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Job request: 10657

Organisation:
ONS
Workspace:
covid_mental_health
ID:
kzchv2foi5wn5esd
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

  • Action:
    generate_cis_visit_level
    Status:
    Status: Succeeded
    Job identifier:
    2ux4uwbot43zgfcv
  • Action:
    transform_cis_wide_to_long
    Status:
    Status: Succeeded
    Job identifier:
    kre5xjmmehtrj55g
  • Action:
    reconcile_snomed_ctv3
    Status:
    Status: Succeeded
    Job identifier:
    hl7yrl4opdg3v3fg
  • Action:
    derive_controls
    Status:
    Status: Failed
    Job identifier:
    e7mtpe5etudtimfd
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    derive_exposed
    Status:
    Status: Failed
    Job identifier:
    f4km2ljawcljdz3t
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    descriptive_stats
    Status:
    Status: Failed
    Job identifier:
    i2xf6l6z5gzizxat
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    adjust_matched_groups
    Status:
    Status: Failed
    Job identifier:
    mwddtuvzuu2256da
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    perform_matching
    Status:
    Status: Failed
    Job identifier:
    qsht647h4y5n4lv4
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
# describes how each step in your analysis should be run

version: '3.0'

expectations:
  population_size: 500

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: 13:33:09

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

Job request

Status
Failed
Backend
TPP
Workspace
covid_mental_health
Requested by
Luke Lorenzi
Branch
main
Force run dependencies
Yes
Git commit hash
b563f1e
Requested actions
  • run_all

Code comparison

Compare the code used in this job request