From 3a1aa7379154954400857e9db1b91091204f9404 Mon Sep 17 00:00:00 2001 From: Alexander VT Date: Thu, 9 Jun 2022 15:56:32 -0500 Subject: [PATCH 01/11] feat(populate-guids): add CLI/SDK functionality to populate a manifest with valid GUIDs --- .secrets.baseline | 20 ++-- gen3/cli/objects.py | 39 +++++++- gen3/index.py | 33 +++++++ gen3/tools/indexing/index_manifest.py | 63 ++++++++++++ tests/test_data/test_populate_guids.csv | 4 + .../test_populate_guids_different_columns.csv | 4 + tests/test_manifests.py | 98 ++++++++++++++++++- 7 files changed, 246 insertions(+), 15 deletions(-) create mode 100644 tests/test_data/test_populate_guids.csv create mode 100644 tests/test_data/test_populate_guids_different_columns.csv diff --git a/.secrets.baseline b/.secrets.baseline index d49240ea8..9f881e8b5 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": "(docs\\/_build|poetry.lock)|^.secrets.baseline$", "lines": null }, - "generated_at": "2022-06-07T20:32:38Z", + "generated_at": "2022-06-09T20:56:24Z", "plugins_used": [ { "name": "AWSKeyDetector" @@ -344,55 +344,55 @@ { "hashed_secret": "6487fa7aea293dfde99cda9c6ccb9161219331c7", "is_verified": false, - "line_number": 110, + "line_number": 120, "type": "Hex High Entropy String" }, { "hashed_secret": "96c9184fb19c9c1618ccf44d141f8029a739891c", "is_verified": false, - "line_number": 426, + "line_number": 436, "type": "Hex High Entropy String" }, { "hashed_secret": "e1da93616713812cb50e0ac845b1e9e305d949f1", "is_verified": false, - "line_number": 562, + "line_number": 572, "type": "Hex High Entropy String" }, { "hashed_secret": "47f42f4c34fddab383b817e689dc0fb75af81266", "is_verified": false, - "line_number": 586, + "line_number": 596, "type": "Hex High Entropy String" }, { "hashed_secret": "300d95dd5d30ab6928ffda6c08c6a129a23e5b39", "is_verified": false, - "line_number": 610, + "line_number": 620, "type": "Hex High Entropy String" }, { "hashed_secret": "f9e664db75c7f23a299b0b055c10e08d47073e93", "is_verified": false, - "line_number": 678, + "line_number": 688, "type": "Hex High Entropy String" }, { "hashed_secret": "7c35c215b326b9463b669b657c1ff9873ff53d9a", "is_verified": false, - "line_number": 819, + "line_number": 829, "type": "Hex High Entropy String" }, { "hashed_secret": "0d515eaf06062d52e8c80abb4d3b713a65396d30", "is_verified": false, - "line_number": 823, + "line_number": 833, "type": "Hex High Entropy String" }, { "hashed_secret": "b4cff7c2af45cdfe66195ec574a7b8832f8621ea", "is_verified": false, - "line_number": 828, + "line_number": 838, "type": "Hex High Entropy String" } ], diff --git a/gen3/cli/objects.py b/gen3/cli/objects.py index 8cbe6abe7..f98bd1127 100644 --- a/gen3/cli/objects.py +++ b/gen3/cli/objects.py @@ -11,6 +11,7 @@ from gen3.tools.indexing.index_manifest import ( index_object_manifest, delete_all_guids, + populate_object_manifest_with_valid_guids, ) from gen3.tools.indexing.verify_manifest import manifest_row_parsers from gen3.utils import get_or_create_event_loop_for_thread @@ -101,7 +102,7 @@ def objects_manifest_verify(ctx, file, max_concurrent_requests): loop = get_or_create_event_loop_for_thread() if not file: - file = click.prompt("Enter Discovery metadata file path to publish") + file = click.prompt("Enter file path to verify") click.echo(f"Verifying {file}...\n Against: {auth.endpoint}") @@ -205,7 +206,7 @@ def objects_manifest_validate_format( line_limit, ): if not file: - file = click.prompt("Enter Discovery metadata file path to validate format for") + file = click.prompt("Enter file path to validate format for") is_valid = is_valid_manifest_format( manifest_path=file, @@ -270,7 +271,7 @@ def objects_manifest_publish( loop = get_or_create_event_loop_for_thread() if not file: - file = click.prompt("Enter Discovery metadata file path to publish") + file = click.prompt("Enter file path to publish") click.echo( f"Publishing/writing object data from {file}...\n to: {auth.endpoint}" @@ -288,6 +289,37 @@ def objects_manifest_publish( ) +@click.command( + help="Populates specified object manifest with valid GUIDs WITHOUT publishing." +) +@click.argument("file", required=False) +@click.option( + "--out-manifest-file", + "out_manifest_file", + help="The path to output manifest", + required=False, +) +@click.pass_context +def objects_manifest_populate_guids( + ctx, + file, + out_manifest_file, +): + auth = ctx.obj["auth_factory"].get() + loop = get_or_create_event_loop_for_thread() + + if not file: + file = click.prompt("Enter file path to populate GUIDs for") + + click.echo(f"Populating GUIDs missing from {file}...") + + populate_object_manifest_with_valid_guids( + commons_url=auth.endpoint, + manifest_file=file, + output_filename=out_manifest_file, + ) + + @click.command(help="Deletes specified object manifest to Gen3 instance.") @click.argument("file", required=True) @click.pass_context @@ -315,4 +347,5 @@ def objects_manifest_delete_all_guids(ctx, file): manifest.add_command(objects_manifest_verify, name="verify") manifest.add_command(objects_manifest_validate_format, name="validate-manifest-format") manifest.add_command(objects_manifest_publish, name="publish") +manifest.add_command(objects_manifest_populate_guids, name="populate-guids") manifest.add_command(objects_manifest_delete_all_guids, name="delete-all-guids") diff --git a/gen3/index.py b/gen3/index.py index 0f69bfd82..4444bfc55 100755 --- a/gen3/index.py +++ b/gen3/index.py @@ -813,6 +813,39 @@ async def async_query_urls(self, pattern, _ssl=None): return response + ## Mint GUID Requests + + @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS) + def get_valid_guids(self, count=None): + """ + Get a list of valid GUIDs without indexing + + Args: + count (int): number of GUIDs to request + + Returns: + List[str]: list of valid indexd GUIDs + """ + url = "/mint/guids" + if count: + url += f"?count={count}" + + response = self.client._get(url) + raise_for_status(response) + return response.json().get("guids", []) + + @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS) + def get_guids_prefix(self): + """ + Get the prefix for GUIDs if there is one + + Returns: + str: prefix for this instance + """ + response = self.client._get("/mint/prefix") + raise_for_status(response) + return response.json().get("prefix") + def _print_func_name(function): return "{}.{}".format(function.__module__, function.