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Job request: 6872

Organisation:
PrescQIPP
Workspace:
the_effects_of_covid-19_on_doac_prescribing
ID:
ed7o7idbpgkvaylg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Rachel Seeley 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_measures
    Status:
    Status: Failed
    Job identifier:
    42nhmudjfieyymr2
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_study_population_2
    Status:
    Status: Failed
    Job identifier:
    b5ztkwpooxtl3ikk
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    4lwx25jrneuyayiv
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2021-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_dose:
    run: python:latest python analysis/calculate_dose_scaled_back.py
    needs: [generate_study_population_1, generate_study_population_2]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather
  
  #generate_study_population_ethnicity:
  #run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=csv
  #outputs:
  #highly_sensitive:
  #cohort: output/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/input*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
    needs: [generate_dose]
    outputs: 
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: output/report.html
        plots: output/*.png

  #generate_dose_match:
  #run: python:latest python analysis/dose_match.py
  #needs: [generate_measures]
  #outputs:
  #moderately_sensitive:
  #figure: output/dose_match.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:52

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

Job request

Status
Failed
Backend
TPP
Workspace
the_effects_of_covid-19_on_doac_prescribing
Requested by
Rachel Seeley
Branch
main
Force run dependencies
No
Git commit hash
8d8c03e
Requested actions
  • generate_study_population_2
  • generate_measures
  • generate_notebook

Code comparison

Compare the code used in this job request