Add method to update pipeline image cache #63
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buehlere
reviewed
Jan 30, 2023
| def _get_cwl_apps(): | ||
| url = urljoin(BEAGLE_ENDPOINT, API['pipelines']) | ||
| params = dict() | ||
| params['page_size'] = 1000000 |
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I've seen some slow downs / bad responses when setting this parameter too high for the files system and runs endpoints. I don't think that should be an issue here since the pipelines list is relatively short. Nonetheless would we maybe want to make this an adjustable parameter somewhere? Magic numbers like these can sometimes be a bit tricky to track down when there's an issue.
| pipeline_folder = find_pipeline_folder.match(git_repo).group(1) | ||
| cwl_path = os.path.join(tmpDir, pipeline_folder, cwl) | ||
| if os.path.exists(cwl_path): | ||
| cache_command = "module load singularity/3.7.1; docker_extract.py -s {} {}".format( |
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Would we also maybe want to make the singularity version a parameter?
| @@ -75,6 +79,7 @@ Usage: | |||
| beaglecli files patch <file_id> [--file-path=<file_path>] [--file-type=<file_type>] [--file-group=<file_group_id>] [--metadata=<metadata>]... [--size=<size>] | |||
| beaglecli files list [--page-size=<page_size>] [--path=<path>]... [--metadata=<metadata>]... [--file-group=<file_group>]... [--file-name=<file_name>]... [--filename-regex=<filename_regex>] [--file-type=<file_type>]... [--all]... [--packaged]... [--force]... | |||
| beaglecli files delete --file-id=<file_id>... | |||
| beaglecli pipeline update-cache <cache_path> | |||
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I wouldn't mind trying the feature out on an example though. Is there a good cache path I could test it out on?
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