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Job request: 4523

Organisation:
University of Manchester
Workspace:
covid-diabetes-outcomes
ID:
2uyjmvdu53zmzso2
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

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: 02:34:25

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-diabetes-outcomes
Requested by
Matthew Carr
Branch
main
Force run dependencies
No
Git commit hash
6bbf83a
Requested actions
  • matching_groups_1_and_2
  • matching_groups_1_and_3
  • matching_groups_1_2_and_3
  • analyses_option1_table1
  • analyses_option1_table2

Code comparison

Compare the code used in this job request