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only use dcm files for export #471

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Merged
merged 3 commits into from
Sep 29, 2022
Merged

only use dcm files for export #471

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8d19082
only use dcm files for export
jackschofield23 Sep 28, 2022
b6ae40c
fix config
jackschofield23 Sep 29, 2022
73a2d7e
update export log to error
jackschofield23 Sep 29, 2022
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4 changes: 2 additions & 2 deletions src/TaskManager/TaskManager/appsettings.Local.json
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Original file line number Diff line number Diff line change
Expand Up @@ -74,8 +74,8 @@
"scuAgentName": "monaiscu"
},
"argoCallback": {
"argoRabbitOverrideEnabled": false,
"argoRabbitOverrideEndpoint": "localhost"
"argoRabbitOverrideEnabled": true,
"argoRabbitOverrideEndpoint": "rabbit-monai"
}
}
},
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2 changes: 1 addition & 1 deletion src/WorkflowManager/Logging/Logging/Log.cs
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Expand Up @@ -94,7 +94,7 @@ public static partial class Log
[LoggerMessage(EventId = 23, Level = LogLevel.Error, Message = "The task {taskId} metadata store update failed. Payload: {payloadId} - Metadata: {metadata}")]
public static partial void TaskMetaDataUpdateFailed(this ILogger logger, string payloadId, string taskId, Dictionary<string, object> metadata);

[LoggerMessage(EventId = 24, Level = LogLevel.Debug, Message = "No files to export for task {taskId} within workflow instance {workflowInstanceId}.")]
[LoggerMessage(EventId = 24, Level = LogLevel.Error, Message = "No files to export for task {taskId} within workflow instance {workflowInstanceId}.")]
public static partial void ExportFilesNotFound(this ILogger logger, string taskId, string workflowInstanceId);

[LoggerMessage(EventId = 25, Level = LogLevel.Error, Message = "Failed to get dicom tag {keyId} in bucket {bucketId}. Payload: {payloadId}")]
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27 changes: 16 additions & 11 deletions src/WorkflowManager/WorkflowExecuter/Services/WorkflowExecuterService.cs
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Expand Up @@ -349,13 +349,6 @@ private async Task HandleDicomExportAsync(WorkflowRevision workflow, WorkflowIns

var artifactValues = GetDicomExports(workflow, workflowInstance, task, exportList);

if (artifactValues.Any() is false)
{
await HandleTaskDestinations(workflowInstance, workflow, task, correlationId);

return;
}

var files = new List<VirtualFileInfo>();
foreach (var artifact in artifactValues)
{
Expand All @@ -365,15 +358,29 @@ private async Task HandleDicomExportAsync(WorkflowRevision workflow, WorkflowIns
workflowInstance.BucketId,
artifact,
true);
if (objects.IsNullOrEmpty() is false)

var dcmFiles = objects?.Where(o => o.FilePath.EndsWith(".dcm"))?.ToList();
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Sometimes, users may not use .dcm extension.

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Does this change also removes the ability to export HL7/FHIR?

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Do we know what other file extensions we will support?

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Currently we only support exporting to the dicom scu endpoint. So when we extend the export to other endpoints we can update supported filetypes.

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We will need to support DICOM, FHIR, and HL7 but no guarantee what file extensions users will use. Therefore, I think we must document the usage, e.g., without .dcm we will not export their DICOM files.


if (dcmFiles?.IsNullOrEmpty() is false)
{
files.AddRange(objects.ToList());
files.AddRange(dcmFiles.ToList());
}
}
}

artifactValues = files.Select(f => f.FilePath).ToArray();

if (artifactValues.IsNullOrEmpty())
{
_logger.ExportFilesNotFound(task.TaskId, workflowInstance.Id);

await UpdateWorkflowInstanceStatus(workflowInstance, task.TaskId, TaskExecutionStatus.Failed);

await CompleteTask(task, workflowInstance, correlationId, TaskExecutionStatus.Failed);

return;
}

await DispatchDicomExport(workflowInstance, task, exportList, artifactValues, correlationId);
}

Expand All @@ -399,8 +406,6 @@ private string[] GetDicomExports(WorkflowRevision workflow, WorkflowInstance wor

if (!task.InputArtifacts.Any())
{
_logger.ExportFilesNotFound(task.TaskId, workflowInstance.Id);

return Array.Empty<string>();
}

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