From 45fafc7d5ea66aec1919d58458a6a9deeeb7c726 Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Mon, 28 Aug 2023 09:28:53 -0500 Subject: [PATCH 01/12] merge_manifests fix for rows with no guid --- gen3/tools/indexing/merge_manifests.py | 58 ++++++++++++++------------ 1 file changed, 32 insertions(+), 26 deletions(-) diff --git a/gen3/tools/indexing/merge_manifests.py b/gen3/tools/indexing/merge_manifests.py index 0e05c2eaa..6ea3e7bb0 100644 --- a/gen3/tools/indexing/merge_manifests.py +++ b/gen3/tools/indexing/merge_manifests.py @@ -106,17 +106,24 @@ def merge_bucket_manifests( headers = set() all_rows = {} + records_with_no_guid = [] for manifest in files: records_from_file, _ = get_and_verify_fileinfos_from_manifest( manifest, include_additional_columns=True ) - records_with_no_guid = [] + # records_with_no_guid = [] for record in records_from_file: # simple case where this is the first time we've seen this hash headers.update(record.keys()) if record[MD5_STANDARD_KEY] not in all_rows: record_to_write = copy.deepcopy(record) all_rows[record_to_write[MD5_STANDARD_KEY]] = [record_to_write] + + new_guid = record.get(GUID_STANDARD_KEY) + if not new_guid: + # since there's no guid specified to differentiate this from other + # entries, we will add metadata to all records later + records_with_no_guid.append(record) else: # if the hash already exists, we need to try and update existing # entries with any new data (and ensure we don't add duplicates) @@ -145,34 +152,33 @@ def merge_bucket_manifests( # for the entries where there was no GUID specified, we will add that metadata # to all previous records - for record in records_with_no_guid: - updated_records = _get_updated_records( - record=record, - existing_records=all_rows.get(record[MD5_STANDARD_KEY], []), - continue_after_error=continue_after_error, - allow_mult_guids_per_hash=allow_mult_guids_per_hash, - columns_with_arrays=columns_with_arrays, - ) - # it's possible a record without a GUID got added if it was the FIRST - # instance of that md5, so we just need to make sure that it's removed - # if there was another GUID provided later on - # - # this also handles the edge case where there were multiple rows for the md5 - # and NO guid was provided (e.g. we want a single combined row of updated values) - any_guid_provided = [ - record.get(GUID_STANDARD_KEY) + for record in records_with_no_guid: + updated_records = _get_updated_records( + record=record, + existing_records=all_rows.get(record[MD5_STANDARD_KEY], []), + continue_after_error=continue_after_error, + allow_mult_guids_per_hash=allow_mult_guids_per_hash, + columns_with_arrays=columns_with_arrays, + ) + # it's possible a record without a GUID got added if it was the FIRST + # instance of that md5, so we just need to make sure that it's removed + # if there was another GUID provided later on + # + # this also handles the edge case where there were multiple rows for the md5 + # and NO guid was provided (e.g. we want a single combined row of updated values) + any_guid_provided = [ + record.get(GUID_STANDARD_KEY) + for record in updated_records.values() + if record.get(GUID_STANDARD_KEY) + ] + if not any_guid_provided: + all_rows[record[MD5_STANDARD_KEY]] = updated_records.values() + else: + all_rows[record[MD5_STANDARD_KEY]] = [ + record for record in updated_records.values() if record.get(GUID_STANDARD_KEY) ] - if not any_guid_provided: - all_rows[record[MD5_STANDARD_KEY]] = updated_records.values() - else: - all_rows[record[MD5_STANDARD_KEY]] = [ - record - for record in updated_records.values() - if record.get(GUID_STANDARD_KEY) - ] - _create_output_file( output_manifest, headers, all_rows, output_manifest_file_delimiter ) From 172b64fc3fa33f0a09c0a63473a2a9ee110f60b9 Mon Sep 17 00:00:00 2001 From: SpencerAxelrod Date: Mon, 28 Aug 2023 14:31:02 +0000 Subject: [PATCH 02/12] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1554905 -> 1553141 bytes docs/_build/doctrees/tools/drs_pull.doctree | Bin 130578 -> 130169 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 101126 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 36402 -> 35919 bytes docs/_build/html/index.html | 8 +++--- docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools.html | 8 +++--- docs/_build/html/tools/drs_pull.html | 6 ++--- docs/_build/html/tools/indexing.html | 26 ++++++++++---------- docs/_build/html/tools/metadata.html | 10 ++++---- 10 files changed, 30 insertions(+), 30 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 938f75edabf21a2fb73f6c9bb45fb5f75f9539e2..cc0330841e2661df8be3a695771bd1f15bfbe032 100644 GIT binary patch delta 92627 zcmb4s2Y6IP_c!;ZXYSs+n+ha>1PC3H&^v^#bVN~AR-F5AtNdXDi%Nm zRMvt5uP7?=QUqzzL3#;Y>UYkWxqD|f8{hxO^RPR6=FFKh=lrIZ?77_M>hV4+c=<{F z$Br4CKPzI?*g;P}n?Eah*q|}}2lgM+A4o%n4;(Z;e^&StLxv8582UM6_>&MbX2gi0 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    -
  • Download
      +
    • Download
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    • Index
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        • -
      • Verify
          +
        • Verify
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          • MAX_CONCURRENT_REQUESTS
          • async_verify_object_manifest()
            • @@ -261,7 +261,7 @@

