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Job request: 7489

Workspace:
covid-diabetes-outcomes
ID:
vdz5w7iu2hielo7c
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: 100

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_table3a:
    #run: stata-mp:latest analysis/130_analyses_option1_table3a_hazardratios.do
    #needs: [data_cleaning]
    #outputs:
      #moderately_sensitive:
        #table1: output/results/option1_table3a_hazardratios.dta

  #analyses_option1_table3b:
    #run: stata-mp:latest analysis/131_analyses_option1_table3b_hazardratios_v2.do
    #needs: [data_cleaning]
    #outputs:
      #moderately_sensitive:
        #table1: output/results/option1_table3b_hazardratios_v2.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_table3a, analyses_option1_table3b, 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_table3a_hazardratios_redacted.dta
        #table6: output/results/option1_table3a_hazardratios_redacted.csv
        #table7: output/results/option1_table3b_hazardratios_v2_redacted.dta
        #table8: output/results/option1_table3b_hazardratios_v2_redacted.csv
        #table9: output/results/option1_table4b_stratified_rateratios_redacted.dta
        #table10: output/results/option1_table4b_stratified_rateratios_redacted.csv
        #table11: output/results/option1_table6_periodspecific_rates_redacted.dta
        #table12: output/results/option1_table6_periodspecific_rates_redacted.csv
        #table13: output/results/option1_table8_splitfollowup_rates_redacted.dta
        #table14: output/results/option1_table8_splitfollowup_rates_redacted.csv
        #table15: output/results/option2_table1a_demographics_groups_1_and_2_redacted.dta
        #table16: output/results/option2_table1a_demographics_groups_1_and_2_redacted.csv
        #table17: output/results/option2_table1b_demographics_groups_1_and_3_redacted.dta
        #table18: output/results/option2_table1b_demographics_groups_1_and_3_redacted.csv
        #table19: output/results/option3_table1_demographics_redacted.dta
        #table20: output/results/option3_table1_demographics_redacted.csv
        #table21: output/results/option3_table2b_rateratios_redacted.dta
        #table22: output/results/option3_table2b_rateratios_redacted.csv
        #table23: output/results/option3_table4b_stratified_rateratios_redacted.dta
        #table24: output/results/option3_table4b_stratified_rateratios_redacted.csv
        #table25: output/results/option3_table6_periodspecific_rates_redacted.dta
        #table26: output/results/option3_table6_periodspecific_rates_redacted.csv
        #table27: output/results/option3_table8_splitfollowup_rates_redacted.dta
        #table28: 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_table3a:
    #run: stata-mp:latest analysis/630_part2_analyses_option1_table3a_hazardratios.do
    #needs: [part2_data_cleaning]
    #outputs:
      #moderately_sensitive:
        #table1: output/results/part2_option1_table3a_hazardratios.dta

  #part2_analyses_option1_table3b:
    #run: stata-mp:latest analysis/631_part2_analyses_option1_table3b_hazardratios_v2.do
    #needs: [part2_data_cleaning]
    #outputs:
      #moderately_sensitive:
        #table1: output/results/part2_option1_table3b_hazardratios_v2.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_table3a, part2_analyses_option1_table3b, part2_analyses_option1_table4b, part2_analyses_option1_table6, part2_analyses_option1_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_table3a_hazardratios_redacted.dta
        #table6: output/results/part2_option1_table3a_hazardratios_redacted.csv
        #table7: output/results/part2_option1_table3b_hazardratios_v2_redacted.dta
        #table8: output/results/part2_option1_table3b_hazardratios_v2_redacted.csv
        #table9: output/results/part2_option1_table4b_stratified_rateratios_redacted.dta
        #table10: output/results/part2_option1_table4b_stratified_rateratios_redacted.csv
        #table11: output/results/part2_option1_table6_periodspecific_rates_redacted.dta
        #table12: output/results/part2_option1_table6_periodspecific_rates_redacted.csv
        #table13: output/results/part2_option1_table8_splitfollowup_rates_redacted.dta
        #table14: output/results/part2_option1_table8_splitfollowup_rates_redacted.csv

  #file_transfer:
    #run: stata-mp:latest analysis/900_file_transfer.do
    #needs: [redaction, part2_redaction]
    #outputs:
      #moderately_sensitive:
        #table1: release/option1_table1_demographics_redacted.csv
        #table2: release/option1_table2b_rateratios_redacted.csv
        #table3: release/option1_table3a_hazardratios_redacted.csv
        #table4: release/option1_table3b_hazardratios_v2_redacted.csv
        #table5: release/option1_table4b_stratified_rateratios_redacted.csv
        #table6: release/option1_table6_periodspecific_rates_redacted.csv
        #table7: release/option1_table8_splitfollowup_rates_redacted.csv
        #table8: release/part2_option1_table1_demographics_redacted.csv
        #table9: release/part2_option1_table2b_rateratios_redacted.csv
        #table10: release/part2_option1_table3a_hazardratios_redacted.csv
        #table11: release/part2_option1_table3b_hazardratios_v2_redacted.csv
        #table12: release/part2_option1_table4b_stratified_rateratios_redacted.csv
        #table13: release/part2_option1_table6_periodspecific_rates_redacted.csv
        #table14: release/part2_option1_table8_splitfollowup_rates_redacted.csv

