diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 645370329..7889809eb 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -20,7 +20,7 @@ jobs: with: ref: ${{github.event.pull_request.head.ref}} repository: ${{github.event.pull_request.head.repo.full_name}} - # Passing a PAT from the PlanXCybrog bot account here, since otherwise commit pushed by this action won't bale able to trigger other actions, see https://github.com/stefanzweifel/git-auto-commit-action?tab=readme-ov-file#commits-made-by-this-action-do-not-trigger-new-workflow-runs + # Passing a PAT from the PlanXCybrog bot account here, since otherwise commits pushed by this action won't be able to trigger other actions, see https://github.com/stefanzweifel/git-auto-commit-action?tab=readme-ov-file#commits-made-by-this-action-do-not-trigger-new-workflow-runs token: ${{ secrets.PLANXCYBORG_PAT }} - name: Set up Python 3.9 uses: actions/setup-python@v1 diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 762ecc015..2af5ae046 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree index 9d8de49d1..056226ad6 100644 Binary files a/docs/_build/doctrees/tools/indexing.doctree and b/docs/_build/doctrees/tools/indexing.doctree differ diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree index d987bd536..f7ae53f72 100644 Binary files a/docs/_build/doctrees/tools/metadata.doctree and b/docs/_build/doctrees/tools/metadata.doctree differ diff --git a/docs/_build/html/_modules/gen3/index.html b/docs/_build/html/_modules/gen3/index.html index ea26f3a80..fd9c58e7a 100644 --- a/docs/_build/html/_modules/gen3/index.html +++ b/docs/_build/html/_modules/gen3/index.html @@ -82,6 +82,7 @@
if not endpoint.endswith(service_location):
endpoint += "/" + service_location
+ self.endpoint = endpoint
self.client = client.IndexClient(endpoint, auth=auth_provider)
### Get Requests
@@ -849,6 +850,10 @@ Source code for gen3.index
"content_updated_date": content_updated_date,
}
rec = self.client.get(guid)
+ if not rec:
+ raise ValueError(
+ f"No indexd record found for GUID '{guid}' at '{self.endpoint}'"
+ )
for k, v in updatable_attrs.items():
if v is not None:
exec(f"rec.{k} = v")
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 83d3aa6c3..eaed4a4ae 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"DRS Download Tools": [[10, null]], "Download": [[11, "module-gen3.tools.indexing.download_manifest"]], "Gen3 Auth Helper": [[0, null]], "Gen3 File Class": [[1, null]], "Gen3 Index Class": [[3, null]], "Gen3 Jobs Class": [[4, null]], "Gen3 Metadata Class": [[5, null]], "Gen3 Object Class": [[6, null]], "Gen3 Query Class": [[7, null]], "Gen3 Submission Class": [[8, null]], "Gen3 Tools": [[9, null]], "Gen3 Workspace Storage": [[13, null]], "Index": [[11, "module-gen3.tools.indexing.index_manifest"]], "Indexing Tools": [[11, null]], "Indices and tables": [[2, "indices-and-tables"]], "Ingest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "Metadata Tools": [[12, null]], "Verify": [[11, "module-gen3.tools.indexing.verify_manifest"]], "Welcome to Gen3 SDK\u2019s documentation!": [[2, null]]}, "docnames": ["auth", "file", "index", "indexing", "jobs", "metadata", "object", "query", "submission", "tools", "tools/drs_pull", "tools/indexing", "tools/metadata", "wss"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["auth.rst", "file.rst", "index.rst", "indexing.rst", "jobs.rst", "metadata.rst", "object.rst", "query.rst", "submission.rst", "tools.rst", "tools/drs_pull.rst", "tools/indexing.rst", "tools/metadata.rst", "wss.rst"], "indexentries": {"_manager (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable._manager", false]], "access_methods (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.access_methods", false]], "acls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ACLS", false]], "async_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create", false]], "async_create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create_aliases", false]], "async_create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_create_record", false]], "async_delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_alias", false]], "async_delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_aliases", false]], "async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.async_download_object_manifest", false]], "async_get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get", false]], "async_get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get_aliases", false]], "async_get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_record", false]], "async_get_records_from_checksum() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_from_checksum", false]], "async_get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_on_page", false]], "async_get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_with_params", false]], "async_ingest_metadata_manifest() (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest", false]], "async_query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_query_urls", false]], "async_query_urls_from_indexd() (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd", false]], "async_run_job_and_wait() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.async_run_job_and_wait", false]], "async_update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update", false]], "async_update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update_aliases", false]], "async_update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_update_record", false]], "async_verify_object_manifest() (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.async_verify_object_manifest", false]], "auth_provider (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.auth_provider", false]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ", false]], "batch_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.batch_create", false]], "cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens", false]], "children (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.children", false]], "column_to_use_as_guid (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID", false]], "commons_url (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.commons_url", false]], "copy() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.copy", false]], "create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create", false]], "create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_aliases", false]], "create_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_blank", false]], "create_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_index_key_path", false]], "create_job() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.create_job", false]], "create_new_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_new_version", false]], "create_object_list() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.create_object_list", false]], "create_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_program", false]], "create_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_project", false]], "create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_record", false]], "created_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.created_time", false]], "curl() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.curl", false]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR", false]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete", false]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias", false]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases", false]], "delete_all_guids() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.delete_all_guids", false]], "delete_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file", false]], "delete_file_locations() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file_locations", false]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path", false]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node", false]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes", false]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object", false]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program", false]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project", false]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record", false]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record", false]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records", false]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download", false]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download", false]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download", false]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type 