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ACED-IDP / gen3_util

Collection of command line tools to interact with a Gen3 instance
MIT License
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feature/manifest #23

Closed bwalsh closed 1 year ago

bwalsh commented 1 year ago

This PR:

For more, see doc

Dependencies:

matthewpeterkort commented 1 year ago

manifest export command appears to be missing object_id option

diff --git a/gen3_util/files/cli.py b/gen3_util/files/cli.py
index 784c449..b033375 100644
--- a/gen3_util/files/cli.py
+++ b/gen3_util/files/cli.py
@@ -137,6 +137,8 @@ def _manifest_upload(config: Config, project_id: str, profile: str, duplicate_ch
 @manifest_group.command(name="export")

 @click.option('--project_id', default=None, required=False, show_default=True,
               help="Gen3 program-project", envvar='PROJECT_ID')
+@click.option('--object_id', default=None, required=False, show_default=True,
+              help="file UUID", envvar='OBJECT_ID')
 @click.pass_obj
 def manifest_export(config: Config, project_id: str, object_id: str):
     """Export the local manifest
matthewpeterkort commented 1 year ago

There should be a command to delete everything in a manifest. That way if you mess up and add 100+ files you don't have to remove them individually or look in the source code to see where the manifest state is stored to delete that

matthewpeterkort commented 1 year ago

BUG when running:

gen3_util files manifest upload --manifest_path guppy/DocumentReference.new.ndjson --profile test --duplicate_check

Manifest with file name format: "file_name": "file:///output/clinical_reports/fa1f97.....6b8e9446a.txt" should ignore the file:///

and not error when uploading with:

Manfiest 2023/10/04 14:41:37 The file you specified "/Users/peterkor/Desktop/NEWGEN3/compose-services-training/gen3_util_test/gen3_util/demo_data/UCL_demo/file:///output/clinical_reports/fd83348...b0d7338.txt" does not exist locally.

bwalsh commented 1 year ago

Moved docs here: https://github.com/ACED-IDP/aced-idp.github.io/pull/1