Job request: 7489

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 Effects of COVID-19 on people with diabetes 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

ID Status Action
bf6kzwqpix4l4zcd succeeded generate_cohort
z4iuwtiomb4j2lmf succeeded generate_cohort_2
pkcvrjfbwe5g4aaw succeeded revised_data_cleaning
fxagzv6zs2imjjkg succeeded revised_analyses_option1_table1
a4fe7h53h3gtqkuu succeeded revised_analyses_option1_table2b
irzxy3rxjjuhzrfz succeeded revised_analyses_option1_table4b
ztqsjbbnzl546iwu succeeded revised_redaction
uvbytego6dug3pso succeeded revised_part2_data_cleaning
qlxxbndssstvvald succeeded revised_part2_analyses_option1_table1
nvreokvqqsjr2p5g failed revised_part2_analyses_option1_table2b
v5hkfcuyl2poxfy3 failed revised_part2_analyses_option1_table4b
2yljbc47fjeij4gd failed revised_part2_redaction

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 171:28:09

Config

  • Backend:
    TPP
  • Workspace:
    covid-diabetes-outcomes
  • Branch:
    main
  • Creator:
    Matt1978b
  • Force run dependencies:
    False
  • 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