From a68bd86c692c76a99fa4921d8356aceb5832e263 Mon Sep 17 00:00:00 2001 From: Alexander VanTol Date: Thu, 2 Dec 2021 15:27:09 -0600 Subject: [PATCH] feat(cli): add initial CLI support for object manifests (#97) * feat(cli): add initial CLI support for object manifests * Apply automatic documentation changes * Apply automatic documentation changes * feat(objects): add more options for click for manifests * Apply automatic documentation changes * Update gen3/tools/indexing/verify_manifest.py Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> * Apply automatic documentation changes * Apply automatic documentation changes * fix(jenkins): update to branch of jenkins lib to test fix * Apply automatic documentation changes * Update Jenkinsfile * feat(delete): add support for deleting GUIDs * Apply automatic documentation changes * fix(download_manifest): make download manifest deterministic, sort array-like columns * fix(python): use python3 * Apply automatic documentation changes * chore(deps): install fastavro * Apply automatic documentation changes * Update gen3/cli/objects.py Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> * Update gen3/cli/objects.py Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> * Apply automatic documentation changes * Update gen3/cli/objects.py Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> * Apply automatic documentation changes * fix(review): adjust based on review, cleanup logging, more performance parsing of GUID, remove unnecessary var * Apply automatic documentation changes * feat(objects): move delete guids out of CLI into SDK so it can be used by both * Apply automatic documentation changes Co-authored-by: Alexander VT Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> --- docs/_build/doctrees/environment.pickle | Bin 226070 -> 228285 bytes docs/_build/doctrees/tools/indexing.doctree | Bin 93366 -> 96031 bytes docs/_build/doctrees/tools/metadata.doctree | Bin 34281 -> 34281 bytes docs/_build/html/_modules/gen3/index.html | 3 +- .../tools/indexing/download_manifest.html | 15 +- .../gen3/tools/indexing/index_manifest.html | 46 + .../gen3/tools/indexing/verify_manifest.html | 2 + docs/_build/html/genindex.html | 2 + docs/_build/html/objects.inv | Bin 1441 -> 1454 bytes docs/_build/html/searchindex.js | 2 +- docs/_build/html/tools/indexing.html | 12 +- docs/_build/html/tools/metadata.html | 2 +- gen3/cli/__main__.py | 6 +- gen3/cli/objects.py | 274 +++++ gen3/index.py | 3 +- gen3/tools/indexing/__init__.py | 2 +- gen3/tools/indexing/download_manifest.py | 15 +- gen3/tools/indexing/index_manifest.py | 46 + gen3/tools/indexing/verify_manifest.py | 2 + poetry.lock | 1034 +++++++++-------- pyproject.toml | 3 +- tests/jenkinsSmoke.sh | 2 +- 22 files changed, 955 insertions(+), 516 deletions(-) create mode 100644 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xDIW)ry}#A@a5>i?Ru2OKplt17uEm( delta 92 zcmaFa&GfRHX~RJcep3qrBLj0&JxgOV6C(qo%@;HbSug|zbYoc21t(VR|7oq?F diff --git a/docs/_build/html/_modules/gen3/index.html b/docs/_build/html/_modules/gen3/index.html index 7f5236d3e..b36c644b8 100644 --- a/docs/_build/html/_modules/gen3/index.html +++ b/docs/_build/html/_modules/gen3/index.html @@ -773,7 +773,8 @@

Source code for gen3.index

 
         """
         rec = self.client.get(guid)
-        rec.delete()
+        if rec:
+            rec.delete()
         return rec
### Query Requests diff --git a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html index 498e969b1..4b921b15e 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html @@ -325,12 +325,21 @@

Source code for gen3.tools.indexing.download_manifest

manifest_row = [ record.get("did"), " ".join( - [url.replace(" ", "%20") for url in record.get("urls")] + sorted( + [url.replace(" ", "%20") for url in record.get("urls")] + ) ), " ".join( - [auth.replace(" ", "%20") for auth in record.get("authz")] + sorted( + [ + auth.replace(" ", "%20") + for auth in record.get("authz") + ] + ) + ), + " ".join( + sorted([a.replace(" ", "%20") for a in record.get("acl")]) ), - " ".join([a.replace(" ", "%20") for a in record.get("acl")]), record.get("hashes", {}).get("md5"), record.get("size"), record.get("file_name"), diff --git a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html index 5d9e49a59..9a8ecfd7d 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html @@ -74,6 +74,7 @@

