From 025eff80d875e3f74007c3919dd6abdbd1692160 Mon Sep 17 00:00:00 2001
From: Alex VanTol <avantol@uchicago.edu>
Date: Wed, 19 Apr 2023 11:00:05 -0500
Subject: [PATCH 1/4] feat(input-manifest): allow an input manifest of only
 guids and populate other columns (prev only md5 supported)

---
 .secrets.baseline                        | 128 ++++++++++++-----------
 gen3/cli/objects.py                      |   2 +-
 gen3/tools/indexing/download_manifest.py |  36 +++++--
 gen3/tools/utils.py                      |  58 +++++++---
 tests/test_manifests.py                  | 114 ++++++++++++++++----
 5 files changed, 232 insertions(+), 106 deletions(-)

diff --git a/.secrets.baseline b/.secrets.baseline
index ac3a65f42..298a9784b 100644
--- a/.secrets.baseline
+++ b/.secrets.baseline
@@ -1,11 +1,11 @@
 {
-  "generated_at": "2022-12-02T22:01:31Z",
+  "version": "1.4.0",
   "plugins_used": [
     {
-      "name": "AWSKeyDetector"
+      "name": "ArtifactoryDetector"
     },
     {
-      "name": "ArtifactoryDetector"
+      "name": "AWSKeyDetector"
     },
     {
       "name": "Base64HighEntropyString",
@@ -31,8 +31,8 @@
       "name": "JwtTokenDetector"
     },
     {
-      "keyword_exclude": null,
-      "name": "KeywordDetector"
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
     },
     {
       "name": "MailchimpDetector"
@@ -53,6 +53,52 @@
       "name": "TwilioKeyDetector"
     }
   ],
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    },
+    {
+      "path": "detect_secrets.filters.regex.should_exclude_file",
+      "pattern": [
+        "(docs\\/_build|poetry.lock)|^.secrets.baseline$"
+      ]
+    }
+  ],
   "results": {
     "docs/howto/metadataTools.md": [
       {
@@ -405,58 +451,58 @@
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
-        "hashed_secret": "96c9184fb19c9c1618ccf44d141f8029a739891c",
+        "hashed_secret": "e1da93616713812cb50e0ac845b1e9e305d949f1",
         "is_verified": false,
-        "line_number": 424
+        "line_number": 133
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
-        "hashed_secret": "e1da93616713812cb50e0ac845b1e9e305d949f1",
+        "hashed_secret": "47f42f4c34fddab383b817e689dc0fb75af81266",
         "is_verified": false,
-        "line_number": 559
+        "line_number": 141
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
-        "hashed_secret": "47f42f4c34fddab383b817e689dc0fb75af81266",
+        "hashed_secret": "300d95dd5d30ab6928ffda6c08c6a129a23e5b39",
         "is_verified": false,
-        "line_number": 583
+        "line_number": 150
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
-        "hashed_secret": "300d95dd5d30ab6928ffda6c08c6a129a23e5b39",
+        "hashed_secret": "96c9184fb19c9c1618ccf44d141f8029a739891c",
         "is_verified": false,
-        "line_number": 607
+        "line_number": 159
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
-        "hashed_secret": "f9e664db75c7f23a299b0b055c10e08d47073e93",
+        "hashed_secret": "7c35c215b326b9463b669b657c1ff9873ff53d9a",
         "is_verified": false,
-        "line_number": 675
+        "line_number": 709
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
-        "hashed_secret": "7c35c215b326b9463b669b657c1ff9873ff53d9a",
+        "hashed_secret": "f9e664db75c7f23a299b0b055c10e08d47073e93",
         "is_verified": false,
-        "line_number": 889
+        "line_number": 743
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "0d515eaf06062d52e8c80abb4d3b713a65396d30",
         "is_verified": false,
-        "line_number": 893
+        "line_number": 965
       },
       {
         "type": "Hex High Entropy String",
         "filename": "tests/test_manifests.py",
         "hashed_secret": "b4cff7c2af45cdfe66195ec574a7b8832f8621ea",
         "is_verified": false,
-        "line_number": 898
+        "line_number": 970
       }
     ],
     "tests/test_submission.py": [
@@ -469,47 +515,5 @@
       }
     ]
   },
-  "version": "1.4.0",
-  "filters_used": [
-    {
-      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_sequential_string"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_templated_secret"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
-    },
-    {
-      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
-      "min_level": 2
-    },
-    {
-      "path": "detect_secrets.filters.regex.should_exclude_file",
-      "pattern": [
-        "(docs\\/_build|poetry.lock)|^.secrets.baseline$"
-      ]
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_lock_file"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
-    },
-    {
-      "path": "detect_secrets.filters.heuristic.is_swagger_file"
-    }
-  ]
+  "generated_at": "2023-04-19T15:59:59Z"
 }
diff --git a/gen3/cli/objects.py b/gen3/cli/objects.py
index 80ca40d95..f429c84a9 100644
--- a/gen3/cli/objects.py
+++ b/gen3/cli/objects.py
@@ -69,7 +69,7 @@ def crosswalk():
     "--input-manifest",
     "input_manifest",
     help="Input file. Read available object data only for records referenced in this file. "
-    "Currently requires at a minimum an `m5d` column with checksum.",
+    "Currently requires at a minimum an `m5d` OR `guid` column to be populated.",
     default=None,
     type=click.Path(writable=True),
     show_default=True,
diff --git a/gen3/tools/indexing/download_manifest.py b/gen3/tools/indexing/download_manifest.py
index 98a84e348..83f5008e1 100644
--- a/gen3/tools/indexing/download_manifest.py
+++ b/gen3/tools/indexing/download_manifest.py
@@ -22,6 +22,7 @@
 """
 import asyncio
 import aiofiles
+import aiohttp
 import click
 import json
 import time
@@ -149,18 +150,23 @@ async def _write_all_index_records_to_file(
     page_chunks = []
 
