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Job request: 4168

Organisation:
Bennett Institute
Workspace:
long-covid-sick-notes
ID:
n7eqywpua5iegvnv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robin Park 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_general_2019
    Status:
    Succeeded
    Job identifier:
    2gf4sm3ojrvkuxfp
  • Action:
    generate_study_population_pneumonia_2019
    Status:
    Failed
    Job identifier:
    zdd4vwrvmfrnvwgx
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_covid_2020
    Status:
    Failed
    Job identifier:
    joccfzsplksedgvy
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_general_2020
    Status:
    Succeeded
    Job identifier:
    rywgzwl2f2q7qrfn
  • Action:
    matching_2019
    Status:
    Failed
    Job identifier:
    vovfl6vxfygw2mf4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    matching_2020
    Status:
    Failed
    Job identifier:
    vnn6e6e4756guhjj
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_covid_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_2020 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_covid_2020.csv

  generate_study_population_general_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2019 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_2019.csv

  generate_study_population_general_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_2020 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_general_2020.csv

  generate_study_population_pneumonia_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia_2019 --output-dir=output/cohorts 
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_pneumonia_2019.csv

  matching_2019:
    run: python:latest python analysis/match_running.py "input_general_2019" "_2019" "2019-02-01" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2020, generate_study_population_general_2019]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_2019.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_2019.csv

  matching_2020:
    run: python:latest python analysis/match_running.py "input_general_2020" "_2020" "2020-02-01" --output-dir=output/cohorts
    needs: [generate_study_population_covid_2020, generate_study_population_general_2020]
    outputs:
      moderately_sensitive:
        matching_report: output/cohorts/matching_report_2020.txt
      highly_sensitive:
        matched_cohort: output/cohorts/matched_matches_2020.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 09:29:52

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

Job request

Status
Failed
Backend
TPP
Workspace
long-covid-sick-notes
Requested by
Robin Park
Branch
master
Force run dependencies
No
Git commit hash
dde614c
Requested actions
  • generate_study_population_covid_2020
  • generate_study_population_general_2019
  • generate_study_population_general_2020
  • generate_study_population_pneumonia_2019
  • matching_2019
  • matching_2020

Code comparison

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