Index

_

__author__ (in module wfexs_backend) __copyright__ (in module wfexs_backend) __download_file_async() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) __enter__() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) __exit__() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) __fetch_schema() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher static method) __gen_sword_dataset_url() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) __get_combined_globals() (wfexs_backend.workflow.WF method) __get_engine_version_str_local() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) __get_sword_opener() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) __instance (wfexs_backend.utils.licences.LicenceMatcherSingleton attribute) (wfexs_backend.utils.passphrase_wrapper.WfExSPassGenSingleton attribute) __license__ (in module wfexs_backend) __list_entity_parts() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __list_payload_entity_parts() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __merge_params_from_file() (wfexs_backend.workflow.WF class method) __missing__() (wfexs_backend.workflow.DefaultMissing method) __new__() (wfexs_backend.common.StrDocEnum method) (wfexs_backend.utils.licences.LicenceMatcherSingleton method) (wfexs_backend.utils.passphrase_wrapper.WfExSPassGenSingleton method) (wfexs_backend.utils.zipfile_path.ZipfilePath method) __official_name__ (in module wfexs_backend) __parseContainersResults() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __parseEnvResults() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __parseInputsResults() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __parseOutputsResults() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __PatchOps() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher class method) __processPayloadEntity() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __processPayloadInput() (wfexs_backend.utils.rocrate.ROCrateToolbox method) __read_yaml_config() (wfexs_backend.workflow.WF static method) __repr (wfexs_backend.utils.zipfile_path.ZipfilePath attribute) __repr__() (wfexs_backend.common.MarshallingStatus method) (wfexs_backend.utils.zipfile_path.ZipfilePath method) __str__() (wfexs_backend.common.ArgTypeMixin method) (wfexs_backend.common.StrDocEnum method) (wfexs_backend.utils.zipfile_path.ZipfilePath method) __truediv__ (wfexs_backend.utils.zipfile_path.ZipfilePath attribute) __update_meta() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher static method) __url__ (in module wfexs_backend) __version__ (in module wfexs_backend) _add_collection_to_crate() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_containers() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_directory_as_dataset() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_file_to_crate() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_GeneratedContent_to_crate() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_GeneratedDirectoryContent_as_dataset() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_wfexs_to_crate() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_workflow_execution_outputs() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _add_workflow_to_crate() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _ancestry() (in module wfexs_backend.utils.zipfile_path) _auth() (wfexs_backend.utils.docker.DockerHelper method) _book_pid_internal() (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) _buildLicensedURI() (wfexs_backend.workflow.WF method) _chunked_file_batch_uploader() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) _chunked_uploader() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) _compute_mime() (wfexs_backend.utils.io_wrappers.MIMETypeIOWrapper method) _computeCanonicalImagePath() (wfexs_backend.container_factories.ContainerCacheHandler method) _computeFingerprint() (wfexs_backend.container_factories.ContainerCacheHandler method) _create_draft_record() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _create_share_links() (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) _curate_orcid_list() (wfexs_backend.workflow.WF method) _current_field_header() (wfexs_backend.utils.io_wrappers.MultipartEncoderIOWrapper method) _customized_book_pid_error_string (wfexs_backend.pushers.AbstractExportPlugin property) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher property) (wfexs_backend.pushers.dataverse_export.DataversePublisher property) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin property) _dedupe (in module wfexs_backend.utils.zipfile_path) _difference() (in module wfexs_backend.utils.zipfile_path) _direct_upload_file_to_draft() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _doMaterializeGitRepo() (wfexs_backend.wfexs_backend.WfExSBackend method) _doMaterializeSoftwareHeritageDirOrContent() (wfexs_backend.wfexs_backend.WfExSBackend method) _download_dir_async() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) _download_file_async() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) _empty() (wfexs_backend.ro_crate.ContainerImage method) (wfexs_backend.ro_crate.SourceCodeFile method) (wfexs_backend.ro_crate.WorkflowDiagram method) _enrichFingerprint() (wfexs_backend.container_factories.docker_container.DockerContainerFactory method) _enrichWorkflowDeps() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) _export_metadata_raw() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _extract_member() (wfexs_backend.utils.zipfile_path.ZipfilePath method) _fake_readinto() (wfexs_backend.utils.io_wrappers.AbstractProxyIOWrapper method) _fetchContentWithURIs() (wfexs_backend.workflow.WF method) _fetchRemoteFile() (wfexs_backend.workflow.WF method) _find_git_repo_in_uri() (wfexs_backend.fetchers.git.GitFetcher class method) _form_upload_file_to_draft() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _formatInputURIFromPlaceHolders() (wfexs_backend.workflow.WF method) _formatStringFromPlaceHolders() (wfexs_backend.workflow.WF method) _gen_headers() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) _gen_trimmed_manifests_signature() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _genContainerPaths() (wfexs_backend.container_factories.ContainerCacheHandler method)

_genDockerTag() (wfexs_backend.container_factories.docker_container.DockerContainerFactory method) _genDockSingContainerTaggedName() (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) _genLicenceText() (wfexs_backend.pushers.dataverse_export.DataversePublisher static method) _genPodmanTag() (wfexs_backend.container_factories.podman_container.PodmanContainerFactory method) _genSingTag() (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) _genTmpContainerPath() (wfexs_backend.container_factories.ContainerCacheHandler method) _genUriMetaCachedFilename() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) _get_community_api_prefix() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_community_metadata() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_community_schema() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_dataverse_collection_url() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _get_engine_version_str() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) _get_entries_schema() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_query_params() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_record_prefix_from_record() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_records_prefix() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _get_wfexs_argparse_internal() (in module wfexs_backend.__main__) _getContainerArchitecture() (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) _getLicences() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _images() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _implied_dirs() (wfexs_backend.utils.zipfile_path.CompleteDirs static method) _init_empty_crate_and_ComputerLanguage() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _inject() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) _injectContent() (wfexs_backend.workflow.WF method) _inspect() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _instantiate_export_plugin() (wfexs_backend.workflow.WF method) _is_child() (wfexs_backend.utils.zipfile_path.ZipfilePath method) _key_fixes() (wfexs_backend.common.MaterializedContent class method) _LicenceMatcher (wfexs_backend.wfexs_backend.WfExSBackend attribute) _load() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _mapping_fixes() (wfexs_backend.common.AbstractGeneratedContent class method) (wfexs_backend.common.LocalWorkflow class method) (wfexs_backend.common.MaterializedContent class method) (wfexs_backend.workflow_engines.MaterializedWorkflowEngine class method) (wfexs_backend.workflow_engines.StagedExecution class method) _marshall() (wfexs_backend.common.ExpectedOutput method) _materialize_word_sets() (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator method) _materializeEngineVersionLocal() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) _materializeSingleContainerSing() (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) _mountEncFS() (in module wfexs_backend.encrypted_fs) _mountGoCryptFS() (in module wfexs_backend.encrypted_fs) _name_set() (wfexs_backend.utils.zipfile_path.CompleteDirs method) (wfexs_backend.utils.zipfile_path.FastLookup method) _next() (wfexs_backend.utils.zipfile_path.ZipfilePath method) _normalize_image_id() (in module wfexs_backend.workflow_engines.cwl_engine) _normalize_sif_id() (in module wfexs_backend.workflow_engines.cwl_engine) _parents() (in module wfexs_backend.utils.zipfile_path) _parse_hh_mm_ss_ff() (in module wfexs_backend.utils.misc) _parse_isoformat_date() (in module wfexs_backend.utils.misc) _parse_isoformat_time() (in module wfexs_backend.utils.misc) _parseContainersFromExecution() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseContainersFromWorkflow() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseEnvFromExecution() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseEnvFromMainEntity() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseInputsFromExecution() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseInputsFromMainEntity() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseMetaStructure() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) _parseOutputsFromExecution() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _parseOutputsFromMainEntity() (wfexs_backend.utils.rocrate.ROCrateToolbox method) _PassGen (wfexs_backend.wfexs_backend.WfExSBackend attribute) _prepare_properties() (wfexs_backend.ro_crate.ContainerImage static method) _prepare_upload_mappings() (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) _process_licence() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _process_licences() (wfexs_backend.ro_crate.WorkflowRunROCrate method) _pull() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) _reconnect() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) _recurse_m() (in module wfexs_backend.utils.marshalling_handling) _recurse_u() (in module wfexs_backend.utils.marshalling_handling) _resolve_swh_id() (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher class method) _rmi() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _save() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _set_fields() (wfexs_backend.utils.io_wrappers.MultipartEncoderIOWrapper method) _split_lines() (wfexs_backend.common.ArgsDefaultWithRawHelpFormatter method) _sword_book_entry() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _sword_book_revision() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _sword_get_collections() (wfexs_backend.pushers.dataverse_export.DataversePublisher method) _tag() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _transferInputs() (wfexs_backend.workflow.WF static method) _tzstring() (in module wfexs_backend.workflow_engines.nextflow_engine) _undeprecate_table() (wfexs_backend.fetchers.RepoType class method) _unmarshall() (wfexs_backend.common.ExpectedOutput class method) _unmarshallExecuteFH() (wfexs_backend.workflow.WF method) _unmarshallExportFH() (wfexs_backend.workflow.WF method) _validate_community_schema() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _validate_entry_schema() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) _value_defaults_fixes() (wfexs_backend.container_factories.Container method) _value_fixes() (wfexs_backend.workflow_engines.WorkflowType class method) _version() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory method) _wakeupEncDir() (in module wfexs_backend.workflow)

A

AbstractContextedExportPlugin (class in wfexs_backend.pushers.abstract_contexted_export) AbstractDockerContainerFactory (class in wfexs_backend.container_factories.abstract_docker_container) AbstractDraftedExportPlugin (class in wfexs_backend.pushers) AbstractExportPlugin (class in wfexs_backend.pushers) AbstractGeneratedContent (class in wfexs_backend.common) AbstractProxyIOWrapper (class in wfexs_backend.utils.io_wrappers) AbstractRepoFetcher (class in wfexs_backend.fetchers) AbstractStatefulFetcher (class in wfexs_backend.fetchers) AbstractStatefulStreamingFetcher (class in wfexs_backend.fetchers) AbstractTokenExportPlugin (class in wfexs_backend.pushers.abstract_token_export) AbstractTokenSandboxedExportPlugin (class in wfexs_backend.pushers.abstract_token_sandboxed_export) AbstractWfExSException AbstractWorkflowEngineType (class in wfexs_backend.workflow_engines) AcceptableLicenceSchemes (in module wfexs_backend.utils.licences) ACCEPTED_CONTAINER_TYPES (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory attribute) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory attribute) ACCEPTED_SING_SCHEMES (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory attribute) AcceptedContainerTypes (wfexs_backend.container_factories.no_container.NoContainerFactory attribute) AcceptsContainer() (wfexs_backend.container_factories.ContainerFactory class method) AcceptsContainerType() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory class method) (wfexs_backend.container_factories.ContainerFactory class method) (wfexs_backend.container_factories.no_container.NoContainerFactory class method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory class method) Action (class in wfexs_backend.ro_crate) action (wfexs_backend.workflow.MaterializedExportAction attribute) action_id (wfexs_backend.workflow.ExportAction attribute) add_creds() (wfexs_backend.utils.docker.DockerHelper method) add_dataset() (wfexs_backend.ro_crate.FixedROCrate method) add_dataset_ext() (wfexs_backend.ro_crate.FixedROCrate method) add_directory (wfexs_backend.ro_crate.FixedROCrate attribute) add_file() (wfexs_backend.ro_crate.FixedROCrate method) add_file_ext() (wfexs_backend.ro_crate.FixedROCrate method) add_workflow() (wfexs_backend.ro_crate.FixedROCrate method) add_workflow_ext() (wfexs_backend.ro_crate.FixedROCrate method) addContainerFactory() (wfexs_backend.wfexs_backend.WfExSBackend method)