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"force_metadata_columns_even_if_empti": 11, "form": 13, "format": [3, 5, 8, 11], "from": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13], "func_to_parse_row": [11, 12], "function": [2, 3, 4, 5, 9, 10, 11, 12], "g": 10, "gen3": [10, 11, 12], "gen3_api_kei": 0, "gen3_oidc_client_creds_secret": 0, "gen3auth": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "gen3fil": [1, 2], "gen3index": [2, 3], "gen3job": [2, 4, 10], "gen3metadata": [2, 5], "gen3object": [2, 6], "gen3queri": [2, 7], "gen3submiss": [2, 8], "gen3wsstorag": [2, 13], "gener": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13], "get": [0, 1, 2, 3, 4, 5, 8, 10, 11, 12, 13], "get_access_token": [0, 2], "get_access_token_from_wt": [0, 2], "get_alias": [2, 5], "get_all_record": [2, 3], "get_dictionary_al": [2, 8], "get_dictionary_nod": [2, 8], "get_fresh_token": [2, 9, 10], "get_graphql_schema": [2, 8], "get_guid_from_fil": 12, "get_guids_prefix": [2, 3], "get_index_key_path": [2, 5], "get_latest_vers": [2, 3], "get_output": [2, 4], "get_presigned_url": [1, 2], "get_program": [2, 8], "get_project": [2, 8], "get_project_dictionari": [2, 8], "get_project_manifest": [2, 8], "get_record": [2, 3], "get_record_doc": [2, 3], "get_records_on_pag": [2, 3], "get_stat": [2, 3], "get_statu": [2, 4], "get_url": [2, 3], "get_valid_guid": [2, 3], "get_vers": [2, 3, 4, 5], "get_with_param": [2, 3], "giangb": 11, "github": [2, 7], "give": 1, "given": [0, 3, 4, 5, 8, 10, 12, 13], "global": [4, 5], "good": 3, "grant": 0, "graph": 8, "graphql": [7, 8], "graphql_queri": [2, 7], "group": 3, "guid": [1, 2, 3, 5, 6, 9, 11, 12], "guid_exampl": 11, "guid_for_row": 12, "guid_from_fil": 12, "guid_type_for_indexed_file_object": [2, 9, 12], "guid_type_for_non_indexed_file_object": [2, 9, 12], "guppi": 7, "ha": [0, 11], "handl": [3, 10], "hardcod": 0, "has_vers": 3, "hash": [3, 11], "hash_typ": 3, "have": [5, 11], "header": 11, "healthi": [3, 4, 5], "help": 11, "helper": 2, "hit": 11, "host": 10, "hostnam": [2, 9, 10], "how": [8, 11], "howto": 10, "http": [0, 7, 11, 12], "i": [0, 1, 2, 3, 4, 5, 8, 10, 11, 12], "id": [0, 1, 3, 5, 10, 11], "idea": 3, "identifi": [3, 5, 9, 11], "idp": 0, "illustr": 11, "immut": 3, "implement": 0, "implic": 11, "import": 11, "includ": [0, 3], "indent": 10, "index": [0, 2, 5, 9], "index_manifest": 11, "index_object_manifest": [2, 9, 11], "indexd": [1, 3, 6, 10, 11, 12], "indexd_field": [11, 12], "indexd_record_page_s": [2, 9, 11], "indexed_file_object_guid": 12, "indic": [0, 11], "infil": 10, "info": [3, 11], "inform": [2, 3, 10], "ingest": [2, 9], "ingest_manifest": 12, "initi": [0, 10], "input": [4, 10, 11], "input_manifest": 11, "instal": [0, 2, 11], "instanc": [1, 3, 6, 7, 8, 9, 10], "instead": [1, 7, 11], "int": [1, 3, 5, 7, 8, 10, 11, 12], "integ": [1, 3, 8], "intend": 0, "interact": [1, 3, 4, 5, 6, 8, 13], "interest": 10, "interpret": 0, "introspect": 8, "involv": 9, "is_healthi": [2, 3, 4, 5], "is_indexed_file_object": 12, "isn": 1, "issu": 0, "its": [1, 3], "job": 2, "job_id": 4, "job_input": 4, "job_nam": 4, "json": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 13], "just": [5, 11, 12], "jwt": 0, "kei": [0, 3, 5, 13], "know": 11, "known": 10, "kwarg": [3, 4, 5], "l": [2, 13], "larg": 9, "last": 10, "latest": 3, "least": 3, "level": 6, "librari": 11, "like": [3, 5, 9, 11, 12], "limit": [1, 3, 5, 12], "linear": 4, "linux": 10, "list": [0, 1, 3, 4, 5, 7, 8, 10, 11, 13], "list_access_in_drs_manifest": [2, 9, 10], "list_drs_object": [2, 9, 10], "list_files_in_drs_manifest": [2, 9, 10], "list_job": [2, 4], "live": [11, 12], "load": [2, 9, 10], "load_manifest": [2, 9, 10], "local": [0, 13], "locat": [1, 6], "lock": 12, "log": [8, 10, 11, 12], "logic": [5, 12], "loop": 11, "ls_path": [2, 13], "maco": 11, "made": 3, "mai": [0, 9, 11], "main": 10, "make": [9, 11], "manag": [1, 5, 10], "mani": [8, 11], "manifest": [2, 8, 9, 10, 11, 12], "manifest_1": 10, "manifest_fil": [11, 12], "manifest_file_delimit": [11, 12], "manifest_row_pars": [11, 12], "map": [0, 11], "mark": 8, "master": 7, "match": [3, 5, 12], "max": 5, "max_concurrent_request": [2, 9, 11, 12], "max_presigned_url_ttl": 1, "max_tri": 8, "maximum": [11, 12], "md": [5, 7, 10, 12], "md5": [2, 3, 9, 11], "md5_hash": 11, "md5sum": [2, 9, 10], "mean": 8, "mechan": 3, "merg": 5, "metadata": [2, 3, 6, 9, 11], "metadata_list": 5, "metadata_sourc": 12, "metadata_typ": 12, "metdata": 12, "method": [1, 7, 10], "minimum": 10, "minut": 0, "mode": 7, "modul": [2, 10, 11], "more": [2, 5, 7, 9, 10], "most": 9, "mostli": 2, "multipl": [8, 11], "must": [1, 5], "my_common": 10, "my_credenti": 10, "my_field": 7, "my_index": 7, "my_program": 7, "my_project": 7, "name": [3, 4, 8, 10, 11, 12, 13], "namespac": [0, 12], "necessari": [3, 5], "need": [3, 7, 10, 11], "nest": 5, "net": 11, "never": 0, "new": [0, 3], "node": 8, "node_nam": 8, "node_typ": 8, "none": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "note": [0, 3, 11, 12], "noth": [3, 6], "now": [1, 8], "num": 5, "num_process": 11, "num_total_fil": 11, "number": [3, 7, 8, 11, 12], "o": 0, "object": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 13], "object_id": [1, 2, 9, 10], "object_list": 10, "object_typ": [2, 9, 10], "objectid": 10, "obtain": [0, 10], "occur": 10, "off": 5, "offset": [5, 7], "oidc": 0, "old": 3, "one": [3, 5, 10, 11], "onli": [3, 5, 7, 8, 10, 11], "open": [8, 10, 11], "open_project": [2, 8], "openid": 0, "opt": 0, "option": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11], "order": [0, 8], "ordered_node_list": 8, "org": 10, "otherwis": 10, "output": [4, 5, 11, 12], "output_dir": 10, "output_filenam": [11, 12], "overrid": [0, 11, 12], "overwrit": 5, "own": 0, "packag": 10, "page": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13], "pagin": 3, "parallel": 11, "param": [3, 5, 8, 10], "paramet": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "pars": [10, 11, 12, 13], "parser": [11, 12], "particular": 0, "pass": [0, 7, 8, 10], "password": [11, 12], "path": [0, 1, 5, 10, 11, 13], "path_to_manifest": 11, "pattern": [3, 12], "pdcdatastor": 11, "pend": 10, "per": [11, 12], "peregrin": 8, "permiss": 10, "persist": 9, "phs0001": 11, "phs0002": 11, "pick": 1, "pla": 11, "place": 11, "planx": 11, "point": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "popul": [10, 12], "posit": [1, 7], "possibl": 10, "post": [0, 11], "pprint": [2, 9, 10], "prefix": 3, "presign": 1, "pretti": 10, "prev_guid": [2, 9, 11], "previou": [3, 11], "previous": 4, "print": [8, 10], "process": 11, "processed_fil": 11, "profil": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "program": [8, 11], "progress": [8, 10], "project": [8, 11], "project_id": [7, 8], "protocol": 1, "provid": [0, 1, 3, 5, 7, 8, 12], "public": [3, 5], "put": 0, "py": 11, "python": [2, 9, 11], "python3": 11, "python_subprocess_command": 11, "queri": [1, 2, 3, 5, 8, 11, 12], "query_str": 7, "query_txt": [7, 8], "query_url": [2, 3], "quickstart": 2, "rather": 0, "raw": [7, 11], "raw_data_download": [2, 7], "rbac": 3, "read": [3, 5, 11], "readm": 2, "reason": 10, "record": [1, 3, 5, 7, 8, 11, 12], "refresh": [0, 10], "refresh_access_token": [0, 2], "refresh_fil": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "refresh_token": 0, "regist": 8, "regular": 7, "relat": 9, "remov": [1, 6, 11, 13], "replac": 11, "replace_url": 11, "repo": 2, "repres": [3, 5, 10], "represent": [1, 3], "request": [0, 1, 3, 5, 8, 11, 12], "requir": 10, "resolv": 10, "resolve_object": [2, 9, 10], "respect": 7, "respons": [0, 1, 3, 4, 5], "result": [1, 8, 10, 11], "retri": 8, "retriev": [1, 8, 10, 12], "return": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11], "return_full_metadata": 5, "rev": 3, "revers": 8, "revis": 3, "right": 1, "rm": [2, 13], "rm_path": [2, 13], "root": [11, 12], "row": [7, 8, 11, 12], "row_offset": 8, "rtype": 3, "run": [8, 11], "s3": [1, 10, 11], "safe": 11, "same": [5, 11, 13], "sampl": [8, 