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Merge pull request #590 from umccr/patch-0.2.3
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Merge pull request #588 from umccr/hotfix/bssh-fastq-copy-quick-fix
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@victorskl
victorskl authored Oct 4, 2024
2 parents 0bcfc7e + 2c58c44 commit 30f245d
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Showing 2 changed files with 29 additions and 32 deletions.
59 changes: 28 additions & 31 deletions ...d/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ def handler(event, context):
(
urlparse(dest_uri).scheme,
urlparse(dest_uri).netloc,
str(Path(dest_project_folder_data_obj.data.details.path) / source_project_data_obj.data.details.name),
str(Path(urlparse(dest_uri).path) / source_project_data_obj.data.details.name),
None, None, None
)
)
Expand Down Expand Up @@ -300,40 +300,37 @@ def handler(event, context):

# if __name__ == "__main__":
# import json
# environ['ICAV2_ACCESS_TOKEN_SECRET_ID'] = 'ICAv2JWTKey-umccr-prod-service-trial'
# environ['AWS_PROFILE'] = 'umccr-production'
# environ['AWS_DEFAULT_REGION'] = 'ap-southeast-2'
# environ['ICAV2_ACCESS_TOKEN_SECRET_ID'] = 'ICAv2JWTKey-umccr-prod-service-production'
# print(
# json.dumps(
# handler(
# event={
# "job_attempt_counter": 1,
# "job_id": "d80ea8f4-b2a4-4b5f-840f-2426584d0495",
# "failed_jobs_list": [],
# "dest_uri": "icav2://7595e8f2-32d3-4c76-a324-c6a85dae87b5/ilmn_primary/2023/231116_A01052_0172_BHVLM5DSX7/3661659/20240307135959/InterOp/",
# "source_uris": [
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/AlignmentMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/EmpiricalPhasingMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/CorrectedIntMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/BasecallingMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/ErrorMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/ExtendedTileMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/OpticalModelMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/QMetricsByLaneOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/ExtractionMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/PFGridMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/ImageMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/TileMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/QMetrics2030Out.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/FWHMGridMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/QMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/EventMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/RegistrationMetricsOut.bin",
# "icav2://b23fb516-d852-4985-adcc-831c12e8cd22/ilmn-runs/bssh_aps2-sh-prod_3661659/InterOp/IndexMetricsOut.bin"
# ],
# "job_status": None,
# "wait_time_seconds": 10
# },
# "job_status": "RUNNING",
# "wait_time_seconds": 20,
# "job_id": "bdfb0a4d-bcae-4670-b51f-9417d23e777a",
# "dest_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/primary/240926_A01052_0232_AHW7LHDSXC/20240928f63332ac/Samples/Lane_4/LPRJ241305/",
# "source_uris": [
# "icav2://9ec02c1f-53ba-47a5-854d-e6b53101adb7/ilmn-analyses/240926_A01052_0232_AHW7LHDSXC_f5e33a_03217c-BclConvert v4_2_7-792cba71-52fa-42b3-85a0-c6593f199353/output/Samples/Lane_4/LPRJ241305/LPRJ241305_S41_L004_R1_001.fastq.gz",
# "icav2://9ec02c1f-53ba-47a5-854d-e6b53101adb7/ilmn-analyses/240926_A01052_0232_AHW7LHDSXC_f5e33a_03217c-BclConvert v4_2_7-792cba71-52fa-42b3-85a0-c6593f199353/output/Samples/Lane_4/LPRJ241305/LPRJ241305_S41_L004_R2_001.fastq.gz"
# ],
# "failed_job_list": []
# },
# context=None
# )
# ),
# indent=4
# )
# )

#
# # {
# # "dest_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/primary/240926_A01052_0232_AHW7LHDSXC/20240928f63332ac/Samples/Lane_4/LPRJ241305/",
# # "source_uris": [
# # "icav2://9ec02c1f-53ba-47a5-854d-e6b53101adb7/ilmn-analyses/240926_A01052_0232_AHW7LHDSXC_f5e33a_03217c-BclConvert v4_2_7-792cba71-52fa-42b3-85a0-c6593f199353/output/Samples/Lane_4/LPRJ241305/LPRJ241305_S41_L004_R1_001.fastq.gz",
# # "icav2://9ec02c1f-53ba-47a5-854d-e6b53101adb7/ilmn-analyses/240926_A01052_0232_AHW7LHDSXC_f5e33a_03217c-BclConvert v4_2_7-792cba71-52fa-42b3-85a0-c6593f199353/output/Samples/Lane_4/LPRJ241305/LPRJ241305_S41_L004_R2_001.fastq.gz"
# # ],
# # "job_id": "bdfb0a4d-bcae-4670-b51f-9417d23e777a",
# # "failed_job_list": [],
# # "job_status": "SUCCEEDED",
# # "wait_time_seconds": 10
# # }
2 changes: 1 addition & 1 deletion lib/workload/components/icav2-copy-files/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ export class ICAv2CopyFilesConstruct extends Construct {
index: 'check_or_launch_job_lambda.py',
handler: 'handler',
memorySize: 1024,
timeout: Duration.seconds(300),
timeout: Duration.seconds(900),
environment: {
ICAV2_ACCESS_TOKEN_SECRET_ID: props.icav2JwtSecretParameterObj.secretName,
},
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