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Job request: 4875

Organisation:
University of Manchester
Workspace:
covid-diabetes-outcomes
ID:
s2jzemaloacuq2v6
View repo View project.yaml

This page shows the technical details of what happened when 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 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: 10000

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_table2b:
    run: stata-mp:latest analysis/121_analyses_option1_table2b_rateratios.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table2b_rateratios.dta

  analyses_option1_table4b:
    run: stata-mp:latest analysis/141_analyses_option1_table4b_stratified_rateratios.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table4b_stratified_rateratios.dta

  analyses_option1_table6:
    run: stata-mp:latest analysis/160_analyses_option1_table6_periodspecific_rates.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table6_periodspecific_rates.dta

  analyses_option1_table8:
    run: stata-mp:latest analysis/180_analyses_option1_table8_splitfollowup_rates.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table8_splitfollowup_rates.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

  analyses_option3_table2b:
    run: stata-mp:latest analysis/321_analyses_option3_table2b_rateratios.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table2b_rateratios.dta

  analyses_option3_table4b:
    run: stata-mp:latest analysis/341_analyses_option3_table4b_stratified_rateratios.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table4b_stratified_rateratios.dta

  analyses_option3_table6:
    run: stata-mp:latest analysis/360_analyses_option3_table6_periodspecific_rates.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table6_periodspecific_rates.dta

  analyses_option3_table8:
    run: stata-mp:latest analysis/380_analyses_option3_table8_splitfollowup_rates.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table8_splitfollowup_rates.dta
  
  redaction:
    run: stata-mp:latest analysis/400_redaction.do
    needs: [analyses_option1_table1, analyses_option1_table2b, analyses_option1_table4b, analyses_option1_table6, analyses_option1_table8, analyses_option2_table1a, analyses_option2_table1b, analyses_option3_table1, analyses_option3_table2b, analyses_option3_table4b, analyses_option3_table6, analyses_option3_table8]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table1_demographics_redacted.dta
        table2: output/results/option1_table1_demographics_redacted.csv
        table3: output/results/option1_table2b_rateratios_redacted.dta
        table4: output/results/option1_table2b_rateratios_redacted.csv
        table5: output/results/option1_table4b_stratified_rateratios_redacted.dta
        table6: output/results/option1_table4b_stratified_rateratios_redacted.csv
        table7: output/results/option1_table6_periodspecific_rates_redacted.dta
        table8: output/results/option1_table6_periodspecific_rates_redacted.csv
        table9: output/results/option1_table8_splitfollowup_rates_redacted.dta
        table10: output/results/option1_table8_splitfollowup_rates_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
        table17: output/results/option3_table2b_rateratios_redacted.dta
        table18: output/results/option3_table2b_rateratios_redacted.csv
        table19: output/results/option3_table4b_stratified_rateratios_redacted.dta
        table20: output/results/option3_table4b_stratified_rateratios_redacted.csv
        table21: output/results/option3_table6_periodspecific_rates_redacted.dta
        table22: output/results/option3_table6_periodspecific_rates_redacted.csv
        table23: output/results/option3_table8_splitfollowup_rates_redacted.dta
        table24: output/results/option3_table8_splitfollowup_rates_redacted.csv

  generate_cohort_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_part2
    outputs:
      highly_sensitive:
        cohort: output/input_part2.csv

  part2_data_cleaning:
    run: stata-mp:latest analysis/510_part2_cleaning.do
    needs: [generate_cohort_2]
    outputs:
      highly_sensitive:
        analysis_dataset: output/input_part2_clean.dta

  part2_matching_groups_1_and_2:
    run: stata-mp:latest analysis/521_part2_matching_groups_1_and_2.do
    needs: [part2_data_cleaning]
    outputs:
      highly_sensitive:
        analysis_dataset: output/matched_part2_groups_1_and_2.dta

  part2_analyses_option1_table1:
    run: stata-mp:latest analysis/610_part2_analyses_option1_table1_demographics.do
    needs: [part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option1_table1_demographics.dta

  part2_analyses_option1_table2b:
    run: stata-mp:latest analysis/621_part2_analyses_option1_table2b_rateratios.do
    needs: [part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option1_table2b_rateratios.dta

