Source Code and Module Documentation (deriva package)
Subpackages
- deriva.config package
- Submodules
- deriva.config.acl_config module
ACLSpecACLSpecListAclCLIAclConfigAclConfig.ACL_TYPESAclConfig.GC_NAMEAclConfig.GLOBUS_PREFIXAclConfig.NC_NAMEAclConfig.ROBOT_PREFIX_FORMATAclConfig.add_node_acl()AclConfig.add_node_acl_binding()AclConfig.apply_acls()AclConfig.create_or_validate_group_table()AclConfig.create_or_validate_schema()AclConfig.create_table()AclConfig.dumps()AclConfig.expand_acl_binding()AclConfig.expand_acl_definition()AclConfig.expand_acl_definitions()AclConfig.expand_group()AclConfig.expand_groups()AclConfig.expand_projection()AclConfig.expand_projection_column()AclConfig.get_group()AclConfig.make_speclist()AclConfig.save_groups()AclConfig.set_acls()AclConfig.set_catalog_acls()AclConfig.set_column_acls()AclConfig.set_fkey_acls()AclConfig.set_node_acl()AclConfig.set_node_acl_bindings()AclConfig.set_schema_acls()AclConfig.set_table_acls()AclConfig.validate_globus_group()AclConfig.validate_group()AclConfig.validate_webauthn_robot()
NoForeignKeyErrorTablemain()
- deriva.config.annotation_config module
AttrConfigAttrConfig.apply_annotations()AttrConfig.find_best_column_specs()AttrConfig.find_best_fkey_specs()AttrConfig.find_best_schema_specs()AttrConfig.find_best_table_specs()AttrConfig.find_corresponding_fkey()AttrConfig.find_named_column()AttrConfig.find_named_schema()AttrConfig.find_named_table()AttrConfig.make_speclist()AttrConfig.node_name()AttrConfig.set_attributes()AttrConfig.set_catalog_annotations()AttrConfig.set_column_annotations()AttrConfig.set_fkey_annotations()AttrConfig.set_node_annotations()AttrConfig.set_schema_annotations()AttrConfig.set_table_annotations()
AttrSpecAttrSpecListNoForeignKeyErrormain()
- deriva.config.base_config module
BaseSpecBaseSpec.ATTRIBUTE_TYPESBaseSpec.column_entry_matches()BaseSpec.config_format()BaseSpec.foreign_key_entry_matches()BaseSpec.get_pattern()BaseSpec.has_node_key()BaseSpec.is_exact_spec()BaseSpec.is_node_spec()BaseSpec.make_pat_name()BaseSpec.matches()BaseSpec.schema_entry_matches()BaseSpec.set_keys()BaseSpec.table_entry_matches()BaseSpec.validate()BaseSpec.validate_node_types()
BaseSpecListBaseSpecList.add_list()BaseSpecList.add_spec()BaseSpecList.find_best_column_spec()BaseSpecList.find_best_foreign_key_name_spec()BaseSpecList.find_best_foreign_key_spec()BaseSpecList.find_best_schema_spec()BaseSpecList.find_best_single_foreign_key_spec()BaseSpecList.find_best_table_spec()BaseSpecList.find_catalog_spec()BaseSpecList.get_specs()
ConfigBaseCLIConfigUtil
- deriva.config.dump_catalog_annotations module
AnnotationsAnnotations.add_catalog_annotations()Annotations.add_column_annotations()Annotations.add_foreign_key_annotations()Annotations.add_schema_annotations()Annotations.add_table_annotations()Annotations.check_consolidation()Annotations.consolidated_column_annotation()Annotations.consolidated_foreign_key_annotation()Annotations.consolidated_schema_annotation()Annotations.consolidated_table_annotation()Annotations.dumps()Annotations.find_relevant_annotations()Annotations.munge_specs()Annotations.types_list()
main()
- Module contents
- deriva.core package
- Subpackages
- deriva.core.utils package
- Submodules
- deriva.core.utils.core_utils module
AttrDictConcurrentUpdateNotModifiedTimeoutHTTPAdapteradd_logging_level()bootstrap()calculate_optimal_transfer_shape()copy_config()format_credential()format_exception()get_new_requests_session()get_oauth_scopes_for_host()get_transfer_summary()init_logging()json_item_handler()load_cookies_from_file()lock_file()make_dirs()read_config()read_credential()resource_path()stob()topo_sorted()urlquote()urlquote_dcctx()write_config()write_credential()
- deriva.core.utils.hash_utils module
- deriva.core.utils.mime_utils module
- deriva.core.utils.version_utils module
- deriva.core.utils.webauthn_utils module
- Module contents
- deriva.core.utils package
- Submodules
- deriva.core.annotation module
- deriva.core.base_cli module
- deriva.core.datapath module
- deriva.core.deriva_binding module
