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Job request: 7113

Organisation:
University of Leeds
Workspace:
all_cause_mortality_with_stratification
ID:
cyoo4hrz54d5qy7u
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
            
    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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:51

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
0c62c46
Requested actions
  • 4wk_onboarding

Code comparison

Compare the code used in this Job Request