From 33b86f5d810696073111a49997ae260b1c7afdd8 Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Wed, 23 Oct 2024 12:45:19 -0500 Subject: [PATCH 01/10] Adding post-indexing validation module --- .../indexing/post_indexing_validation.py | 342 ++++++++++++++++++ 1 file changed, 342 insertions(+) create mode 100644 gen3/tools/indexing/post_indexing_validation.py diff --git a/gen3/tools/indexing/post_indexing_validation.py b/gen3/tools/indexing/post_indexing_validation.py new file mode 100644 index 000000000..9bbec405b --- /dev/null +++ b/gen3/tools/indexing/post_indexing_validation.py @@ -0,0 +1,342 @@ +""" +Module for running post-indexing validation. +validate_manifest takes as input a manifest, an api credentials file, and an output path +then runs an async coroutine attempting to obtain a pre-signed url, download a file from each bucket +to verify it has been indexed, and generate a report in csv format. + +The output format is as follows: +| ACL | Bucket | Protocol | Presigned URL Status | Download Status | GUID | +""" + + +import csv +import aiohttp +import asyncio +from gen3.auth import Gen3Auth +from cdislogging import get_logger, get_stream_handler + + +logger = get_logger(__name__) +logger.addHandler(get_stream_handler()) +logger.setLevel("INFO") + + +class GuidError(Exception): + pass + + +class Record: + def __init__(self, guid, bucket, protocol, acl, access_token, commons, size): + self.guid = guid + self.bucket = bucket + self.protocol = protocol + self.acl = acl + self.commons = commons + self.size = size + self.download_status = -1 + self.headers = { + "accept": "application/json", + "authorization": f"bearer {access_token}", + } + + async def get_presigned_url(self, semaphore, session): + """ + Generates a presigned_url for the given guid and protocol at the specified commons. + + Runs concurrently as many as the provided semaphore will allow. + + Args: + semaphore: an asyncio semaphore + session: an aiohttp client session connected to the commons + + """ + async with semaphore: + try: + url = ( + self.commons + + f"/user/data/download/{self.guid}?protocol={self.protocol}" + ) + async with session.get(url, headers=self.headers) as response: + if response.ok: + # url = response.get() + self.response, self.response_status = ( + await response.json(), + response.status, + ) + else: + logger.info( + f"Response unsuccessful; returned with status {response.status}" + ) + self.response, self.response_status = {}, response.status + except Exception as e: + logger.error(f"Error fetching presigned URL {url}: {e}") + self.response, self.response_status = {}, -1 + + self.presigned_url = None + if self.response: + logger.info(f"presigned-url response: {self.response}") + self.presigned_url = self.response.get("url") + else: + logger.warning( + f"FAILED TO GET PRESIGNED-URL: status_code = {self.response_status}" + ) + + async def download_file(self, semaphore, session): + """ + Downloads a file from the provided url, which is a generated presigned_url. + + Runs concurrently as many as the provided semaphore will allow. + + Args: + semaphore: an asyncio semaphore + session: an aiohttp client session connected to the commons + + """ + async with semaphore: + try: + async with session.get( + self.presigned_url, headers={"Range": "bytes=0-1023"} + ) as response: + if response.ok: + await response.read() + self.download_status = response.status + else: + self.download_status = response.status + except Exception as e: + logger.error(f"Error downloading file from {self.presigned_url}: {e}") + self.download_status = -1 + + +class Records: + def __init__(self, semaphore, session, auth): + self.access_token = auth.get_access_token() + self.commons = auth.endpoint + self.semaphore = semaphore + self.session = session + self.record_dict = {} + self.record_sizes = {} + self.headers = { + "accept": "application/json", + "authorization": f"bearer {self.access_token}", + } + + def read_records_from_manifest(self, manifest): + """ + Parses a manifest and creates a dictionary of Record objects. + + Args: + manifest (str): the location of a manifest file + """ + if manifest[-3:] == "tsv": + sep = "\t" + else: + sep == "," + with open(manifest, mode="r") as f: + csv_reader = csv.DictReader(f, delimiter=sep) + rows = [row for row in csv_reader] + + try: + guid_cols = {"GUID", "guid", "id"} + guid_col = list(guid_cols.intersection(set(csv_reader.fieldnames)))[0] + except IndexError: + raise GuidError( + "Manifest file has no column named 'GUID', 'guid', or 'id'" + ) + + for row in rows: + url_parsed = False + size = row["size"] + guid = row[guid_col] + for acl in row["acl"].split(" "): + if acl != "admin": + for url in row["url"].split(" "): + if "://" not in url: + continue + else: + protocol, bucket = ( + url.split("://")[0].replace("[", ""), + url.split("/")[2], + ) + key = (bucket, protocol, acl) + if key not in self.record_dict or int( + self.record_dict[key].size + ) >= int(size): + record = Record( + guid, + bucket, + protocol, + acl, + self.access_token, + self.commons, + size, + ) + self.record_dict[key] = record + url_parsed = True + + if url_parsed == False: + logger.warning(f"No url parsed for record {guid}") + + async def get_presigned_url_list(self): + """ + Attempts to obtain a presigned url for every record. + Runs concurrently according to defined semaphore. + """ + tasks = [] + for (bucket, protocol, acl), record in self.record_dict.items(): + logger.info( + f"picking one indexd record with GUID {record.guid} from acl {acl}" + ) + logger.info(f"checking guid {record.guid} with protocol {protocol}...") + tasks.append( + ( + record.get_presigned_url(self.semaphore, self.session), + protocol, + acl, + bucket, + record.guid, + ) + ) + + self.presigned_results = await asyncio.gather(*[task[0] for task in tasks]) + + async def download_files(self): + """ + Attempts to download a file for every record where a presigned url was able to be obtained. + Runs concurrently according to defined semaphore. + """ + download_tasks = [] + for (bucket, protocol, acl), record in self.record_dict.items(): + if record.presigned_url: + logger.info( + f"Attempting to download from presigned URL: {record.presigned_url}" + ) + download_tasks.append( + ( + record.download_file(self.semaphore, self.session), + record.protocol, + record.acl, + record.response_status, + record.bucket, + record.guid, + ) + ) + else: + logger.warning( + f"No presigned url associated with record {record.guid} from acl {acl}" + ) + download_tasks.append( + ( + None, + record.protocol, + record.acl, + record.response_status, + record.bucket, + record.guid, + ) + ) + + self.download_responses = await asyncio.gather( + *[task[0] for task in download_tasks if task[0] is not None] + ) + + def save_download_check_results_to_csv(self, csv_filename): + """ + Generates results from presigned url generation and file downloads. + Output format is: | ACL | Bucket | Protocol | Presigned URL Status | Download Status | GUID | + + Args: + csv_filename (str): the relative file path of the output csv + """ + download_results = [] + for record in self.record_dict.values(): + download_results.append( + { + "acl": record.acl, + "bucket": record.bucket, + "protocol": record.protocol, + "presigned_url_status": record.response_status, + "download_status": record.download_status, + "guid": record.guid, + } + ) + + # Check if the results list is empty + if not download_results: + logger.warning("No results to save.") + return + + # Define the CSV file header + fieldnames = [ + "ACL", + "Bucket", + "Protocol", + "Presigned URL Status", + "Download Status", + "GUID", + ] + + with open(csv_filename, mode="w", newline="") as csv_file: + writer = csv.DictWriter(csv_file, fieldnames=fieldnames) + + # Write the header row + writer.writeheader() + + # Iterate through the DownloadCheckResult instances and write each row + for result in download_results: + writer.writerow( + { + "ACL": result["acl"], + "Bucket": result["bucket"], + "Protocol": result["protocol"], + "Presigned URL Status": result["presigned_url_status"], + "Download Status": result["download_status"], + "GUID": result["guid"], + } + ) + + logger.info(f"Results saved to {csv_filename}") + + +async def _validate_manifest_coro(MANIFEST, api_key, output_file): + """ + Manifest validation coroutine. + Takes as input a manifest location, the location of an api credentials file, and an output file + Attempts to obtain a presigned url from a record from each bucket then download the file. + Outputs report in csv format. + + Args: + MANIFEST (str): the location of a manifest file + api_key (str): the location