addExportPlugin() (wfexs_backend.wfexs_backend.WfExSBackend method) AdditionalType2ContainerType (in module wfexs_backend.utils.rocrate) addRawSchemeHandlers() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) addSchemeHandlers() (wfexs_backend.wfexs_backend.WfExSBackend method) addStagedWorkflowDetails() (wfexs_backend.ro_crate.WorkflowRunROCrate method) addStatefulSchemeHandlers() (wfexs_backend.wfexs_backend.WfExSBackend method) addWorkflowEngine() (wfexs_backend.wfexs_backend.WfExSBackend method) addWorkflowExecution() (wfexs_backend.ro_crate.WorkflowRunROCrate method) addWorkflowExpectedOutputs() (wfexs_backend.ro_crate.WorkflowRunROCrate method) addWorkflowInputs() (wfexs_backend.ro_crate.WorkflowRunROCrate method) aiohttp_caching_document_loader() (in module wfexs_backend.utils.pyld_caching) alias (wfexs_backend.utils.docker.DockerTagMetadata attribute) allow_other (wfexs_backend.common.StagedSetup attribute) analyze_nf_content() (in module wfexs_backend.utils.groovy_parsing) applicationCategory (wfexs_backend.utils.rocrate.ContainerTypeMetadata attribute) ApplicationCategory2ContainerType (in module wfexs_backend.utils.rocrate) Apptainer (wfexs_backend.common.ContainerType attribute) architecture (wfexs_backend.container_factories.Container attribute) (wfexs_backend.container_factories.ContainerFactory property) (wfexs_backend.container_factories.docker_container.DockerContainerFactory property) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory property) ArgsDefaultWithRawHelpFormatter (class in wfexs_backend.common) argtype() (wfexs_backend.common.ArgTypeMixin class method) ArgTypeMixin (class in wfexs_backend.common) asyncio_run() (in module wfexs_backend.fetchers.internal.ftp_downloader) ATOM_CONTENT_TYPE (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) ATOM_NAMESPACE (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) ATOM_PREFIX (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) Attribution (class in wfexs_backend.common) AttributionRole (class in wfexs_backend.common) attributions (wfexs_backend.common.LicensedURI attribute) augmentCWLInputs() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) augmentedInputs (wfexs_backend.workflow_engines.StagedExecution attribute) augmentNextflowInputs() (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) autoFilled (wfexs_backend.common.MaterializedInput attribute)

B

B2SHARE_API_PREFIX (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) B2SHARE_DOI_PREFIX (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) B2SHARE_RECORD_PREFIX (in module wfexs_backend.fetchers.doi) B2SHARE_RECORD_REST (in module wfexs_backend.fetchers.b2share) B2SHARE_SCHEME (in module wfexs_backend.fetchers.b2share) B2SHAREPublisher (class in wfexs_backend.pushers.b2share_export) BANNED_PATCH_OPS_KEYS (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) BANNED_SCHEMA_KEYS (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) bin2dataurl() (in module wfexs_backend.utils.contents) BitBucket (wfexs_backend.fetchers.RepoGuessFlavor attribute) block (wfexs_backend.workflow.ExportItem attribute) BLOCK_STATEMENTS_RULE (in module wfexs_backend.utils.groovy_parsing)

book_pid() (wfexs_backend.pushers.AbstractExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.cache_export.CacheExportPlugin method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) bootstrap_config() (wfexs_backend.wfexs_backend.WfExSBackend class method) build_pid_from_repo() (wfexs_backend.fetchers.AbstractRepoFetcher method) (wfexs_backend.fetchers.git.GitFetcher method) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher method) bypassSchemeHandler() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) bypassSchemeHandlers() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method)

C

C_DOCKER_REGEX (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) C_URL_REGEX (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) Cache (wfexs_backend.__main__.WfExS_Commands attribute) CACHE_METADATA_SCHEMA (wfexs_backend.cache_handler.SchemeHandlerCacheHandler attribute) cached_parse_and_digest_groovy_content() (in module wfexs_backend.utils.groovy_parsing) CachedContent (class in wfexs_backend.cache_handler) cacheDir (wfexs_backend.container_factories.ContainerFactory property) CacheExportPlugin (class in wfexs_backend.pushers.cache_export) cacheFetch() (wfexs_backend.wfexs_backend.WfExSBackend method) CacheHandlerException CacheHandlerSchemeException CacheOfflineException cacheROcrate() (wfexs_backend.wfexs_backend.WfExSBackend method) cacheROCrateDir (wfexs_backend.wfexs_backend.WfExSBackend property) cacheTRSFilesDir (wfexs_backend.wfexs_backend.WfExSBackend property) CacheType (class in wfexs_backend.common) cacheWorkflow() (wfexs_backend.wfexs_backend.WfExSBackend method) cacheWorkflowDir (wfexs_backend.wfexs_backend.WfExSBackend property) cacheWorkflowInputsDir (wfexs_backend.wfexs_backend.WfExSBackend property) cardinality (wfexs_backend.common.ExpectedOutput attribute) CardinalityMapping (wfexs_backend.workflow.WF attribute) CC_BY_40_LICENCE (in module wfexs_backend.common) CC_BY_40_LicenceDescription (in module wfexs_backend.common) checkout (wfexs_backend.fetchers.RemoteRepo attribute) choose_domain() (wfexs_backend.utils.docker.DockerHelper method) clazz (wfexs_backend.workflow_engines.WorkflowType attribute) cleanup() (wfexs_backend.workflow.WF method) clear_tasks() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader static method) clonable (wfexs_backend.cache_handler.CachedContent attribute) (wfexs_backend.common.MaterializedContent attribute) close() (wfexs_backend.utils.io_wrappers.AbstractProxyIOWrapper method) closed (wfexs_backend.utils.io_wrappers.AbstractProxyIOWrapper property) CLOSURE_RULE (in module wfexs_backend.utils.groovy_parsing) code (wfexs_backend.fetchers.FetcherException attribute) Collection (class in wfexs_backend.ro_crate) command (wfexs_backend.container_factories.ContainerFactory property) COMMON_RULE (in module wfexs_backend.utils.groovy_parsing) community_custom_metadata (wfexs_backend.workflow.ExportAction attribute) CompleteDirs (class in wfexs_backend.utils.zipfile_path) compute_sha1_git_from_any() (in module wfexs_backend.utils.digests) compute_sha1_git_from_bytes() (in module wfexs_backend.utils.digests) compute_sha1_git_from_dir() (in module wfexs_backend.utils.digests) compute_sha1_git_from_file() (in module wfexs_backend.utils.digests) compute_sha1_git_from_stream() (in module wfexs_backend.utils.digests) compute_sha1_git_from_string() (in module wfexs_backend.utils.digests) ComputeDigestFromDirectory() (in module wfexs_backend.utils.digests) ComputeDigestFromFile() (in module wfexs_backend.utils.digests) ComputeDigestFromFileLike() (in module wfexs_backend.utils.digests) ComputeDigestFromGeneratedContentList() (in module wfexs_backend.utils.digests) ComputeDigestFromObject() (in module wfexs_backend.utils.digests) Conceptualization (wfexs_backend.common.AttributionRole attribute) Conda (wfexs_backend.common.ContainerType attribute) CONDA_CHILD (in module wfexs_backend.utils.groovy_parsing) condas (wfexs_backend.utils.groovy_parsing.NfProcess attribute) config (wfexs_backend.common.MarshallingStatus attribute) CONFIG_SCHEMA (wfexs_backend.wfexs_backend.WfExSBackend attribute) config_validate() (in module wfexs_backend.utils.misc) configuration local-config security-config wf-config configuredContainerType (wfexs_backend.workflow_engines.AbstractWorkflowEngineType property) ConfigValidate (wfexs_backend.__main__.WfExS_Commands attribute) ConfigValidationException consolidated_workflow_dir (wfexs_backend.common.StagedSetup attribute) ContactPoint (class in wfexs_backend.ro_crate) Container (class in wfexs_backend.container_factories) CONTAINER_CHILD (in module wfexs_backend.utils.groovy_parsing) CONTAINER_DOCKERIMAGE_SHORT (in module wfexs_backend.utils.rocrate)

CONTAINER_SIFIMAGE_SHORT (in module wfexs_backend.utils.rocrate) container_type (wfexs_backend.common.MarshallingStatus attribute) (wfexs_backend.common.StagedSetup attribute) ContainerCacheHandler (class in wfexs_backend.container_factories) ContainerEngineException ContainerFactory (class in wfexs_backend.container_factories) ContainerFactoryException ContainerImage (class in wfexs_backend.ro_crate) ContainerImageAdditionalType (class in wfexs_backend.utils.rocrate) ContainerNotFoundException Containers (wfexs_backend.common.CratableItem attribute) containers (wfexs_backend.utils.groovy_parsing.NfProcess attribute) (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) containers_dir (wfexs_backend.common.StagedSetup attribute) containers_path (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) ContainerTaggedName (class in wfexs_backend.common) ContainerType (class in wfexs_backend.common) containerType (wfexs_backend.container_factories.ContainerFactory property) ContainerType() (wfexs_backend.container_factories.ContainerFactory class method) (wfexs_backend.container_factories.docker_container.DockerContainerFactory class method) (wfexs_backend.container_factories.no_container.NoContainerFactory class method) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory class method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory class method) ContainerType2AdditionalType (in module wfexs_backend.utils.rocrate) ContainerTypeMetadata (class in wfexs_backend.utils.rocrate) ContainerTypeMetadataDetails (in module wfexs_backend.utils.rocrate) ContainerYAMLConstructor() (wfexs_backend.container_factories.Container class method) ContConfigPat (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) content_type (wfexs_backend.utils.io_wrappers.MultipartEncoderIOWrapper property) ContentKind (class in wfexs_backend.common) ContentWithURIs (wfexs_backend.common.ContentKind attribute) contentWithURIs (wfexs_backend.common.MaterializedInput attribute) ContentWithURIsDesc (class in wfexs_backend.common) ContentWithURIsMIMEs (in module wfexs_backend.utils.rocrate) context_name (wfexs_backend.workflow.ExportAction attribute) ControlAction (class in wfexs_backend.ro_crate) copy2_nofollow() (in module wfexs_backend.utils.contents) copy_nofollow() (in module wfexs_backend.utils.contents) copy_to() (wfexs_backend.utils.zipfile_path.ZipfilePath method) CratableItem (class in wfexs_backend.common) create_augmented_context() (in module wfexs_backend.common) create_job_directories() (wfexs_backend.workflow_engines.WorkflowEngine method) create_remote_path() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) create_share_links() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) CreateAction (class in wfexs_backend.ro_crate) CreateProvenanceROCrate (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) createRawWorkDir() (wfexs_backend.wfexs_backend.WfExSBackend method) createResultsResearchObject() (wfexs_backend.workflow.WF method) CreateStagedROCrate (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) createStageResearchObject() (wfexs_backend.workflow.WF method) createYAMLFile() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) creation (wfexs_backend.common.StagedSetup attribute) Credentials (class in wfexs_backend.utils.docker) CRYPT4GH_PASSPHRASE_KEY (wfexs_backend.wfexs_backend.WfExSBackend attribute) CRYPT4GH_PRIVKEY_KEY (wfexs_backend.wfexs_backend.WfExSBackend attribute) CRYPT4GH_PUBKEY_KEY (wfexs_backend.wfexs_backend.WfExSBackend attribute) CRYPT4GH_SECTION (wfexs_backend.wfexs_backend.WfExSBackend attribute) ct_applicationCategory (wfexs_backend.utils.rocrate.ContainerTypeMetadata attribute) curate_licence_list() (wfexs_backend.wfexs_backend.WfExSBackend method) custom_metadata (wfexs_backend.workflow.ExportAction attribute) CWL_REPO (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) CWL_UTILS_PYTHON_PACKAGE (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) CWL_UTILS_REPO (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) CWLClass2WfExS (in module wfexs_backend.utils.contents) CWLDesc2Content() (in module wfexs_backend.utils.contents) CWLTOOL_MAX_PYVER (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) CWLTOOL_PYTHON_PACKAGE (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) CWLTOOL_REPO (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) CWLWorkflowEngine (class in wfexs_backend.workflow_engines.cwl_engine)

