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Job request: 17383

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
collateral-imd
ID:
fexd5gd3kpqqmcvp
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ruth Costello 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_study_population_dm
    Status:
    Status: Succeeded
    Job identifier:
    7d4vupxplas2ppa2
  • Action:
    generate_study_population_resp
    Status:
    Status: Succeeded
    Job identifier:
    npfaeqwtxvd672ga
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    7fkl7zp3mt35rmy5
    Error:
    nonzero_exit: Job exited with an error: A transient database error occurred, your job may run if you try it again, if it keeps failing then contact tech support
  • Action:
    generate_study_population_static
    Status:
    Status: Succeeded
    Job identifier:
    s3ttfck242fv4wvm
  • Action:
    join_cohorts_dm
    Status:
    Status: Succeeded
    Job identifier:
    xooecdiy5yeotdys
  • Action:
    join_cohorts_resp
    Status:
    Status: Succeeded
    Job identifier:
    oi65mfzrkfuro6nk
  • Action:
    calculate_measures_dm
    Status:
    Status: Succeeded
    Job identifier:
    pbviwrgcttisd7dk
  • Action:
    calculate_measures_resp
    Status:
    Status: Succeeded
    Job identifier:
    dn34aajgmurh6vgl
  • Action:
    join_cohorts
    Status:
    Status: Failed
    Job identifier:
    tugmrbjpnzblcqpv
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures
    Status:
    Status: Failed
    Job identifier:
    czpxtvznybujxoyl
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    graphs
    Status:
    Status: Failed
    Job identifier:
    flgightspwe66o34
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
# General population cohort
  generate_study_population:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition
      --index-date-range "2018-03-01 to 2021-12-31 by month" 
      --output-dir=output/measures 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv

  generate_study_population_static:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_static
    outputs:
      highly_sensitive:
        cohort: output/input_static.csv

  join_cohorts:
    run: >
        cohort-joiner:v0.0.56
          --lhs output/measures/input_*.csv
          --rhs output/input_static.csv
          --output-dir output/measures/joined
    needs: [generate_study_population, generate_study_population_static]
    outputs: 
      highly_sensitive:
        cohort: output/measures/joined/input_*.csv

  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition --output-dir=output/measures/joined
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure: output/measures/joined/measure_*_rate.csv
# Diabetes subpopulation
  generate_study_population_dm:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_dm
      --index-date-range "2018-03-01 to 2021-12-31 by month" 
      --output-dir=output/measures 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_dm_*.csv

  join_cohorts_dm:
    run: >
        cohort-joiner:v0.0.56
          --lhs output/measures/input_dm_*.csv
          --rhs output/input_static.csv
          --output-dir output/measures/joined
    needs: [generate_study_population_dm, generate_study_population_static]
    outputs: 
      highly_sensitive:
        cohort: output/measures/joined/input_dm_*.csv

  calculate_measures_dm:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_dm --output-dir=output/measures/joined
    needs: [join_cohorts_dm]
    outputs:
      moderately_sensitive:
        measure: output/measures/joined/measure_dm*_rate.csv

# Respiratory subpopulation
  generate_study_population_resp:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_resp
      --index-date-range "2018-03-01 to 2021-12-31 by month" 
      --output-dir=output/measures 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_resp_*.csv

  join_cohorts_resp:
    run: >
        cohort-joiner:v0.0.56
          --lhs output/measures/input_resp_*.csv
          --rhs output/input_static.csv
          --output-dir output/measures/joined
    needs: [generate_study_population_resp, generate_study_population_static]
    outputs: 
      highly_sensitive:
        cohort: output/measures/joined/input_resp_*.csv

  calculate_measures_resp:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_resp --output-dir=output/measures/joined
    needs: [join_cohorts_resp]
    outputs:
      moderately_sensitive:
        measure: output/measures/joined/measure_resp_*_rate.csv

  create_baseline_tables:
    run: stata-mp:latest analysis/101_baseline_tables.do
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        log: logs/table1_descriptives.log
        output: output/tables/baseline_table_*.csv

  graphs:
    run: stata-mp:latest analysis/102_graphs.do
    needs: [calculate_measures, calculate_measures_dm, calculate_measures_resp]
    outputs:
      moderately_sensitive:
        log: logs/graphs.log
        output: output/graphs/line_*.svg
        data: output/graphs/line_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 21:22:32

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

Job request

Status
Failed
Backend
TPP
Workspace
collateral-imd
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
95c12fa
Requested actions
  • generate_study_population
  • generate_study_population_static
  • join_cohorts
  • calculate_measures
  • generate_study_population_dm
  • join_cohorts_dm
  • calculate_measures_dm
  • generate_study_population_resp
  • join_cohorts_resp
  • calculate_measures_resp
  • graphs

Code comparison

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