__name__) diff --git a/gen3/tools/indexing/index_manifest.py b/gen3/tools/indexing/index_manifest.py index a9cb23a66..2b60ef8ed 100644 --- a/gen3/tools/indexing/index_manifest.py +++ b/gen3/tools/indexing/index_manifest.py @@ -458,6 +458,69 @@ def index_object_manifest( return files, headers +def populate_object_manifest_with_valid_guids( + commons_url, manifest_file, output_filename=None +): + """ + Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs + for the given commons. + + NOTE: This DOES NOT index anything, it only works client side to populate the manifest + with valid GUIDs (which are obtained from the server). No records are created + as part of this function call. + + Args: + commons_url (str): root domain for commons where indexd lives + manifest_file (str): file path for input manifest file to populate empty GUIDs + output_filename(str): output file name for manifest + """ + if not output_filename: + file, extension = os.path.splitext(manifest_file) + output_filename = file + "_populated_guids" + extension + + try: + records, headers = get_and_verify_fileinfos_from_manifest( + manifest_file, manifest_file_delimiter=None, include_additional_columns=True + ) + except Exception as exc: + logging.error( + f"Can not read records and headers from input manifest: {manifest_file}." + ) + raise + + # ensure GUID column exists + try: + headers.index(GUID_STANDARD_KEY) + except ValueError: + headers.insert(0, GUID_STANDARD_KEY) + + index = Gen3Index(commons_url) + valid_guids = index.get_valid_guids(count=10000) + + # modify records to include a valid GUID if it doesn't exist + new_records = [] + for record in records: + if not record.get(GUID_STANDARD_KEY): + record[GUID_STANDARD_KEY] = valid_guids.pop() + + # if we run out of valid GUIDs, get some more + if not valid_guids: + valid_guids = index.get_valid_guids(count=10000) + + new_records.append(record) + + assert len(new_records) == len(records) + + output_filename = os.path.abspath(output_filename) + logging.info(f"Writing output to {output_filename}") + + # remove existing output if it exists + if os.path.isfile(output_filename): + os.unlink(output_filename) + + _write_csv(os.path.join(CURRENT_DIR, output_filename), new_records, headers) + + @click.command() @click.option( "--commons-url", diff --git a/tests/test_data/test_populate_guids.csv b/tests/test_data/test_populate_guids.csv new file mode 100644 index 000000000..b4fd3ab6e --- /dev/null +++ b/tests/test_data/test_populate_guids.csv @@ -0,0 +1,4 @@ +guid,authz,acl,file_size,md5,urls +,/programs/DEV/projects/test,DEV test,123,a1234567891234567890123456789012,gs://test/test.txt s3://testaws/aws/test.txt +,/programs/DEV/projects/test2,DEV,235,c1234567891234567890123456789012,gs://test/test.txt s3://testaws/aws/test.txt +dg.TEST/9c205cd7-c399-4503-9f49-5647188bde66,/programs/DEV/projects/test3 /programs/DEV/projects/test3bak,DEV test3,334,b1334567891334567890133456789013,gs://test/test.txt s3://testaws/aws/test.txt diff --git a/tests/test_data/test_populate_guids_different_columns.csv b/tests/test_data/test_populate_guids_different_columns.csv new file mode 100644 index 000000000..1dc4ea3be --- /dev/null +++ b/tests/test_data/test_populate_guids_different_columns.csv @@ -0,0 +1,4 @@ +file_size,md5,urls,foobar +123,a1234567891234567890123456789012,gs://test/test.txt s3://testaws/aws/test.txt,foobar1 +235,c1234567891234567890123456789012,gs://test/test.txt,foobar2 +334,b1334567891334567890133456789013,gs://test/test.txt,foobar3 diff --git a/tests/test_manifests.py b/tests/test_manifests.py index 86e1e742a..3b77cff28 100644 --- a/tests/test_manifests.py +++ b/tests/test_manifests.py @@ -10,9 +10,19 @@ from gen3.tools.indexing import async_download_object_manifest from gen3.tools.indexing.index_manifest import ( index_object_manifest, + populate_object_manifest_with_valid_guids, +) +from gen3.tools.utils import ( + get_and_verify_fileinfos_from_tsv_manifest, + GUID_STANDARD_KEY, + FILENAME_STANDARD_KEY, + SIZE_STANDARD_KEY, + MD5_STANDARD_KEY, + ACL_STANDARD_KEY, + URLS_STANDARD_KEY, + AUTHZ_STANDARD_KEY, + PREV_GUID_STANDARD_KEY, ) -from gen3.tools.utils import get_and_verify_fileinfos_from_tsv_manifest - CURRENT_DIR = os.path.dirname(os.path.realpath(__file__)) @@ -922,3 +932,87 @@ def test_index_manifest_packages_failure(data, gen3_index, gen3_auth, logfile): for error in data["expected_error_msgs"]: assert error in logfile.read() + + +@pytest.mark.parametrize( + "data", + [ + {"manifest": "test_populate_guids.csv"}, + {"manifest": "test_populate_guids_different_columns.csv"}, + ], +) +def test_objects_manifest_populate_guids(data, gen3_index, gen3_auth, logfile): + """ + Test that the output of the populate GUIDs functionality is as expected + + guid,md5 + dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b,a1234567891234567890123456789012 + dg.TEST/1e9d3103-cbe2-4c39-917c-b3abad4750d2,c1234567891234567890123456789012 + dg.TEST/9c205cd7-c399-4503-9f49-5647188bde66,b1334567891334567890133456789013 + """ + input_filename = f"{CURRENT_DIR}/test_data/{data['manifest']}" + output_filename = ( + f"{CURRENT_DIR}/test_data/{data['manifest'].rstrip('.csv')}_output.csv" + ) + + input_files, input_headers = get_and_verify_fileinfos_from_tsv_manifest( + input_filename + ) + + existing_guids = [] + records_from_input = {} + for file in input_files: + records_from_input[file[MD5_STANDARD_KEY]] = file + + existing_guid = file.get(GUID_STANDARD_KEY) + if existing_guid: + existing_guids.append(existing_guid) + + # mock with GUIDs + mocked_valid_guids = [ + "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", + "dg.TEST/1e9d3103-cbe2-4c39-917c-b3abad4750d2", + "dg.TEST/9c205cd7-c399-4503-9f49-5647188bde66", + ] + + with patch( + "gen3.tools.indexing.index_manifest.Gen3Index.get_valid_guids", MagicMock() + ) as mock_indexd_valid_guids: + mock_indexd_valid_guids.return_value = mocked_valid_guids + populate_object_manifest_with_valid_guids( + commons_url=gen3_index.client.url, + manifest_file=f"{CURRENT_DIR}/test_data/{data['manifest']}", + output_filename=output_filename, + ) + + output_files, headers = get_and_verify_fileinfos_from_tsv_manifest(output_filename) + + # cleanup output + if os.path.isfile(output_filename): + os.unlink(output_filename) + + # ensure output has valid input headers + for header in input_headers: + if header in [ + GUID_STANDARD_KEY, + SIZE_STANDARD_KEY, + MD5_STANDARD_KEY, + ACL_STANDARD_KEY, + AUTHZ_STANDARD_KEY, + URLS_STANDARD_KEY, + FILENAME_STANDARD_KEY, + PREV_GUID_STANDARD_KEY, + ]: + assert headers.index() >= 0 + + records_from_output = {} + for file in output_files: + records_from_output[file[MD5_STANDARD_KEY]] = file + + # ensure that for every record in the input manifest: + # the record exists in the output and it now has a valid GUID (whether it be + # one that already existed in the input OR a new GUID from the population logic) + valid_guids = existing_guids + mocked_valid_guids + for record_md5, record in records_from_input.items(): + assert record_md5 in records_from_output + assert records_from_output[record_md5].get(GUID_STANDARD_KEY) in valid_guids From 9ed4c513e17d7d6f9ff56dbaaa68c1e1fdc5d5f2 Mon Sep 17 00:00:00 2001 From: Avantol13 Date: Thu, 9 Jun 2022 20:59:02 +0000 Subject: [PATCH 02/11] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 306980 -> 310983 bytes docs/_build/doctrees/indexing.doctree | Bin 139195 -> 145291 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 87834 -> 94216 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 36345 -> 36345 bytes docs/_build/html/_modules/gen3/index.html | 35 +++++++++- .../gen3/tools/indexing/index_manifest.html | 63 ++++++++++++++++++ docs/_build/html/genindex.html | 12 +++- docs/_build/html/indexing.html | 31 +++++++++ docs/_build/html/objects.inv | Bin 1823 -> 1859 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 23 ++++++- docs/_build/html/tools/metadata.html | 2 +- 12 files changed, 161 insertions(+), 7 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index c6eb4fb4f32d3acbff36ab46249d2eff30ea04a9..6243b86a6da42f8523d9e8e83bdee5853592e4d4 100644 GIT binary patch delta 11713 zcmb_CX?PS>wp3LUlFm-{mC8aE60)#{K!C8w(saTiq5`&^bSLR1=?>}6Ft|m>r+m>U zk`pX_E{GerfWaVvum~yy!oIj8;PS>99R){cM*Y-z=bWnUR2aW`&iB3i$i4S$_iXpx zb8pwP7l!u!Jaq7#gV%3P-8T3@+6|U$Q>a}*XNvk{vAMACz z>j_`usJC~th4HY^*5t7?HrLl9-r=&@e-EeAqDlhXRZe@g7lkm);i~o1_XCWc=BfsV 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                 raise_for_status(response)
                 response = await response.json()
 
