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Job request: 153

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
households
ID:
ohpck2hitmatf6fa
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

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
        allvars_csv: hh_analysis_datasetALLVARS.csv
        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

  household_analysis:
    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

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
Kevin Wing
Branch
master
Force run dependencies
No
Git commit hash
293666a
Requested actions
  • household_analysis

Code comparison

Compare the code used in this Job Request