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Job request: 12419

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

This page shows the technical details of what happened when the authorised researcher Klaudia Rzepnicka 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:
    combine_codelists
    Status:
    Status: Succeeded
    Job identifier:
    4al4xrstvcpkpddb
  • Action:
    generate_wide_health_non_mh
    Status:
    Status: Failed
    Job identifier:
    cnejszc5h3hu5vyi
    Error:
    nonzero_exit: Job exited with error code 3: A transient database error occurred, your job may run if you try it again, if it keeps failing then contact tech support
  • Action:
    generate_wide_health_mh
    Status:
    Status: Succeeded
    Job identifier:
    j6jv57wjpu6d6svo
  • Action:
    generate_wide_non_health
    Status:
    Status: Succeeded
    Job identifier:
    dqhzo3e75tzozw27
  • Action:
    transform_cis_wide_to_long
    Status:
    Status: Failed
    Job identifier:
    fos3hnm5opkvfkov
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    combine_wide_data
    Status:
    Status: Failed
    Job identifier:
    fiigar3vsfryyisn
    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: 1000

actions:

    combine_codelists:
        run: r:latest analysis/combine_codelists.R
        outputs:
            highly_sensitive:
                cmd: 'codelists/ons-cmd-codes.csv'
                smi: 'codelists/ons-smi-codes.csv'
                self_harm : 'codelists/ons-self-harm-codes.csv'
                
    generate_wide_non_health:
        run: cohortextractor:latest generate_cohort --study-definition study_definition_non_health --with-end-date-fix
        needs: [combine_codelists]
        outputs:
            highly_sensitive:
                cohort: output/input_non_health.csv
    
    generate_wide_health_mh:
        run: cohortextractor:latest generate_cohort --study-definition study_definition_health_mh --with-end-date-fix
        needs: [combine_codelists]
        outputs:
            highly_sensitive:
                cohort: output/input_health_mh.csv
                
    generate_wide_health_non_mh:
        run: cohortextractor:latest generate_cohort --study-definition study_definition_health_non_mh --with-end-date-fix
        needs: [combine_codelists]
        outputs:
            highly_sensitive:
                cohort: output/input_health_non_mh.csv
                
    combine_wide_data:
        run: r:latest analysis/combine_wide_data.R
        needs: [generate_wide_non_health, generate_wide_health_mh, generate_wide_health_non_mh]
        outputs:
            highly_sensitive:
                cohort: output/input_cis_wide.csv
        
    transform_cis_wide_to_long:
        run: r:latest analysis/cis_wide_to_long.R
        needs: [combine_wide_data]
        outputs:
            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:
                incidence: output/incidence_group.csv
                prevalence: output/prevalence_group.csv
                exacerbated: output/exacerbated_group.csv
    
    adjust_matched_groups:
        run: r:latest analysis/adjust_groups.R
        needs: [perform_matching]
        outputs:
            highly_sensitive:
                incidence: output/adjusted_incidence_group.csv
                prevalence: output/adjusted_prevalence_group.csv
    
    descriptive_stats:
        run: r:latest analysis/descriptive_statistics.R
        needs: [adjust_matched_groups]
        outputs:
            moderately_sensitive:
                incidence_cat_stats: output/incidence_cat_stats.csv
                incidence_con_stats: output/incidence_con_stats.csv
                prevalence_cat_stats: output/prevalence_cat_stats.csv
                prevalence_con_stats: output/prevalence_con_stats.csv
    
    cumulative_incidence:
        run: r:latest analysis/cumulative_incidence_curves.R
        needs: [adjust_matched_groups]
        outputs:
            highly_sensitive:
                inc_t: output/incidence_t.csv
                prev_t: output/prevalence_t.csv
            moderately_sensitive:
                inc_surv: output/incidence_surv.jpg
                prev_surv: output/prevalence_surv.jpg
                
    hazard_ratios:
        run: r:latest analysis/hazard_ratios.R
        needs: [cumulative_incidence]
        outputs:
            moderately_sensitive:
                temp: output/hr_placeholder.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 51:29:35

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
Klaudia Rzepnicka
Branch
main
Force run dependencies
Yes
Git commit hash
33bdaa1
Requested actions
  • generate_wide_non_health
  • generate_wide_health_mh
  • generate_wide_health_non_mh
  • combine_wide_data
  • transform_cis_wide_to_long

Code comparison

Compare the code used in this job request