Source code for gen3.tools.indexing.index_manifest

import sys import traceback +from gen3.index import Gen3Index from gen3.auth import Gen3Auth from gen3.tools.indexing.manifest_columns import ( GUID_COLUMN_NAMES, @@ -680,6 +681,51 @@

Source code for gen3.tools.indexing.index_manifest

logging.basicConfig(filename="index_object_manifest.log", level=logging.DEBUG) logging.getLogger().addHandler(logging.StreamHandler(sys.stdout)) index_object_manifest_cli() + + +
[docs]def delete_all_guids(auth, file): + """ + Delete all GUIDs specified in the object manifest. + + WARNING: THIS COMPLETELY REMOVES INDEX RECORDS. USE THIS ONLY IF YOU KNOW + THE IMPLICATIONS. + """ + index = Gen3Index(auth.endpoint, auth_provider=auth) + if not index.is_healthy(): + logging.debug( + f"uh oh! The indexing service is not healthy in the commons {auth.endpoint}" + ) + exit() + + # try to get delimeter based on file ext + file_ext = os.path.splitext(file) + if file_ext[-1].lower() == ".tsv": + manifest_file_delimiter = "\t" + else: + # default, assume CSV + manifest_file_delimiter = "," + + with open(file, "r", encoding="utf-8-sig") as input_file: + csvReader = csv.DictReader(input_file, delimiter=manifest_file_delimiter) + fieldnames = csvReader.fieldnames + + logging.debug(f"got fieldnames from {file}: {fieldnames}") + + # figure out which permutation of the name GUID is being used 1 time + # then use it for all future rows + guid_name = "guid" + for name in ["guid", "GUID", "did", "DID"]: + if name in fieldnames: + guid_name = name + + logging.debug(f"using {guid_name} to retrieve GUID to delete...") + + for row in csvReader: + guid = row.get(guid_name) + + if guid: + logging.debug(f"deleting GUID record:{guid}") + logging.debug(index.delete_record(guid=guid))
diff --git a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html index 115af1bae..b84e9a20f 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html @@ -247,6 +247,8 @@

Source code for gen3.tools.indexing.verify_manifest

# default, assume CSV manifest_file_delimiter = "," + logging.debug(f"detected {manifest_file_delimiter} as delimiter between columns") + await _verify_all_index_records_in_file( commons_url, manifest_file, diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index e8c64eb2b..4fbdee2b5 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -144,6 +144,8 @@

D

  • delete() (gen3.metadata.Gen3Metadata method) +
    • +
  • delete_all_guids() (in module gen3.tools.indexing.index_manifest)
  • delete_index_key_path() (gen3.metadata.Gen3Metadata method)
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Auth Helper","Gen3 File Class","Welcome to Gen3 SDK\u2019s documentation!","Gen3 Index Class","Gen3 Jobs Class","Gen3 Metadata Class","Gen3 Query Class","Gen3 Submission Class","Gen3 Tools","Indexing Tools","Metadata Tools","Gen3 Workspace Storage"],titleterms:{"class":[1,3,4,5,6,7],auth:0,document:2,download:9,file:1,gen3:[0,1,2,3,4,5,6,7,8,11],helper:0,index:[3,9],indic:2,ingest:10,job:4,metadata:[5,10],queri:6,sdk:2,storag:11,submiss:7,tabl:2,tool:[8,9,10],verifi:9,welcom:2,workspac:11}}) \ No newline at end of file diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index fd59dc846..34fae2529 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -228,6 +228,16 @@

    Indexing Tools +
    +gen3.tools.indexing.index_manifest.delete_all_guids(auth, file)[source]¶
    +

    Delete all GUIDs specified in the object manifest.

    +
    +
    WARNING: THIS COMPLETELY REMOVES INDEX RECORDS. USE THIS ONLY IF YOU KNOW

    THE IMPLICATIONS.