D

DATA_SCHEME (in module wfexs_backend.fetchers.data) DataCuration (wfexs_backend.common.AttributionRole attribute) DATAVERSE_VALID_LICENCES (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) DataversePublisher (class in wfexs_backend.pushers.dataverse_export) DatetimeEncoder (class in wfexs_backend.utils.misc) datetimeFromISOFormat() (in module wfexs_backend.utils.misc) DEBUG_LOGGING_FORMAT (in module wfexs_backend.__main__) decompose_docker_tagged_name (wfexs_backend.container_factories.Container property) deep_update() (in module wfexs_backend.utils.groovy_parsing) default() (wfexs_backend.utils.misc.DatetimeEncoder method) DEFAULT_ALIAS (wfexs_backend.utils.docker.DockerHelper attribute) DEFAULT_APPTAINER_CMD (in module wfexs_backend.common) DEFAULT_ASPERA_CMD (wfexs_backend.fetchers.fasp.FASPFetcher attribute) DEFAULT_B2SHARE_COMMUNITY (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) DEFAULT_CONTAINER_TYPE (in module wfexs_backend.common) DEFAULT_CWLTOOL_VERSION (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) DEFAULT_DESCRIPTION_TYPE (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) DEFAULT_DIGEST_ALGORITHM (in module wfexs_backend.utils.digests) DEFAULT_DIGEST_BUFFER_SIZE (in module wfexs_backend.utils.digests) DEFAULT_DOCKER_CMD (in module wfexs_backend.common) DEFAULT_DOCKER_REGISTRY (in module wfexs_backend.container_factories) (wfexs_backend.utils.docker.DockerHelper attribute) DEFAULT_DOT_CMD (in module wfexs_backend.common) DEFAULT_ENCRYPTED_FS_CMD (in module wfexs_backend.encrypted_fs) DEFAULT_ENCRYPTED_FS_IDLE_TIMEOUT (in module wfexs_backend.encrypted_fs) DEFAULT_ENCRYPTED_FS_TYPE (in module wfexs_backend.encrypted_fs) DEFAULT_ENGINE_MODE (in module wfexs_backend.common) DEFAULT_FTP_PORT (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader attribute) DEFAULT_FUSERMOUNT_CMD (in module wfexs_backend.common) DEFAULT_GIT_CMD (wfexs_backend.fetchers.git.GitFetcher attribute) DEFAULT_JAVA_CMD (in module wfexs_backend.common) DEFAULT_LIMIT_THROUGHPUT (wfexs_backend.fetchers.fasp.FASPFetcher attribute) DEFAULT_LOCAL_CONFIG_RELNAME (in module wfexs_backend.__main__) DEFAULT_MAX_CPUS (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_MAX_RETRIES (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader attribute) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_NEXTFLOW_DOCKER_IMAGE (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_NEXTFLOW_ENTRYPOINT (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_NEXTFLOW_VERSION (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_NEXTFLOW_VERSION_20_04 (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_NEXTFLOW_VERSION_WITH_PODMAN (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DEFAULT_PASS (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader attribute) DEFAULT_PASSPHRASE_LENGTH (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator attribute) (wfexs_backend.wfexs_backend.WfExSBackend attribute) DEFAULT_PODMAN_CMD (in module wfexs_backend.common) DEFAULT_PRIORITY (in module wfexs_backend.fetchers) (in module wfexs_backend.workflow_engines) DEFAULT_PROGS (in module wfexs_backend.common) DEFAULT_REMOTE_PATH_SEPARATOR (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin attribute) DEFAULT_RO_EXTENSION (wfexs_backend.wfexs_backend.WfExSBackend attribute) DEFAULT_SINGULARITY_CMD (in module wfexs_backend.common) DEFAULT_SPDX_VERSION (wfexs_backend.utils.licences.LicenceMatcher attribute) DEFAULT_STATIC_BASH_CMDS (in module wfexs_backend.workflow_engines.nextflow_engine) DEFAULT_STATIC_PS_CMDS (in module wfexs_backend.workflow_engines.nextflow_engine) DEFAULT_TRS_ENDPOINT (wfexs_backend.workflow.WF attribute) DEFAULT_USER (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader attribute) DEFAULT_WORD_SETS (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator attribute) DefaultCardinality (wfexs_backend.workflow.WF attribute) DefaultMissing (class in wfexs_backend.workflow) DefaultNoLicenceTuple (in module wfexs_backend.common) deploy_containers() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.WorkflowEngine method) deployContainers() (wfexs_backend.container_factories.ContainerFactory method) deploySingleContainer() (wfexs_backend.container_factories.ContainerFactory method) (wfexs_backend.container_factories.docker_container.DockerContainerFactory method) (wfexs_backend.container_factories.no_container.NoContainerFactory method) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method)

describeDocumentedLicences() (wfexs_backend.utils.licences.LicenceMatcher method) describeFetchableSchemes() (wfexs_backend.wfexs_backend.WfExSBackend method) describeGitRepo() (in module wfexs_backend) describeRegisteredSchemes() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) description (wfexs_backend.common.LicenceDescription attribute) (wfexs_backend.common.StrDocEnum attribute) (wfexs_backend.fetchers.AbstractStatefulFetcher property) (wfexs_backend.fetchers.DocumentedProtocolFetcher attribute) (wfexs_backend.fetchers.DocumentedStatefulProtocolFetcher attribute) (wfexs_backend.fetchers.fasp.FASPFetcher property) (wfexs_backend.fetchers.git.GitFetcher property) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher property) (wfexs_backend.fetchers.wiktionary.WiktionaryFetcher property) (wfexs_backend.workflow.ExportAction attribute) deserializeDataURI() (in module wfexs_backend.fetchers.data) DEVEL_CWLTOOL_PACKAGE (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) DEVEL_CWLTOOL_REPO (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) DEVEL_CWLTOOL_VERSION (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) diagram (wfexs_backend.workflow_engines.StagedExecution attribute) Died (wfexs_backend.common.ExecutionStatus attribute) digest() (wfexs_backend.utils.io_wrappers.DigestIOWrapper method) DigestIOWrapper (class in wfexs_backend.utils.io_wrappers) dir (wfexs_backend.common.LocalWorkflow attribute) DIR_RETRIES (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) Directory (wfexs_backend.common.ContentKind attribute) discard_booked_pid() (wfexs_backend.pushers.AbstractExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.cache_export.CacheExportPlugin method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) disclosable (wfexs_backend.common.MaterializedInput attribute) Docker (wfexs_backend.common.ContainerType attribute) (wfexs_backend.common.EngineMode attribute) (wfexs_backend.utils.rocrate.ContainerImageAdditionalType attribute) DOCKER_PROTO (in module wfexs_backend.container_factories.abstract_docker_container) DOCKER_REGISTRY (wfexs_backend.utils.docker.DockerHelper attribute) DOCKER_SCHEME (in module wfexs_backend.container_factories) DOCKER_URI_PREFIX (in module wfexs_backend.container_factories) DockerContainerFactory (class in wfexs_backend.container_factories.docker_container) DockerHelper (class in wfexs_backend.utils.docker) DockerHelperException DockerTagMetadata (class in wfexs_backend.utils.docker) DocumentedProtocolFetcher (class in wfexs_backend.fetchers) DocumentedStatefulProtocolFetcher (class in wfexs_backend.fetchers) DOI_HANDLE_REST (in module wfexs_backend.fetchers.doi) DOI_RA_REST (in module wfexs_backend.fetchers.doi) DOI_SCHEME (in module wfexs_backend.fetchers.doi) domain (wfexs_backend.utils.docker.Credentials attribute) doMaterializeRepo() (wfexs_backend.wfexs_backend.WfExSBackend method) download() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) download_async() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) download_dir() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) download_dir_async() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) download_file() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) download_file_async() (wfexs_backend.fetchers.internal.ftp_downloader.FTPDownloader method) downloadContent() (wfexs_backend.wfexs_backend.WfExSBackend method) downloadContentFrom_gs() (in module wfexs_backend.fetchers.gs) downloadContentFrom_s3() (in module wfexs_backend.fetchers.s3) downloadContentFromDRS() (in module wfexs_backend.fetchers.drs) draft_id (wfexs_backend.pushers.DraftEntry attribute) DraftEntry (class in wfexs_backend.pushers) DRS_SCHEME (in module wfexs_backend.fetchers.drs) DSLEnablePat (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) DXFFat (class in wfexs_backend.utils.docker)

E

effectiveCheckout (wfexs_backend.common.LocalWorkflow attribute) elems (wfexs_backend.workflow.MaterializedExportAction attribute) ENABLED (wfexs_backend.container_factories.ContainerFactory attribute) (wfexs_backend.fetchers.AbstractStatefulFetcher attribute) (wfexs_backend.pushers.AbstractExportPlugin attribute) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) (wfexs_backend.pushers.cache_export.CacheExportPlugin attribute) (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin attribute) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin attribute) enabled (wfexs_backend.workflow_engines.WorkflowType attribute) enableDefaultParanoidMode() (wfexs_backend.wfexs_backend.WfExSBackend method) enableParanoidMode() (wfexs_backend.workflow.WF method) EncFS (wfexs_backend.encrypted_fs.EncryptedFSType attribute) encodingFormat (wfexs_backend.common.ContentWithURIsDesc attribute) ENCRYPTED_FS_MOUNT_IMPLEMENTATIONS (in module wfexs_backend.encrypted_fs) EncryptedFSException EncryptedFSType (class in wfexs_backend.encrypted_fs) ended (wfexs_backend.workflow_engines.StagedExecution attribute) ENGINE_NAME (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) (wfexs_backend.workflow_engines.WorkflowEngine attribute) engine_path (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) engine_tweaks_dir (wfexs_backend.common.StagedSetup attribute) engine_url (wfexs_backend.workflow_engines.AbstractWorkflowEngineType property) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine property) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine property) engine_version() (wfexs_backend.container_factories.ContainerFactory method) (wfexs_backend.container_factories.no_container.NoContainerFactory method) EngineMode (class in wfexs_backend.common) engineName (wfexs_backend.workflow_engines.WorkflowType attribute) Environment (wfexs_backend.common.ExportItemType attribute) environment (wfexs_backend.container_factories.ContainerFactory property) (wfexs_backend.workflow_engines.StagedExecution attribute) ERROR_PROCESS_NAME (in module wfexs_backend.utils.groovy_parsing) Execute (wfexs_backend.__main__.WfExS_Commands attribute) executeWorkflow() (wfexs_backend.workflow.WF method) ExecuteWorkflow() (wfexs_backend.workflow_engines.WorkflowEngine class method) execution (wfexs_backend.common.MarshallingStatus attribute) EXECUTION_CRATE_FILE (wfexs_backend.workflow.WF attribute)

execution_stats (wfexs_backend.common.MarshallingStatus attribute) executionInputs() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) ExecutionStatus (class in wfexs_backend.common) exists() (wfexs_backend.utils.zipfile_path.ZipfilePath method) exitVal (wfexs_backend.workflow_engines.StagedExecution attribute) expectedCardinality (wfexs_backend.common.MaterializedOutput attribute) ExpectedOutput (class in wfexs_backend.common) Export (wfexs_backend.__main__.WfExS_Commands attribute) export (wfexs_backend.common.MarshallingStatus attribute) EXPORT_ACTIONS_SCHEMA (wfexs_backend.workflow.WF attribute) EXPORT_FORMATS (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) export_stamps (wfexs_backend.common.MarshallingStatus attribute) ExportAction (class in wfexs_backend.workflow) ExportActionException ExportCrate (wfexs_backend.__main__.WfExS_Commands attribute) ExportItem (class in wfexs_backend.workflow) ExportItemType (class in wfexs_backend.common) ExportMapping (class in wfexs_backend.pushers.nextcloud_export) ExportPluginException ExportResults (wfexs_backend.__main__.WfExS_Commands attribute) exportResults() (wfexs_backend.workflow.WF method) exportResultsFromFiles() (wfexs_backend.workflow.WF method) ExportROCrate2Payloads (wfexs_backend.workflow.WF attribute) ExportStage (wfexs_backend.__main__.WfExS_Commands attribute) extract_nested_assignments() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_condas() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_config_includeconfigs() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_config_plugins() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_containers() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_features() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_includes() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_process() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_templates() (in module wfexs_backend.utils.groovy_parsing) extract_nextflow_workflow() (in module wfexs_backend.utils.groovy_parsing) extract_process_features() (in module wfexs_backend.utils.groovy_parsing) extract_strings() (in module wfexs_backend.utils.groovy_parsing) extract_values_as_pairs() (in module wfexs_backend.utils.groovy_parsing) extractWorkflowMetadata() (wfexs_backend.utils.rocrate.ROCrateToolbox method) extrapolated_inputs_dir (wfexs_backend.common.StagedSetup attribute) extrapolated_local (wfexs_backend.common.MaterializedContent attribute)

