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Job request: 7682

Organisation:
University of Leeds
Workspace:
all_cause_mortality_with_stratification
ID:
uotbrbmovgf2thbu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ciarán D. McInerney requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    generate_study_population_2
    Status:
    Status: Failed
    Job identifier:
    crxivyuzga5ywvhf
    Error:
    nonzero_exit: Job exited with error code 4: New data is being imported into the database, please try again in a few hours
  • Action:
    COVIDSurg_compare
    Status:
    Status: Failed
    Job identifier:
    bjddcxlebpzfp2wg
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

    # generate_study_population:
        # run: cohortextractor:latest generate_cohort --study-definition study_definition
        # outputs:
            # highly_sensitive:
                # cohort: output/input.csv
                
    generate_study_population_2:
        run: cohortextractor:latest generate_cohort --study-definition study_definition_2
        outputs:
            highly_sensitive:
                cohort: output/input_2.csv

    # generate_study_population_cohort_check:
        # run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
        # outputs:
            # highly_sensitive:
                # cohort: output/input_*.csv
            
    # generate_study_population_codelist_check:
        # run: cohortextractor:latest generate_cohort --study-definition study_definition_codelist_check
        # outputs:
            # highly_sensitive:
                # cohort: output/input_*.csv
                
    # generate_study_population_vacc_check_anyTest:
        # run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc_check_anyTest
        # outputs:
            # highly_sensitive:
                # cohort: output/input_vacc_check.csv
    
    # generate_study_population_vacc_check_posTest:
        # run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc_check_posTest
        # outputs:
            # highly_sensitive:
                # cohort: output/input_vacc_check_posTest.csv
    
    # check_cohort:
        # run: r:latest analysis/check_cohort.R
        # needs: [generate_study_population_cohort_check]
        # outputs:
            # moderately_sensitive:
                # cohort: output/check_cohort.csv
                
    # check_codelist:
        # run: r:latest analysis/check_codelist.R
        # needs: [generate_study_population_codelist_check]
        # outputs:
            # moderately_sensitive:
                # cohort: output/check_codelist.csv
                
    # 4wk_onboarding:
        # run: r:latest analysis/report.R
        # needs: [generate_study_population]
        # outputs:
            # moderately_sensitive:
                # n_patients: output/count_patients.csv
                ##cohort1: output/plot_postOp_mortality_30day.png
                # subtable_table1_ageGroup: output/table1_ageGroup.csv
                # subtable_table1_Sex: output/table1_Sex.csv
                # subtable_table1_30dayMortality: output/table1_postOp_mortality_30day.csv
                # table1_df_4wk: output/table1_4wk_onboarding.csv
                ##table1_kable_4wk: output/Table1_4wk_onboarding.png
                # subtable_table1_ageGroup_3mths: output/table1_ageGroup_3mths.csv
                # subtable_table1_Sex_3mths: output/table1_Sex_3mths.csv
                # subtable_table1_30dayMortality_3mths: output/table1_postOp_mortality_30day_3mths.csv
                # table1_df_4wk_3mths: output/table1_4wk_onboarding_3mths.csv
                ##table1_kable_4wk_3mths: output/Table1_4wk_onboarding_3mths.png
                # subtable_table1_ageGroup_6mths: output/table1_ageGroup_6mths.csv
                # subtable_table1_Sex_6mths: output/table1_Sex_6mths.csv
                # subtable_table1_30dayMortality_6mths: output/table1_postOp_mortality_30day_6mths.csv
                # table1_df_4wk_6mths: output/table1_4wk_onboarding_6mths.csv
                ##table1_kable_4wk_6mths: output/Table1_4wk_onboarding_6mths.png
                # tableVacc_30dayMortality: output/tableVacc_postOp_mortality_30day.csv
                # tableVacc_df: output/table_Vaccination_status.csv
                ##tableVacc_kable: output/TableVacc.png
                # tableVacc_30dayMortality_3mths: output/tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_df_3mths: output/table_Vaccination_status_3mths.csv
                ##tableVacc_kable_3mths: output/TableVacc_3mths.png
                # tableVacc_30dayMortality_6mths: output/tableVacc_postOp_mortality_30day_6mths.csv
                # tableVacc_df_6mths: output/table_Vaccination_status_6mths.csv
                ##tableVacc_kable_6mths: output/TableVacc_6mths.png
    