    +
    +
    +
    +
    gen3.tools.indexing.index_manifest.get_and_verify_fileinfos_from_manifest(manifest_file, include_additional_columns=False)[source]¶
    @@ -365,7 +375,7 @@

    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-1635802075.480863.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-1638375560.236531.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 8ef51ad0d..b9dca5ee3 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-1635802075.9364202.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-1638375560.7279043.log', get_guid_from_file=True, metadata_type=None)[source]¶

    Ingest all metadata records into a manifest csv

    Parameters
    diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py index 775e94061..b3dd8adfa 100644 --- a/gen3/cli/__main__.py +++ b/gen3/cli/__main__.py @@ -5,6 +5,7 @@ import gen3.cli.wss as wss import gen3.cli.discovery as discovery import gen3.cli.configure as configure +import gen3.cli.objects as objects import gen3 @@ -26,7 +27,7 @@ def get(self): "--auth", "auth_config", default=os.getenv("GEN3_API_KEY", None), - help="""authentication source: + help="""authentication source: "idp://wts/" is an identity provider in a Gen3 workspace, "accesstoken:///" is an access token, otherwise a path to an api key or basename of key under ~/.gen3/; @@ -41,7 +42,7 @@ def get(self): ) @click.pass_context def main(ctx=None, auth_config=None, endpoint=None): - """Gen3 sdk commands""" + """Gen3 Command Line Interface""" ctx.ensure_object(dict) ctx.obj["auth_config"] = auth_config ctx.obj["endpoint"] = endpoint @@ -53,5 +54,6 @@ def main(ctx=None, auth_config=None, endpoint=None): main.add_command(wss.wss) main.add_command(discovery.discovery) main.add_command(configure.configure) +main.add_command(objects.objects) main() diff --git a/gen3/cli/objects.py b/gen3/cli/objects.py new file mode 100644 index 000000000..6483b3fa5 --- /dev/null +++ b/gen3/cli/objects.py @@ -0,0 +1,274 @@ +import asyncio +import click +import csv +import logging +import os +import sys +from urllib.parse import urlparse + +from gen3.tools import indexing +from gen3.tools.indexing import ( + is_valid_manifest_format, + index_object_manifest, + delete_all_guids, +) +from gen3.tools.indexing.verify_manifest import manifest_row_parsers + + +@click.group() +def objects(): + """Commands for reading and editing objects""" + pass + + +@objects.group() +def manifest(): + """For working with minimal object metadata manifests""" + pass + + +@click.command( + help="Creates an object manifest of current data by reading from the Gen3 instance." +) +@click.option( + "--output-file", + "output_file", + default="object-manifest.csv", + help="filename for output", + type=click.Path(writable=True), +) +@click.option( + "--num-processes", + "num_processes", + default=4, + help="Number of parallel Python processes to start", + type=int, +) +@click.option( + "--max-concurrent-requests", + "max_concurrent_requests", + help="Maximum concurrent requests to Gen3", + default=24, + type=int, +) +@click.pass_context +def objects_manifest_read(ctx, output_file, num_processes, max_concurrent_requests): + auth = ctx.obj["auth_factory"].get() + loop = asyncio.get_event_loop() + click.echo(f"Getting minimal object metadata from {auth.endpoint}") + loop.run_until_complete( + indexing.async_download_object_manifest( + auth.endpoint, + output_filename=output_file, + num_processes=num_processes, + max_concurrent_requests=max_concurrent_requests, + ) + ) + click.echo(output_file) + + +@click.command( + help="Verifies that a Gen3 instance contains the data in the specified object manifest." +) +@click.argument("file", required=False) +@click.option( + "--max-concurrent-requests", + "max_concurrent_requests", + help="Maximum concurrent requests to Gen3", + default=24, + type=int, +) +@click.pass_context +def objects_manifest_verify(ctx, file, max_concurrent_requests): + auth = ctx.obj["auth_factory"].get() + loop = asyncio.get_event_loop() + + if not file: + file = click.prompt("Enter Discovery metadata file path to publish") + + click.echo(f"Verifying {file}...