From 2c07651e11eca6288b973688b8f8861e7a032f5f Mon Sep 17 00:00:00 2001 From: Alexander VanTol Date: Thu, 24 Aug 2023 10:22:50 -0500 Subject: [PATCH] =?UTF-8?q?feat(drs-pull-objects):=20initial=20support=20f?= =?UTF-8?q?or=20supplying=20a=20list=20of=20DRS=20I=E2=80=A6=20(#195)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat(drs-pull-objects): initial support for supplying a list of DRS IDs to download * Apply automatic documentation changes * feat(logging): add arg for silencing logging (that way we can ensure click.echos are the only stdout) * feat(drs-pull): correctly allow list of object IDs as an arg, support JSON output * Apply automatic documentation changes * chore(spelling): fix typo * Apply automatic documentation changes * chore(drs-pull): refactor to reduce function calls, support passing a list of objects to underlying download functions * Apply automatic documentation changes * chore(tests): fix test and version * Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1563011 -> 1554905 bytes docs/_build/doctrees/tools/drs_pull.doctree | Bin 136459 -> 130578 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 101131 -> 101126 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 36397 -> 36402 bytes .../gen3/tools/download/drs_download.html | 19 ++- docs/_build/html/genindex.html | 2 - docs/_build/html/index.html | 1 - docs/_build/html/objects.inv | Bin 1898 -> 1894 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools.html | 1 - docs/_build/html/tools/drs_pull.html | 22 ---- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- docs/howto/drsDownloading.md | 7 ++ gen3/cli/__main__.py | 19 ++- gen3/cli/drs_pull.py | 113 ++++++++++++++++-- gen3/tools/download/drs_download.py | 14 +-- pyproject.toml | 2 +- tests/download_tests/test_download.py | 7 +- 19 files changed, 148 insertions(+), 65 deletions(-) diff --git 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diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree index 2ac638912084b4860c88fef6c18e654d1f2388cf..19f96a3f2cebb3e68f2d9ee24a5096a8d506ddae 100644 GIT binary patch delta 182 zcmZ2GhiTIsCYA=)sp=b9-fFVUWn^HOWGBB_M9Y?u&%(mY+{9SV!ob|b+{AM71_PVT zv$T&hGuCfT(sx9c-n_w}m4ne^@`0h%i|D_e1e0037cGK2sC delta 178 zcmdlqhiUB`CYA=)sY)AJ-fFVUVPs&KJYP?4v#^#OBd@ukxq-2zp1FyMk(tTncx`4D z#=6bP`i^KaljF5*Hor6QDYa8HGFW@S TN~Liq%@Bjgqq#uCiYo*FSource code for gen3.tools.download.drs_download
def _download_obj( hostname, auth, - object_id, + object_ids, output_dir=".", show_progress=False, unpack_packages=True, @@ -1222,7 +1222,7 @@

Source code for gen3.tools.download.drs_download

Args: hostname (str): hostname of Gen3 commons to use for access and WTS auth: Gen3 Auth instance - object_id (str): DRS object id + object_ids (List[str]): DRS object id output_dir: directory to save downloaded files to show_progress: show progress bar unpack_packages (bool): set to False to disable the unpacking of downloaded packages @@ -1237,7 +1237,7 @@

Source code for gen3.tools.download.drs_download

logger.critical(f"Unable to authenticate your credentials with {hostname}") return None - object_list = [Downloadable(object_id=object_id)] + object_list = [Downloadable(object_id=object_id) for object_id in object_ids] downloader = DownloadManager( hostname=hostname, auth=auth, @@ -1430,12 +1430,10 @@

Source code for gen3.tools.download.drs_download

-
-[docs] -def download_drs_object( +def download_drs_objects( hostname, auth, - object_id, + object_ids, output_dir, show_progress=True, unpack_packages=True, @@ -1446,7 +1444,7 @@

Source code for gen3.tools.download.drs_download

Args: hostname (str): hostname of Gen3 commons to use for access and WTS auth: Gen3 Auth instance - object_id (str): DRS object id + object_ids (List[str]): DRS object ids output_dir: directory to save downloaded files to unpack_packages (bool): set to False to disable the unpacking of downloaded packages delete_unpacked_packages (bool): set to True to delete package files after unpacking them @@ -1457,13 +1455,12 @@