            Welcome to Gen3 SDK’s documentation!Metadata Tools
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"titleterms": {"gen3": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13], "auth": 0, "helper": 0, "file": 1, "class": [1, 3, 4, 5, 6, 7, 8], "welcom": 2, "sdk": 2, "": 2, "document": 2, "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, "module-gen3.tools.download.drs_download"]], "Indexing Tools": [[11, "indexing-tools"]], "Download": [[11, "module-gen3.tools.indexing.download_manifest"]], "Index": [[11, "module-gen3.tools.indexing.index_manifest"]], "Verify": [[11, "module-gen3.tools.indexing.verify_manifest"]], "Metadata Tools": [[12, "metadata-tools"]], "Ingest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "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, 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"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 dacf213a1..00687b817 100644 --- a/docs/_build/html/tools.html +++ b/docs/_build/html/tools.html @@ -87,7 +87,7 @@

                  Gen3 ToolsIndexing Tools

Verify all file object records into a manifest csv

Parameters:
@@ -435,7 +435,7 @@

Navigation

  • Gen3 Tools
    • DRS Download Tools
    • Indexing Tools
        -
      • Download
          +
        • Download
          • -
        • Index
            +
          • Index
            • -
          • Verify
              +
            • Verify
              • CURRENT_DIR
              • MAX_CONCURRENT_REQUESTS
              • async_verify_object_manifest()
                • diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 02b342e9a..27980da2a 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -33,9 +33,9 @@

                Metadata Tools

                -
                -

                Ingest

                -

                Tools for ingesting a CSV/TSV metadata manifest into the Metdata Service.

                +
                +

                Ingest

                +

                Tools for ingesting a CSV/TSV metadata manifest into the Metdata Service.

                gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID
                @@ -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-1692886743.8074749.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-1693233058.6020522.log', get_guid_from_file=True, metadata_type=None)[source]