F

FailedContainerTag (class in wfexs_backend.container_factories.singularity_container) FASP_PROTO (wfexs_backend.fetchers.fasp.FASPFetcher attribute) FASPFetcher (class in wfexs_backend.fetchers.fasp) FastLookup (class in wfexs_backend.utils.zipfile_path) Fetch (wfexs_backend.__main__.WfExS_Cache_Commands attribute) fetch() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) (wfexs_backend.fetchers.AbstractStatefulFetcher method) (wfexs_backend.fetchers.AbstractStatefulStreamingFetcher method) (wfexs_backend.fetchers.fasp.FASPFetcher method) (wfexs_backend.fetchers.git.GitFetcher method) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher method) (wfexs_backend.fetchers.wiktionary.WiktionaryFetcher method) fetchB2SHARE() (in module wfexs_backend.fetchers.b2share) fetchClassicURL() (in module wfexs_backend.fetchers.http) fetchDOI() (in module wfexs_backend.fetchers.doi) fetcher (wfexs_backend.fetchers.DocumentedProtocolFetcher attribute) fetcher_class (wfexs_backend.fetchers.DocumentedStatefulProtocolFetcher attribute) FetcherException FetcherInstanceException fetchFile() (in module wfexs_backend.fetchers.file) fetchFTPURL() (in module wfexs_backend.fetchers.ftp) fetchInputs() (wfexs_backend.workflow.WF method) fetchOSFIO() (in module wfexs_backend.fetchers.osf_io) fetchPRIDEProject() (in module wfexs_backend.fetchers.pride) fetchSSHURL() (in module wfexs_backend.fetchers.sftp) fetchTRSFiles() (in module wfexs_backend.fetchers.trs_files) fetchWorkflow() (wfexs_backend.workflow.WF method) fetchZenodo() (in module wfexs_backend.fetchers.zenodo) File (wfexs_backend.common.ContentKind attribute) filename (wfexs_backend.utils.io_wrappers.MultipartFile attribute) (wfexs_backend.utils.zipfile_path.ZipfilePath property) filledFrom (wfexs_backend.common.MaterializedOutput attribute) fillFrom (wfexs_backend.common.ExpectedOutput attribute) findAndAddContainerFactoriesFromModule() (wfexs_backend.wfexs_backend.WfExSBackend method) findAndAddContainerFactoriesFromModuleName() (wfexs_backend.wfexs_backend.WfExSBackend method) findAndAddExportPluginsFromModule() (wfexs_backend.wfexs_backend.WfExSBackend method) findAndAddExportPluginsFromModuleName() (wfexs_backend.wfexs_backend.WfExSBackend method) findAndAddSchemeHandlersFromModule() (wfexs_backend.wfexs_backend.WfExSBackend method)

findAndAddSchemeHandlersFromModuleName() (wfexs_backend.wfexs_backend.WfExSBackend method) findAndAddWorkflowEnginesFromModule() (wfexs_backend.wfexs_backend.WfExSBackend method) findAndAddWorkflowEnginesFromModuleName() (wfexs_backend.wfexs_backend.WfExSBackend method) fingerprint (wfexs_backend.cache_handler.CachedContent attribute) (wfexs_backend.common.MaterializedContent attribute) (wfexs_backend.container_factories.Container attribute) (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) Finished (wfexs_backend.common.ExecutionStatus attribute) FixedDataset (class in wfexs_backend.ro_crate) FixedFile (class in wfexs_backend.ro_crate) FixedMixin (class in wfexs_backend.ro_crate) FixedROCrate (class in wfexs_backend.ro_crate) FixedWorkflow (class in wfexs_backend.ro_crate) footer (wfexs_backend.utils.io_wrappers.MultipartEncoderIOWrapper property) FormalAnalysis (wfexs_backend.common.AttributionRole attribute) FormalParameter (class in wfexs_backend.ro_crate) formatParams() (wfexs_backend.workflow.WF method) FromDescription() (wfexs_backend.wfexs_backend.WfExSBackend class method) fromDescription() (wfexs_backend.wfexs_backend.WfExSBackend method) FromDescription() (wfexs_backend.workflow.WF class method) FromFile() (wfexs_backend.security_context.SecurityContextVault class method) fromFiles() (wfexs_backend.wfexs_backend.WfExSBackend method) FromFiles() (wfexs_backend.workflow.WF class method) fromForm() (wfexs_backend.wfexs_backend.WfExSBackend method) FromForm() (wfexs_backend.workflow.WF class method) fromPreviousInstanceDeclaration() (wfexs_backend.wfexs_backend.WfExSBackend method) FromPreviousInstanceDeclaration() (wfexs_backend.workflow.WF class method) fromPreviousROCrate() (wfexs_backend.wfexs_backend.WfExSBackend method) FromPreviousROCrate() (wfexs_backend.workflow.WF class method) FromStagedRecipe() (wfexs_backend.workflow.WF class method) FromStagedSetup() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType class method) (wfexs_backend.workflow_engines.WorkflowEngine class method) fromWorkDir() (wfexs_backend.wfexs_backend.WfExSBackend method) FromWorkDir() (wfexs_backend.workflow.WF class method) FTPDownloader (class in wfexs_backend.fetchers.internal.ftp_downloader) Full (wfexs_backend.utils.rocrate.ReproducibilityLevel attribute) FundingAcquisition (wfexs_backend.common.AttributionRole attribute) fungen (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator property) FUSE_SYSTEM_CONF (wfexs_backend.workflow.WF attribute)

G

gen_repo_desc() (wfexs_backend.fetchers.RemoteRepo method) gen_workflow_pid() (wfexs_backend.wfexs_backend.WfExSBackend method) generate_nickname() (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator method) generate_passphrase() (wfexs_backend.wfexs_backend.WfExSBackend class method) generate_passphrase_random() (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator method) generateCanonicalTag() (wfexs_backend.container_factories.ContainerFactory method) (wfexs_backend.container_factories.docker_container.DockerContainerFactory method) (wfexs_backend.container_factories.no_container.NoContainerFactory method) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) GeneratedContent (class in wfexs_backend.common) GeneratedDirectoryContent (class in wfexs_backend.common) generateDotWorkflow() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine static method) generateSecuredWorkdirPassphrase() (wfexs_backend.wfexs_backend.WfExSBackend method) generateWorkflowMetaFromJSONLD() (wfexs_backend.utils.rocrate.ROCrateToolbox method) genParserSub() (in module wfexs_backend.__main__) genStagedContainersDirPaths() (wfexs_backend.container_factories.ContainerCacheHandler method) get_api_prefix() (wfexs_backend.pushers.abstract_token_export.AbstractTokenExportPlugin method) (wfexs_backend.pushers.abstract_token_sandboxed_export.AbstractTokenSandboxedExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) get_checkout() (wfexs_backend.fetchers.RemoteRepo method) get_community_metadata() (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) get_fat_manifest() (wfexs_backend.utils.docker.DXFFat method) get_fat_manifest_and_dcd() (wfexs_backend.utils.docker.DXFFat method) get_fat_manifest_and_response() (wfexs_backend.utils.docker.DXFFat method) get_file_bucket_prefix() (wfexs_backend.pushers.abstract_token_export.AbstractTokenExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) GET_LICENCES_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) get_maximum_file_descriptors() (in module wfexs_backend.utils.misc) get_opener_with_auth() (in module wfexs_backend.utils.misc) get_parsed_manifest_and_dcd() (wfexs_backend.utils.docker.DXFFat method) get_pid_draftentry() (wfexs_backend.pushers.AbstractExportPlugin method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) get_pid_metadata() (wfexs_backend.pushers.AbstractExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.cache_export.CacheExportPlugin method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) get_share_link_info() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) get_uri() (wfexs_backend.common.LicenceDescription method) get_wfexs_argparse() (in module wfexs_backend.__main__) get_WfExS_version() (in module wfexs_backend) get_WfExS_version_str() (in module wfexs_backend) getCacheHandler() (wfexs_backend.wfexs_backend.WfExSBackend method) getConfiguredContainerType() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.WorkflowEngine method) getContainerFactoryClass() (wfexs_backend.wfexs_backend.WfExSBackend method) getContext() (wfexs_backend.security_context.SecurityContextVault method) getDefaultParanoidMode() (wfexs_backend.wfexs_backend.WfExSBackend method) GetEngineVersion() (wfexs_backend.workflow_engines.WorkflowEngine static method)

getExportPluginClass() (wfexs_backend.wfexs_backend.WfExSBackend method) getFusermountParams() (wfexs_backend.wfexs_backend.WfExSBackend method) GetGeneratedDirectoryContent() (in module wfexs_backend.utils.contents) GetGeneratedDirectoryContentFromList() (in module wfexs_backend.utils.contents) getHashDir() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler static method) getinfo() (wfexs_backend.utils.zipfile_path.CompleteDirs method) GetLicenceMatcher() (wfexs_backend.wfexs_backend.WfExSBackend class method) getMarshallingStatus() (wfexs_backend.workflow.WF method) getMaterializedContainers() (wfexs_backend.workflow.WF method) getMaterializedWorkflow() (wfexs_backend.workflow.WF method) GetNeededPrograms() (wfexs_backend.fetchers.AbstractStatefulFetcher class method) (wfexs_backend.fetchers.fasp.FASPFetcher class method) (wfexs_backend.fetchers.git.GitFetcher class method) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher class method) (wfexs_backend.fetchers.wiktionary.WiktionaryFetcher class method) getOrCreateRawWorkDirFromInstanceId() (wfexs_backend.wfexs_backend.WfExSBackend method) GetPassGen() (wfexs_backend.wfexs_backend.WfExSBackend class method) getPID() (wfexs_backend.workflow.WF method) GetSchemeHandlers() (wfexs_backend.fetchers.AbstractStatefulFetcher class method) (wfexs_backend.fetchers.fasp.FASPFetcher class method) (wfexs_backend.fetchers.git.GitFetcher class method) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher class method) (wfexs_backend.fetchers.wiktionary.WiktionaryFetcher class method) getStagedSetup() (wfexs_backend.workflow.WF method) getting-started inst-gearshift installation installation; devel installation; easy-setup-wfexs installation; prerequisites installation; sof_dep secure_dirs sys-requirments getWorkflowBundleFromURI() (wfexs_backend.wfexs_backend.WfExSBackend method) getWorkflowEngineClass() (wfexs_backend.wfexs_backend.WfExSBackend method) getWorkflowRepoFromROCrateFile() (wfexs_backend.wfexs_backend.WfExSBackend method) getWorkflowRepoFromTRS() (wfexs_backend.wfexs_backend.WfExSBackend method) Git (wfexs_backend.fetchers.RepoType attribute) GIT_PROTO (wfexs_backend.fetchers.git.GitFetcher attribute) GIT_PROTO_PREFIX (wfexs_backend.fetchers.git.GitFetcher attribute) GIT_SCHEMES (wfexs_backend.fetchers.git.GitFetcher attribute) GitFetcher (class in wfexs_backend.fetchers.git) GitHub (wfexs_backend.fetchers.RepoGuessFlavor attribute) GITHUB_NETLOC (in module wfexs_backend.fetchers.git) GITHUB_SCHEME (wfexs_backend.fetchers.git.GitFetcher attribute) GitLab (wfexs_backend.fetchers.RepoGuessFlavor attribute) glob (wfexs_backend.common.ExpectedOutput attribute) (wfexs_backend.common.MaterializedOutput attribute) GoCryptFS (wfexs_backend.encrypted_fs.EncryptedFSType attribute) guess_flavor (wfexs_backend.fetchers.RemoteRepo attribute) guess_repo_params() (wfexs_backend.wfexs_backend.WfExSBackend method) GuessedCardinalityMapping (wfexs_backend.workflow_engines.WorkflowEngine attribute) GuessedOutputKindMapping (wfexs_backend.workflow_engines.WorkflowEngine attribute) GuessRepoParams() (wfexs_backend.fetchers.AbstractRepoFetcher class method) (wfexs_backend.fetchers.git.GitFetcher class method) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher class method)

H

has_explicit_outputs (wfexs_backend.workflow_engines.WorkflowType property) HasExplicitOutputs() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType class method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine class method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine class method)

HEAD_LABEL (wfexs_backend.fetchers.git.GitFetcher attribute) hexDigest() (in module wfexs_backend.utils.digests) hexdigest() (wfexs_backend.utils.io_wrappers.DigestIOWrapper method) hook_pyld_cache() (in module wfexs_backend.utils.pyld_caching)