10], "sandbox": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "save": 10, "save_directori": 10, "schema": 8, "scope": [0, 1], "screen": 8, "script": 2, "search": [0, 2, 3], "second": [1, 4], "secret": 0, "see": [7, 10, 11], "self": 10, "semaphon": 12, "semaphor": 12, "separ": [0, 11], "server": 10, "servic": [1, 3, 4, 5, 6, 8, 11, 12, 13], "service_loc": [3, 4, 5], "session": 11, "set": [0, 1, 5, 10], "setup": 2, "sheepdog": 8, "should": [0, 8, 11], "show": 10, "show_progress": 10, "shown": 11, "sign": 1, "signpost": 3, "similar": 10, "simpl": 3, "simpli": 11, "sinc": 3, "singl": [1, 5, 8], "size": [2, 3, 9, 10, 11], "skip": 8, "sleep": 4, "so": 11, "some": [0, 2], "someth": 11, "sort": 7, "sort_field": 7, "sort_object": 7, "sourc": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "space": [0, 11], "specif": [5, 8, 11, 12], "specifi": [0, 1, 3, 11, 13], "spreadsheet": 8, "src_path": 13, "src_urlstr": 13, "src_w": 13, "src_wskei": 13, "ssl": [3, 4, 5], "start": [4, 7, 8, 10], "start_tim": [2, 9, 10], "static": 10, "statu": [2, 4, 9, 10], "storag": [1, 2, 6], "store": [1, 3, 10], "str": [0, 1, 3, 4, 5, 7, 8, 10, 11, 12], "string": [0, 3, 5, 11, 13], "strip": 11, "sub": 8, "subject": [7, 8], "submiss": 2, "submit": [8, 11], "submit_additional_metadata_column": 11, "submit_fil": [2, 8], "submit_record": [2, 8], "submitter_id": 7, "success": 10, "successfulli": 10, "suffici": 3, "suppli": 3, "support": [0, 1, 5, 8, 11], "sure": 1, "synchron": 11, "syntax": 7, "system": [6, 7, 8, 9], "t": [1, 5, 11], "tab": 11, "task": 9, "temporari": 11, "test": 11, "test1": 11, "test2": 11, "test3": 11, "test4": 11, "test5": 11, "text": [1, 7, 8], "than": [0, 5], "thei": [0, 10], "them": [10, 11], "thi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "those": 11, "thread": 11, "thread_num": 11, "threadcontrol": [2, 9, 11], "through": [8, 11], "tier": 7, "time": [1, 3, 8, 10, 11], "timestamp": 10, "tmp_folder": [2, 9, 11], "token": [0, 10], "tool": 2, "total": 11, "treat": [1, 5], "tree": 10, "true": [3, 4, 5, 6, 7, 8, 10, 11, 12], "try": 0, "tsv": [8, 11, 12], "tupl": [0, 3, 11, 12], "type": [1, 3, 4, 5, 7, 8, 10, 11, 12], "typic": 10, "uc": 7, "unaccess": 7, "under": [0, 8, 13], "uniqu": [1, 5], "unknown": 10, "unpack": 10, "unpack_packag": 10, "until": [4, 10], "up": [5, 9], "updat": [2, 3, 5, 10, 11], "update_alias": [2, 5], "update_blank": [2, 3], "update_record": [2, 3], "updated_tim": [2, 9, 10], "upload": [1, 2, 3, 8, 13], "upload_fil": [1, 2], "upload_file_to_guid": [1, 2], "upload_url": [2, 13], "url": [1, 2, 3, 9, 10, 11, 12, 13], "urls_metadata": 3, "us": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "usag": 11, "use_agg_md": 5, "user": [0, 10, 12], "user_access": [2, 9, 10], "usual": 12, "utcnow": 1, "util": 9, "uuid": [1, 3, 8], "uuid1": 8, "uuid2": 8, "valid": [3, 7], "valu": [0, 1, 3, 5, 7, 10, 11], "value_from_indexd": 11, "value_from_manifest": 11, "variabl": [0, 7, 8], "variou": 2, "verbos": [7, 8], "verif": 11, "verifi": [2, 9], "verify_manifest": 11, "verify_object_manifest": 11, "version": [3, 4, 5], "vital_statu": 7, "w": 13, "wa": 0, "wai": 10, "wait": 4, "want": [0, 3, 8], "warn": 11, "we": [3, 11], "web": 0, "what": 5, "when": [0, 3, 7, 10, 12], "where": [0, 3, 5, 11, 12], "whether": [3, 4, 5, 8, 11, 12], "which": [8, 10], "while": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "whose": 5, "within": [0, 2, 9], "without": [3, 5], "won": 5, "work": [0, 10], "workaround": 11, "worksheet": 8, "workspac": [0, 2], "wrapper": 10, "write": 11, "ws_urlstr": 13, "wskei": 13, "wss": 13, "wt": [0, 10], "x": 11, "xlsx": 8, "you": [0, 3, 8, 11], "your": 0}, "titles": ["Gen3 Auth Helper", "Gen3 File Class", "Welcome to Gen3 SDK\u2019s documentation!", "Gen3 Index Class", "Gen3 Jobs Class", "Gen3 Metadata Class", "Gen3 Object Class", "Gen3 Query Class", "Gen3 Submission Class", "Gen3 Tools", "DRS Download Tools", "Indexing Tools", "Metadata Tools", "Gen3 Workspace Storage"], "titleterms": {"": 2, "auth": 0, "class": [1, 3, 4, 5, 6, 7, 8], "document": 2, "download": [10, 11], "dr": 10, "file": 1, "gen3": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13], "helper": 0, "index": [3, 11], "indic": 2, "ingest": 12, "job": 4, "metadata": [5, 12], "object": 6, "queri": 7, "sdk": 2, "storag": 13, "submiss": 8, "tabl": 2, "tool": [9, 10, 11, 12], "verifi": 11, "welcom": 2, "workspac": 13}})
