clearer error when values are missing #7939
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #7939 +/- ##
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Coverage ? 86.241%
Complexity ? 35201
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Files ? 2173
Lines ? 165016
Branches ? 17792
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Hits ? 142311
Misses ? 16378
Partials ? 6327 |
mcovarr
approved these changes
Jul 25, 2022
| @@ -990,29 +990,38 @@ task ClinvarSignificance { | |||
| # "other", | |||
| # "not provided"] | |||
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| bq query --nouse_legacy_sql --project_id=~{query_project_id} --format=csv 'SELECT | |||
| bq query --nouse_legacy_sql --project_id=~{query_project_id} --format=csv 'SELECT | |||
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| echo "false" > ~{pf_file} | ||
| # if the result of the query has any rows, that means gvs_all_an has not been calculated correctly | ||
| if [[ $NUMRESULTS -ge 13 && $INCLUVALUES = "0" ]]; then | ||
| # if the result of the query less than 13 rows, that means clinvar_classification must not have all the expected values |
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Suggested change
| # if the result of the query less than 13 rows, that means clinvar_classification must not have all the expected values | |
| # If the result of the query has fewer than 13 rows, that means clinvar_classification must not have all the expected values. |
| # if the result of the query has any rows, that means gvs_all_an has not been calculated correctly | ||
| if [[ $NUMRESULTS -ge 13 && $INCLUVALUES = "0" ]]; then | ||
| # if the result of the query less than 13 rows, that means clinvar_classification must not have all the expected values | ||
| if [[ $NUMRESULTS -ge 13 && $NUMMISS = "0" ]]; then |
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Suggested change
| if [[ $NUMRESULTS -ge 13 && $NUMMISS = "0" ]]; then | |
| if [[ $NUMRESULTS -ge 13 && $NUMMISS -eq 0 ]]; then |
| index($0,"not provided"))}' bq_clinvar_classes.csv) | ||
| ~{fq_vat_table}, UNNEST(clinvar_classification) AS unnested_clinvar_classification'| sed "2 d" > bq_clinvar_classes.csv | ||
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| echo "affects" >> expected_clinvar_classes.csv |
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TOL this could be DRYed
echo 'affects
association
benign
.
.
.
uncertain significance' > expected_clinvar_classes.csv
gbggrant
approved these changes
Jul 26, 2022
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This was referenced Mar 17, 2023
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In the VAT validation, give clearer error msg about which clinvar classification values are missing