                Ingest all metadata records into a manifest csv

                Parameters:
                @@ -190,7 +190,7 @@

                Navigation

              • DRS Download Tools
              • Indexing Tools
              • Metadata Tools
                  -
                • Ingest
                    +
                  • Ingest
                    • COLUMN_TO_USE_AS_GUID
                    • GUID_TYPE_FOR_INDEXED_FILE_OBJECT
                    • GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT
                      • From b9349e0483b9681d5bd7382c89eee9491a3ff303 Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Mon, 28 Aug 2023 09:45:47 -0500 Subject: [PATCH 03/12] remove comment --- gen3/tools/indexing/merge_manifests.py | 1 - 1 file changed, 1 deletion(-) diff --git a/gen3/tools/indexing/merge_manifests.py b/gen3/tools/indexing/merge_manifests.py index 6ea3e7bb0..5a80e32e4 100644 --- a/gen3/tools/indexing/merge_manifests.py +++ b/gen3/tools/indexing/merge_manifests.py @@ -111,7 +111,6 @@ def merge_bucket_manifests( records_from_file, _ = get_and_verify_fileinfos_from_manifest( manifest, include_additional_columns=True ) - # records_with_no_guid = [] for record in records_from_file: # simple case where this is the first time we've seen this hash headers.update(record.keys()) From 559f35fffe45a3578e614d6e377a902f011291b3 Mon Sep 17 00:00:00 2001 From: SpencerAxelrod Date: Mon, 28 Aug 2023 14:48:18 +0000 Subject: [PATCH 04/12] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1553141 -> 1553141 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35919 -> 35919 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index cc0330841e2661df8be3a695771bd1f15bfbe032..aa7f839dff029bb4296bfbe1075882c78520de38 100644 GIT binary patch delta 9845 zcma)Cd01A}*7v;g2=6(YK|sX;k{J|nz!7If5ld5Z$O#9o0SPpjP--fuX}##OBGa78 zGA-2Yl+|_4OmEiJa>_DIKtMrLbNJTY`)t&Ezwddzf8O<5^V-uoXCJun$Cw*`jM==b zMWOM<+}x6drp)Z|NX*aYXH0*&WT8)9cJ{Q~_~$b6#!VcTH?CeVaeD5vIr-D3l`M4R z=8u1FYHse->@0NS=18YzP0V-+qm9eYn^LmS#@VS^lM((`C|#$b(vm$sGh;#?`c0ZT zEyMdnSlBby4GkJBv@terdTw4x=3k7ra~~nN#sn^zK*(yj6B~)(E4Yo!EM#@wHDS#I 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2dbcd31e50f008fe0c24dc2ed68f5a345f1bf02d..a9ad6a6e2673eaff1495d83734e5568118a3ade3 100644 GIT binary patch delta 113 zcmZqeV{7eWYuLiL-Ad5Jz|vUH$k5c%%)&x1CqG?%^8Cf3+wWR2ny~U9%Wao+V0^-j ZA~c=XhtVBXB*BN#21R813LnN;D**E69cusp delta 113 zcmZqeV{7eWYuLiL-Ad5dz|=y|*udDr!pKZ7CqG?%^8Cf3+wWR2ny~U9%Wao+V0^-j ZA~c=XhtVBXB*BN#21R813LnN;D*)<^9XIndexing 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-1693233058.3038826.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-1693234093.2159688.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 27980da2a..d7860a28e 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

                      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-1693233058.6020522.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-1693234093.5807943.log', get_guid_from_file=True, metadata_type=None)[source]

                      Ingest all metadata records into a manifest csv

                      Parameters:
                      From 2de3a7c7a16d9a84d0e686bfe1e5d9eb71530e0d Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Mon, 28 Aug 2023 10:19:07 -0500 Subject: [PATCH 05/12] fix comments --- gen3/tools/indexing/merge_manifests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gen3/tools/indexing/merge_manifests.py b/gen3/tools/indexing/merge_manifests.py index 5a80e32e4..56752ea43 100644 --- a/gen3/tools/indexing/merge_manifests.py +++ b/gen3/tools/indexing/merge_manifests.py @@ -149,8 +149,8 @@ def merge_bucket_manifests( ) all_rows[record[MD5_STANDARD_KEY]] = updated_records.values() - # for the entries where there was no GUID specified, we will add that metadata - # to all previous records + # for the entries where there was no GUID specified, we will add that metadata + # to all previous records for record in records_with_no_guid: updated_records = _get_updated_records( record=record, From 603e9c9f10ade351389d8b245dd58b306629a34f Mon Sep 17 00:00:00 2001 From: SpencerAxelrod Date: Mon, 28 Aug 2023 15:20:51 +0000 Subject: [PATCH 06/12] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1553141 -> 1553136 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35919 -> 35914 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index aa7f839dff029bb4296bfbe1075882c78520de38..41245f2786c17aef8c77f5eecbef9b475e34d2ae 100644 GIT binary patch delta 11148 zcma)Cd01A}*5|zQ$ornNnFX9cL1qrC4dc|{YaOe~sMQD!bGD41D@?Tq{>dCydoISS`YdSXUl;f#X(iZav0IYrYe%8XAJ zqK2hlk}q#^5pt)_n3-4pVe6<^e{P(_O=sj!t0=QIL6fgw67&1yoV?l3mbZzDntR#c z=T~N9#)-2Fiz<9q7;Wbkf^m^CT+)T$HF6{7OVHQ2j*MUMsu|BA!V{c2#?HG 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"gen3-submission-class"]], "Gen3 Tools": [[9, "gen3-tools"]], "DRS Download Tools": [[10, "module-gen3.tools.download.drs_download"]], "Indexing Tools": [[11, "indexing-tools"]], "Download": [[11, "module-gen3.tools.indexing.download_manifest"]], "Index": [[11, "module-gen3.tools.indexing.index_manifest"]], "Verify": [[11, "module-gen3.tools.indexing.verify_manifest"]], "Metadata Tools": [[12, "metadata-tools"]], "Ingest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "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, 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"attribute", "Python attribute"], "3": ["py", "module", "Python module"], "4": ["py", "function", "Python function"]}, "titleterms": {"gen3": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13], "auth": 0, "helper": 0, "file": 1, "class": [1, 3, 4, 5, 6, 7, 8], "welcom": 2, "sdk": 2, "": 2, "document": 2, "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, "module-gen3.tools.download.drs_download"]], "Indexing Tools": [[11, "indexing-tools"]], "Download": [[11, "module-gen3.tools.indexing.download_manifest"]], "Index": [[11, "module-gen3.tools.indexing.index_manifest"]], "Verify": [[11, "module-gen3.tools.indexing.verify_manifest"]], "Metadata Tools": [[12, "metadata-tools"]], "Ingest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "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_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/indexing.html b/docs/_build/html/tools/indexing.html index f15d537eb..ee8166867 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -380,7 +380,7 @@