of an api credentials file + output_file (str): the relative path of the output csv + """ + logger.info("STARTING...") + concurrent_limit = 5 + auth = Gen3Auth(refresh_file=api_key) + access_token = auth.get_access_token() + + semaphore = asyncio.Semaphore(concurrent_limit) + + async with aiohttp.ClientSession() as session: + headers = { + "accept": "application/json", + "authorization": f"bearer {access_token}", + } + + records = Records(semaphore, session, auth) + + records.read_records_from_manifest(MANIFEST) + await records.get_presigned_url_list() + await records.download_files() + records.save_download_check_results_to_csv(output_file) + + +def validate_manifest(MANIFEST, api_key, output_file="results.csv"): + """ + The driver for _validate_manifest_coro + + Args: + MANIFEST (str): the location of a manifest file + api_key (str): the location of an api credentials file + output_file (str): the relative path of the output csv + """ + asyncio.run(_validate_manifest_coro(MANIFEST, api_key, output_file)) From ee958ce960b9849a3bcd24d03669e65b7a6456fb Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Wed, 23 Oct 2024 17:49:09 +0000 Subject: [PATCH 02/10] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 447288 -> 447288 bytes docs/_build/doctrees/tools/indexing.doctree | 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"gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", "tools"]], "gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "get_access_token_from_wts"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "download_single"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"], [1, 1, 1, "", "upload_file_to_guid"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], "gen3.jobs": [[4, 0, 1, "", "Gen3Jobs"]], "gen3.jobs.Gen3Jobs": [[4, 1, 1, "", "async_run_job_and_wait"], [4, 1, 1, "", "create_job"], [4, 1, 1, "", "get_output"], [4, 1, 1, "", "get_status"], [4, 1, 1, "", "get_version"], [4, 1, 1, "", "is_healthy"], [4, 1, 1, "", "list_jobs"]], "gen3.metadata": [[5, 0, 1, "", "Gen3Metadata"]], "gen3.metadata.Gen3Metadata": [[5, 1, 1, "", "async_create"], [5, 1, 1, "", "async_create_aliases"], [5, 1, 1, "", "async_delete_alias"], [5, 1, 1, "", "async_delete_aliases"], [5, 1, 1, "", "async_get"], [5, 1, 1, "", "async_get_aliases"], [5, 1, 1, "", "async_update"], [5, 1, 1, "", "async_update_aliases"], [5, 2, 1, "", "auth_provider"], [5, 1, 1, "", "batch_create"], [5, 1, 1, "", "create"], [5, 1, 1, "", "create_aliases"], [5, 1, 1, "", "create_index_key_path"], [5, 1, 1, "", "delete"], [5, 1, 1, "", "delete_alias"], [5, 1, 1, "", "delete_aliases"], [5, 1, 1, "", "delete_index_key_path"], [5, 2, 1, "", "endpoint"], [5, 1, 1, "", "get"], [5, 1, 1, "", "get_aliases"], [5, 1, 1, "", "get_index_key_paths"], [5, 1, 1, "", "get_version"], [5, 1, 1, "", "is_healthy"], [5, 1, 1, "", "query"], [5, 1, 1, "", "update"], [5, 1, 1, "", "update_aliases"]], "gen3.object": [[6, 0, 1, "", "Gen3Object"]], "gen3.object.Gen3Object": [[6, 1, 1, "", "delete_object"]], "gen3.query": [[7, 0, 1, "", "Gen3Query"]], "gen3.query.Gen3Query": [[7, 1, 1, "", "graphql_query"], [7, 1, 1, "", "query"], [7, 1, 1, "", "raw_data_download"]], "gen3.submission": [[8, 0, 1, "", "Gen3Submission"]], "gen3.submission.Gen3Submission": [[8, 1, 1, "", "create_program"], [8, 1, 1, "", "create_project"], [8, 1, 1, "", "delete_node"], [8, 1, 1, "", "delete_nodes"], [8, 1, 1, "", "delete_program"], [8, 1, 1, "", "delete_project"], [8, 1, 1, "", "delete_record"], [8, 1, 1, "", "delete_records"], [8, 1, 1, "", "export_node"], [8, 1, 1, "", "export_record"], [8, 1, 1, "", "get_dictionary_all"], [8, 1, 1, "", "get_dictionary_node"], [8, 1, 1, "", "get_graphql_schema"], [8, 1, 1, "", "get_programs"], [8, 1, 1, "", "get_project_dictionary"], [8, 1, 1, "", "get_project_manifest"], [8, 1, 1, "", "get_projects"], [8, 1, 1, "", "open_project"], [8, 1, 1, "", "query"], [8, 1, 1, "", "submit_file"], [8, 1, 1, "", "submit_record"]], "gen3.tools.download": [[10, 3, 0, "-", "drs_download"]], 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"gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", "tools"]], "gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "get_access_token_from_wts"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "download_single"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"], [1, 1, 1, "", "upload_file_to_guid"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], "gen3.jobs": [[4, 0, 1, "", "Gen3Jobs"]], "gen3.jobs.Gen3Jobs": [[4, 1, 1, "", "async_run_job_and_wait"], [4, 1, 1, "", "create_job"], [4, 1, 1, "", "get_output"], [4, 1, 1, "", "get_status"], [4, 1, 1, "", "get_version"], [4, 1, 1, "", "is_healthy"], [4, 1, 1, "", "list_jobs"]], "gen3.metadata": [[5, 0, 1, "", "Gen3Metadata"]], "gen3.metadata.Gen3Metadata": [[5, 1, 1, "", "async_create"], [5, 1, 1, "", "async_create_aliases"], [5, 1, 1, "", "async_delete_alias"], [5, 1, 1, "", "async_delete_aliases"], [5, 1, 1, "", "async_get"], [5, 1, 1, "", "async_get_aliases"], [5, 1, 1, "", "async_update"], [5, 1, 1, "", "async_update_aliases"], [5, 2, 1, "", "auth_provider"], [5, 1, 1, "", "batch_create"], [5, 1, 1, "", "create"], [5, 1, 1, "", "create_aliases"], [5, 1, 1, "", "create_index_key_path"], [5, 1, 1, "", "delete"], [5, 1, 1, "", "delete_alias"], [5, 1, 1, "", "delete_aliases"], [5, 1, 1, "", "delete_index_key_path"], [5, 2, 1, "", "endpoint"], [5, 1, 1, "", "get"], [5, 1, 1, "", "get_aliases"], [5, 1, 1, "", "get_index_key_paths"], [5, 1, 1, "", "get_version"], [5, 1, 1, "", "is_healthy"], [5, 1, 1, "", "query"], [5, 1, 1, "", "update"], [5, 1, 1, "", "update_aliases"]], "gen3.object": [[6, 0, 1, "", "Gen3Object"]], "gen3.object.Gen3Object": [[6, 1, 1, "", "delete_object"]], "gen3.query": [[7, 0, 1, "", "Gen3Query"]], "gen3.query.Gen3Query": [[7, 1, 1, "", "graphql_query"], [7, 1, 1, "", "query"], [7, 1, 1, "", "raw_data_download"]], "gen3.submission": [[8, 0, 1, "", "Gen3Submission"]], "gen3.submission.Gen3Submission": [[8, 1, 1, "", "create_program"], [8, 1, 1, "", "create_project"], [8, 1, 1, "", "delete_node"], [8, 1, 1, "", "delete_nodes"], [8, 1, 1, "", "delete_program"], [8, 1, 1, "", "delete_project"], [8, 1, 1, "", "delete_record"], [8, 1, 1, "", "delete_records"], [8, 1, 1, "", "export_node"], [8, 1, 1, "", "export_record"], [8, 1, 1, "", "get_dictionary_all"], [8, 1, 1, "", "get_dictionary_node"], [8, 1, 1, "", "get_graphql_schema"], [8, 1, 1, "", "get_programs"], [8, 1, 1, "", "get_project_dictionary"], [8, 1, 1, "", "get_project_manifest"], [8, 1, 1, "", "get_projects"], [8, 1, 1, "", "open_project"], [8, 1, 1, "", "query"], [8, 1, 1, "", "submit_file"], [8, 1, 1, "", "submit_record"]], "gen3.tools.download": [[10, 3, 0, "-", "drs_download"]], "gen3.tools.download.drs_download": [[10, 0, 1, "", "DownloadManager"], [10, 0, 1, "", "DownloadStatus"], [10, 0, 1, "", "Downloadable"], [10, 0, 1, "", "Manifest"], [10, 4, 1, "", "download_files_in_drs_manifest"], [10, 4, 1, "", "list_access_in_drs_manifest"], [10, 4, 1, "", "list_drs_object"], [10, 4, 1, "", "list_files_in_drs_manifest"]], "gen3.tools.download.drs_download.DownloadManager": [[10, 1, 1, "", "cache_hosts_wts_tokens"], [10, 1, 1, "", "download"], [10, 1, 1, "", "get_fresh_token"], [10, 1, 1, "", "resolve_objects"], [10, 1, 1, "", "user_access"]], "gen3.tools.download.drs_download.DownloadStatus": [[10, 2, 1, "", "end_time"], [10, 2, 1, "", "start_time"], [10, 2, 1, "", "status"]], "gen3.tools.download.drs_download.Downloadable": [[10, 2, 1, "", "_manager"], [10, 2, 1, "", "access_methods"], [10, 2, 1, "", "children"], [10, 2, 1, "", "created_time"], [10, 1, 1, "", "download"], [10, 2, 1, "", "file_name"], [10, 2, 1, "", "file_size"], [10, 2, 1, "", "hostname"], [10, 2, 1, "", "object_id"], [10, 2, 1, "", "object_type"], [10, 1, 1, "", "pprint"], [10, 2, 1, "", "updated_time"]], "gen3.tools.download.drs_download.Manifest": [[10, 2, 1, "", "commons_url"], [10, 1, 1, "", "create_object_list"], [10, 2, 1, "", "file_name"], [10, 2, 1, "", "file_size"], [10, 1, 1, "", "load"], [10, 1, 1, "", "load_manifest"], [10, 2, 1, "", "md5sum"], [10, 2, 1, "", "object_id"]], "gen3.tools.indexing": [[11, 3, 0, "-", "download_manifest"], [11, 3, 0, "-", "index_manifest"], [11, 3, 0, "-", "verify_manifest"]], "gen3.tools.indexing.download_manifest": [[11, 2, 1, "", "CURRENT_DIR"], [11, 2, 1, "", "INDEXD_RECORD_PAGE_SIZE"], [11, 2, 1, "", "MAX_CONCURRENT_REQUESTS"], [11, 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a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index 5d64bda23..e11fe0f37 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -381,7 +381,7 @@

Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1728061593.9082778.log')[source]
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1729705745.146578.log')[source]

Verify all file object records into a manifest csv

Parameters:
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 2367ba622..e5b15e728 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -102,7 +102,7 @@

Metadata Tools
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1728061594.165499.log', get_guid_from_file=True, metadata_type=None)[source]
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1729705745.417489.log', get_guid_from_file=True, metadata_type=None)[source]

Ingest all metadata records into a manifest csv

Parameters:
From 9aaf1e2502a6d9acee84fb46830532009fabb17e Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Thu, 31 Oct 2024 15:32:46 -0500 Subject: [PATCH 03/10] Added tests --- .../indexing/post_indexing_validation.py | 19 +- poetry.lock | 2130 +++++++++-------- pyproject.toml | 4 +- tests/test_post_indexing_validation.py | 171 ++ 4 files changed, 1376 insertions(+), 948 deletions(-) create mode 100644 tests/test_post_indexing_validation.py diff --git a/gen3/tools/indexing/post_indexing_validation.py b/gen3/tools/indexing/post_indexing_validation.py index 9bbec405b..702a75fdc 100644 --- a/gen3/tools/indexing/post_indexing_validation.py +++ b/gen3/tools/indexing/post_indexing_validation.py @@ -58,7 +58,6 @@ async def get_presigned_url(self, semaphore, session): ) async with session.get(url, headers=self.headers) as response: if response.ok: - # url = response.get() self.response, self.response_status = ( await response.json(), response.status, @@ -130,7 +129,7 @@ def read_records_from_manifest(self, manifest): if manifest[-3:] == "tsv": sep = "\t" else: - sep == "," + sep = "," with open(manifest, mode="r") as f: csv_reader = csv.DictReader(f, delimiter=sep) rows = [row for row in csv_reader] @@ -260,6 +259,8 @@ def save_download_check_results_to_csv(self, csv_filename): } ) + self.download_results = download_results + # Check if the results list is empty if not download_results: logger.warning("No results to save.") @@ -297,7 +298,7 @@ def save_download_check_results_to_csv(self, csv_filename): logger.info(f"Results saved to {csv_filename}") -async def _validate_manifest_coro(MANIFEST, api_key, output_file): +async def _validate_manifest_coro(MANIFEST, auth, output_file): """ Manifest validation coroutine. Takes as input a manifest location, the location of an api credentials file, and an output file @@ -311,26 +312,20 @@ async def _validate_manifest_coro(MANIFEST, api_key, output_file): """ logger.info("STARTING...") concurrent_limit = 5 - auth = Gen3Auth(refresh_file=api_key) - access_token = auth.get_access_token() semaphore = asyncio.Semaphore(concurrent_limit) async with aiohttp.ClientSession() as session: - headers = { - "accept": "application/json", - "authorization": f"bearer {access_token}", - } - records = Records(semaphore, session, auth) records.read_records_from_manifest(MANIFEST) await records.get_presigned_url_list() await records.download_files() records.save_download_check_results_to_csv(output_file) + return records -def validate_manifest(MANIFEST, api_key, output_file="results.csv"): +def validate_manifest(MANIFEST, auth, output_file="results.csv"): """ The driver for _validate_manifest_coro @@ -339,4 +334,4 @@ def validate_manifest(MANIFEST, api_key, output_file="results.csv"): api_key (str): the location of an api credentials file output_file (str): the relative path of the output csv """ - asyncio.run(_validate_manifest_coro(MANIFEST, api_key, output_file)) + return asyncio.run(_validate_manifest_coro(MANIFEST, auth, output_file)) diff --git a/poetry.lock b/poetry.lock index 2c3c22f58..5bf9fc1dc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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"importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [extras] fhir = ["fhirclient"] @@ -2275,4 +2535,4 @@ fhir = ["fhirclient"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <4" -content-hash = "75e3c8c64a23003501cb2e531df1b6a2c0bb2dd085dc40bf7cc3480efd5e1595" +content-hash = "2d200420be8310df4e3efc6ead3ee481f67b729e40fe2a931859ea8bcb4435ed" diff --git a/pyproject.toml b/pyproject.toml index 6d604835a..9563c34d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,12 +44,13 @@ gen3users = "*" # A list of all of the optional dependencies, some of which are included in the # below `extras`. They can be opted into by apps. fhirclient = { version = "*", optional = true } +pytest-asyncio = "^0.24.0" [tool.poetry.extras] fhir = ["fhirclient"] [tool.poetry.dev-dependencies] -pytest = "^6.0.0" +pytest = "*" pytest-cov = "*" requests-mock = "*" cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "1.0.0" } @@ -67,6 +68,7 @@ build-backend = "poetry.masonry.api" [tool.pytest.ini_options] minversion = "6.0" addopts = "-vv" +asyncio_mode = "auto" testpaths = [ "tests", ] diff --git a/tests/test_post_indexing_validation.py b/tests/test_post_indexing_validation.py new file mode 100644 index 000000000..8c04aa255 --- /dev/null +++ b/tests/test_post_indexing_validation.py @@ -0,0 +1,171 @@ +import pytest +import os +from gen3.tools.indexing.post_indexing_validation import ( + Record, + Records, + _validate_manifest_coro, +) +from unittest import mock +from unittest.mock import MagicMock, AsyncMock, mock_open +from aiohttp import ClientResponse +import gen3 +import time +import base64 + +cwd = os.path.dirname(os.path.realpath(__file__)) + + +read_data = "guid,md5,size,acl,url\n255e396f-f1f8-11e9-9a07-0a80fada099c,473d83400bc1bc9dc635e334faddf33d,363455714,['Open'],['s3://pdcdatastore/test1.raw']\n255e396f-f1f8-11e9-9a07-0a80fada098d,473d83400bc1bc9dc635e334faddd33c,343434344,['Open'],['s3://pdcdatastore/test2.raw']\n255e396f-f1f8-11e9-9a07-0a80fada097c,473d83400bc1bc9dc635e334fadd433c,543434443,['phs0001'],['s3://pdcdatastore/test3.raw']" + + +class MockResponse: + def __init__(self, status, ok=True, json={"url": "my_presigned_url"}): + self.status = status + self.ok = ok + self.status = status + self.json_data = json + + async def text(self): + return self._text + + async def __aexit__(self, exc_type, exc, tb): + pass + + async def __aenter__(self): + return self + + async def read(self): + pass + + async def json(self): + return self.json_data + + +@pytest.mark.asyncio +async def test_validate_manifest_coro_with_200(): + hostname = "test.datacommons.io" + exp = time.time() + 300 + decoded_info = {"aud": "123", "exp": exp, "iss": f"http://{hostname}"} + test_key = { + "api_key": "whatever." # pragma: allowlist secret + + base64.urlsafe_b64encode( + ('{"iss": "http://%s", "exp": %d }' % (hostname, exp)).encode("utf-8") + ).decode("utf-8") + + ".whatever" + } + get_mock = MockResponse(200) + with mock.patch( + "gen3.auth.get_access_token_with_key" + ) as mock_access_token, mock.patch( + "gen3.auth.Gen3Auth._write_to_file" + ) as mock_write_to_file, mock.patch( + "gen3.auth.decode_token" + ) as mock_decode_token, mock.patch( + "aiohttp.ClientSession.get" + ) as mock_request, mock.patch( + "csv.DictWriter.writerow" + ) as mock_writerow, mock.patch( + "csv.DictWriter.writeheader" + ) as mock_writeheader, mock.patch( + "builtins.open", mock_open(read_data=read_data) + ) as mock_file_open: + mock_access_token.return_value = "new_access_token" + mock_write_to_file().return_value = True + mock_decode_token.return_value = decoded_info + mock_request.return_value = get_mock + mock_writerow.return_value = None + mock_writeheader.return_value = None + + input = f"{cwd}/test_data/manifest3.csv" + output = f"{cwd}/test_data/post_indexing_output.csv" + + auth = gen3.auth.Gen3Auth(refresh_token=test_key) + auth.get_access_token() + records = await _validate_manifest_coro(input, auth, output) + + mock_file_open.assert_called_with( + f"{cwd}/test_data/post_indexing_output.csv", mode="w", newline="" + ) + mock_writeheader.assert_called_once() + mock_writerow.assert_called_with( + { + "ACL": "['phs0001']", + "Bucket": "pdcdatastore", + "Protocol": "'s3", + "Presigned URL Status": 200, + "Download Status": 200, + "GUID": "255e396f-f1f8-11e9-9a07-0a80fada097c", + } + ) + + presigned_statuses = [] + download_statuses = [] + for record in records.download_results: + presigned_statuses.append(record["presigned_url_status"]) + download_statuses.append(record["download_status"]) + assert set(presigned_statuses) == {200} and set(download_statuses) == {200} + + +@pytest.mark.asyncio +async def test_validate_manifest_coro_with_401(): + hostname = "test.datacommons.io" + exp = time.time() + 300 + decoded_info = {"aud": "123", "exp": exp, "iss": f"http://{hostname}"} + test_key = { + "api_key": "whatever." # pragma: allowlist secret + + base64.urlsafe_b64encode( + ('{"iss": "http://%s", "exp": %d }' % (hostname, exp)).encode("utf-8") + ).decode("utf-8") + + ".whatever" + } + get_mock = MockResponse(401, False, {}) + with mock.patch( + "gen3.auth.get_access_token_with_key" + ) as mock_access_token, mock.patch( + "gen3.auth.Gen3Auth._write_to_file" + ) as mock_write_to_file, mock.patch( + "gen3.auth.decode_token" + ) as mock_decode_token, mock.patch( + "aiohttp.ClientSession.get" + ) as mock_request, mock.patch( + "csv.DictWriter.writerow" + ) as mock_writerow, mock.patch( + "csv.DictWriter.writeheader" + ) as mock_writeheader, mock.patch( + "builtins.open", mock_open(read_data=read_data) + ) as mock_file_open: + mock_access_token.return_value = "new_access_token" + mock_write_to_file().return_value = True + mock_decode_token.return_value = decoded_info + mock_request.return_value = get_mock + mock_writerow.return_value = None + mock_writeheader.return_value = None + + input = f"{cwd}/test_data/manifest3.csv" + output = f"{cwd}/test_data/post_indexing_output.csv" + + auth = gen3.auth.Gen3Auth(refresh_token=test_key) + auth.get_access_token() + records = await _validate_manifest_coro(input, auth, output) + + mock_file_open.assert_called_with( + f"{cwd}/test_data/post_indexing_output.csv", mode="w", newline="" + ) + mock_writeheader.assert_called_once() + mock_writerow.assert_called_with( + { + "ACL": "['phs0001']", + "Bucket": "pdcdatastore", + "Protocol": "'s3", + "Presigned URL Status": 401, + "Download Status": -1, + "GUID": "255e396f-f1f8-11e9-9a07-0a80fada097c", + } + ) + + presigned_statuses = [] + download_statuses = [] + for record in records.download_results: + presigned_statuses.append(record["presigned_url_status"]) + download_statuses.append(record["download_status"]) + assert set(presigned_statuses) == {401} and set(download_statuses) == {-1} From c46b32a2d6a968a6ebf864090cba7340583c7789 Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Thu, 31 Oct 2024 20:35:50 +0000 Subject: [PATCH 04/10] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 447288 -> 447288 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100192 -> 100197 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35904 -> 35909 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 7229618060e768cc4d551ea3a8c884dbf7ed52aa..0fa0361309209b5540b52607a99a0674fa63cd40 100644 GIT binary patch delta 9136 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"delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project", false]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record", false]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record", false]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records", false]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download", false]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download", false]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download", false]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", "tools"]], "gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "get_access_token_from_wts"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "download_single"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"], [1, 1, 1, "", "upload_file_to_guid"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], "gen3.jobs": [[4, 0, 1, "", "Gen3Jobs"]], "gen3.jobs.Gen3Jobs": [[4, 1, 1, "", "async_run_job_and_wait"], [4, 1, 1, "", "create_job"], [4, 1, 1, "", "get_output"], [4, 1, 1, "", "get_status"], [4, 1, 1, "", "get_version"], [4, 1, 1, "", "is_healthy"], [4, 1, 1, "", "list_jobs"]], "gen3.metadata": [[5, 0, 1, "", "Gen3Metadata"]], "gen3.metadata.Gen3Metadata": [[5, 1, 1, "", "async_create"], [5, 1, 1, "", "async_create_aliases"], [5, 1, 1, "", "async_delete_alias"], [5, 1, 1, "", "async_delete_aliases"], [5, 1, 1, "", "async_get"], [5, 1, 1, "", "async_get_aliases"], [5, 1, 1, "", "async_update"], [5, 1, 1, "", "async_update_aliases"], [5, 2, 1, "", "auth_provider"], [5, 1, 1, "", "batch_create"], [5, 1, 1, "", "create"], [5, 1, 1, "", "create_aliases"], [5, 1, 1, "", "create_index_key_path"], [5, 1, 1, "", "delete"], [5, 1, 1, "", "delete_alias"], [5, 1, 1, "", "delete_aliases"], [5, 1, 1, "", "delete_index_key_path"], [5, 2, 1, "", "endpoint"], [5, 1, 1, "", "get"], [5, 1, 1, "", "get_aliases"], [5, 1, 1, "", "get_index_key_paths"], [5, 1, 1, "", "get_version"], [5, 1, 1, "", "is_healthy"], [5, 1, 1, "", "query"], [5, 1, 1, "", "update"], [5, 1, 1, "", "update_aliases"]], "gen3.object": [[6, 0, 1, "", "Gen3Object"]], "gen3.object.Gen3Object": [[6, 1, 1, "", "delete_object"]], "gen3.query": [[7, 0, 1, "", "Gen3Query"]], "gen3.query.Gen3Query": [[7, 1, 1, "", "graphql_query"], [7, 1, 1, "", "query"], [7, 1, 1, "", "raw_data_download"]], "gen3.submission": [[8, 0, 1, "", "Gen3Submission"]], "gen3.submission.Gen3Submission": [[8, 1, 1, "", "create_program"], [8, 1, 1, "", "create_project"], [8, 1, 1, "", "delete_node"], [8, 1, 1, "", "delete_nodes"], [8, 1, 1, "", "delete_program"], [8, 1, 1, "", "delete_project"], [8, 1, 1, "", "delete_record"], [8, 1, 1, "", "delete_records"], [8, 1, 1, "", "export_node"], [8, 1, 1, "", "export_record"], [8, 1, 1, "", "get_dictionary_all"], [8, 1, 1, "", "get_dictionary_node"], [8, 1, 1, "", "get_graphql_schema"], [8, 1, 1, "", "get_programs"], [8, 1, 1, "", "get_project_dictionary"], [8, 1, 1, "", "get_project_manifest"], [8, 1, 1, "", "get_projects"], [8, 1, 1, "", "open_project"], [8, 1, 1, "", "query"], [8, 1, 1, "", "submit_file"], [8, 1, 1, "", "submit_record"]], "gen3.tools.download": [[10, 3, 0, "-", "drs_download"]], 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"gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", "tools"]], "gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "get_access_token_from_wts"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "download_single"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"], [1, 1, 1, "", "upload_file_to_guid"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], "gen3.jobs": [[4, 0, 1, "", "Gen3Jobs"]], "gen3.jobs.Gen3Jobs": [[4, 1, 1, "", "async_run_job_and_wait"], [4, 1, 1, "", "create_job"], [4, 1, 1, "", "get_output"], [4, 1, 1, "", "get_status"], [4, 1, 1, "", "get_version"], [4, 1, 1, "", "is_healthy"], [4, 1, 1, "", "list_jobs"]], "gen3.metadata": [[5, 0, 1, "", "Gen3Metadata"]], "gen3.metadata.Gen3Metadata": [[5, 1, 1, "", "async_create"], [5, 1, 1, "", "async_create_aliases"], [5, 1, 1, "", "async_delete_alias"], [5, 1, 1, "", "async_delete_aliases"], [5, 1, 1, "", "async_get"], [5, 1, 1, "", "async_get_aliases"], [5, 1, 1, "", "async_update"], [5, 1, 1, "", "async_update_aliases"], [5, 2, 1, "", "auth_provider"], [5, 1, 1, "", "batch_create"], [5, 1, 1, "", "create"], [5, 1, 1, "", "create_aliases"], [5, 1, 1, "", "create_index_key_path"], [5, 1, 1, "", "delete"], [5, 1, 1, "", "delete_alias"], [5, 1, 1, "", "delete_aliases"], [5, 1, 1, "", "delete_index_key_path"], [5, 2, 1, "", "endpoint"], [5, 1, 1, "", "get"], [5, 1, 1, "", "get_aliases"], [5, 1, 1, "", "get_index_key_paths"], [5, 1, 1, "", "get_version"], [5, 1, 1, "", "is_healthy"], [5, 1, 1, "", "query"], [5, 1, 1, "", "update"], [5, 1, 1, "", "update_aliases"]], "gen3.object": [[6, 0, 1, "", "Gen3Object"]], "gen3.object.Gen3Object": [[6, 1, 1, "", "delete_object"]], "gen3.query": [[7, 0, 1, "", "Gen3Query"]], "gen3.query.Gen3Query": [[7, 1, 1, "", "graphql_query"], [7, 1, 1, "", "query"], [7, 1, 1, "", "raw_data_download"]], "gen3.submission": [[8, 0, 1, "", "Gen3Submission"]], "gen3.submission.Gen3Submission": [[8, 1, 1, "", "create_program"], [8, 1, 1, "", "create_project"], [8, 1, 1, "", "delete_node"], [8, 1, 1, "", "delete_nodes"], [8, 1, 1, "", "delete_program"], [8, 1, 1, "", "delete_project"], [8, 1, 1, "", "delete_record"], [8, 1, 1, "", "delete_records"], [8, 1, 1, "", "export_node"], [8, 1, 1, "", "export_record"], [8, 1, 1, "", "get_dictionary_all"], [8, 1, 1, "", "get_dictionary_node"], [8, 1, 1, "", "get_graphql_schema"], [8, 1, 1, "", "get_programs"], [8, 1, 1, "", "get_project_dictionary"], [8, 1, 1, "", "get_project_manifest"], [8, 1, 1, "", "get_projects"], [8, 1, 1, "", "open_project"], [8, 1, 1, "", "query"], [8, 1, 1, "", "submit_file"], [8, 1, 1, "", "submit_record"]], "gen3.tools.download": [[10, 3, 0, "-", "drs_download"]], "gen3.tools.download.drs_download": [[10, 0, 1, "", "DownloadManager"], [10, 0, 1, "", "DownloadStatus"], [10, 0, 1, "", "Downloadable"], [10, 0, 1, "", "Manifest"], [10, 4, 1, "", "download_files_in_drs_manifest"], [10, 4, 1, "", "list_access_in_drs_manifest"], [10, 4, 1, "", "list_drs_object"], [10, 4, 1, "", "list_files_in_drs_manifest"]], "gen3.tools.download.drs_download.DownloadManager": [[10, 1, 1, "", "cache_hosts_wts_tokens"], [10, 1, 1, "", "download"], [10, 1, 1, "", "get_fresh_token"], [10, 1, 1, "", "resolve_objects"], [10, 1, 1, "", "user_access"]], "gen3.tools.download.drs_download.DownloadStatus": [[10, 2, 1, "", "end_time"], [10, 2, 1, "", "start_time"], [10, 2, 1, "", "status"]], "gen3.tools.download.drs_download.Downloadable": [[10, 2, 1, "", "_manager"], [10, 2, 1, "", "access_methods"], [10, 2, 1, "", "children"], [10, 2, 1, "", "created_time"], [10, 1, 1, "", "download"], [10, 2, 1, "", "file_name"], [10, 2, 1, "", "file_size"], [10, 2, 1, "", "hostname"], [10, 2, 1, "", "object_id"], [10, 2, 1, "", "object_type"], [10, 1, 1, "", "pprint"], [10, 2, 1, "", "updated_time"]], "gen3.tools.download.drs_download.Manifest": [[10, 2, 1, "", "commons_url"], [10, 1, 1, "", "create_object_list"], [10, 2, 1, "", "file_name"], [10, 2, 1, "", "file_size"], [10, 1, 1, "", "load"], [10, 1, 1, "", "load_manifest"], [10, 2, 1, "", "md5sum"], [10, 2, 1, "", "object_id"]], "gen3.tools.indexing": [[11, 3, 0, "-", "download_manifest"], [11, 3, 0, "-", "index_manifest"], [11, 3, 0, "-", "verify_manifest"]], "gen3.tools.indexing.download_manifest": [[11, 2, 1, "", "CURRENT_DIR"], [11, 2, 1, "", "INDEXD_RECORD_PAGE_SIZE"], [11, 2, 1, "", "MAX_CONCURRENT_REQUESTS"], [11, 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a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index e11fe0f37..a2154cd50 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -381,7 +381,7 @@

Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1729705745.146578.log')[source]
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730406946.6368155.log')[source]

Verify all file object records into a manifest csv

Parameters:
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index e5b15e728..6038936a2 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -102,7 +102,7 @@

Metadata Tools
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1729705745.417489.log', get_guid_from_file=True, metadata_type=None)[source]
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730406946.8912847.log', get_guid_from_file=True, metadata_type=None)[source]

Ingest all metadata records into a manifest csv

Parameters:
From 5bf4ebea557a34f415e1b2c30927651a00906e4c Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Fri, 1 Nov 2024 10:14:15 -0500 Subject: [PATCH 05/10] Fix pytest dependency to be between 8.2 and 9 --- poetry.lock | 186 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 94 insertions(+), 94 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5bf9fc1dc..77af0689d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2006,17 +2006,17 @@ testing = ["coverage (>=6.2)", "hypothesis (>=5.7.1)"] [[package]] name = "pytest-cov" -version = "5.0.0" +version = "6.0.0" description = "Pytest plugin for measuring coverage." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "pytest-cov-5.0.0.tar.gz", hash = "sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857"}, - {file = "pytest_cov-5.0.0-py3-none-any.whl", hash = "sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652"}, + {file = 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"gen3.tools.indexing.verify_manifest.async_verify_object_manifest", false]], "auth_provider (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.auth_provider", false]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ", false]], "batch_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.batch_create", false]], "cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens", false]], "children (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.children", false]], "column_to_use_as_guid (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID", false]], "commons_url (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.commons_url", false]], "copy() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.copy", false]], "create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create", false]], "create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_aliases", false]], "create_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_blank", false]], "create_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_index_key_path", false]], "create_job() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.create_job", false]], "create_new_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_new_version", false]], "create_object_list() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.create_object_list", false]], "create_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_program", false]], "create_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_project", false]], "create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_record", false]], "created_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.created_time", false]], "curl() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.curl", false]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR", false]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete", false]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias", false]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases", false]], "delete_all_guids() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.delete_all_guids", false]], "delete_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file", false]], "delete_file_locations() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file_locations", false]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path", false]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node", false]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes", false]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object", false]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program", false]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project", false]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record", false]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record", false]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records", false]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download", false]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download", false]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download", false]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() 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"gen3.tools.indexing.index_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR", false]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete", false]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias", false]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases", false]], "delete_all_guids() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.delete_all_guids", false]], "delete_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file", false]], "delete_file_locations() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file_locations", false]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path", false]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node", false]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes", false]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object", false]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program", false]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project", false]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record", false]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record", false]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records", false]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download", false]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download", false]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download", false]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", "tools"]], "gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "get_access_token_from_wts"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "download_single"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"], [1, 1, 1, "", "upload_file_to_guid"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], 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11, "welcom": 2, "workspac": 13}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index a2154cd50..d84cb8c5e 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -381,7 +381,7 @@

Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730406946.6368155.log')[source]
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730474120.877882.log')[source]

Verify all file object records into a manifest csv

Parameters:
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 6038936a2..dd8b51ea1 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -102,7 +102,7 @@

Metadata Tools
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730406946.8912847.log', get_guid_from_file=True, metadata_type=None)[source]
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730474121.131172.log', get_guid_from_file=True, metadata_type=None)[source]