     # used when an input manifest is provided, this will only read record info for
-    # the records referenced in the manifest based on their checksums
+    # the records referenced in the manifest based on their checksums or guids
     record_chunks = []
 
     if input_manifest:
-        # create chunks of checksums
+        # create chunks of requested records
         logging.debug(f"parsing input file {input_manifest}")
-        input_records, headers = get_and_verify_fileinfos_from_manifest(input_manifest)
+
+        # allow returning invalid b/c the input manifest won't always have complete
+        # information. e.g. it may not have a checksum b/c only a GUID column is provided
+        input_records, headers = get_and_verify_fileinfos_from_manifest(
+            input_manifest, return_invalid_records=True
+        )
         num_input_records = len(input_records)
 
         if not num_input_records:
             raise AttributeError(
-                f"No valid records found in provided input file: {input_manifest}. "
+                f"No records found in provided input file: {input_manifest}. "
                 "Please check previous logs."
             )
 
@@ -201,7 +207,7 @@ async def _write_all_index_records_to_file(
             "|||".join(map(json.dumps, record_chunks[x])) if record_chunks else "|||"
         )
 
-        # write record_checksum chunks to temporary files since the size can overload
+        # write requested records chunks to temporary files since the size can overload
         # command line arguments
         input_records_chunk_filename = TMP_FOLDER + f"input/input_records_chunk_{x}.txt"
         logging.info(
@@ -401,11 +407,12 @@ async def _put_records_from_input_manifest_in_queue(
 
     Args:
         commons_url (str): root domain for commons where indexd lives
-        input_record (int/str): indexd record to request (must contain checksum)
+        input_record (int/str): indexd record to request (must contain checksum OR guid)
         lock (asyncio.Semaphore): semaphones used to limit ammount of concurrent http
             connections
         queue (asyncio.Queue): queue to put indexd records in
     """
+    guid = input_record.get(GUID_STANDARD_KEY)
     checksum = input_record.get(MD5_STANDARD_KEY)
 
     index = Gen3Index(commons_url)
@@ -415,9 +422,20 @@ async def _put_records_from_input_manifest_in_queue(
         if "https" not in commons_url:
             ssl = False
 
-        records = await index.async_get_records_from_checksum(
-            checksum=checksum, _ssl=ssl
-        )
+        records = []
+        if guid:
+            try:
+                matched_record = await index.async_get_record(guid=guid, _ssl=ssl)
+                records.append(matched_record)
+            except aiohttp.client_exceptions.ClientResponseError as exc:
+                # this means the GUID likely doesn't exist or there was an error
+                # receiving it. In this case, log and ignore
+                logging.debug(f"guid: {guid} not found. Error: {exc}")
+        else:
+            matched_records = await index.async_get_records_from_checksum(
+                checksum=checksum, _ssl=ssl
+            )
+            records += matched_records
 
         # if nothing was found, we still want to output the input record
         if not records:
diff --git a/gen3/tools/utils.py b/gen3/tools/utils.py
index 578097789..3e4b19fcb 100644
--- a/gen3/tools/utils.py
+++ b/gen3/tools/utils.py
@@ -64,7 +64,10 @@
 
 
 def get_and_verify_fileinfos_from_manifest(
-    manifest_file, manifest_file_delimiter=None, include_additional_columns=False
+    manifest_file,
+    manifest_file_delimiter=None,
+    include_additional_columns=False,
+    return_invalid_records=False,
 ):
     """
     Wrapper for above function to determine the delimiter based on file extention
@@ -82,11 +85,15 @@ def get_and_verify_fileinfos_from_manifest(
         manifest_file=manifest_file,
         manifest_file_delimiter=manifest_file_delimiter,
         include_additional_columns=include_additional_columns,
+        return_invalid_records=return_invalid_records,
     )
 
 
 def get_and_verify_fileinfos_from_tsv_manifest(
-    manifest_file, manifest_file_delimiter="\t", include_additional_columns=False
+    manifest_file,
+    manifest_file_delimiter="\t",
+    include_additional_columns=False,
+    return_invalid_records=False,
 ):
     """
     get and verify file infos from tsv manifest
@@ -150,7 +157,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                 ):
                     fieldnames[fieldnames.index(current_column_name)] = MD5_STANDARD_KEY
                     output_column_name = MD5_STANDARD_KEY
-                    if not _verify_format(row[current_column_name], MD5_FORMAT):
+                    if (
+                        not _verify_format(row[current_column_name], MD5_FORMAT)
+                        and not return_invalid_records
+                    ):
                         logging.error(
                             f"ERROR: {row[current_column_name]} is not in md5 format"
                         )
@@ -161,7 +171,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                 ):
                     fieldnames[fieldnames.index(current_column_name)] = ACL_STANDARD_KEY
                     output_column_name = ACL_STANDARD_KEY
-                    if not _verify_format(row[current_column_name], ACL_FORMAT):
+                    if (
+                        not _verify_format(row[current_column_name], ACL_FORMAT)
+                        and not return_invalid_records
+                    ):
                         logging.error(
                             f"ERROR: {row[current_column_name]} is not in acl format"
                         )
@@ -174,7 +187,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                         fieldnames.index(current_column_name)
                     ] = URLS_STANDARD_KEY
                     output_column_name = URLS_STANDARD_KEY
-                    if not _verify_format(row[current_column_name], URL_FORMAT):
+                    if (
+                        not _verify_format(row[current_column_name], URL_FORMAT)
+                        and not return_invalid_records
+                    ):
                         logging.error(
                             f"ERROR: {row[current_column_name]} is not in urls format"
                         )
@@ -187,7 +203,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                         fieldnames.index(current_column_name)
                     ] = AUTHZ_STANDARD_KEY
                     output_column_name = AUTHZ_STANDARD_KEY
-                    if not _verify_format(row[current_column_name], AUTHZ_FORMAT):
+                    if (
+                        not _verify_format(row[current_column_name], AUTHZ_FORMAT)
+                        and not return_invalid_records
+                    ):
                         logging.error(
                             f"ERROR: {row[current_column_name]} is not in authz format"
                         )
@@ -200,7 +219,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                         fieldnames.index(current_column_name)
                     ] = SIZE_STANDARD_KEY
                     output_column_name = SIZE_STANDARD_KEY
-                    if not _verify_format(row[current_column_name], SIZE_FORMAT):
+                    if (
+                        not _verify_format(row[current_column_name], SIZE_FORMAT)
+                        and not return_invalid_records
+                    ):
                         logging.error(
                             f"ERROR: {row[current_column_name]} is not in int format"
                         )
@@ -214,8 +236,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     ] = PREV_GUID_STANDARD_KEY
                     output_column_name = PREV_GUID_STANDARD_KEY
                     # only validate format if value is provided (since this is optional)
-                    if row[current_column_name] and not _verify_format(
-                        row[current_column_name], UUID_FORMAT
+                    if (
+                        row[current_column_name]
+                        and not _verify_format(row[current_column_name], UUID_FORMAT)
+                        and not return_invalid_records
                     ):
                         logging.error(
                             f"ERROR: {row[current_column_name]} is not in UUID_FORMAT format"
@@ -226,7 +250,10 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     and current_column_name.lower() == RECORD_TYPE_STANDARD_KEY
                 ):
                     output_column_name = RECORD_TYPE_STANDARD_KEY
-                    if row[current_column_name] not in RECORD_TYPE_ALLOWED_VALUES:
+                    if (
+                        row[current_column_name] not in RECORD_TYPE_ALLOWED_VALUES
+                        and not return_invalid_records
+                    ):
                         logging.error(
                             f"ERROR: '{row[current_column_name]}' is not one of the valid record types: {RECORD_TYPE_ALLOWED_VALUES}"
                         )
@@ -247,8 +274,11 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                         # don't break
                         pass
 