  part2_analyses_option1_table4b:
    run: stata-mp:latest analysis/641_part2_analyses_option1_table4b_stratified_rateratios.do
    needs: [part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option1_table4b_stratified_rateratios.dta

  part2_analyses_option1_table6:
    run: stata-mp:latest analysis/660_part2_analyses_option1_table6_periodspecific_rates.do
    needs: [part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option1_table6_periodspecific_rates.dta

  part2_analyses_option1_table8:
    run: stata-mp:latest analysis/680_part2_analyses_option1_table8_splitfollowup_rates.do
    needs: [part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option1_table8_splitfollowup_rates.dta

  part2_analyses_option2_table1:
    run: stata-mp:latest analysis/710_part2_analyses_option2_table1_demographics.do
    needs: [part2_matching_groups_1_and_2]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option2_table1_demographics.dta

  part2_analyses_option2_table2b:
    run: stata-mp:latest analysis/721_part2_analyses_option2_table2b_rateratios.do
    needs: [part2_matching_groups_1_and_2]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option2_table2b_rateratios.dta

  part2_analyses_option2_table4b:
    run: stata-mp:latest analysis/741_part2_analyses_option2_table4b_stratified_rateratios.do
    needs: [part2_matching_groups_1_and_2]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option2_table4b_stratified_rateratios.dta

  part2_analyses_option2_table6:
    run: stata-mp:latest analysis/760_part2_analyses_option2_table6_periodspecific_rates.do
    needs: [part2_matching_groups_1_and_2]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option2_table6_periodspecific_rates.dta

  part2_analyses_option2_table8:
    run: stata-mp:latest analysis/780_part2_analyses_option2_table8_splitfollowup_rates.do
    needs: [part2_matching_groups_1_and_2]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option2_table8_splitfollowup_rates.dta

  part2_redaction:
    run: stata-mp:latest analysis/800_part2_redaction.do
    needs: [part2_analyses_option1_table1, part2_analyses_option1_table2b, part2_analyses_option1_table4b, part2_analyses_option1_table6, part2_analyses_option1_table8, part2_analyses_option2_table1, part2_analyses_option2_table2b, part2_analyses_option2_table4b, part2_analyses_option2_table6, part2_analyses_option2_table8]
    outputs:
      moderately_sensitive:
        table1: output/results/part2_option1_table1_demographics_redacted.dta
        table2: output/results/part2_option1_table1_demographics_redacted.csv
        table3: output/results/part2_option1_table2b_rateratios_redacted.dta
        table4: output/results/part2_option1_table2b_rateratios_redacted.csv
        table5: output/results/part2_option1_table4b_stratified_rateratios_redacted.dta
        table6: output/results/part2_option1_table4b_stratified_rateratios_redacted.csv
        table7: output/results/part2_option1_table6_periodspecific_rates_redacted.dta
        table8: output/results/part2_option1_table6_periodspecific_rates_redacted.csv
        table9: output/results/part2_option1_table8_splitfollowup_rates_redacted.dta
        table10: output/results/part2_option1_table8_splitfollowup_rates_redacted.csv
        table11: output/results/part2_option2_table1_demographics_redacted.dta
        table12: output/results/part2_option2_table1_demographics_redacted.csv
        table13: output/results/part2_option2_table2b_rateratios_redacted.dta
        table14: output/results/part2_option2_table2b_rateratios_redacted.csv
        table15: output/results/part2_option2_table4b_stratified_rateratios_redacted.dta
        table16: output/results/part2_option2_table4b_stratified_rateratios_redacted.csv
        table17: output/results/part2_option2_table6_periodspecific_rates_redacted.dta
        table18: output/results/part2_option2_table6_periodspecific_rates_redacted.csv
        table19: output/results/part2_option2_table8_splitfollowup_rates_redacted.dta
        table20: output/results/part2_option2_table8_splitfollowup_rates_redacted.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 208:41:06

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-diabetes-outcomes
Requested by
Matthew Carr
Branch
main
Force run dependencies
Yes
Git commit hash
2e9d959
Requested actions
  • run_all