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Update ingest for VIDRL flat files #164

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Update ingest for VIDRL flat files #164

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d4eb286
read_flat_vidrl: add column map to script
joverlee521 Oct 8, 2024
3ac788f
read_flat_vidrl: Update column map
joverlee521 Oct 8, 2024
facbe78
read_flat_vidrl: replace pandas with csv module
joverlee521 Oct 8, 2024
5c80788
vidrl_upload: refactor human serum id to separate function
joverlee521 Oct 8, 2024
a9d4e14
read_flat_vidrl: standardize human sera strain/id/type
joverlee521 Oct 8, 2024
fd56875
read_flat_vidrl: Include "assay_date"
joverlee521 Oct 8, 2024
e5edcf3
read_flat_vidrl: Validate records
joverlee521 Oct 14, 2024
349c72f
vidrl_upload: refactor curate_flat_records
joverlee521 Oct 15, 2024
d16f37c
read_flat_vidrl: ingest reference_panel.csv file
joverlee521 Oct 15, 2024
ceff42b
read_flat_vidrl: Parse human serum passage from `reference passage`
joverlee521 Oct 16, 2024
fe2685c
read_flat_vidrl: Clean up `virus_strain` that includes "pool" suffix
joverlee521 Nov 4, 2024
ad39ce2
read_flat_vidrl: Check for potential duplicate _reference_panel files
joverlee521 Nov 5, 2024
10a5ad3
Update flat records column map
joverlee521 Nov 19, 2024
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6 changes: 0 additions & 6 deletions source-data/vidrl_flat_file_column_map.tsv
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22 changes: 12 additions & 10 deletions tdb/elife_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,18 +49,20 @@ def format_measurements(self, measurements, **kwargs):
self.format_subtype(meas)
self.format_assay_type(meas)
self.format_date(meas)
tmp = kwargs['fstem'].split('-')[0]
if len(tmp) > 8:
tmp = tmp[:(8-len(tmp))]
elif len(tmp) < 8:
meas['assay_date'] = "XXXX-XX-XX"
else:
if tmp[0:2] == '20':
meas['assay_date'] = "{}-{}-{}".format(tmp[0:4],tmp[4:6],tmp[6:8])
# Only overwrite the "assay_date" if it's not already available
if meas.get("assay_date", None) is None:
tmp = kwargs['fstem'].split('-')[0]
if len(tmp) > 8:
tmp = tmp[:(8-len(tmp))]
elif len(tmp) < 8:
meas['assay_date'] = "XXXX-XX-XX"
else:
if tmp[0:2] == '20':
meas['assay_date'] = "{}-{}-{}".format(tmp[0:4],tmp[4:6],tmp[6:8])
else:
meas['assay_date'] = "XXXX-XX-XX"
if 'assay_date' not in meas.keys() or meas['assay_date'] is None:
meas['assay_date'] = "XXXX-XX-XX"
if 'assay_date' not in meas.keys() or meas['assay_date'] is None:
meas['assay_date'] = "XXXX-XX-XX"
self.format_passage(meas, 'serum_passage', 'serum_passage_category')
self.format_passage(meas, 'virus_passage', 'virus_passage_category')
self.format_ref(meas)
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