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Job request: 16670

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt_longcovid_vaccines
ID:
pfcxsfshlwiravw2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alasdair Henderson 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

  • Action:
    clean_the_data
    Status:
    Status: Succeeded
    Job identifier:
    gm5mjtakp5esdski
  • Action:
    poisson_rates
    Status:
    Status: Succeeded
    Job identifier:
    klxnvig2a6xnypdw

Pipeline

Show project.yaml 
version: '3.0'

expectations:
 population_size: 1000

actions:

  generate_dataset_cases:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_cases.py --output output/dataset_cases.csv.gz
    outputs:
      highly_sensitive:
        dataset_cases: output/dataset_cases.csv.gz
  
  generate_dataset_controls:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_controls.py --output output/dataset_controls.csv.gz
    outputs:
      highly_sensitive:
        dataset_controls: output/dataset_controls.csv.gz
  
  generate_dataset_lc_pre_vacc:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_longcovid_prevaccine.py --output output/dataset_lc_pre_vacc.csv.gz
    outputs:
      highly_sensitive:
        dataset_controls: output/dataset_lc_pre_vacc.csv.gz
  
  clean_the_data: 
    run: > 
      r:latest
        analysis/010_cleandata.R
    needs: [generate_dataset_cases, generate_dataset_controls]
    outputs: 
      highly_sensitive:
        cleandata: output/clean_dataset.gz.parquet 
        timedata: output/timeupdate_dataset.gz.parquet

  crude_rates:
    run: >
      r:latest
        analysis/020_cruderates.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        cruderates: output/tab021_crude_lc_rates.csv
        tuvrates:  output/tab022_tuv_lc_rates.csv
  
  plot_incidence:
    run: >
      r:latest
        analysis/030_plotrates.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        cuminc: output/fig1_cumulative_incidence.pdf
        rawcountsplot: output/fig2_raw_counts_bysex.pdf
  
  poisson_rates:
    run: >
      r:latest
        analysis/040_poisson_regressions.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        poissonrates: output/tab023_poissonrates.csv
        irrplot: output/fig3_rate_ratios.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:26:12

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

Job information

Status
Succeeded
Backend
TPP
Workspace
openprompt_longcovid_vaccines
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
No
Git commit hash
f238d86
Requested actions
  • clean_the_data
  • poisson_rates

Code comparison

Compare the code used in this Job Request