I

ID_CHILD (in module wfexs_backend.utils.groovy_parsing) ID_JSON_FILENAME (wfexs_backend.wfexs_backend.WfExSBackend attribute) IdentifiedWorkflow (class in wfexs_backend.wfexs_backend) IDENTIFIER_RULE (in module wfexs_backend.utils.groovy_parsing) identifyMaterializedOutputs() (wfexs_backend.workflow_engines.WorkflowEngine method) identifyROCrate() (wfexs_backend.utils.rocrate.ROCrateToolbox method) identifyWorkflow() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) (wfexs_backend.workflow_engines.WorkflowEngine method) image_signature (wfexs_backend.container_factories.Container attribute) implicit (wfexs_backend.common.MaterializedInput attribute) Import (wfexs_backend.__main__.WfExS_Commands attribute) INCLUDE_CHILD (in module wfexs_backend.utils.groovy_parsing) INCLUDE_PROCESS_RULE (in module wfexs_backend.utils.groovy_parsing) INCLUDECONFIG_CHILD (in module wfexs_backend.utils.groovy_parsing) Init (wfexs_backend.__main__.WfExS_Commands attribute) initialize() (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator method) initialized (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator property) Inject (wfexs_backend.__main__.WfExS_Cache_Commands attribute) inject() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) Input (wfexs_backend.common.CacheType attribute) INPUT_DECLARATIONS_FILENAME (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute)

Inputs (wfexs_backend.common.CratableItem attribute) inputs_dir (wfexs_backend.common.StagedSetup attribute) instance (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) instance_id (wfexs_backend.common.StagedSetup attribute) instantiateEngine() (wfexs_backend.wfexs_backend.WfExSBackend method) instantiateRepoFetcher() (wfexs_backend.wfexs_backend.WfExSBackend method) instantiateStatefulFetcher() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) (wfexs_backend.wfexs_backend.WfExSBackend method) Intangible (class in wfexs_backend.ro_crate) intermediate_dir (wfexs_backend.common.StagedSetup attribute) INTERNAL_ID_PAT (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) INTERNAL_TRS_SCHEME_PREFIX (in module wfexs_backend.fetchers.trs_files) INTROSPECT_VALIDATOR_MAPPER (in module wfexs_backend.pushers.b2share_export) invalidate() (wfexs_backend.container_factories.ContainerCacheHandler method) InvalidFetcherException Investigation (wfexs_backend.common.AttributionRole attribute) is_damaged (wfexs_backend.common.StagedSetup attribute) is_dir() (wfexs_backend.utils.zipfile_path.ZipfilePath method) is_encrypted (wfexs_backend.common.StagedSetup attribute) is_file() (wfexs_backend.utils.zipfile_path.ZipfilePath method) IS_ROCRATE_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) is_spdx (wfexs_backend.common.LicenceDescription attribute) is_uri() (in module wfexs_backend.utils.misc) iter_namespace() (in module wfexs_backend.utils.misc) iterdir() (wfexs_backend.utils.zipfile_path.ZipfilePath method)

J

job_id (wfexs_backend.workflow_engines.StagedExecution attribute)

joinpath() (wfexs_backend.utils.zipfile_path.ZipfilePath method) jsonFilterDecodeFromStream() (in module wfexs_backend.utils.misc)

K

kind (wfexs_backend.cache_handler.CachedContent attribute) (wfexs_backend.common.ExpectedOutput attribute) (wfexs_backend.common.MaterializedContent attribute) (wfexs_backend.common.MaterializedOutput attribute)

kind_or_resolved (wfexs_backend.fetchers.ProtocolFetcherReturn attribute)

L

label (wfexs_backend.utils.groovy_parsing.NfPlugin attribute) langVersion (wfexs_backend.common.LocalWorkflow attribute) launchWorkflow() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) (wfexs_backend.workflow_engines.WorkflowEngine method) lazy_import() (in module wfexs_backend.utils.misc) LEAF_TYPE_2_ADDITIONAL_TYPE (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) LEAF_TYPE_2_OUTPUT_ADDITIONAL_TYPE (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) LEGACY_ROCRATE_JSONLD_FILENAME (in module wfexs_backend.utils.rocrate) LicenceDescription (class in wfexs_backend.common) LicenceMatcher (class in wfexs_backend.utils.licences) LicenceMatcherSingleton (class in wfexs_backend.utils.licences) licences (wfexs_backend.cache_handler.CachedContent attribute) (wfexs_backend.common.LicensedURI attribute) (wfexs_backend.fetchers.ProtocolFetcherReturn attribute) (wfexs_backend.workflow.ExportAction attribute) licensed_uri (wfexs_backend.common.MaterializedContent attribute) LicensedURI (class in wfexs_backend.common) LimitedStreamIOWrapper (class in wfexs_backend.utils.io_wrappers) link_or_copy() (in module wfexs_backend.utils.contents) link_or_copy_pathlib() (in module wfexs_backend.utils.contents) link_or_symlink_pathlib() (in module wfexs_backend.utils.contents) List (wfexs_backend.__main__.WfExS_Cache_Commands attribute) (wfexs_backend.__main__.WfExS_Export_Commands attribute) (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) list() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method)

list_containers() (in module wfexs_backend.docs_module) list_export_plugins() (in module wfexs_backend.docs_module) list_fetchers() (in module wfexs_backend.docs_module) list_licences() (in module wfexs_backend.docs_module) LIST_PARTS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) list_workflow_engines() (in module wfexs_backend.docs_module) ListContainerFactories (wfexs_backend.__main__.WfExS_Commands attribute) listContainerFactoryClasses() (wfexs_backend.wfexs_backend.WfExSBackend method) listExportPluginNames() (wfexs_backend.wfexs_backend.WfExSBackend method) ListFetchers (wfexs_backend.__main__.WfExS_Commands attribute) listImplementedContainerTypes() (wfexs_backend.wfexs_backend.WfExSBackend method) ListLicences (wfexs_backend.__main__.WfExS_Commands attribute) listMaterializedExportActions() (wfexs_backend.workflow.WF method) ListPushers (wfexs_backend.__main__.WfExS_Commands attribute) listStagedWorkflows() (wfexs_backend.wfexs_backend.WfExSBackend method) listWorkflowEngineClasses() (wfexs_backend.wfexs_backend.WfExSBackend method) ListWorkflowEngines (wfexs_backend.__main__.WfExS_Commands attribute) listWorkflowEngines() (wfexs_backend.wfexs_backend.WfExSBackend method) load_with_datetime() (in module wfexs_backend.utils.misc) local (wfexs_backend.common.AbstractGeneratedContent attribute) Local (wfexs_backend.common.EngineMode attribute) local (wfexs_backend.common.MaterializedContent attribute) local_filename (wfexs_backend.pushers.nextcloud_export.ExportMapping attribute) localPath (wfexs_backend.container_factories.Container attribute) LocalWorkflow (class in wfexs_backend.common) locateExportItems() (wfexs_backend.workflow.WF method) logfile (wfexs_backend.workflow_engines.StagedExecution attribute) LOGGING_FORMAT (in module wfexs_backend.__main__)

M

main() (in module wfexs_backend.__main__) make() (wfexs_backend.utils.zipfile_path.CompleteDirs class method) manifest (wfexs_backend.utils.docker.DockerTagMetadata attribute) MANIFEST_CHILD (in module wfexs_backend.utils.groovy_parsing) mappings_uploader() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) marshall_namedtuple() (in module wfexs_backend.utils.marshalling_handling) marshallConfig() (wfexs_backend.workflow.WF method) marshallExecute() (wfexs_backend.workflow.WF method) marshallExport() (wfexs_backend.workflow.WF method) MarshallingStatus (class in wfexs_backend.common) marshallStage() (wfexs_backend.workflow.WF method) match_LongLicence() (wfexs_backend.utils.licences.LicenceMatcher method) match_ShortLicence() (wfexs_backend.utils.licences.LicenceMatcher method) matCheckOutputs (wfexs_backend.workflow_engines.StagedExecution attribute) matchLicence() (wfexs_backend.utils.licences.LicenceMatcher method) matchWorkflowType() (wfexs_backend.wfexs_backend.WfExSBackend method) materialize_containers() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.WorkflowEngine method) materialize_repo() (wfexs_backend.fetchers.AbstractRepoFetcher method) (wfexs_backend.fetchers.git.GitFetcher method) (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher method) materializeContainers() (wfexs_backend.container_factories.ContainerFactory method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) MaterializedContainerImage (class in wfexs_backend.ro_crate) MaterializedContent (class in wfexs_backend.common) MaterializedContent2AbstractGeneratedContent() (in module wfexs_backend.utils.contents) MaterializedExportAction (class in wfexs_backend.workflow) MaterializedInput (class in wfexs_backend.common) MaterializedOutput (class in wfexs_backend.common) MaterializedWorkflowEngine (class in wfexs_backend.workflow_engines) materializeEngine() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.WorkflowEngine method) materializeEngineVersion() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) (wfexs_backend.workflow_engines.WorkflowEngine method) materializeInputs() (wfexs_backend.workflow.WF method) materializeSingleContainer() (wfexs_backend.container_factories.ContainerFactory method) (wfexs_backend.container_factories.docker_container.DockerContainerFactory method) (wfexs_backend.container_factories.no_container.NoContainerFactory method) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory method) (wfexs_backend.container_factories.singularity_container.SingularityContainerFactory method) materializeWorkflow() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) (wfexs_backend.workflow_engines.WorkflowEngine method) materializeWorkflowAndContainers() (wfexs_backend.workflow.WF method) MaterializeWorkflowAndContainers() (wfexs_backend.workflow_engines.WorkflowEngine class method) MAX_RAND_CHARS (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator attribute) MAXFD (in module wfexs_backend.utils.misc) meta_dir (wfexs_backend.common.StagedSetup attribute) META_JSON_POSTFIX (in module wfexs_backend.common) metadata (wfexs_backend.common.URIWithMetadata attribute) (wfexs_backend.pushers.DraftEntry attribute) Metadata (wfexs_backend.utils.rocrate.ReproducibilityLevel attribute) metadata_array (wfexs_backend.cache_handler.CachedContent attribute) (wfexs_backend.common.MaterializedContent attribute) (wfexs_backend.fetchers.ProtocolFetcherReturn attribute) metadataLocalPath (wfexs_backend.container_factories.Container attribute) Methodology (wfexs_backend.common.AttributionRole attribute) mime (wfexs_backend.utils.io_wrappers.MultipartFile attribute) mime() (wfexs_backend.utils.io_wrappers.MIMETypeIOWrapper method) MIMETypeIOWrapper (class in wfexs_backend.utils.io_wrappers) MIN_RAND_CHARS (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator attribute) Minimal (wfexs_backend.utils.rocrate.ReproducibilityLevel attribute) module wfexs_backend wfexs_backend.__main__ wfexs_backend.cache_handler wfexs_backend.common wfexs_backend.container_factories wfexs_backend.container_factories.abstract_docker_container wfexs_backend.container_factories.docker_container wfexs_backend.container_factories.no_container wfexs_backend.container_factories.podman_container wfexs_backend.container_factories.singularity_container wfexs_backend.docs_module wfexs_backend.encrypted_fs wfexs_backend.fetchers wfexs_backend.fetchers.b2share wfexs_backend.fetchers.data wfexs_backend.fetchers.doi wfexs_backend.fetchers.drs wfexs_backend.fetchers.fasp wfexs_backend.fetchers.file wfexs_backend.fetchers.ftp wfexs_backend.fetchers.git wfexs_backend.fetchers.gs wfexs_backend.fetchers.http wfexs_backend.fetchers.internal wfexs_backend.fetchers.internal.ftp_downloader wfexs_backend.fetchers.osf_io wfexs_backend.fetchers.pride wfexs_backend.fetchers.s3 wfexs_backend.fetchers.sftp wfexs_backend.fetchers.swh wfexs_backend.fetchers.trs_files wfexs_backend.fetchers.wiktionary wfexs_backend.fetchers.zenodo wfexs_backend.pushers wfexs_backend.pushers.abstract_contexted_export wfexs_backend.pushers.abstract_token_export wfexs_backend.pushers.abstract_token_sandboxed_export wfexs_backend.pushers.b2share_export wfexs_backend.pushers.cache_export wfexs_backend.pushers.dataverse_export wfexs_backend.pushers.nextcloud_export wfexs_backend.pushers.zenodo_export wfexs_backend.ro_crate wfexs_backend.security_context wfexs_backend.side_caches wfexs_backend.utils wfexs_backend.utils.contents wfexs_backend.utils.digests wfexs_backend.utils.docker wfexs_backend.utils.groovy_parsing wfexs_backend.utils.io_wrappers wfexs_backend.utils.licences wfexs_backend.utils.marshalling_handling wfexs_backend.utils.misc wfexs_backend.utils.orcid wfexs_backend.utils.passphrase_wrapper wfexs_backend.utils.pyld_caching wfexs_backend.utils.rocrate wfexs_backend.utils.zipfile_path wfexs_backend.wfexs_backend wfexs_backend.workflow wfexs_backend.workflow_engines wfexs_backend.workflow_engines.cwl_engine wfexs_backend.workflow_engines.nextflow_engine

