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Job request: 2036

Organisation:
Workspace:
online_consultation
ID:
ecnwx6fak5i4bykj
View repo View project.yaml

This page shows the technical details of what happened when 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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.

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_unlist: output/tables/gt_ocpop_unlisted.csv
        #rdata2_unlist: output/tables/gt_gpcpop_unlisted.csv
        tb04: output/tables/tb04_gpcr_agesex.csv
        gtpng1: output/tables/gt_ocpop.html
        gtpng2: output/tables/gt_gpcpop.html
        #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
        #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
        fig07: output/plots/sc03_fig07_ctv3nattrends.svg
        fig08: output/plots/sc03_fig08_ctv3nattrends.svg
        fig05: output/plots/sc03_fig05_ctv3pracnatcoverage.svg
        fig06: output/plots/sc03_fig06_ctv3pracbyregcoverage.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
        figlogquant: output/plots/plot_logquantiles_*_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

### Weekly tallies to compare with OC/VC supplier data
  generate_cohorts_weekly2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_weekly --index-date-range "2020-01-06 to 2021-03-22 by week" --output-dir=output/measures-week
    outputs:
      highly_sensitive:
        cohort: output/measures-week/input_measures_weekly_*.csv

  generate_measures_weekly2021:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures_weekly --output-dir=output/measures-week
    needs: [generate_cohorts_weekly2021]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures-week/measure_*.csv

  run_model_weekly2021:
    run: r:latest analysis/04-weekly2021.R
    needs: [generate_cohorts_weekly2021,generate_measures_weekly2021]
    outputs:
      moderately_sensitive:
        log: logs/log-04-weekly2021.txt
        tab1: output/tables/sc04-weeklynattrend.csv

#### Clinical history
  generate_cohorts_v2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_v2
    outputs:
      highly_sensitive:
        cohort: output/input_v2.csv

  run_model_v2:
    run: r:latest analysis/05-createClinicalConditiontables.R
    needs: [generate_cohorts_v2]
    outputs:
      moderately_sensitive:
        log: logs/log-05-createClinicalConditiontables.txt
        gthtml1: output/tables/gt_econsult_pop_pre.html
        gthtml2: output/tables/gt_econsult_pop_post.html
        gthtml3: output/tables/gt_econsult_consultpop_pre.html
        gthtml4: output/tables/gt_econsult_consultpop_post.html

### SNOMED check
  generate_cohorts_checksnomed:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_checksnomed
    outputs:
      highly_sensitive:
        cohort: output/input_checksnomed.csv


  run_model_checksnomed:
    run: r:latest analysis/0a-snomedcheck.R
    needs: [generate_cohorts_checksnomed]
    outputs:
      moderately_sensitive:
        log: logs/log-0a-snomedcheck.txt
        tab1: output/tables/sc0a_snomedcheck_tallies.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: 03:34:01

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

Job information

Status
Succeeded
Backend
TPP
Workspace
online_consultation
Requested by
Martina Fonseca
Branch
master
Force run dependencies
Yes
Git commit hash
2bc8cab
Requested actions
  • run_model_v2

Code comparison

Compare the code used in this Job Request