Refactored Snakemake workflow and generate example output #41
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Updated the dockerfile to use a two stage process. Snakemake image is used as the runtime environment. Supports / Partially addresses #17
Updated snakemake workflow to work with Dockerfile. Also fixes module not found error by exposing pythonpath. Partially addresses #17
- Temporary fix for ValueError with multiple context URLs (#34) by returning empty context for URLs that don't match allowed_urls_pattern.
FromAsCasing - FROM and AS should be in the same case.
- Added get_max_id_from_files method. - If --workflow-ids argument is not provided, created_files.json should contain all workflows downloaded. get_max_id_from_files() finds the maximum ID in the sourced workflows. - Part of wider effort to address #17
Removes list_expected_files() method.
- Added progress bar and removed line-by-line logging for easier evaluation of download and processing progress. - Addresses #33
- Added preliminary module create_ro_crate to create an RO crate for a given file. - Addresses #37
- Added a rule in Snakemake workflow to create an RO crate. - Addresses #37
Addresses #37
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This PR primarily addresses: #37, #34, #33, #28, #17
The snakemake workflow consists of 3 main rules:
source_ro_cratessources the RO crates and checks their outputmerge_filescreates the merged.ttlfilecreate_ro_cratecreates thero-crate-metadata.jsonfileThe example
.ttlfile consists of all versions of all publicly accessible RO crates on WorkflowHub.