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Job request: 7400

Organisation:
University of Leeds
Workspace:
all_cause_mortality_with_stratification
ID:
pzpl3xdyxv2wdrso
View repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

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
                PNV_OS_NC_counts.csv: output/PNV_OS_NC_counts.csv
                PWV_OS_NC_counts.csv: output/PWV_OS_NC_counts.csv
                PNV_OS_C_counts.csv: output/PNV_OS_C_counts.csv
                PWV_OS_C_counts.csv: output/PWV_OS_C_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:46

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

Job information

Status
Succeeded
Backend
TPP
Workspace
all_cause_mortality_with_stratification
Requested by
Ciarán D. McInerney
Branch
main
Force run dependencies
No
Git commit hash
cbfbff0
Requested actions
  • COVIDSurg_compare

Code comparison

Compare the code used in this Job Request