opencga-app/app/misc/clients/java_client_generator.py +++ b/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)) diff --git a/opencga-app/app/misc/clients/javascript_client_generator.py b/opencga-app/app/misc/clients/javascript_client_generator.py index b6955e46fe4..2ac2fb88667 100644 --- a/opencga-app/app/misc/clients/javascript_client_generator.py +++ b/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') diff --git a/opencga-app/app/misc/clients/python_client_generator.py b/opencga-app/app/misc/clients/python_client_generator.py index 8a0ba4320c6..ada636dc5c1 100644 --- a/opencga-app/app/misc/clients/python_client_generator.py +++ b/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('') diff --git a/opencga-app/app/misc/clients/r_client_generator.py b/opencga-app/app/misc/clients/r_client_generator.py index f07735c62a0..2d2a4840a97 100644 --- a/opencga-app/app/misc/clients/r_client_generator.py +++ b/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/}") diff --git a/opencga-app/app/misc/clients/rest_client_generator.py b/opencga-app/app/misc/clients/rest_client_generator.py index b4c5800e751..53ed2bdfd8f 100644 --- a/opencga-app/app/misc/clients/rest_client_generator.py +++ b/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.' diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java index eb6f7ae747c..3f5f7cee80f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java +++ b/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; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 1ff476d5003..d6bd902fff1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/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; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index f2bcf34a63c..33d53de3bf8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/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; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java new file mode 100644 index 00000000000..425fd72353f --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java new file mode 100644 index 00000000000..0c0273e7820 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java new file mode 100644 index 00000000000..b99e0a9f1d5 --- /dev/null +++ b/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 { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java new file mode 100644 index 00000000000..06a78900ab0 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java new file mode 100644 index 00000000000..96f702d96f4 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java new file mode 100644 index 00000000000..7efdea6a56a --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java new file mode 100644 index 00000000000..a35f794d130 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java new file mode 100644 index 00000000000..48cd8ce2f3b --- /dev/null +++ b/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 { + } + +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java new file mode 100644 index 00000000000..747feb3bbcb --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java new file mode 100644 index 00000000000..58625266d9b --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java new file mode 100644 index 00000000000..452e99d627f --- /dev/null +++ b/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 { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java new file mode 100644 index 00000000000..18e6272d7a6 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java new file mode 100644 index 00000000000..f37d46cb9f2 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java new file mode 100644 index 00000000000..0530e369b04 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java new file mode 100644 index 00000000000..a0c0938de73 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java new file mode 100644 index 00000000000..9b21dcdbc9c --- /dev/null +++ b/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 { + } +} \ No newline at end of file diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java new file mode 100644 index 00000000000..ef72a501f44 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java new file mode 100644 index 00000000000..5dac53d4688 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java new file mode 100644 index 00000000000..7b33bd7d709 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java new file mode 100644 index 00000000000..b4d243ee279 --- /dev/null +++ b/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 { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java new file mode 100644 index 00000000000..7008388f42e --- /dev/null +++ b/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 { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java new file mode 100644 index 00000000000..1f23c1b331c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java @@ -0,0 +1,16 @@ +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_name_field_in_cohort_1902", + description = "Add new name field to Cohort #1902", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220228, deprecatedSince = "3.0.0") +public class AddNameFieldInCohort extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java new file mode 100644 index 00000000000..1aa51b53014 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.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_new_allowed_biotype", + description = "Add new allowed biotype 'guide_RNA', #1856", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211209, deprecatedSince = "3.0.0") +public class AddNewAllowedBiotype extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java new file mode 100644 index 00000000000..099dd960790 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.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 = "new_file_internal_index_1850", + description = "Add new FileInternalVariant and FileInternalAlignment index #1850", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211127, deprecatedSince = "3.0.0") +public class AddNewFileInternalIndex_1850 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java new file mode 100644 index 00000000000..21218e3222d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.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_sample_internal_variant_1851", + description = "Add new SampleInternalVariant #1851", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211129, deprecatedSince = "3.0.0") +public class AddSampleInternalVariant_1851 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java new file mode 100644 index 00000000000..7731a4510fe --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java @@ -0,0 +1,16 @@ +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 = "change_interpretation_method", + description = "Remove list of methods from Interpretations #1841", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211112, deprecatedSince = "3.0.0") +public class ChangeInterpretationMethods extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java new file mode 100644 index 00000000000..6de2592fbaa --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java @@ -0,0 +1,16 @@ +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_clinical_variant_evidence_review", + description = "Add new ClinicalVariantEvidenceReview object, #1874", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220112, deprecatedSince = "3.0.0") +public class ClinicalVariantEvidenceMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java new file mode 100644 index 00000000000..7ddea73508c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java @@ -0,0 +1,18 @@ +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 = "delete_unused_variablesets", + description = "Delete unused VariableSets, #1859", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211210, deprecatedSince = "3.0.0") +public class DeleteUnusedVariableSets extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java new file mode 100644 index 00000000000..fd160750475 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.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 = "fix_family_references_in_individual", + description = "Fix Family references, #TASK-489", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220324, deprecatedSince = "3.0.0") +public class FixFamilyReferences extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java new file mode 100644 index 00000000000..d642d8499af --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java @@ -0,0 +1,18 @@ +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 = "fix_non_existing_mois_from_panels", + description = "Remove non-existing MOIs from Panels", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20220111, deprecatedSince = "3.0.0") +public class FixNonExistingMoIFromPanels extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java new file mode 100644 index 00000000000..b7ff196615b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.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 = "improve_ca_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "3.0.0") +public class ImproveClinicalAnalysisQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java new file mode 100644 index 00000000000..16043d38b26 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.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 = "improve_file_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "3.0.0") +public class ImproveFileQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java new file mode 100644 index 00000000000..b3350e099f3 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java @@ -0,0 +1,16 @@ +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 = "improve_individual_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "3.0.0") +public class ImproveIndividualQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java new file mode 100644 index 00000000000..39b2df0d2a2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java @@ -0,0 +1,16 @@ +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 = "improveVariableSetNamesAndDescriptions", + description = "Improve VariableSet names and descriptions", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211210) +public class ImproveVariableSetNamesAndDescriptions extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java new file mode 100644 index 00000000000..af85465d69e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java @@ -0,0 +1,16 @@ +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 = "remove_file_docs_from_clinical_analyses", + description = "Store references of File in Clinical Analysis and not full File documents #1837", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211102, deprecatedSince = "3.0.0") +public class RemoveFileDocsFromCA extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java new file mode 100644 index 00000000000..7b00543f9a5 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java @@ -0,0 +1,16 @@ +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 = "remove_parallel_indexes", + description = "Remove parallel array indexes #CU-20jc4tx", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220310, deprecatedSince = "3.0.0") +public class RemoveParallelIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java new file mode 100644 index 00000000000..821fb020a28 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java @@ -0,0 +1,16 @@ +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 = "rename_family_quality_control_fields", + description = "Rename FamilyQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "3.0.0") +public class RenameFamilyQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java new file mode 100644 index 00000000000..c3c5d4ff7f8 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java @@ -0,0 +1,16 @@ +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 = "rename_file_quality_control_fields", + description = "Rename FileQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "3.0.0") +public class RenameFileQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java new file mode 100644 index 00000000000..6df5fc82131 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java @@ -0,0 +1,16 @@ +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 = "rename_individual_quality_control_fields", + description = "Rename IndividualQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "3.0.0") +public class RenameIndividualQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java new file mode 100644 index 00000000000..bd4ad966774 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.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 = "rename_interpretation_stats_field", + description = "Rename interpretation stats field #1819", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211115, deprecatedSince = "3.0.0") +public class RenameInterpretationFindingStats extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java new file mode 100644 index 00000000000..0c5b36cdf93 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java @@ -0,0 +1,18 @@ +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 = "rename_sample_quality_control_fields", + description = "Rename SampleQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211119, deprecatedSince = "3.0.0") +public class RenameSampleQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java new file mode 100644 index 00000000000..9a43d99ac53 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java @@ -0,0 +1,16 @@ +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_variant_caller_interpretation_configuration", + description = "Add default variant caller Interpretation Study configuration #1822", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210916, deprecatedSince = "3.0.0") +public class addDefaultVariantCallerInterpretationStudyConfiguration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java new file mode 100644 index 00000000000..28e32235bb0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java @@ -0,0 +1,10 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.MigrationTool; + +public abstract class AddInternalLastModified extends MigrationTool { + + protected void addInternalModificationDate(String collection) { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java new file mode 100644 index 00000000000..c127e7b2695 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_clinical.internal", description = "Add internal modificationDate to Clinical #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToClinicalInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java new file mode 100644 index 00000000000..0aaccf98b74 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_cohort.internal", description = "Add internal modificationDate to Cohort #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToCohortInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java new file mode 100644 index 00000000000..914b6351a0c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_family.internal", description = "Add internal modificationDate to Family #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToFamilyInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java new file mode 100644 index 00000000000..7ffc3cf7f37 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_file.internal", description = "Add internal modificationDate to File #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToFileInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java new file mode 100644 index 00000000000..05ca7bc522d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_individual.internal", description = "Add internal modificationDate to Individual #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToIndividualInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java new file mode 100644 index 00000000000..9340231dfde --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_interpretation.internal", description = "Add internal modificationDate to Interpretation #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToInterpretationInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java new file mode 100644 index 00000000000..543e02f328e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_job.internal", description = "Add internal modificationDate to Job #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToJobInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java new file mode 100644 index 00000000000..82a3142a222 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_modificationDate_to_project.internal", description = "Add internal modificationDate to Project #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToProjectInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java new file mode 100644 index 00000000000..875bbaa26a7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_sample.internal", description = "Add internal modificationDate to Sample #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToSampleInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java new file mode 100644 index 00000000000..987a742cb5d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_study.internal", description = "Add internal modificationDate to Study #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "3.0.0") +public class AddModificationDateToStudyInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java new file mode 100644 index 00000000000..ac1c112d0a1 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.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_interpretation_stats", + description = "Add interpretation stats #1819", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20210908, deprecatedSince = "3.0.0") +public class addInterpretationStats extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java new file mode 100644 index 00000000000..efd1107ba7b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java @@ -0,0 +1,10 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.MigrationTool; + +public abstract class AddRegistrationDate extends MigrationTool { + + protected void addRegistrationDate(String collection) { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java new file mode 100644 index 00000000000..14a48ed90be --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_clinical.internal", description = "Add registrationDate to Clinical #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToClinicalInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java new file mode 100644 index 00000000000..a7dcf145b33 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_cohort.internal", description = "Add registrationDate to Cohort #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToCohortInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java new file mode 100644 index 00000000000..66f375ce955 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_family.internal", description = "Add registrationDate to Family #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToFamilyInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java new file mode 100644 index 00000000000..cfa29de842a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_file.internal", description = "Add registrationDate to File #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToFileInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java new file mode 100644 index 00000000000..58d233f6d7f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_individual.internal", description = "Add registrationDate to Individual #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToIndividualInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java new file mode 100644 index 00000000000..115b4e4fc6c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_interpretation.internal", description = "Add registrationDate to Interpretation #1804", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToInterpretationInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java new file mode 100644 index 00000000000..c56124cdda6 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_job.internal", description = "Add registrationDate to Job #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToJobInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java new file mode 100644 index 00000000000..ae3f65b70d9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_registrationDate_to_project.internal", description = "Add registrationDate to Project #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToProjectInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java new file mode 100644 index 00000000000..e317c667a98 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_sample.internal", description = "Add registrationDate to Sample #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToSampleInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java new file mode 100644 index 00000000000..7d036f65bc4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_study.internal", description = "Add registrationDate to Study #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "3.0.0") +public class AddRegistrationDateToStudyInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java new file mode 100644 index 00000000000..d995f4ba97f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.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_rga_index_summary_to_study_internal", + description = "Add RGA Index information to Study Internal #", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210719, deprecatedSince = "3.0.0") +public class addRgaIndexToStudyInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java new file mode 100644 index 00000000000..25e93347812 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1795; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_familyIds_in_individual", description = "Add new list of familyIds in Individual #1795", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "3.0.0") +public class AddFamilyIdsInIndividual extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java new file mode 100644 index 00000000000..b6d1d3ff298 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1796; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_cohortIds_in_sample", description = "Add new list of cohortIds in Sample #1796", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "3.0.0") +public class AddCohortIdsInSample extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java new file mode 100644 index 00000000000..fcb2313cb39 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_clinical_status_models", + description = "Complete Clinical Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, + deprecatedSince = "3.0.0") +public class CompleteClinicalStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java new file mode 100644 index 00000000000..692e58cc397 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_cohort_status_models", + description = "Complete Cohort Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteCohortStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java new file mode 100644 index 00000000000..5c1bfbfc2aa --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_family_status_models", + description = "Complete Family Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteFamilyStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java new file mode 100644 index 00000000000..c1c84058b5c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_file_status_models", + description = "Complete File Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteFileStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java new file mode 100644 index 00000000000..cb7fda578ca --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_individual_status_models", + description = "Complete Individual Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteIndividualStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java new file mode 100644 index 00000000000..dad8a984810 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_interpretation_status_models", + description = "Complete Interpretation Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteInterpretationStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java new file mode 100644 index 00000000000..4a08d4695e7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_job_status_models", + description = "Complete Job Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteJobStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java new file mode 100644 index 00000000000..8311dcc2153 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_panel_status_models", + description = "Complete Panel Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompletePanelStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java new file mode 100644 index 00000000000..09ce8a4fc88 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_project_status_models", + description = "Complete Project Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteProjectStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java new file mode 100644 index 00000000000..bb9b3e54086 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_sample_status_models", + description = "Complete Sample Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteSampleStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java new file mode 100644 index 00000000000..8b119d92cc4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_study_status_models", + description = "Complete Study Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteStudyStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java new file mode 100644 index 00000000000..937e6d3f9fb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_user_status_models", + description = "Complete User Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "3.0.0") +public class CompleteUserStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java new file mode 100644 index 00000000000..9a5eb6cec84 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "individual_ontology_term_migration_#1853", + description = "Change sex and ethnicity types for OntologyTermAnnotation #1855", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211203, deprecatedSince = "3.0.0") +public class IndividualOntologyTermMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java new file mode 100644 index 00000000000..e6659fb4ad7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "new_study_data_model_fields_#1853", + description = "New Study 'sources', 'type' and 'additionalInfo' fields #1853", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211202, deprecatedSince = "3.0.0") +public class NewStudyDataModelFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java new file mode 100644 index 00000000000..a054a6a0566 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "sample_source_treatments_#1854", + description = "Sample source, treatments, processing and collection changes #1854", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211201, patch = 2, deprecatedSince = "3.0.0") +public class SampleProcessingAndCollectionChanges extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java new file mode 100644 index 00000000000..bd3f00937e9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java @@ -0,0 +1,18 @@ +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 = "rename_variableset_field", + description = "Rename Variable variableSet field to variables #1823", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210920, deprecatedSince = "3.0.0") +public class renameVariableSetFieldFromVariable extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java new file mode 100644 index 00000000000..609d50c915a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "synchronize_catalog_storage_1850_1851", + description = "Synchronize catalog storage #1850 #1851", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220118, deprecatedSince = "3.0.0") +public class SynchronizeCatalogStorage extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java new file mode 100644 index 00000000000..2965c326760 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "update_sample_index_status_1901", + description = " Improve sample-index multi-schema management. #1901", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220302, deprecatedSince = "3.0.0") +public class UpdateSampleIndexStatus extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java new file mode 100644 index 00000000000..7173a402e96 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_biotypes", + description = "Add missing biotypes, #TASK-625", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220412, deprecatedSince = "3.0.0") +public class AddMissingBiotypes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java new file mode 100644 index 00000000000..0cd9ba5ff1b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_gene_name_index", + description = "Add Panel gene.name index #TASK-602", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220406, deprecatedSince = "3.0.0") +public class AddPanelGeneNameIndex extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java new file mode 100644 index 00000000000..49b4b252f60 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_shared_project", + description = "Initialise sharedProjects #TASK-702", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, deprecatedSince = "3.0.0") +public class InitSharedProjectField extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java new file mode 100644 index 00000000000..cd11e50f8aa --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "sample_index_configuration_add_missing_status", + description = "Sample index configuration add missing status #TASK-512", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220328, deprecatedSince = "3.0.0") +public class SampleIndexConfigurationAddMissingStatus extends StorageMigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java new file mode 100644 index 00000000000..52a95ccf66e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_locked_to_interpretation_TASK-552", + description = "Add new 'locked' field to Interpretation #TASK-552", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220401, + deprecatedSince = "3.0.0") +public class AddLockedToInterpretation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java new file mode 100644 index 00000000000..e2edbf68060 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_internal_field-TASK_734", + description = "Add 'internal' to Panel data model #TASK-734", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220509, + deprecatedSince = "3.0.0") +public class AddPanelInternalField extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java new file mode 100644 index 00000000000..8cbd5a59eef --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "autoincrement_version_TASK-323", + description = "Reorganise data in new collections (autoincrement version) #TASK-323", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + offline = true, + date = 20220512, + deprecatedSince = "3.0.0") +public class AutoIncrementVersion extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java new file mode 100644 index 00000000000..81d3f1e8628 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "init_sampleIndexConfiguration-TASK550", + description = "Initialise SampleIndexConfiguration in Study internal #TASK-550", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, + deprecatedSince = "3.0.0") +public class InitSampleIndexConfiguration extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java new file mode 100644 index 00000000000..9f4f30213fb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_cellbase_from_project_internal_to_project_TASK-354", + description = "Move cellbase from project.internal to project #TASK-354", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220422, + deprecatedSince = "3.0.0") + +public class MoveCellbaseFromProjectInternalToProject extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java new file mode 100644 index 00000000000..2a1532c6da4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_deleted_collections_TASK-359", + description = "Rename deleted collections #TASK-359", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, + deprecatedSince = "3.0.0") +public class RenameDeletedCollections extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java new file mode 100644 index 00000000000..b39a56cdbec --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_variant_storage_tool_ids_TASK-705", + description = "Rename variant storage tool ids #TASK-705", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220506, + deprecatedSince = "3.0.0") +public class RenameDeprecatedVariantStorageToolId extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java new file mode 100644 index 00000000000..be328bbeb6a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "update_jwt_secret_key_TASK-807", + description = "Update JWT secret key #TASK-807", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220513, + deprecatedSince = "3.0.0") +public class UpdateJWTSecretKey extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java new file mode 100644 index 00000000000..df2e308a727 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id="add_missing_columns_to_phoenix_TASK-789", description = "Add missing 1000G columns to phoenix #TASK-789", + version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "3.0.0" +) +public class AddMissingColumnsToPhoenix extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java new file mode 100644 index 00000000000..2c645980391 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "bugfix_move_cellbase_from_project_internal_to_project_TASK-1100", + description = "Bugfix: Move cellbase from project.internal to project #TASK-1100", version = "2.3.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220620, + deprecatedSince = "3.0.0") + +public class MoveCellbaseFromProjectInternalToProjectBugFix extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java new file mode 100644 index 00000000000..8f3886c50e8 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_status_type_TASK-607", + description = "Automatically close cases depending on the new clinical status type #TASK-607", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220610, + deprecatedSince = "3.0.0") +public class AddClinicalStatusType_607 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java new file mode 100644 index 00000000000..6dcab05694a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_private_dueDate_TASK-803", + description = "Add private _dueDate to ClinicalAnalysis #TASK-803", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220530, + deprecatedSince = "3.0.0") +public class AddPrivateDueDate_803 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java new file mode 100644 index 00000000000..af93d04de7d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "index_panel_source_TASK-473", + description = "Index panel source #TASK-473", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220530, + deprecatedSince = "3.0.0") +public class IndexPanelSource extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java new file mode 100644 index 00000000000..0759d4c7bf1 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_10.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_endDate_on_finished_jobs" , + description = "Add missing end date on finished jobs", + version = "2.4.10", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20221026, + deprecatedSince = "3.0.0" +) +public class AddMissingEndDateOnFinishedJobs extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java new file mode 100644 index 00000000000..e2fb99933cf --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_11; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "synchronize_catalog_storage_statuses", + description = "Synchronize catalog internal statuses from storage, #TASK-1304", version = "2.4.11", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20221117, + deprecatedSince = "3.0.0") +public class SynchronizeCatalogStorageStatuses extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java new file mode 100644 index 00000000000..ec0b49baae3 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_11.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "signature_fittings" , + description = "Replace fitting for fittings in Signature", + version = "2.4.11", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20221109, + deprecatedSince = "3.0.0" +) +public class SignatureFittingsMigration extends MigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java new file mode 100644 index 00000000000..8e5825e3de7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_2.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_discussion_TASK-1472", + description = "Add ClinicalDiscussion #TASK-1472", version = "2.4.2", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220727, + deprecatedSince = "3.0.0") +public class AddClinicalDiscussion extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java new file mode 100644 index 00000000000..aba0267d65b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_2.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "recover_proband_samples_in_cases_TASK-1470", + description = "Recover lost samples in clinical collection #TASK-1470", version = "2.4.2", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220725, + patch = 2, + deprecatedSince = "3.0.0") +public class RecoverProbandSamplesInCases extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java new file mode 100644 index 00000000000..7951810b105 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_3.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "migrate_to_clinical_acmg_TASK-1194", + description = "Migrate to ClinicalAcmg #TASK-1194", version = "2.4.3", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220809, + deprecatedSince = "3.0.0") +public class MigrateToClinicalAcmg extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java new file mode 100644 index 00000000000..2d4e2cb14a8 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_3.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "shorten_indexed_field_variables-1386", + description = "Shorten indexed field variables #TASK-1386", version = "2.4.3", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220809, + deprecatedSince = "3.0.0") +public class ShortenIndexedFieldVariables extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java new file mode 100644 index 00000000000..e26df11c03c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "avoidCaseStatusIdNull-1938", + description = "Avoid nullable status id in Clinical Analysis #TASK-1938", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220914, + deprecatedSince = "3.0.0") +public class AvoidCaseStatusIdNullMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java new file mode 100644 index 00000000000..07a19a12fdb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_biotype_allowed_keys_TASK-1849", + description = "Remove biotype and consequence type allowed keys from variable sets #TASK-1849", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220905, + deprecatedSince = "3.0.0") +public class RemoveBiotypeAllowedKeysMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java new file mode 100644 index 00000000000..069e1a86e6e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "invalidate_variant_archives_migration-633", + description = "Invalidate variant archives from variant storage hadoop #TASK-633", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220825, + deprecatedSince = "3.0.0") +public class InvalidateVariantArchivesMigration extends StorageMigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java new file mode 100644 index 00000000000..06f1d871a80 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_6_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_cellbase_data_release" , + description = "Add default cellbase data release if missing", + version = "2.6.0", + domain = Migration.MigrationDomain.STORAGE, + language = Migration.MigrationLanguage.JAVA, + patch = 2, + date = 20230104, + deprecatedSince = "3.0.0" +) +public class AddCellbaseDataRelease extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java new file mode 100644 index 00000000000..ce425e3434b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_7_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "panel_roles_and_modesOfInheritance" , + description = "Change panel cancer.role and modeOfInheritance for cancer.roles[] and modesOfInheritance[]", + version = "2.7.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230117, + deprecatedSince = "3.0.0" +) +public class CancerRoleAndModeOfInheritanceMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java new file mode 100644 index 00000000000..0be802202c4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_8_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "calculate_pedigree_graph" , + description = "Calculate Pedigree Graph for all the families", + version = "2.8.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230313, + deprecatedSince = "3.0.0" +) +public class CalculatePedigreeGraphMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java new file mode 100644 index 00000000000..e3b093906c4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_8_6.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "mark_unknown_largest_variant_length" , + description = "Mark as unknown largest variant length", + version = "2.8.6", + domain = Migration.MigrationDomain.STORAGE, + language = Migration.MigrationLanguage.JAVA, + patch = 1, + date = 20230927, + deprecatedSince = "3.0.0" +) +public class MarkUnknownLargestVariantLength extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java new file mode 100644 index 00000000000..7dbd590c27e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_9_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_cellbase_token_2_api_key" , + description = "Rename CellBase Token to ApiKey", + version = "2.9.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230829, + deprecatedSince = "3.0.0" +) +public class RenameCellBaseToken2ApiKey extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java similarity index 70% rename from opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java rename to opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 0b9982c6f71..9b226c0ea1a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -1,12 +1,12 @@ -package org.opencb.opencga.app.migrations.v3_0_0; +package org.opencb.opencga.app.migrations.v3.v3_0_0; import org.opencb.opencga.catalog.migration.Migration; -import org.opencb.opencga.catalog.migration.MigrationException; import org.opencb.opencga.catalog.migration.MigrationTool; import org.opencb.opencga.core.config.Configuration; @Migration(id = "add_organizations", description = "Add new Organization layer #TASK-4389", version = "3.0.0", - language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20231212) + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20231212, + deprecatedSince = "3.1.0") public class OrganizationMigration extends MigrationTool { public OrganizationMigration(Configuration configuration, String adminPassword, String userId) { @@ -14,7 +14,6 @@ public OrganizationMigration(Configuration configuration, String adminPassword, @Override protected void run() throws Exception { - throw MigrationException.outdatedMigration(getAnnotation(), "3.1.0"); } } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/AuthOriginSimplificationMigration.java similarity index 98% rename from opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigration.java rename to opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/AuthOriginSimplificationMigration.java index e913941bafd..e1b331fa987 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/AuthOriginSimplificationMigration.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.app.migrations.v3_1_0; +package org.opencb.opencga.app.migrations.v3.v3_1_0; import com.mongodb.client.model.Filters; import com.mongodb.client.model.Projections; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/NoteMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/NoteMigration.java similarity index 98% rename from opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/NoteMigration.java rename to opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/NoteMigration.java index a842905fc70..c5fb031f1da 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/NoteMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/NoteMigration.