  #checks:
    #run: stata-mp:latest analysis/910_checks_ethnicity.do
    #needs: [generate_cohort]
    #outputs:
      #moderately_sensitive:
        #table1: output/checks/ethnicity.dta
        #table2: output/checks/ethnicity.csv

  revised_data_cleaning:
    run: stata-mp:latest analysis/revised_010_cleaning.do
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/input_part1_clean.dta

  revised_analyses_option1_table1:
    run: stata-mp:latest analysis/revised_110_analyses_option1_table1_demographics.do
    needs: [revised_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_option1_table1_demographics.dta

  revised_analyses_option1_table2b:
    run: stata-mp:latest analysis/revised_121_analyses_option1_table2b_rateratios.do
    needs: [revised_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_option1_table2b_rateratios.dta

  revised_analyses_option1_table4b:
    run: stata-mp:latest analysis/revised_141_analyses_option1_table4b_stratified_rateratios.do
    needs: [revised_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_option1_table4b_stratified_rateratios.dta

  revised_redaction:
    run: stata-mp:latest analysis/revised_400_redaction.do
    needs: [revised_analyses_option1_table1, revised_analyses_option1_table2b, revised_analyses_option1_table4b]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_option1_table1_demographics_redacted.dta
        table2: output/revised_results/revised_option1_table1_demographics_redacted.csv
        table3: output/revised_results/revised_option1_table2b_rateratios_redacted.dta
        table4: output/revised_results/revised_option1_table2b_rateratios_redacted.csv
        table5: output/revised_results/revised_option1_table4b_stratified_rateratios_redacted.dta
        table6: output/revised_results/revised_option1_table4b_stratified_rateratios_redacted.csv

  revised_part2_data_cleaning:
    run: stata-mp:latest analysis/revised_510_part2_cleaning.do
    needs: [generate_cohort_2]
    outputs:
      highly_sensitive:
        analysis_dataset: output/input_part2_clean.dta

  revised_part2_analyses_option1_table1:
    run: stata-mp:latest analysis/revised_610_part2_analyses_option1_table1_demographics.do
    needs: [revised_part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_part2_option1_table1_demographics.dta

  revised_part2_analyses_option1_table2b:
    run: stata-mp:latest analysis/revised_621_part2_analyses_option1_table2b_rateratios.do
    needs: [revised_part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_part2_option1_table2b_rateratios.dta

  revised_part2_analyses_option1_table4b:
    run: stata-mp:latest analysis/revised_641_part2_analyses_option1_table4b_stratified_rateratios.do
    needs: [revised_part2_data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_part2_option1_table4b_stratified_rateratios.dta

  revised_part2_redaction:
    run: stata-mp:latest analysis/revised_800_part2_redaction.do
    needs: [revised_part2_analyses_option1_table1, revised_part2_analyses_option1_table2b, revised_part2_analyses_option1_table4b]
    outputs:
      moderately_sensitive:
        table1: output/revised_results/revised_part2_option1_table1_demographics_redacted.dta
        table2: output/revised_results/revised_part2_option1_table1_demographics_redacted.csv
        table3: output/revised_results/revised_part2_option1_table2b_rateratios_redacted.dta
        table4: output/revised_results/revised_part2_option1_table2b_rateratios_redacted.csv
        table5: output/revised_results/revised_part2_option1_table4b_stratified_rateratios_redacted.dta
        table6: output/revised_results/revised_part2_option1_table4b_stratified_rateratios_redacted.csv

  revised_file_transfer:
    run: stata-mp:latest analysis/revised_900_file_transfer.do
    needs: [revised_redaction, revised_part2_redaction]
    outputs:
      moderately_sensitive:
        table1: revised_release/revised_option1_table1_demographics_redacted.csv
        table2: revised_release/revised_option1_table2b_rateratios_redacted.csv
        table3: revised_release/revised_option1_table4b_stratified_rateratios_redacted.csv
        table4: revised_release/revised_part2_option1_table1_demographics_redacted.csv
        table5: revised_release/revised_part2_option1_table2b_rateratios_redacted.csv
        table6: revised_release/revised_part2_option1_table4b_stratified_rateratios_redacted.csv

Timeline

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  • Finished:

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Job information

Status
Failed 
Completed successfully
Backend
TPP
Workspace
covid-diabetes-outcomes
Requested by
Matthew Carr
Branch
main
Force run dependencies
No
Git commit hash
0fc59cf
Requested actions
  • generate_cohort
  • generate_cohort_2
  • revised_data_cleaning
  • revised_analyses_option1_table1
  • revised_analyses_option1_table2b
  • revised_analyses_option1_table4b
  • revised_redaction
  • revised_part2_data_cleaning
  • revised_part2_analyses_option1_table1
  • revised_part2_analyses_option1_table2b
  • revised_part2_analyses_option1_table4b
  • revised_part2_redaction