-            if not {URLS_STANDARD_KEY, MD5_STANDARD_KEY, SIZE_STANDARD_KEY}.issubset(
-                set(output_row.keys())
+            if (
+                not {URLS_STANDARD_KEY, MD5_STANDARD_KEY, SIZE_STANDARD_KEY}.issubset(
+                    set(output_row.keys())
+                )
+                and not return_invalid_records
             ):
                 logging.error(
                     f"ERROR: '{row[current_column_name]}' (columns names: "
@@ -270,7 +300,9 @@ def get_and_verify_fileinfos_from_tsv_manifest(
 
     if not pass_verification:
         logging.error("The manifest is not in the correct format!!!")
-        return [], []
+
+        if not return_invalid_records:
+            return [], []
 
     return files, fieldnames
 
diff --git a/tests/test_manifests.py b/tests/test_manifests.py
index 07069efa2..1e5a20af5 100644
--- a/tests/test_manifests.py
+++ b/tests/test_manifests.py
@@ -378,18 +378,18 @@ def test_download_manifest_with_input_manifest(monkeypatch, gen3_index):
             assert "42" == record.get("file_size")
 
 
-def test_download_manifest_with_invalid_input_manifest(monkeypatch, gen3_index):
+def test_download_manifest_with_incomplete_input_manifest(monkeypatch, gen3_index):
     """
-    Test that dowload manifest errors when
-    provided an initial input manifest with an invalid format
+    Test that dowload manifest still works even when
+    provided an initial input manifest that's incomplete
     """
     with open("input.csv", "w+") as file:
         file.writelines(
             [
-                "guid,urls,authz,acl,md5,file_size,file_name\n",
-                ",gs://foo/bar,programs/foo/projects/bar,,a1234567891234567890123456789012,42,\n",
-                ",gs://foo/bar,programs/foo/projects/bar,,x1234567891234567890123456789012,42,\n",
-                ",gs://foo/bar,programs/foo/projects/bar,,f1234567891234567890123456789012,234,\n",
+                "guid\n",
+                "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b\n",
+                "dg.TEST/does_not_exist\n",
+                "dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce\n",
             ]
         )
 
@@ -431,19 +431,88 @@ def test_download_manifest_with_invalid_input_manifest(monkeypatch, gen3_index):
     monkeypatch.setattr(download_manifest, "INDEXD_RECORD_PAGE_SIZE", 2)
 
     loop = get_or_create_event_loop_for_thread()
-    # ensure error is raised
-    try:
-        loop.run_until_complete(
-            async_download_object_manifest(
-                "http://localhost:8001",
-                output_filename="object-manifest.csv",
-                num_processes=1,
-                input_manifest="input.csv",
-            )
+    loop.run_until_complete(
+        async_download_object_manifest(
+            "http://localhost:8001",
+            output_filename="object-manifest.csv",
+            num_processes=1,
+            input_manifest="input.csv",
         )
+    )
+
+    records = {}
+    try:
+        with open("object-manifest.csv") as file:
+            # skip header
+            next(file)
+            for line in file:
+                guid, urls, authz, acl, md5, file_size, file_name = line.split(",")
+                guid = guid.strip("\n")
+                urls = urls.split(" ")
+                authz = authz.split(" ")
+                acl = acl.split(" ")
+                file_size = file_size.strip("\n")
+                file_name = file_name.strip("\n")
+
+                records[guid] = {
+                    "urls": urls,
+                    "authz": authz,
+                    "acl": acl,
+                    "md5": md5,
+                    "file_size": file_size,
+                    "file_name": file_name,
+                }
+    except Exception:
+        # unexpected file format, fail test
         assert False
-    except AttributeError:
-        assert True
+
+    # should have 3 records in the output manifest but only 2 have checksums (b/c they
+    # were the only ones with matches in indexd)
+    assert len(records) == 3
+
+    # ensure downloaded manifest populates expected info for a record
+    assert "gs://test/test.txt" in records.get(
+        "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}
+    ).get("urls", [])
+    assert "s3://testaws/aws/test.txt" in records.get(
+        "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}
+    ).get("urls", [])
+    assert "/programs/DEV/projects/test" in records.get(
+        "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}
+    ).get("authz", [])
+    assert "DEV" in records.get("dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}).get(
+        "acl", []
+    )
+    assert "test" in records.get(
+        "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}
+    ).get("acl", [])
+    assert "123" in records.get("dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}).get(
+        "file_size"
+    )
+    assert "a1234567891234567890123456789012" in records.get(
+        "dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}
+    ).get("md5")
+    assert not records.get("dg.TEST/f2a39f98-6ae1-48a5-8d48-825a0c52a22b", {}).get(
+        "file_name"
+    )
+
+    assert "gs://test/test4%20space.txt" in records.get(
+        "dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce", {}
+    ).get("urls", [])
+    assert "s3://test/test4%20space.txt" in records.get(
+        "dg.TEST/a802e27d-4a5b-42e3-92b0-ba19e81b9dce", {}
+    ).get("urls", [])
+
+    # ensure downloaded manifest populates expected info for input with a missing record
+    for key, record in records.items():
+        if not key:
+            assert "gs://foo/bar" in record.get("urls", [])
+            assert "programs/foo/projects/bar" in record.get("authz", [])
+            assert (
+                record["md5"]
+                == "51234567891234567890123456789012"  # pragma: allowlist secret
+            )
+            assert "42" == record.get("file_size")
 