\n Against: {auth.endpoint}") + + loop = asyncio.new_event_loop() + asyncio.set_event_loop(loop) + + loop.run_until_complete( + indexing.async_verify_object_manifest( + auth.endpoint, + manifest_file=file, + max_concurrent_requests=max_concurrent_requests, + ) + ) + + +@click.command( + help="Validates that the format of the specified object manifest is correct." +) +@click.argument("file", required=False) +@click.option( + "--allowed-protocols", + "allowed_protocols", + help=""" + space-delimited string list of allowed protocols for url validation. (default: "s3 gs") + + Note that if allowed_protocols is provided, url values will only be + validated using the provided protocols (e.g. if + allowed_protocols="http https" an error would be raised when + validating "s3://valid_bucket/valid_key" url) + """, + default="s3 gs", +) +@click.option( + "--allow-base64-encoded-md5", + "allow_base64_encoded_md5", + help=""" + whether or not Base64 encoded md5 values are allowed. (default: False) + + if False, only hexadecimal encoded 128-bit md5 values are considered valid, + and Base64 encoded values will be logged as errors. + + if arg provided, both hexadecimal and Base64 encoded 128-bit md5 values are considered + valid + """, + is_flag=True, + default=False, +) +@click.option( + "--error-on-empty-url", + "error_on_empty_url", + help=""" + whether to treat completely empty url values as errors (default: False) + + for the following example manifest, if error_on_empty_url is False, + a warning would be logged for the completely empty url value on + line 2. if error_on_empty_url is True, an error would be generated + instead + ``` + md5,url,size + 1596f493ba9ec53023fca640fb69bd3b,,42 + ``` + + note that regardless of error_on_empty_url, errors will be + generated no matter what for arrays or quotes from which urls could + not be extracted. for example, for the following manifest, errors + would be generated for the url value on lines 2, 3, 4, and 5 + ``` + md5,url,size + 1596f493ba9ec53023fca640fb69bd30,"",42 + 1596f493ba9ec53023fca640fb69bd31,'',43 + 1596f493ba9ec53023fca640fb69bd32,[],44 + 1596f493ba9ec53023fca640fb69bd33,["", ""],45 + ``` + """, + is_flag=True, + default=False, +) +@click.option( + "--line-limit", + "line_limit", + help=""" + number of lines in manifest to validate including the header. if + not provided, every line is validated. (default: None) + + This can be helpful as a way to only attempt validation of a few rows to get + an idea if there are large format issues without needing to run against every + row in the manifest. + """, + default=None, + type=int, +) +@click.pass_context +def objects_manifest_validate_format( + ctx, + file, + allowed_protocols, + allow_base64_encoded_md5, + error_on_empty_url, + line_limit, +): + if not file: + file = click.prompt("Enter Discovery metadata file path to validate format for") + + is_valid = is_valid_manifest_format( + manifest_path=file, + column_names_to_enums=None, + allowed_protocols=allowed_protocols.split(" "), + allow_base64_encoded_md5=allow_base64_encoded_md5, + error_on_empty_url=error_on_empty_url, + line_limit=line_limit, + ) + + # non-zero exit code + if not is_valid: + sys.exit(1) + + +@click.command(help="Publishes specified object manifest to Gen3 instance.") +@click.argument("file", required=False) +@click.option( + "--thread-num", + "thread_num", + help="number of threads for indexing", + default=8, + type=int, +) +@click.option( + "--append-urls", + "append_urls", + help=""" + If supplied, will append urls for existing records. e.g. existing urls will + still exist and new ones will be added + + By default the newly provided urls will REPLACE existing urls + """, + is_flag=True, + default=False, +) +@click.pass_context +def objects_manifest_publish(ctx, file, thread_num, append_urls): + auth = ctx.obj["auth_factory"].get() + loop = asyncio.get_event_loop() + + if not file: + file = click.prompt("Enter Discovery metadata file path to publish") + + click.echo( + f"Publishing/writing object data from {file}...