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Job request: 26172

Organisation:
King's College London
Workspace:
inflammatory_rheum
ID:
i4qn2yc4mb4aldgs
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Mark Russell 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_dataset_gca
    Status:
    Succeeded
    Job identifier:
    hqlppbamrhvrugpw
  • Action:
    gca_cleaning
    Status:
    Succeeded
    Job identifier:
    harvafurewz7rnme
  • Action:
    gca_datatables
    Status:
    Succeeded
    Job identifier:
    2nufgydwp5gucxon
  • Action:
    gca_temporal_plots
    Status:
    Succeeded
    Job identifier:
    47rdt5yeikx2t4gq

Pipeline

Show project.yaml 
version: '4.0'

actions:    
  generate_dataset_incidence:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_incidence.py
      --output output/dataset_incidence.csv
      --
      --studystart_date "2016-04-01"
      --studyend_date "2025-03-31"
      --studyfup_date "2026-03-31"
      --diseases_list eia rheumatoid psa axialspa undiffia gca sjogren ssc sle myositis anca
      --registration_months 12
    outputs:
      highly_sensitive:
        cohort: output/dataset_incidence.csv

  generate_dataset_incidence_ref:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_incidence_ref.py 
      --output output/dataset_incidence_ref.csv
      --
      --studystart_date "2016-04-01"
      --studyend_date "2025-03-31"
    outputs:
      highly_sensitive:
        cohort: output/dataset_incidence_ref.csv

  reference_cleaning:
    run: stata-mp:latest analysis/003_reference_cleaning.do
    needs: [generate_dataset_incidence_ref]
    outputs:
      moderately_sensitive:
        log1: logs/reference_cleaning.log   
        table1: output/tables/reference_table_rounded.csv        

  generate_dataset_gca:
      run: ehrql:v1 generate-dataset analysis/dataset_definition_gca.py 
        --output output/dataset_gca.csv
        --
        --studystart_date "2016-04-01"
        --studyend_date "2025-03-31"
        --studyfup_date "2026-03-31"
        --diseases_list eia rheumatoid psa axialspa undiffia gca sjogren ssc sle myositis anca
        --registration_months 12
      needs: [generate_dataset_incidence]
      outputs:
        highly_sensitive:
          cohort: output/dataset_gca.csv

  gca_cleaning:
    run: stata-mp:latest analysis/101_gca_cleaning.do "2016-04-01" "2025-03-31" "2026-03-31"
    needs: [generate_dataset_gca]
    outputs:
      highly_sensitive:
        log1: logs/gca_cleaning.log   
        data1: output/data/gca_processed.dta

  gca_datatables:
    run: stata-mp:latest analysis/201_gca_datatables.do "2016-04-01" "2025-03-31" "2026-03-31"
    needs: [gca_cleaning]
    outputs:
      moderately_sensitive:
        log1: logs/gca_datatables.log   
        table1: output/tables/gca_datatable_*.csv

  gca_temporal_plots:
    run: stata-mp:latest analysis/301_gca_plots.do "2016-04-01" "2025-03-31" "2026-03-31" "2020-03-01"
    needs: [gca_datatables]
    outputs:
      moderately_sensitive:
        log1: logs/gca_plots.log   
        figure1: output/figures/gca_plot_*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:11:18

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

Job request

Status
Succeeded
Backend
TPP
Workspace
inflammatory_rheum
Requested by
Mark Russell
Branch
main
Force run dependencies
No
Git commit hash
ff88721
Requested actions
  • generate_dataset_gca
  • gca_cleaning
  • gca_datatables
  • gca_temporal_plots

Code comparison

Compare the code used in this job request