Mount (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) MountWorkDir (wfexs_backend.__main__.WfExS_Commands attribute) MultipartEncoderIOWrapper (class in wfexs_backend.utils.io_wrappers) MultipartFile (class in wfexs_backend.utils.io_wrappers) MyWorkflowType() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType class method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine class method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine class method)

N

N2T_NET_SERVICE (in module wfexs_backend.fetchers.drs) name (wfexs_backend.common.Attribution attribute) (wfexs_backend.common.ExpectedOutput attribute) (wfexs_backend.common.MaterializedInput attribute) (wfexs_backend.common.MaterializedOutput attribute) (wfexs_backend.utils.groovy_parsing.NfProcess attribute) (wfexs_backend.utils.groovy_parsing.NfWorkflow attribute) (wfexs_backend.utils.zipfile_path.ZipfilePath property) (wfexs_backend.workflow.ExportItem attribute) (wfexs_backend.workflow_engines.WorkflowType attribute) NAME_PART_RULE (in module wfexs_backend.utils.groovy_parsing) NAMELESS_W_RULE (in module wfexs_backend.utils.groovy_parsing) namelist() (wfexs_backend.utils.zipfile_path.CompleteDirs method) (wfexs_backend.utils.zipfile_path.FastLookup method) newSetup() (wfexs_backend.wfexs_backend.WfExSBackend method) NextcloudContentExporter (class in wfexs_backend.pushers.nextcloud_export) NextcloudExportPlugin (class in wfexs_backend.pushers.nextcloud_export) NEXTFLOW_CONFIG_FILENAME (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) NEXTFLOW_IO (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) NEXTFLOW_REPO (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute)

NextflowWorkflowEngine (class in wfexs_backend.workflow_engines.nextflow_engine) NfInclude (class in wfexs_backend.utils.groovy_parsing) NfIncludeConfig (class in wfexs_backend.utils.groovy_parsing) NfPlugin (class in wfexs_backend.utils.groovy_parsing) NfProcess (class in wfexs_backend.utils.groovy_parsing) NfWorkflow (class in wfexs_backend.utils.groovy_parsing) nickname (wfexs_backend.common.StagedSetup attribute) nihDigester() (in module wfexs_backend.utils.digests) NO_WRAPPER_CWLTOOL_VERSION (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) NoContainer (wfexs_backend.common.ContainerType attribute) NoContainerFactory (class in wfexs_backend.container_factories.no_container) NoCratableItem (in module wfexs_backend.common) NODEJS_CONTAINER_TAG (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) NODEJS_WRAPPER (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) NoLicence (in module wfexs_backend.common) NoLicenceDescription (in module wfexs_backend.common) NoLicenceShort (in module wfexs_backend.common) normalizeRawWorkingDirectory() (wfexs_backend.wfexs_backend.WfExSBackend method) nullProcessDigest() (in module wfexs_backend.utils.digests) NXF_VER_PAT (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute)

O

OBTAIN_EXECUTION_ENV_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_EXECUTION_INPUTS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_EXECUTION_OUTPUTS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_RUN_CONTAINERS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_RUNS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_WORKFLOW_ENV_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_WORKFLOW_INPUTS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_WORKFLOW_OUTPUTS_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OBTAIN_WORKFLOW_PID_SPARQL (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) OfflineExecute (wfexs_backend.__main__.WfExS_Commands attribute) (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) OfflineQueueExecute (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) open() (wfexs_backend.utils.zipfile_path.ZipfilePath method) operatingSystem (wfexs_backend.container_factories.Container attribute) OPERATIONAL_CONTAINER_TAGS (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) operational_containers (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute)

orcid (wfexs_backend.common.ResolvedORCID attribute) ORCID_CURIE (in module wfexs_backend.utils.orcid) ORCID_HOST (in module wfexs_backend.utils.orcid) ORCID_PATTERN (in module wfexs_backend.utils.orcid) ORCID_URL_PREFIX (in module wfexs_backend.utils.orcid) OrganizeAction (class in wfexs_backend.ro_crate) origTaggedName (wfexs_backend.common.ContainerTaggedName attribute) OSF_IO_RECORD_PREFIX (in module wfexs_backend.fetchers.doi) OSF_IO_RECORD_REST (in module wfexs_backend.fetchers.osf_io) OSF_IO_SCHEME (in module wfexs_backend.fetchers.osf_io) Other (wfexs_backend.fetchers.RepoType attribute) Output (wfexs_backend.common.ExportItemType attribute) OutputClassMapping (wfexs_backend.workflow.WF attribute) outputMetaDir (wfexs_backend.workflow_engines.StagedExecution attribute) Outputs (wfexs_backend.common.CratableItem attribute) outputs_dir (wfexs_backend.common.StagedSetup attribute) outputsDir (wfexs_backend.workflow_engines.StagedExecution attribute)

P

P_RULE (in module wfexs_backend.utils.groovy_parsing) Param (wfexs_backend.common.ExportItemType attribute) parent (wfexs_backend.utils.zipfile_path.ZipfilePath property) ParseAndRemoveCredentials() (wfexs_backend.fetchers.AbstractStatefulFetcher static method) parseAndValidateSecurityContextFile() (wfexs_backend.wfexs_backend.WfExSBackend method) parseExpectedOutputs() (wfexs_backend.workflow.WF method) parseExportActions() (wfexs_backend.workflow.WF method) parseOrCreateRawWorkDir() (wfexs_backend.wfexs_backend.WfExSBackend method) ParseRawAttribution() (wfexs_backend.common.Attribution class method) ParseRawAttributions() (wfexs_backend.common.Attribution class method) partial_fingerprint (wfexs_backend.utils.docker.DockerTagMetadata attribute) password (wfexs_backend.utils.docker.Credentials attribute) path (wfexs_backend.cache_handler.CachedContent attribute) (wfexs_backend.utils.groovy_parsing.NfInclude attribute) (wfexs_backend.utils.groovy_parsing.NfIncludeConfig attribute) (wfexs_backend.utils.rocrate.ROCratePayload attribute) Path2AbstractGeneratedContent() (in module wfexs_backend.utils.contents) path_relative_to() (in module wfexs_backend.utils.zipfile_path) PathArgType (in module wfexs_backend.__main__) PATHEXP_RULE (in module wfexs_backend.utils.groovy_parsing) pid (wfexs_backend.common.Attribution attribute) (wfexs_backend.common.MarshallingStatus attribute) (wfexs_backend.pushers.DraftEntry attribute) pids (wfexs_backend.workflow.MaterializedExportAction attribute) plugin_id (wfexs_backend.workflow.ExportAction attribute) PLUGIN_NAME (wfexs_backend.pushers.AbstractExportPlugin attribute) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) (wfexs_backend.pushers.cache_export.CacheExportPlugin attribute) (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin attribute) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin attribute) PluginName() (wfexs_backend.pushers.AbstractExportPlugin class method) PLUGINS_CHILD (in module wfexs_backend.utils.groovy_parsing) Podman (wfexs_backend.common.ContainerType attribute) PODMAN_CWLTOOL_VERSION (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) PodmanContainerFactory (class in wfexs_backend.container_factories.podman_container) populate_side_caches() (in module wfexs_backend.side_caches) PopulateSideCaches (wfexs_backend.__main__.WfExS_Commands attribute) PRE_CLOSURE_NAME (in module wfexs_backend.utils.groovy_parsing) PRE_IDENTIFIER_NAME (in module wfexs_backend.utils.groovy_parsing)

preferred_id (wfexs_backend.workflow.ExportAction attribute) preferred_scheme (wfexs_backend.workflow.ExportAction attribute) preferredFilename (wfexs_backend.common.AbstractGeneratedContent attribute) (wfexs_backend.common.ExpectedOutput attribute) preferredName (wfexs_backend.common.URIWithMetadata attribute) prettyFilename (wfexs_backend.common.MaterializedContent attribute) PRIDE_PROJECT_SCHEME (in module wfexs_backend.fetchers.pride) PRIDE_PROJECTS_REST (in module wfexs_backend.fetchers.pride) PRIORITY (wfexs_backend.fetchers.AbstractRepoFetcher attribute) (wfexs_backend.fetchers.AbstractStatefulFetcher attribute) priority (wfexs_backend.fetchers.DocumentedProtocolFetcher attribute) (wfexs_backend.fetchers.DocumentedStatefulProtocolFetcher attribute) (wfexs_backend.workflow_engines.WorkflowType attribute) PROCESS_CHILD (in module wfexs_backend.utils.groovy_parsing) process_dir_entries() (in module wfexs_backend.utils.digests) processCacheCommand() (in module wfexs_backend.__main__) processExportCommand() (in module wfexs_backend.__main__) processListContainerFactoriesCommand() (in module wfexs_backend.__main__) processListFetchersCommand() (in module wfexs_backend.__main__) processListLicencesCommand() (in module wfexs_backend.__main__) processListPushersCommand() (in module wfexs_backend.__main__) processListWorkflowEnginesCommand() (in module wfexs_backend.__main__) processStagedWorkdirCommand() (in module wfexs_backend.__main__) profiles (wfexs_backend.workflow_engines.StagedExecution attribute) ProjectAdministration (wfexs_backend.common.AttributionRole attribute) PropertyValue (class in wfexs_backend.ro_crate) ProspectiveProvenance (wfexs_backend.common.CratableItem attribute) ProtocolFetcherReturn (class in wfexs_backend.fetchers) ProvenanceCrate (wfexs_backend.common.ExportItemType attribute) publish_draft_record() (wfexs_backend.pushers.AbstractDraftedExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) publish_draft_record_by_id() (wfexs_backend.pushers.AbstractDraftedExportPlugin method) PURL_NAMESPACE (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) PURL_PREFIX (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) push() (wfexs_backend.pushers.abstract_token_export.AbstractTokenExportPlugin method) (wfexs_backend.pushers.AbstractExportPlugin method) (wfexs_backend.pushers.cache_export.CacheExportPlugin method) pyld_cache_initialize() (in module wfexs_backend.utils.pyld_caching)

Q

query() (wfexs_backend.container_factories.ContainerCacheHandler method) query_n2t() (in module wfexs_backend.fetchers.drs) query_tag() (wfexs_backend.utils.docker.DockerHelper method)

Queued (wfexs_backend.common.ExecutionStatus attribute) queued (wfexs_backend.workflow_engines.StagedExecution attribute) queueExecution() (wfexs_backend.workflow.WF method)

