Skip to content

Job request: 10680

Organisation:
ONS
Workspace:
covid_mental_health
ID:
pu5w5gvc6je773wt
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Luke Lorenzi 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 
# describes how each step in your analysis should be run

version: '3.0'

expectations:
  population_size: 5000

actions:
    generate_cis_visit_level:
        run: cohortextractor:latest generate_cohort --study-definition study_definition_cis_wide
        outputs:
            highly_sensitive:
                cohort: output/input_cis_wide.csv
    
    transform_cis_wide_to_long:
        run: r:latest analysis/cis_wide_to_long.R
        needs: [generate_cis_visit_level]
        outputs:
            moderately_sensitive:
                cohort: output/cis_wide_dimensions.csv
            highly_sensitive:
                cohort: output/input_cis_long.csv
    
    reconcile_snomed_ctv3:
        run: r:latest analysis/reconcile_snomed_ctv3.R
        needs: [transform_cis_wide_to_long]
        outputs:
            highly_sensitive:
                cohort: output/input_reconciled.csv
    
    derive_exposed:
        run: r:latest analysis/exposed_population.R
        needs: [reconcile_snomed_ctv3]
        outputs:
            highly_sensitive:
                cohort: output/cis_exposed.csv
    
    derive_controls:
        run: r:latest analysis/control_population.R
        needs: [reconcile_snomed_ctv3]
        outputs:
            highly_sensitive:
                cohort: output/cis_control.csv
                
    # perform_matching:
    #     run: r:latest analysis/create_controls.R
    #     needs: [derive_exposed, derive_controls]
    #     outputs:
    #         highly_sensitive:
    #             cohort: output/matched_groups.csv
    
    # adjust_matched_groups:
    #     run: r:latest analysis/adjust_groups.R
    #     needs: [perform_matching]
    #     outputs:
    #         highly_sensitive:
    #             cohort: output/adjusted_groups.csv
    
    # descriptive_stats:
    #     run: r:latest analysis/descriptive_statistics.R
    #     needs: [adjust_matched_groups]
    #     outputs:
    #         moderately_sensitive:
    #             cat_stats: output/cat_stats.csv
    #             con_stats: output/cont_stats.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:23

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid_mental_health
Requested by
Luke Lorenzi
Branch
main
Force run dependencies
No
Git commit hash
40beb1f
Requested actions
  • reconcile_snomed_ctv3

Code comparison

Compare the code used in this job request