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Job request: 9447

Organisation:
University of Bristol
Workspace:
lockdown-and-vulnerable-groups
ID:
odgqsg6r63hit2k6
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Scott Walter 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_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-02 to 2020-01-13 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-20 to 2020-06-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-08 to 2020-10-19 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-10-26 to 2021-03-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-08 to 2021-06-14 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/in*.csv.gz

  generate_study_population_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-06-21 to 2021-09-27 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/i*.csv.gz


  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv


  run_subgroup_setup:
    run: stata-mp:latest analysis/subgroup_data_setup.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        subgroup1: output/dva_female.dta
        subgroup2: output/dva_male.dta
        subgroup3: output/dva_all.dta
        subgroup4: output/intdis_sub14.dta
        subgroup5: output/intdis_over14.dta
        subgroup6: output/intdis_all.dta
        subgroup7: output/RCGPsafeguard_sub18.dta
        subgroup8: output/CovidNewCaseCounts.dta

  run_model_dva_female:
    run: stata-mp:latest analysis/model_DVA_female.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_dva_female0: output/CITS_dva_female.xlsx
        model_dva_female1: output/dva_female2.dta
        model_dva_female2: output/dva_female2_ld1.dta
        model_dva_female3: output/dva_ratioLoess_f1.svg
        model_dva_female4: output/diagnostics/dva_diagnostics_f1.svg
        model_dva_female5: output/dva_female_plot1.svg
        model_dva_female6: output/dva_female2_ld2.dta
        model_dva_female7: output/dva_ratioLoess_f2.svg
        model_dva_female8: output/diagnostics/dva_diagnostics_f2.svg
        model_dva_female9: output/dva_female_plot2.svg

  run_model_dva_male:
    run: stata-mp:latest analysis/model_DVA_male.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_dva_male0: output/CITS_dva_male.xlsx
        model_dva_male1: output/dva_male2.dta
        model_dva_male2: output/dva_male2_ld1.dta
        model_dva_male3: output/dva_ratioLoess_m1.svg
        model_dva_male4: output/diagnostics/dva_diagnostics_m1.svg
        model_dva_male5: output/dva_male_plot1.svg
        model_dva_male6: output/dva_male2_ld2.dta
        model_dva_male7: output/dva_ratioLoess_m2.svg
        model_dva_male8: output/diagnostics/dva_diagnostics_m2.svg
        model_dva_male9: output/dva_male_plot2.svg

  run_model_dva_all:
    run: stata-mp:latest analysis/model_DVA_all.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_dva_all0: output/CITS_dva.xlsx
        model_dva_all1: output/dva_all2.dta
        model_dva_all2: output/dva_all2_ld1.dta
        model_dva_all3: output/dva_ratioLoess1.svg
        model_dva_all4: output/diagnostics/dva_diagnostics1.svg
        model_dva_all5: output/dva_plot1.svg
        model_dva_all6: output/dva_all2_ld2.dta
        model_dva_all7: output/dva_ratioLoess2.svg
        model_dva_all8: output/diagnostics/dva_diagnostics2.svg
        model_dva_all9: output/dva_plot2.svg

  run_model_opioid:
    run: stata-mp:latest analysis/model_opioid.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_opioid0: output/CITS_opioid.xlsx
        model_opioid1: output/opioid.dta
        model_opioid2: output/opioid_ld1.dta
        model_opioid3: output/opioid_ratioLoess1.svg
        model_opioid4: output/diagnostics/opioid_diagnostics1.svg
        model_opioid5: output/opioid_plot1.svg
        model_opioid6: output/opioid_ld2.dta
        model_opioid7: output/opioid_ratioLoess2.svg
        model_opioid8: output/diagnostics/opioid_diagnostics2.svg
        model_opioid9: output/opioid_plot2.svg

  run_model_alc:
    run: stata-mp:latest analysis/model_alc.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_alc0: output/CITS_alc.xlsx
        model_alc1: output/alc.dta
        model_alc2: output/alc_ld1.dta
        model_alc3: output/alc_ratioLoess1.svg
        model_alc4: output/diagnostics/alc_diagnostics1.svg
        model_alc5: output/alc_plot1.svg
        model_alc6: output/alc_ld2.dta
        model_alc7: output/alc_ratioLoess2.svg
        model_alc8: output/diagnostics/alc_diagnostics2.svg
        model_alc9: output/alc_plot2.svg

