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Job request: 5936

Organisation:
NICE
Workspace:
post_covid_nice_compliance
ID:
q2firixnecmanrnj
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.

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_cohorts:
    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
        debug_nuts_1_region: output/debug_nuts_1_region.csv

  compliance_ratios:
    run: r:latest analysis/guideline_compliance_ratios.R
    needs: [generate_acute_cohort, generate_og_pc_cohort]
    outputs:
      moderately_sensitive:
        pc_counts: output/ratios.csv
        ref_rates: output/ref_rates_by_month.csv
        
  descriptive_coding_script:
    run: r:latest analysis/descriptive_coding_script.R
    needs: [generate_cohort_all]
    outputs:
      moderately_sensitive:
        Fig1: output/Fig_1.png
        Fig1_numbers: output/Fig_1_numbers.csv
        Fig2: output/Fig_2.png
        Fig2_numbers: output/Fig_2_numbers.csv
        Fig3: output/Fig_3.png
        Fig3_numbers: output/Fig_3_numbers.csv
        Table_1: output/Table_1.csv
        Table_2: output/Table_2.csv
        Table_3: output/Table_3.csv
        RefDiag_tab: output/RefDiag_tab.csv

  HE_compliance_summary:
    run: r:latest analysis/HE_compliance_summary.R
    needs: [generate_acute_cohort]
    outputs:
      moderately_sensitive:
        HE_summary_table_1_1: output/monthly_summary_tab_1_1.csv
        HE_summary_fig_1_1_age: output/line_chart_1_1_age_group.png
        HE_summary_fig_1_1_eth: output/line_chart_1_1_ethnicity.png
        HE_summary_fig_1_1_IMD: output/line_chart_1_1_imd.png
        HE_summary_fig_1_1_region: output/line_chart_1_1_region.png
        HE_summary_fig_1_1_sex: output/line_chart_1_1_sex.png
        HE_summary_fig_1_1_total: output/line_chart_1_1_total.png
        HE_summary_table_1_8: output/monthly_summary_tab_1_8.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
JobRequestError: generate_cohort_all failed on a previous run and must be re-run
Backend
EMIS
Workspace
post_covid_nice_compliance
Requested by
Robert Willans
Branch
master
Force run dependencies
No
Git commit hash
627b37a
Requested actions
  • descriptive_coding_script

Code comparison

Compare the code used in this job request