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Job request: 1441

Organisation:
Workspace:
onlineconsultations_run01_cutdown
ID:
rjbcla5qrxswklvw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Martina Fonseca 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 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_cohorts_main:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ori
    outputs:
      highly_sensitive:
        cohort: output/input_ori.csv

  run_model:
    run: r:latest analysis/01-createSDtables.R
    needs: [generate_cohorts_main]
    outputs:
      moderately_sensitive:
        log: logs/log-01-createSDtables.txt
        #gtpng1: output/tables/gt_ocpop.png
        #gtpng2: output/tables/gt_gpcpop.png
        rdata1: output/tables/gt_ocpop.RData
        rdata2: output/tables/gt_gpcpop.RData
        #tb01: output/tables/tb01_gpcr_region.csv
        #tb02: output/tables/tb02_gpcr_stp.csv # guidance says to not output identifiable regions
        tb04: output/tables/tb04_gpcr_agesex.csv
        tb05: output/tables/tb05_gpcr_ethnicity.csv
        tb06: output/tables/tb06_gpcr_ruc.csv
        tb07: output/tables/tb07_gpcr_care.csv
        tb08: output/tables/tb08_gpcr_dis.csv
        tb09: output/tables/tb09_gpcr_imd.csv

  # https://docs.opensafely.org/en/latest/measures/
  generate_cohorts_long:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_bycode --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_measures_bycode_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures_bycode --output-dir=output/measures
    needs: [generate_cohorts_long]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  run_model_long:
    run: r:latest analysis/03-createnattrends_codes.R
    needs: [generate_cohorts_long]
    outputs:
      moderately_sensitive:
        log: logs/log-03-createnattrends.txt
        tb01: output/tables/sc03_tb01_nattrends.csv
        fig01: output/plots/sc03_fig01_nattrends.svg
        fig02: output/plots/sc03_fig02_nattrends.svg
        fig03: output/plots/sc03_fig03_pracnatcoverage.svg
        fig04: output/plots/sc03_fig04_pracbyregcoverage.svg

  run_model_measures:
    run: r:latest analysis/02-createtemporal.R
    needs: [generate_cohorts_long,generate_measures]
    outputs:
      moderately_sensitive:
        log: logs/log-02-createtemporal.txt
        red_measures: output/tables/redacted_*.csv
        #tb01: output/measures_gpc_pop.csv # redundant into. omit output
        fig01: output/plots/plot_overall_gpc_pop.svg
        #figall: output/plots/plot_each_OC_*_practice.svg
        figquant: output/plots/plot_quantiles_OC_*_practice.svg


  run_model_measuresDEBUG:
    run: r:latest analysis/02-createtemporal_debug.R
    needs: [generate_cohorts_long,generate_measures]
    outputs:
      moderately_sensitive:
        log: logs/log-02-createtemporal-debug.txt
        #tb01: output/measures_gpc_pop_debug.csv
        #fig01: output/plots/plot_overall_gpc_pop_debug.svg
        #figall: output/plots/plot_each_debug_*_practice.svg
        #figquant: output/plots/plot_quantiles_debug_*_practice.svg
        #figquant2: output/plots/plot_quantiles2_debug_*_practice.svg

  run_model_redactedmeasures:
    run: r:latest analysis/02a-createredactedmeasure.R
    needs: [generate_cohorts_long,generate_measures]
    outputs:
      moderately_sensitive:
        log: logs/log-02a-createredactedmeasure.txt
        red_measures: output/tables/redacted2a_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:54:39

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

Job request

Status
Succeeded
Backend
TPP
Workspace
onlineconsultations_run01_cutdown
Requested by
Martina Fonseca
Branch
mf-edit-23Mar
Force run dependencies
No
Git commit hash
ec36e42
Requested actions
  • run_all

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