 
 def _mock_get_guid(guid, **kwargs):
@@ -635,7 +704,6 @@ def test_read_manifest():
 
 
 def test_index_manifest(gen3_index, indexd_server):
-
     rec1 = gen3_index.create_record(
         did="255e396f-f1f8-11e9-9a07-0a80fada099c",
         hashes={"md5": "473d83400bc1bc9dc635e334faddf33c"},
@@ -800,7 +868,9 @@ def test_index_manifest_additional_metadata_force(
     guid = "111e396f-f1f8-11e9-9a07-0a80fada0900"
     assert indexd_records[guid]["file_name"] == "file.txt"
     assert indexd_records[guid]["size"] == 111
-    assert indexd_records[guid]["hashes"] == {"md5": "111d83400bc1bc9dc635e334faddf33c"}
+    assert indexd_records[guid]["hashes"] == {
+        "md5": "111d83400bc1bc9dc635e334faddf33c"  # pragma: allowlist secret
+    }
     assert indexd_records[guid]["authz"] == ["/open"]
     assert indexd_records[guid]["urls"] == ["s3://my-data-bucket/dg.111/path/file.txt"]
     assert guid in mds_records
@@ -808,7 +878,9 @@ def test_index_manifest_additional_metadata_force(
     guid = "222e396f-f1f8-11e9-9a07-0a80fada0900"
     assert indexd_records[guid]["file_name"] == "file.txt"
     assert indexd_records[guid]["size"] == 222
-    assert indexd_records[guid]["hashes"] == {"md5": "222d83400bc1bc9dc635e334faddf33c"}
+    assert indexd_records[guid]["hashes"] == {
+        "md5": "222d83400bc1bc9dc635e334faddf33c"  # pragma: allowlist secret
+    }
     assert indexd_records[guid]["authz"] == ["/open"]
     assert indexd_records[guid]["urls"] == ["s3://my-data-bucket/dg.222/path/file.txt"]
     assert guid in mds_records

From c413fffb9b55008f574cee281963781f26683bab Mon Sep 17 00:00:00 2001
From: Avantol13 <Avantol13@users.noreply.github.com>
Date: Wed, 19 Apr 2023 16:02:04 +0000
Subject: [PATCH 2/4] Apply automatic documentation changes

---
 docs/_build/doctrees/environment.pickle       | Bin 1553139 -> 1553989 bytes
 docs/_build/doctrees/tools/indexing.doctree   | Bin 99440 -> 99435 bytes
 docs/_build/doctrees/tools/metadata.doctree   | Bin 35609 -> 35609 bytes
 .../tools/indexing/download_manifest.html     |  36 +++++++++++++-----
 docs/_build/html/searchindex.js               |   2 +-
 docs/_build/html/tools/indexing.html          |   2 +-
 docs/_build/html/tools/metadata.html          |   2 +-
 7 files changed, 30 insertions(+), 12 deletions(-)

diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
index 1b3685cad747f19b693b394133a15e3ba3651e4c..b9cc97029a732776a937f85e4b6ddaace7c1f2d6 100644
GIT binary patch
delta 11240
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diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree
index 9945e68698b71364dad26de2ece429e65e4a35c0..44ceb08e6dbcab490c95ebc157f9bf34c5360bd4 100644
GIT binary patch
delta 185
zcmey+!S=d?tzily4`cXNUdBmgjBmCtFk`&U$Y*G2WMF7$p=V)iW@%x$y~~2Jo0;VT
zBLl<s{br1NFyx=uGH&H&w3{Aa!Kkf{s#h;3KV5xF27Bz3tl7*A44REoYNu#qu=YR{
T%ivO+AqG`}?v#8lMn)?DNwqTD

delta 182
zcmaFe!S<nptzily4`a+$UdBmgjBmFuFk`&U$Zue3Y+-0&q-S7YXlQ9_zP;0ev74FY
zA|nIC_Wfpzdl*I06zJvTr>kpD{<Sx5yPF+jAUC7^bVDyjZFF;{U-V>@fXc~YGh#{x
Td+d}9u^#N&w`X}VGFkxuVwNy|

diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree
index 9be9131a5219fb3978fb08a4bb6297b4e0d4fc58..5d296cc899d798c81232c840239c905d509f127b 100644
GIT binary patch
delta 115
zcmbO^jcMjIrVUA&{DziB28M=~dPW9jhQ{Vbn+r8vSkVP17i!vU(y!yd5brhj#SnXG
N?u0J3*~;R65CEC;9UuSz

delta 115
zcmbO^jcMjIrVUA&{064R7KRo^dPWw;CT0dEn+r8vSkVP17i!vU(y!yd5brhj#SnXG
N?u0J3*~;R65CEjg9Z~=Q

diff --git a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
index 992f4c86e..bf1aab73a 100644
--- a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
+++ b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
@@ -54,6 +54,7 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">import</span> <span class="nn">asyncio</span>
 <span class="kn">import</span> <span class="nn">aiofiles</span>
+<span class="kn">import</span> <span class="nn">aiohttp</span>
 <span class="kn">import</span> <span class="nn">click</span>
 <span class="kn">import</span> <span class="nn">json</span>
 <span class="kn">import</span> <span class="nn">time</span>
@@ -181,18 +182,23 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
     <span class="n">page_chunks</span> <span class="o">=</span> <span class="p">[]</span>
 
