Job request: 4677

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
sqmkgm7auwtqrlh5 succeeded analyses_option1_table1
6laa4w2fpgeyyk3q succeeded analyses_option1_table2
r7cs5lq4utolwlta succeeded analyses_option1_table3
vzveif5jmfua4jna succeeded analyses_option1_table4
jawjoyxfrl35sqit succeeded analyses_option1_table5
de6wchuyiqlg5b6s succeeded analyses_option2_table1a
cfo6fuzqqy4qaj4k succeeded analyses_option2_table1b
37z4de7oarnskn6x succeeded analyses_option3_table1
tpl4afy7pyw7mwok succeeded analyses_option3_table2
stvrnyy5i2dikws6 succeeded analyses_option3_table3
i4qp5ir6fl45h6px succeeded analyses_option3_table4
asqmk4hr2dbt3shn succeeded analyses_option3_table5
ibnskyxrt6pm5fj7 succeeded data_cleaning
al3bqflofg3bdanq succeeded generate_cohort
l6dkslgfuqydom7i succeeded matching_groups_1_2_and_3
zrzwba6zgl6f6zkv succeeded matching_groups_1_and_2
2paffn5ngkgotlgf succeeded matching_groups_1_and_3
jzwe5ht3fsw6vg7w succeeded redaction
zsaqazkb74o6cbd4 succeeded analyses_option1_table3_v2
y6vr6udfbipyjht5 succeeded analyses_option1_table5_v2
skuhigtwzyojepqk succeeded analyses_option3_table3_v2
b6c2c7uppzifn74e succeeded analyses_option3_table5_v2

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 200000

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_table3_v2:
    run: stata-mp:latest analysis/131_analyses_option1_table3_hazardratios_v2.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table3_hazardratios_v2.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_option1_table5_v2:
    run: stata-mp:latest analysis/151_analyses_option1_table5_stratified_hazardratios_v2.do
    needs: [data_cleaning]
    outputs:
      moderately_sensitive:
        table1: output/results/option1_table5_stratified_hazardratios_v2.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_table2:
    run: stata-mp:latest analysis/320_analyses_option3_table2_rates.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table2_rates.dta

  analyses_option3_table3:
    run: stata-mp:latest analysis/330_analyses_option3_table3_hazardratios.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table3_hazardratios.dta

  analyses_option3_table3_v2:
    run: stata-mp:latest analysis/331_analyses_option3_table3_hazardratios_v2.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table3_hazardratios_v2.dta

  analyses_option3_table4:
    run: stata-mp:latest analysis/340_analyses_option3_table4_stratified_rates.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table4_stratified_rates.dta

  analyses_option3_table5:
    run: stata-mp:latest analysis/350_analyses_option3_table5_stratified_hazardratios.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table5_stratified_hazardratios.dta

  analyses_option3_table5_v2:
    run: stata-mp:latest analysis/351_analyses_option3_table5_stratified_hazardratios_v2.do
    needs: [matching_groups_1_2_and_3]
    outputs:
      moderately_sensitive:
        table1: output/results/option3_table5_stratified_hazardratios_v2.dta

  redaction:
    run: stata-mp:latest analysis/999_redaction.do
    needs: [analyses_option1_table1, analyses_option1_table2, analyses_option1_table3, analyses_option1_table3_v2, analyses_option1_table4, analyses_option1_table5, analyses_option1_table5_v2, analyses_option2_table1a, analyses_option2_table1b, analyses_option3_table1, analyses_option3_table2, analyses_option3_table3, analyses_option3_table3_v2, analyses_option3_table4, analyses_option3_table5, analyses_option3_table5_v2]
    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_table3_hazardratios_v2_redacted.dta
        table8: output/results/option1_table3_hazardratios_v2_redacted.csv
        table9: output/results/option1_table4_stratified_rates_redacted.dta
        table10: output/results/option1_table4_stratified_rates_redacted.csv
        table11: output/results/option1_table5_stratified_hazardratios_redacted.dta
        table12: output/results/option1_table5_stratified_hazardratios_redacted.csv
        table13: output/results/option1_table5_stratified_hazardratios_v2_redacted.dta
        table14: output/results/option1_table5_stratified_hazardratios_v2_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_table2_rates_redacted.dta
        table22: output/results/option3_table2_rates_redacted.csv
        table23: output/results/option3_table3_hazardratios_redacted.dta
        table24: output/results/option3_table3_hazardratios_redacted.csv
        table25: output/results/option3_table3_hazardratios_v2_redacted.dta
        table26: output/results/option3_table3_hazardratios_v2_redacted.csv
        table27: output/results/option3_table4_stratified_rates_redacted.dta
        table28: output/results/option3_table4_stratified_rates_redacted.csv
        table29: output/results/option3_table5_stratified_hazardratios_redacted.dta
        table30: output/results/option3_table5_stratified_hazardratios_redacted.csv
        table31: output/results/option3_table5_stratified_hazardratios_v2_redacted.dta
        table32: output/results/option3_table5_stratified_hazardratios_v2_redacted.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 26:49:12

Config