  run_model_drug:
    run: stata-mp:latest analysis/model_drug.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_drug0: output/CITS_drug.xlsx
        model_drug1: output/drug.dta
        model_drug2: output/drug_ld1.dta
        model_drug3: output/drug_ratioLoess1.svg
        model_drug4: output/diagnostics/drug_diagnostics1.svg
        model_drug5: output/drug_plot1.svg
        model_drug6: output/drug_ld2.dta
        model_drug7: output/drug_ratioLoess2.svg
        model_drug8: output/diagnostics/drug_diagnostics2.svg
        model_drug9: output/drug_plot2.svg

  run_model_misuse:
    run: stata-mp:latest analysis/model_misuse.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_misuse0: output/CITS_misuse.xlsx
        model_misuse1: output/misuse.dta
        model_misuse2: output/misuse_ld1.dta
        model_misuse3: output/misuse_ratioLoess1.svg
        model_misuse4: output/diagnostics/misuse_diagnostics1.svg
        model_misuse5: output/misuse_plot1.svg
        model_misuse6: output/misuse_ld2.dta
        model_misuse7: output/misuse_ratioLoess2.svg
        model_misuse8: output/diagnostics/misuse_diagnostics2.svg
        model_misuse9: output/misuse_plot2.svg

  run_model_safeguard:
    run: stata-mp:latest analysis/model_RCGPsafeguard.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_safeguard0: output/CITS_safeguard.xlsx
        model_safeguard1: output/safeguard.dta
        model_safeguard2: output/safeguard_ld1.dta
        model_safeguard3: output/safeguard_ratioLoess1.svg
        model_safeguard4: output/diagnostics/safeguard_diagnostics1.svg
        model_safeguard5: output/safeguard_plot1.svg
        model_safeguard6: output/safeguard_ld2.dta
        model_safeguard7: output/safeguard_ratioLoess2.svg
        model_safeguard8: output/diagnostics/safeguard_diagnostics2.svg
        model_safeguard9: output/safeguard_plot2.svg

  run_model_intdis_sub14:
    run: stata-mp:latest analysis/model_intdis_sub14.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_intdis_sub0: output/CITS_intdis_sub14.xlsx
        model_intdis_sub1: output/intdis_sub14_2.dta
        model_intdis_sub2: output/intdis_sub14_2_ld1.dta
        model_intdis_sub3: output/intdis_ratioLoess_jr1.svg
        model_intdis_sub4: output/diagnostics/intdis_diagnostics_jr1.svg
        model_intdis_sub5: output/intdis_sub14_plot1.svg
        model_intdis_sub6: output/intdis_sub14_2_ld2.dta
        model_intdis_sub7: output/intdis_ratioLoess_jr2.svg
        model_intdis_sub8: output/diagnostics/intdis_diagnostics_jr2.svg
        model_intdis_sub9: output/intdis_sub14_plot2.svg

  run_model_intdis_over14:
    run: stata-mp:latest analysis/model_intdis_over14.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_intdis_over0: output/CITS_intdis_over14.xlsx
        model_intdis_over1: output/intdis_over14_2.dta
        model_intdis_over2: output/intdis_over14_2_ld1.dta
        model_intdis_over3: output/intdis_ratioLoess_sr1.svg
        model_intdis_over4: output/diagnostics/intdis_diagnostics_sr1.svg
        model_intdis_over5: output/intdis_over14_plot1.svg
        model_intdis_over6: output/intdis_over14_2_ld2.dta
        model_intdis_over7: output/intdis_ratioLoess_sr2.svg
        model_intdis_over8: output/diagnostics/intdis_diagnostics_sr2.svg
        model_intdis_over9: output/intdis_over14_plot2.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:12:37

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

Job information

Status
Succeeded
Backend
TPP
Workspace
lockdown-and-vulnerable-groups
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
2e38eec
Requested actions
  • run_model_dva_female
  • run_model_dva_male
  • run_model_dva_all
  • run_model_opioid
  • run_model_alc
  • run_model_drug
  • run_model_misuse
  • run_model_safeguard
  • run_model_intdis_sub14
  • run_model_intdis_over14

Code comparison

Compare the code used in this Job Request