From 0cc7067c53e4a0e25b521b24386a61c8c6eea006 Mon Sep 17 00:00:00 2001 From: Miguel Covarrubias Date: Thu, 14 Jul 2022 14:02:04 -0400 Subject: [PATCH 1/2] Fix bad check for missing workflow name [VS-520] --- scripts/variantstore/wdl/extract/workflow_compute_costs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/extract/workflow_compute_costs.py b/scripts/variantstore/wdl/extract/workflow_compute_costs.py index e74e8ab266b..19eed2a1bbb 100644 --- a/scripts/variantstore/wdl/extract/workflow_compute_costs.py +++ b/scripts/variantstore/wdl/extract/workflow_compute_costs.py @@ -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. From d6e0b9afa27d1f84b72725a194296abdd70ea5d4 Mon Sep 17 00:00:00 2001 From: Miguel Covarrubias Date: Thu, 14 Jul 2022 14:13:58 -0400 Subject: [PATCH 2/2] docker references --- .dockstore.yml | 3 +-- scripts/variantstore/wdl/GvsAssignIds.wdl | 2 +- .../variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl | 2 +- scripts/variantstore/wdl/GvsCallsetCost.wdl | 2 +- scripts/variantstore/wdl/GvsCreateAltAllele.wdl | 2 +- scripts/variantstore/wdl/GvsCreateVAT.wdl | 2 +- scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl | 4 ++-- scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl | 4 ++-- scripts/variantstore/wdl/GvsImportGenomes.wdl | 2 +- scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl | 2 +- scripts/variantstore/wdl/GvsUtils.wdl | 2 +- 11 files changed, 13 insertions(+), 14 deletions(-) diff --git a/.dockstore.yml b/.dockstore.yml index b5eec8c9996..fddf8458f22 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -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 diff --git a/scripts/variantstore/wdl/GvsAssignIds.wdl b/scripts/variantstore/wdl/GvsAssignIds.wdl index 034e7c0c381..3acd3b027e6 100644 --- a/scripts/variantstore/wdl/GvsAssignIds.wdl +++ b/scripts/variantstore/wdl/GvsAssignIds.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl b/scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl index 2d96415f35f..becca84600a 100644 --- a/scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl +++ b/scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsCallsetCost.wdl b/scripts/variantstore/wdl/GvsCallsetCost.wdl index b414ea688a6..71ac9778bf7 100644 --- a/scripts/variantstore/wdl/GvsCallsetCost.wdl +++ b/scripts/variantstore/wdl/GvsCallsetCost.wdl @@ -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 { diff --git a/scripts/variantstore/wdl/GvsCreateAltAllele.wdl b/scripts/variantstore/wdl/GvsCreateAltAllele.wdl index 1ef602e2aaf..af8e05320c6 100644 --- a/scripts/variantstore/wdl/GvsCreateAltAllele.wdl +++ b/scripts/variantstore/wdl/GvsCreateAltAllele.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsCreateVAT.wdl b/scripts/variantstore/wdl/GvsCreateVAT.wdl index f46f6b55541..01110a612f0 100644 --- a/scripts/variantstore/wdl/GvsCreateVAT.wdl +++ b/scripts/variantstore/wdl/GvsCreateVAT.wdl @@ -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" diff --git a/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl b/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl index 0155d249bc3..008982cf756 100644 --- a/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl +++ b/scripts/variantstore/wdl/GvsCreateVATAnnotations.wdl @@ -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 @@ -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" diff --git a/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl b/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl index b1965fb4035..a143836bf43 100644 --- a/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl +++ b/scripts/variantstore/wdl/GvsCreateVATFromAnnotations.wdl @@ -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" @@ -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" diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl index 041b1a1dc8a..42e46f507fe 100644 --- a/scripts/variantstore/wdl/GvsImportGenomes.wdl +++ b/scripts/variantstore/wdl/GvsImportGenomes.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl b/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl index 3b1f20037d3..cebef00195f 100644 --- a/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl +++ b/scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl @@ -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 diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl index 4e577a022e4..a4f30c9381a 100644 --- a/scripts/variantstore/wdl/GvsUtils.wdl +++ b/scripts/variantstore/wdl/GvsUtils.wdl @@ -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