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Ingest Error Handling Fixes [VS-261] #7841
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,151 @@ | ||
| version 1.0 | ||
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| import "GvsAssignIds.wdl" as GvsAssignIds | ||
| import "GvsImportGenomes.wdl" as GvsImportGenomes | ||
| import "GvsUtils.wdl" as GvsUtils | ||
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| workflow GvsIngestTieout { | ||
| input { | ||
| String project | ||
| String reference_dataset_name | ||
| String branch_name | ||
| Array[String] sample_names | ||
| Array[File] input_vcfs | ||
| Array[File] input_vcf_indexes | ||
| String? service_account_json_path | ||
| } | ||
|
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| call GvsUtils.BuildGATKJarAndCreateDataset { | ||
| input: | ||
| branch_name = branch_name, | ||
| dataset_prefix = "ingest_tieout" | ||
| } | ||
|
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| call GvsAssignIds.GvsAssignIds { | ||
| input: | ||
| project_id = project, | ||
| dataset_name = BuildGATKJarAndCreateDataset.dataset_name, | ||
| external_sample_names = sample_names, | ||
| assign_ids_gatk_override = BuildGATKJarAndCreateDataset.jar, | ||
| service_account_json_path = service_account_json_path | ||
| } | ||
|
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| call GvsImportGenomes.GvsImportGenomes { | ||
| input: | ||
| go = GvsAssignIds.done, | ||
| dataset_name = BuildGATKJarAndCreateDataset.dataset_name, | ||
| project_id = project, | ||
| external_sample_names = sample_names, | ||
| input_vcfs = input_vcfs, | ||
| input_vcf_indexes = input_vcf_indexes, | ||
| load_data_gatk_override = BuildGATKJarAndCreateDataset.jar, | ||
| service_account_json_path = service_account_json_path | ||
| } | ||
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| call IngestTieout { | ||
| input: | ||
| dataset_name = BuildGATKJarAndCreateDataset.dataset_name, | ||
| reference_dataset_name = reference_dataset_name, | ||
| project = project, | ||
| stderrs = GvsImportGenomes.load_data_stderrs | ||
| } | ||
| } | ||
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| task IngestTieout { | ||
| input { | ||
| Boolean? go | ||
| String dataset_name | ||
| String reference_dataset_name | ||
| String project | ||
| Array[File] stderrs | ||
| } | ||
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| parameter_meta { | ||
| stderrs: { | ||
| localization_optional: true | ||
| } | ||
| } | ||
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| command <<< | ||
| set -o xtrace | ||
| fail=0 | ||
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| check_table() { | ||
| local table_name=$1 | ||
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| bq query --location=US --project_id=~{project} --format=csv --use_legacy_sql=false \ | ||
| "select actual.sample_id, expected.sample_id from | ||
| (select sample_id, count(*) as count from \`spec-ops-aou.~{dataset_name}.${table_name}\` group by sample_id) actual full outer join | ||
| (select sample_id, count(*) as count from \`spec-ops-aou.~{reference_dataset_name}.${table_name}\` group by sample_id) expected on actual.sample_id = expected.sample_id | ||
| where actual.count != expected.count OR actual.sample_id is null OR expected.sample_id is null" > differences.txt | ||
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| if [[ -s differences.txt ]]; then | ||
| fail=1 | ||
| echo "${table_name} row counts are mismatched for the following samples:" | ||
| cat differences.txt | ||
| fi | ||
| } | ||
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| # This task is currently being called with a sample set of 2000 so it only needs to check a single vet and | ||
| # ref_ranges table each. If this code were to be called with a sample set of more than 4000 it should test all | ||
| # the additional vet and ref_ranges tables that would be introduced. | ||
| if [[ ~{length(stderrs)} -gt 4000 ]]; then | ||
| echo "IngestTieout invoked with a sample set of size ~{length(stderrs)} but is currently limited to sample sets no larger than 4000." | ||
| exit 1 | ||
| fi | ||
|
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| check_table "ref_ranges_001" | ||
| check_table "vet_001" | ||
|
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| mkdir logs | ||
| cd logs | ||
|
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| # Get everything up to and including the /call-LoadData/ part of the GCS path. | ||
| gcs_prefix=$(echo ~{stderrs[0]} | sed -E 's!(.*/call-LoadData/).*!\1!') | ||
|
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| # Recursively copy everything under this path. | ||
| gsutil -m cp -r ${gcs_prefix} . | ||
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| # Find the stderr files in the call execution directories but not the ones in the pipelines-logs directories. | ||
| find call-LoadData -name pipelines-logs -prune -o -name stderr -print > stderr_fofn.txt | ||
| echo "Found $(wc -l stderr_fofn.txt | awk '{print $1}') stderr files in call directories" | ||
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| cat stderr_fofn.txt | xargs grep StatusRuntimeException | tee exceptions.txt | ||
| if [[ $? -ne 0 ]]; then | ||
| fail=1 | ||
| echo "Did not find any StatusRuntimeExceptions among the stderr files!" | ||
| else | ||
| grep UNAVAILABLE exceptions.txt | ||
| if [[ $? -ne 0 ]]; then | ||
| fail=1 | ||
| echo "No UNAVAILABLE StatusRuntimeExceptions found for run!" | ||
| fi | ||
| grep -E 'ABORTED|INTERNAL|CANCELLED' exceptions.txt | ||
| if [[ $? -ne 0 ]]; then | ||
| fail=1 | ||
| echo "No retryable StatusRuntimeExceptions (ABORTED, INTERNAL, CANCELLED) found for run!" | ||
| fi | ||
| fi | ||
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| cd .. | ||
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| if [[ $fail -ne 0 ]]; then | ||
| exit 1; | ||
| fi | ||
| >>> | ||
|
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| output { | ||
| File stderr_fofn = "logs/stderr_fofn.txt" | ||
| File exceptions = "logs/exceptions.txt" | ||
| Boolean done = true | ||
| } | ||
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| runtime { | ||
| docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:latest" | ||
| memory: "14 GB" | ||
| disks: "local-disk 2000 HDD" | ||
| preemptible: 3 | ||
| cpu: 4 | ||
| } | ||
| } |
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This is almost completely a cut/paste of a task from the quickstart integration test to
GvsUtils.wdlso it could be reused.