-        return response
+ return response + + ## Mint GUID Requests + +
[docs] @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS) + def get_valid_guids(self, count=None): + """ + Get a list of valid GUIDs without indexing + + Args: + count (int): number of GUIDs to request + + Returns: + List[str]: list of valid indexd GUIDs + """ + url = "/mint/guids" + if count: + url += f"?count={count}" + + response = self.client._get(url) + raise_for_status(response) + return response.json().get("guids", [])
+ +
[docs] @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS) + def get_guids_prefix(self): + """ + Get the prefix for GUIDs if there is one + + Returns: + str: prefix for this instance + """ + response = self.client._get("/mint/prefix") + raise_for_status(response) + return response.json().get("prefix")
def _print_func_name(function): diff --git a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html index 5a9a2c77d..d2591a404 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html @@ -492,6 +492,69 @@

Source code for gen3.tools.indexing.index_manifest

return files, headers
+
[docs]def populate_object_manifest_with_valid_guids( + commons_url, manifest_file, output_filename=None +): + """ + Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs + for the given commons. + + NOTE: This DOES NOT index anything, it only works client side to populate the manifest + with valid GUIDs (which are obtained from the server). No records are created + as part of this function call. + + Args: + commons_url (str): root domain for commons where indexd lives + manifest_file (str): file path for input manifest file to populate empty GUIDs + output_filename(str): output file name for manifest + """ + if not output_filename: + file, extension = os.path.splitext(manifest_file) + output_filename = file + "_populated_guids" + extension + + try: + records, headers = get_and_verify_fileinfos_from_manifest( + manifest_file, manifest_file_delimiter=None, include_additional_columns=True + ) + except Exception as exc: + logging.error( + f"Can not read records and headers from input manifest: {manifest_file}." + ) + raise + + # ensure GUID column exists + try: + headers.index(GUID_STANDARD_KEY) + except ValueError: + headers.insert(0, GUID_STANDARD_KEY) + + index = Gen3Index(commons_url) + valid_guids = index.get_valid_guids(count=10000) + + # modify records to include a valid GUID if it doesn't exist + new_records = [] + for record in records: + if not record.get(GUID_STANDARD_KEY): + record[GUID_STANDARD_KEY] = valid_guids.pop() + + # if we run out of valid GUIDs, get some more + if not valid_guids: + valid_guids = index.get_valid_guids(count=10000) + + new_records.append(record) + + assert len(new_records) == len(records) + + output_filename = os.path.abspath(output_filename) + logging.info(f"Writing output to {output_filename}") + + # remove existing output if it exists + if os.path.isfile(output_filename): + os.unlink(output_filename) + + _write_csv(os.path.join(CURRENT_DIR, output_filename), new_records, headers)
+ + @click.command() @click.option( "--commons-url", diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index 52dfbf46b..31557fabd 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -333,13 +333,15 @@

G

  • get_dictionary_all() (gen3.submission.Gen3Submission method)
    • - - +
    • get_fresh_token() (gen3.tools.download.drs_download.DownloadManager method)
    • get_graphql_schema() (gen3.submission.Gen3Submission method) +
      • +
    • get_guids_prefix() (gen3.index.Gen3Index method)
    • get_index_key_paths() (gen3.metadata.Gen3Metadata method)
      • @@ -370,6 +372,8 @@

      G

    • get_status() (gen3.jobs.Gen3Jobs method)
    • get_urls() (gen3.index.Gen3Index method) +
      • +
    • get_valid_guids() (gen3.index.Gen3Index method)
    • get_version() (gen3.index.Gen3Index method) @@ -506,10 +510,12 @@

      O

      P

      diff --git a/docs/_build/html/indexing.html b/docs/_build/html/indexing.html index c1a021d7b..81116edb4 100644 --- a/docs/_build/html/indexing.html +++ b/docs/_build/html/indexing.html @@ -312,6 +312,20 @@

      Gen3 Index Class +
      +get_guids_prefix()[source]
      +

      Get the prefix for GUIDs if there is one

      +
      +
      Returns:
      +

      prefix for this instance

      +
      +
      Return type:
      +

      str

      +
      +
      +
      +
      get_latest_version(guid, has_version=False)[source]
      @@ -389,6 +403,23 @@

      Gen3 Index Class +
      +get_valid_guids(count=None)[source]
      +

      Get a list of valid GUIDs without indexing

      +
      +
      Parameters:
      +

      count (int) – number of GUIDs to request

      +
      +
      Returns:
      +

      list of valid indexd GUIDs

      +
      +
      Return type:
      +

      List[str]

      +
      +
      +

      +
      get_version()[source]
      diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv index fa43b62537b877cd671252d8d76e8ebceb793d5a..11f365cb127d7ff2a0cf6c3a6ead41e5e395eaf1 100644 GIT binary patch delta 1759 zcmV<51|a#L4#N(Rcz?}yqc#-Y`zhShZbRGCGn?6^Hpyff#~J@L)7j|AAR7`uj3nZ? ztG-5GuTN6_fx#xWk;D$8`+Zlsy7x-r${UpZ=D~tR-YtK+<`2Vs_c2HyrNdu`vLRw= z^5aj#tHI_-)(Z-f2tbNhgu_b^8^iz%0z@fb_yuL%&;+dsqJL2*hIO1E$#BCT>Z6kl zCuF@4C5R!g*0@SZ7a&M*09lMP+KockDd%I2HyH}Sp_$LZi#)+Fyr}DO7NR$ayc17# z3(2N9+nh#tknXYo1O!1oXo3Pv!iLgLG-BZHI4D>XoPr=i!3!-?H6ft*Ao-)?)n<+=aEl8QoEZ9Zw9t}bq*fCH`xJ{G`8pE2Xt=R@%hVWC5FwbbXlH`9OQ|}U8t1~!$@m$ssDH$N<`4C?TQ;1K)!CmE8Q|{$ z%tEk*aWjLR<GdLGh^XAq@N;R;_VZ6%OnllU*?C`*N^>7=-~Aux}=C*asbm!Qp1 z1a5&a9^ayFGjYm3%Rq}&8dKp&l4f50tPi&)bblebOeZ`+ayvB7wpMIMQ)j@Y{UF03 za!5rTaXB*Cp3R}jTK0anWY%UwZ#gE+$!uyWH=`6eI*bGHeGT$mJ3mG{W^^%Pc{j*QLPDEMVT0ml(VQ1a(wWN}>xT)<;70BL%f+&d+Jw^! zAP-0oVah1jGF?$>@f;apbrv;!FwW$H{BCz3a(N1w}+xc-$(OS6>dC z`H`X&M<2lA6dfLYT=7!|`I_0Y25lRs?0<08thqTM^u&@lGj`CUII@q#E$ zLZZU72X?uY@5v>lhJJFHq?T3F4EEJ?Nl)Xyd!iRhNq?PJc^AZCuk>t}_tgJ9C;9`C zW2aFcIUIZZq_%OjPGBXO7vMC-87*u2PJ3D&;`Ky|uh4FcT`6!MolR<|ky%l@OMg`j z%J!p;J$D*@(3ch5n!$bgC?9}$yZ`97E;4zNbV4osf`T}cI_eg8p+y#I^orl73itMr zw2o|36&EX`H$1y}qH9(n+fQ`w6MCcNZ00{K!1!*~?uPGFI?oc{J&gUYV=(ha)7cn2 zUf=p)e)r9Ht7LNh6^y12{^_g3~jq+2dNeRIg?$e#~bZLRLQ>mimJRCS&cXd7Lw}X8h{Wri zvy^f`=PGCqX?s{54ppceuHRZuaa9TC0%8VF*t=OYZnyV)blzxsznnaP#S|>(KDeHr z$R6($r_U%5d|>g{qt6%48IW56e++K!?tL)*{j)z>^r!4$`p~z+PJU&kLittsR!g1s zEE`4pYj)~}w)E1li<&J}_kXRP=$v7qZ)%oVUNoK&=Lhk;S+=nCGu_0yQM{$q%s`kH-q2LD%vJj%_gJ~XzH(Y;Kd7hb`P_>tJ*v1`gY9dp3b7Es2hC&pk$m$2KOE2I z!}1GggP_fCS~dd8U_!1AZu5(lB)oSF1?HhwN0gDMM)!ot3(aAGhB|-;{{z97htOeu BWxoIb delta 1723 zcmV;s21NP84xbK?cz?@w+cps0>nqgLZq2r*C!6eCNlBbqmZL|VW`hHfkjR)M7yz`Q zuKFAOy?#mYB1KBHBof0NMa;be3}yxZ2ilVKHxK6`^xn&-Tlp}|_HX?db3Xias2f6& z#6SKtycujyWIaD;u>vGSgfzGYu_Xdw-zS_SL7z$54$a7h5q}=GV%S76(G2h8Lv?hz z;f$;okeCR9HWpVZX#+$t^|6R(%G*&WJ7sdL(KaOkIyUn~c%H=+2Um4HN(1s;Bk$Bx z)k3-{O1I|`9_IVhM?NE14w@04vY@846^$A=90x}mMibKz%m`?g)2@P({N97M=UhH5wJxarP{{vwFvz6mb+19E)(@ z1?`s0Y!>UBgj#38uXN2d{-b=TE}FXGjI2$&EKiYqkAH9)pdF6tspBGt&35u-JDi$j znu{zK?Qtq9a^4=-}uWPVJBCJeC4i;A&f-n&u8H z$LmN33ggWVEV)VqjJ`wxVTuL|!J>68Ia@NVvG7A@!@%H?4rTOA_A<$tlTJ4}vsG}# zgLQ|bL4QW0R5(qPlh>&*uaAbiku~LvRwS?Fk5(LdMd}W}J_zahEAfR!&-7z8581{G zh{C66i7%Bl66mpM{HJ1+g+kMGR@~b%oQ2NmE4!0t7CAvr_GC@i^)DM+TY$sFKfq%{VK}rJxNX3D;fJ}B^12kE~-p`fH z*=*!{MwtMaO-ltcN|mF7$X6e>u-vuF^D8hT#E2DTk*K&Ik_1CAS{LR(T*`qf1BYZy za2jn07l543qox^2q2l&*8RNiHpyt}Cjd&TPK z1%Hg!m%1y0B zfU&FSFja}uas-$X$xq{#Vtdz*RSd?E5!2HNis-q7QQ9_Q7K2ZEzV7X@Y ztijp_lpU|@#V!y+Pc11$N&xS!XRCU~?|=F+iRXt=95556J+SMod`~W^HT09qG_@{Q zrns-3YkD62-4nf9O8V=($-5{DdZicptf&5G8M7aVfStyC&p;_XDLuh1~YE)~E>XPp`}GD~W>R8^yFKH9i*C&3$gO90jk@ady?K!57( z;iKOsPxVO>gj)FpM^UPER4opnMHg!9ir=RSc>8EtAlsD1#nR|C&#s^7>Xpdm6W!~C z-e@(SPac+Nd^c})!&fSu7m4p4#*@!uG@p!S^D%n7eLq2qyDt-1CDYr_Xf%5$1~H#} zT1^(q1+0?g^bx(A-H#{07BW@2@_)Te2WQ>pI#s6V0_8JxHt%+H?_}R&y4CW-7eGEB ze?DS;zq%U((oM&20NEbrlRpt~4_!m`h;A9molr2MsbDld-N1F?T+Klp(SD*=m#(&X zWKNnO@n?U+h4%|#(Pj@8-$!&%5p+!3L#jSjVG^o+>um3`EGq@nCAu^Au76i>o9+D? zoj01@uci-ZIYX<(1l=yqgz_tu;tL8CA6owPIFYN^9O-p=GDh$2?k8yW`^U*>*`Kn9 z*+bt7TlrNt6~?cMw^r)BXSpak+<7zil(m-zZPe_zx%~9R7lJZ-=dnn+s_}xjJQZj4 z8p<`G#;;IqfG0QFuK^$341c^1a(cJs8XQYHK)R_iSM@u>&f8I4;~H`iyj3@HZz}(e z7%Hxz{=3Hq5@&=Bbp5L$TK-YMi0c1NjFelc{%AMV(lK6>SjiV}4MyLo92~?fX+`3R z#6C@kbZ(Indexing Tools +
      +gen3.tools.indexing.index_manifest.populate_object_manifest_with_valid_guids(commons_url, manifest_file, output_filename=None)[source]
      +

      Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs +for the given commons.

      +
      +
      NOTE: This DOES NOT index anything, it only works client side to populate the manifest

      with valid GUIDs (which are obtained from the server). No records are created +as part of this function call.

      +
      +
      +
      +
      Parameters:
      +
        +

      • commons_url (str) – root domain for commons where indexd lives

        • +

      • manifest_file (str) – file path for input manifest file to populate empty GUIDs

        • +

      • output_filename (str) – output file name for manifest

        • +
      +
      +
      +
      +

      Verify

      @@ -340,7 +361,7 @@

      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-1654789636.6798043.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-1654808338.3985054.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 827ab8497..1978655fc 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1654789636.9773014.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-1654808338.7157485.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
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      +gen3.tools.indexing.index_manifest.populate_object_manifest_with_valid_guids(commons_url, manifest_file, output_filename=None)[source]
      +

      Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs +for the given commons.

      +
      +
      NOTE: This DOES NOT index anything, it only works client side to populate the manifest

      with valid GUIDs (which are obtained from the server). No records are created +as part of this function call.

      +
      +
      +
      +
      Parameters:
      +
        +

      • commons_url (str) – root domain for commons where indexd lives

        • +

      • manifest_file (str) – file path for input manifest file to populate empty GUIDs

        • +

      • output_filename (str) – output file name for manifest

        • +
      +
      +
      +
      +

      Verify

      @@ -340,7 +361,7 @@

      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-1654807944.3028057.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-1654871231.116127.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 da4286ad3..099daded2 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1654807944.560571.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-1654871231.617515.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
      From 90ca6d6e5a862f3efd6217260c02b5ee2b77705d Mon Sep 17 00:00:00 2001 From: Avantol13 Date: Fri, 10 Jun 2022 20:32:35 +0000 Subject: [PATCH 04/11] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 307194 -> 311197 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 87829 -> 94216 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 36345 -> 36340 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 23 +++++++++++++++++++- docs/_build/html/tools/metadata.html | 2 +- 6 files changed, 24 insertions(+), 3 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 271deea41bddc14231ae18a18fd60ce70fc38af2..e17c4faa7a083f743aa3d569955f9816aa497ba4 100644 GIT binary patch delta 12085 zcmbVyd3;nwwlH;XlclqhedT5`3klf}2!TK%LBXcOCgKc8(@A%dZj$bp?jDA5iN1Lw 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      +gen3.tools.indexing.index_manifest.populate_object_manifest_with_valid_guids(commons_url, manifest_file, output_filename=None)[source]
      +

      Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs +for the given commons.

      +
      +
      NOTE: This DOES NOT index anything, it only works client side to populate the manifest

      with valid GUIDs (which are obtained from the server). No records are created +as part of this function call.

      +
      +
      +
      +
      Parameters:
      +
        +

      • commons_url (str) – root domain for commons where indexd lives

        • +

      • manifest_file (str) – file path for input manifest file to populate empty GUIDs

