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Job request: 1472

Organisation:
Workspace:
onlineconsultations_runmaster
ID:
e6c74qs5cw6eilex
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

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        
        rdata1_discl: output/tables/gt_ocpop_unformatted.csv
        rdata2_discl: output/tables/gt_gpcpop_unformatted.csv
        #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_*_practice.svg
        figquant: output/plots/plot_quantiles_*_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


### SRO template pipeline
  SROtem_generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  SROtem_generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice_count.csv

  
  SROtem_generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
      needs: [SROtem_generate_study_population]
      outputs:
        moderately_sensitive:
          measure_csv: output/measure_*.csv

  SROtem_get_patient_count:
    run: python:latest python analysis/SROtem_get_patients_counts.py
    needs: [SROtem_generate_study_population]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/SRO-Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [SROtem_generate_measures, SROtem_generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        notebook: output/SRO-Notebook.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
JobRequestError: generate_cohorts_long failed on a previous run and must be re-run
Backend
TPP
Workspace
onlineconsultations_runmaster
Requested by
Martina Fonseca
Branch
master
Force run dependencies
No
Git commit hash
3563e61
Requested actions
  • run_model_measures

Code comparison

Compare the code used in this Job Request