Source code for gen3.tools.download.drs_download

return _download_obj( hostname, auth, - object_id, + object_ids, output_dir, show_progress, unpack_packages, delete_unpacked_packages, - )
- + )
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index 76528c186..3c8704b10 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -220,8 +220,6 @@

D

  • (gen3.wss.Gen3WsStorage method)
    • -
  • download_drs_object() (in module gen3.tools.download.drs_download) -
  • download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)
  • download_single() (gen3.file.Gen3File method) diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index 0e611b039..57f5e27e3 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -223,7 +223,6 @@

    Welcome to Gen3 SDK’s documentation!Manifest.load_manifest()

    • -
  • download_drs_object()
  • download_files_in_drs_manifest()
  • list_access_in_drs_manifest()
  • list_drs_object()
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"indic": 2, "tabl": 2, "index": [3, 11], "job": 4, "metadata": [5, 12], "object": 6, "queri": 7, "submiss": 8, "tool": [9, 10, 11, 12], "dr": 10, "download": [10, 11], "verifi": 11, "ingest": 12, "workspac": 13, "storag": 13}, "envversion": {"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, "sphinx": 60}, "alltitles": {"Gen3 Auth Helper": [[0, "gen3-auth-helper"]], "Gen3 File Class": [[1, "gen3-file-class"]], "Welcome to Gen3 SDK\u2019s documentation!": [[2, "welcome-to-gen3-sdk-s-documentation"]], "Indices and tables": [[2, "indices-and-tables"]], "Gen3 Index Class": [[3, "gen3-index-class"]], "Gen3 Jobs Class": [[4, "gen3-jobs-class"]], "Gen3 Metadata Class": [[5, "gen3-metadata-class"]], "Gen3 Object Class": [[6, "gen3-object-class"]], "Gen3 Query Class": [[7, "gen3-query-class"]], "Gen3 Submission Class": [[8, "gen3-submission-class"]], "Gen3 Tools": [[9, "gen3-tools"]], "DRS Download Tools": [[10, "drs-download-tools"]], "Indexing Tools": [[11, "indexing-tools"]], "Download": [[11, "download"]], "Index": [[11, "index"]], "Verify": [[11, "verify"]], "Metadata Tools": [[12, "metadata-tools"]], "Ingest": [[12, "ingest"]], "Gen3 Workspace Storage": [[13, "gen3-workspace-storage"]]}, "indexentries": {"gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth"]], "curl() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.curl"]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token"]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts"]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token"]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File"]], "delete_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file"]], "delete_file_locations() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file_locations"]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single"]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url"]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file"]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid"]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index"]], "async_create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_create_record"]], "async_get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_record"]], "async_get_records_from_checksum() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_from_checksum"]], "async_get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_on_page"]], "async_get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_with_params"]], "async_query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_query_urls"]], "async_update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_update_record"]], "create_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_blank"]], "create_new_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_new_version"]], "create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_record"]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record"]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get"]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records"]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix"]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version"]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record"]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc"]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records"]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page"]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats"]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls"]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids"]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version"]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions"]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params"]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy"]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls"]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank"]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record"]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs"]], "async_run_job_and_wait() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.async_run_job_and_wait"]], "create_job() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.create_job"]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output"]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status"]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version"]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy"]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs"]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata"]], "async_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create"]], "async_create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create_aliases"]], "async_delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_alias"]], "async_delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_aliases"]], "async_get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get"]], "async_get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get_aliases"]], "async_update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update"]], "async_update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update_aliases"]], "auth_provider (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.auth_provider"]], "batch_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.batch_create"]], "create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create"]], "create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_aliases"]], "create_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_index_key_path"]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete"]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias"]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases"]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path"]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint"]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get"]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases"]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths"]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version"]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy"]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query"]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update"]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases"]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object"]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object"]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query"]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query"]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query"]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download"]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission"]], "create_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_program"]], "create_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_project"]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node"]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes"]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program"]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project"]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record"]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records"]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node"]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record"]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all"]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node"]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema"]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs"]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary"]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest"]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects"]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project"]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query"]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file"]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record"]], "gen3.tools": [[9, "module-gen3.tools"]], "module": [[9, "module-gen3.tools"], [10, "module-gen3.tools.download.drs_download"], [11, "module-gen3.tools.indexing.download_manifest"], [11, "module-gen3.tools.indexing.index_manifest"], [11, "module-gen3.tools.indexing.verify_manifest"], [12, "module-gen3.tools.metadata.ingest_manifest"]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager"]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus"]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable"]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest"]], "_manager (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable._manager"]], "access_methods (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.access_methods"]], "cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens"]], "children (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.children"]], "commons_url (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.commons_url"]], "create_object_list() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.create_object_list"]], "created_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.created_time"]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download"]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download"]], "download_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_drs_object"]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest"]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time"]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name"]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name"]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size"]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size"]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download"]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token"]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname"]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest"]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object"]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest"]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load"]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest"]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum"]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id"]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id"]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type"]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint"]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects"]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time"]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status"]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time"]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access"]], "acls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ACLS"]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ"]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR"]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID"]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE"]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS"]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS"]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5"]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID"]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE"]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER"]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl"]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS"]], "async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.async_download_object_manifest"]], "async_verify_object_manifest() (in