\n to: {auth.endpoint}" + ) + + index_object_manifest( + commons_url=auth.endpoint, + manifest_file=file, + thread_num=thread_num, + auth=auth, + replace_urls=not append_urls, + ) + + +@click.command(help="Deletes specified object manifest to Gen3 instance.") +@click.argument("file", required=True) +@click.pass_context +def objects_manifest_delete_all_guids(ctx, file): + auth = ctx.obj["auth_factory"].get() + loop = asyncio.get_event_loop() + + if not file: + file = click.prompt("Enter Discovery metadata file path to delete") + + click.echo(f" DELETING ALL GUIDS\n from: {file}\n in: {auth.endpoint}") + click.confirm( + f"Are you sure you want to DELETE ALL GUIDS in {auth.endpoint} as specified by this file: {file}?", + abort=True, + ) + click.confirm( + f"Please confirm again, this is irreversible. All GUIDs specified specified in {file} will be deleted from {auth.endpoint}. You are sure?", + abort=True, + ) + + delete_all_guids(auth, file) + + +manifest.add_command(objects_manifest_read, name="read") +manifest.add_command(objects_manifest_verify, name="verify") +manifest.add_command(objects_manifest_validate_format, name="validate-manifest-format") +manifest.add_command(objects_manifest_publish, name="publish") +manifest.add_command(objects_manifest_delete_all_guids, name="delete-all-guids") diff --git a/gen3/index.py b/gen3/index.py index fc0dac3ce..a50b1a297 100755 --- a/gen3/index.py +++ b/gen3/index.py @@ -740,7 +740,8 @@ def delete_record(self, guid): """ rec = self.client.get(guid) - rec.delete() + if rec: + rec.delete() return rec ### Query Requests diff --git a/gen3/tools/indexing/__init__.py b/gen3/tools/indexing/__init__.py index 9cb79940b..5c8556994 100644 --- a/gen3/tools/indexing/__init__.py +++ b/gen3/tools/indexing/__init__.py @@ -1,5 +1,5 @@ from gen3.tools.indexing.download_manifest import async_download_object_manifest from gen3.tools.indexing.verify_manifest import async_verify_object_manifest -from gen3.tools.indexing.index_manifest import index_object_manifest +from gen3.tools.indexing.index_manifest import index_object_manifest, delete_all_guids from gen3.tools.indexing.merge_manifests import merge_bucket_manifests from gen3.tools.indexing.validate_manifest_format import is_valid_manifest_format diff --git a/gen3/tools/indexing/download_manifest.py b/gen3/tools/indexing/download_manifest.py index a5bceb8ef..58810ea4c 100644 --- a/gen3/tools/indexing/download_manifest.py +++ b/gen3/tools/indexing/download_manifest.py @@ -292,12 +292,21 @@ async def _parse_from_queue(queue): manifest_row = [ record.get("did"), " ".join( - [url.replace(" ", "%20") for url in record.get("urls")] + sorted( + [url.replace(" ", "%20") for url in record.get("urls")] + ) ), " ".join( - [auth.replace(" ", "%20") for auth in record.get("authz")] + sorted( + [ + auth.replace(" ", "%20") + for auth in record.get("authz") + ] + ) + ), + " ".join( + sorted([a.replace(" ", "%20") for a in record.get("acl")]) ), - " ".join([a.replace(" ", "%20") for a in record.get("acl")]), record.get("hashes", {}).get("md5"), record.get("size"), record.get("file_name"), diff --git a/gen3/tools/indexing/index_manifest.py b/gen3/tools/indexing/index_manifest.py index 9e24da614..6f7e2d1cc 100644 --- a/gen3/tools/indexing/index_manifest.py +++ b/gen3/tools/indexing/index_manifest.py @@ -41,6 +41,7 @@ import sys import traceback +from gen3.index import Gen3Index from gen3.auth import Gen3Auth from gen3.tools.indexing.manifest_columns import ( GUID_COLUMN_NAMES, @@ -647,3 +648,48 @@ def index_object_manifest_cli( logging.basicConfig(filename="index_object_manifest.log", level=logging.DEBUG) logging.getLogger().addHandler(logging.StreamHandler(sys.stdout)) index_object_manifest_cli() + + +def delete_all_guids(auth, file): + """ + Delete all GUIDs specified in the object manifest. + + WARNING: THIS COMPLETELY REMOVES INDEX RECORDS. USE THIS ONLY IF YOU KNOW + THE IMPLICATIONS. + """ + index = Gen3Index(auth.endpoint, auth_provider=auth) + if not index.is_healthy(): + logging.debug( + f"uh oh! The indexing service is not healthy in the commons {auth.endpoint}" + ) + exit() + + # try to get delimeter based on file ext + file_ext = os.path.splitext(file) + if file_ext[-1].lower() == ".tsv": + manifest_file_delimiter = "\t" + else: + # default, assume CSV + manifest_file_delimiter = "," + + with open(file, "r", encoding="utf-8-sig") as input_file: + csvReader = csv.DictReader(input_file, delimiter=manifest_file_delimiter) + fieldnames = csvReader.fieldnames + + logging.debug(f"got fieldnames from {file}: {fieldnames}") + + # figure out which permutation of the name GUID is being used 1 time + # then use it for all future rows + guid_name = "guid" + for name in ["guid", "GUID", "did", "DID"]: + if name in fieldnames: + guid_name = name + + logging.debug(f"using {guid_name} to retrieve GUID to delete...") + + for row in csvReader: + guid = row.get(guid_name) + + if guid: + logging.debug(f"deleting GUID record:{guid}") + logging.debug(index.delete_record(guid=guid)) diff --git a/gen3/tools/indexing/verify_manifest.py b/gen3/tools/indexing/verify_manifest.py index 19d189f39..cfc45402e 100644 --- a/gen3/tools/indexing/verify_manifest.py +++ b/gen3/tools/indexing/verify_manifest.py @@ -214,6 +214,8 @@ async def async_verify_object_manifest( # default, assume CSV manifest_file_delimiter = "," + logging.debug(f"detected {manifest_file_delimiter} as delimiter between columns") + await _verify_all_index_records_in_file( commons_url, manifest_file, diff --git a/poetry.lock b/poetry.lock index d2c823466..e3e91e3e4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -8,7 +8,7 @@ python-versions = "*" [[package]] name = "aiohttp" -version = "3.7.3" +version = "3.7.4.post0" description = "Async http client/server framework (asyncio)" category = "main" optional = false @@ -17,7 +17,7 @@ python-versions = ">=3.6" [package.dependencies] async-timeout = ">=3.0,<4.0" attrs = ">=17.3.0" -chardet = ">=2.0,<4.0" +chardet = ">=2.0,<5.0" idna-ssl = {version = ">=1.0", markers = "python_version < \"3.7\""} multidict = ">=4.5,<7.0" typing-extensions = ">=3.6.5" @@ -60,21 +60,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "20.3.0" +version = "21.2.0" description = "Classes Without Boilerplate" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"] -docs = ["furo", "sphinx", "zope.interface"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"] +docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] [[package]] name = "authlib" -version = "0.15.2" +version = "0.15.4" description = "The ultimate Python library in building OAuth and OpenID Connect servers." category = "dev" optional = false @@ -109,7 +109,7 @@ xmltodict = ">=0.9,<1.0" [[package]] name = "babel" -version = "2.9.0" +version = "2.9.1" description = "Internationalization utilities" category = "dev" optional = false @@ -120,7 +120,7 @@ pytz = ">=2015.7" [[package]] name = "backoff" -version = "1.10.0" +version = "1.11.1" description = "Function decoration for backoff and retry" category = "main" optional = false @@ -138,7 +138,7 @@ python-versions = "*" name = "cdiserrors" version = "0.1.2" description = "The auth system for the gdcapi." -category = "dev" +category = "main" optional = false python-versions = "*" @@ -172,7 +172,7 @@ resolved_reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024" [[package]] name = "certifi" -version = "2020.12.5" +version = "2021.5.30" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -180,7 +180,7 @@ python-versions = "*" [[package]] name = "cffi" -version = "1.14.4" +version = "1.14.6" description = "Foreign Function Interface for Python calling C code." category = "dev" optional = false @@ -191,25 +191,40 @@ pycparser = "*" [[package]] name = "chardet" -version = "3.0.4" +version = "4.0.0" description = "Universal encoding detector for Python 2 and 3" category = "main" optional = false -python-versions = "*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[[package]] +name = "charset-normalizer" +version = "2.0.6" +description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" +optional = false +python-versions = ">=3.5.0" + +[package.extras] +unicode_backport = ["unicodedata2"] [[package]] name = "click" -version = "7.1.2" +version = "8.0.1" description = "Composable command line interface toolkit" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "colorama" version = "0.4.4" description = "Cross-platform colored terminal text." -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" @@ -226,50 +241,37 @@ immutables = ">=0.9" [[package]] name = "cryptography" -version = "3.3.1" +version = "3.4.8" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." category = "dev" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" +python-versions = ">=3.6" [package.dependencies] cffi = ">=1.12" -six = ">=1.4.1" [package.extras] docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"] docstest = ["doc8", "pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"] pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"] +sdist = ["setuptools-rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] -test = ["pytest (>=3.6.0,!