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Job request: 16869

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt_longcovid_vaccines
ID:
ucr4kewibnjzuylh
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:
    generate_dataset_cases
    Status:
    Status: Succeeded
    Job identifier:
    b42pvfadmlici3ps
  • Action:
    generate_dataset_lc_pre_vacc
    Status:
    Status: Succeeded
    Job identifier:
    izdks3r4lvbk5wj7
  • Action:
    generate_dataset_controls
    Status:
    Status: Succeeded
    Job identifier:
    lkyumwbaruiji6zv
  • Action:
    clean_the_data
    Status:
    Status: Succeeded
    Job identifier:
    scqnidu2ybbf6oiu
  • Action:
    poisson_rates
    Status:
    Status: Failed
    Job identifier:
    tfenwii22md7rc4y
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    crude_rates
    Status:
    Status: Succeeded
    Job identifier:
    lmpv4je2igd22rts
  • Action:
    plot_incidence
    Status:
    Status: Succeeded
    Job identifier:
    5wbctf7il2pma4br
  • Action:
    poisson_plots
    Status:
    Status: Failed
    Job identifier:
    prypaq7cqvdqenxv
    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 
        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: 
        txt1: output/data_properties/clean_dataset_skim.txt
        txt2: output/data_properties/clean_dataset_tabulate.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]
    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:
    run: >
      r:latest
        analysis/040_poisson_regressions.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        poissonrates: output/tab023_poissonrates.csv

  poisson_plots:
    run: >
      r:latest
        analysis/041_plot_poisson_results.R
    needs: [poisson_rates]
    outputs: 
      moderately_sensitive: 
        poissonplots_all: output/figures/fig3a_rate_ratios.pdf
        poissonplots_lc: output/figures/fig3b_rate_ratios_longcovid.pdf
        poissonplots_control: output/figures/fig3c_rate_ratios_controloutcome.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 35:43:32

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

Job information

Status
Failed
Backend
TPP
Workspace
openprompt_longcovid_vaccines
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
Yes
Git commit hash
afbace5
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request