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Job request: 24437

Organisation:
King's College London
Workspace:
zoster_incidence_imids
ID:
k43jfruxxopb4edu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Zijing Yang 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:
    KM_plot
    Status:
    Status: Succeeded
    Job identifier:
    7gbaytec7sk6xp4r
  • Action:
    KM_age_plot
    Status:
    Status: Succeeded
    Job identifier:
    cjxstqtwwrrwlji6
  • Action:
    KM_gender_plot
    Status:
    Status: Succeeded
    Job identifier:
    2ma7sww66ettp6jv

Pipeline

Show project.yaml 
version: '4.0'

actions:
  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset.arrow
    outputs:
      highly_sensitive:
        dataset: output/dataset.arrow

  data_cleaning:
    run: r:latest analysis/data_cleaning.R
    needs:
    - generate_dataset
    outputs:
      highly_sensitive:
        table1: output/dt.csv

  Baseline_table:
    run: r:latest analysis/baseline_table.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1: output/Baseline_table.csv

  Incidence_table:
    run: r:latest analysis/Incidence_imids_diag_V2.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1: output/zoster_by_month_and_imids.csv

  Incidence_gender_table:
    run: r:latest analysis/Incidence_imids_diag_gender.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1: output/zoster_by_month_imids_gender.csv



  KM_plot:
    run: r:latest analysis/km_survival.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        plot1:  output/km_zoster_combined.png
       
  KM_age_plot:
    run: r:latest analysis/KM_sub_age.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        plot1:  output/km_zoster_imid_age.png
        plot_ad: output/km_zoster_AD_age.png
        plot_ra: output/km_zoster_RA_age.png
        plot_ibd: output/km_zoster_IBD_age.png
        plot_ps: output/km_zoster_PS_age.png
        plot_hs: output/km_zoster_HS_age.png
        plot_as: output/km_zoster_AS_age.png
        plot_psa: output/km_zoster_PsA_age.png

  KM_gender_plot:
    run: r:latest analysis/KM_sub_gender.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        plot1:  output/km_zoster_imid_gender.png
        plot_ad: output/km_zoster_AD_gender.png
        plot_ra: output/km_zoster_RA_gender.png
        plot_ibd: output/km_zoster_IBD_gender.png
        plot_ps: output/km_zoster_PS_gender.png
        plot_hs: output/km_zoster_HS_gender.png
        plot_as: output/km_zoster_AS_gender.png
        plot_psa: output/km_zoster_PsA_gender.png

  Incidence_plot:
    run: r:latest analysis/incidence_plot.R
    needs:
    - data_cleaning
    - Incidence_table
    - Incidence_gender_table
    outputs:
      moderately_sensitive:
        plot1_inc:  output/zoster_inc_individual_imid.png
        plot2_inc:  output/zoster_inc_all_imid.png
        plot1_cum:  output/zoster_cum_individual_imid.png
        plot2_cum:  output/zoster_cum_all_imid.png
        plot3_inc:  output/zoster_individual_imid_gender.png
        plot4_inc:  output/zoster_all_imid_gender.png
        plot3_cum:  output/zoster_cum_individual_imid_gender.png
        plot4_cum:  output/zoster_cum_all_imid_gender.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:11

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

Job request

Status
Succeeded
Backend
TPP
Workspace
zoster_incidence_imids
Requested by
Zijing Yang
Branch
main
Force run dependencies
No
Git commit hash
fc8967f
Requested actions
  • KM_plot
  • KM_age_plot
  • KM_gender_plot

Code comparison

Compare the code used in this job request