R

Raw (wfexs_backend.fetchers.RepoType attribute) raw_metadata (wfexs_backend.pushers.DraftEntry attribute) raw_work_dir (wfexs_backend.common.StagedSetup attribute) read_bytes() (wfexs_backend.utils.zipfile_path.ZipfilePath method) read_text() (wfexs_backend.utils.zipfile_path.ZipfilePath method) readable() (wfexs_backend.utils.io_wrappers.AbstractProxyIOWrapper method) readinto() (wfexs_backend.utils.io_wrappers.DigestIOWrapper method) (wfexs_backend.utils.io_wrappers.LimitedStreamIOWrapper method) (wfexs_backend.utils.io_wrappers.MIMETypeIOWrapper method) (wfexs_backend.utils.io_wrappers.MultipartEncoderIOWrapper method) ReadROCrateMetadata() (in module wfexs_backend.utils.rocrate) readSecuredWorkdirPassphrase() (wfexs_backend.wfexs_backend.WfExSBackend method) ReadSecurityContextFile() (wfexs_backend.security_context.SecurityContextVault class method) real_unlink_if_exists() (in module wfexs_backend.utils.contents) reason (wfexs_backend.fetchers.FetcherException attribute) record (wfexs_backend.common.ResolvedORCID attribute) record_fetch_metadata (wfexs_backend.common.ResolvedORCID attribute) REFS_HEADS_PREFIX (wfexs_backend.fetchers.git.GitFetcher attribute) REFS_TAGS_PREFIX (wfexs_backend.fetchers.git.GitFetcher attribute) REGISTER_CONSTRUCTOR (in module wfexs_backend.container_factories) RegisterYAMLConstructor() (wfexs_backend.container_factories.Container class method) registries (wfexs_backend.common.ContainerTaggedName attribute) RegistryPat (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) registryServer (wfexs_backend.utils.docker.DockerTagMetadata attribute) rel_path (wfexs_backend.fetchers.RemoteRepo attribute) (wfexs_backend.utils.rocrate.ROCratePayload attribute) RELATIVE_ROCRATE_NS (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) RELATIVE_ROCRATE_SCHEME (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) RELATIVE_ROCRATE_SPARQL_BASE (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) relative_to() (wfexs_backend.utils.zipfile_path.ZipfilePath method) relPath (wfexs_backend.common.LocalWorkflow attribute) relPathFiles (wfexs_backend.common.LocalWorkflow attribute) remote_basename (wfexs_backend.pushers.nextcloud_export.ExportMapping attribute) remote_dirname (wfexs_backend.pushers.nextcloud_export.ExportMapping attribute) remote_repo (wfexs_backend.wfexs_backend.IdentifiedWorkflow attribute)

RemoteRepo (class in wfexs_backend.fetchers) RemoteWordlistResource (class in wfexs_backend.utils.passphrase_wrapper) Remove (wfexs_backend.__main__.WfExS_Cache_Commands attribute) (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) remove() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) remove_remote_path() (wfexs_backend.pushers.nextcloud_export.NextcloudContentExporter method) removeStagedWorkflows() (wfexs_backend.wfexs_backend.WfExSBackend method) repo (wfexs_backend.utils.docker.DockerTagMetadata attribute) repo_type (wfexs_backend.fetchers.RemoteRepo attribute) repo_url (wfexs_backend.fetchers.RemoteRepo attribute) RepoGuessException RepoGuessFlavor (class in wfexs_backend.fetchers) RepoType (class in wfexs_backend.fetchers) ReproducibilityLevel (class in wfexs_backend.utils.rocrate) resolve() (wfexs_backend.utils.zipfile_path.ZipfilePath method) resolve_dir() (wfexs_backend.utils.zipfile_path.CompleteDirs method) ResolvedORCID (class in wfexs_backend.common) Resources (wfexs_backend.common.AttributionRole attribute) ReStage (wfexs_backend.__main__.WfExS_Commands attribute) RetrospectiveProvenance (wfexs_backend.common.CratableItem attribute) RevContentWithURIsMIMEs (in module wfexs_backend.utils.rocrate) ROCrate (wfexs_backend.common.CacheType attribute) ROCRATE_JSONLD_FILENAME (in module wfexs_backend.utils.rocrate) rocrate_programming_language (wfexs_backend.workflow_engines.WorkflowType attribute) ROCrateGenerationException ROCratePayload (class in wfexs_backend.utils.rocrate) ROCrateToolbox (class in wfexs_backend.utils.rocrate) ROCrateToolboxException roles (wfexs_backend.common.Attribution attribute) ROOT_RULE (in module wfexs_backend.utils.groovy_parsing) Run (wfexs_backend.__main__.WfExS_Export_Commands attribute) runLocalNextflowCommand() (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) runNextflowCommand() (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) runNextflowCommandInDocker() (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) Running (wfexs_backend.common.ExecutionStatus attribute)

S

sa_id (wfexs_backend.utils.rocrate.ContainerTypeMetadata attribute) SANDBOX_B2SHARE_API_PREFIX (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) SANDBOX_B2SHARE_DOI_PREFIX (wfexs_backend.pushers.b2share_export.B2SHAREPublisher attribute) SANDBOX_ZENODO_PREFIX (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin attribute) scantree() (in module wfexs_backend.utils.digests) SCHEMA_ORG_PREFIX (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) SCHEMA_SALAD_PYTHON_PACKAGE (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) SCHEMAS_REL_DIR (in module wfexs_backend.utils.misc) (wfexs_backend.wfexs_backend.WfExSBackend attribute) SCHEME_PAT (wfexs_backend.wfexs_backend.WfExSBackend attribute) SCHEME_PATTERN (wfexs_backend.security_context.SecurityContextVault attribute) SchemeHandlerCacheHandler (class in wfexs_backend.cache_handler) secContext (wfexs_backend.common.LicensedURI attribute) secondaryFiles (wfexs_backend.common.GeneratedContent attribute) (wfexs_backend.common.GeneratedDirectoryContent attribute) secondaryInputs (wfexs_backend.common.MaterializedInput attribute) secure_exec (wfexs_backend.common.StagedSetup attribute) SECURITY_CONTEXT_SCHEMA (wfexs_backend.security_context.SecurityContextVault attribute) SecurityContextVault (class in wfexs_backend.security_context) SecurityContextVaultException set_wfexs_context() (wfexs_backend.pushers.abstract_contexted_export.AbstractContextedExportPlugin method) setup (wfexs_backend.common.ContentWithURIsDesc attribute) (wfexs_backend.workflow.ExportAction attribute) setupEngine() (wfexs_backend.workflow.WF method) setupWorkdir() (wfexs_backend.workflow.WF method) sftpCopy() (in module wfexs_backend.fetchers.sftp) Shell (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) shellFirstStagedWorkflow() (wfexs_backend.wfexs_backend.WfExSBackend method) short (wfexs_backend.common.LicenceDescription attribute) shortname (wfexs_backend.workflow_engines.WorkflowType attribute) sideContainers() (wfexs_backend.workflow_engines.AbstractWorkflowEngineType method) (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.WorkflowEngine method) signature (wfexs_backend.common.AbstractGeneratedContent attribute) (wfexs_backend.container_factories.Container attribute) (wfexs_backend.utils.rocrate.ROCratePayload attribute) simpleContainerFileName() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) (wfexs_backend.workflow_engines.WorkflowEngine method) sing_tag (wfexs_backend.container_factories.singularity_container.FailedContainerTag attribute) Singularity (wfexs_backend.common.ContainerType attribute) (wfexs_backend.utils.rocrate.ContainerImageAdditionalType attribute) SingularityContainerFactory (class in wfexs_backend.container_factories.singularity_container) size (wfexs_backend.utils.io_wrappers.MultipartFile attribute) Software (wfexs_backend.common.AttributionRole attribute) SOFTWARE_HERITAGE_SCHEME (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SoftwareHeritage (wfexs_backend.fetchers.RepoType attribute) SoftwareHeritageFetcher (class in wfexs_backend.fetchers.swh) source_type (wfexs_backend.container_factories.Container attribute) SourceCodeFile (class in wfexs_backend.ro_crate) SPARQL_NS (wfexs_backend.utils.rocrate.ROCrateToolbox attribute) SPDX_JSON_URL_TEMPLATE (wfexs_backend.utils.licences.LicenceMatcher attribute) Stage (wfexs_backend.__main__.WfExS_Commands attribute) stage (wfexs_backend.common.MarshallingStatus attribute)

STAGE_DEFINITION_SCHEMA (wfexs_backend.workflow.WF attribute) StageCrate (wfexs_backend.common.ExportItemType attribute) staged_containers_dir (wfexs_backend.workflow_engines.AbstractWorkflowEngineType property) (wfexs_backend.workflow_engines.WorkflowEngine property) STAGED_CRATE_FILE (wfexs_backend.workflow.WF attribute) StagedExecution (class in wfexs_backend.workflow_engines) StagedSetup (class in wfexs_backend.common) StagedWorkDir (wfexs_backend.__main__.WfExS_Commands attribute) stageWorkDir() (wfexs_backend.workflow.WF method) staging_recipe (wfexs_backend.workflow.WF property) started (wfexs_backend.workflow_engines.StagedExecution attribute) STATS_DAG_DOT_FILE (in module wfexs_backend.workflow_engines) Status (wfexs_backend.__main__.WfExS_Cache_Commands attribute) (wfexs_backend.__main__.WfExS_Staged_WorkDir_Commands attribute) status (wfexs_backend.workflow_engines.StagedExecution attribute) statusStagedWorkflows() (wfexs_backend.wfexs_backend.WfExSBackend method) StrContainerAdditionalType2ContainerImageAdditionalType (in module wfexs_backend.utils.rocrate) StrDocEnum (class in wfexs_backend.common) stream (wfexs_backend.utils.io_wrappers.MultipartFile attribute) streamfetch() (wfexs_backend.fetchers.AbstractStatefulStreamingFetcher method) stringifyDigest() (in module wfexs_backend.utils.digests) stringifyFilenameDigest() (in module wfexs_backend.utils.digests) structureAsNXFParams() (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine method) subend (wfexs_backend.utils.passphrase_wrapper.RemoteWordlistResource attribute) substart (wfexs_backend.utils.passphrase_wrapper.RemoteWordlistResource attribute) Supervision (wfexs_backend.common.AttributionRole attribute) SUPPORTED_CONTAINER_TYPES (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) SUPPORTED_SECURE_EXEC_CONTAINER_TYPES (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine attribute) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute) SupportedContainerTypes() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine class method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine class method) (wfexs_backend.workflow_engines.WorkflowEngine class method) SupportedSecureExecContainerTypes() (wfexs_backend.workflow_engines.cwl_engine.CWLWorkflowEngine class method) (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine class method) (wfexs_backend.workflow_engines.WorkflowEngine class method) SupportsContainerFactory() (wfexs_backend.workflow_engines.WorkflowEngine class method) SupportsContainerType() (wfexs_backend.workflow_engines.WorkflowEngine class method) supportsFeature() (wfexs_backend.container_factories.ContainerFactory method) SupportsSecureExecContainerFactory() (wfexs_backend.workflow_engines.WorkflowEngine class method) SupportsSecureExecContainerType() (wfexs_backend.workflow_engines.WorkflowEngine class method) SWH_API_REST (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWH_API_REST_CONTENT (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWH_API_REST_KNOWN (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWH_API_REST_RELEASE (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWH_API_REST_RESOLVE (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWH_API_REST_REVISION (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWH_API_REST_VAULT_FLAT (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) SWORD_APP_NAMESPACE (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) SWORD_APP_PREFIX (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) SWORD_TERMS_NAMESPACE (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) SWORD_TERMS_PREFIX (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) syntheticOutput (wfexs_backend.common.ExpectedOutput attribute) (wfexs_backend.common.MaterializedOutput attribute)

T

tag (wfexs_backend.container_factories.singularity_container.FailedContainerTag attribute) (wfexs_backend.fetchers.RemoteRepo attribute) taggedName (wfexs_backend.container_factories.Container attribute) tell() (wfexs_backend.utils.io_wrappers.AbstractProxyIOWrapper method) temp_dir (wfexs_backend.common.StagedSetup attribute) TEMPLATE_CHILD (in module wfexs_backend.utils.groovy_parsing) templates (wfexs_backend.utils.groovy_parsing.NfProcess attribute) title (wfexs_backend.workflow.ExportAction attribute) transfer() (wfexs_backend.container_factories.ContainerCacheHandler method) translate_glob_args() (in module wfexs_backend.utils.misc) TRIMMABLE_MANIFEST_KEYS (wfexs_backend.container_factories.docker_container.DockerContainerFactory attribute) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory attribute) trimmable_manifest_keys() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory class method) (wfexs_backend.container_factories.docker_container.DockerContainerFactory class method) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory class method) TROJAN_CONFIG_FILENAME (wfexs_backend.workflow_engines.nextflow_engine.NextflowWorkflowEngine attribute)