                      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-1693234093.2159688.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-1693236046.1047835.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 d7860a28e..0e1e68c4e 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

                      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-1693234093.5807943.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-1693236046.485695.log', get_guid_from_file=True, metadata_type=None)[source]

                      Ingest all metadata records into a manifest csv

                      Parameters:
                      From 79936758d2ad5f6aa3895d9cf56fbfc8c5db1c73 Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Thu, 30 Nov 2023 14:43:05 -0600 Subject: [PATCH 07/12] Revert "Apply automatic documentation changes" This reverts commit 603e9c9f10ade351389d8b245dd58b306629a34f. --- docs/_build/doctrees/environment.pickle | Bin 1553136 -> 1553141 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35914 -> 35919 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 41245f2786c17aef8c77f5eecbef9b475e34d2ae..aa7f839dff029bb4296bfbe1075882c78520de38 100644 GIT binary patch delta 11041 zcma)Cd0drM`scme%iX#6eGiM^0tzULEG~%qh6{?K87{bm3odsYP!T7y)Z8H^sY^WC 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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() 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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, 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"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/indexing.html b/docs/_build/html/tools/indexing.html index ee8166867..f15d537eb 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -380,7 +380,7 @@

                      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-1693236046.1047835.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-1693234093.2159688.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 0e1e68c4e..d7860a28e 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

                      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-1693236046.485695.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-1693234093.5807943.log', get_guid_from_file=True, metadata_type=None)[source]

                      Ingest all metadata records into a manifest csv

                      Parameters:
                      From a7b78d11c6ab4f2c0e630cf17e13080d9df74026 Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Tue, 5 Dec 2023 23:09:31 -0600 Subject: [PATCH 08/12] Revert "Apply automatic documentation changes" This reverts commit 559f35fffe45a3578e614d6e377a902f011291b3. --- docs/_build/doctrees/environment.pickle | Bin 1553141 -> 1553141 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35919 -> 35919 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index aa7f839dff029bb4296bfbe1075882c78520de38..cc0330841e2661df8be3a695771bd1f15bfbe032 100644 GIT binary patch delta 9845 zcma)CcXU-nx98kmlY7qOrcr{BNO~oN-g_uPK|qSMP$DLg5F3&xXdnRuy&>Czh|&}b 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z!qM7O68(N!qM>Ic8huV8^}Ix*FG_T{LZV%j61BT3QDvP(mv2fm>{g6~+iyuUrW z{+8&|y9~`+G$nv8ni9Aqp8wxU=9l5@PXRPydEkU#@ppiuk@7DBGomDlh>@r$R-zx` eBpRI{(fU>rJ>6QON{R9_Z$v1#aq{!W$Ndkr+LRUm diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree index a9ad6a6e2673eaff1495d83734e5568118a3ade3..2dbcd31e50f008fe0c24dc2ed68f5a345f1bf02d 100644 GIT binary patch delta 113 zcmZqeV{7eWYuLiL-Ad5dz|=y|*udDr!pKZ7CqG?%^8Cf3+wWR2ny~U9%Wao+V0^-j ZA~c=XhtVBXB*BN#21R813LnN;D*)<^9XIndexing 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-1693234093.2159688.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-1693233058.3038826.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 d7860a28e..27980da2a 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

