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Job request: 6555

Organisation:
Bennett Institute
Workspace:
hypertension-sro
ID:
jmo6fwsa6wyqbi6b
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Milan Wiedemann 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_hyp003
    Status:
    Status: Failed
    Job identifier:
    s3rbab5iuchrgqu6
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population_hyp001
    Status:
    Status: Failed
    Job identifier:
    naxfhjdb5fov6w2b
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    join_measures
    Status:
    Status: Failed
    Job identifier:
    k6kouri5g67fgf6y
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_hyp_report
    Status:
    Status: Failed
    Job identifier:
    kc2rh2ujs3z5hjhg
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures_hyp001
    Status:
    Status: Failed
    Job identifier:
    sl34tqlt3poxazeh
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures_hyp003
    Status:
    Status: Failed
    Job identifier:
    uawqzaae7vx3xuo4
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  # Study populations
  # Extract latests ethnicity record for cohort
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output/indicators 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_ethnicity.feather

  # Extract cohort for indicator HYP001 by month 
  generate_study_population_hyp001:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp001 
      --index-date-range "2019-01-01 to 2022-01-01 by month" 
      --output-dir=output/indicators
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp001_*.feather

  # Extract cohort for indicator HYP003 by month 
  generate_study_population_hyp003:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp003 
      --index-date-range "2019-01-01 to 2022-01-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp003_*.feather
  
  # Extract cohort for indicator HYP007 by month 
  generate_study_population_hyp007:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp007 
      --index-date-range "2019-01-01 to 2022-01-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp007_*.feather

  # join_ethnicity:
  #   run: >
  #     cohort-joiner:v0.0.9
  #       --lhs output/indicators/input_hyp001_*.feather
  #       --rhs output/indicators/input_ethnicity.feather
  #       --output-dir output/indicators/joined
  #   needs: [generate_study_population_ethnicity, generate_study_population_hyp001]
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/indicators/joined/input_hyp*.csv

  # Measures
  # Generate measures for indicator HYP001 by month
  generate_measures_hyp001:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp001 
       --output-dir=output/indicators
     needs: [generate_study_population_hyp001]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/measure_hyp001_*_rate.csv

 # Generate measures for indicator HYP003 by month
  generate_measures_hyp003:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp003 
       --output-dir=output/indicators
     needs: [generate_study_population_hyp003]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/measure_hyp003_*_rate.csv

  # Generate measures for indicator HYP007 by month
  generate_measures_hyp007:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp007 
       --output-dir=output/indicators
     needs: [generate_study_population_hyp007]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/measure_hyp007_*_rate.csv
  
  # Join all measure files for each indicator
  join_measures:
    run: r:latest analysis/join_measures.R
    needs: [generate_measures_hyp001]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_hyp001.csv

# Generate notebooks
  generate_hyp_report:
    run: r:latest -e 'rmarkdown::render("analysis/hypertension-sro-report.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
    needs: [join_measures]
    outputs:
      moderately_sensitive:
        report: output/notebooks/hypertension-sro-report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:38:42

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

Job request

Status
Failed
Backend
TPP
Workspace
hypertension-sro
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
Yes
Git commit hash
9e1523f
Requested actions
  • generate_study_population_hyp001
  • generate_study_population_hyp003
  • generate_measures_hyp001
  • generate_measures_hyp003
  • join_measures
  • generate_hyp_report

Code comparison

Compare the code used in this job request