Job request: 17574
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- sotrovimab_molnupiravir
- ID:
- ejwsbj6p6jbicufg
This page shows the technical details of what happened when the authorised researcher Bang Zheng 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.
Jobs
-
- Job identifier:
-
2bq6lgpjw3jobbew
-
- Job identifier:
-
lqviiv2k6n63rcp6
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 500000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
data_preparation:
run: stata-mp:latest analysis/data_preparation_and_descriptives.do
needs: [generate_study_population]
outputs:
moderately_sensitive:
log: logs/data_preparation.log
highly_sensitive:
data: output/main.dta
cox_regression:
run: stata-mp:latest analysis/cox.do
needs: [data_preparation]
outputs:
moderately_sensitive:
log: logs/cox.log
figure1: output/phtest.svg
figure2: output/phtest_psw.svg
multiple_imputation:
run: stata-mp:latest analysis/multiple_imputation.do
needs: [data_preparation]
outputs:
moderately_sensitive:
log: logs/MI.log
generate_study_population_update_codelist:
run: cohortextractor:latest generate_cohort --study-definition study_definition_update_codelist
outputs:
highly_sensitive:
cohort: output/update_codelist/input_update_codelist.csv
data_preparation_update_codelist:
run: stata-mp:latest analysis/data_preparation_and_descriptives_update_codelist.do
needs: [generate_study_population_update_codelist]
outputs:
moderately_sensitive:
log: logs/data_preparation_update_codelist.log
highly_sensitive:
data: output/update_codelist/main_update_codelist.dta
cox_regression_update_codelist:
run: stata-mp:latest analysis/cox_update_codelist.do
needs: [data_preparation_update_codelist]
outputs:
moderately_sensitive:
log: logs/cox_update_codelist.log
figure1: output/update_codelist/phtest.svg
figure2: output/update_codelist/phtest_psw.svg
generate_study_population_BA2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_BA2
outputs:
highly_sensitive:
cohort: output/BA2/input_BA2.csv
data_preparation_BA2:
run: stata-mp:latest analysis/data_preparation_and_descriptives_BA2.do
needs: [generate_study_population_BA2]
outputs:
moderately_sensitive:
log: logs/data_preparation_BA2.log
highly_sensitive:
data: output/BA2/main_BA2.dta
cox_regression_BA2:
run: stata-mp:latest analysis/cox_BA2.do
needs: [data_preparation_BA2]
outputs:
moderately_sensitive:
log: logs/cox_BA2.log
figure1: output/BA2/phtest.svg
figure2: output/BA2/phtest_psw.svg
generate_study_population_ukrr:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr.csv
data_preparation_ukrr:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr.do
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr.log
highly_sensitive:
data: output/ukrr/main_ukrr.dta
cox_regression_ukrr:
run: stata-mp:latest analysis/cox_ukrr.do
needs: [data_preparation_ukrr]
outputs:
moderately_sensitive:
log: logs/cox_ukrr.log
figure1: output/ukrr/phtest.svg
figure2: output/ukrr/phtest_psw.svg
figure3: output/ukrr/psgraph.svg
multiple_imputation_ukrr:
run: stata-mp:latest analysis/multiple_imputation_ukrr.do
needs: [data_preparation_ukrr]
outputs:
moderately_sensitive:
log: logs/MI_ukrr.log
data_preparation_ukrr_raw_rate:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_raw_rate.do
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr_raw_rate.log
generate_study_population_ukrr_update:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr_update
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr_update.csv
data_preparation_ukrr_update:
run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_update.do
needs: [generate_study_population_ukrr_update]
outputs:
moderately_sensitive:
log: logs/data_preparation_ukrr_update.log
highly_sensitive:
data: output/ukrr/main_ukrr_update.dta
cox_regression_ukrr_update:
run: stata-mp:latest analysis/cox_ukrr_update.do
needs: [data_preparation_ukrr_update]
outputs:
moderately_sensitive:
log: logs/cox_ukrr_update.log
figure1: output/ukrr/phtest_update.svg
figure2: output/ukrr/phtest_psw_update.svg
figure3: output/ukrr/psgraph_update.svg
generate_study_population_anaphylaxis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis
outputs:
highly_sensitive:
cohort: output/input_anaphylaxis.csv
anaphylaxis:
run: stata-mp:latest analysis/anaphylaxis.do
needs: [generate_study_population_anaphylaxis]
outputs:
moderately_sensitive:
log: logs/anaphylaxis.log
generate_study_population_anaphylaxis_untreated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_untreated
outputs:
highly_sensitive:
cohort: output/input_anaphylaxis_untreated.csv
anaphylaxis_untreated:
run: stata-mp:latest analysis/anaphylaxis_untreated.do
needs: [generate_study_population_anaphylaxis_untreated]
outputs:
moderately_sensitive:
log: logs/anaphylaxis_untreated.log
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:08:44
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- sotrovimab_molnupiravir
- Requested by
- Bang Zheng
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 107e79a
- Requested actions
-
-
anaphylaxis
-
anaphylaxis_untreated
-
Code comparison
Compare the code used in this Job Request