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Job request: 25006

Organisation:
King's College London
Workspace:
zoster_incidence_imids
ID:
hkls6niorctblc5n
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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: '4.0'

actions:


  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_2.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_V2.py --output output/Incidence_age_gender_measure.csv
    outputs:
      highly_sensitive:
        measure: output/Incidence_age_gender_measure.csv
        
  Baseline_table:
    run: r:latest analysis/baseline_table.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table_imids: output/baseline_by_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


  Vaccination_table:
    run: r:latest analysis/vaccination_region_year.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        tableq: output/vaccination_summary.csv
        table2: output/eligiable_vaccination_summary.csv

  Incidence_crude_table:
    run: r:latest analysis/Incidence_imids_diag_V3.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1: output/Crude_incidence_allimids.csv

  Incidence_adjusted_table:
    run: r:latest analysis/Incidence_imids_age_gender_V2.R
    needs:
    - data_cleaning
    outputs:
     moderately_sensitive:
        table1: output/Ajusted_incidence_allimids.csv

  Incidence_adjusted_incident_table:
    run: r:latest analysis/Incidence_imids_age_gender_incident.R
    needs:
    - data_cleaning
    outputs:
     moderately_sensitive:
        table1: output/Ajusted_incidence_allimids_incident.csv

  Incidence_adjusted_region_table:
    run: r:latest analysis/Incidence_imids_age_gender_region_V1.R
    needs:
    - data_cleaning
    outputs:
     moderately_sensitive:
        table1: output/Adjusted_incidence_by_region.csv
        table2: output/Adjusted_incidence_by_region_period.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
        table3:  output/regression_IRR_IMID_adjusted.csv
        table4:  output/regression_IRR_by_IMID_adjusted.csv  

  Regresison_IRR_COVID:
    run: r:latest analysis/Regresison_IRR_COVID.R
    needs:
    - data_cleaning
    outputs:
      moderately_sensitive:
        table1:  output/Regression_IRR_all_models.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



  Incidence_plot:
    run: r:latest analysis/incidence_plot.R
    needs:
    - data_cleaning
    - Incidence_adjusted_table
    outputs:
      moderately_sensitive:
        plot1_inc:  output/Incidence_adjusted_monthly.png
        plot2_inc:  output/Incidence_adjusted_3monthrolling.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 28:27:35

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

Job information

Status
Failed
Backend
TPP
Workspace
zoster_incidence_imids
Requested by
Zijing Yang
Branch
main
Force run dependencies
No
Git commit hash
2315b94
Requested actions
  • generate_dataset
  • data_cleaning
  • generate_zoster_prevalence
  • Baseline_table
  • Vaccination_table
  • Incidence_crude_table
  • Incidence_adjusted_table
  • Incidence_adjusted_incident_table
  • Incidence_adjusted_region_table
  • Regresison_IRR_COVID
  • Incidence_plot

Code comparison

Compare the code used in this Job Request