                      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-1693234093.5807943.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-1693233058.6020522.log', get_guid_from_file=True, metadata_type=None)[source]

                      Ingest all metadata records into a manifest csv

                      Parameters:
                      From 2b7a64609c2be82b02873dcac24904c8482c61f6 Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Tue, 5 Dec 2023 23:09:51 -0600 Subject: [PATCH 09/12] Revert "Apply automatic documentation changes" This reverts commit 172b64fc3fa33f0a09c0a63473a2a9ee110f60b9. --- docs/_build/doctrees/environment.pickle | Bin 1553141 -> 1554905 bytes docs/_build/doctrees/tools/drs_pull.doctree | Bin 130169 -> 130578 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 101126 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35919 -> 36402 bytes docs/_build/html/index.html | 8 +++--- docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools.html | 8 +++--- docs/_build/html/tools/drs_pull.html | 6 ++--- docs/_build/html/tools/indexing.html | 26 ++++++++++---------- docs/_build/html/tools/metadata.html | 10 ++++---- 10 files changed, 30 insertions(+), 30 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle 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zQO*@ZQ@Kgb+-UG9EauZ;LrV8y>0FNG(TH|@*89?TLPFBcNlz{_&>Hr)RuNIV6r!B3 zqFkwa*>|6xev=${+0KK6s@@%b$;FX7*sT;o(&aG@A(L$nCs)$O^RdRp@HHRSZnW#= ZYO6xS=tUZ@k5=eFykM$Cm~72Y{U5YHY83zg diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index bf4d4bba6..57f5e27e3 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -230,7 +230,7 @@

                      Welcome to Gen3 SDK’s documentation!Indexing Tools
                        -
                      • Download
                          +
                        • Download
                          • -
                        • Index
                            +
                          • Index
                            • -
                          • Verify
                              +
                            • Verify
                              • CURRENT_DIR
                              • MAX_CONCURRENT_REQUESTS
                              • async_verify_object_manifest()
                                • @@ -261,7 +261,7 @@

                                Welcome to Gen3 SDK’s documentation!Metadata Tools
                                  -
                                • Ingest
                                    +
                                  • Ingest
                                    • COLUMN_TO_USE_AS_GUID
                                    • GUID_TYPE_FOR_INDEXED_FILE_OBJECT
                                    • GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT
                                      • diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index 175ad7349..a470ed6b5 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["auth", "file", "index", "indexing", "jobs", "metadata", "object", "query", "submission", "tools", "tools/drs_pull", "tools/indexing", "tools/metadata", "wss"], "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"], "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"], "terms": 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"Gen3 Query Class": [[7, "gen3-query-class"]], "Gen3 Submission Class": [[8, "gen3-submission-class"]], "Gen3 Tools": [[9, "gen3-tools"]], "DRS Download Tools": [[10, "module-gen3.tools.download.drs_download"]], "Indexing Tools": [[11, "indexing-tools"]], "Download": [[11, "module-gen3.tools.indexing.download_manifest"]], "Index": [[11, "module-gen3.tools.indexing.index_manifest"]], "Verify": [[11, "module-gen3.tools.indexing.verify_manifest"]], "Metadata Tools": [[12, "metadata-tools"]], "Ingest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "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"]], 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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_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 00687b817..dacf213a1 100644 --- a/docs/_build/html/tools.html +++ b/docs/_build/html/tools.html @@ -87,7 +87,7 @@

                                      Gen3 ToolsIndexing Tools

                      Verify all file object records into a manifest csv

                      Parameters:
                      @@ -435,7 +435,7 @@

                      Navigation

                    • Gen3 Tools
                      • DRS Download Tools
                      • Indexing Tools
                          -
                        • Download
                            +
                          • Download
                            • -
                          • Index
                              +
                            • Index
                              • -
                            • Verify
                                +
                              • Verify
                                • CURRENT_DIR
                                • MAX_CONCURRENT_REQUESTS
                                • async_verify_object_manifest()
                                  • diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 27980da2a..02b342e9a 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -33,9 +33,9 @@

                                  Metadata Tools

                                  -
                                  -

                                  Ingest

                                  -

                                  Tools for ingesting a CSV/TSV metadata manifest into the Metdata Service.

