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115
centaur/src/main/resources/standardTestCases/drs_tests/gcpbatch_drs_usa_jdr.wdl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| version 1.0 | ||
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| workflow drs_usa_jdr { | ||
| input { | ||
| File file1 | ||
| File file2 | ||
| } | ||
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| call localize_jdr_drs_with_usa { | ||
| input: | ||
| file1 = file1, | ||
| file2 = file2 | ||
| } | ||
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| call skip_localize_jdr_drs_with_usa { | ||
| input: | ||
| file1 = file1, | ||
| file2 = file2 | ||
| } | ||
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| call read_drs_with_usa { | ||
| input: | ||
| file1 = file1, | ||
| file2 = file2 | ||
| } | ||
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| output { | ||
| String path1 = localize_jdr_drs_with_usa.path1 | ||
| String path2 = localize_jdr_drs_with_usa.path2 | ||
| String hash1 = localize_jdr_drs_with_usa.hash1 | ||
| String hash2 = localize_jdr_drs_with_usa.hash2 | ||
| Float size1 = localize_jdr_drs_with_usa.size1 | ||
| Float size2 = localize_jdr_drs_with_usa.size2 | ||
| String cloud1 = skip_localize_jdr_drs_with_usa.path1 | ||
| String cloud2 = skip_localize_jdr_drs_with_usa.path2 | ||
| Map[String, String] map1 = read_drs_with_usa.map1 | ||
| Map[String, String] map2 = read_drs_with_usa.map2 | ||
| } | ||
| } | ||
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| task localize_jdr_drs_with_usa { | ||
| input { | ||
| File file1 | ||
| File file2 | ||
| } | ||
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| command <<< | ||
| echo ~{file1} > path1 | ||
| echo ~{file2} > path2 | ||
| md5sum ~{file1} | cut -c1-32 > hash1 | ||
| md5sum ~{file2} | cut -c1-32 > hash2 | ||
| >>> | ||
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| output { | ||
| String path1 = read_string("path1") | ||
| String path2 = read_string("path2") | ||
| String hash1 = read_string("hash1") | ||
| String hash2 = read_string("hash2") | ||
| Float size1 = size(file1) | ||
| Float size2 = size(file2) | ||
| } | ||
|
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| runtime { | ||
| docker: "ubuntu:latest" | ||
| backend: "GCPBATCH-usa" | ||
| } | ||
| } | ||
|
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| task skip_localize_jdr_drs_with_usa { | ||
| input { | ||
| File file1 | ||
| File file2 | ||
| } | ||
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| parameter_meta { | ||
| file1: { localization_optional: true } | ||
| file2: { localization_optional: true } | ||
| } | ||
|
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| command <<< | ||
| echo ~{file1} > path1 | ||
| echo ~{file2} > path2 | ||
| >>> | ||
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| output { | ||
| String path1 = read_string("path1") | ||
| String path2 = read_string("path2") | ||
| } | ||
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| runtime { | ||
| docker: "ubuntu:latest" | ||
| backend: "GCPBATCH-usa" | ||
| } | ||
| } | ||
|
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| task read_drs_with_usa { | ||
| input { | ||
| File file1 | ||
| File file2 | ||
| } | ||
|
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| command <<< | ||
| echo file is read by the engine | ||
| >>> | ||
|
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| output { | ||
| Map[String, String] map1 = read_json(file1) | ||
| Map[String, String] map2 = read_json(file2) | ||
| } | ||
|
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||
| runtime { | ||
| docker: "ubuntu:latest" | ||
| backend: "GCPBATCH-usa" | ||
| } | ||
| } |
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2 changes: 1 addition & 1 deletion
2
centaur/src/main/resources/standardTestCases/drs_usa_jdr_preresolve.test
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36 changes: 36 additions & 0 deletions
36
centaur/src/main/resources/standardTestCases/gcpbatch_drs_usa_jdr.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| name: gcpbatch_drs_usa_jdr | ||
| testFormat: WorkflowSuccess | ||
| backends: ["GCPBATCH-usa"] | ||
| tags: [ drs ] | ||
| skipDescribeEndpointValidation: true | ||
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| files { | ||
| workflow: drs_tests/gcpbatch_drs_usa_jdr.wdl | ||
| options-dir: "Error: BA-6546 The environment variable CROMWELL_BUILD_RESOURCES_DIRECTORY must be set/export pointing to a valid path such as '${YOUR_CROMWELL_DIR}/target/ci/resources'" | ||
| options-dir: ${?CROMWELL_BUILD_RESOURCES_DIRECTORY} | ||
| options: ${files.options-dir}/papi_v2_usa.options.json | ||
| inputs: drs_tests/drs_usa_jdr.inputs | ||
| } | ||
|
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| metadata { | ||
| workflowName: drs_usa_jdr | ||
| status: Succeeded | ||