    # vacc_definition_check_anyTest:
        # run: r:latest analysis/vacc_check.R
        # needs: [generate_study_population_vacc_check_anyTest]
        # outputs:
            # moderately_sensitive:
                # tableVacc_30dayMortality_3mths_SNOMED: output/SNOMED_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_30dayMortality_3mths_TPP: output/TPP_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_30dayMortality_3mths_AlwynSNOMED: output/AlwynSNOMED_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_30dayMortality_3mths_AlwynTPP: output/AlwynTPP_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_df_check_3mths_SNOMED: output/SNOMED_table_Vaccination_status_3mths.csv
                # tableVacc_df_check_3mths_TPP: output/TPP_table_Vaccination_status_3mths.csv
                # tableVacc_df_check_3mths_AlwynSNOMED: output/AlwynSNOMED_table_Vaccination_status_3mths.csv
                # tableVacc_df_check_3mths_AlwynTPP: output/AlwynTPP_table_Vaccination_status_3mths.csv
                
    # vacc_definition_check_posTest:
        # run: r:latest analysis/vacc_check.R
        # needs: [generate_study_population_vacc_check_posTest]
        # outputs:
            # moderately_sensitive:
                # tableVacc_30dayMortality_3mths_SNOMED: output/SNOMED_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_30dayMortality_3mths_TPP: output/TPP_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_30dayMortality_3mths_AlwynSNOMED: output/AlwynSNOMED_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_30dayMortality_3mths_AlwynTPP: output/AlwynTPP_tableVacc_postOp_mortality_30day_3mths.csv
                # tableVacc_df_check_3mths_SNOMED: output/SNOMED_table_Vaccination_status_3mths.csv
                # tableVacc_df_check_3mths_TPP: output/TPP_table_Vaccination_status_3mths.csv
                # tableVacc_df_check_3mths_AlwynSNOMED: output/AlwynSNOMED_table_Vaccination_status_3mths.csv
                # tableVacc_df_check_3mths_AlwynTPP: output/AlwynTPP_table_Vaccination_status_3mths.csv
                
    COVIDSurg_compare:
        run: r:latest analysis/Make_table_COVIDSurg_compare.R
        needs: [generate_study_population_2]
        outputs:
            moderately_sensitive:
                table_counts: output/table_Count_of_patients_in_each_cohort_in_each_era_across_all_intervals.csv
                table_mortality_intervals: output/table_30day_post-op_mortality_in_each_era_across_all_intervals.csv
                table_mortality_totals: output/table_30day_post-op_mortality_for_each_cohort_in_each_era.csv
                plotData_C: output/plotData_OS_C6m.csv
                plotData_NC: output/plotData_OS_NC6m.csv
                figure_NC_3m: output/noCancer_3monthly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_NC_2m: output/noCancer_2monthly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_NC_1m: output/noCancer_1monthly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_NC_wk: output/noCancer_weekly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_C_3m: output/cancer_3monthly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_C_2m: output/cancer_2monthly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_C_1m: output/cancer_1monthly_summary_proportion_surgeries_7wks_after_pos_test.png
                figure_C_wk: output/cancer_weekly_summary_proportion_surgeries_7wks_after_pos_test.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:20

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status
Failed
Backend
TPP
Workspace
all_cause_mortality_with_stratification
Requested by
Ciarán D. McInerney
Branch
main
Force run dependencies
Yes
Git commit hash
bf04255
Requested actions
  • run_all

Code comparison

Compare the code used in this job request