\ No newline at end of file
diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html
index 836cef697..cc616d9d0 100644
--- a/docs/_build/html/tools/indexing.html
+++ b/docs/_build/html/tools/indexing.html
@@ -381,7 +381,7 @@ Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1739488230.1381567.log')[source]¶
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1745256298.5438318.log')[source]¶
Verify all file object records into a manifest csv
- Parameters:
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html
index e29816a6d..95ea2c064 100644
--- a/docs/_build/html/tools/metadata.html
+++ b/docs/_build/html/tools/metadata.html
@@ -102,7 +102,7 @@ Metadata Tools
-
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1739488230.392749.log', get_guid_from_file=True, metadata_type=None)[source]¶
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1745256298.8196251.log', get_guid_from_file=True, metadata_type=None)[source]¶
Ingest all metadata records into a manifest csv
- Parameters:
diff --git a/gen3/cli/discovery.py b/gen3/cli/discovery.py
index 7ca574053..5e22dabc2 100644
--- a/gen3/cli/discovery.py
+++ b/gen3/cli/discovery.py
@@ -55,7 +55,7 @@ def discovery():
"guid_field",
help=(
'The column / field name within the metadata that will be used as GUIDs, if not specified, will try to find a column \ field named "guid" from the metadata.'
- "If that field doesn't exists in a certain metadata record, that record will be skipped from publishing."
+ "If that field doesn't exist in a certain metadata record, that record will be skipped from publishing."
),
default=None,
show_default=True,
diff --git a/gen3/index.py b/gen3/index.py
index 5b8947fc7..f420f5c2f 100755
--- a/gen3/index.py
+++ b/gen3/index.py
@@ -48,6 +48,7 @@ def __init__(self, endpoint=None, auth_provider=None, service_location="index"):
if not endpoint.endswith(service_location):
endpoint += "/" + service_location
+ self.endpoint = endpoint
self.client = client.IndexClient(endpoint, auth=auth_provider)
### Get Requests
@@ -747,6 +748,10 @@ def update_record(
"content_updated_date": content_updated_date,
}
rec = self.client.get(guid)
+ if not rec:
+ raise ValueError(
+ f"No indexd record found for GUID '{guid}' at '{self.endpoint}'"
+ )
for k, v in updatable_attrs.items():
if v is not None:
exec(f"rec.{k} = v")
diff --git a/gen3/tools/metadata/discovery.py b/gen3/tools/metadata/discovery.py
index 8fcc4bfc5..e88334429 100644
--- a/gen3/tools/metadata/discovery.py
+++ b/gen3/tools/metadata/discovery.py
@@ -403,7 +403,7 @@ async def publish_discovery_metadata(
endpoint (str): HOSTNAME of a Gen3 environment, defaults to None
omit_empty_values (bool): whether to exclude fields with empty values from the published discovery metadata, defaults to False
guid_type (str): intended GUID type for publishing, defaults to discovery_metadata
- guid_field (str): specify a field from the metadata that will be used as GUIDs, if not specified, will try to find a field named "guid" from the metadata, if that field doesn't exists in a certain metadata record, that record will be skipped from publishing, defaults to None
+ guid_field (str): specify a field from the metadata that will be used as GUIDs, if not specified, will try to find a field named "guid" from the metadata, if that field doesn't exist in a certain metadata record, that record will be skipped from publishing, defaults to None
is_unregistered_metadata (bool): (for use by "study registration" feature only) whether to publish metadata as unregistered study metadata, defaults to False
reset_unregistered_metadata (bool): (for use by "study registration" feature only) whether to reset existing study metadata back to unregistered study metadata if they exists in the local file, defaults to False
update_registered_metadata (bool): (for use by "study registration" feature only) whether to update existing study metadata with new values if they exists in the local file, defaults to True