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Job request: 6837

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-collateral
ID:
h6cvz4b5djdc4apr
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Rohini Mathur 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
    Status:
    Status: Failed
    Job identifier:
    suk36re7ep3qxlrx
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    calculate_measures_resp
    Status:
    Status: Succeeded
    Job identifier:
    o4krnlnqy3yocsuz
  • Action:
    graphs_resp
    Status:
    Status: Succeeded
    Job identifier:
    jdxaexlmg6rr4ya3
  • Action:
    graphs_mh_cvd
    Status:
    Status: Failed
    Job identifier:
    s2capurkwtxbft65
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures
    Status:
    Status: Failed
    Job identifier:
    ocv2u4o2lotd7cfe
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  # Generates study population for CV, mental health outcomes
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv
  # Generates study population for diabetes outcomes
  generate_study_population_dm:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/dm --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/dm/input_dm_*.csv

  # Generates study population for respiratory outcomes
  generate_study_population_resp:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_resp --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/resp --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/resp/input_resp_*.csv

  # Generates study population for mortality
  generate_study_population_mortality:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_mortality --index-date-range "2019-02-01 to 2022-01-31 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/mortality/input_mortality_*.csv
  
  # Generates summary measures for CV and mental health outcomes
  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_*.csv
  # Generates summary measures for diabetes outcomes  
  calculate_measures_dm:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_dm --output-dir=output/measures/dm
    needs: [generate_study_population_dm]
    outputs:
      moderately_sensitive:
        measure: output/measures/dm/measure_dm_*.csv

  # Generates summary measures for respiratory outcomes  
  calculate_measures_resp:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_resp --output-dir=output/measures/resp
    needs: [generate_study_population_resp]
    outputs:
      moderately_sensitive:
        measure: output/measures/resp/measure_*.csv

  # Generates summary measures for mortality outcomes  
  calculate_measures_mortality:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_mortality --output-dir=output/measures/mortality
    needs: [generate_study_population_mortality]
    outputs:
      moderately_sensitive:
        measure: output/measures/mortality/measure_*.csv
  
  # Generates graphs for CVD & mental health outcomes
  graphs_mh_cvd:
    run: stata-mp:latest analysis/graphs_mh_cvd.do 
    needs: [calculate_measures]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mh_cvd.log
        output: output/line_*.eps
      highly_sensitive:
        output: output/measures/measure_*
  # Generates graphs for diabetes outcomes
  graphs_dm:
    run: stata-mp:latest analysis/graphs_dm.do 
    needs: [calculate_measures_dm]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_dm.log
        output: output/line_dm_*.eps
  # Generate graphs for respiratory outcomes
  graphs_resp:
    run: stata-mp:latest analysis/graphs_resp.do 
    needs: [calculate_measures_resp]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_resp.log
        output: output/line_resp_*.eps

  # Generate graphs for mortality
  graphs_mortality:
    run: stata-mp:latest analysis/graphs_mortality.do 
    needs: [calculate_measures_mortality]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mortality.log
        output: output/line_mortality_*.eps

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:18:08

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-collateral
Requested by
Rohini Mathur
Branch
main
Force run dependencies
No
Git commit hash
9bd6960
Requested actions
  • generate_study_population
  • calculate_measures
  • calculate_measures_resp
  • graphs_mh_cvd
  • graphs_resp

Code comparison

Compare the code used in this job request