Job request: 4875

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
dngmsfaqvfxfizyn succeeded analyses_option1_table1
7ki56snr6wadm3pa succeeded analyses_option1_table6
couudrma3z5gfkqi succeeded analyses_option2_table1a
4pud7l53nbdoik6q succeeded analyses_option2_table1b
blfni7wywzmnz77z succeeded analyses_option3_table1
e6zqiunhwdug7obp succeeded analyses_option3_table6
es6miybqcmh3rdak succeeded data_cleaning
52mfylj7en7yd7rr succeeded generate_cohort
fbdhsvk3mke6qdjb succeeded matching_groups_1_2_and_3
5vgt3fgf4wgkp3co succeeded matching_groups_1_and_2
ir4joy2oqmhj5myv succeeded matching_groups_1_and_3
uxo7beg53q7lfagc succeeded redaction
ypkiqa2jabejr2sw succeeded analyses_option1_table2b
vxdi5krx7xx7pobl succeeded analyses_option1_table4b
xpdcshqojkmsgga4 succeeded analyses_option1_table8
p7in4hpa7ylh6gdd succeeded analyses_option3_table2b
ktscp5fi37bm4esf succeeded analyses_option3_table4b
puiorfoe4x7euj3a succeeded analyses_option3_table8
nmkv6plgp3o2lp4d succeeded generate_cohort_2
palyel3jxczqiura succeeded part2_data_cleaning
zybfyrtmkk4eszzg failed part2_matching_groups_1_and_2
2pc7ot5dani62b6p succeeded part2_analyses_option1_table1
igndu3o3trm3x4cg succeeded part2_analyses_option1_table2b
dvhbpri2dweqzjk2 failed part2_analyses_option1_table4b
v6r3nnofc5tfanpt succeeded part2_analyses_option1_table6
teepjgm3clzoodb4 succeeded part2_analyses_option1_table8
hgzxm52wkf2bnz6t failed part2_analyses_option2_table1
ynmdzaelulljxzun failed part2_analyses_option2_table2b
che472evb4fahcfl failed part2_analyses_option2_table4b
lxjcn577y7wtoege failed part2_analyses_option2_table6
uzhhe362hkjtmckj failed part2_analyses_option2_table8
keemqvedrqw4s6fh failed part2_redaction

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 208:41:06

Config