- deriva.core.deriva_server module
- deriva.core.ermrest_catalog module
DerivaServerErmrestAliasErmrestCatalogErmrestCatalog.alias_targetErmrestCatalog.catalog_idErmrestCatalog.clone_catalog()ErmrestCatalog.connect()ErmrestCatalog.create()ErmrestCatalog.delete()ErmrestCatalog.delete_ermrest_catalog()ErmrestCatalog.deriva_serverErmrestCatalog.exists()ErmrestCatalog.getAsFile()ErmrestCatalog.getCatalogModel()ErmrestCatalog.getCatalogSchema()ErmrestCatalog.getDefaultColumns()ErmrestCatalog.getPathBuilder()ErmrestCatalog.getTableColumns()ErmrestCatalog.getTableSchema()ErmrestCatalog.get_as_file()ErmrestCatalog.latest_snapshot()ErmrestCatalog.resolve_rid()ErmrestCatalog.splitQualifiedCatalogName()ErmrestCatalog.table_schemasErmrestCatalog.validateRowColumns()
ErmrestCatalogMutationErrorErmrestSnapshotResolveRidResult
- deriva.core.ermrest_config module
- deriva.core.ermrest_model module
ArrayTypeColumnDomainTypeFindAssociationResultForeignKeyForeignKey.alter()ForeignKey.apply()ForeignKey.catalogForeignKey.clear()ForeignKey.column_mapForeignKey.columnsForeignKey.define()ForeignKey.digest_referenced_columns()ForeignKey.drop()ForeignKey.foreign_keyForeignKey.nameForeignKey.name_in_model()ForeignKey.namesForeignKey.prejson()ForeignKey.uri_path
KeyKeyedListModelModel.apply()Model.bulk_uploadModel.catalogModel.chaise_configModel.clear()Model.column()Model.column_defaultsModel.configure_baseline_catalog()Model.configure_baseline_ermrest_client()Model.configure_baseline_ermrest_group()Model.create_schema()Model.digest_fkeys()Model.displayModel.export_2019Model.export_fragment_definitionsModel.fkey()Model.fromcatalog()Model.fromfile()Model.generatedModel.immutableModel.non_deletableModel.prejson()Model.table()Model.uri_path
NoChangeQuantifierSchemaSchema.alter()Schema.apply()Schema.catalogSchema.clear()Schema.column_defaultsSchema.create_table()Schema.define()Schema.define_www()Schema.displaySchema.drop()Schema.export_2019Schema.export_fragment_definitionsSchema.generatedSchema.immutableSchema.non_deletableSchema.prejson()Schema.uri_path
TableTable.alter()Table.alternativesTable.apply()Table.catalogTable.citationTable.clear()Table.column_defaultsTable.columnsTable.create_column()Table.create_fkey()Table.create_key()Table.create_reference()Table.default_key_column_search_orderTable.define()Table.define_asset()Table.define_association()Table.define_page()Table.define_vocabulary()Table.displayTable.drop()Table.export_2019Table.export_fragment_definitionsTable.find_associations()Table.fkey_by_column_map()Table.fkeys_by_columns()Table.generatedTable.google_datasetTable.immutableTable.indexing_preferencesTable.is_association()Table.key_by_columns()Table.non_deletableTable.prejson()Table.source_definitionsTable.sqlite3_ddl()Table.sqlite3_table_name()Table.system_column_defs()Table.system_fkey_defs()Table.system_key_defs()Table.table_displayTable.uri_pathTable.visible_columnsTable.visible_foreign_keysTable.viz_3d_display
TypeUpdateMappingsequivalent()find_tables_with_foreign_keys()make_id()make_type()object_annotation()presence_annotation()sql_identifier()sql_literal()strip_nochange()
- deriva.core.hatrac_cli module
- deriva.core.hatrac_store module
HatracHashMismatchHatracJobAbortedHatracJobPausedHatracJobTimeoutHatracStoreHatracStore.cancel_upload_job()HatracStore.content_equals()HatracStore.create_namespace()HatracStore.create_upload_job()HatracStore.del_acl()HatracStore.del_obj()HatracStore.delete_namespace()HatracStore.finalize_upload_job()HatracStore.get_acl()HatracStore.get_obj()HatracStore.get_upload_job()HatracStore.is_valid_namespace()HatracStore.put_loc()HatracStore.put_obj()HatracStore.put_obj_chunked()HatracStore.retrieve_namespace()HatracStore.set_acl()
- deriva.core.polling_ermrest_catalog module
- Module contents
- Subpackages
- deriva.transfer package
- Subpackages
- deriva.transfer.download package
- Subpackages
- deriva.transfer.download.processors package
- Subpackages
- deriva.transfer.download.processors.postprocess package
- Submodules
- deriva.transfer.download.processors.postprocess.identifier_post_processor module
