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Job request: 24802

Organisation:
King's College London
Workspace:
zoster_incidence_imids
ID:
wauxfc4vfxe3ou5z
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

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


  generate_zoster_prevalence:
    run: ehrql:v1 generate-measures analysis/population_measure.py --output output/had_event_by_sex_age.arrow
    outputs:
      highly_sensitive:
        measure: output/had_event_by_sex_age.arrow
        
  Baseline_table:
    run: r:latest analysis/baseline_table.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table_zoster: output/baseline_by_zoster.csv
        table_imids: output/baseline_by_imids.csv
        table_ra: output/baseline_RA_zoster.csv
        table_psa: output/baseline_PsA_zoster.csv
        table_ibd: output/baseline_IBD_zoster.csv
        table_ps: output/baseline_PS_zoster.csv
        table_hs: output/baseline_HS_zoster.csv
        table_as: output/baseline_AS_zoster.csv
        table_ad: output/baseline_AD_zoster.csv

  Incidence_table:
    run: r:latest analysis/Incidence_imids_diag_V2.1.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1: output/zoster_by_month_and_imids.csv


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

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

  Incidence_age_gender_table:
    run: r:latest analysis/Incidence_imids_diag_age_gender.R
    needs:
    - data_cleaning
    outputs:
     moderately_sensitive:
        table1: output/zoster_by_month_gender_age_index_std.csv
        table2: output/zoster_by_month_age_std.csv    
        table3: output/zoster_by_month_gender_std.csv

  Incidence_age_gender_mea_table:
    run: r:latest analysis/Incidence_imids_age_gender_mea.R
    needs:
    - data_cleaning
    - generate_zoster_prevalence
    outputs:
     moderately_sensitive:
        table1: output/zoster_by_month_gender_age_index_mea_std.csv
        table2: output/zoster_by_month_age_mea_std.csv    
        table3: output/zoster_by_month_gender_mea_std.csv

  Proportion_age_gender_notrend:
    run: r:latest analysis/Proportion_age_gender_imids.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table_age_gender: output/proportion_all_IMIDs_zoster_age_gender.csv
        table_age: output/proportion_all_IMIDs_zoster_by_age.csv
        table_gender: output/proportion_all_IMIDs_zoster_by_gender.csv
        
  IRR_IRD:
    run: r:latest analysis/IRR_COVID.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1:  output/regression_IRR_IMID.csv
        table2:  output/regression_IRR_by_IMID.csv


  CRR_IRD:
    run: r:latest analysis/HR_IMIDs.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1:  output/Competing_newly_IMID.csv.csv
        table2:  output/Competing_newly_each_IMID.csv.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_age_gender_table
    outputs:
      moderately_sensitive:
        plot1_inc:  output/zoster_std_imid.png
        plot2_inc:  output/zoster_std_gender.png
        plot3_inc:  output/zoster_std_age.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:35:14

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
8a4a63d
Requested actions
  • generate_dataset
  • data_cleaning
  • practice_registrations_table
  • Vaccince_information

Code comparison

Compare the code used in this job request