module gen3.tools.indexing.verify_manifest)": [[11, 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(gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_create_record"]], "async_get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_record"]], "async_get_records_from_checksum() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_from_checksum"]], "async_get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_on_page"]], "async_get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_with_params"]], "async_query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_query_urls"]], "async_update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_update_record"]], "create_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_blank"]], "create_new_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_new_version"]], "create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_record"]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record"]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get"]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records"]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix"]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version"]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record"]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc"]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records"]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page"]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats"]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls"]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids"]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version"]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions"]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params"]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy"]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls"]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank"]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record"]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs"]], "async_run_job_and_wait() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.async_run_job_and_wait"]], "create_job() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.create_job"]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output"]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status"]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version"]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy"]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs"]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata"]], "async_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create"]], "async_create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create_aliases"]], "async_delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_alias"]], "async_delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_aliases"]], "async_get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get"]], "async_get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get_aliases"]], "async_update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update"]], "async_update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update_aliases"]], "auth_provider (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.auth_provider"]], "batch_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.batch_create"]], "create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create"]], "create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_aliases"]], "create_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_index_key_path"]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete"]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias"]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases"]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path"]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint"]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get"]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases"]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths"]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version"]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy"]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query"]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update"]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases"]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object"]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object"]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query"]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query"]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query"]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download"]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission"]], "create_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_program"]], "create_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_project"]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node"]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes"]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program"]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project"]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record"]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records"]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node"]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record"]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all"]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node"]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema"]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs"]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary"]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest"]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects"]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project"]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query"]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file"]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record"]], "gen3.tools": [[9, "module-gen3.tools"]], "module": [[9, "module-gen3.tools"], [10, "module-gen3.tools.download.drs_download"], [11, "module-gen3.tools.indexing.download_manifest"], [11, "module-gen3.tools.indexing.index_manifest"], [11, "module-gen3.tools.indexing.verify_manifest"], [12, "module-gen3.tools.metadata.ingest_manifest"]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager"]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus"]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable"]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest"]], "_manager (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable._manager"]], "access_methods (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.access_methods"]], "cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens"]], "children (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.children"]], "commons_url (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.commons_url"]], "create_object_list() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.create_object_list"]], "created_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.created_time"]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download"]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download"]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest"]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time"]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name"]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name"]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size"]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size"]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download"]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token"]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname"]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest"]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object"]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest"]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load"]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest"]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum"]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id"]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id"]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type"]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint"]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects"]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time"]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status"]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time"]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access"]], "acls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ACLS"]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ"]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR"]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID"]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE"]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS"]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS"]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5"]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID"]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE"]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER"]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl"]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS"]], "async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.async_download_object_manifest"]], "async_verify_object_manifest() (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.async_verify_object_manifest"]], "delete_all_guids() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.delete_all_guids"]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest"]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest"]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest"]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest"]], "column_to_use_as_guid (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID"]], "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"]], "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"]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS"]], "async_ingest_metadata_manifest() (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest"]], "async_query_urls_from_indexd() (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd"]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage"]], "copy() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.copy"]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download"]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url"]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls"]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path"]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm"]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path"]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload"]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url"]]}}) \ No newline at end of file diff --git a/docs/_build/html/tools.html b/docs/_build/html/tools.html index 7411d62fe..dacf213a1 100644 --- a/docs/_build/html/tools.html +++ b/docs/_build/html/tools.html @@ -80,7 +80,6 @@

