feat: experiments results file ingestion #488
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v-rocheleau
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Mar 6, 2024
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davidlougheed
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #488 +/- ##
========================================
Coverage 88.34% 88.35%
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Files 128 128
Lines 4642 4645 +3
Branches 684 684
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+ Hits 4101 4104 +3
Misses 389 389
Partials 152 152 ☔ View full report in Codecov by Sentry. |
davidlougheed
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v-rocheleau
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davidlougheed
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davidlougheed
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davidlougheed
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Jun 18, 2024
| for experiment in data.get('experiments', []): | ||
| for result in experiment.get('experiment_results', []): | ||
| filename = result.get('filename', '') | ||
| file_path = '' |
| if filename in files: | ||
| file_found = True | ||
| file_path = os.path.join(root, filename) | ||
| path_list.append({'filename': filename, 'url': file_path}) |
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why is the file path key here "url"? should this be a "path"?
v-rocheleau
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Jun 19, 2024
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This PR introduces a new workflow that
-Accepts an input directory with experiment files, ensuring filenames match those in the experiment results JSON.
-Manages a json file containing experiment metadata and results to prepare for further processing.
-Downloads external resources referenced by URLs in the json to a temporary folder, preparing them for drs ingestion.
-Uploads the specified files to the DRS, creating DRS objects. https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.2.0/docs/
-Updates the experiment results json with drs URIs in the url field post-ingestion, directly linking experiment data to its DRS objects.
-After updating the JSON with new URLs, the experiments are ingested, completing the process.