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Job request: 1028

Organisation:
Workspace:
online_consultation
ID:
oddwjj7etjrwy76y
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jonny Pearson 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
        #rdata1: output/gt_ocpop.RData
        #rdata2: output/gt_gpcpop.RData
        tb01: output/tb01_gpcr_region.csv
        tb02: output/tb02_gpcr_stp.csv
        tb04: output/tb04_gpcr_agesex.csv
        tb05: output/tb05_gpcr_ethnicity.csv
        tb06: output/tb06_gpcr_ruc.csv
        tb07: output/tb07_gpcr_care.csv
        tb08: output/tb08_gpcr_dis.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/sc03_tb01_nattrends.csv
        fig01: output/sc03_fig01_nattrends.svg
        fig02: output/sc03_fig02_nattrends.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
        tb01: output/measures_gpc_pop.csv
        fig01: output/plots/plot_overall_gpc_pop.svg
        figall: output/plots/plot_each_OC_*_practice.svg
        figquant: output/plots/plot_quantiles_OC_*_practice.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:36:35

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

Job request

Status
Failed
Backend
TPP
Workspace
online_consultation
Requested by
Jonny Pearson
Branch
master
Force run dependencies
No
Git commit hash
79d1aa2
Requested actions
  • run_all

Code comparison

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