     <span class="c1"># used when an input manifest is provided, this will only read record info for</span>
-    <span class="c1"># the records referenced in the manifest based on their checksums</span>
+    <span class="c1"># the records referenced in the manifest based on their checksums or guids</span>
     <span class="n">record_chunks</span> <span class="o">=</span> <span class="p">[]</span>
 
     <span class="k">if</span> <span class="n">input_manifest</span><span class="p">:</span>
-        <span class="c1"># create chunks of checksums</span>
+        <span class="c1"># create chunks of requested records</span>
         <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;parsing input file </span><span class="si">{</span><span class="n">input_manifest</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">input_records</span><span class="p">,</span> <span class="n">headers</span> <span class="o">=</span> <span class="n">get_and_verify_fileinfos_from_manifest</span><span class="p">(</span><span class="n">input_manifest</span><span class="p">)</span>
+
+        <span class="c1"># allow returning invalid b/c the input manifest won&#39;t always have complete</span>
+        <span class="c1"># information. e.g. it may not have a checksum b/c only a GUID column is provided</span>
+        <span class="n">input_records</span><span class="p">,</span> <span class="n">headers</span> <span class="o">=</span> <span class="n">get_and_verify_fileinfos_from_manifest</span><span class="p">(</span>
+            <span class="n">input_manifest</span><span class="p">,</span> <span class="n">return_invalid_records</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
         <span class="n">num_input_records</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">input_records</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="ow">not</span> <span class="n">num_input_records</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;No valid records found in provided input file: </span><span class="si">{</span><span class="n">input_manifest</span><span class="si">}</span><span class="s2">. &quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;No records found in provided input file: </span><span class="si">{</span><span class="n">input_manifest</span><span class="si">}</span><span class="s2">. &quot;</span>
                 <span class="s2">&quot;Please check previous logs.&quot;</span>
             <span class="p">)</span>
 
@@ -233,7 +239,7 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
             <span class="s2">&quot;|||&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">,</span> <span class="n">record_chunks</span><span class="p">[</span><span class="n">x</span><span class="p">]))</span> <span class="k">if</span> <span class="n">record_chunks</span> <span class="k">else</span> <span class="s2">&quot;|||&quot;</span>
         <span class="p">)</span>
 
-        <span class="c1"># write record_checksum chunks to temporary files since the size can overload</span>
+        <span class="c1"># write requested records chunks to temporary files since the size can overload</span>
         <span class="c1"># command line arguments</span>
         <span class="n">input_records_chunk_filename</span> <span class="o">=</span> <span class="n">TMP_FOLDER</span> <span class="o">+</span> <span class="sa">f</span><span class="s2">&quot;input/input_records_chunk_</span><span class="si">{</span><span class="n">x</span><span class="si">}</span><span class="s2">.txt&quot;</span>
         <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
@@ -433,11 +439,12 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
 
 <span class="sd">    Args:</span>
 <span class="sd">        commons_url (str): root domain for commons where indexd lives</span>
-<span class="sd">        input_record (int/str): indexd record to request (must contain checksum)</span>
+<span class="sd">        input_record (int/str): indexd record to request (must contain checksum OR guid)</span>
 <span class="sd">        lock (asyncio.Semaphore): semaphones used to limit ammount of concurrent http</span>
 <span class="sd">            connections</span>
 <span class="sd">        queue (asyncio.Queue): queue to put indexd records in</span>
 <span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">guid</span> <span class="o">=</span> <span class="n">input_record</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">GUID_STANDARD_KEY</span><span class="p">)</span>
     <span class="n">checksum</span> <span class="o">=</span> <span class="n">input_record</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">MD5_STANDARD_KEY</span><span class="p">)</span>
 
     <span class="n">index</span> <span class="o">=</span> <span class="n">Gen3Index</span><span class="p">(</span><span class="n">commons_url</span><span class="p">)</span>
@@ -447,9 +454,20 @@ <h1>Source code for gen3.tools.indexing.download_manifest</h1><div class="highli
         <span class="k">if</span> <span class="s2">&quot;https&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">commons_url</span><span class="p">:</span>
             <span class="n">ssl</span> <span class="o">=</span> <span class="kc">False</span>
 
-        <span class="n">records</span> <span class="o">=</span> <span class="k">await</span> <span class="n">index</span><span class="o">.</span><span class="n">async_get_records_from_checksum</span><span class="p">(</span>
-            <span class="n">checksum</span><span class="o">=</span><span class="n">checksum</span><span class="p">,</span> <span class="n">_ssl</span><span class="o">=</span><span class="n">ssl</span>
-        <span class="p">)</span>
+        <span class="n">records</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">if</span> <span class="n">guid</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">matched_record</span> <span class="o">=</span> <span class="k">await</span> <span class="n">index</span><span class="o">.</span><span class="n">async_get_record</span><span class="p">(</span><span class="n">guid</span><span class="o">=</span><span class="n">guid</span><span class="p">,</span> <span class="n">_ssl</span><span class="o">=</span><span class="n">ssl</span><span class="p">)</span>
+                <span class="n">records</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">matched_record</span><span class="p">)</span>
+            <span class="k">except</span> <span class="n">aiohttp</span><span class="o">.</span><span class="n">client_exceptions</span><span class="o">.</span><span class="n">ClientResponseError</span> <span class="k">as</span> <span class="n">exc</span><span class="p">:</span>
+                <span class="c1"># this means the GUID likely doesn&#39;t exist or there was an error</span>
+                <span class="c1"># receiving it. In this case, log and ignore</span>
+                <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;guid: </span><span class="si">{</span><span class="n">guid</span><span class="si">}</span><span class="s2"> not found. Error: </span><span class="si">{</span><span class="n">exc</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">matched_records</span> <span class="o">=</span> <span class="k">await</span> <span class="n">index</span><span class="o">.</span><span class="n">async_get_records_from_checksum</span><span class="p">(</span>
+                <span class="n">checksum</span><span class="o">=</span><span class="n">checksum</span><span class="p">,</span> <span class="n">_ssl</span><span class="o">=</span><span class="n">ssl</span>
+            <span class="p">)</span>
+            <span class="n">records</span> <span class="o">+=</span> <span class="n">matched_records</span>
 