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.app.migrations.v3_1_0; +package org.opencb.opencga.app.migrations.v3.v3_1_0; import com.mongodb.MongoNamespace; import com.mongodb.client.MongoCollection; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java index 7fb3b1dabf8..3c5ddea26d3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java @@ -54,6 +54,11 @@ */ boolean manual() default false; + /** + * @return the version when the migration was deprecated. + */ + String deprecatedSince() default ""; + enum MigrationDomain { CATALOG, STORAGE diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java index e59e1e659e3..000c46d57dc 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java @@ -21,8 +21,9 @@ public static MigrationException offlineMigrationException(Migration migration) + "cannot be accessed and run try again with '--offline' flag."); } - public static MigrationException outdatedMigration(Migration migration, String version) { - return new MigrationException("Migration '" + migration.id() + "' is outdated since version " + version + ". Please, update the " - + "migration from the previous latest version."); + public static MigrationException deprecatedMigration(Migration migration) { + return new MigrationException("Migration '" + migration.id() + "' can't be run since version '" + + migration.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); } + } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java index 7809f4fb0f7..10b247a6d0d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java @@ -622,6 +622,10 @@ private MigrationRun run(String organizationId, Class r String token) throws MigrationException { Migration annotation = getMigrationAnnotation(runnableMigration); + if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { + throw MigrationException.deprecatedMigration(annotation); + } + MigrationTool migrationTool; try { migrationTool = runnableMigration.newInstance(); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java index 47a701f0ed2..219e1178652 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java @@ -4,6 +4,7 @@ import com.mongodb.client.MongoCursor; import com.mongodb.client.model.IndexOptions; import com.mongodb.client.model.WriteModel; +import org.apache.commons.lang3.StringUtils; import org.bson.Document; import org.bson.conversions.Bson; import org.opencb.commons.ProgressLogger; @@ -78,6 +79,10 @@ public final void setup(Configuration configuration, CatalogManager catalogManag public final void execute() throws MigrationException { try { + Migration annotation = getAnnotation(); + if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { + throw MigrationException.deprecatedMigration(annotation); + } run(); } catch (MigrationException e) { throw e; diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 21ccff3b4da..d63a1ad3478 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 363efca3f8f..398851faed5 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 3d6e69ee4cb..195b5ad36f3 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,11 +1,11 @@ # ############################################################################## ## OrganizationClient -setGeneric("organizationClient", function(OpencgaR, organization, id, endpointName, params=NULL, ...) +setGeneric("organizationClient", function(OpencgaR, id, organization, endpointName, params=NULL, ...) standardGeneric("organizationClient")) # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -15,37 +15,37 @@ setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, group, id, variableSet, templateId, study, studies, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, group, id, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, members, folder, files, annotationSet, file, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, members, samples, annotationSet, sample, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, annotationSet, individual, individuals, members, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -65,7 +65,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, members, interpretation, clinicalAnalysis, clinicalAnalyses, interpretations, annotationSet, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -80,7 +80,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 675d8f0c9bb..f9d9f038ae1 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -62,7 +61,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, interpretation, clinicalAnalysis, clinicalAnalyses, interpretations, annotationSet, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 771d7d16480..e510a05eba8 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -38,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index dc1ad726ed4..de04b212196 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -37,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 52d5b80e3f6..41ff659c258 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -54,7 +53,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, files, annotationSet, file, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index b134810eeb3..a6053502605 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -31,7 +30,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index ab204922c49..9a3bc092adc 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -38,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individual, individuals, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index c48e3ae9691..df80a2c29cc 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -39,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 8fd2202e69f..8da8f31ca44 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 868d718b61c..ecd586a9ed7 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/R/R/Organization-methods.R b/opencga-client/src/main/R/R/Organization-methods.R index fd5681c5378..3efaf5eec2f 100644 --- a/opencga-client/src/main/R/R/Organization-methods.R +++ b/opencga-client/src/main/R/R/Organization-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -34,7 +33,7 @@ #' [*]: Required parameter #' @export -setMethod("organizationClient", "OpencgaR", function(OpencgaR, organization, id, endpointName, params=NULL, ...) { +setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/organizations/create: diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index 6f9d0bebb47..b23b8043f55 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 41235ecea72..380d33ea815 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index b61ca7558ca..a5434ddb451 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -38,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, samples, annotationSet, sample, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 81f0e582a7c..95104111011 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -49,7 +48,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, members, group, id, variableSet, templateId, study, studies, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, group, id, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 4b6e2d76c67..ffc1c599ca9 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. @@ -40,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/anonymous: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 8bc5c25558b..95fba46fac9 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # 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. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index a74cbd784c4..928fd361341 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -37,7 +37,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -46,7 +45,6 @@ /** * This class contains methods for the Admin webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: admin */ public class AdminClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 5d3cef8c796..ca1e1ecc744 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -49,7 +48,6 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index f12aa75b765..976ea17a4f6 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -55,7 +55,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -64,7 +63,6 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java deleted file mode 100644 index 67bb142fc41..00000000000 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java +++ /dev/null @@ -1,914 +0,0 @@ -/* -* Copyright 2015-2022 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.client.rest.clients; - -import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant; -import org.opencb.commons.datastore.core.FacetField; -import org.opencb.commons.datastore.core.ObjectMap; -import org.opencb.opencga.client.config.ClientConfiguration; -import org.opencb.opencga.client.exceptions.ClientException; -import org.opencb.opencga.client.rest.AbstractParentClient; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByGeneSummary; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividual; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividualSummary; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByVariant; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByVariantSummary; -import org.opencb.opencga.core.models.analysis.knockout.RgaKnockoutByGene; -import org.opencb.opencga.core.models.clinical.CancerTieringInterpretationAnalysisParams; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysis; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysisAclUpdateParams; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysisCreateParams; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysisUpdateParams; -import org.opencb.opencga.core.models.clinical.Interpretation; -import org.opencb.opencga.core.models.clinical.InterpretationCreateParams; -import org.opencb.opencga.core.models.clinical.InterpretationUpdateParams; -import org.opencb.opencga.core.models.clinical.RgaAnalysisParams; -import org.opencb.opencga.core.models.clinical.TeamInterpretationAnalysisParams; -import org.opencb.opencga.core.models.clinical.TieringInterpretationAnalysisParams; -import org.opencb.opencga.core.models.clinical.ZettaInterpretationAnalysisParams; -import org.opencb.opencga.core.models.job.Job; -import org.opencb.opencga.core.models.study.configuration.ClinicalAnalysisStudyConfiguration; -import org.opencb.opencga.core.response.RestResponse; - - -/* -* WARNING: AUTOGENERATED CODE -* -* This code was generated by a tool. -* Autogenerated on: 2022-08-02 08:25:32 ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x -* -* 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. -*/ - - -/** - * This class contains methods for the Clinical webservices. - * Client version: 2.3.3-SNAPSHOT [fb5e7ed17448243b10ddd619bdf973e4b20b0a74] ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - * PATH: analysis/clinical - */ -public class ClinicalClient extends AbstractParentClient { - - public ClinicalClient(String token, ClientConfiguration configuration) { - super(token, configuration); - } - - /** - * Update the set of permissions granted for the member. - * @param members Comma separated list of user or group IDs. - * @param action Action to be performed [ADD, SET, REMOVE or RESET]. - * @param data JSON containing the parameters to add ACLs. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * propagate: Propagate permissions to related families, individuals, samples and files. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse updateAcl(String members, String action, ClinicalAnalysisAclUpdateParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("action", action); - params.put("body", data); - return execute("analysis", null, "clinical/acl", members, "update", params, POST, ObjectMap.class); - } - - /** - * Update Clinical Analysis configuration. - * @param data Configuration params to update. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse updateClinicalConfiguration(ClinicalAnalysisStudyConfiguration data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/clinical/configuration", null, "update", params, POST, ObjectMap.class); - } - - /** - * Create a new clinical analysis. - * @param data JSON containing clinical analysis information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * skipCreateDefaultInterpretation: Flag to skip creating and initialise an empty default primary interpretation (Id will be - * '{clinicalAnalysisId}.1'). This flag is only considered if no Interpretation object is passed. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse create(ClinicalAnalysisCreateParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical", null, "create", params, POST, ClinicalAnalysis.class); - } - - /** - * Clinical Analysis distinct method. - * @param field Field for which to obtain the distinct values. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. - * files: Clinical Analysis files. - * sample: Sample associated to the proband or any member of a family. - * individual: Proband or any member of a family. - * proband: Clinical Analysis proband. - * probandSamples: Clinical Analysis proband samples. - * family: Clinical Analysis family. - * familyMembers: Clinical Analysis family members. - * familyMemberSamples: Clinical Analysis family members samples. - * panels: Clinical Analysis panels. - * locked: Locked Clinical Analyses. - * analystId: Clinical Analysis analyst id. - * priority: Clinical Analysis priority. - * flags: Clinical Analysis flags. - * creationDate: Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * dueDate: Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * qualityControlSummary: Clinical Analysis quality control summary. - * release: Release when it was created. - * status: Filter by status. - * internalStatus: Filter by internal status. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse distinct(String field, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("field", field); - return execute("analysis", null, "clinical", null, "distinct", params, GET, ObjectMap.class); - } - - /** - * Interpretation distinct method. - * @param field Field for which to obtain the distinct values. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. - * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. - * clinicalAnalysisId: Clinical Analysis id. - * analystId: Analyst ID. - * methodName: Interpretation method name. - * panels: Interpretation panels. - * primaryFindings: Interpretation primary findings. - * secondaryFindings: Interpretation secondary findings. - * creationDate: Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * status: Filter by status. - * internalStatus: Filter by internal status. - * release: Release when it was created. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse distinctInterpretation(String field, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("field", field); - return execute("analysis", null, "clinical/interpretation", null, "distinct", params, GET, ObjectMap.class); - } - - /** - * Search clinical interpretations. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * sort: Sort the results. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. - * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. - * clinicalAnalysisId: Clinical Analysis id. - * analystId: Analyst ID. - * methodName: Interpretation method name. - * panels: Interpretation panels. - * primaryFindings: Interpretation primary findings. - * secondaryFindings: Interpretation secondary findings. - * creationDate: Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * status: Filter by status. - * internalStatus: Filter by internal status. - * release: Release when it was created. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse searchInterpretation(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/interpretation", null, "search", params, GET, Interpretation.class); - } - - /** - * Clinical interpretation information. - * @param interpretations Comma separated list of clinical interpretation IDs up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * version: Comma separated list of interpretation versions. 'all' to get all the interpretation versions. Not supported if - * multiple interpretation ids are provided. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse infoInterpretation(String interpretations, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/interpretation", interpretations, "info", params, GET, Interpretation.class); - } - - /** - * Run cancer tiering interpretation analysis. - * @param data Cancer tiering interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterCancerTiering(CancerTieringInterpretationAnalysisParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/cancerTiering", null, "run", params, POST, Job.class); - } - - /** - * Run TEAM interpretation analysis. - * @param data TEAM interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterTeam(TeamInterpretationAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/team", null, "run", params, POST, Job.class); - } - - /** - * Run tiering interpretation analysis. - * @param data Tiering interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterTiering(TieringInterpretationAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/tiering", null, "run", params, POST, Job.class); - } - - /** - * Run Zetta interpretation analysis. - * @param data Zetta interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterZetta(ZettaInterpretationAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/zetta", null, "run", params, POST, Job.class); - } - - /** - * RGA aggregation stats. - * @param field List of fields separated by semicolons, e.g.: clinicalSignificances;type. For nested fields use >>, e.g.: - * type>>clinicalSignificances;knockoutType. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse aggregationStatsRga(String field, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("field", field); - return execute("analysis", null, "clinical/rga", null, "aggregationStats", params, GET, FacetField.class); - } - - /** - * Query gene RGA. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * includeIndividual: Include only the comma separated list of individuals to the response. - * skipIndividual: Number of individuals to skip. - * limitIndividual: Limit number of individuals returned (default: 1000). - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryRgaGene(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/gene", null, "query", params, GET, RgaKnockoutByGene.class); - } - - /** - * RGA gene summary stats. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse summaryRgaGene(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/gene", null, "summary", params, GET, KnockoutByGeneSummary.class); - } - - /** - * Generate Recessive Gene Analysis secondary index. - * @param data Recessive Gene Analysis index params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * auxiliarIndex: Index auxiliar collection to improve performance assuming RGA is completely indexed. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runRgaIndex(RgaAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/rga/index", null, "run", params, POST, Job.class); - } - - /** - * Query individual RGA. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryRgaIndividual(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/individual", null, "query", params, GET, KnockoutByIndividual.class); - } - - /** - * RGA individual summary stats. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse summaryRgaIndividual(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/individual", null, "summary", params, GET, KnockoutByIndividualSummary.class); - } - - /** - * Query variant RGA. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * includeIndividual: Include only the comma separated list of individuals to the response. - * skipIndividual: Number of individuals to skip. - * limitIndividual: Limit number of individuals returned (default: 1000). - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryRgaVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/variant", null, "query", params, GET, KnockoutByVariant.class); - } - - /** - * RGA variant summary stats. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse summaryRgaVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/variant", null, "summary", params, GET, KnockoutByVariantSummary.class); - } - - /** - * Clinical analysis search. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. - * files: Clinical Analysis files. - * sample: Sample associated to the proband or any member of a family. - * individual: Proband or any member of a family. - * proband: Clinical Analysis proband. - * probandSamples: Clinical Analysis proband samples. - * family: Clinical Analysis family. - * familyMembers: Clinical Analysis family members. - * familyMemberSamples: Clinical Analysis family members samples. - * panels: Clinical Analysis panels. - * locked: Locked Clinical Analyses. - * analystId: Clinical Analysis analyst id. - * priority: Clinical Analysis priority. - * flags: Clinical Analysis flags. - * creationDate: Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * dueDate: Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * qualityControlSummary: Clinical Analysis quality control summary. - * release: Release when it was created. - * status: Filter by status. - * internalStatus: Filter by internal status. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse search(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", null, "search", params, GET, ClinicalAnalysis.class); - } - - /** - * Fetch actionable clinical variants. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * sample: Sample ID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse actionableVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/variant", null, "actionable", params, GET, ClinicalVariant.class); - } - - /** - * Fetch clinical variants. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * approximateCount: Get an approximate count, instead of an exact total count. Reduces execution time. - * approximateCountSamplingSize: Sampling size to get the approximate count. Larger values increase accuracy but also increase - * execution time. - * savedFilter: Use a saved filter at User level. - * id: List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T. - * region: List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: - * 2,3:100000-200000. - * type: List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION, - * DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL. - * study: Filter variants from the given studies, these can be either the numeric ID or the alias with the format - * organization@project:study. - * file: Filter variants from the files specified. This will set includeFile parameter when not provided. - * filter: Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: - * PASS,LowGQX. - * qual: Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. e.g.: >123.4. - * fileData: Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file - * is specified, will use all files from "file" filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can - * be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - * sample: Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This - * filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) - * operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) - * operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. - * 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, - * regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, - * HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with - * segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - * compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . - * sampleData: Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will - * use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be - * combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. - * sampleAnnotation: Selects some samples using metadata information from Catalog. e.g. - * age>20;phenotype=hpo:123,hpo:456;name=smith. - * cohort: Select variants with calculated stats for the selected cohorts. - * cohortStatsRef: Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsAlt: Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsMaf: Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsMgf: Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsPass: Filter PASS frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8. - * missingAlleles: Number of missing alleles: [{study:}]{cohort}[<|>|<=|>=]{number}. - * missingGenotypes: Number of missing genotypes: [{study:}]{cohort}[<|>|<=|>=]{number}. - * score: Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}. - * family: Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). - * familyDisorder: Specify the disorder to use for the family segregation. - * familySegregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, - * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. - * familyMembers: Sub set of the members of a given family. - * familyProband: Specify the proband child to use for the family segregation. - * gene: List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter. - * ct: List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' - * and 'protein_altering'. - * xref: List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, - * dbSNP, ClinVar, HPO, Cosmic, ... - * biotype: List of biotypes, e.g. protein_coding. - * proteinSubstitution: Protein substitution scores include SIFT and PolyPhen. You can query using the score - * {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. - * conservation: Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. phastCons>0.5,phylop<0.1,gerp>0.1. - * populationFrequencyAlt: Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - * populationFrequencyRef: Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - * populationFrequencyMaf: Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - * transcriptFlag: List of transcript flags. e.g. canonical, CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc, - * TSO500. - * geneTraitId: List of gene trait association id. e.g. "umls:C0007222" , "OMIM:269600". - * go: List of GO (Gene Ontology) terms. e.g. "GO:0002020". - * expression: List of tissues of interest. e.g. "lung". - * proteinKeyword: List of Uniprot protein variant annotation keywords. - * drug: List of drug names. - * functionalScore: Functional score: {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , cadd_raw<=0.3. - * clinical: Clinical source: clinvar, cosmic. - * clinicalSignificance: Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic. - * clinicalConfirmedStatus: Clinical confirmed status. - * customAnnotation: Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}. - * panel: Filter by genes from the given disease panel. - * panelModeOfInheritance: Filter genes from specific panels that match certain mode of inheritance. Accepted values : [ - * autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - * compoundHeterozygous ]. - * panelConfidence: Filter genes from specific panels that match certain confidence. Accepted values : [ high, medium, low, - * rejected ]. - * panelRoleInCancer: Filter genes from specific panels that match certain role in cancer. Accepted values : [ both, oncogene, - * tumorSuppressorGene, fusion ]. - * panelFeatureType: Filter elements from specific panels by type. Accepted values : [ gene, region, str, variant ]. - * panelIntersection: Intersect panel genes and regions with given genes and regions from que input query. This will prevent - * returning variants from regions out of the panel. - * trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,... - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/variant", null, "query", params, GET, ClinicalVariant.class); - } - - /** - * Returns the acl of the clinical analyses. If member is provided, it will only return the acl for the member. - * @param clinicalAnalyses Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * member: User or group ID. - * silent: Boolean to retrieve all possible entries that are queried for, false to raise an exception whenever one of the entries - * looked for cannot be shown for whichever reason. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse acl(String clinicalAnalyses, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", clinicalAnalyses, "acl", params, GET, ObjectMap.class); - } - - /** - * Delete clinical analyses. - * @param clinicalAnalyses Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * force: Force deletion if the ClinicalAnalysis contains interpretations or is locked. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse delete(String clinicalAnalyses, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", clinicalAnalyses, "delete", params, DELETE, ClinicalAnalysis.class); - } - - /** - * Update clinical analysis attributes. - * @param clinicalAnalyses Comma separated list of clinical analysis IDs. - * @param data JSON containing clinical analysis information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * commentsAction: Action to be performed if the array of comments is being updated. - * flagsAction: Action to be performed if the array of flags is being updated. - * filesAction: Action to be performed if the array of files is being updated. - * panelsAction: Action to be performed if the array of panels is being updated. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse update(String clinicalAnalyses, ClinicalAnalysisUpdateParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical", clinicalAnalyses, "update", params, POST, ClinicalAnalysis.class); - } - - /** - * Clinical analysis info. - * @param clinicalAnalysis Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse info(String clinicalAnalysis, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", clinicalAnalysis, "info", params, GET, ClinicalAnalysis.class); - } - - /** - * Create a new Interpretation. - * @param clinicalAnalysis Clinical analysis ID. - * @param data JSON containing clinical interpretation information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: [[organization@]project:]study id. - * setAs: Set interpretation as. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse createInterpretation(String clinicalAnalysis, InterpretationCreateParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", null, "create", params, POST, Interpretation.class); - } - - /** - * Clear the fields of the main interpretation of the Clinical Analysis. