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Job request: 7191

Organisation:
University of Leeds
Workspace:
all_cause_mortality_with_stratification
ID:
ulsdcxw4wbwlbtzi
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_cohort_check:
        # run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
        # outputs:
            # highly_sensitive:
                # cohort: output/input_*.csv
            
    # check_cohort:
        # run: r:latest analysis/check_cohort.R
        # needs: [generate_study_population_cohort_check]
        # outputs:
            # moderately_sensitive:
                # cohort: output/check_cohort.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_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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:35

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
Yes
Git commit hash
ccbe66e
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request