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| "outputs.drs_usa_jdr.path1" = | ||
| "/mnt/disks/cromwell_root/drs_localization_paths/CromwellSimpleWithFilerefs/hello_jade.json" | ||
| "outputs.drs_usa_jdr.path2" = | ||
| "/mnt/disks/cromwell_root/drs_localization_paths/CromwellSimpleWithFilerefs2/hello_jade_2.json" | ||
| "outputs.drs_usa_jdr.hash1" = "faf12e94c25bef7df62e4a5eb62573f5" | ||
| "outputs.drs_usa_jdr.hash2" = "19e1b021628130fda04c79ee9a056b67" | ||
| "outputs.drs_usa_jdr.size1" = 18.0 | ||
| "outputs.drs_usa_jdr.size2" = 38.0 | ||
| # This JDR file has a gsUri that doesn't end in /fileName so it must be downloaded with the DRS localizer | ||
| "outputs.drs_usa_jdr.cloud1" = | ||
| "/mnt/disks/cromwell_root/drs_localization_paths/CromwellSimpleWithFilerefs/hello_jade.json" | ||
| # This JDR file has a gsUri that can skip localization | ||
| "outputs.drs_usa_jdr.cloud2" = | ||
| "gs://broad-jade-dev-data-bucket/e1941fb9-6537-4e1a-b70d-34352a3a7817/ad783b60-aeba-4055-8f7b-194880f37259/hello_jade_2.json" | ||
| "outputs.drs_usa_jdr.map1.hello" = "jade" | ||
| "outputs.drs_usa_jdr.map2.hello" = "jade" | ||
| "outputs.drs_usa_jdr.map2.attempt" = "2" | ||
| } |
40 changes: 40 additions & 0 deletions
40
centaur/src/main/resources/standardTestCases/gcpbatch_drs_usa_jdr_preresolve.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| name: gcpbatch_drs_usa_jdr_preresolve | ||
| testFormat: WorkflowSuccess | ||
| backends: ["GCPBATCH-usa"] | ||
| tags: [ drs ] | ||
| skipDescribeEndpointValidation: true | ||
|
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| files { | ||
| workflow: drs_tests/gcpbatch_drs_usa_jdr.wdl | ||
| options-dir: "Error: BA-6546 The environment variable CROMWELL_BUILD_RESOURCES_DIRECTORY must be set/export pointing to a valid path such as '${YOUR_CROMWELL_DIR}/target/ci/resources'" | ||
| options-dir: ${?CROMWELL_BUILD_RESOURCES_DIRECTORY} | ||
| options: ${files.options-dir}/gcpbatch_papi_v2_usa_preresolve.options.json | ||
| inputs: drs_tests/drs_usa_jdr.inputs | ||
| } | ||
|
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| metadata { | ||
| workflowName: drs_usa_jdr | ||
| status: Succeeded | ||
|
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| "outputs.drs_usa_jdr.path1" = | ||
| "/mnt/disks/cromwell_root/drs_localization_paths/CromwellSimpleWithFilerefs/hello_jade.json" | ||
| # This JDR file has a gsUri that can be preresolved to a regular GCS file for improved localization performance. | ||
| # However this means that the file's container path is determined by the GCS localization logic and not the | ||
| # `localizationPath`-aware DRS localization logic. The GCS localization logic always uses a containerized version | ||
| # of the GCS path, which is what this expectation represents. | ||
| "outputs.drs_usa_jdr.path2" = | ||
| "/mnt/disks/cromwell_root/broad-jade-dev-data-bucket/e1941fb9-6537-4e1a-b70d-34352a3a7817/ad783b60-aeba-4055-8f7b-194880f37259/hello_jade_2.json" | ||
| "outputs.drs_usa_jdr.hash1" = "faf12e94c25bef7df62e4a5eb62573f5" | ||
| "outputs.drs_usa_jdr.hash2" = "19e1b021628130fda04c79ee9a056b67" | ||
| "outputs.drs_usa_jdr.size1" = 18.0 | ||
| "outputs.drs_usa_jdr.size2" = 38.0 | ||
| # This JDR file has a gsUri that doesn't end in /fileName so it must be downloaded with the DRS localizer | ||
| "outputs.drs_usa_jdr.cloud1" = | ||
| "/mnt/disks/cromwell_root/drs_localization_paths/CromwellSimpleWithFilerefs/hello_jade.json" | ||
| # This JDR file has a gsUri that can skip localization | ||
| "outputs.drs_usa_jdr.cloud2" = | ||
| "gs://broad-jade-dev-data-bucket/e1941fb9-6537-4e1a-b70d-34352a3a7817/ad783b60-aeba-4055-8f7b-194880f37259/hello_jade_2.json" | ||
| "outputs.drs_usa_jdr.map1.hello" = "jade" | ||
| "outputs.drs_usa_jdr.map2.hello" = "jade" | ||
| "outputs.drs_usa_jdr.map2.attempt" = "2" | ||
| } |
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12 changes: 12 additions & 0 deletions
12
src/ci/resources/gcpbatch_papi_v2_usa_preresolve.options.json.ctmpl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| {{with $cromwellServiceAccount := secret (printf "secret/dsde/cromwell/common/cromwell-service-account.json")}} | ||
| { | ||
| "google_compute_service_account": "{{$cromwellServiceAccount.Data.client_email}}", | ||
| "user_service_account_json": "{{$cromwellServiceAccount.Data | toJSON | replaceAll "\\" "\\\\" | replaceAll "\"" "\\\"" }}", | ||
| "google_project": "broad-dsde-cromwell-dev", | ||
| "jes_gcs_root": "gs://cloud-cromwell-dev-self-cleaning/cromwell_execution/ci", | ||
| {{/* We're re-using the WDL with the same inputs in multiple tests, make sure we don't accidentally cache hit */}} | ||
| "read_from_cache": false, | ||
| {{/* Test pre-resolving DrsPath to GcsPath */}} | ||
| "override_preresolve_for_test": true | ||
| } | ||
| {{end}} |
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