    Gen3 ToolsManifest.load_manifest() -
  • download_drs_object()
  • download_files_in_drs_manifest()
  • list_access_in_drs_manifest()
  • list_drs_object()
    • diff --git a/docs/_build/html/tools/drs_pull.html b/docs/_build/html/tools/drs_pull.html index 47572cefd..6fe4c33ff 100644 --- a/docs/_build/html/tools/drs_pull.html +++ b/docs/_build/html/tools/drs_pull.html @@ -405,27 +405,6 @@

    DRS Download Tools -
    -gen3.tools.download.drs_download.download_drs_object(hostname, auth, object_id, output_dir, show_progress=True, unpack_packages=True, delete_unpacked_packages=False) → None[source]
    -

    A convenience function used to download a single DRS object. -:param hostname: hostname of Gen3 commons to use for access and WTS -:type hostname: str -:param auth: Gen3 Auth instance -:param object_id: DRS object id -:type object_id: str -:param output_dir: directory to save downloaded files to -:param unpack_packages: set to False to disable the unpacking of downloaded packages -:type unpack_packages: bool -:param delete_unpacked_packages: set to True to delete package files after unpacking them -:type delete_unpacked_packages: bool

    -
    -
    Returns:
    -

    List of DownloadStatus objects for the DRS object

    -
    -
    -
    -
    gen3.tools.download.drs_download.download_files_in_drs_manifest(hostname, auth, infile, output_dir, show_progress=True, unpack_packages=True, delete_unpacked_packages=False) → None[source]
    @@ -569,7 +548,6 @@

    Navigation

  • Manifest.load_manifest()
    • -
  • download_drs_object()
  • download_files_in_drs_manifest()
  • list_access_in_drs_manifest()
  • list_drs_object()
    • diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index 9ffe61161..77273cc4a 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -380,7 +380,7 @@

    Verify
    -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-1692717039.3338752.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-1692886743.381985.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 b3764f4aa..02b342e9a 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

    Ingest
    -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-1692717039.744264.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-1692886743.8074749.log', get_guid_from_file=True, metadata_type=None)[source]

