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Fix bad check for missing workflow name [VS-520] #7943

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merged 2 commits into from
Jul 14, 2022
Merged

Fix bad check for missing workflow name [VS-520] #7943

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0cc7067
Fix bad check for missing workflow name [VS-520]
mcovarr Jul 14, 2022
d6e0b9a
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mcovarr Jul 14, 2022
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3 changes: 1 addition & 2 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -231,8 +231,7 @@ workflows:
branches:
- master
- ah_var_store
- vs_475_read_cost_observability
- vs_518_throw_on_fiss_api_error
- cost_robustitude
- name: MitochondriaPipeline
subclass: WDL
primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsAssignIds.wdl
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Expand Up @@ -214,7 +214,7 @@ task CreateCostObservabilityTable {
fi
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
}
output {
Boolean done = true
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
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Expand Up @@ -264,7 +264,7 @@ task Add_AS_MAX_VQSLOD_ToVcf {
File input_vcf
String output_basename

String docker = "us.gcr.io/broad-dsde-methods/variantstore:rsa_metadata_from_python_20220628"
String docker = "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
Int cpu = 1
Int memory_mb = 3500
Int disk_size_gb = ceil(2*size(input_vcf, "GiB")) + 50
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCallsetCost.wdl
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Expand Up @@ -62,7 +62,7 @@ task WorkflowComputeCosts {
>>>

runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
}

output {
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateAltAllele.wdl
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Expand Up @@ -204,7 +204,7 @@ task PopulateAltAlleleTable {
$SERVICE_ACCOUNT_STANZA
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "3 GB"
disks: "local-disk 10 HDD"
cpu: 1
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsCreateVAT.wdl
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Expand Up @@ -155,7 +155,7 @@ task MakeSubpopulationFiles {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "1 GB"
preemptible: 3
cpu: "1"
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl
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Expand Up @@ -186,7 +186,7 @@ task ExtractAnAcAfFromVCF {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
maxRetries: 3
memory: "16 GB"
preemptible: 3
Expand Down Expand Up @@ -317,7 +317,7 @@ task PrepAnnotationJson {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "8 GB"
preemptible: 5
cpu: "1"
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl
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Expand Up @@ -92,7 +92,7 @@ task GetAnnotations {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "1 GB"
preemptible: 3
cpu: "1"
Expand Down Expand Up @@ -151,7 +151,7 @@ task PrepAnnotationJson {
# ------------------------------------------------
# Runtime settings:
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "8 GB"
preemptible: 5
cpu: "1"
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsImportGenomes.wdl
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Expand Up @@ -426,7 +426,7 @@ task CurateInputLists {
--output_files True
>>>
runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "3 GB"
disks: "local-disk 100 HDD"
bootDiskSizeGb: 15
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
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Expand Up @@ -116,7 +116,7 @@ task PrepareRangesCallsetTask {
}

runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
memory: "3 GB"
disks: "local-disk 100 HDD"
bootDiskSizeGb: 15
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsUtils.wdl
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Expand Up @@ -367,7 +367,7 @@ task ScaleXYBedValues {
}

runtime {
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_13"
docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_2022_07_14"
maxRetries: 3
memory: "7 GB"
preemptible: 3
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4 changes: 2 additions & 2 deletions scripts/variantstore/wdl/extract/workflow_compute_costs.py
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Expand Up @@ -47,11 +47,11 @@ def compute_costs(workspace_namespace, workspace_name, excluded_submission_ids,
workflow_ids = [w['workflowId'] for w in workflows]
for workflow_id in workflow_ids:
workflow = get_workflow_metadata(workspace_namespace, workspace_name, submission_id, workflow_id)
workflow_name = workflow['workflowName']
if not workflow_name:
if 'workflowName' not in workflow:
warning(f"Workflow {workflow_id} has no workflow name, skipping cost calculation.")
continue

workflow_name = workflow['workflowName']
if workflow_name.startswith('Gvs'):
if len(workflow_ids) == 1:
# If this run is < 1 day old the cost data may not yet be available.
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