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Job request: 4560

Organisation:
NHSE/I
Workspace:
carehomeprescribing
ID:
igasg4jy64bihtv3
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Greg Eydmann 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_ethnicity
    Status:
    Status: Failed
    Job identifier:
    4n6wwtsluxk6sk37
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    jep42ga6b3kjkg5e
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_control
    Status:
    Status: Failed
    Job identifier:
    y3utftj735n4mydq
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    describe
    Status:
    Status: Failed
    Job identifier:
    lt7xm2g766noj2tx
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    kdpcrgih4c56c472
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity_control
    Status:
    Status: Failed
    Job identifier:
    cromvnsjanjfcd2n
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures_control
    Status:
    Status: Failed
    Job identifier:
    p2qpyh3uqa4lhh72
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    ubczoiv47n3unh7t
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:


  generate_study_population:
    run: cohortextractor:latest generate_cohort --index-date-range "2019-03-01 to 2021-3-01 by month" --study-definition study_definition --output-dir=output/inputs
    outputs:
      highly_sensitive:
        cohort: output/inputs/input_*.csv

  generate_study_population_control:
    run: cohortextractor:latest generate_cohort --index-date-range "2019-3-01 to 2021-3-01 by month" --study-definition study_definition_control --output-dir=output/control
    outputs:
      highly_sensitive:
        cohort: output/control/input_control_*.csv
        
        
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/inputs 
    outputs:
      highly_sensitive:     
        cohort: output/inputs/input_ethnicity.csv

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py    
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/inputs/input*.csv


  join_ethnicity_control:
    run: python:latest python analysis/join_ethnicity_control.py    
    needs: [generate_study_population_control, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/control/input*.csv
        
          # Generate measures
          
  generate_measures_control:
      run: cohortextractor:latest generate_measures --study-definition study_definition_control --output-dir=output/control
      needs: [join_ethnicity_control]
      outputs:
        moderately_sensitive:
          measure_csv: output/control/measure_control_*.csv


  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/inputs
      needs: [join_ethnicity]
      outputs:
        moderately_sensitive:
          measure_csv: output/inputs/measure_a*.csv
               
  describe:
    run: python:latest python analysis/descriptives.py
    needs: [generate_measures,join_ethnicity,generate_measures_control]
    outputs:
      moderately_sensitive:
        cohort: output/graphs/*.html
        tables: output/descriptives/descriptive_statistics_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:46

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

Job request

Status
Failed
Backend
TPP
Workspace
carehomeprescribing
Requested by
Greg Eydmann
Branch
main
Force run dependencies
No
Git commit hash
8689345
Requested actions
  • generate_study_population
  • generate_study_population_control
  • generate_study_population_ethnicity
  • join_ethnicity
  • join_ethnicity_control
  • generate_measures_control
  • generate_measures
  • describe

Code comparison

Compare the code used in this job request