Job request: 925
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- absolute-risks
- ID:
- oxxfe7fnli6ujssq
This page shows the technical details of what happened when the authorised researcher Elizabeth (Fizz) Williamson requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the list of jobs with the
pipeline section below, you can infer what
security level
various outputs were written to. Researchers can never directly
view outputs marked as
highly_sensitive
;
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.
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_cohort1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01"
outputs:
highly_sensitive:
cohort: output/input_2020-03-01.csv
generate_cohort2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01"
outputs:
highly_sensitive:
cohort: output/input_2020-09-01.csv
clean:
run: stata-mp:latest analysis/001_clean_input_data.do
needs: [generate_cohort1, generate_cohort2]
outputs:
highly_sensitive:
clean1: analysis/data_base_cohort1.dta
clean2: analysis/data_base_cohort2.dta
create_analysis:
run: stata-mp:latest analysis/002_create_ld_analysis_dataset.do
needs: [clean]
outputs:
highly_sensitive:
an_data1: analysis/data_ldanalysis_cohort1.dta
an_data2: analysis/data_ldanalysis_cohort2.dta
create_analysis_ar:
run: stata-mp:latest analysis/003_create_ar_analysis_dataset.do
needs: [clean]
outputs:
highly_sensitive:
an_data1: analysis/data_aranalysis_cohort1.dta
an_data2: analysis/data_aranalysis_cohort2.dta
describe_cohort:
run: stata-mp:latest analysis/AL001_describe_cohort.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL001_describe_cohort.log
tabulate_cohort:
run: stata-mp:latest analysis/AL002_tabulate_cohort_descriptives.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL002_tabulate_cohort_descriptives.log
model: output/basetable1.txt
cox_regression:
run: stata-mp:latest analysis/AL004_cox_regression.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_cox_regression.log
hrs_adult: output/output_hrs_main.out
rates_adult: output/output_rates.out
cox_regression_child:
run: stata-mp:latest analysis/AL005_cox_regression_child.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL005_cox_regression_child.log
hrs_child: output/output_hrs_main_child.out
rates_child: output/output_rates_child.out
cumulative_incidence:
run: stata-mp:latest analysis/AL003_cumulative_incidence.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL003_cumulative_incidence.log
graph1: output/cumincidence_coviddeath.svg
graph2: output/cumincidence_composite.svg
cox_regression1:
run: stata-mp:latest analysis/AL004_1_cox_regression.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_1_cox_regression.log
hrs_adult: output/output_hrs_main_2_coviddeath_ldr_group.out
rates_adult: output/output_rates_2_coviddeath_ldr_group.out
cox_regression2:
run: stata-mp:latest analysis/AL004_2_cox_regression.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_2_cox_regression.log
hrs_adult: output/output_hrs_main_2_covidadmission_ldr_group.out
rates_adult: output/output_rates_2_covidadmission_ldr_group.out
cox_regression3:
run: stata-mp:latest analysis/AL004_3_cox_regression.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_3_cox_regression.log
hrs_adult: output/output_hrs_main_1_coviddeath_ldr_group.out
rates_adult: output/output_rates_1_coviddeath_ldr_group.out
cox_regression4:
run: stata-mp:latest analysis/AL004_4_cox_regression.do
needs: [create_analysis]
outputs:
moderately_sensitive:
log: logs/AL004_4_cox_regression.log
hrs_adult: output/output_hrs_main_1_covidadmission_ldr_group.out
rates_adult: output/output_rates_1_covidadmission_ldr_group.out4
cox_regression3_ar:
run: stata-mp:latest analysis/AAR001_3_cox_regression.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_3_cox_regression.log
hrfemale: output/hr_coviddeath_wave1_male0.txt
hrmale: output/hr_coviddeath_wave1_male1.txt
cox_regression4_ar:
run: stata-mp:latest analysis/AAR001_4_cox_regression.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_4_cox_regression.log
hrfemale: output/hr_coviddeath_wave2_male0.txt
hrmale: output/hr_coviddeath_wave2_male1.txt
cox_regression1_ar:
run: stata-mp:latest analysis/AAR001_1_cox_regression.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_1_cox_regression.log
hrfemale: output/hr_covidadmission_wave1_male0.txt
hrmale: output/hr_covidadmission_wave1_male1.txt
cox_regression2_ar:
run: stata-mp:latest analysis/AAR001_2_cox_regression.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR001_2_cox_regression.log
hrfemale: output/hr_covidadmission_wave2_male0.txt
hrmale: output/hr_covidadmission_wave2_male1.txt
ar_1:
run: stata-mp:latest analysis/AAR002_1_risk_by_age.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_1_risk_by_age.log
arfemale: output/ar_wave1_male0_covidadmission.out
armale: output/ar_wave1_male1_covidadmission.out
garfemale: output/ar_wave1_male0_covidadmission.svg
garmale: output/ar_wave1_male1_covidadmission.svg
ar_2:
run: stata-mp:latest analysis/AAR002_2_risk_by_age.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_2_risk_by_age.log
arfemale: output/ar_wave2_male0_covidadmission.out
armale: output/ar_wave2_male1_covidadmission.out
garfemale: output/ar_wave2_male0_covidadmission.svg
garmale: output/ar_wave2_male1_covidadmission.svg
ar_3:
run: stata-mp:latest analysis/AAR002_3_risk_by_age.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_3_risk_by_age.log
arfemale: output/ar_wave1_male0_coviddeath.out
armale: output/ar_wave1_male1_coviddeath.out
garfemale: output/ar_wave1_male0_coviddeath.svg
garmale: output/ar_wave1_male1_coviddeath.svg
ar_4:
run: stata-mp:latest analysis/AAR002_4_risk_by_age.do
needs: [create_analysis_ar]
outputs:
moderately_sensitive:
log: logs/AAR002_4_risk_by_age.log
arfemale: output/ar_wave2_male0_coviddeath.out
armale: output/ar_wave2_male1_coviddeath.out
garfemale: output/ar_wave2_male0_coviddeathn.svg
garmale: output/ar_wave2_male1_coviddeath.svg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime:
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
JobRequestError: Internal error
- Backend
- TPP
- Workspace
- absolute-risks
- Requested by
- Elizabeth (Fizz) Williamson
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- cd3940a
- Requested actions
-
-
create_analysis_ar
-
ar_1
-
ar_2
-
ar_3
-
ar_4
-
Code comparison
Compare the code used in this Job Request