Restore withdrawn [VS-581] #8006
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8006 +/- ##
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Coverage ? 86.243%
Complexity ? 35201
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Files ? 2173
Lines ? 165004
Branches ? 17791
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Hits ? 142304
Misses ? 16373
Partials ? 6327 |
gbggrant
approved these changes
Aug 30, 2022
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| NUMROWS=$(python3 -c "csvObj=open('num_rows.csv','r');csvContents=csvObj.read();print(csvContents.split('\n')[1]);") | ||
| SELECT COUNT(*) FROM `~{fq_sample_table}` WHERE |
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I believe the input fq_sample_table_lastmodified_timestamp is no longer needed.
| help='File containing list of samples to extract, 1 per line. ' + | ||
| 'All samples in this file will be included in the cohort regardless of `withdrawn` status in the `sample_info` table.') | ||
| sample_args.add_argument('--fq_cohort_sample_names', type=str, | ||
| help='FQN of cohort table to extract, contains "sample_name" column. ' + |
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Please spell out FQN (I actually had to look it 😁 )
mcovarr
commented
Aug 30, 2022
| samples.sample_id NOT IN (SELECT sample_id FROM `~{dataset_name}.sample_load_status` WHERE status="FINISHED") AND | ||
| samples.withdrawn is NULL | ||
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| ' > sample_map |
mcovarr
commented
Aug 30, 2022
| SELECT IFNULL(MIN(sample_id),0) as min, IFNULL(MAX(sample_id),0) as max FROM `~{dataset_name}.~{table_name}` | ||
| AS samples JOIN `~{temp_table}` AS temp ON samples.sample_name = temp.sample_name | ||
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| ' > results |
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rsasch
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This was referenced Mar 17, 2023
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Putting this out for early review as I slowly continue to test the changes. 'Hide whitespace' highly recommended when viewing the diffs due to PEP8-fueled horizontal whitespace fixes in a couple of Python scripts.