    Ingest all metadata records into a manifest csv

    Parameters:
    diff --git a/docs/howto/drsDownloading.md b/docs/howto/drsDownloading.md index 173b75590..05e93df77 100644 --- a/docs/howto/drsDownloading.md +++ b/docs/howto/drsDownloading.md @@ -67,6 +67,12 @@ You should see something like: Datafile05_T.csv : 100%|████████████████████████████████████████████████████████████████████████| 3.72M/3.72M [00:01<00:00, 1.92MiB/s] ``` +To download a list of files, you can use the `drs-pull objects` command: + +``` +gen3 --endpoint my-commons.org --auth drs-pull objects dg.XXTS/181af989-5d66-4139-91e7-69f4570ccd41 dg.XX22/221af922-2222-2239-22e7-62f4570cc222 +``` + ### Listing Files and Access #### List Contents @@ -93,6 +99,7 @@ BIG_DataCollection.5.2.1.7695.1700.100392922143281268049004312967/1.3.6.1.4.1.14 ├── BIG_Datafile.177741488444741406265552879434.dcm#1592595549340161 527.66 KB test.datacommons4.io 09/19/2020, 09:12:09 └── BIG_Datafile.193538014659307853778370216921.dcm#1592595549438034 527.66 KB test.datacommons4.io 09/18/2020, 14:48:53 ``` + #### List Access Given a manifest or DRS object id, you can query the access rights for that object's host commons, or in the case of a manifest all of the host commons diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index bbc61f087..dcfa1ad9d 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -1,6 +1,7 @@ import click import os import sys +import logging import cdislogging import pkg_resources @@ -68,6 +69,13 @@ def get(self): default=False, help="only show ERROR logs", ) +@click.option( + "--silent", + "silent", + is_flag=True, + default=False, + help="don't show ANY logs", +) @click.option( "--version", help="Show Gen3 Version", @@ -80,6 +88,7 @@ def main( verbose_logs, very_verbose_logs, only_error_logs, + silent, version, ): """Gen3 Command Line Interface""" @@ -90,7 +99,15 @@ def main( if version: click.echo(pkg_resources.get_distribution("gen3").version) - if very_verbose_logs: + if silent: + # we still need to define the logger, the log_level here doesn't + # really matter b/c we immediately disable all logging + logger = cdislogging.get_logger( + __name__, format=gen3.LOG_FORMAT, log_level="debug" + ) + # disables all logging + logging.disable(logging.CRITICAL) + elif very_verbose_logs: logger = cdislogging.get_logger( __name__, format=gen3.LOG_FORMAT, log_level="debug" ) diff --git a/gen3/cli/drs_pull.py b/gen3/cli/drs_pull.py index 319bdb753..dc8f0e9a1 100644 --- a/gen3/cli/drs_pull.py +++ b/gen3/cli/drs_pull.py @@ -1,11 +1,13 @@ import click +import json + from cdislogging import get_logger from gen3.tools.download.drs_download import ( list_files_in_drs_manifest, list_drs_object, download_files_in_drs_manifest, - download_drs_object, + download_drs_objects, list_access_in_drs_manifest, ) @@ -94,7 +96,6 @@ def download_manifest( @click.command() @click.argument("object_id") -@click.argument("output-dir", default=".") @click.option( "--no-progress", is_flag=True, @@ -113,6 +114,11 @@ def download_manifest( help="delete package files after unpacking them", show_default=True, ) +@click.option( + "--output-dir", + default=".", + show_default=True, +) @click.pass_context def download_object( ctx, @@ -129,11 +135,11 @@ def download_object( gen3 --endpoint mydata.org drs-pull object dg.XXXT/181af989-5d66-4139-91e7-69f4570ccd41 """ - click.echo(f"GA4GH DRS Object Streaming Starting...") - res = download_drs_object( + logger.info(f"GA4GH DRS Object Streaming Starting...") + res = download_drs_objects( ctx.obj["endpoint"], ctx.obj["auth_factory"].get(), - object_id, + [object_id], output_dir, no_progress, not no_unpack_packages, @@ -141,17 +147,101 @@ def download_object( ) success = True + + results = { + "succeeded": [], + "failed": [], + } + for drs_object_id in res: - if drs_object_id in res and res[drs_object_id].status != "downloaded": - click.echo(f"Object {drs_object_id} download failed.") + if drs_object_id in res and res[drs_object_id].status == "downloaded": + results["succeeded"].append(drs_object_id) + else: + logger.error(f"Object {drs_object_id} download failed.") success = False + results["failed"].append(drs_object_id) if success: - click.echo("All objects downloaded successfully.") + logger.info("All objects downloaded successfully.") else: - click.echo( - f"One or more objects have failed to be downloaded. Please check previous failure messages to see which ones have failed." - ) + logger.error(f"One or more objects have failed to be downloaded. Details:") + + click.echo(json.dumps(results)) + + +@click.command() +@click.argument("object_ids", nargs=-1) +@click.option( + "--output-dir", + default=".", + show_default=True, +) +@click.option( + "--no-progress", + is_flag=True, + help="Hide the progress bar when downloading", + show_default=True, +) +@click.option( + "--no-unpack-packages", + is_flag=True, + help="disable the unpacking of downloaded packages", + show_default=True, +) +@click.option( + "--delete-unpacked-packages", + is_flag=True, + help="delete package files after unpacking them", + show_default=True, +) +@click.pass_context +def