Job request: 4875
- Organisation:
- University of Manchester
- Workspace:
- covid-diabetes-outcomes
- ID:
- s2jzemaloacuq2v6
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.
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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
-