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Job request: 9301

Organisation:
University of Bristol
Workspace:
post-covid-unvaccinated
ID:
3iokyfuzegkyz7bv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Kurt Taylor 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  preprocess_data:
    run: r:latest analysis/preprocess/preprocess_data.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_stage0.txt
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/review/descriptives/QA_summary.csv
        refactoring: output/not-for-review/meta_data_factors.csv
        IE_criteria: output/review/descriptives/cohort_flow*.csv
        histograms: output/not-for-review/numeric_histograms_*.svg
      highly_sensitive:
        cohort: output/input_stage1*.rds

  stage1_end_date_table:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates*.rds

  stage2_missing_table1:
    run: r:latest analysis/descriptives/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range*.csv
        DateChecks: output/not-for-review/Check_dates_range*.csv
        Descriptive_Table: output/review/descriptives/Table1*.csv

  stage3_diabetes_flow:
    run: r:latest analysis/descriptives/diabetes_flowchart.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values*.csv

  ## Stage 4 - Table 2 

  stage4_table_2:
    run: 'r:latest analysis/descriptives/table_2.R '
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2*.csv

  stage4_venn_diagram:
    run: r:latest analysis/descriptives/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*.svg
        venn_diagram_number_check: output/review/venn-diagrams/venn_diagram_number_check*.csv

  ## Apply cox model for t1dm 

  Analysis_cox_t1dm:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_t1dm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_t1dm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_t1dm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_t1dm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_t1dm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_t1dm.csv

  ## Apply cox model for t2dm 

  Analysis_cox_t2dm:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_t2dm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_t2dm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_t2dm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_t2dm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_t2dm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_t2dm.csv

  ## Apply cox model for otherdm 

  Analysis_cox_otherdm:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_otherdm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_otherdm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_otherdm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_otherdm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_otherdm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_otherdm.csv

  ## Apply cox model for gestationaldm 

  Analysis_cox_gestationaldm:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_gestationaldm.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_gestationaldm.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_gestationaldm_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_gestationaldm.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_gestationaldm.csv
        compiled_event_counts: output/review/model/compiled_event_counts_gestationaldm.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
GitRepoNotReachableError: Could not read from https://github.com/opensafely/post-covid-unvaccinated
Backend
TPP
Workspace
post-covid-unvaccinated
Requested by
Kurt Taylor
Branch
main
Force run dependencies
Yes
Git commit hash
3644af9
Requested actions
  • run_all

Code comparison

Compare the code used in this job request