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Job request: 17462

Organisation:
PrescQIPP
Workspace:
the_effects_of_covid-19_on_dfms_prescribing
ID:
5iemoyhsolbgxsxy
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.

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=csv
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  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=csv
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv
  
  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-01-01 to 2023-04-01 by month" --output-dir=output --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv
 
  generate_indication:
    run: python:latest python analysis/indication_variables.py
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv
  
  generate_medication:
    run: python:latest python analysis/medication_variables.py
    needs: [generate_indication]
    outputs:
      highly_sensitive:
        cohort: output/in*.csv

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

  generate_report:
    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

Timeline

  • Created:

  • Started:

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  • Runtime:

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

Job request

Status
Failed 
JobRequestError: All requested actions were already scheduled to run
Backend
TPP
Workspace
the_effects_of_covid-19_on_dfms_prescribing
Requested by
Rachel Seeley
Branch
main
Force run dependencies
No
Git commit hash
44ad72c
Requested actions
  • generate_report

Code comparison

Compare the code used in this job request