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Job request: 13559

Organisation:
ONS
Workspace:
covid_mental_health
ID:
5siq6yq2glvo6wtl
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

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
                bmi: output/bmi_summary_table_info_before_cap.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
                incidence_bmi: output/incidence_cont_bmi_stats.csv
                prevalence_bmi: output/prevalence_cont_bmi_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/inc_hr_placeholder.csv
                temp2: output/prev_hr_placeholder.csv
                cox_inc1: output/cox_graph_inc_no_adj.jpg
                cox_inc2: output/cox_graph_inc_min_adj.jpg
                cox_inc3: output/cox_graph_inc_full_adj.jpg
                cox_prev1: output/cox_graph_prev_no_adj.jpg
                cox_prev2: output/cox_graph_prev_min_adj.jpg
                cox_prev3: output/cox_graph_prev_full_adj.jpg
                res_inc1: output/res_no_inc.jpg
                res_inc2: output/res_min_inc.jpg 
                res_inc3: output/res_full_inc.jpg
                res_prev1: output/res_no_prev.jpg
                res_prev2: output/res_min_prev.jpg
                res_prev3: output/res_full_prev.jpg
                sch_res1: output/schoenfled_inc_no.csv
                sch_res2: output/schoenfled_inc_min.csv
                sch_res3: output/schoenfled_inc_full.csv
                sch_res4: output/schoenfled_prev_no.csv
                sch_res5: output/schoenfled_prev_min.csv
                sch_res6: output/schoenfled_prev_full.csv

    event_rates_incidence:
        run: r:latest analysis/event_rates_incidence.R
        needs: [cumulative_incidence]
        outputs:
            moderately_sensitive:
                incidence_event_rates: output/event_counts_and_rates_incidence.csv

    event_rates_prevalence:
        run: r:latest analysis/event_rates_prevalence.R
        needs: [cumulative_incidence]
        outputs:
            moderately_sensitive:
                incidence_event_rates: output/event_counts_and_rates_prevalence.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 62:26:27

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
Klaudia Rzepnicka
Branch
main
Force run dependencies
No
Git commit hash
0e0b08a
Requested actions
  • generate_wide_non_health
  • generate_wide_health_mh
  • generate_wide_health_non_mh
  • combine_wide_data
  • transform_cis_wide_to_long
  • reconcile_snomed_ctv3
  • derive_exposed
  • derive_controls
  • perform_matching
  • adjust_matched_groups
  • descriptive_stats
  • cumulative_incidence
  • hazard_ratios
  • event_rates_incidence
  • event_rates_prevalence

Code comparison

Compare the code used in this job request