=3.9.0,!=3.9.1,!=3.9.2)", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] +test = ["pytest (>=6.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] [[package]] name = "debtcollector" -version = "2.2.0" +version = "2.3.0" description = "A collection of Python deprecation patterns and strategies that help you collect your technical debt in a non-destructive manner." category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] +importlib-metadata = {version = ">=1.7.0", markers = "python_version < \"3.8\""} pbr = ">=2.0.0,<2.1.0 || >2.1.0" six = ">=1.10.0" wrapt = ">=1.7.0" -[[package]] -name = "dictionaryutils" -version = "3.0.0" -description = "" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -cdislogging = ">=1.0,<2.0" -jsonschema = ">=2.5.1" -PyYAML = ">=5.1,<6.0" -requests = ">=2.18,<3.0" - [[package]] name = "doiclient" version = "0.1" @@ -323,7 +325,7 @@ requests = ">=2.23.0,<3.0.0" [[package]] name = "fastavro" -version = "1.2.1" +version = "1.4.7" description = "Fast read/write of AVRO files" category = "main" optional = false @@ -339,7 +341,7 @@ zstandard = ["zstandard"] name = "flask" version = "1.1.1" description = "A simple framework for building complex web applications." -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" @@ -354,19 +356,6 @@ dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxco docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] dotenv = ["python-dotenv"] -[[package]] -name = "gdcdictionary" -version = "1.2.0" -description = "Gen3 generic data dictionary" -category = "main" -optional = false -python-versions = "*" - -[package.dependencies] -dictionaryutils = "*" -jsonschema = ">=2.5.1" -PyYAML = ">=5.1,<6.0" - [[package]] name = "gen3authz" version = "0.4.0" @@ -441,11 +430,11 @@ http2 = ["h2 (>=3.0.0,<4.0.0)"] [[package]] name = "idna" -version = "2.10" +version = "3.2" description = "Internationalized Domain Names in Applications (IDNA)" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.5" [[package]] name = "idna-ssl" @@ -460,40 +449,49 @@ idna = ">=2.0" [[package]] name = "immutables" -version = "0.14" +version = "0.16" description = "Immutable Collections" category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" + +[package.dependencies] +typing-extensions = {version = ">=3.7.4.3", markers = "python_version < \"3.8\""} + +[package.extras] +test = ["flake8 (>=3.8.4,<3.9.0)", "pycodestyle (>=2.6.0,<2.7.0)", "mypy (>=0.910)", "pytest (>=6.2.4,<6.3.0)"] [[package]] name = "importlib-metadata" -version = "1.7.0" +version = "4.8.1" description = "Read metadata from Python packages" category = "main" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] +typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} zipp = ">=0.5" [package.extras] -docs = ["sphinx", "rst.linker"] -testing = ["packaging", "pep517", "importlib-resources (>=1.3)"] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +perf = ["ipython"] +testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" -version = "3.3.0" +version = "5.2.2" description = "Read resources from Python packages" category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" +python-versions = ">=3.6" [package.dependencies] -zipp = {version = ">=0.4", markers = "python_version < \"3.8\""} +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["sphinx", "rst.linker", "jaraco.packaging"] +docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"] [[package]] name = "indexclient" @@ -545,7 +543,7 @@ python-versions = "*" [[package]] name = "iso8601" -version = "0.1.13" +version = "0.1.16" description = "Simple module to parse ISO 8601 dates" category = "dev" optional = false @@ -553,25 +551,25 @@ python-versions = "*" [[package]] name = "itsdangerous" -version = "1.1.0" -description = "Various helpers to pass data to untrusted environments and back." -category = "dev" +version = "2.0.1" +description = "Safely pass data to untrusted environments and back." +category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [[package]] name = "jinja2" -version = "2.11.2" +version = "3.0.1" description = "A very fast and expressive template engine." -category = "dev" +category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" [package.dependencies] -MarkupSafe = ">=0.23" +MarkupSafe = ">=2.0" [package.extras] -i18n = ["Babel (>=0.8)"] +i18n = ["Babel (>=2.7)"] [[package]] name = "jsonschema" @@ -586,15 +584,15 @@ format = ["rfc3987", "strict-rfc3339", "webcolors"] [[package]] name = "markupsafe" -version = "1.1.1" +version = "2.0.1" description = "Safely add untrusted strings to HTML/XML markup." -category = "dev" +category = "main" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=3.6" [[package]] name = "msgpack" -version = "1.0.1" +version = "1.0.2" description = "MessagePack (de)serializer." category = "dev" optional = false @@ -621,7 +619,7 @@ importlib-resources = {version = "*", markers = "python_version < \"3.7\""} [[package]] name = "netifaces" -version = "0.10.9" +version = "0.11.0" description = "Portable network interface information." category = "dev" optional = false @@ -629,7 +627,7 @@ python-versions = "*" [[package]] name = "numpy" -version = "1.19.4" +version = "1.19.5" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -637,7 +635,7 @@ python-versions = ">=3.6" [[package]] name = "oslo.config" -version = "8.4.0" +version = "8.7.1" description = "Oslo Configuration API" category = "dev" optional = false @@ -648,7 +646,7 @@ debtcollector = ">=1.2.0" importlib-metadata = {version = ">=1.7.0", markers = "python_version < \"3.8\""} netaddr = ">=0.7.18" "oslo.i18n" = ">=3.15.3" -PyYAML = ">=3.12" +PyYAML = ">=5.1" requests = ">=2.18.0" rfc3986 = ">=1.2.0" stevedore = ">=1.20.0" @@ -659,7 +657,7 @@ test = ["bandit (>=1.6.0,<1.7.0)", "coverage (>=4.0,!=4.4)", "fixtures (>=3.0.0) [[package]] name = "oslo.i18n" -version = "5.0.1" +version = "5.1.0" description = "Oslo i18n library" category = "dev" optional = false @@ -667,11 +665,10 @@ python-versions = ">=3.6" [package.dependencies] pbr = ">=2.0.0,<2.1.0 || >2.1.0" -six = ">=1.10.0" [[package]] name = "oslo.serialization" -version = "4.0.1" +version = "4.2.0" description = "Oslo Serialization library" category = "dev" optional = false @@ -685,7 +682,7 @@ pytz = ">=2013.6" [[package]] name = "oslo.utils" -version = "4.7.0" +version = "4.10.0" description = "Oslo Utility library" category = "dev" optional = false @@ -701,15 +698,14 @@ packaging = ">=20.4" pbr = ">=2.0.0,<2.1.0 || >2.1.0" pyparsing = ">=2.1.0" pytz = ">=2013.6" -six = ">=1.10.0" [[package]] name = "packaging" -version = "20.8" +version = "21.0" description = "Core utilities for Python packages" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] pyparsing = ">=2.0.2" @@ -732,7 +728,7 @@ test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"] [[package]] name = "pbr" -version = "5.5.1" +version = "5.6.0" description = "Python Build Reasonableness" category = "dev" optional = false @@ -740,17 +736,18 @@ python-versions = ">=2.6" [[package]] name = "pluggy" -version = "0.13.1" +version = "1.0.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} [package.extras] dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "prettytable" @@ -762,11 +759,11 @@ python-versions = "*" [[package]] name = "psycopg2" -version = "2.8.6" +version = "2.9.1" description = "psycopg2 - Python-PostgreSQL Database Adapter" category = "dev" optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +python-versions = ">=3.6" [[package]] name = "py" @@ -807,24 +804,18 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "pypfb" -version = "0.5.0" +version = "0.1.0" description = "Python SDK for PFB format" category = "main" optional = false -python-versions = 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[tool.poetry] name = "gen3" homepage = "https://gen3.org/" -version = "4.2.0" +version = "4.4.0" description = "Gen3 CLI and Python SDK" authors = ["Center for Translational Data Science at the University of Chicago "] license = "Apache-2.0" @@ -27,6 +27,7 @@ backoff = "*" click = "*" pandas = "*" pypfb = "<1.0.0" +fastavro = "^1.4.7" [tool.poetry.dev-dependencies] pytest = ">=3.2.3" diff --git a/tests/jenkinsSmoke.sh b/tests/jenkinsSmoke.sh index 39a42b537..ab9efd15c 100644 --- a/tests/jenkinsSmoke.sh +++ b/tests/jenkinsSmoke.sh @@ -15,6 +15,6 @@ export PATH="/var/jenkins_home/.local/bin:$PATH" export GEN3_API_KEY="accesstoken:///$(gen3 api access-token cdis.autotest@gmail.com)" poetry config virtualenvs.path "${WORKSPACE}/pysdkvirtenv" --local -poetry env use python3.8 +poetry env use python3 poetry install -vv poetry run bash tests/smokeTest.sh test-all