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Job request: 221

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
households
ID:
bryky5srizhjqdfj
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Seb Bacon requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    os_test
    Status:
    Job identifier:
    2zqpxgaxivs6plq6-manually-set

Pipeline

Show project.yaml 
version: "1.0"
actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --output-dir=/workspace
    outputs:
      highly_sensitive:
        cohort: input.csv

  prepare_data:
    run: stata-mp:latest analysis/01_hh_cr_analysis_dataset.do
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        allvars: hh_analysis_datasetALLVARS.dta
        redvars: hh_analysis_datasetREDVARS.dta

  descriptive_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/opensafely_eda_test_notebook.ipynb --execute --to html --output-dir=/workspace --ExecutePreprocessor.timeout=86400
    needs: [prepare_data]
    outputs:
      moderately_sensitive:
        notebook: opensafely_eda_test_notebook.html
        ages: analysis/ages.png
        hhsize: analysis/hh_sizes.png
        cases: analysis/hh_cases_*.png

    run: jupyter:latest jupyter nbconvert /workspace/analysis/opensafely_age_hh.ipynb --execute --to html --output-dir=/workspace --ExecutePreprocessor.timeout=86400
    needs: [prepare_data]
    outputs:
      moderately_sensitive:
        notebook: opensafely_age_hh.html
        notebook_log: analysis/opensafely_age_hh.log

  vo_test:
    run: python:latest python analysis/fit_vo.py 20
    needs: []
    outputs:
      moderately_sensitive:
        vo: vo.txt

  os_test:
    run: python:latest python analysis/opensafely_age_hh.py
    needs: [prepare_data]
    outputs:
      moderately_sensitive:
        log: opensafely_age_hh.log

Timeline

  • Created:

  • Started:

  • Runtime:

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

Job information

Status
Failed
Backend
TPP
Workspace
households
Requested by
Seb Bacon
Branch
master
Force run dependencies
No
Git commit hash
d2b03ea
Requested actions
  • os_test

Code comparison

Compare the code used in this Job Request