        • +

      • output_filename (str) – output file name for manifest

        • +
      +
      +
      +
      +

      Verify

      @@ -340,7 +361,7 @@

      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-1654874771.190345.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-1654893151.5314457.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 489f2422c..04f8046f8 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1654874771.4957037.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-1654893151.903162.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
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"error": [10, 11, 12], "continu": 10, "downloadstatu": 10, "save": 10, "show": 10, "bar": 10, "disabl": 10, "unpack": 10, "packag": 10, "after": 10, "them": [10, 11], "get_fresh_token": 10, "drs_hostnam": 10, "known": 10, "otherwis": 10, "success": 10, "resolve_object": 10, "resolv": 10, "permiss": 10, "wai": 10, "determin": [10, 11, 12], "reason": 10, "pend": 10, "start_tim": 10, "end_tim": 10, "objectid": 10, "datamanag": 10, "occur": 10, "attribut": [10, 11], "object_id": 10, "object_typ": 10, "drsobjecttyp": 10, "unknown": 10, "file_s": [10, 11], "updated_tim": 10, "created_tim": 10, "access_method": 10, "factori": 10, "children": 10, "popul": [10, 11, 12], "server": [10, 11], "requir": 10, "byte": 10, "timestamp": 10, "last": 10, "g": 10, "child": 10, "bundl": 10, "_manag": 10, "self": 10, "pprint": 10, "indent": 10, "pretti": 10, "In": 10, "similar": 10, "linux": 10, "tree": 10, "command": 10, "md5sum": 10, "commons_url": [10, 11, 12], "typic": 10, "discoveri": 10, "cach": 10, "files": 10, "static": 10, "create_object_list": 10, "bownload": 10, "successfulli": 10, "pars": [10, 11, 12, 13], "load_manifest": 10, "download_drs_object": 10, "output_dir": 10, "conveni": 10, "download_files_in_drs_manifest": 10, "infil": 10, "list_access_in_drs_manifest": 10, "list_drs_object": 10, "list_files_in_drs_manifest": 10, "wrapper": 10, "cli": 10, "process": 11, "coroutin": 11, "asyncio": [11, 12], "librari": 11, "comma": 11, "separ": 11, "header": 11, "space": 11, "download_manifest": 11, "current_dir": 11, "indexd_record_page_s": 11, "per": [11, 12], "max_concurrent_request": [11, 12], "maximum": [11, 12], "desir": 11, "concurr": [11, 12], "across": 11, "thread": 11, "tmp_folder": 11, "folder": 11, "place": 11, "temporari": 11, "write": 11, "safe": 11, "so": 11, "To": 11, "workaround": 11, "concat": 11, "async_download_object_manifest": 11, "output_filenam": [11, 12], "num_process": 11, "24": [11, 12], "input_manifest": 11, "root": [11, 12], "domain": [11, 12], "live": [11, 12], "parallel": 11, "hit": 11, "total": 11, "help": 11, "everyth": 11, "attempt": 11, "tab": 11, "session": 11, "column": [11, 12], "shown": 11, "below": 11, "255e396f": 11, "f1f8": 11, "11e9": 11, "9a07": 11, "0a80fada099c": 11, "473d83400bc1bc9dc635e334faddf33c": 11, "363455714": 11, "pdcdatastor": 11, "test1": 11, "0a80fada098c": 11, "473d83400bc1bc9dc635e334faddd33c": 11, "343434344": 11, "test2": 11, "0a80fada097c": 11, "473d83400bc1bc9dc635e334fadd433c": 11, "543434443": 11, "phs0001": 11, "phs0002": 11, "test3": 11, "0a80fada096c": 11, "test4": 11, "0a80fada010c": 11, "473d83400bc1bc9dc635e334fadde33c": 11, "test5": 11, "index_manifest": 11, "prev_guid": 11, "usag": 11, "py": 11, "giangb": 11, "planx": 11, "pla": 11, "net": 11, "manifest_fil": [11, 12], "path_to_manifest": 11, "replace_url": 11, "thread_num": 11, "api_kei": 11, "threadcontrol": 11, "processed_fil": 11, "num_total_fil": 11, "synchron": 11, "delete_all_guid": 11, "warn": 11, "IF": 11, "know": 11, "THE": 11, "implic": 11, "index_object_manifest": 11, "manifest_file_delimit": [11, 12], "submit_additional_metadata_column": 11, "loop": 11, "ha": 11, "password": [11, 12], "flag": 11, "replac": 11, "delimit": 11, "guid_exampl": 11, "md5_hash": 11, "fieldnam": 11, "There": 11, "those": 11, "abov": 11, "overrid": [11, 12], "assum": 11, "altern": 11, "behavior": 11, "simpli": 11, "manifest_row_pars": [11, 12], "custom": 11, "import": 11, "verify_manifest": 11, "def": 11, "_get_authz_from_row": 11, "strip": 11, "parser": [11, 12], "verify_object_manifest": 11, "verif": 11, "error_nam": 11, "value_from_manifest": 11, "actual": 11, "value_from_indexd": 11, "93d9af72": 11, "b0f1": 11, "450c": 11, "a5c6": 11, "7d3d8d2083b4": 11, "dev": 11, "test": 11, "async_verify_object_manifest": 11, "_get_acl_from_row": 11, "_get_file_name_from_row": 11, "_get_file_size_from_row": 11, "_get_guid_from_row": 11, "_get_md5_from_row": 11, "_get_urls_from_row": 11, "1654627682": [], "4302042": [], "indexd_field": [11, 12], "func_to_parse_row": [11, 12], "delimet": [11, 12], "metdata": 12, "ingest_manifest": 12, "column_to_use_as_guid": 12, "guid_type_for_indexed_file_object": 12, "guid_type_for_non_indexed_file_object": 12, "NOT": [11, 12], "guid_from_fil": 12, "_get_guid_for_row": 12, "indexed_file_object_guid": 12, "_query_for_associated_indexd_record_guid": 12, "guid_for_row": 12, "elsewher": 12, "async_ingest_metadata_manifest": 12, "metadata_sourc": 12, "672043": [], "get_guid_from_fil": 12, "metadata_typ": 12, "namespac": 12, "dbgap": 12, "usual": 12, "fill": 12, "_guid_typ": 12, "is_indexed_file_object": 12, "async_query_urls_from_indexd": 12, "lock": 12, "semaphor": 12, "semaphon": 12, "ammount": 12, "connect": 12, "wss": 13, "gen3wsstorag": 13, "copi": 13, "src_urlstr": 13, "dest_urlstr": 13, "appropri": 13, "src_w": 13, "src_wskei": 13, "dest_path": 13, "disk": 13, "download_url": 13, "ws": 13, "wskei": 13, "ls": 13, "ls_path": 13, "ws_urlstr": 13, "form": 13, "rm": 13, "rm_path": 13, "src_path": 13, "dest_w": 13, "dest_wskei": 13, "upload_url": 13, "1654634067": [], "5923028": [], "8967967": [], "1654789636": [], "6798043": [], "9773014": [], "1654807944": [], "3028057": [], "560571": [], "1654874610": [], "345438": [], "6664228": [], "1654874771": [], "190345": [], "4957037": [], "1654887195": [], "1666398": [], "5790925": [], "get_guids_prefix": 3, "prefix": 3, "get_valid_guid": 3, "count": 3, "populate_object_manifest_with_valid_guid": 11, "minim": 11, "miss": 11, "anyth": 11, "side": 11, "No": 11, "part": 11, "1655136811": [11, 12], "5685084": 11, "982317": 12}, "objects": {"gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], "gen3.jobs": [[4, 0, 1, "", "Gen3Jobs"]], "gen3.jobs.Gen3Jobs": [[4, 1, 1, "", "async_run_job_and_wait"], [4, 1, 1, "", "create_job"], [4, 1, 1, "", "get_output"], [4, 1, 1, "", "get_status"], [4, 1, 1, "", "get_version"], [4, 1, 1, "", "is_healthy"], [4, 1, 1, "", "list_jobs"]], "gen3.metadata": [[5, 0, 1, "", "Gen3Metadata"]], "gen3.metadata.Gen3Metadata": [[5, 1, 1, "", "async_create"], [5, 1, 1, "", "async_get"], [5, 1, 1, "", "async_update"], [5, 2, 1, "", "auth_provider"], [5, 1, 1, "", "batch_create"], [5, 1, 1, "", "create"], [5, 1, 1, "", "create_index_key_path"], [5, 1, 1, "", "delete"], [5, 1, 1, "", "delete_index_key_path"], [5, 2, 1, "", "endpoint"], [5, 1, 1, "", "get"], [5, 1, 1, "", "get_index_key_paths"], [5, 1, 1, "", "get_version"], [5, 1, 1, "", "is_healthy"], [5, 1, 1, "", "query"], [5, 1, 1, "", "update"]], "gen3.object": [[6, 0, 1, "", "Gen3Object"]], "gen3.object.Gen3Object": [[6, 1, 1, "", "delete_object"]], "gen3.query": [[7, 0, 1, "", "Gen3Query"]], "gen3.query.Gen3Query": [[7, 1, 1, "", "graphql_query"], [7, 1, 1, "", "query"], [7, 1, 1, "", "raw_data_download"]], "gen3.submission": [[8, 0, 1, "", "Gen3Submission"]], "gen3.submission.Gen3Submission": [[8, 1, 1, "", "create_program"], [8, 1, 1, "", "create_project"], [8, 1, 1, "", "delete_node"], [8, 1, 1, "", "delete_nodes"], [8, 1, 1, "", "delete_program"], [8, 1, 1, "", "delete_project"], [8, 1, 1, "", "delete_record"], [8, 1, 1, "", "delete_records"], [8, 1, 1, "", "export_node"], [8, 1, 1, "", "export_record"], [8, 1, 1, "", "get_dictionary_all"], [8, 1, 1, "", "get_dictionary_node"], [8, 1, 1, "", "get_graphql_schema"], [8, 1, 1, "", "get_programs"], [8, 1, 1, "", "get_project_dictionary"], [8, 1, 1, "", "get_project_manifest"], [8, 1, 1, "", "get_projects"], [8, 1, 1, "", "open_project"], [8, 1, 1, "", "query"], [8, 1, 1, "", "submit_file"], [8, 1, 1, "", "submit_record"]], "gen3": [[9, 3, 0, "-", "tools"]], "gen3.tools.download": [[10, 3, 0, "-", "drs_download"]], "gen3.tools.download.drs_download": [[10, 0, 1, "", "DownloadManager"], [10, 0, 1, "", "DownloadStatus"], [10, 0, 1, "", "Downloadable"], [10, 0, 1, "", "Manifest"], [10, 4, 1, "", "download_drs_object"], [10, 4, 1, "", "download_files_in_drs_manifest"], [10, 4, 1, "", "list_access_in_drs_manifest"], [10, 4, 1, "", "list_drs_object"], [10, 4, 1, "", "list_files_in_drs_manifest"]], "gen3.tools.download.drs_download.DownloadManager": [[10, 1, 1, "", "cache_hosts_wts_tokens"], [10, 1, 1, "", "download"], [10, 1, 1, "", "get_fresh_token"], [10, 1, 1, "", "resolve_objects"], [10, 1, 1, "", "user_access"]], "gen3.tools.download.drs_download.DownloadStatus": [[10, 2, 1, "", "end_time"], [10, 2, 1, "", "start_time"], [10, 2, 1, "", "status"]], "gen3.tools.download.drs_download.Downloadable": [[10, 2, 1, "", "_manager"], [10, 2, 1, "", "access_methods"], [10, 2, 1, "", "children"], [10, 2, 1, "", "created_time"], [10, 1, 1, "", "download"], [10, 2, 1, "", "file_name"], [10, 2, 1, "", "file_size"], [10, 2, 1, "", "hostname"], [10, 2, 1, "", "object_id"], [10, 2, 1, "", "object_type"], [10, 1, 1, "", "pprint"], [10, 2, 1, "", "updated_time"]], "gen3.tools.download.drs_download.Manifest": [[10, 2, 1, "", "commons_url"], [10, 1, 1, "", "create_object_list"], [10, 2, 1, "", "file_name"], [10, 2, 1, "", "file_size"], [10, 1, 1, "", "load"], [10, 1, 1, "", "load_manifest"], [10, 2, 1, "", "md5sum"], [10, 2, 1, "", "object_id"]], "gen3.tools.indexing": [[11, 3, 0, "-", "download_manifest"], [11, 3, 0, "-", "index_manifest"], [11, 3, 0, "-", "verify_manifest"]], "gen3.tools.indexing.download_manifest": [[11, 2, 1, "", "CURRENT_DIR"], [11, 2, 1, "", "INDEXD_RECORD_PAGE_SIZE"], [11, 2, 1, "", "MAX_CONCURRENT_REQUESTS"], [11, 2, 1, "", "TMP_FOLDER"], [11, 4, 1, "", "async_download_object_manifest"]], "gen3.tools.indexing.index_manifest": [[11, 2, 1, "", "ACLS"], [11, 2, 1, "", "AUTHZ"], [11, 2, 1, "", "CURRENT_DIR"], [11, 2, 1, "", "GUID"], [11, 2, 1, "", "MD5"], [11, 2, 1, "", "PREV_GUID"], [11, 2, 1, "", "SIZE"], [11, 0, 1, "", "ThreadControl"], [11, 2, 1, "", "URLS"], [11, 4, 1, "", "delete_all_guids"], [11, 4, 1, "", "index_object_manifest"], [11, 4, 1, "", "populate_object_manifest_with_valid_guids"]], "gen3.tools.indexing.verify_manifest": [[11, 2, 1, "", "CURRENT_DIR"], [11, 2, 1, "", "MAX_CONCURRENT_REQUESTS"], [11, 4, 1, "", "async_verify_object_manifest"]], "gen3.tools.metadata": [[12, 3, 0, "-", "ingest_manifest"]], "gen3.tools.metadata.ingest_manifest": [[12, 2, 1, "", "COLUMN_TO_USE_AS_GUID"], [12, 2, 1, "", "GUID_TYPE_FOR_INDEXED_FILE_OBJECT"], [12, 2, 1, "", "GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT"], [12, 2, 1, "", "MAX_CONCURRENT_REQUESTS"], [12, 4, 1, "", "async_ingest_metadata_manifest"], [12, 4, 1, "", "async_query_urls_from_indexd"]], "gen3.wss": [[13, 0, 1, "", "Gen3WsStorage"]], "gen3.wss.Gen3WsStorage": [[13, 1, 1, "", "copy"], [13, 1, 1, "", "download"], [13, 1, 1, "", "download_url"], [13, 1, 1, "", "ls"], [13, 1, 1, "", "ls_path"], [13, 1, 1, "", "rm"], [13, 1, 1, "", "rm_path"], [13, 1, 1, "", "upload"], [13, 1, 1, "", "upload_url"]]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:attribute", "3": "py:module", "4": "py:function"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "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, "s": 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": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index d51943f09..287e1e359 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -285,6 +285,27 @@