         <span class="c1"># if nothing was found, we still want to output the input record</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">records</span><span class="p">:</span>
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index d6b971a97..f2d4d0ec2 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, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "endpoint": [0, 1, 2, 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, "client_credenti": 0, "client_scop": 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, 5, 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], "contain": [0, 2, 5, 8, 9, 10, 11, 12], "download": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13], "json": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 13], "web": 0, "option": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11], "work": [0, 10], "workspac": [0, 2], "default": [0, 1, 3, 7, 8, 11, 12], "env": 0, "gen3_api_kei": 0, "credenti": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 13], "set": [0, 1, 5, 10], "includ": [0, 3], "search": [0, 2, 3], "path": [0, 1, 5, 10, 11, 13], "valu": [0, 1, 3, 5, 7, 10, 11], "doe": [0, 12], "interpret": 0, "wt": [0, 10], "an": [0, 3, 6, 8, 10, 11], "accesstoken": 0, "If": [0, 1, 7, 11, 12], "can": [0, 3, 4, 8, 11, 12], "specifi": [0, 1, 3, 11, 13], "local": [0, 13], "indic": [0, 11], "environ": 0, "fenc": [0, 1], "tupl": [0, 3, 11, 12], "client_id": 0, "client_secret": 0, "oidc": 0, "client": [0, 3], "ha": [0, 11], "grant": 0, "allow": [0, 6, 8, 10, 11, 12], "obtain": [0, 10], "space": [0, 11], "separ": [0, 11], "list": [0, 1, 3, 4, 5, 7, 8, 10, 11, 13], "scope": [0, 1], "user": [0, 10, 12], "data": [0, 1, 3, 5, 7, 8, 10, 11], "openid": 0, "exampl": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11, 13], "thi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "point": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "sandbox": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "common": [0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13], "while": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "profil": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "page": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13], "instal": [0, 2, 11], "crdc": 0, "some": [0, 2], "arbitrari": 0, "kei": [0, 3, 5, 13], "variabl": [0, 7, 8], "rather": 0, "than": [0, 5], "pass": [0, 7, 8, 10], "argument": [0, 13], "constructor": 0, "id": [0, 1, 3, 5, 10, 11], "secret": 0, "note": [0, 3, 11, 12], "should": [0, 8, 11], "never": 0, "hardcod": 0, "http": [0, 7, 11, 12], "datacommon": 0, "o": 0, "gen3_oidc_client_creds_secret": 0, "initi": [0, 10], "follow": [0, 11], "curl": [0, 2], "given": [0, 3, 4, 5, 8, 10, 12, 13], "ex": [0, 11, 12], "return": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11], "respons": [0, 1, 3, 4, 5], "under": [0, 8, 13], "index": [0, 2, 5, 9], "authz": [0, 1, 2, 3, 9, 10, 11], "map": [0, 11], "get": [0, 1, 2, 3, 4, 5, 8, 10, 11, 12, 13], "post": [0, 11], "put": 0, "delet": [0, 1, 2, 3, 5, 6, 8, 10, 11], "i": [0, 1, 2, 3, 4, 5, 8, 10, 11, 12], "els": [0, 12], "filenam": [0, 8, 10, 11, 12], "get_access_token": [0, 2], "auto": [0, 2], "within": [0, 2, 9], "5": [0, 5], "minut": 0, "get_access_token_from_wt": [0, 2], "try": 0, "fetch": 0, "namespac": [0, 12], "refresh_access_token": [0, 2], "new": [0, 3], "gen3fil": [1, 2], "auth_provid": [1, 2, 3, 4, 5, 6, 7, 8, 13], "object": [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 13], "For": [1, 5, 6, 7, 8, 9, 11], "interact": [1, 3, 4, 5, 6, 8, 13], "manag": [1, 5, 10], "featur": [1, 6], "A": [1, 3, 4, 5, 6, 7, 8, 10, 11, 13], "servic": [1, 3, 4, 5, 6, 8, 11, 12, 13], "presign": 1, "url": [1, 2, 3, 9, 10, 11, 12, 13], "right": 1, "now": [1, 8], "instanc": [1, 3, 6, 7, 8, 9, 10], "auth": [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "delete_fil": [1, 2], "guid": [1, 2, 3, 5, 6, 9, 11, 12], "method": [1, 7, 10], "deprec": 1, "delete_file_loc": [1, 2, 6], "instead": [1, 7, 11], "all": [1, 3, 4, 5, 6, 7, 8, 10, 11, 12], "locat": [1, 6], "store": [1, 3, 10], "remov": [1, 6, 11, 13], "its": [1, 3], "record": [1, 3, 5, 7, 8, 11, 12], "indexd": [1, 3, 6, 10, 11, 12], "uuid": [1, 3, 8], "text": [1, 7, 8], "result": [1, 8, 10, 11], "type": [1, 3, 4, 5, 7, 8, 10, 11, 12], "download_singl": [1, 2], "object_id": [1, 2, 9, 10], "singl": [1, 5, 8, 10], "": [1, 4, 8, 10, 11], "uniqu": [1, 5], "get_presigned_url": [1, 2], "protocol": 1, "retriev": [1, 8, 10, 12], "give": 1, "limit": [1, 3, 5, 12], "time": [1, 8, 10, 11], "pick": 1, "avail": [1, 2, 10, 11], "queri": [1, 2, 3, 5, 8, 11, 12], "upload_fil": [1, 2], "file_nam": [1, 2, 3, 9, 10, 11], "expires_in": 1, "bucket": [1, 6], "upload": [1, 2, 3, 8, 13], "author": 1, "storag": [1, 2, 6], "s3": [1, 10, 11], "az": 1, "isn": 1, "t": [1, 5, 11], "int": [1, 3, 5, 7, 8, 10, 11, 12], "amount": [1, 9], "second": [1, 4], "sign": 1, "datetim": [1, 10], "utcnow": 1, "Be": 1, "sure": 1, "posit": [1, 7], "integ": [1, 3, 8], "also": 1, "treat": [1, 5], "max_presigned_url_ttl": 1, "configur": 1, "must": [1, 5], "allowed_data_upload_bucket": 1, "data_upload_bucket": 1, "represent": [1, 3], "document": [1, 3], "upload_file_to_guid": [1, 2], "exist": [1, 3, 5, 6, 9, 12], "readm": 2, "python": [2, 9, 11], "github": [2, 7], "repo": 2, "setup": 2, "inform": [2, 3, 10], "along": 2, "quickstart": 2, "script": 2, "more": [2, 5, 7, 9, 10], "detail": [2, 7, 10], "about": [2, 3], "variou": 2, "function": [2, 3, 4, 5, 9, 10, 11, 12], "mostli": 2, "docstr": 2, "code": [2, 8], "helper": 2, "gen3index": [2, 3], "async_create_record": [2, 3], "async_get_record": [2, 3], "async_get_records_from_checksum": [2, 3], "async_get_records_on_pag": [2, 3], "async_get_with_param": [2, 3], "async_query_url": [2, 3], "async_update_record": [2, 3], "create_blank": [2, 3], "create_new_vers": [2, 3], "create_record": [2, 3], "delete_record": [2, 3, 8], "get_all_record": [2, 3], "get_guids_prefix": [2, 3], "get_latest_vers": [2, 3], "get_record": [2, 3], "get_record_doc": [2, 3], "get_records_on_pag": [2, 3], "get_stat": [2, 3], "get_url": [2, 3], "get_valid_guid": [2, 3], "get_vers": [2, 3, 4, 5], "get_with_param": [2, 3], "is_healthi": [2, 3, 4, 5], "query_url": [2, 3], "update_blank": [2, 3], "update_record": [2, 3], "job": 2, "gen3job": [2, 4, 10], "async_run_job_and_wait": [2, 4], "create_job": [2, 4], "get_output": [2, 4], "get_statu": [2, 4], "list_job": [2, 4], "metadata": [2, 3, 6, 9, 11], "gen3metadata": [2, 5], "async_cr": [2, 5], "async_create_alias": [2, 5], "async_delete_alia": [2, 5], "async_delete_alias": [2, 5], "async_get": [2, 5], "async_get_alias": [2, 5], "async_upd": [2, 5], "async_update_alias": [2, 5], "batch_creat": [2, 5], "creat": [2, 3, 4, 5, 6, 8, 10, 11], "create_alias": [2, 5], "create_index_key_path": [2, 5], "delete_alia": [2, 5], "delete_alias": [2, 5], "delete_index_key_path": [2, 5], "get_alias": [2, 5], "get_index_key_path": [2, 5], "updat": [2, 3, 5, 10, 11], "update_alias": [2, 5], "gen3object": 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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"]], "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, "": 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": 8, "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": 57}, "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_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_drs_object"]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest"]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time"]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name"]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name"]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size"]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size"]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download"]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token"]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname"]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest"]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object"]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest"]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load"]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest"]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum"]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id"]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id"]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type"]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint"]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects"]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time"]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status"]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time"]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access"]], "acls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ACLS"]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ"]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR"]], "current_dir (in module 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\ No newline at end of file
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"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": 57}, "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_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_drs_object"]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest"]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time"]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name"]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name"]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size"]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size"]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download"]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token"]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname"]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest"]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object"]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest"]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load"]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest"]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum"]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id"]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id"]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type"]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint"]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects"]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time"]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status"]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time"]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access"]], "acls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ACLS"]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ"]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR"]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID"]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE"]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS"]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS"]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5"]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID"]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE"]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER"]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl"]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS"]], "async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.async_download_object_manifest"]], "async_verify_object_manifest() (in module gen3.tools.indexing.verify_manifest)": [[11, "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 f94b99b95..fc22b67f9 100644
--- a/docs/_build/html/tools/indexing.html
+++ b/docs/_build/html/tools/indexing.html
@@ -381,7 +381,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Permalink
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.indexing.verify_manifest.async_verify_object_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1680538182.0011957.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1681920118.836989.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Permalink to this definition">¶</a></dt>
 <dd><p>Verify all file object records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html
index 076c9b35f..f90c0aa65 100644
--- a/docs/_build/html/tools/metadata.html
+++ b/docs/_build/html/tools/metadata.html
@@ -102,7 +102,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1680538182.2834604.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1681920119.2061372.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Permalink to this definition">¶</a></dt>
 <dd><p>Ingest all metadata records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

