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Job request: 7167

Organisation:
University of Bristol
Workspace:
lockdown-and-vulnerable-groups
ID:
pe5jtvi44oao45hc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Scott Walter 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

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 "2020-02-24 to 2020-03-09 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-16 to 2020-03-30 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz
        # note that the file pattern should be distinct for each action otherwise 
        # when you run this action, previous outputs matching this pattern will be removed.
        # May need to make sure each action covers a specific period e.g. a single month or whole year so that the output pattern is input_2020_*.csv etc. 

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-04-06 to 2020-04-20 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv




#  generate_study_population:
#    run: cohortextractor:latest generate_cohort --study-definition study_definition1 --index-date-range "2020-03-16 to 2020-03-30 by week" --skip-existing --output-format=csv --output-dir=output
#    outputs:
#      highly_sensitive:
#        cohort: output/input_*.csv
#
#  generate_measures:
#    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing
#    needs: [generate_study_population]
#    outputs:
#      highly_sensitive:
#        measure_csv: output/measure_*_rate.csv

#  run_model
#    run: stata-mp:latest analysis/model.do
#    needs: [generate_study_population]
#    outputs:
#      moderately_sensitive:
#        model: output/practice_variables.dta
#        model2: output/practice_variables.xlsx

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:47

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

Job request

Status
Succeeded
Backend
TPP
Workspace
lockdown-and-vulnerable-groups
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
12fa456
Requested actions
  • generate_measures

Code comparison

Compare the code used in this job request