TRS (wfexs_backend.common.CacheType attribute) (wfexs_backend.fetchers.RepoType attribute) trs_descriptor (wfexs_backend.workflow_engines.WorkflowType attribute) TRS_DESCRIPTOR_INFIX (in module wfexs_backend.fetchers.trs_files) TRS_FILES_SUFFIX (in module wfexs_backend.fetchers.trs_files) TRS_METADATA_FILE (wfexs_backend.wfexs_backend.WfExSBackend attribute) TRS_QUERY_CACHE_FILE (wfexs_backend.wfexs_backend.WfExSBackend attribute) TRS_SCHEME_PREFIX (in module wfexs_backend.fetchers.trs_files) TRS_TOOL_FILES_FILE (wfexs_backend.workflow.WF attribute) TRS_TOOLS_PATH (wfexs_backend.workflow.WF attribute) type (wfexs_backend.common.ContainerTaggedName attribute) (wfexs_backend.workflow.ExportItem attribute) TYPES (wfexs_backend.ro_crate.ContainerImage attribute) (wfexs_backend.ro_crate.FixedWorkflow attribute) (wfexs_backend.ro_crate.MaterializedContainerImage attribute) (wfexs_backend.ro_crate.SourceCodeFile attribute) (wfexs_backend.ro_crate.WorkflowDiagram attribute)

U

UDocker (wfexs_backend.common.ContainerType attribute) unmarshall_namedtuple() (in module wfexs_backend.utils.marshalling_handling) unmarshallConfig() (wfexs_backend.workflow.WF method) unmarshallExecute() (wfexs_backend.workflow.WF method) unmarshallExport() (wfexs_backend.workflow.WF method) unmarshallStage() (wfexs_backend.workflow.WF method) unmountWorkdir() (wfexs_backend.workflow.WF method) unstringifyDigest() (in module wfexs_backend.utils.digests) update() (wfexs_backend.container_factories.ContainerCacheHandler method) update_record_metadata() (wfexs_backend.pushers.AbstractDraftedExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method) update_record_metadata_by_id() (wfexs_backend.pushers.AbstractDraftedExportPlugin method) upload_file_to_draft() (wfexs_backend.pushers.AbstractDraftedExportPlugin method) (wfexs_backend.pushers.b2share_export.B2SHAREPublisher method) (wfexs_backend.pushers.dataverse_export.DataversePublisher method) (wfexs_backend.pushers.nextcloud_export.NextcloudExportPlugin method) (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin method)

upload_file_to_draft_by_id() (wfexs_backend.pushers.AbstractDraftedExportPlugin method) uri (wfexs_backend.common.AbstractGeneratedContent attribute) (wfexs_backend.common.LicensedURI attribute) (wfexs_backend.common.URIWithMetadata attribute) (wfexs_backend.utils.passphrase_wrapper.RemoteWordlistResource attribute) uriMatch (wfexs_backend.workflow_engines.WorkflowType attribute) uris (wfexs_backend.common.LicenceDescription attribute) uriTemplate (wfexs_backend.workflow_engines.WorkflowType attribute) URIWithMetadata (class in wfexs_backend.common) url (wfexs_backend.common.ResolvedORCID attribute) (wfexs_backend.workflow_engines.WorkflowType attribute) usage own_workflow test_workflow username (wfexs_backend.utils.docker.Credentials attribute)

V

VALID_LICENCES_MAPPING (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute) VALID_NI_ALGOS (in module wfexs_backend.utils.digests) Validate (wfexs_backend.__main__.WfExS_Cache_Commands attribute) validate() (wfexs_backend.cache_handler.SchemeHandlerCacheHandler method) validate_orcid() (in module wfexs_backend.utils.orcid) validateConfigFiles() (wfexs_backend.wfexs_backend.WfExSBackend method) Validation (wfexs_backend.common.AttributionRole attribute) Value (wfexs_backend.common.ContentKind attribute)

values (wfexs_backend.common.GeneratedDirectoryContent attribute) (wfexs_backend.common.MaterializedInput attribute) (wfexs_backend.common.MaterializedOutput attribute) VAR_RULE (in module wfexs_backend.utils.groovy_parsing) variant_name() (wfexs_backend.container_factories.abstract_docker_container.AbstractDockerContainerFactory class method) (wfexs_backend.container_factories.docker_container.DockerContainerFactory class method) (wfexs_backend.container_factories.podman_container.PodmanContainerFactory class method) version (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) Visualization (wfexs_backend.common.AttributionRole attribute)

W

W_RULE (in module wfexs_backend.utils.groovy_parsing) WAIT_SECS (wfexs_backend.fetchers.swh.SoftwareHeritageFetcher attribute) web_url (wfexs_backend.fetchers.RemoteRepo attribute) WF (class in wfexs_backend.workflow) WFException wfexs_backend module wfexs_backend.__main__ module wfexs_backend.cache_handler module wfexs_backend.common module wfexs_backend.container_factories module wfexs_backend.container_factories.abstract_docker_container module wfexs_backend.container_factories.docker_container module wfexs_backend.container_factories.no_container module wfexs_backend.container_factories.podman_container module wfexs_backend.container_factories.singularity_container module wfexs_backend.docs_module module wfexs_backend.encrypted_fs module wfexs_backend.fetchers module wfexs_backend.fetchers.b2share module wfexs_backend.fetchers.data module wfexs_backend.fetchers.doi module wfexs_backend.fetchers.drs module wfexs_backend.fetchers.fasp module wfexs_backend.fetchers.file module wfexs_backend.fetchers.ftp module wfexs_backend.fetchers.git module wfexs_backend.fetchers.gs module wfexs_backend.fetchers.http module wfexs_backend.fetchers.internal module wfexs_backend.fetchers.internal.ftp_downloader module wfexs_backend.fetchers.osf_io module wfexs_backend.fetchers.pride module wfexs_backend.fetchers.s3 module wfexs_backend.fetchers.sftp module wfexs_backend.fetchers.swh module wfexs_backend.fetchers.trs_files module wfexs_backend.fetchers.wiktionary module wfexs_backend.fetchers.zenodo module wfexs_backend.pushers module wfexs_backend.pushers.abstract_contexted_export module wfexs_backend.pushers.abstract_token_export module wfexs_backend.pushers.abstract_token_sandboxed_export module wfexs_backend.pushers.b2share_export module wfexs_backend.pushers.cache_export module wfexs_backend.pushers.dataverse_export module wfexs_backend.pushers.nextcloud_export module wfexs_backend.pushers.zenodo_export module wfexs_backend.ro_crate module wfexs_backend.security_context module wfexs_backend.side_caches module wfexs_backend.utils module wfexs_backend.utils.contents module

wfexs_backend.utils.digests module wfexs_backend.utils.docker module wfexs_backend.utils.groovy_parsing module wfexs_backend.utils.io_wrappers module wfexs_backend.utils.licences module wfexs_backend.utils.marshalling_handling module wfexs_backend.utils.misc module wfexs_backend.utils.orcid module wfexs_backend.utils.passphrase_wrapper module wfexs_backend.utils.pyld_caching module wfexs_backend.utils.rocrate module wfexs_backend.utils.zipfile_path module wfexs_backend.wfexs_backend module wfexs_backend.workflow module wfexs_backend.workflow_engines module wfexs_backend.workflow_engines.cwl_engine module wfexs_backend.workflow_engines.nextflow_engine module WfExS_Cache_Commands (class in wfexs_backend.__main__) WfExS_Commands (class in wfexs_backend.__main__) WfExS_Export_Commands (class in wfexs_backend.__main__) WFEXS_PASSPHRASE_SCHEME (wfexs_backend.utils.passphrase_wrapper.WfExSPassphraseGenerator attribute) WfExS_Staged_WorkDir_Commands (class in wfexs_backend.__main__) WFEXS_TERMS_BASE (in module wfexs_backend.utils.rocrate) WFEXS_TERMS_CONTEXT (in module wfexs_backend.utils.rocrate) WFEXS_TERMS_NAMESPACE (in module wfexs_backend.utils.rocrate) WfExSBackend (class in wfexs_backend.wfexs_backend) WfExSBackendException WfExSPassGenSingleton (class in wfexs_backend.utils.passphrase_wrapper) WfExSPassphraseGenerator (class in wfexs_backend.utils.passphrase_wrapper) WFWarning what (wfexs_backend.workflow.ExportAction attribute) when (wfexs_backend.workflow.MaterializedExportAction attribute) WIKTIONARY_PROTO (wfexs_backend.fetchers.wiktionary.WiktionaryFetcher attribute) WiktionaryFetcher (class in wfexs_backend.fetchers.wiktionary) with_name() (wfexs_backend.utils.zipfile_path.ZipfilePath method) work_dir (wfexs_backend.common.StagedSetup attribute) WORKDIR_CONSOLIDATED_WORKFLOW_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_CONTAINERS_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_ENGINE_TWEAKS_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_EXTRAPOLATED_INPUTS_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_INPUTS_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_INTERMEDIATE_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_MARSHALLED_EXECUTE_FILE (in module wfexs_backend.workflow_engines) WORKDIR_MARSHALLED_EXPORT_FILE (in module wfexs_backend.workflow_engines) WORKDIR_MARSHALLED_STAGE_FILE (in module wfexs_backend.workflow_engines) WORKDIR_META_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_OUTPUTS_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_PASSPHRASE_FILE (in module wfexs_backend.workflow_engines) WORKDIR_STATS_RELDIR (in module wfexs_backend.workflow_engines) WORKDIR_STDERR_FILE (in module wfexs_backend.workflow_engines) WORKDIR_STDOUT_FILE (in module wfexs_backend.workflow_engines) WORKDIR_WORKFLOW_META_FILE (in module wfexs_backend.workflow_engines) WORKDIR_WORKFLOW_RELDIR (in module wfexs_backend.workflow_engines) workdirToBagit() (wfexs_backend.workflow.WF method) Workflow (wfexs_backend.common.CacheType attribute) (wfexs_backend.common.CratableItem attribute) workflow (wfexs_backend.workflow_engines.MaterializedWorkflowEngine attribute) WORKFLOW_CHILD (in module wfexs_backend.utils.groovy_parsing) workflow_config (wfexs_backend.common.StagedSetup attribute) workflow_dir (wfexs_backend.common.StagedSetup attribute) WORKFLOW_RUN_BASE (in module wfexs_backend.utils.rocrate) WORKFLOW_RUN_CONTEXT (in module wfexs_backend.utils.rocrate) WORKFLOW_RUN_NAMESPACE (in module wfexs_backend.utils.rocrate) workflow_type (wfexs_backend.common.MarshallingStatus attribute) (wfexs_backend.wfexs_backend.IdentifiedWorkflow attribute) WorkflowDiagram (class in wfexs_backend.ro_crate) WorkflowEngine (class in wfexs_backend.workflow_engines) WorkflowEngineException WorkflowEngineInstallException WORKFLOWHUB_RECORD_PREFIX (in module wfexs_backend.fetchers.doi) WorkflowHubShortLicencesList (in module wfexs_backend.utils.licences) WorkflowRunROCrate (class in wfexs_backend.ro_crate) WorkflowType (class in wfexs_backend.workflow_engines) workflowType (wfexs_backend.workflow_engines.AbstractWorkflowEngineType property) WorkingDirectory (wfexs_backend.common.ExportItemType attribute) writable() (wfexs_backend.utils.io_wrappers.AbstractProxyIOWrapper method) write() (wfexs_backend.ro_crate.FixedDataset method) (wfexs_backend.ro_crate.FixedFile method) writeWRROC() (wfexs_backend.ro_crate.WorkflowRunROCrate method) WritingOriginalDraft (wfexs_backend.common.AttributionRole attribute) WritingReviewEditing (wfexs_backend.common.AttributionRole attribute)

X

XML_NS (wfexs_backend.pushers.dataverse_export.DataversePublisher attribute)

Z

ZENODO_LICENSE_REST (in module wfexs_backend.fetchers.zenodo) ZENODO_NEW_RECORD_PREFIX (in module wfexs_backend.fetchers.doi) ZENODO_OLD_LICENSE_REST (in module wfexs_backend.fetchers.zenodo) ZENODO_PREFIX (wfexs_backend.pushers.zenodo_export.ZenodoExportPlugin attribute) ZENODO_RECORD_PREFIX (in module wfexs_backend.fetchers.doi)

ZENODO_RECORD_REST (in module wfexs_backend.fetchers.zenodo) ZENODO_SCHEME (in module wfexs_backend.fetchers.zenodo) ZenodoExportPlugin (class in wfexs_backend.pushers.zenodo_export) zip_root (wfexs_backend.utils.zipfile_path.ZipfilePath property) ZipfilePath (class in wfexs_backend.utils.zipfile_path)