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretations Interpretation IDs of the Clinical Analysis. - * @param params Map containing any of the following optional parameters. - * study: [[organization@]project:]study ID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse clearInterpretation(String clinicalAnalysis, String interpretations, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", params, POST, - Interpretation.class); - } - - /** - * Delete interpretation. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretations Interpretation IDs of the Clinical Analysis. - * @param params Map containing any of the following optional parameters. - * study: [[organization@]project:]study ID. - * setAsPrimary: Interpretation id to set as primary from the list of secondaries in case of deleting the actual primary one. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse deleteInterpretation(String clinicalAnalysis, String interpretations, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "delete", params, DELETE, - Interpretation.class); - } - - /** - * Revert to a previous interpretation version. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretation Interpretation ID. - * @param version Version to revert to. - * @param params Map containing any of the following optional parameters. - * study: [[organization@]project:]study ID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse revertInterpretation(String clinicalAnalysis, String interpretation, int version, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("version", version); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", params, POST, - Interpretation.class); - } - - /** - * Update interpretation fields. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretation Interpretation ID. - * @param data JSON containing clinical interpretation information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: [[organization@]project:]study ID. - * primaryFindingsAction: Action to be performed if the array of primary findings is being updated. - * methodsAction: Action to be performed if the array of methods is being updated. - * secondaryFindingsAction: Action to be performed if the array of secondary findings is being updated. - * commentsAction: Action to be performed if the array of comments is being updated. To REMOVE or REPLACE, the date will need to - * be provided to identify the comment. - * panelsAction: Action to be performed if the array of panels is being updated. - * setAs: Set interpretation as. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse updateInterpretation(String clinicalAnalysis, String interpretation, InterpretationUpdateParams - data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", params, POST, - Interpretation.class); - } -} diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 127e40de626..0bcb27158a8 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -36,7 +36,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -45,7 +44,6 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: cohorts */ public class CohortClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index d55854b6127..ead924800fa 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -44,7 +43,6 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 663903149db..368cf2eb4a5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -44,7 +43,6 @@ /** * This class contains methods for the Family webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: families */ public class FamilyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 0fe1fba1940..09cc5ab8c25 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -52,7 +51,6 @@ /** * This class contains methods for the File webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: files */ public class FileClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 0e14eba34d8..e1eb10bd8a1 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -36,7 +35,6 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 5598bf2ec81..571f7b8953f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -44,7 +43,6 @@ /** * This class contains methods for the Individual webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: individuals */ public class IndividualClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 02037990104..523523ab4b3 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -36,7 +36,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -45,7 +44,6 @@ /** * This class contains methods for the Job webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: jobs */ public class JobClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 8826ff88f90..8401614fec4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -37,7 +36,6 @@ /** * This class contains methods for the Meta webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: meta */ public class MetaClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java index e1ec2b30ebf..aebe0ba61f5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java @@ -33,7 +33,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -42,7 +41,6 @@ /** * This class contains methods for the Organization webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: organizations */ public class OrganizationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 23b5a0f0afd..53ecaea4610 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -31,7 +31,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -40,7 +39,6 @@ /** * This class contains methods for the Project webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: projects */ public class ProjectClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index 5f69fa0997a..811dcbfe08c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -44,7 +43,6 @@ /** * This class contains methods for the Sample webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: samples */ public class SampleClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 02383dedf92..71e89be53fb 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -47,7 +47,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -56,7 +55,6 @@ /** * This class contains methods for the Study webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: studies */ public class StudyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index bdadc50c29b..ee290b40d21 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -45,7 +44,6 @@ /** * This class contains methods for the User webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: users */ public class UserClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 58f15654b8d..93ae92a1d88 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -71,7 +70,6 @@ /** * This class contains methods for the Variant webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index 31b832fd1bd..9731eb2bcc0 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * 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. @@ -59,7 +58,6 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 7fcab038434..3f6204d4165 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 1ec703a5d46..0b374aab6a5 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index e445a613946..265e9e28a2b 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 6f9ac1e3c22..dcd44092cc6 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 4343bc420dc..b23920896d2 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 245c24abe04..55a5ac0caf6 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index 0a085be817c..80c275318ef 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 1bef974d359..02af95b1363 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index ce94d506024..fb33520e6db 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 1d2aa95b0cc..e9014ed296f 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 6d9869452f1..0a536de0c03 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Organization.js b/opencga-client/src/main/javascript/Organization.js index a429ccf6868..4385a545eb0 100644 --- a/opencga-client/src/main/javascript/Organization.js +++ b/opencga-client/src/main/javascript/Organization.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index e58af550ded..524221df852 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index f4ae4e29625..48edf930fc8 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index d13f1d427c3..1be4598d5bc 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index e478e03db6f..843416dd14e 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index c341d110c64..177fdffdae3 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index a178fbbddcf..6f2ce1afafa 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * 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 + * + * 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. @@ -12,7 +15,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * 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. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index ead2235886b..7311fa7e5dd 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/admin """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 313d3223ade..4924a3e1233 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/analysis/alignment """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index d43bfa65210..e66873eba68 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/analysis/clinical """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py deleted file mode 100644 index 3c42c2e0a16..00000000000 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py +++ /dev/null @@ -1,1005 +0,0 @@ -""" -WARNING: AUTOGENERATED CODE - - This code was generated by a tool. - Autogenerated on: 2022-08-02 08:25:32 ->>>>>>> develop ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - - 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. -""" - -from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient - - -class Clinical(_ParentRestClient): - """ - This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.3.3-SNAPSHOT [fb5e7ed17448243b10ddd619bdf973e4b20b0a74] ->>>>>>> develop ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - PATH: /{apiVersion}/analysis/clinical - """ - - def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs): - super(Clinical, self).__init__(configuration, token, login_handler, *args, **kwargs) - - def update_acl(self, members, action, data=None, **options): - """ - Update the set of permissions granted for the member. - PATH: /{apiVersion}/analysis/clinical/acl/{members}/update - - :param dict data: JSON containing the parameters to add ACLs. - (REQUIRED) - :param str action: Action to be performed [ADD, SET, REMOVE or RESET]. - (REQUIRED) - :param str members: Comma separated list of user or group IDs. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool propagate: Propagate permissions to related families, - individuals, samples and files. - """ - - options['action'] = action - return self._post(category='analysis', resource='update', subcategory='clinical/acl', second_query_id=members, data=data, **options) - - def update_clinical_configuration(self, data=None, **options): - """ - Update Clinical Analysis configuration. - PATH: /{apiVersion}/analysis/clinical/clinical/configuration/update - - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param dict data: Configuration params to update. - """ - - return self._post(category='analysis', resource='update', subcategory='clinical/clinical/configuration', data=data, **options) - - def create(self, data=None, **options): - """ - Create a new clinical analysis. - PATH: /{apiVersion}/analysis/clinical/create - - :param dict data: JSON containing clinical analysis information. - (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool skip_create_default_interpretation: Flag to skip creating - and initialise an empty default primary interpretation (Id will be - '{clinicalAnalysisId}.1'). This flag is only considered if no - Interpretation object is passed. - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis', resource='create', subcategory='clinical', data=data, **options) - - def distinct(self, field, **options): - """ - Clinical Analysis distinct method. - PATH: /{apiVersion}/analysis/clinical/distinct - - :param str field: Field for which to obtain the distinct values. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Clinical Analysis UUIDs up to - a maximum of 100. - :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. - :param str files: Clinical Analysis files. - :param str sample: Sample associated to the proband or any member of a - family. - :param str individual: Proband or any member of a family. - :param str proband: Clinical Analysis proband. - :param str proband_samples: Clinical Analysis proband samples. - :param str family: Clinical Analysis family. - :param str family_members: Clinical Analysis family members. - :param str family_member_samples: Clinical Analysis family members - samples. - :param str panels: Clinical Analysis panels. - :param bool locked: Locked Clinical Analyses. - :param str analyst_id: Clinical Analysis analyst id. - :param str priority: Clinical Analysis priority. - :param str flags: Clinical Analysis flags. - :param str creation_date: Clinical Analysis Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Clinical Analysis Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str due_date: Clinical Analysis due date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str quality_control_summary: Clinical Analysis quality control - summary. - :param str release: Release when it was created. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - options['field'] = field - return self._get(category='analysis', resource='distinct', subcategory='clinical', **options) - - def distinct_interpretation(self, field, **options): - """ - Interpretation distinct method. - PATH: /{apiVersion}/analysis/clinical/interpretation/distinct - - :param str field: Field for which to obtain the distinct values. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Interpretation UUIDs up to a - maximum of 100. - :param str clinical_analysis_id: Clinical Analysis id. - :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. - :param str panels: Interpretation panels. - :param str primary_findings: Interpretation primary findings. - :param str secondary_findings: Interpretation secondary findings. - :param str creation_date: Interpretation Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Interpretation Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param str release: Release when it was created. - """ - - options['field'] = field - return self._get(category='analysis', resource='distinct', subcategory='clinical/interpretation', **options) - - def search_interpretation(self, **options): - """ - Search clinical interpretations. - PATH: /{apiVersion}/analysis/clinical/interpretation/search - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool sort: Sort the results. