update translator service to bclconvert manager #299
Conversation
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Morning Ray. Great start. Could you do me favour; can you create a github issue/ticket with the same description - and, label "pipeline" "refactor". Then, pls link it to; this PR > Development > Link issue from this repository (at the right panel) Thank so much. |
Also reformatted python file and added example execution
…ert-manager Thanks @alexiswl , will merge and test it later
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Hi @reisingerf @victorskl @alexiswl ;
(Non-SUCCEEDED Event without payload) {
"portalRunId": '20xxxxxxxxxx',
"executionId": "valid_payload_id",
"timestamp": "2024-00-25T00:07:00Z",
"status": "SUCCEEDED",
"workflowName": "BclConvert",
"workflowVersion": "4.2.7",
"workflowRunName": "123456_A1234_0000_TestingPattern",
}(SUCCEEDED Event) {
"portalRunId": '20xxxxxxxxxx',
"executionId": "valid_payload_id",
"timestamp": "2024-00-25T00:07:00Z",
"status": "SUCCEEDED",
"workflowName": "BclConvert",
"workflowVersion": "4.2.7",
"workflowRunName": "123456_A1234_0000_TestingPattern",
"payload": {
"refId": None,
"version": "0.1.0",
"data": {
"projectId": "valid_project_id",
"analysisId": "valid_payload_id",
"userReference": "123456_A1234_0000_TestingPattern",
"timeCreated": "2024-01-01T00:11:35Z",
"timeModified": "2024-01-01T01:24:29Z",
"pipelineId": "valid_pipeline_id",
"pipelineCode": "BclConvert v0_0_0",
"pipelineDescription": "BclConvert pipeline.",
"pipelineUrn": "urn:ilmn:ica:pipeline:123456-abcd-efghi-1234-acdefg1234a#BclConvert_v0_0_0"
"instrumentRunId": "12345_A12345_1234_ABCDE12345",
"basespaceRunId": "1234567",
"samplesheetB64gz": "H4sIAFGBVWYC/9VaUW+jOBD+Kyvu9VqBgST0njhWh046..."
}
}
} |
| 'id_type': {'S': 'db_uuid'}, | ||
| 'analysis_id': {'S': internal_ica_event.detail.payload.get('data', '').get("analysisId", '')}, | ||
| 'analysis_status': {'S': internal_ica_event.detail.status}, | ||
| # 'SUCCEEDED', 'FAILED', 'INPROGRESS', 'ABORTED', 'UNKNOWN |
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Where does "UNKNOWN" come from?
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this may come from old draft, already deleted.
| "portalRunId": '20xxxxxxxxxx', | ||
| "executionId": "valid_payload_id", | ||
| "timestamp": "2024-00-25T00:07:00Z", | ||
| "status": "SUCCEEDED", |
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This should probably not be "SUCCEEDED".
The code will use whatever was the status from the input event, right?
| "workflowVersion": "4.2.7", | ||
| workflowRunName: "123456_A1234_0000_TestingPattern", | ||
| "payload": { | ||
| "refId": None, |
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"refId" is no longer needed. (I think the code is already updated)
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refId deleted as not required
| # Convert from entity module to internal event details | ||
| def get_event_details(event) -> WorkflowRunStateChange: | ||
| # Extract relevant fields from the event payload | ||
| analysis_status = event.get("eventParameters", {}).get("analysisStatus", '') |
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Would "UNSPECIFIED" be a better default?
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| event_name, version = parse_event_code(pipeline.get("code", '')) | ||
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| if analysis_status != "SUCCEEDED": |
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An empty payload for all non-SUCCEEDED events is fine for now.
In the future we may want to handle all known statuses, for example add an error message payload for FAILED events. Happy to put that on the backlog though.
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sure, new backlog added here
I think for non-final status "Requested", "Queued", "Initializing", "Preparing Inputs", "In Progress", "Generating outputs", "Aborting", we can leave it empty;
for final status "Aborted", "Failed", "Succeeded", we may need add additional specific information in the future.
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Just heads up; this file is deprecated and superseded by JSON Schema in main branch. When you rebase to main, pls see if you can adapt to the latest arrangement. It should be the same meaning in schema-wise.
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sure, will deleted the deprecated PayloadDataSucceeded file.
Update translator service to bclconvert manager
As discussed,
new schema example