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Fix analysis path generation for outputs
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@alexiswl
alexiswl committed Nov 6, 2024
1 parent 83a6cb9 commit deb8862
Showing 1 changed file with 188 additions and 4 deletions.
192 changes: 188 additions & 4 deletions ...-pipeline-manager/lambdas/generate_output_data_payload_py/generate_output_data_payload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,53 @@
"""

from urllib.parse import (
urlparse, urlunparse
)
from pathlib import Path


def strip_path_from_url(url: str) -> str:
"""
Strip the path from the url
:param url:
:return:
"""
url_obj = urlparse(url)

return str(
urlunparse(
(
url_obj.scheme,
url_obj.netloc,
"/",
None, None, None
)
)
)


def join_url_paths(url: str, path_ext: str) -> str:
"""
Join the url paths
:param url: str
:param path_ext: str
:return: url
"""
url_obj = urlparse(url)
url_path = Path(url_obj.path) / path_ext

return str(
urlunparse(
(
url_obj.scheme,
url_obj.netloc,
str(url_path),
None, None, None
)
)
)


def handler(event, context):
"""
Expand Down Expand Up @@ -53,15 +100,28 @@ def handler(event, context):

# Set the outputs
return_dict["data_payload"]["outputs"] = {
"caseUrl": f"{pieriandx_base_url.replace("cgw-api/v2.0.0/", "")}/cgw/order/viewOrderDetails/{case_id}",
"vcfOutputUrl": f"{pieriandx_base_url.replace("cgw-api/v2.0.0/", "")}/cgw/informatics/downloadJobOutputAnalysisFile?caseId={case_id}&jobId={job_id}&accessionNumber={case_accession_number}&fileName=main.vcf",
"reportPdfUrl": f"{pieriandx_base_url.replace("cgw-api/v2.0.0/", "")}/cgw/report/openPdfReport/{report_id}",
"biomarkerReportUrl": f"{pieriandx_base_url.replace("cgw-api/v2.0.0/", "")}/cgw/informatics/downloadJobOutputAnalysisFile?caseId={case_id}&jobId={job_id}&accessionNumber={case_accession_number}&fileName={sample_name}_BiomarkerReport.txt"
"caseUrl": join_url_paths(
strip_path_from_url(pieriandx_base_url),
f"/cgw/order/viewOrderDetails/{case_id}"
),
"vcfOutputUrl": join_url_paths(
strip_path_from_url(pieriandx_base_url),
f"/cgw/informatics/downloadJobOutputAnalysisFile?caseId={case_id}&jobId={job_id}&accessionNumber={case_accession_number}&fileName=main.vcf"
),
"reportPdfUrl": join_url_paths(
strip_path_from_url(pieriandx_base_url),
f"/cgw/report/openPdfReport/{report_id}"
),
"biomarkerReportUrl": join_url_paths(
strip_path_from_url(pieriandx_base_url),
f"/cgw/informatics/downloadJobOutputAnalysisFile?caseId={case_id}&jobId={job_id}&accessionNumber={case_accession_number}&fileName={sample_name}_BiomarkerReport.txt"
),
}

return return_dict


# DEV
# if __name__ == "__main__":
# import json
#
Expand Down Expand Up @@ -181,3 +241,127 @@ def handler(event, context):
# # }
# # }
# # }


