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Fix parsing of Cromwell tasks to accommodate reattempted tasks #695

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May 1, 2024
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Fix parsing of Cromwell tasks to accommodate reattempted tasks #695

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5 changes: 3 additions & 2 deletions src/Tes/TaskSubmitters/CromwellTaskSubmitter.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,10 @@ public partial class CromwellTaskSubmitter() : TaskSubmitter(SubmitterName)
public const string SubmitterName = "cromwell";

// Parses out the task and shard along with its workflow name & id from the execution path. Note that is expected to be the most deeply nested workflow.
[GeneratedRegex("/*?/(.+)/([^/]+)/([0-9A-Fa-f]{8}[-][0-9A-Fa-f]{4}[-][0-9A-Fa-f]{4}[-][0-9A-Fa-f]{4}[-][0-9A-Fa-f]{12})/call-([^/]+)(?:/shard-([^/]+))?/execution/rc", RegexOptions.Singleline)]
[GeneratedRegex("/*?/(.+)/([^/]+)/([0-9A-Fa-f]{8}[-][0-9A-Fa-f]{4}[-][0-9A-Fa-f]{4}[-][0-9A-Fa-f]{4}[-][0-9A-Fa-f]{12})/call-([^/]+)(?:/shard-([^/]+))?(?:/attempt-([^/]+))?/execution/rc", RegexOptions.Singleline)]
// examples: /cromwell-executions/test/daf1a044-d741-4db9-8eb5-d6fd0519b1f1/call-hello/execution/rc
// examples: /cromwell-executions/test/daf1a044-d741-4db9-8eb5-d6fd0519b1f1/call-hello/test-subworkflow/b5227f73-f6e8-43be-8b18-520b1fd789b6/call-subworkflow/shard-8/execution/rc
// examples: /cromwell-executions/test/daf1a044-d741-4db9-8eb5-d6fd0519b1f1/call-hello/test-subworkflow/b5227f73-f6e8-43be-8b18-520b1fd789b6/call-subworkflow/shard-8/attempt-2/execution/rc
private static partial Regex CromwellPathRegex();

// Parses the task instance name from the description
Expand Down Expand Up @@ -91,7 +92,7 @@ private static bool IsCromwellCommandScript(TesInput inputFile) =>
// match.Groups[4] <= task name
// match.Groups[5] <= shard, if present

if (match.Success && match.Captures.Count == 1 && match.Groups.Count == 6)
if (match.Success && match.Captures.Count == 1 && match.Groups.Count == 7)
{
var workflowName = path[2];
var workflowId = path[3]; // This is how we set WorkflowId before making this pre-submitter determinable
Expand Down
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