Job request: 8406
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- covid-collateral
- ID:
- kyy4d6bolbn6euiy
This page shows the technical details of what happened when the authorised researcher Ruth Costello 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:
-
pg37jo6z45ow74i5
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- Job identifier:
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hknwr53svz337u7t
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- Job identifier:
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coxm3jo7g7emjika
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- Job identifier:
-
b76ukmw2v4vrenxm
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- Job identifier:
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jymsioppg3gw3ab3
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- Job identifier:
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we2kdlbnllyuoipl
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- Job identifier:
-
zaol3i7h7ysukoeb
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
# Generating static variables
generate_study_population_static:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static.csv
# Generates study population for CV - start date = 2018-03-01
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv
# Join static and time-varying variables
join_cohorts_cvd:
run: >
cohort-joiner:v0.0.30
--lhs output/measures/input_*.csv
--rhs output/input_static.csv
--output-dir output/measures/cvd
needs: [generate_study_population, generate_study_population_static]
outputs:
highly_sensitive:
cohort: output/measures/cvd/input_*.csv
# Generates study population for mental health outcomes - start date = 2018-03-01
generate_study_population_mh:
run: cohortextractor:latest generate_cohort --study-definition study_definition_mh --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_mh_*.csv
# Join static and time-varying variables
join_cohorts_mh:
run: >
cohort-joiner:v0.0.30
--lhs output/measures/input_mh_*.csv
--rhs output/input_static.csv
--output-dir output/measures/mh
needs: [generate_study_population_mh, generate_study_population_static]
outputs:
highly_sensitive:
cohort: output/measures/mh/input_mh_*.csv
# Generates study population for diabetes outcomes
generate_study_population_dm:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/dm --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/dm/input_dm_*.csv
# Generates study population for respiratory outcomes
generate_study_population_resp:
run: cohortextractor:latest generate_cohort --study-definition study_definition_resp --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/resp --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/resp/input_resp_*.csv
# Generates study population for mortality
generate_study_population_mortality:
run: cohortextractor:latest generate_cohort --study-definition study_definition_mortality --index-date-range "2019-02-01 to 2022-01-31 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/mortality/input_mortality_*.csv
# Generates study populations for baseline tables at 3 timepoints
generate_study_population_tables_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/tables/input_tables_2019-01-01.csv
generate_study_population_tables_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/tables/input_tables_2020-01-01.csv
generate_study_population_tables_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/tables/input_tables_2021-01-01.csv
# Generates baseline tables
create_baseline_tables:
run: stata-mp:latest analysis/baseline_tables.do
needs: [generate_study_population_tables_2019, generate_study_population_tables_2020, generate_study_population_tables_2021]
outputs:
moderately_sensitive:
output: output/tables/baseline_table_*.csv
# Generates summary measures for CV
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures/cvd
needs: [join_cohorts_cvd]
outputs:
moderately_sensitive:
measure: output/measures/cvd/measure_*_rate.csv
# Generates summary measures for mental health outcomes
calculate_measures_mh:
run: cohortextractor:latest generate_measures --study-definition study_definition_mh --output-dir=output/measures/mh
needs: [join_cohorts_mh]
outputs:
moderately_sensitive:
measure: output/measures/mh/measure_*_rate.csv
# Generates summary measures for diabetes outcomes
calculate_measures_dm:
run: cohortextractor:latest generate_measures --study-definition study_definition_dm --output-dir=output/measures/dm
needs: [generate_study_population_dm]
outputs:
moderately_sensitive:
measure: output/measures/dm/measure_dm_*_rate.csv
# Generates summary measures for respiratory outcomes
calculate_measures_resp:
run: cohortextractor:latest generate_measures --study-definition study_definition_resp --output-dir=output/measures/resp
needs: [generate_study_population_resp]
outputs:
moderately_sensitive:
measure: output/measures/resp/measure_*_rate.csv
# Generates summary measures for mortality outcomes
calculate_measures_mortality:
run: cohortextractor:latest generate_measures --study-definition study_definition_mortality --output-dir=output/measures/mortality
needs: [generate_study_population_mortality]
outputs:
moderately_sensitive:
measure: output/measures/mortality/measure_*_rate.csv
# Generates graphs for CVD & mental health outcomes
graphs_mh_cvd:
run: stata-mp:latest analysis/graphs_mh_cvd.do
needs: [calculate_measures, calculate_measures_mh]
outputs:
moderately_sensitive:
log: logs/graphs_mh_cvd.log
output: output/graphs/line_*.svg
# Generates graphs for diabetes outcomes
graphs_dm:
run: stata-mp:latest analysis/graphs_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/graphs_dm.log
output: output/graphs/line_dm_*.svg
highly_sensitive:
output: output/collapsed/collapse_measure_dm_*
# Generate graphs for respiratory outcomes
graphs_resp:
run: stata-mp:latest analysis/graphs_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/graphs_resp.log
output: output/graphs/line_resp_*.svg
# Generate graphs for mortality
graphs_mortality:
run: stata-mp:latest analysis/graphs_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/graphs_mortality.log
output: output/graphs/line_mortality_*.svg
highly_sensitive:
output: output/collapsed/collapse_measure_*
# Running analysis scripts
model_checks_dm:
run: stata-mp:latest analysis/model_check_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/model_checks_dm.log
output: output/time_series/dm_*.svg
model_checks_resp:
run: stata-mp:latest analysis/model_check_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/model_checks_resp.log
output: output/time_series/resp_*.svg
model_checks_cvd:
run: stata-mp:latest analysis/model_check_cvd.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/model_checks_cvd.log
output: output/time_series/cvd_*.svg
model_checks_mh:
run: stata-mp:latest analysis/model_check_mh.do
needs: [calculate_measures_mh]
outputs:
moderately_sensitive:
log: logs/model_checks_mh.log
output: output/time_series/mh_*.svg
model_checks_mortality:
run: stata-mp:latest analysis/model_check_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/model_checks_mortality.log
output: output/time_series/mortality_*.svg
time_series_resp:
run: stata-mp:latest analysis/time_series_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/tsreg_resp.log
output: output/time_series/tsreg_resp*.csv
time_series_dm:
run: stata-mp:latest analysis/time_series_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/tsreg_dm.log
output: output/time_series/tsreg_dm*.csv
time_series_cvd:
run: stata-mp:latest analysis/time_series_cvd.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/tsreg_cvd.log
output: output/time_series/tsreg_cvd_*.csv
time_series_mh:
run: stata-mp:latest analysis/time_series_mh.do
needs: [calculate_measures_mh]
outputs:
moderately_sensitive:
log: logs/tsreg_mh.log
output: output/time_series/tsreg_mh*.csv
time_series_mortality:
run: stata-mp:latest analysis/time_series_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/tsreg_mortality.log
output: output/time_series/tsreg_mortality*.csv
Timeline
-
Created:
-
Finished:
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Runtime:
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- covid-collateral
- Requested by
- Ruth Costello
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 09061ed
- Requested actions
-
-
calculate_measures
-
calculate_measures_mh
-
graphs_mh_cvd
-
model_checks_cvd
-
model_checks_mh
-
time_series_cvd
-
time_series_mh
-
Code comparison
Compare the code used in this Job Request