Ingest all metadata records into a manifest csv

Parameters:
From b953f6c40aa9003173ee2282b295a2fb76f459d6 Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Fri, 1 Nov 2024 10:17:54 -0500 Subject: [PATCH 07/10] remove duplicate line --- tests/test_post_indexing_validation.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_post_indexing_validation.py b/tests/test_post_indexing_validation.py index 8c04aa255..30738728c 100644 --- a/tests/test_post_indexing_validation.py +++ b/tests/test_post_indexing_validation.py @@ -22,7 +22,6 @@ class MockResponse: def __init__(self, status, ok=True, json={"url": "my_presigned_url"}): self.status = status self.ok = ok - self.status = status self.json_data = json async def text(self): From e3171a77e131ddb57b96da66d9d84b6dd115e634 Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Fri, 1 Nov 2024 15:18:58 +0000 Subject: [PATCH 08/10] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 447288 -> 447288 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100192 -> 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(gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_aliases", false]], "create_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_blank", false]], "create_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_index_key_path", false]], "create_job() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.create_job", false]], "create_new_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_new_version", false]], "create_object_list() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.create_object_list", false]], "create_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_program", false]], "create_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_project", false]], "create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_record", false]], "created_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.created_time", false]], "curl() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.curl", false]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR", false]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR", false]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete", false]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias", false]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases", false]], "delete_all_guids() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.delete_all_guids", false]], "delete_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file", false]], "delete_file_locations() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file_locations", false]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path", false]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node", false]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes", false]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object", false]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program", false]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project", false]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record", false]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record", false]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records", false]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download", false]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download", false]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download", false]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", 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"gen3.tools.download.drs_download.Downloadable.download", false]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download", false]], "download() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download", false]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest", false]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single", false]], "download_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.download_url", false]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable", false]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager", false]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus", false]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time", false]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint", false]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node", false]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record", false]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name", false]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name", false]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size", false]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size", false]], "gen3.tools": [[9, "module-gen3.tools", false]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download", false]], "gen3.tools.indexing.download_manifest": [[11, "module-gen3.tools.indexing.download_manifest", false]], "gen3.tools.indexing.index_manifest": [[11, "module-gen3.tools.indexing.index_manifest", false]], "gen3.tools.indexing.verify_manifest": [[11, "module-gen3.tools.indexing.verify_manifest", false]], "gen3.tools.metadata.ingest_manifest": [[12, "module-gen3.tools.metadata.ingest_manifest", false]], "gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth", false]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File", false]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index", false]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs", false]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata", false]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object", false]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query", false]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission", false]], "gen3wsstorage (class in gen3.wss)": [[13, "gen3.wss.Gen3WsStorage", false]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get", false]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get", false]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token", false]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts", false]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases", false]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records", false]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all", false]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node", false]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token", false]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema", false]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix", false]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths", false]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version", false]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output", false]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url", false]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs", false]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary", false]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest", false]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects", false]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record", false]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc", false]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records", false]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page", false]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats", false]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status", false]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls", false]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids", false]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version", false]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version", false]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version", false]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions", false]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params", false]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query", false]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID", false]], "guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT", false]], "guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT", false]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname", false]], "index_object_manifest() (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.index_object_manifest", false]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE", false]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy", false]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy", false]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy", false]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest", false]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object", false]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest", false]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs", false]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load", false]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest", false]], "ls() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls", false]], "ls_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.ls_path", false]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest", false]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS", false]], "max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)": [[12, "gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS", false]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5", false]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum", false]], "module": [[9, "module-gen3.tools", false], [10, "module-gen3.tools.download.drs_download", false], [11, "module-gen3.tools.indexing.download_manifest", false], [11, "module-gen3.tools.indexing.index_manifest", false], [11, "module-gen3.tools.indexing.verify_manifest", false], [12, "module-gen3.tools.metadata.ingest_manifest", false]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id", false]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id", false]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type", false]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project", false]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint", false]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID", false]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query", false]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query", false]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query", false]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls", false]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download", false]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token", false]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects", false]], "rm() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm", false]], "rm_path() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.rm_path", false]], "size (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.SIZE", false]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time", false]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status", false]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file", false]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record", false]], "threadcontrol (class in gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ThreadControl", false]], "tmp_folder (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.TMP_FOLDER", false]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update", false]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases", false]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank", false]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record", false]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time", false]], "upload() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload", false]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file", false]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid", false]], "upload_url() (gen3.wss.gen3wsstorage method)": [[13, "gen3.wss.Gen3WsStorage.upload_url", false]], "urls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.URLS", false]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access", false]]}, "objects": {"gen3": [[9, 3, 0, "-", "tools"]], "gen3.auth": [[0, 0, 1, "", "Gen3Auth"]], "gen3.auth.Gen3Auth": [[0, 1, 1, "", "curl"], [0, 1, 1, "", "get_access_token"], [0, 1, 1, "", "get_access_token_from_wts"], [0, 1, 1, "", "refresh_access_token"]], "gen3.file": [[1, 0, 1, "", "Gen3File"]], "gen3.file.Gen3File": [[1, 1, 1, "", "delete_file"], [1, 1, 1, "", "delete_file_locations"], [1, 1, 1, "", "download_single"], [1, 1, 1, "", "get_presigned_url"], [1, 1, 1, "", "upload_file"], [1, 1, 1, "", "upload_file_to_guid"]], "gen3.index": [[3, 0, 1, "", "Gen3Index"]], "gen3.index.Gen3Index": [[3, 1, 1, "", "async_create_record"], [3, 1, 1, "", "async_get_record"], [3, 1, 1, "", "async_get_records_from_checksum"], [3, 1, 1, "", "async_get_records_on_page"], [3, 1, 1, "", "async_get_with_params"], [3, 1, 1, "", "async_query_urls"], [3, 1, 1, "", "async_update_record"], [3, 1, 1, "", "create_blank"], [3, 1, 1, "", "create_new_version"], [3, 1, 1, "", "create_record"], [3, 1, 1, "", "delete_record"], [3, 1, 1, "", "get"], [3, 1, 1, "", "get_all_records"], [3, 1, 1, "", "get_guids_prefix"], [3, 1, 1, "", "get_latest_version"], [3, 1, 1, "", "get_record"], [3, 1, 1, "", "get_record_doc"], [3, 1, 1, "", "get_records"], [3, 1, 1, "", "get_records_on_page"], [3, 1, 1, "", "get_stats"], [3, 1, 1, "", "get_urls"], [3, 1, 1, "", "get_valid_guids"], [3, 1, 1, "", "get_version"], [3, 1, 1, "", "get_versions"], [3, 1, 1, "", "get_with_params"], [3, 1, 1, "", "is_healthy"], [3, 1, 1, "", "query_urls"], [3, 1, 1, "", "update_blank"], [3, 1, 1, "", "update_record"]], "gen3.jobs": [[4, 0, 1, "", "Gen3Jobs"]], "gen3.jobs.Gen3Jobs": [[4, 1, 1, "", "async_run_job_and_wait"], [4, 1, 1, "", "create_job"], [4, 1, 1, "", "get_output"], [4, 1, 1, "", "get_status"], [4, 1, 1, "", "get_version"], [4, 1, 1, "", "is_healthy"], [4, 1, 1, "", "list_jobs"]], "gen3.metadata": [[5, 0, 1, "", "Gen3Metadata"]], "gen3.metadata.Gen3Metadata": [[5, 1, 1, "", "async_create"], [5, 1, 1, "", "async_create_aliases"], [5, 1, 1, "", "async_delete_alias"], [5, 1, 1, "", "async_delete_aliases"], [5, 1, 1, "", "async_get"], [5, 1, 1, "", "async_get_aliases"], [5, 1, 1, "", "async_update"], [5, 1, 1, "", "async_update_aliases"], [5, 2, 1, "", "auth_provider"], [5, 1, 1, "", "batch_create"], [5, 1, 1, "", "create"], [5, 1, 1, "", "create_aliases"], [5, 1, 1, "", "create_index_key_path"], [5, 1, 1, "", "delete"], [5, 1, 1, "", "delete_alias"], [5, 1, 1, "", "delete_aliases"], [5, 1, 1, "", "delete_index_key_path"], [5, 2, 1, "", "endpoint"], [5, 1, 1, "", "get"], [5, 1, 1, "", "get_aliases"], [5, 1, 1, "", "get_index_key_paths"], [5, 1, 1, "", "get_version"], [5, 1, 1, "", "is_healthy"], [5, 1, 1, "", "query"], [5, 1, 1, "", "update"], [5, 1, 1, "", "update_aliases"]], "gen3.object": [[6, 0, 1, "", "Gen3Object"]], "gen3.object.Gen3Object": [[6, 1, 1, "", "delete_object"]], "gen3.query": [[7, 0, 1, "", "Gen3Query"]], "gen3.query.Gen3Query": [[7, 1, 1, "", "graphql_query"], [7, 1, 1, "", "query"], [7, 1, 1, "", "raw_data_download"]], "gen3.submission": [[8, 0, 1, "", "Gen3Submission"]], "gen3.submission.Gen3Submission": [[8, 1, 1, "", "create_program"], [8, 1, 1, "", "create_project"], [8, 1, 1, "", "delete_node"], [8, 1, 1, "", "delete_nodes"], [8, 1, 1, "", "delete_program"], [8, 1, 1, "", "delete_project"], [8, 1, 1, "", "delete_record"], [8, 1, 1, "", "delete_records"], [8, 1, 1, "", "export_node"], [8, 1, 1, "", "export_record"], [8, 1, 1, "", "get_dictionary_all"], [8, 1, 1, "", "get_dictionary_node"], [8, 1, 1, "", "get_graphql_schema"], [8, 1, 1, "", 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"path_to_manifest": 11, "pattern": [3, 12], "pdcdatastor": 11, "pend": 10, "per": [11, 12], "peregrin": 8, "permiss": 10, "persist": 9, "phs0001": 11, "phs0002": 11, "pick": 1, "pla": 11, "place": 11, "planx": 11, "point": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "popul": [10, 12], "posit": [1, 7], "possibl": 10, "post": [0, 11], "pprint": [2, 9, 10], "prefix": 3, "presign": 1, "pretti": 10, "prev_guid": [2, 9, 11], "previou": [3, 11], "previous": 4, "print": [8, 10], "process": 11, "processed_fil": 11, "profil": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "program": [8, 11], "progress": [8, 10], "project": [8, 11], "project_id": [7, 8], "protocol": 1, "provid": [0, 1, 3, 5, 7, 8, 12], "public": [3, 5], "put": 0, "py": 11, "python": [2, 9, 11], "python3": 11, "python_subprocess_command": 11, "queri": [1, 2, 3, 5, 8, 11, 12], "query_str": 7, "query_txt": [7, 8], "query_url": [2, 3], "quickstart": 2, "rather": 0, "raw": [7, 11], "raw_data_download": [2, 7], "rbac": 3, "read": [3, 5, 11], "readm": 2, "reason": 10, "record": [1, 3, 5, 7, 8, 11, 12], "refresh": [0, 10], "refresh_access_token": [0, 2], "refresh_fil": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "refresh_token": 0, "regist": 8, "regular": 7, "relat": 9, "remov": [1, 6, 11, 13], "replac": 11, "replace_url": 11, "repo": 2, "repres": [3, 5, 10], "represent": [1, 3], "request": [0, 1, 3, 5, 8, 11, 12], "requir": 10, "resolv": 10, "resolve_object": [2, 9, 10], "respect": 7, "respons": [0, 1, 3, 4, 5], "result": [1, 8, 10, 11], "retri": 8, "retriev": [1, 8, 10, 12], "return": [0, 1, 3, 4, 5, 6, 7, 8, 10, 11], "return_full_metadata": 5, "rev": 3, "revers": 8, "revis": 3, "right": 1, "rm": [2, 13], "rm_path": [2, 13], "root": [11, 12], "row": [7, 8, 11, 12], "row_offset": 8, "rtype": 3, "run": [8, 11], "s3": [1, 10, 11], "safe": 11, "same": [5, 11, 13], "sampl": [8, 10], "sandbox": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "save": 10, "save_directori": 10, "schema": 8, "scope": [0, 1], "screen": 8, "script": 2, "search": [0, 2, 3], "second": [1, 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"subject": [7, 8], "submiss": 2, "submit": [8, 11], "submit_additional_metadata_column": 11, "submit_fil": [2, 8], "submit_record": [2, 8], "submitter_id": 7, "success": 10, "successfulli": 10, "suffici": 3, "suppli": 3, "support": [0, 1, 5, 8, 11], "sure": 1, "synchron": 11, "syntax": 7, "system": [6, 7, 8, 9], "t": [1, 5, 11], "tab": 11, "task": 9, "temporari": 11, "test": 11, "test1": 11, "test2": 11, "test3": 11, "test4": 11, "test5": 11, "text": [1, 7, 8], "than": [0, 5], "thei": [0, 10], "them": [10, 11], "thi": [0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13], "those": 11, "thread": 11, "thread_num": 11, "threadcontrol": [2, 9, 11], "through": [8, 11], "tier": 7, "time": [1, 3, 8, 10, 11], "timestamp": 10, "tmp_folder": [2, 9, 11], "token": [0, 10], "tool": 2, "total": 11, "treat": [1, 5], "tree": 10, "true": [3, 4, 5, 6, 7, 8, 10, 11, 12], "try": 0, "tsv": [8, 11, 12], "tupl": [0, 3, 11, 12], "type": [1, 3, 4, 5, 7, 8, 10, 11, 12], "typic": 10, "uc": 7, "unaccess": 7, "under": [0, 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3, 7, 10, 12], "where": [0, 3, 5, 11, 12], "whether": [3, 4, 5, 8, 11, 12], "which": [8, 10], "while": [0, 1, 3, 4, 5, 6, 7, 8, 10, 13], "whose": 5, "within": [0, 2, 9], "without": [3, 5], "won": 5, "work": [0, 10], "workaround": 11, "worksheet": 8, "workspac": [0, 2], "wrapper": 10, "write": 11, "ws_urlstr": 13, "wskei": 13, "wss": 13, "wt": [0, 10], "x": 11, "xlsx": 8, "you": [0, 3, 8, 11], "your": 0}, "titles": ["Gen3 Auth Helper", "Gen3 File Class", "Welcome to Gen3 SDK\u2019s documentation!", "Gen3 Index Class", "Gen3 Jobs Class", "Gen3 Metadata Class", "Gen3 Object Class", "Gen3 Query Class", "Gen3 Submission Class", "Gen3 Tools", "DRS Download Tools", "Indexing Tools", "Metadata Tools", "Gen3 Workspace Storage"], "titleterms": {"": 2, "auth": 0, "class": [1, 3, 4, 5, 6, 7, 8], "document": 2, "download": [10, 11], "dr": 10, "file": 1, "gen3": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13], "helper": 0, "index": [3, 11], "indic": 2, "ingest": 12, "job": 4, "metadata": [5, 12], "object": 6, "queri": 7, "sdk": 2, "storag": 13, "submiss": 8, "tabl": 2, "tool": [9, 10, 11, 12], "verifi": 11, "welcom": 2, "workspac": 13}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index d84cb8c5e..0db027cab 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -381,7 +381,7 @@

Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730474120.877882.log')[source]
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730474334.0718453.log')[source]

Verify all file object records into a manifest csv

Parameters:
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index dd8b51ea1..687118881 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -102,7 +102,7 @@

Metadata Tools
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730474121.131172.log', get_guid_from_file=True, metadata_type=None)[source]
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730474334.3628798.log', get_guid_from_file=True, metadata_type=None)[source]

Ingest all metadata records into a manifest csv

Parameters:
From 106f05f13def4d9c75f98d80f6a54cbb25747c53 Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Fri, 1 Nov 2024 12:01:19 -0500 Subject: [PATCH 09/10] updating poetry.lock --- poetry.lock | 56 ++++++++++++++++++++--------------------------------- 1 file changed, 21 insertions(+), 35 deletions(-) diff --git a/poetry.lock b/poetry.lock index 77af0689d..08a6bcc6a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -773,18 +773,19 @@ resolved_reference = "38c0f1ab42edf3efb1ad6348d7dbdff81b131360" [[package]] name = "drsclient" -version = "0.2.3" +version = "0.3.0" description = "GA4GH DRS Client" optional = false -python-versions = ">=3.9,<4.0" +python-versions = "<4.0,>=3.9" files = [ - {file = "drsclient-0.2.3.tar.gz", hash = "sha256:679061eacfb04f7fdccf709924f03b907af024481eb4c9ff123d87080cf4f344"}, + {file = "drsclient-0.3.0-py3-none-any.whl", hash = "sha256:076d0c68afdfb229472e4de2867b7b773f279e968f1d6e45391d01c5fb6d28f1"}, + {file = "drsclient-0.3.0.tar.gz", hash = "sha256:bf1e53ad1e651cfd206f33bf1455eb12c505970ed81dea02c32c9e40a26d83a0"}, ] [package.dependencies] asyncio = ">=3.4.3,<4.0.0" backoff = ">=1.10.0,<2.0.0" -httpx = ">=0.23.0,<0.24.0" +httpx = ">=0.27.0,<0.28.0" requests = ">=2.23.0,<3.0.0" [[package]] @@ -1068,47 +1069,49 @@ resolved_reference = "f122072ee245216da5e4260f718d6f886db81773" [[package]] name = "httpcore" -version = "0.16.3" +version = "1.0.6" description = "A minimal low-level HTTP client." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "httpcore-0.16.3-py3-none-any.whl", hash = "sha256:da1fb708784a938aa084bde4feb8317056c55037247c787bd7e19eb2c2949dc0"}, - {file = "httpcore-0.16.3.tar.gz", hash = "sha256:c5d6f04e2fc530f39e0c077e6a30caa53f1451096120f1f38b954afd0b17c0cb"}, + {file = "httpcore-1.0.6-py3-none-any.whl", hash = "sha256:27b59625743b85577a8c0e10e55b50b5368a4f2cfe8cc7bcfa9cf00829c2682f"}, + {file = "httpcore-1.0.6.tar.gz", hash = "sha256:73f6dbd6eb8c21bbf7ef8efad555481853f5f6acdeaff1edb0694289269ee17f"}, ] [package.dependencies] -anyio = ">=3.0,<5.0" certifi = "*" h11 = ">=0.13,<0.15" -sniffio = "==1.*" [package.extras] +asyncio = ["anyio (>=4.0,<5.0)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] +trio = ["trio (>=0.22.0,<1.0)"] [[package]] name = "httpx" -version = "0.23.3" +version = "0.27.2" description = "The next generation HTTP client." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "httpx-0.23.3-py3-none-any.whl", hash = "sha256:a211fcce9b1254ea24f0cd6af9869b3d29aba40154e947d2a07bb499b3e310d6"}, - {file = "httpx-0.23.3.tar.gz", hash = "sha256:9818458eb565bb54898ccb9b8b251a28785dd4a55afbc23d0eb410754fe7d0f9"}, + {file = "httpx-0.27.2-py3-none-any.whl", hash = "sha256:7bb2708e112d8fdd7829cd4243970f0c223274051cb35ee80c03301ee29a3df0"}, + {file = "httpx-0.27.2.tar.gz", hash = "sha256:f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2"}, ] [package.dependencies] +anyio = "*" certifi = "*" -httpcore = ">=0.15.0,<0.17.0" -rfc3986 = {version = ">=1.3,<2", extras = ["idna2008"]} +httpcore = "==1.*" +idna = "*" sniffio = "*" [package.extras] brotli = ["brotli", "brotlicffi"] -cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<13)"] +cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] +zstd = ["zstandard (>=0.18.0)"] [[package]] name = "humanfriendly" @@ -2158,23 +2161,6 @@ requests = ">=2.22,<3" [package.extras] fixture = ["fixtures"] -[[package]] -name = "rfc3986" -version = "1.5.0" -description = "Validating URI References per RFC 3986" -optional = false -python-versions = "*" -files = [ - {file = "rfc3986-1.5.0-py2.py3-none-any.whl", hash = "sha256:a86d6e1f5b1dc238b218b012df0aa79409667bb209e58da56d0b94704e712a97"}, - {file = "rfc3986-1.5.0.tar.gz", hash = "sha256:270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835"}, -] - -[package.dependencies] -idna = {version = "*", optional = true, markers = "extra == \"idna2008\""} - -[package.extras] -idna2008 = ["idna"] - [[package]] name = "setuptools" version = "75.3.0" @@ -2535,4 +2521,4 @@ fhir = ["fhirclient"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <4" -content-hash = "ece63c924b844229d07ba0267a7e0ef7378cc97a3afc8ea0f704874829959fbe" +content-hash = "411ab09f8936af57b3b0b442f9d2c710e289c4ccf25470cfdb854ed4ebd9b268" From ba1610fe17f9754f1cce499d908a37e67c570449 Mon Sep 17 00:00:00 2001 From: jacob50231 Date: Fri, 1 Nov 2024 17:02:22 +0000 Subject: [PATCH 10/10] Apply automatic documentation changes --- docs/_build/doctrees/environment.pickle | Bin 447288 -> 447288 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 100197 -> 100192 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 35909 -> 35909 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 2 +- docs/_build/html/tools/metadata.html | 2 +- 6 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"auth": 0, "class": [1, 3, 4, 5, 6, 7, 8], "document": 2, "download": [10, 11], "dr": 10, "file": 1, "gen3": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13], "helper": 0, "index": [3, 11], "indic": 2, "ingest": 12, "job": 4, "metadata": [5, 12], "object": 6, "queri": 7, "sdk": 2, "storag": 13, "submiss": 8, "tabl": 2, "tool": [9, 10, 11, 12], "verifi": 11, "welcom": 2, "workspac": 13}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index 0db027cab..add013c7c 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -381,7 +381,7 @@

Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730474334.0718453.log')[source]
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1730480538.391207.log')[source]

Verify all file object records into a manifest csv

Parameters:
diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 687118881..ea6eb1537 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -102,7 +102,7 @@

Metadata Tools
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730474334.3628798.log', get_guid_from_file=True, metadata_type=None)[source]
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1730480538.6421762.log', get_guid_from_file=True, metadata_type=None)[source]

Ingest all metadata records into a manifest csv

Parameters: