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Integrate PPP specific evidence parsers with the other parsers #3477

Closed DSuveges closed 2 months ago

DSuveges commented 2 months ago

So far the data update, and therefore the evidence generation of the PPP was not particularly regular, which made the integration of these parsers not essential. Although the snakefile contained the rules to run these parsers, it gave the false impression that once we run the --until all rule, PPP evidence is also updated in the right buckets. But that was not the case.

Task:

DSuveges commented 2 months ago

From the parser's snakefile:

# At this point parsing the PPP datasources are not yet as integrated as to add these files to the complete set of output:
PPP_sources = [
    ('ot_crispr.json.gz', GS.remote(f"{config['OT_CRISPR']['outputBucket']}/ot_crispr-{timeStamp}.json.gz")),
    ('validation_lab.json.gz', GS.remote(f"{config['ValidationLab']['outputBucket']}/validation_lab-{timeStamp}.json.gz")),
    ('encore.json.gz', GS.remote(f"{config['Encore']['outputBucket']}/encore-{timeStamp}.json.gz"))
]