                                  +
                                  +

                                  Ingest

                                  +

                                  Tools for ingesting a CSV/TSV metadata manifest into the Metdata Service.

                                  gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID
                                  @@ -101,7 +101,7 @@

                                  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-1693233058.6020522.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:
                                  @@ -190,7 +190,7 @@

                                  Navigation

                                • DRS Download Tools
                                • Indexing Tools
                                • Metadata Tools
                                    -
                                  • Ingest
                                      +
                                    • Ingest
                                      • COLUMN_TO_USE_AS_GUID
                                      • GUID_TYPE_FOR_INDEXED_FILE_OBJECT
                                      • GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT
                                        • From 58470f54ffcf2b05643bf305f608106639bf5341 Mon Sep 17 00:00:00 2001 From: SpencerAxelrod Date: Wed, 6 Dec 2023 05:11:32 +0000 Subject: [PATCH 10/12] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1553136 -> 1553141 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35914 -> 35919 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index fd6a32ce442154ea34b40a4f524cd458549097fc..2a95767eb60dd87c47926682405599feb7cec384 100644 GIT binary patch delta 11230 zcma)Cd0bW1zGolKJny}jK?V_JkU=AEW|)qYO5QUw@~4%T>Zi__nO9zFEi9V!)QrNy83p;}rN)9up1jF(%S(Nq zE-WlB)oiBBDV#8?Xy(lFQUf26td2=UDnK*YMvUnI|JqpCV 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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 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"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/indexing.html b/docs/_build/html/tools/indexing.html index e93f4ffa9..52f8a7a9a 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -380,7 +380,7 @@

                                        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-1700678999.9725351.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-1701839488.6993823.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 a16694a81..06c2691a1 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

                                        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-1700679000.272037.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-1701839489.0258799.log', get_guid_from_file=True, metadata_type=None)[source]

