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Job request: 4149

Organisation:
NICE
Workspace:
post_covid_nice_compliance
ID:
sky37ub7adw5647d
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robert Willans 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_acute_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_any_acute_covid_pri_care
    outputs:
      highly_sensitive:
        cohort: output/input_any_acute_covid_pri_care.csv
        
  generate_og_pc_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ongoing_post_covid
    outputs:
      highly_sensitive:
        cohort: output/input_ongoing_post_covid.csv
        
  generate_cohort_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all
    outputs:
      highly_sensitive:
        cohort: output/input_all.csv

  debug_cohort:
    run: r:latest analysis/debug_script.R
    needs: [generate_acute_cohort, generate_og_pc_cohort, generate_cohort_all]
    outputs:
      moderately_sensitive:
        debug_oc: output/debug_oc_counts.csv
        debug_ac: output/debug_ac_counts.csv
        debug_all_counts: output/debug_all_counts.csv
        debug_all_crosstab: output/debug_all_diag_refer_crosstab.csv

  describe:
    run: r:latest analysis/report.R
    needs: [generate_acute_cohort, generate_og_pc_cohort, generate_cohort_all]
    outputs:
      moderately_sensitive:
        pc_counts: output/ratios.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:06:34

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

Job request

Status
Succeeded
Backend
TPP
Workspace
post_covid_nice_compliance
Requested by
Robert Willans
Branch
master
Force run dependencies
No
Git commit hash
2ca2dc4
Requested actions
  • generate_cohort_all

Code comparison

Compare the code used in this job request