From b7a33bc2f0196552f68d7e01e1357270b6c115f5 Mon Sep 17 00:00:00 2001
From: Avantol13 <Avantol13@users.noreply.github.com>
Date: Wed, 6 Dec 2023 20:47:18 +0000
Subject: [PATCH 3/4] Apply automatic documentation changes

---
 docs/_build/doctrees/environment.pickle     | Bin 1553136 -> 1553996 bytes
 docs/_build/doctrees/tools/indexing.doctree | Bin 100101 -> 100101 bytes
 docs/_build/doctrees/tools/metadata.doctree | Bin 35609 -> 35919 bytes
 docs/_build/html/searchindex.js             |   2 +-
 docs/_build/html/tools/indexing.html        |   2 +-
 docs/_build/html/tools/metadata.html        |  31 ++++++++++----------
 6 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
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diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree
index 1984d47cea8ed2a999883ef6168ca97590f87cae..24020246768e8d406333864fd4d7ca427f74636b 100644
GIT binary patch
delta 128
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ce8`P1I-S>t(FH>=!H3ZjU2yvfAI4ZK0HHD<UH||9

delta 128
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diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree
index 5d296cc899d798c81232c840239c905d509f127b..c18cc1bf381ae72f823eb8a5e6141c5b910b17d2 100644
GIT binary patch
delta 6023
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\ No newline at end of file
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"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..75709bd2c 100644
--- a/docs/_build/html/tools/indexing.html
+++ b/docs/_build/html/tools/indexing.html
@@ -380,7 +380,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Link to th
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.indexing.verify_manifest.async_verify_object_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1700678999.9725351.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1701895635.1045384.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition">¶</a></dt>
 <dd><p>Verify all file object records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html
index f90c0aa65..12009d4bd 100644
--- a/docs/_build/html/tools/metadata.html
+++ b/docs/_build/html/tools/metadata.html
@@ -1,17 +1,16 @@
-
 <!DOCTYPE html>
 
