Hello,
My files are being accepted now, but they are failing with the following.
STDERR: 2024-08-30T09:29:24.576352821Z 2024-08-30 09:29:13,786 - [INFO] - Report Generation Started
STDERR: 2024-08-30T09:29:24.576356359Z 2024-08-30 09:29:13,786 - [INFO] - Initialization Started
STDERR: 2024-08-30T09:29:24.576360029Z {
STDERR: 2024-08-30T09:29:24.576363436Z "config_file": {
STDERR: 2024-08-30T09:29:24.576366925Z "run_name": "MIDI_1_1_Testing",
STDERR: 2024-08-30T09:29:24.576370465Z "input_data_path": "submission/mappings",
STDERR: 2024-08-30T09:29:24.576374148Z "output_data_path": "results",
STDERR: 2024-08-30T09:29:24.576377796Z "answer_db_file": "/usr/local/bin/MIDI_validation_script/midi_1_1_answer_data_1.db",
STDERR: 2024-08-30T09:29:24.576381524Z "uid_mapping_file": "submission/mappings/uid_mapping.csv",
STDERR: 2024-08-30T09:29:24.576385184Z "patid_mapping_file": "submission/mappings/patient_id_mapping.csv",
STDERR: 2024-08-30T09:29:24.576388904Z "multiprocessing": "True",
STDERR: 2024-08-30T09:29:24.576411729Z "multiprocessing_cpus": "5",
STDERR: 2024-08-30T09:29:24.576416348Z "log_path": "logs",
STDERR: 2024-08-30T09:29:24.576424621Z "log_level": "info",
STDERR: 2024-08-30T09:29:24.576426004Z "report_series": "True"
STDERR: 2024-08-30T09:29:24.576434727Z }
STDERR: 2024-08-30T09:29:24.576439804Z }
STDERR: 2024-08-30T09:29:24.576446806Z 2024-08-30 09:29:13,788 - [ERROR] - An unexpected error occurred: Execution failed on sql 'select * from validation_results': no such table: validation_results
STDERR: 2024-08-30T09:29:24.576452404Z 2024-08-30 09:29:13,788 - [INFO] - Reports Generation Complete - Duration: (2, 21)
STDERR: 2024-08-30T09:29:24.576453748Z [job test.cwl] Max memory used: 0MiB
STDERR: 2024-08-30T09:29:24.576453748Z INFO:cwltool:[job test.cwl] Max memory used: 0MiB
STDERR: 2024-08-30T09:29:24.576453748Z [job test.cwl] Job error:
STDERR: 2024-08-30T09:29:24.576453748Z ("Error collecting output for parameter 'discrepancy_internal':\nMIDI-B-De-identification-main/steps/test.cwl:61:7: Did not find output file with glob pattern: '['results/MIDI_1_1_Testing/discrepancy_report_internal.csv']'", {})
STDERR: 2024-08-30T09:29:24.576454444Z ERROR:cwltool:[job test.cwl] Job error:
STDERR: 2024-08-30T09:29:24.576458909Z ("Error collecting output for parameter 'discrepancy_internal':\nMIDI-B-De-identification-main/steps/test.cwl:61:7: Did not find output file with glob pattern: '['results/MIDI_1_1_Testing/discrepancy_report_internal.csv']'", {})
STDERR: 2024-08-30T09:29:24.576462935Z [job test.cwl] completed permanentFail
Regards,
Chris
Created by Chris Ablett ChrisAb I checked and I do not have identical names:
idold,idnew
1011144680,3185783787
1014584441,1104323522
id_old,id_new
1.1.284.1.1.4850980.4.279.1093639058163472900,1.2.840.113654.2.174.69.246960692683834061411240334060983237351
1.1.284.1.1.4850980.4.279.1483659926933632803,1.2.840.113654.2.174.69.70272056236193826317492168924246263028
I suspect issue might be I am missing the _ character in the patient id mappings. I will try that.
Regards,
Chris In the mapping files, you may have an identical header name in two columns of "$$\(id\_old\)$$". Should be "$$\(id\_old\)$$" and "$$\(id\_new\)$$". Su@phmoer (submission ID 9749213) I am pretty sure file names are correct as I had an issue with them earlier and got a different error. They seem to be being accepted now:
patient_id_mapping.csv
uid_mapping.csv Can you double-check the mapping file names? They should be uid_mapping.csv, and patient_id_mapping.csv.
Drop files to upload
Submission Workflow Failing - no such table: validation_results page is loading…