# # PROD
# if __name__ == "__main__":
# import json
#
# print(
# json.dumps(
# handler(
# {
# "pieriandx_base_url": "https://app.pieriandx.com/cgw-api/v2.0.0",
# "inputs": {
# "instrumentRunId": "241101_A01052_0236_BHVJNMDMXY",
# "panelVersion": "main",
# "caseMetadata": {
# "isIdentified": False,
# "caseAccessionNumber": "L2401562__V2__20241106c25602c7",
# "externalSpecimenId": "CMM0.5pc-10646979",
# "sampleType": "validation",
# "specimenLabel": "primarySpecimen",
# "indication": "NA",
# "diseaseCode": 55342001,
# "specimenCode": "122561005",
# "sampleReception": {
# "dateAccessioned": "2024-11-07T08:39:55+1100",
# "dateCollected": "2024-11-07T08:39:55+1100",
# "dateReceived": "2024-11-07T08:39:55+1100"
# },
# "study": {
# "id": "Control",
# "subjectIdentifier": "Sera-ctDNA-Comp05pc"
# }
# },
# "dataFiles": {
# "microsatOutputUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Logs_Intermediates/DragenCaller/L2401562/L2401562.microsat_output.json",
# "tmbMetricsUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Logs_Intermediates/Tmb/L2401562/L2401562.tmb.metrics.csv",
# "cnvVcfUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562.cnv.vcf.gz",
# "hardFilteredVcfUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562.hard-filtered.vcf.gz",
# "fusionsUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562_Fusions.csv",
# "metricsOutputUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562_MetricsOutput.tsv",
# "samplesheetUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Logs_Intermediates/SampleSheetValidation/SampleSheet_Intermediate.csv"
# }
# },
# "job_id": "302091",
# "report_id": "312010",
# "case_id": "336486",
# "report_status": "complete",
# "case_accession_number": "L2401562__V2__20241106c25602c7",
# "engine_parameters": {
# "caseId": "336486",
# "informaticsJobId": "302091"
# },
# "tags": {
# "metadataFromRedCap": False,
# "isIdentified": False,
# "libraryId": "L2401562",
# "sampleType": "validation",
# "projectId": "Control",
# "instrumentRunId": "241101_A01052_0236_BHVJNMDMXY",
# "panelVersion": "main"
# },
# "sample_name": "L2401562"
# },
# None
# ),
# indent=4
# )
# )
#
# # {
# # "data_payload": {
# # "inputs": {
# # "instrumentRunId": "241101_A01052_0236_BHVJNMDMXY",
# # "panelVersion": "main",
# # "caseMetadata": {
# # "isIdentified": false,
# # "caseAccessionNumber": "L2401562__V2__20241106c25602c7",
# # "externalSpecimenId": "CMM0.5pc-10646979",
# # "sampleType": "validation",
# # "specimenLabel": "primarySpecimen",
# # "indication": "NA",
# # "diseaseCode": 55342001,
# # "specimenCode": "122561005",
# # "sampleReception": {
# # "dateAccessioned": "2024-11-07T08:39:55+1100",
# # "dateCollected": "2024-11-07T08:39:55+1100",
# # "dateReceived": "2024-11-07T08:39:55+1100"
# # },
# # "study": {
# # "id": "Control",
# # "subjectIdentifier": "Sera-ctDNA-Comp05pc"
# # }
# # },
# # "dataFiles": {
# # "microsatOutputUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Logs_Intermediates/DragenCaller/L2401562/L2401562.microsat_output.json",
# # "tmbMetricsUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Logs_Intermediates/Tmb/L2401562/L2401562.tmb.metrics.csv",
# # "cnvVcfUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562.cnv.vcf.gz",
# # "hardFilteredVcfUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562.hard-filtered.vcf.gz",
# # "fusionsUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562_Fusions.csv",
# # "metricsOutputUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Results/L2401562/L2401562_MetricsOutput.tsv",
# # "samplesheetUri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202411052080dbdd/Logs_Intermediates/SampleSheetValidation/SampleSheet_Intermediate.csv"
# # }
# # },
# # "engineParameters": {
# # "caseId": "336486",
# # "informaticsJobId": "302091"
# # },
# # "tags": {
# # "metadataFromRedCap": false,
# # "isIdentified": false,
# # "libraryId": "L2401562",
# # "sampleType": "validation",
# # "projectId": "Control",
# # "instrumentRunId": "241101_A01052_0236_BHVJNMDMXY",
# # "panelVersion": "main"
# # },
# # "outputs": {
# # "caseUrl": "https://app.pieriandx.com/cgw/order/viewOrderDetails/336486",
# # "vcfOutputUrl": "https://app.pieriandx.com/cgw/informatics/downloadJobOutputAnalysisFile?caseId=336486&jobId=302091&accessionNumber=L2401562__V2__20241106c25602c7&fileName=main.vcf",
# # "reportPdfUrl": "https://app.pieriandx.com/cgw/report/openPdfReport/312010",
# # "biomarkerReportUrl": "https://app.pieriandx.com/cgw/informatics/downloadJobOutputAnalysisFile?caseId=336486&jobId=302091&accessionNumber=L2401562__V2__20241106c25602c7&fileName=L2401562_BiomarkerReport.txt"
# # }
# # }
# # }

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