FAIRIdentifierPostProcessorFAIRIdentifierPostProcessor.IDENTIFIER_NAMESPACEFAIRIdentifierPostProcessor.IDENTIFIER_SERVICEFAIRIdentifierPostProcessor.IDENTIFIER_SERVICE_TESTFAIRIdentifierPostProcessor.IDENTIFIER_SERVICE_WRITER_SCOPEFAIRIdentifierPostProcessor.TEST_IDENTIFIER_NAMESPACEFAIRIdentifierPostProcessor.load_identifier_client()FAIRIdentifierPostProcessor.process()
- deriva.transfer.download.processors.postprocess.transfer_post_processor module
- deriva.transfer.download.processors.postprocess.workspace_post_processor module
- Module contents
- deriva.transfer.download.processors.query package
- Submodules
- deriva.transfer.download.processors.query.bag_fetch_query_processor module
- deriva.transfer.download.processors.query.base_query_processor module
- deriva.transfer.download.processors.query.file_download_query_processor module
- Module contents
- deriva.transfer.download.processors.transform package
- deriva.transfer.download.processors.postprocess package
- Submodules
- deriva.transfer.download.processors.base_processor module
- Module contents
- Subpackages
- deriva.transfer.download.processors package
- Submodules
- deriva.transfer.download.deriva_download module
- deriva.transfer.download.deriva_download_cli module
- Module contents
- Subpackages
- deriva.transfer.upload package
- Submodules
- deriva.transfer.upload.deriva_upload module
DerivaUploadDerivaUpload.DefaultConfigFileNameDerivaUpload.DefaultServerListFileNameDerivaUpload.DefaultTransferStateBaseNameDerivaUpload.DefaultTransferStateFileNameDerivaUpload.acquire_dependent_locks()DerivaUpload.archive_preprocessing_enabled()DerivaUpload.cancel()DerivaUpload.cleanup()DerivaUpload.cleanupTransferState()DerivaUpload.defaultFileCallback()DerivaUpload.delTransferState()DerivaUpload.delete_dependent_locks()DerivaUpload.find_file_in_dir_hierarchy()DerivaUpload.getAssetMapping()DerivaUpload.getCatalogTable()DerivaUpload.getConfigPath()DerivaUpload.getCurrentConfigFilePath()DerivaUpload.getDefaultConfigFilePath()DerivaUpload.getDefaultServer()DerivaUpload.getDeployedConfigFilePath()DerivaUpload.getDeployedConfigPath()DerivaUpload.getFileDisplayName()DerivaUpload.getFileHashes()DerivaUpload.getFileSize()DerivaUpload.getFileStatusAsArray()DerivaUpload.getRemoteConfig()DerivaUpload.getServers()DerivaUpload.getTransferState()DerivaUpload.getTransferStateFileName()DerivaUpload.getTransferStateStatus()DerivaUpload.getUpdatedConfig()DerivaUpload.getVersion()DerivaUpload.getVersionCompatibility()DerivaUpload.guessContentType()DerivaUpload.initialize()DerivaUpload.interpolateDict()DerivaUpload.interrupt_handler()DerivaUpload.isFileNewer()DerivaUpload.isVersionCompatible()DerivaUpload.loadTransferState()DerivaUpload.pruneDict()DerivaUpload.reset()DerivaUpload.scanDirectory()DerivaUpload.setConfig()DerivaUpload.setCredentials()DerivaUpload.setServer()DerivaUpload.setTransferState()DerivaUpload.set_dcctx_cid()DerivaUpload.uploadFile()DerivaUpload.uploadFiles()DerivaUpload.validateFile()DerivaUpload.writeTransferState()
EnumFileUploadStateGenericUploaderUploadEntry
- deriva.transfer.upload.deriva_upload_cli module
- Module contents
- deriva.transfer.backup package
- deriva.transfer.restore package
- Submodules
- deriva.transfer.restore.deriva_restore module
DerivaRestoreDerivaRestore.BASE_ASSETS_INPUT_PATHDerivaRestore.BASE_DATA_INPUT_PATHDerivaRestore.RESTORE_STATE_URLDerivaRestore.check_column_compatibility()DerivaRestore.cleanup_restored_catalog()DerivaRestore.copy_cdef()DerivaRestore.copy_kdef()DerivaRestore.copy_sdef()DerivaRestore.copy_tdef_core()DerivaRestore.copy_tdef_fkeys()DerivaRestore.get_json_recordset()DerivaRestore.get_table_path()DerivaRestore.load_json_file()DerivaRestore.open_json_stream_file()DerivaRestore.prune_parts()DerivaRestore.restore()DerivaRestore.set_config()DerivaRestore.set_credentials()DerivaRestore.upload_assets()
- deriva.transfer.restore.deriva_restore_cli module
- Module contents
- deriva.transfer.download package
- Module contents
- Subpackages
- deriva.seo package