Job request: 7489
- Workspace:
- covid-diabetes-outcomes
- ID:
- vdz5w7iu2hielo7c
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
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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
-
Created:
-
Started:
-
Finished:
-
Runtime:
These timestamps are generated and stored using the UTC timezone on the backend.
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
-