-<html lang="en">
+<html lang="en" data-content_root="../">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
     <title>Metadata Tools &#8212; Gen3 SDK  documentation</title>
-    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
-    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-    <script src="../_static/doctools.js"></script>
-    <script src="../_static/sphinx_highlight.js"></script>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=4f649999" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=039e1c02" />
+    <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Gen3 Workspace Storage" href="../wss.html" />
@@ -33,13 +32,13 @@
           <div class="body" role="main">
             
   <section id="metadata-tools">
-<h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink to this heading">¶</a></h1>
+<h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Link to this heading">¶</a></h1>
 <section id="module-gen3.tools.metadata.ingest_manifest">
-<span id="ingest"></span><h2>Ingest<a class="headerlink" href="#module-gen3.tools.metadata.ingest_manifest" title="Permalink to this heading">¶</a></h2>
+<span id="ingest"></span><h2>Ingest<a class="headerlink" href="#module-gen3.tools.metadata.ingest_manifest" title="Link to this heading">¶</a></h2>
 <p>Tools for ingesting a CSV/TSV metadata manifest into the Metdata Service.</p>
 <dl class="py attribute">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID">
-<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">COLUMN_TO_USE_AS_GUID</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">COLUMN_TO_USE_AS_GUID</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID" title="Link to this definition">¶</a></dt>
 <dd><p>file column containing guid to use</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
@@ -50,7 +49,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT">
-<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">GUID_TYPE_FOR_INDEXED_FILE_OBJECT</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">GUID_TYPE_FOR_INDEXED_FILE_OBJECT</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT" title="Link to this definition">¶</a></dt>
 <dd><p>type to populate in mds when guid exists
 in indexd</p>
 <dl class="field-list simple">
@@ -62,7 +61,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT">
-<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT" title="Link to this definition">¶</a></dt>
 <dd><p>type to populate in mds when guid does
 NOT exist in indexd</p>
 <dl class="field-list simple">
@@ -91,7 +90,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS">
-<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">MAX_CONCURRENT_REQUESTS</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">MAX_CONCURRENT_REQUESTS</span></span><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS" title="Link to this definition">¶</a></dt>
 <dd><p>Maximum concurrent requests to mds for ingestion</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
@@ -102,7 +101,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1681920119.2061372.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1701895635.3887937.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition">¶</a></dt>
 <dd><p>Ingest all metadata records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -137,7 +136,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Permalink
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_query_urls_from_indexd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pattern</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lock</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_query_urls_from_indexd"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_query_urls_from_indexd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pattern</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lock</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_query_urls_from_indexd"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd" title="Link to this definition">¶</a></dt>
 <dd><p>Gets a semaphore then requests a record for the given pattern</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

From 6622f1ac9f4e8ac9442d293ffedd6a9853b7651f Mon Sep 17 00:00:00 2001
From: Avantol13 <Avantol13@users.noreply.github.com>
Date: Thu, 7 Dec 2023 16:06:38 +0000
Subject: [PATCH 4/4] Apply automatic documentation changes

---
 docs/_build/doctrees/environment.pickle     | Bin 1553996 -> 1553996 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 078180a2c6ecf46ca02305514e267fd3fdf23ce2..ca98f8da959e137d884776d95fb13c15bb6146c1 100644
GIT binary patch
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"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
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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 75709bd2c..69660157f 100644
--- a/docs/_build/html/tools/indexing.html
+++ b/docs/_build/html/tools/indexing.html
@@ -380,7 +380,7 @@ <h1>Indexing Tools<a class="headerlink" href="#indexing-tools" title="Link to th
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.indexing.verify_manifest.async_verify_object_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1701895635.1045384.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.indexing.verify_manifest.</span></span><span class="sig-name descname"><span class="pre">async_verify_object_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'acl':</span> <span class="pre">&lt;function</span> <span class="pre">_get_acl_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'authz':</span> <span class="pre">&lt;function</span> <span class="pre">_get_authz_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_name':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_name_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'file_size':</span> <span class="pre">&lt;function</span> <span class="pre">_get_file_size_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'guid':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'md5':</span> <span class="pre">&lt;function</span> <span class="pre">_get_md5_from_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'urls':</span> <span class="pre">&lt;function</span> <span class="pre">_get_urls_from_row&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='verify-manifest-errors-1701965194.2907536.log'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/indexing/verify_manifest.html#async_verify_object_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.indexing.verify_manifest.async_verify_object_manifest" title="Link to this definition">¶</a></dt>
 <dd><p>Verify all file object records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html
index 12009d4bd..0427be900 100644
--- a/docs/_build/html/tools/metadata.html
+++ b/docs/_build/html/tools/metadata.html
@@ -101,7 +101,7 @@ <h1>Metadata Tools<a class="headerlink" href="#metadata-tools" title="Link to th
 
 <dl class="py function">
 <dt class="sig sig-object py" id="gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest">
-<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1701895635.3887937.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition">¶</a></dt>
+<em class="property"><span class="k"><span class="pre">async</span></span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gen3.tools.metadata.ingest_manifest.</span></span><span class="sig-name descname"><span class="pre">async_ingest_metadata_manifest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">commons_url</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auth=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_concurrent_requests=24</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_row_parsers={'guid_for_row':</span> <span class="pre">&lt;function</span> <span class="pre">_get_guid_for_row&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">'indexed_file_object_guid':</span> <span class="pre">&lt;function</span> <span class="pre">_query_for_associated_indexd_record_guid&gt;}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifest_file_delimiter=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_filename='ingest-metadata-manifest-errors-1701965194.6133904.log'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_guid_from_file=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metadata_type=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gen3/tools/metadata/ingest_manifest.html#async_ingest_metadata_manifest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest" title="Link to this definition">¶</a></dt>
 <dd><p>Ingest all metadata records into a manifest csv</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>