      Indexing Tools +
      +gen3.tools.indexing.index_manifest.populate_object_manifest_with_valid_guids(commons_url, manifest_file, output_filename=None)[source]
      +

      Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs +for the given commons.

      +
      +
      NOTE: This DOES NOT index anything, it only works client side to populate the manifest

      with valid GUIDs (which are obtained from the server). No records are created +as part of this function call.

      +
      +
      +
      +
      Parameters:
      +
        +

      • commons_url (str) – root domain for commons where indexd lives

        • +

      • manifest_file (str) – file path for input manifest file to populate empty GUIDs

        • +

      • output_filename (str) – output file name for manifest

        • +
      +
      +
      +

      +

      Verify

      @@ -340,7 +361,7 @@

      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-1654887195.1666398.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-1655136811.5685084.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 ea9c87a51..7a2e696e3 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1654887195.5790925.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-1655136811.982317.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
      From dbcc944d13e7ff51cc002c84abca4321d6edb43e Mon Sep 17 00:00:00 2001 From: Avantol13 Date: Mon, 1 Aug 2022 17:45:12 +0000 Subject: [PATCH 06/11] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 311182 -> 319666 bytes docs/_build/doctrees/indexing.doctree | Bin 145291 -> 144585 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 94216 -> 103405 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 36340 -> 35851 bytes docs/_build/html/objects.inv | Bin 1859 -> 1866 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 45 ++++++++++++++++++-- docs/_build/html/tools/metadata.html | 4 +- 8 files changed, 45 insertions(+), 6 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index f71a741147f84d5f81d2c82379fa3348e33db4ab..7c88452f678ed740bdb41f29ebfec64330ad11af 100644 GIT binary patch delta 30830 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zA?&mr#m%uHW#LD0kNB$gzmTEe8p=Pqd_qZ%$Uv6dYNFL&B$TN9*T_h?mFSOjQz@Om z6-tDB`Bq`%HO|3aOq13mo_|mh;1qG^Rto0hKmPmYUpnNHMT#;e|1I*vpiJ9GEM+QJ zX!V~B)jxUPuqIwzH&mkXhNzM(L#i&_2s4GK?jvdx4qL{b@2<)Q1)ZpMLs>$fd24!V z_kffZeb-3osIi?<^SI*^pEb3qQfy7x{yL7*rEVE1RTM!IL`^N~on8XWRr@3Nxxv12 zT4z6~r|S9Kiz+>;xLSklYpV*e5Wfe_WBQSN^8h~_&*sDO3uuF&&2L&Z0?J@Qt`2VV ji - + Indexing Tools — Gen3 SDK documentation @@ -245,7 +245,7 @@

      Indexing Tools
      -gen3.tools.indexing.index_manifest.index_object_manifest(commons_url, manifest_file, thread_num, auth=None, replace_urls=True, manifest_file_delimiter=None, output_filename='indexing-output-manifest.csv', submit_additional_metadata_columns=False)[source]
      +gen3.tools.indexing.index_manifest.index_object_manifest(commons_url, manifest_file, thread_num, auth=None, replace_urls=True, manifest_file_delimiter=None, output_filename='indexing-output-manifest.csv', submit_additional_metadata_columns=False, force_metadata_columns_even_if_empty=True)[source]

