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Job request: 16912

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt_longcovid_vaccines
ID:
fgmwr3wyqufopkz3
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 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_cases
    Status:
    Succeeded
    Job identifier:
    jqcnbpcsg4unipg2
  • Action:
    generate_dataset_controls
    Status:
    Succeeded
    Job identifier:
    otahsjjsc466q6wd
  • Action:
    generate_dataset_lc_pre_vacc
    Status:
    Succeeded
    Job identifier:
    wbri4kainwom7lfd
  • Action:
    clean_the_data
    Status:
    Succeeded
    Job identifier:
    ojextqyhudjvv6tm
  • Action:
    crude_rates
    Status:
    Succeeded
    Job identifier:
    rpyyu7k4ghp5k3rj
  • Action:
    time_update_data
    Status:
    Succeeded
    Job identifier:
    rcpz4fietjcwblk2
  • Action:
    poisson_rates_static
    Status:
    Succeeded
    Job identifier:
    bxwvsqzksnepzf3p
  • Action:
    poisson_rates_timeupdated
    Status:
    Failed
    Job identifier:
    yvnsktmklyyys34p
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    plot_incidence
    Status:
    Succeeded
    Job identifier:
    4lp2v7iecz3rv7at
  • Action:
    poisson_plots
    Status:
    Failed
    Job identifier:
    eyw52n5euqk32iwk
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
 population_size: 20000

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 
      moderately_sensitive: 
        txt1: output/data_properties/clean_dataset_skim.txt
        txt2: output/data_properties/clean_dataset_tabulate.txt

  time_update_data: 
    run: >
      r:latest
        analysis/011_timeupdate_data.R
    needs: [clean_the_data]
    outputs: 
      highly_sensitive: 
        timedata_longcovid: output/timeupdate_dataset_lc_all.gz.parquet
        timedata_longcovid_dx: output/timeupdate_dataset_lc_dx.gz.parquet
        timedata_fracture: output/timeupdate_dataset_fracture.gz.parquet
      moderately_sensitive: 
        txt3: output/data_properties/timeupdated_dataset_skim.txt

  crude_rates:
    run: >
      r:latest
        analysis/020_cruderates.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        cruderates: output/tab021_crude_lc_rates.csv
  
  plot_incidence:
    run: >
      r:latest
        analysis/030_plotrates.R
    needs: [clean_the_data, time_update_data]
    outputs:
      moderately_sensitive:
        cuminc: output/figures/fig1_cumulative_incidence.pdf
        rawcountsplot: output/figures/fig2_raw_counts_line.pdf
        rawcount: output/figures/fig2b_raw_counts_column.pdf
        vaccinegap: output/supplementary/fig_agegap_vaccines.pdf

  poisson_rates_static:
    run: >
      r:latest
        analysis/040_poisson_regressions_staticvars.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        poissonrates: output/tab023_poissonrates_static.csv

  poisson_rates_timeupdated:
    run: >
      r:latest
        analysis/041_poisson_regressions_timeupdated.R
    needs: [time_update_data]
    outputs:
      moderately_sensitive:
        poissonrates: output/tab023_poissonrates_timeupdated.csv

  poisson_plots:
    run: >
      r:latest
        analysis/042_plot_poisson_results.R
    needs: [poisson_rates_static, poisson_rates_timeupdated]
    outputs: 
      moderately_sensitive: 
        poissonplots_all: output/figures/fig3a_rate_ratios.pdf
        poissonplots_lc: output/figures/fig3b_rate_ratios_longcovid.pdf
        poissonplots_lc_adjusted: output/figures/fig3c_rate_ratios_longcovid_adjustedonly.pdf
        poissonplots_control: output/figures/fig3d_rate_ratios_controloutcome.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 16:22:20

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

Job request

Status
Failed
Backend
TPP
Workspace
openprompt_longcovid_vaccines
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
Yes
Git commit hash
4b1f4d8
Requested actions
  • run_all

Code comparison

Compare the code used in this job request