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Job request: 4530

Organisation:
University of Manchester
Workspace:
covid-diabetes-outcomes
ID:
iqxy44x3u34bvg2v
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Matthew Carr 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: 100000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_part1
    outputs:
      highly_sensitive:
        cohort: output/input_part1.csv

  data_cleaning:
    run: stata-mp:latest analysis/010_cleaning.do
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/input_part1_clean.dta

  matching_groups_1_and_2:
    run: stata-mp:latest analysis/021_matching_groups_1_and_2.do
    needs: [data_cleaning]
    outputs:
      highly_sensitive:
        analysis_dataset: output/matched_groups_1_and_2.dta

  matching_groups_1_and_3:
    run: stata-mp:latest analysis/022_matching_groups_1_and_3.do
    needs: [data_cleaning]
    outputs:
      highly_sensitive:
        analysis_dataset: output/matched_groups_1_and_3.dta

  matching_groups_1_2_and_3:
    run: stata-mp:latest analysis/023_matching_groups_1_2_and_3.do
    needs: [matching_groups_1_and_2, matching_groups_1_and_3]
    outputs:
      highly_sensitive:
        analysis_dataset: output/matched_groups_1_2_and_3.dta

  analyses_option1_table1:
    run: stata-mp:latest analysis/110_analyses_option1_table1_demographics.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table1_demographics.dta

  analyses_option1_table2:
    run: stata-mp:latest analysis/120_analyses_option1_table2_rates.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table2_rates.dta

  analyses_option1_table3:
    run: stata-mp:latest analysis/130_analyses_option1_table3_hazardratios.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table3_hazardratios.dta

  analyses_option1_table4:
    run: stata-mp:latest analysis/140_analyses_option1_table4_stratified_rates.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table4_stratified_rates.dta

  analyses_option1_table5:
    run: stata-mp:latest analysis/150_analyses_option1_table5_stratified_hazardratios.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table5_stratified_hazardratios.dta    

  analyses_option2_table1a:
    run: stata-mp:latest analysis/210_analyses_option2_table1a_demographics_groups_1_and_2.do
    needs: [matching_groups_1_and_2]
    outputs:
      moderately_sensitive:
        table1: output/results/option2_table1a_demographics_groups_1_and_2.dta

  analyses_option2_table1b:
    run: stata-mp:latest analysis/211_analyses_option2_table1b_demographics_groups_1_and_3.do
    needs: [matching_groups_1_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option2_table1b_demographics_groups_1_and_3.dta

  analyses_option3_table1:
    run: stata-mp:latest analysis/310_analyses_option3_table1_demographics.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table1_demographics.dta

  redaction:
    run: stata-mp:latest analysis/999_redaction.do
    needs: [analyses_option1_table1, analyses_option1_table2, analyses_option1_table3, analyses_option1_table4, analyses_option1_table5, analyses_option2_table1a, analyses_option2_table1b, analyses_option3_table1]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table1_demographics_redacted.dta
        table2: output/results/option1_table1_demographics_redacted.csv
        table3: output/results/option1_table2_rates_redacted.dta
        table4: output/results/option1_table2_rates_redacted.csv
        #table5: output/results/option1_table3_hazardratios_redacted.dta
        #table6: output/results/option1_table3_hazardratios_redacted.csv
        #table7: output/results/option1_table4_stratified_rates_redacted.dta
        #table8: output/results/option1_table4_stratified_rates_redacted.csv
        #table9: output/results/option1_table5_stratified_hazardratios_redacted.dta
        #table10: output/results/option1_table5_stratified_hazardratios_redacted.csv
        #table11: output/results/option2_table1a_demographics_groups_1_and_2_redacted.dta
        #table12: output/results/option2_table1a_demographics_groups_1_and_2_redacted.csv
        #table13: output/results/option2_table1b_demographics_groups_1_and_3_redacted.dta
        #table14: output/results/option2_table1b_demographics_groups_1_and_3_redacted.csv
        #table15: output/results/option3_table1_demographics_redacted.dta
        #table16: output/results/option3_table1_demographics_redacted.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
JobRequestError: analyses_option1_table3 failed on a previous run and must be re-run
Backend
TPP
Workspace
covid-diabetes-outcomes
Requested by
Matthew Carr
Branch
main
Force run dependencies
No
Git commit hash
be15c43
Requested actions
  • analyses_option2_table1a
  • analyses_option2_table1b
  • analyses_option3_table1
  • redaction

Code comparison

Compare the code used in this Job Request