      Loop through all the files in the manifest, update/create records in indexd update indexd if the url is not in the record url list or acl has changed

      @@ -259,6 +259,45 @@

      Indexing Tools +
      guid, …, columnA, columnB, ColumnC

      1, …, dataA, , +2, …, , dataB,

      +
      +

      +
      +
      Resulting metadata if force_metadata_columns_even_if_empty=True :
      +
      ”1”: {

      “columnA”: “dataA”, +“columnB”: “”, +“ColumnC”: “”,

      +
      +
      +

      }, +“2”: {

      +
      +

      ”columnA”: “”, +“columnB”: “dataB”, +“ColumnC”: “”,

      +
      +

      },

      +
      +
      Resulting metadata if force_metadata_columns_even_if_empty=False :
      +
      ”1”: {

      “columnA”: “dataA”,

      +
      +
      +

      }, +“2”: {

      +
      +

      ”columnB”: “dataB”,

      +
      +

      },

      +
      +

      +

      Returns:
      @@ -361,7 +400,7 @@

      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-1655136811.5685084.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-1659375909.1640186.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 7a2e696e3..0a9fddc65 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -4,7 +4,7 @@ - + Metadata Tools — Gen3 SDK documentation @@ -104,7 +104,7 @@

      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-1655136811.982317.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-1659375909.522224.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
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           def get_valid_guids(self, count=None):
         """
         Get a list of valid GUIDs without indexing
-
         Args:
             count (int): number of GUIDs to request
-
         Returns:
             List[str]: list of valid indexd GUIDs
         """
-        url = "/mint/guids"
+        url = "/guid/mint"
         if count:
             url += f"?count={count}"
 
         response = self.client._get(url)
-        raise_for_status(response)
+        response.raise_for_status()
         return response.json().get("guids", [])
      [docs] @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS) def get_guids_prefix(self): """ Get the prefix for GUIDs if there is one - Returns: str: prefix for this instance """ - response = self.client._get("/mint/prefix") - raise_for_status(response) + response = self.client._get("/guid/prefix") + response.raise_for_status() return response.json().get("prefix")
      diff --git a/docs/_build/html/indexing.html b/docs/_build/html/indexing.html index 31318be2e..dbe06dcd6 100644 --- a/docs/_build/html/indexing.html +++ b/docs/_build/html/indexing.html @@ -315,15 +315,9 @@

      Gen3 Index Class
      get_guids_prefix()[source]
      -

      Get the prefix for GUIDs if there is one

      -
      -
      Returns:
      -

      prefix for this instance

      -
      -
      Return type:
      -

      str

      -
      -
      +

      Get the prefix for GUIDs if there is one +:returns: prefix for this instance +:rtype: str

      @@ -406,16 +400,15 @@

      Gen3 Index Class
      get_valid_guids(count=None)[source]
      -

      Get a list of valid GUIDs without indexing

      +

      Get a list of valid GUIDs without indexing +:param count: number of GUIDs to request +:type count: int

      -
      Parameters:
      -

      count (int) – number of GUIDs to request

      -
      -
      Returns:
      -

      list of valid indexd GUIDs

      +
      Returns:
      +

      list of valid indexd GUIDs

      -
      Return type:
      -

      List[str]

      +
      Return type:
      +

      List[str]

      diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index a9d52e303..63ca6841c 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": {"class": [0, 2, 10, 11, 13], "gen3auth": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "endpoint": [0, 1, 3, 4, 5, 7, 8, 13], "none": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "refresh_fil": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "refresh_token": 0, "idp": 0, "sourc": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "base": [0, 1, 3, 4, 5, 6, 7, 8, 9, 11, 13], "authbas": 0, "us": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "request": [0, 1, 3, 8, 11, 12], "implement": 0, "order": [0, 8], "support": [0, 1, 5, 8, 11], "jwt": 0, "authent": 0, "gener": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13], "access": [0, 1, 3, 7, 10], "token": [0, 10], "from": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13], "provid": [0, 1, 3, 5, 7, 8, 12], "refresh": [0, 10], "file": [0, 2, 3, 4, 8, 9, 10, 11, 12, 13], "string": [0, 3, 5, 11, 13], "automat": 0, "when": [0, 3, 7, 10, 12], "thei": [0, 10], "expir": [0, 1], "paramet": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "str": [0, 1, 3, 4, 5, 7, 8, 10, 11, 12], "opt": 0, "The": [0, 1, 2, 3, 5, 8, 10, 11], 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"sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index 58232f5b0..49677aa35 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -400,7 +400,7 @@

      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-1659375909.1640186.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-1660165119.312618.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 0a9fddc65..ae77f0258 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1659375909.522224.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-1660165119.6884966.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
      From ec67e361ea41c3614176b8463e39a06a7e2a6b07 Mon Sep 17 00:00:00 2001 From: Avantol13 Date: Mon, 15 Aug 2022 15:12:42 +0000 Subject: [PATCH 08/11] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 320151 -> 320151 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 103400 -> 103400 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35856 -> 35856 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 020ac893952866c3579a6fa3f15f8139e3ec2ca7..2c57e3efc39fbefc597c6acf5e68b74ba48b9d9d 100644 GIT binary patch delta 5680 zcmbU_X;hR~mcFlwDnJ&IeJK#Cf+a`+1__EFC2%vkrst%4W^&Bj_g+z$oSZ&$=Ffe1 zfA`*Z-|~G@m$%gA-J*#|@~E$_HrB{}-_9ZY!1gAJvRFxTCv|8*=W|f_pprWcA{fX73=t*8;s^4R^ 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"GUID_TYPE_FOR_INDEXED_FILE_OBJECT"], [12, 2, 1, "", "GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT"], [12, 2, 1, "", "MAX_CONCURRENT_REQUESTS"], [12, 4, 1, "", "async_ingest_metadata_manifest"], [12, 4, 1, "", "async_query_urls_from_indexd"]], "gen3.wss": [[13, 0, 1, "", "Gen3WsStorage"]], "gen3.wss.Gen3WsStorage": [[13, 1, 1, "", "copy"], [13, 1, 1, "", "download"], [13, 1, 1, "", "download_url"], [13, 1, 1, "", "ls"], [13, 1, 1, "", "ls_path"], [13, 1, 1, "", "rm"], [13, 1, 1, "", "rm_path"], [13, 1, 1, "", "upload"], [13, 1, 1, "", "upload_url"]]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:attribute", "3": "py:module", "4": "py:function"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "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, "s": [], "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, "": 2}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index 49677aa35..de70a1f79 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -400,7 +400,7 @@

      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-1660165119.312618.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-1660576358.150224.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 ae77f0258..b03e8dd5b 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1660165119.6884966.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-1660576358.5508597.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
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z8yFgzZjbd~>}F=Y2vn#sdE#anh$0bGMS3~;>FS!(8~7OGwoCaj268jnPu~~Gs3VL; h+4M$#Mq#MD3>Nt*8SJrBGQ@fyCZM~?P_H}L=f delta 208 zcmaF6obAPOwuUK;wv3Cn+A*5CvAkhqV3=;_%_uW@#Rl2!8{8NdF!Gw3n;Dy0=oy+C z7#W#tkMm&cW@fzrRHrd{;$|6$8etSQdO7*&>YCFV_!#51%lI({ax>aZKN!iVqlT$! oN(OuEl&mSt3=Eo$Q);JZWU%%?)Jo$}n;`~OfaWacD8^Nm00(wEssI20 diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree index aedb10bf3aad9a822f682ff1a06225fe9e212eb1..24f8e699b13844ed4933ceef3aa92315cda32802 100644 GIT binary patch delta 164 zcmbO*gQrMc1Mxq3F6 z+cb|eGuCbP({)6X-8@&Xm4nfJ@&$8KArx(TIr-`8lOLK0LnNg!C8uPt$4j7&< LwR5wu#ou56K%*}+ delta 176 zcmeC4!8Bn86H5c@RMw3wH`E#DZoaD?&&X$LZf0z1p=WApU}0)$K6$pD&E{6kIndexing 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-1660576358.150224.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-1660677351.9370115.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 b03e8dd5b..28c8be9f8 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -104,7 +104,7 @@

      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-1660576358.5508597.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-1660677352.260972.log', get_guid_from_file=True, metadata_type=None)[source]

      Ingest all metadata records into a manifest csv

      Parameters:
      From d9c2b0c4a432e008075082103e0061d2e2d573b0 Mon Sep 17 00:00:00 2001 From: Avantol13 Date: Wed, 6 Dec 2023 20:48:33 +0000 Subject: [PATCH 10/11] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 1553136 -> 1564684 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 106609 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35914 -> 35919 bytes .../gen3/tools/indexing/index_manifest.html | 49 +++++++++++------- docs/_build/html/index.html | 1 + docs/_build/html/objects.inv | Bin 1894 -> 1912 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools.html | 1 + docs/_build/html/tools/indexing.html | 24 ++++++++- docs/_build/html/tools/metadata.html | 2 +- 10 files changed, 56 insertions(+), 23 deletions(-) diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index fd6a32ce442154ea34b40a4f524cd458549097fc..dfe83b371d7f7103701cc88192ce8a3f6a32ca4b 100644 GIT binary patch delta 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a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree index 3b74e55ada6a5d7b3b7301ff01b6fae18dac7ecd..129c8c02eac5d5678a3eab2df1b991926917c8f6 100644 GIT binary patch delta 169 zcmX>#gX#PXCYA=)sV*B?mT0idWn^HOJTY8u^C=BmMt(yJOH*@013eQXb29@YwdZuHVYR=rQ@Nxe10=eG3VQj4Ya=dO7*&>QgeN`0UQT|x`s9N-!Vp;*EV5HF*kh+;i1mQA MquIOpzC}SW0NSH3?f?J) diff --git a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html index 788fedb12..8b9050049 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html @@ -1,18 +1,15 @@ - - + gen3.tools.indexing.index_manifest — Gen3 SDK documentation - - - - - - - + + + + + @@ -102,8 +99,10 @@

      Source code for gen3.tools.indexing.index_manifest

      logging = get_logger("__name__") -
      [docs]class ThreadControl(object): - """ +
      +[docs] +class ThreadControl(object): + """ Class for thread synchronization """ @@ -113,8 +112,9 @@

      Source code for gen3.tools.indexing.index_manifest

      self.num_total_files = num_total_files
      + def _write_csv(filename, files, fieldnames=None): - """ + """ write to csv file Args: @@ -157,7 +157,7 @@

      Source code for gen3.tools.indexing.index_manifest

      force_metadata_columns_even_if_empty, fi, ): - """ + """ Index a single file, and submit additional metadata to the metadata service if provided Args: @@ -384,7 +384,9 @@

      Source code for gen3.tools.indexing.index_manifest

      thread_control.mutexLock.release() -
      [docs]def index_object_manifest( +
      +[docs] +def index_object_manifest( commons_url, manifest_file, thread_num, @@ -395,7 +397,7 @@

      Source code for gen3.tools.indexing.index_manifest

      submit_additional_metadata_columns=False, force_metadata_columns_even_if_empty=True, ): - """ + """ Loop through all the files in the manifest, update/create records in indexd update indexd if the url is not in the record url list or acl has changed @@ -529,10 +531,13 @@

      Source code for gen3.tools.indexing.index_manifest

      return files, headers
      -
      [docs]def populate_object_manifest_with_valid_guids( + +
      +[docs] +def populate_object_manifest_with_valid_guids( commons_url, manifest_file, output_filename=None ): - """ + """ Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs for the given commons. @@ -592,6 +597,7 @@

      Source code for gen3.tools.indexing.index_manifest

      _write_csv(os.path.join(CURRENT_DIR, output_filename), new_records, headers)
      + @click.command() @click.option( "--commons-url", @@ -642,7 +648,7 @@

      Source code for gen3.tools.indexing.index_manifest

      manifest_file_delimiter, out_manifest_file, ): - """ + """ Commandline interface for indexing a given manifest to indexd Args: @@ -681,8 +687,10 @@

      Source code for gen3.tools.indexing.index_manifest

      index_object_manifest_cli() -
      [docs]def delete_all_guids(auth, file): - """ +
      +[docs] +def delete_all_guids(auth, file): + """ Delete all GUIDs specified in the object manifest. WARNING: THIS COMPLETELY REMOVES INDEX RECORDS. USE THIS ONLY IF YOU KNOW @@ -724,6 +732,7 @@

      Source code for gen3.tools.indexing.index_manifest

      if guid: logging.debug(f"deleting GUID record:{guid}") logging.debug(index.delete_record(guid=guid))
      +
      diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index bf4d4bba6..d5fedd197 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -250,6 +250,7 @@

      Welcome to Gen3 SDK’s documentation!ThreadControl
    • delete_all_guids()
    • index_object_manifest()
      • +
    • populate_object_manifest_with_valid_guids()
    • Verify
        diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv index 8f2fb369e10a277a49c29de1f9aeb6fd64436a33..194f72c5f2b14896686623a8103d7c6e29fd0523 100644 GIT binary patch delta 498 zcmVQEA6owP zIFTFY9O*}a$r!!6yPu%h?;j_lWq-;ZW)FQUY~@$oR2aW1u3CSo^Pc6R=+N(JJ{8bj z8njWfa~??K#gyw+5k_!O1TDn)D?Rjk`}f409V1`Kp+_6=hR zd*-d^sWj^tEw&-Z=%}z=Q1iH#3!m1tnR;nO*`a5~=rU@pKt>fOnE7E{i@9b13p4&G zeQt0lZ&ullik@~o528koseo2shXSZUEY<%({g{3tUq8SP$MeOocuiR&X!4te2LWR+ oC07ME`9(t#J~)N}%h0PLibynf_nERMo?)L1Z2%Ac2Z7wMZfn%^r~m)} delta 480 zcmV<60U!SO4(1N9kp+L@!uy%9XtM{4?;|>>2s)eA@q#B z>t)tvd%s5Kjb`_&=>uBM&}uP3w~I5O{7O0Zf&#^dmVZ4? zaWY!=r|e<&(6_=?e$`Ed@vGvhl{)WPE{YD#m!@xDduh-{&5nPYF1*itAtUEIQZk%gyEa?F0rpkQ6(h+vvj;ft)$VKp0 zb(h~%zEv73uA%;h>jQ~1!UnoXRS_*eoH3&MOQw->D>WbOrdm42YZ5E@;;O;u=H9_U z%#v0lK9ks|36X!!Z4@lVfBg5)zkDbq^Ms^Af5G&_ph(*%EJZ3eX!9kHnV;@Lt%#RR zs76%x4I9ZKq^i=jFf)jGen3 ToolsThreadControl
      • delete_all_guids()
      • index_object_manifest()
        • +
      • populate_object_manifest_with_valid_guids()
    • Verify
        diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index e93f4ffa9..3b49c9208 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -325,6 +325,27 @@

        Indexing Tools +
        +gen3.tools.indexing.index_manifest.populate_object_manifest_with_valid_guids(commons_url, manifest_file, output_filename=None)[source]
        +

        Given a minimal file object manifest, populate any missing GUIDs with valid GUIDs +for the given commons.

        +
        +
        NOTE: This DOES NOT index anything, it only works client side to populate the manifest

        with valid GUIDs (which are obtained from the server). No records are created +as part of this function call.

        +
        +
        +
        +
        Parameters:
        +
          +

        • commons_url (str) – root domain for commons where indexd lives

          • +

        • manifest_file (str) – file path for input manifest file to populate empty GUIDs

          • +

        • output_filename (str) – output file name for manifest

          • +
        +
        +
        +

      • +

      Verify

      @@ -380,7 +401,7 @@

      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-1701895710.1259124.log')[source]

      Verify all file object records into a manifest csv

      Parameters:
      @@ -455,6 +476,7 @@

      Navigation

    • ThreadControl
    • delete_all_guids()
    • index_object_manifest()
      • +
    • populate_object_manifest_with_valid_guids()
    • Verify

      • Verify

      @@ -380,7 +401,7 @@

      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-1701900364.6706986.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-1701965244.9268556.log')[source]

      Verify all file object records into a manifest csv

      Parameters:
      @@ -455,6 +476,7 @@

      Navigation

    • ThreadControl
    • delete_all_guids()
    • index_object_manifest()
      • +
    • populate_object_manifest_with_valid_guids()
    • Verify