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Job request: 6249

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-collateral
ID:
a7tzvigd6yh45umz
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 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_study_population_resp
    Status:
    Status: Failed
    Job identifier:
    rzxopkxb2ipgz2rc
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population_dm
    Status:
    Status: Failed
    Job identifier:
    c7i3klhko52c7rxy
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    tyxtsgyvpf2uxk6w
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population_mortality
    Status:
    Status: Failed
    Job identifier:
    en6jvnkokwdwpgqa
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    calculate_measures_mortality
    Status:
    Status: Failed
    Job identifier:
    avo74tcvak6mxsxi
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    graphs_mh_cvd
    Status:
    Status: Failed
    Job identifier:
    332nzfijbfaidqfe
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures_resp
    Status:
    Status: Failed
    Job identifier:
    mxikn7rcarf4xdhr
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    graphs_mortality
    Status:
    Status: Failed
    Job identifier:
    7ywjwsf6iymwkgcj
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures
    Status:
    Status: Failed
    Job identifier:
    wbnafa5etpvontkf
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    calculate_measures_dm
    Status:
    Status: Failed
    Job identifier:
    tkwjwuvzpiq36iyc
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    graphs_resp
    Status:
    Status: Failed
    Job identifier:
    lmu2ct5aalmwwqrd
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    graphs_dm
    Status:
    Status: Failed
    Job identifier:
    2q6xwvlu5w4tvput
    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 "2020-03-01 to 2020-06-01 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 "2020-03-01 to 2020-06-01 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 "2020-03-01 to 2020-06-01 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 "2020-03-01 to 2020-06-01 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
  # 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: 01:43:44

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-collateral
Requested by
Rohini Mathur
Branch
main
Force run dependencies
Yes
Git commit hash
9499a5b
Requested actions
  • run_all

Code comparison

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