Fix up FQ and race condition issues with volatile tasks work [VS-478] #7888
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RoriCremer
reviewed
Jun 9, 2022
| @@ -11,6 +11,8 @@ workflow GvsCreateAltAllele { | |||
| String? service_account_json_path | |||
| } | |||
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| String fq_alt_allele_table = "~{dataset_name}.alt_allele" | |||
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do we want project name in this too to keep it consistent?
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yup, that turns out to be a required fix.
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7888 +/- ##
================================================
Coverage ? 86.291%
Complexity ? 35196
================================================
Files ? 2170
Lines ? 164888
Branches ? 17785
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Hits ? 142284
Misses ? 16280
Partials ? 6324 |
mcovarr
changed the title
mcovarr
commented
Jun 10, 2022
| @@ -11,6 +11,8 @@ workflow GvsCreateAltAllele { | |||
| String? service_account_json_path | |||
| } | |||
|
|
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| String fq_alt_allele_table = "~{project_id}.~{dataset_name}.alt_allele" | |||
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bug 1: alt allele table must be fully qualified
| @@ -110,7 +110,7 @@ workflow GvsExtractCallset { | |||
| call Utils.GetBQTableLastModifiedDatetime as FilterSetInfoTimestamp { | |||
| input: | |||
| query_project = project_id, | |||
| fq_table = "filter_set_info", | |||
| fq_table = "~{fq_gvs_dataset}.filter_set_info", | |||
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bug 3: same as bug 1, BQ table name must be fully qualified here.
| @@ -27,8 +29,9 @@ workflow GvsCreateAltAllele { | |||
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| call Utils.GetBQTableLastModifiedDatetime { | |||
| input: | |||
| go = CreateAltAlleleTable.done, | |||
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bug 2: getting the last modified datetime of the alt allele table should run only after the alt allele table has been created
…non_fq_invocations
RoriCremer
approved these changes
Jun 10, 2022
This was referenced Mar 17, 2023
Closed
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Integration test successful https://app.terra.bio/#workspaces/broad-firecloud-dsde/VS-415%20GVS%20Quickstart%20Default%20Extract%20Scatter/job_history/73ac71db-0488-46be-a8e8-7f00e795edec