                                        Ingest all metadata records into a manifest csv

                                        Parameters:
                                        From 40f9e45161da10d7f27c4d40feb5c5d79acbf334 Mon Sep 17 00:00:00 2001 From: Spencer Axelrod Date: Wed, 6 Dec 2023 16:04:52 -0600 Subject: [PATCH 11/12] add test for no guid merge order --- .../expected-merged-output-manifest.tsv | 2 ++ .../input/manifest_WITHOUT_guid.tsv | 2 ++ .../input/manifest_with_guid.tsv | 2 ++ tests/merge_manifests/test_manifest_merge.py | 31 +++++++++++++++++++ 4 files changed, 37 insertions(+) create mode 100644 tests/merge_manifests/no_guid_same_md5_order/expected-merged-output-manifest.tsv create mode 100644 tests/merge_manifests/no_guid_same_md5_order/input/manifest_WITHOUT_guid.tsv create mode 100644 tests/merge_manifests/no_guid_same_md5_order/input/manifest_with_guid.tsv diff --git a/tests/merge_manifests/no_guid_same_md5_order/expected-merged-output-manifest.tsv b/tests/merge_manifests/no_guid_same_md5_order/expected-merged-output-manifest.tsv new file mode 100644 index 000000000..2255f7db1 --- /dev/null +++ b/tests/merge_manifests/no_guid_same_md5_order/expected-merged-output-manifest.tsv @@ -0,0 +1,2 @@ +guid size md5 acl authz urls metadata +dg.4503/1234abcd 1193060 2de45cf5e6b2639c98b56b679cffc119 admin phsXXXXXX.c1 AUTHZ_HERE gs://path s3://path some_data diff --git a/tests/merge_manifests/no_guid_same_md5_order/input/manifest_WITHOUT_guid.tsv b/tests/merge_manifests/no_guid_same_md5_order/input/manifest_WITHOUT_guid.tsv new file mode 100644 index 000000000..4a3373440 --- /dev/null +++ b/tests/merge_manifests/no_guid_same_md5_order/input/manifest_WITHOUT_guid.tsv @@ -0,0 +1,2 @@ +guid size md5 acl authz urls metadata + 1193060 2de45cf5e6b2639c98b56b679cffc119 phsXXXXXX.c1 admin AUTHZ_HERE gs://path s3://path some_data \ No newline at end of file diff --git a/tests/merge_manifests/no_guid_same_md5_order/input/manifest_with_guid.tsv b/tests/merge_manifests/no_guid_same_md5_order/input/manifest_with_guid.tsv new file mode 100644 index 000000000..427b44603 --- /dev/null +++ b/tests/merge_manifests/no_guid_same_md5_order/input/manifest_with_guid.tsv @@ -0,0 +1,2 @@ +guid size md5 acl authz urls metadata +dg.4503/1234abcd 1193060 2de45cf5e6b2639c98b56b679cffc119 phsXXXXXX.c1 admin AUTHZ_HERE gs://path s3://path some_data \ No newline at end of file diff --git a/tests/merge_manifests/test_manifest_merge.py b/tests/merge_manifests/test_manifest_merge.py index 62e3cae93..e6997ffc3 100644 --- a/tests/merge_manifests/test_manifest_merge.py +++ b/tests/merge_manifests/test_manifest_merge.py @@ -121,6 +121,37 @@ def test_size_mismatch(): ) +def test_no_guid_input_order(): + """ + Test merging two input manifests with that have the same md5, but one has no guid. + Ensure that the order of the input results in the same correct output. + """ + file_order_1 = [ + "tests/merge_manifests/no_guid_same_md5_order/input/manifest_with_guid.tsv", + "tests/merge_manifests/no_guid_same_md5_order/input/manifest_WITHOUT_guid.tsv", + ] + file_order_2 = [ + "tests/merge_manifests/no_guid_same_md5_order/input/manifest_WITHOUT_guid.tsv", + "tests/merge_manifests/no_guid_same_md5_order/input/manifest_with_guid.tsv", + ] + merge_bucket_manifests( + files=file_order_1, + output_manifest_file_delimiter=None, + output_manifest="merged-output-test-manifest.tsv", + ) + assert _get_tsv_data("merged-output-test-manifest.tsv") == _get_tsv_data( + "tests/merge_manifests/no_guid_same_md5_order/expected-merged-output-manifest.tsv" + ) + merge_bucket_manifests( + files=file_order_2, + output_manifest_file_delimiter=None, + output_manifest="merged-output-test-manifest.tsv", + ) + assert _get_tsv_data("merged-output-test-manifest.tsv") == _get_tsv_data( + "tests/merge_manifests/no_guid_same_md5_order/expected-merged-output-manifest.tsv" + ) + + def _get_tsv_data(manifest, delimiter="\t"): """ Returns a list of rows sorted by md5 for the given manifest. From 48d3015c3f470c8a5a7a297903f5281f79a258f8 Mon Sep 17 00:00:00 2001 From: SpencerAxelrod Date: Wed, 6 Dec 2023 22:06:07 +0000 Subject: [PATCH 12/12] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1553141 -> 1553141 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35919 -> 35919 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 2a95767eb60dd87c47926682405599feb7cec384..d3ea12c690ae101ace6e99e5900ab8dd14761d78 100644 GIT binary patch delta 11057 zcma)Cd0bW1_V?VGJD+p7%pxi%2r`N&&f<&`nqv;(fWv(TD9{|1l?vie7g<{5(`OF( zGJRogQ?q)hEy?r?7BNex6Ss85vk^m^o)|ZnGuxGbeABuR~Z zGpsX% zu*p;KOvOrXz3)L>uzsbt(O1$bM5^_z=@c$q_U-Nz)|$q)q9VH7EsXdyU{*JL*E>bn 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b#Em96o!5ua65g*b3 delta 120 zcmX>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-1701839488.6993823.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-1701900364.6706986.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 06c2691a1..35c815644 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -101,7 +101,7 @@

                                        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-1701839489.0258799.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-1701900364.9645383.log', get_guid_from_file=True, metadata_type=None)[source]

                                        Ingest all metadata records into a manifest csv

                                        Parameters: