Job request: 21447

Organisation:: University of Bristol
Workspace:: lockdown-and-vulnerable-groups
ID:: azc454zo27nr7uuc

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

Action:

model_alcmisuse

Status:

Status: Succeeded

Job identifier:

56r4efvdfp7euetd
Action:

model_drugmisuse

Status:

Status: Succeeded

Job identifier:

l3zanusuxrvhzwo3
Action:

model_dvafemale

Status:

Status: Succeeded

Job identifier:

yk6mef3lhwcwqhf7
Action:

model_dvamale

Status:

Status: Succeeded

Job identifier:

y5ee53ec2ap5hcz3
Action:

model_intdisover14

Status:

Status: Succeeded

Job identifier:

yk6omhafr3ojqywq
Action:

model_intdissub14

Status:

Status: Succeeded

Job identifier:

x46a55vppv6gs6ok
Action:

model_opioid

Status:

Status: Succeeded

Job identifier:

3czgdn65qt24x32f
Action:

model_rcgpsafeguard

Status:

Status: Succeeded

Job identifier:

f6rryoigc2go56ux
Action:

combine_results

Status:

Status: Succeeded

Job identifier:

6lzop6xslcig63jr

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


  subgroup_setup:
    run: stata-mp:latest analysis/subgroup_data_setup.do
    needs: 
    - generate_measures
    outputs:
      highly_sensitive:
        subgroup1: output/measure_dvafemale_rate.dta
        subgroup2: output/measure_dvamale_rate.dta
        subgroup3: output/measure_intdissub14_rate.dta
        subgroup4: output/measure_intdisover14_rate.dta
        subgroup5: output/measure_rcgpsafeguard_rate.dta
        subgroup6: output/measure_alcmisuse_rate.dta
        subgroup7: output/measure_drugmisuse_rate.dta
        subgroup8: output/measure_opioid_rate.dta

  model_alcmisuse:
    run: stata-mp:latest analysis/model.do alcmisuse
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/alcmisuse_RR_LD1.dta
        results2: output/alcmisuse_RD_LD1.dta
        results3: output/alcmisuse_RR_LD2.dta
        results4: output/alcmisuse_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/alcmisuse_diagnostics1.svg
        diagnostics2: output/diagnostics/alcmisuse_diagnostics2.svg
        plot1: output/alcmisuse_plot1.svg
        plot2: output/alcmisuse_plot2.svg

  model_drugmisuse:
    run: stata-mp:latest analysis/model.do drugmisuse
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/drugmisuse_RR_LD1.dta
        results2: output/drugmisuse_RD_LD1.dta
        results3: output/drugmisuse_RR_LD2.dta
        results4: output/drugmisuse_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/drugmisuse_diagnostics1.svg
        diagnostics2: output/diagnostics/drugmisuse_diagnostics2.svg
        plot1: output/drugmisuse_plot1.svg
        plot2: output/drugmisuse_plot2.svg

  model_opioid:
    run: stata-mp:latest analysis/model.do opioid
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/opioid_RR_LD1.dta
        results2: output/opioid_RD_LD1.dta
        results3: output/opioid_RR_LD2.dta
        results4: output/opioid_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/opioid_diagnostics1.svg
        diagnostics2: output/diagnostics/opioid_diagnostics2.svg
        plot1: output/opioid_plot1.svg
        plot2: output/opioid_plot2.svg

  model_dvafemale:
    run: stata-mp:latest analysis/model.do dvafemale
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/dvafemale_RR_LD1.dta
        results2: output/dvafemale_RD_LD1.dta
        results3: output/dvafemale_RR_LD2.dta
        results4: output/dvafemale_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/dvafemale_diagnostics1.svg
        diagnostics2: output/diagnostics/dvafemale_diagnostics2.svg
        plot1: output/dvafemale_plot1.svg
        plot2: output/dvafemale_plot2.svg

  model_dvamale:
    run: stata-mp:latest analysis/model.do dvamale
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/dvamale_RR_LD1.dta
        results2: output/dvamale_RD_LD1.dta
        results3: output/dvamale_RR_LD2.dta
        results4: output/dvamale_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/dvamale_diagnostics1.svg
        diagnostics2: output/diagnostics/dvamale_diagnostics2.svg
        plot1: output/dvamale_plot1.svg
        plot2: output/dvamale_plot2.svg

  model_intdissub14:
    run: stata-mp:latest analysis/model.do intdissub14
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/intdissub14_RR_LD1.dta
        results2: output/intdissub14_RD_LD1.dta
        results3: output/intdissub14_RR_LD2.dta
        results4: output/intdissub14_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/intdissub14_diagnostics1.svg
        diagnostics2: output/diagnostics/intdissub14_diagnostics2.svg
        plot1: output/intdissub14_plot1.svg
        plot2: output/intdissub14_plot2.svg

  model_intdisover14:
    run: stata-mp:latest analysis/model.do intdisover14
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/intdisover14_RR_LD1.dta
        results2: output/intdisover14_RD_LD1.dta
        results3: output/intdisover14_RR_LD2.dta
        results4: output/intdisover14_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/intdisover14_diagnostics1.svg
        diagnostics2: output/diagnostics/intdisover14_diagnostics2.svg
        plot1: output/intdisover14_plot1.svg
        plot2: output/intdisover14_plot2.svg


  model_rcgpsafeguard:
    run: stata-mp:latest analysis/model.do rcgpsafeguard
    needs:
    - subgroup_setup
    outputs:
      highly_sensitive:
        results1: output/rcgpsafeguard_RR_LD1.dta
        results2: output/rcgpsafeguard_RD_LD1.dta
        results3: output/rcgpsafeguard_RR_LD2.dta
        results4: output/rcgpsafeguard_RD_LD2.dta
      moderately_sensitive:
        diagnostics1: output/diagnostics/rcgpsafeguard_diagnostics1.svg
        diagnostics2: output/diagnostics/rcgpsafeguard_diagnostics2.svg
        plot1: output/rcgpsafeguard_plot1.svg
        plot2: output/rcgpsafeguard_plot2.svg

  combine_results:
    run: stata-mp:latest analysis/combine_results.do
    needs:
    - model_alcmisuse
    - model_drugmisuse
    - model_opioid
    - model_dvafemale
    - model_dvamale
    - model_intdissub14
    - model_intdisover14
    - model_rcgpsafeguard
    outputs:
      moderately_sensitive:
        results: output/CITS_results.csv

Timeline

Created: 5 months ago 30 Nov 2023 21:01:07 UTC
Started: 5 months ago 30 Nov 2023 20:59:23 UTC
Finished: 5 months ago 30 Nov 2023 21:03:21 UTC
Runtime: 00:10:55

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: 28cc250
Requested actions: model_alcmisuse

model_drugmisuse

model_opioid

model_dvafemale

model_dvamale

model_intdissub14

model_intdisover14

model_rcgpsafeguard

combine_results

Code comparison

Compare the code used in this Job Request