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Interpretation UUIDs up to a - maximum of 100. - :param str clinical_analysis_id: Clinical Analysis id. - :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. - :param str panels: Interpretation panels. - :param str primary_findings: Interpretation primary findings. - :param str secondary_findings: Interpretation secondary findings. - :param str creation_date: Interpretation Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Interpretation Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param str release: Release when it was created. - """ - - return self._get(category='analysis', resource='search', subcategory='clinical/interpretation', **options) - - def info_interpretation(self, interpretations, **options): - """ - Clinical interpretation information. - PATH: /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info - - :param str interpretations: Comma separated list of clinical - interpretation IDs up to a maximum of 100. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str version: Comma separated list of interpretation versions. - 'all' to get all the interpretation versions. Not supported if - multiple interpretation ids are provided. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - return self._get(category='analysis', resource='info', subcategory='clinical/interpretation', second_query_id=interpretations, **options) - - def run_interpreter_cancer_tiering(self, data=None, **options): - """ - Run cancer tiering interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run - - :param dict data: Cancer tiering interpretation analysis params. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/cancerTiering', data=data, **options) - - def run_interpreter_exomiser(self, data=None, **options): - """ - Run exomiser interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/exomiser/run - - :param dict data: Exomizer interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options) - - def run_interpreter_team(self, data=None, **options): - """ - Run TEAM interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/team/run - - :param dict data: TEAM interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/team', data=data, **options) - - def run_interpreter_tiering(self, data=None, **options): - """ - Run tiering interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/tiering/run - - :param dict data: Tiering interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/tiering', data=data, **options) - - def run_interpreter_zetta(self, data=None, **options): - """ - Run Zetta interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/zetta/run - - :param dict data: Zetta interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/zetta', data=data, **options) - - def aggregation_stats_rga(self, field, **options): - """ - RGA aggregation stats. - PATH: /{apiVersion}/analysis/clinical/rga/aggregationStats - - :param str field: List of fields separated by semicolons, e.g.: - clinicalSignificances;type. For nested fields use >>, e.g.: - type>>clinicalSignificances;knockoutType. (REQUIRED) - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - options['field'] = field - return self._get(category='analysis', resource='aggregationStats', subcategory='clinical/rga', **options) - - def query_rga_gene(self, **options): - """ - Query gene RGA. - PATH: /{apiVersion}/analysis/clinical/rga/gene/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str include_individual: Include only the comma separated list - of individuals to the response. - :param int skip_individual: Number of individuals to skip. - :param int limit_individual: Limit number of individuals returned - (default: 1000). - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/rga/gene', **options) - - def summary_rga_gene(self, **options): - """ - RGA gene summary stats. - PATH: /{apiVersion}/analysis/clinical/rga/gene/summary - - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='summary', subcategory='clinical/rga/gene', **options) - - def run_rga_index(self, data=None, **options): - """ - Generate Recessive Gene Analysis secondary index. - PATH: /{apiVersion}/analysis/clinical/rga/index/run - - :param dict data: Recessive Gene Analysis index params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - :param bool auxiliar_index: Index auxiliar collection to improve - performance assuming RGA is completely indexed. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/rga/index', data=data, **options) - - def query_rga_individual(self, **options): - """ - Query individual RGA. - PATH: /{apiVersion}/analysis/clinical/rga/individual/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/rga/individual', **options) - - def summary_rga_individual(self, **options): - """ - RGA individual summary stats. - PATH: /{apiVersion}/analysis/clinical/rga/individual/summary - - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='summary', subcategory='clinical/rga/individual', **options) - - def query_rga_variant(self, **options): - """ - Query variant RGA. - PATH: /{apiVersion}/analysis/clinical/rga/variant/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str include_individual: Include only the comma separated list - of individuals to the response. - :param int skip_individual: Number of individuals to skip. - :param int limit_individual: Limit number of individuals returned - (default: 1000). - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/rga/variant', **options) - - def summary_rga_variant(self, **options): - """ - RGA variant summary stats. - PATH: /{apiVersion}/analysis/clinical/rga/variant/summary - - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='summary', subcategory='clinical/rga/variant', **options) - - def search(self, **options): - """ - Clinical analysis search. - PATH: /{apiVersion}/analysis/clinical/search - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Clinical Analysis UUIDs up to - a maximum of 100. - :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. - :param str files: Clinical Analysis files. - :param str sample: Sample associated to the proband or any member of a - family. - :param str individual: Proband or any member of a family. - :param str proband: Clinical Analysis proband. - :param str proband_samples: Clinical Analysis proband samples. - :param str family: Clinical Analysis family. - :param str family_members: Clinical Analysis family members. - :param str family_member_samples: Clinical Analysis family members - samples. - :param str panels: Clinical Analysis panels. - :param bool locked: Locked Clinical Analyses. - :param str analyst_id: Clinical Analysis analyst id. - :param str priority: Clinical Analysis priority. - :param str flags: Clinical Analysis flags. - :param str creation_date: Clinical Analysis Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Clinical Analysis Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str due_date: Clinical Analysis due date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str quality_control_summary: Clinical Analysis quality control - summary. - :param str release: Release when it was created. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - return self._get(category='analysis', resource='search', subcategory='clinical', **options) - - def actionable_variant(self, **options): - """ - Fetch actionable clinical variants. - PATH: /{apiVersion}/analysis/clinical/variant/actionable - - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str sample: Sample ID. - """ - - return self._get(category='analysis', resource='actionable', subcategory='clinical/variant', **options) - - def query_variant(self, **options): - """ - Fetch clinical variants. - PATH: /{apiVersion}/analysis/clinical/variant/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param bool approximate_count: Get an approximate count, instead of an - exact total count. Reduces execution time. - :param int approximate_count_sampling_size: Sampling size to get the - approximate count. Larger values increase accuracy but also - increase execution time. - :param str saved_filter: Use a saved filter at User level. - :param str id: List of IDs, these can be rs IDs (dbSNP) or variants in - the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T. - :param str region: List of regions, these can be just a single - chromosome name or regions in the format chr:start-end, e.g.: - 2,3:100000-200000. - :param str type: List of types, accepted values are SNV, MNV, INDEL, - SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION, - DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. - SNV,INDEL. - :param str study: Filter variants from the given studies, these can be - either the numeric ID or the alias with the format - user@project:study. - :param str file: Filter variants from the files specified. This will - set includeFile parameter when not provided. - :param str filter: Specify the FILTER for any of the files. If 'file' - filter is provided, will match the file and the filter. e.g.: - PASS,LowGQX. - :param str qual: Specify the QUAL for any of the files. If 'file' - filter is provided, will match the file and the qual. e.g.: >123.4. - :param str file_data: Filter by file data (i.e. FILTER, QUAL and INFO - columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file - is specified, will use all files from 'file' filter. e.g. AN>200 or - file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. - e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - :param str sample: Filter variants by sample genotype. This will - automatically set 'includeSample' parameter when not provided. This - filter accepts multiple 3 forms: 1) List of samples: Samples that - contain the main variant. Accepts AND (;) and OR (,) operators. - e.g. HG0097,HG0098 . 2) List of samples with genotypes: - {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. - HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will - also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice - versa. When filtering by multi-allelic genotypes, any secondary - allele will match, regardless of its position e.g. 1/2 will match - with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: - HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. - HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation - mode: {sample}:{segregation}. Only one sample accepted.Accepted - segregation modes: [ autosomalDominant, autosomalRecessive, - XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. Value is case insensitive. - e.g. HG0097:DeNovo Sample must have parents defined and indexed. . - :param str sample_data: Filter by any SampleData field from samples. - [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will - use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or - HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined. - e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. - :param str sample_annotation: Selects some samples using metadata - information from Catalog. e.g. - age>20;phenotype=hpo:123,hpo:456;name=smith. - :param str cohort: Select variants with calculated stats for the - selected cohorts. - :param str cohort_stats_ref: Reference Allele Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_alt: Alternate Allele Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_maf: Minor Allele Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_mgf: Minor Genotype Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_pass: Filter PASS frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8. - :param str missing_alleles: Number of missing alleles: - [{study:}]{cohort}[<|>|<=|>=]{number}. - :param str missing_genotypes: Number of missing genotypes: - [{study:}]{cohort}[<|>|<=|>=]{number}. - :param str score: Filter by variant score: - [{study:}]{score}[<|>|<=|>=]{number}. - :param str family: Filter variants where any of the samples from the - given family contains the variant (HET or HOM_ALT). - :param str family_disorder: Specify the disorder to use for the family - segregation. - :param str family_segregation: Filter by segregation mode from a given - family. Accepted values: [ autosomalDominant, autosomalRecessive, - XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. - :param str family_members: Sub set of the members of a given family. - :param str family_proband: Specify the proband child to use for the - family segregation. - :param str gene: List of genes, most gene IDs are accepted (HGNC, - Ensembl gene, ...). This is an alias to 'xref' parameter. - :param str ct: List of SO consequence types, e.g. - missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts - aliases 'loss_of_function' and 'protein_altering'. - :param str xref: List of any external reference, these can be genes, - proteins or variants. Accepted IDs include HGNC, Ensembl genes, - dbSNP, ClinVar, HPO, Cosmic, ... - :param str biotype: List of biotypes, e.g. protein_coding. - :param str protein_substitution: Protein substitution scores include - SIFT and PolyPhen. You can query using the score - {protein_score}[<|>|<=|>=]{number} or the description - {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. - :param str conservation: Filter by conservation score: - {conservation_score}[<|>|<=|>=]{number} e.g. - phastCons>0.5,phylop<0.1,gerp>0.1. - :param str population_frequency_alt: Alternate Population Frequency: - {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - :param str population_frequency_ref: Reference Population Frequency: - {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - :param str population_frequency_maf: Population minor allele - frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - 1000G:ALL<0.01. - :param str transcript_flag: List of transcript flags. e.g. canonical, - CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc, - TSO500. - :param str gene_trait_id: List of gene trait association id. e.g. - 'umls:C0007222' , 'OMIM:269600'. - :param str go: List of GO (Gene Ontology) terms. e.g. 'GO:0002020'. - :param str expression: List of tissues of interest. e.g. 'lung'. - :param str protein_keyword: List of Uniprot protein variant annotation - keywords. - :param str drug: List of drug names. - :param str functional_score: Functional score: - {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , - cadd_raw<=0.3. - :param str clinical: Clinical source: clinvar, cosmic. - :param str clinical_significance: Clinical significance: benign, - likely_benign, likely_pathogenic, pathogenic. - :param bool clinical_confirmed_status: Clinical confirmed status. - :param str custom_annotation: Custom annotation: - {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}. - :param str panel: Filter by genes from the given disease panel. - :param str panel_mode_of_inheritance: Filter genes from specific - panels that match certain mode of inheritance. Accepted values : [ - autosomalDominant, autosomalRecessive, XLinkedDominant, - XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - compoundHeterozygous ]. - :param str panel_confidence: Filter genes from specific panels that - match certain confidence. Accepted values : [ high, medium, low, - rejected ]. - :param str panel_role_in_cancer: Filter genes from specific panels - that match certain role in cancer. Accepted values : [ both, - oncogene, tumorSuppressorGene, fusion ]. - :param str panel_feature_type: Filter elements from specific panels by - type. Accepted values : [ gene, region, str, variant ]. - :param bool panel_intersection: Intersect panel genes and regions with - given genes and regions from que input query. This will prevent - returning variants from regions out of the panel. - :param str trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.: - IDs, histologies, descriptions,... - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/variant', **options) - - def acl(self, clinical_analyses, **options): - """ - Returns the acl of the clinical analyses. If member is provided, it - will only return the acl for the member. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl - - :param str clinical_analyses: Comma separated list of clinical - analysis IDs or names up to a maximum of 100. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str member: User or group ID. - :param bool silent: Boolean to retrieve all possible entries that are - queried for, false to raise an exception whenever one of the - entries looked for cannot be shown for whichever reason. - """ - - return self._get(category='analysis', resource='acl', subcategory='clinical', second_query_id=clinical_analyses, **options) - - def delete(self, clinical_analyses, **options): - """ - Delete clinical analyses. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete - - :param str clinical_analyses: Comma separated list of clinical - analysis IDs or names up to a maximum of 100. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool force: Force deletion if the ClinicalAnalysis contains - interpretations or is locked. - """ - - return self._delete(category='analysis', resource='delete', subcategory='clinical', second_query_id=clinical_analyses, **options) - - def update(self, clinical_analyses, data=None, **options): - """ - Update clinical analysis attributes. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update - - :param dict data: JSON containing clinical analysis information. - (REQUIRED) - :param str clinical_analyses: Comma separated list of clinical - analysis IDs. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str comments_action: Action to be performed if the array of - comments is being updated. Allowed values: ['ADD', 'REMOVE', - 'REPLACE'] - :param str flags_action: Action to be performed if the array of flags - is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str files_action: Action to be performed if the array of files - is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str panels_action: Action to be performed if the array of - panels is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis', resource='update', subcategory='clinical', second_query_id=clinical_analyses, data=data, **options) - - def info(self, clinical_analysis, **options): - """ - Clinical analysis info. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info - - :param str clinical_analysis: Comma separated list of clinical - analysis IDs or names up to a maximum of 100. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - return self._get(category='analysis', resource='info', subcategory='clinical', second_query_id=clinical_analysis, **options) - - def create_interpretation(self, clinical_analysis, data=None, **options): - """ - Create a new Interpretation. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create - - :param dict data: JSON containing clinical interpretation information. - (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: [[user@]project:]study id. - :param str set_as: Set interpretation as. Allowed values: ['PRIMARY', - 'SECONDARY'] - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis/clinical', resource='create', query_id=clinical_analysis, subcategory='interpretation', data=data, **options) - - def clear_interpretation(self, clinical_analysis, interpretations, **options): - """ - Clear the fields of the main interpretation of the Clinical Analysis. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear - - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str interpretations: Interpretation IDs of the Clinical - Analysis. (REQUIRED) - :param str study: [[user@]project:]study ID. - """ - - return self._post(category='analysis/clinical', resource='clear', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretations, **options) - - def delete_interpretation(self, clinical_analysis, interpretations, **options): - """ - Delete interpretation. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete - - :param str interpretations: Interpretation IDs of the Clinical - Analysis. (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str study: [[user@]project:]study ID. - :param str set_as_primary: Interpretation id to set as primary from - the list of secondaries in case of deleting the actual primary one. - """ - - return self._delete(category='analysis/clinical', resource='delete', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretations, **options) - - def revert_interpretation(self, clinical_analysis, interpretation, version, **options): - """ - Revert to a previous interpretation version. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert - - :param int version: Version to revert to. (REQUIRED) - :param str interpretation: Interpretation ID. (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str study: [[user@]project:]study ID. - """ - - options['version'] = version - return self._post(category='analysis/clinical', resource='revert', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, **options) - - def update_interpretation(self, clinical_analysis, interpretation, data=None, **options): - """ - Update interpretation fields. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update - - :param dict data: JSON containing clinical interpretation information. - (REQUIRED) - :param str interpretation: Interpretation ID. (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: [[user@]project:]study ID. - :param str primary_findings_action: Action to be performed if the - array of primary findings is being updated. Allowed values: ['ADD', - 'SET', 'REMOVE', 'REPLACE'] - :param str methods_action: Action to be performed if the array of - methods is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str secondary_findings_action: Action to be performed if the - array of secondary findings is being updated. Allowed values: - ['ADD', 'SET', 'REMOVE', 'REPLACE'] - :param str comments_action: Action to be performed if the array of - comments is being updated. To REMOVE or REPLACE, the date will need - to be provided to identify the comment. Allowed values: ['ADD', - 'REMOVE', 'REPLACE'] - :param str panels_action: Action to be performed if the array of - panels is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str set_as: Set interpretation as. Allowed values: ['PRIMARY', - 'SECONDARY'] - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis/clinical', resource='update', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, data=data, **options) - diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 5772cf02ee5..f38109debed 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/cohorts """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 0688b1f4c07..dff08d5a0f8 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/panels """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index e13a27bddf0..278c306bfe6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/families """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 0d9c9655f4b..f922f15b910 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/files """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index c7e9bb9efeb..2b850d3c6fb 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/ga4gh """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index a3c184edacd..515ca12ca0b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/individuals """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 22d31ddfacd..459007a179f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/jobs """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 130fa0aa824..39c13a7bcb7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/meta """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py index 681e988c54d..a3124bfcf45 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Organization(_ParentRestClient): """ This class contains methods for the 'Organizations' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/organizations """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 28bf4f3e914..dd650ac0f26 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/projects """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 8f6753319e5..6b10aac717f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/samples """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index b6f496bf061..57826554192 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/studies """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 6bc479ff5f0..93451319d3d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/users """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index db47d5553a7..e1d63675309 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/analysis/variant """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index ffaa0dbb2e4..e726e9dd2db 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 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. @@ -14,7 +13,6 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/operation """ diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..6863e08197c 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -392,7 +392,9 @@ CodeGen - false + + !skipCodeGen + diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java index b9082449a32..f94a917e20f 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java @@ -54,14 +54,18 @@ private void generateLibrary(String clientsGeneratorDir, String language, String System.out.println("outDir " + outDir); String binary = clientsGeneratorDir + "/" + language + "_client_generator.py"; ProcessBuilder processBuilder = new ProcessBuilder("python3", binary, restFilePath, outDir); + System.out.println("python3 " + binary + " " + restFilePath + " " + outDir); Process p; try { p = processBuilder.start(); BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream())); + BufferedReader error = new BufferedReader(new InputStreamReader(p.getErrorStream())); String line; while ((line = input.readLine()) != null) { logger.info("{} library generator: {}", language, line); - System.out.println(language + " library generator: " + line); + } + while ((line = error.readLine()) != null) { + logger.error("{} library generator: {}", language, line); } p.waitFor(); input.close(); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java index d4f85542ddf..1d58459b343 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java @@ -25,8 +25,6 @@ import java.io.File; import java.io.IOException; -import java.text.SimpleDateFormat; -import java.util.Date; public class AutoCompleteWriter extends ParentClientRestApiWriter { @@ -37,23 +35,6 @@ public AutoCompleteWriter(RestApi restApi, CommandLineConfiguration config) { @Override protected String getClassImports(String key) { StringBuilder sb = new StringBuilder(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - sb.append("/*\n"); - sb.append("* Copyright 2015-").append(sdf.format(new Date())).append(" OpenCB\n"); - sb.append("*\n"); - sb.append("* Licensed under the Apache License, Version 2.0 (the \"License\");\n"); - sb.append("* you may not use this file except in compliance with the License.\n"); - sb.append("* You may obtain a copy of the License at\n"); - sb.append("*\n"); - sb.append("* http://www.apache.org/licenses/LICENSE-2.0\n"); - sb.append("*\n"); - sb.append("* Unless required by applicable law or agreed to in writing, software\n"); - sb.append("* distributed under the License is distributed on an \"AS IS\" BASIS,\n"); - sb.append("* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n"); - sb.append("* See the License for the specific language governing permissions and\n"); - sb.append("* limitations under the License.\n"); - sb.append("*/\n"); - sb.append("\n"); sb.append("package ").append(config.getOptions().getParserPackage()).append(";\n"); sb.append("\n"); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java index bfa784319b7..90b8977decc 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java @@ -28,7 +28,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.text.SimpleDateFormat; import java.util.HashSet; import java.util.Set; @@ -45,7 +44,6 @@ protected String getClassImports(String key) { StringBuilder sb = new StringBuilder(); RestCategory restCategory = availableCategories.get(key); CategoryConfig categoryConfig = availableCategoryConfigs.get(key); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); sb.append("package ").append(config.getOptions().getOptionsPackage()).append(";\n\n"); sb.append("import com.beust.jcommander.JCommander;\n"); sb.append("import com.beust.jcommander.Parameter;\n"); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java index 121166bd9d2..669a5151c61 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java @@ -27,8 +27,6 @@ import java.io.File; import java.io.IOException; -import java.text.SimpleDateFormat; -import java.util.Date; public class ParserCliRestApiWriter extends ParentClientRestApiWriter { @@ -39,23 +37,6 @@ public ParserCliRestApiWriter(RestApi restApi, CommandLineConfiguration config) @Override protected String getClassImports(String key) { StringBuilder sb = new StringBuilder(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - sb.append("/*\n"); - sb.append("* Copyright 2015-").append(sdf.format(new Date())).append(" OpenCB\n"); - sb.append("*\n"); - sb.append("* Licensed under the Apache License, Version 2.0 (the \"License\");\n"); - sb.append("* you may not use this file except in compliance with the License.\n"); - sb.append("* You may obtain a copy of the License at\n"); - sb.append("*\n"); - sb.append("* http://www.apache.org/licenses/LICENSE-2.0\n"); - sb.append("*\n"); - sb.append("* Unless required by applicable law or agreed to in writing, software\n"); - sb.append("* distributed under the License is distributed on an \"AS IS\" BASIS,\n"); - sb.append("* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n"); - sb.append("* See the License for the specific language governing permissions and\n"); - sb.append("* limitations under the License.\n"); - sb.append("*/\n"); - sb.append("\n"); sb.append("package ").append(config.getOptions().getParserPackage()).append(";\n"); sb.append("\n"); diff --git a/pom.xml b/pom.xml index b187199de8b..634283dace0 100644 --- a/pom.xml +++ b/pom.xml @@ -43,6 +43,7 @@ + 3.2.0_dev 3.2.0_dev 6.2.0-SNAPSHOT