download_objects( + ctx, + output_dir: str, + object_ids: list, + no_progress: bool, + no_unpack_packages: bool, + delete_unpacked_packages: bool, +): + """ + Download DRS objects by their object ids + The user credentials use the Gen3Auth class so the Gen3Auth options are applicable (--auth and --endpoint) + An example: + gen3 --endpoint mydata.org drs-pull objects dg.XXXT/181af989-5d66-4139-91e7-69f4570ccd41 dg.YYYT/221af989-2266-2239-22e7-22f4570ccd22 + + """ + success = True + + results = { + "succeeded": [], + "failed": [], + } + + logger.info(f"GA4GH DRS Object Streaming Starting...") + logger.debug(f"object_ids: {object_ids}") + res = download_drs_objects( + ctx.obj["endpoint"], + ctx.obj["auth_factory"].get(), + object_ids, + output_dir, + no_progress, + not no_unpack_packages, + delete_unpacked_packages, + ) + for drs_object_id in res: + if drs_object_id in res and res[drs_object_id].status == "downloaded": + results["succeeded"].append(drs_object_id) + else: + logger.error(f"Object {drs_object_id} download failed.") + success = False + results["failed"].append(drs_object_id) + + if success: + logger.info("All objects downloaded successfully.") + else: + logger.error(f"One or more objects have failed to be downloaded. Details:") + + click.echo(json.dumps(results)) @click.group() @@ -162,4 +252,5 @@ def drs_pull(): drs_pull.add_command(download_manifest, name="manifest") drs_pull.add_command(download_object, name="object") +drs_pull.add_command(download_objects, name="objects") drs_pull.add_command(list_files_or_access, name="ls") diff --git a/gen3/tools/download/drs_download.py b/gen3/tools/download/drs_download.py index 03f57a030..e22752395 100644 --- a/gen3/tools/download/drs_download.py +++ b/gen3/tools/download/drs_download.py @@ -1138,7 +1138,7 @@ def _download( def _download_obj( hostname, auth, - object_id, + object_ids, output_dir=".", show_progress=False, unpack_packages=True, @@ -1149,7 +1149,7 @@ def _download_obj( Args: hostname (str): hostname of Gen3 commons to use for access and WTS auth: Gen3 Auth instance - object_id (str): DRS object id + object_ids (List[str]): DRS object id output_dir: directory to save downloaded files to show_progress: show progress bar unpack_packages (bool): set to False to disable the unpacking of downloaded packages @@ -1164,7 +1164,7 @@ def _download_obj( logger.critical(f"Unable to authenticate your credentials with {hostname}") return None - object_list = [Downloadable(object_id=object_id)] + object_list = [Downloadable(object_id=object_id) for object_id in object_ids] downloader = DownloadManager( hostname=hostname, auth=auth, @@ -1348,10 +1348,10 @@ def download_files_in_drs_manifest( ) -def download_drs_object( +def download_drs_objects( hostname, auth, - object_id, + object_ids, output_dir, show_progress=True, unpack_packages=True, @@ -1362,7 +1362,7 @@ def download_drs_object( Args: hostname (str): hostname of Gen3 commons to use for access and WTS auth: Gen3 Auth instance - object_id (str): DRS object id + object_ids (List[str]): DRS object ids output_dir: directory to save downloaded files to unpack_packages (bool): set to False to disable the unpacking of downloaded packages delete_unpacked_packages (bool): set to True to delete package files after unpacking them @@ -1373,7 +1373,7 @@ def download_drs_object( return _download_obj( hostname, auth, - object_id, + object_ids, output_dir, show_progress, unpack_packages, diff --git a/pyproject.toml b/pyproject.toml index 29dbbf4c2..e8725ede1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "gen3" homepage = "https://gen3.org/" -version = "4.20.5" +version = "4.21.0" description = "Gen3 CLI and Python SDK" authors = ["Center for Translational Data Science at the University of Chicago "] license = "Apache-2.0" diff --git a/tests/download_tests/test_download.py b/tests/download_tests/test_download.py index 6918acc92..9b08d7cff 100644 --- a/tests/download_tests/test_download.py +++ b/tests/download_tests/test_download.py @@ -287,7 +287,6 @@ def test_get_external_wts_oidc(wts_oidc, hostname): def test_download_file_from_url_failures(download_dir): with requests_mock.Mocker() as m: - m.get( url=f"https://test.commons1.io/ga4gh/drs/v1/objects/blah/access/s3", headers={"content-length": "10"}, @@ -536,7 +535,7 @@ def test_download_objects( results = _download_obj( hostname, auth, - "dg.XXTS/b96018c5-db06-4af8-a195-28e339ba815e", + ["dg.XXTS/b96018c5-db06-4af8-a195-28e339ba815e"], download_dir.join("_download_obj"), ) for id, item in results.items(): @@ -640,7 +639,7 @@ def test_download_objects( results = _download_obj( hostname, auth, - "dg.XXTS/b96018c5-db06-4af8-a195-28e339ba815e", + ["dg.XXTS/b96018c5-db06-4af8-a195-28e339ba815e"], download_dir.join("_download_obj"), ) assert results is None @@ -844,7 +843,6 @@ def test_list_no_auth( manifest_file, expected, ): - test_key = { "api_key": "whatever." # pragma: allowlist secret + base64.urlsafe_b64encode( @@ -899,7 +897,6 @@ def test_unpackage_objects( download_test_files, hostname, ): - exp = time.time() + 300 test_key = { "api_key": "whatever." # pragma: allowlist secret