Job request: 6414
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- covid-collateral
- ID:
- j47d4s7zie6t5vxb
This page shows the technical details of what happened when the authorised researcher Rohini Mathur 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:
-
ijka2ia2q4j6kkla - Error:
- nonzero_exit: Job exited with error code 1
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- Job identifier:
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nlepl7m75ki26rdg - Error:
- nonzero_exit: Job exited with error code 1
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- Job identifier:
-
6irsma3bimdnvdxs - Error:
- nonzero_exit: Job exited with error code 1
-
- Job identifier:
-
2sfvz7vnxssjbr7c - Error:
- nonzero_exit: Job exited with error code 1
-
- Job identifier:
-
tm6gm7kxw5ng3scn - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
lnhr32nzdsd7bbsc - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
3abcb2h7staatdrz - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
twj2tlbo4h57xi5f - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
e2tpz24krv4oeql2 - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
oltgdxlfvexoq4qp - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
6s27zsfpegpfz5wr - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
yapg7oti5y4fkuuh - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
# Generates study population for CV, mental health outcomes
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2020-06-01 by month" --output-dir=output/measures --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv
# Generates study population for diabetes outcomes
generate_study_population_dm:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2020-03-01 to 2020-06-01 by month" --output-dir=output/measures/dm --output-format=csv --skip-existing
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 "2020-03-01 to 2020-06-01 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 "2020-03-01 to 2020-06-01 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/mortality/input_mortality_*.csv
# Generates summary measures for CV and mental health outcomes
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure: output/measures/measure_*.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_*.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_*.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_*.csv
# Generates graphs for CVD & mental health outcomes
graphs_mh_cvd:
run: stata-mp:latest analysis/graphs_mh_cvd.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/graphs_mh_cvd.log
output: output/line_*.eps
# 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/line_dm_*.eps
# 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/line_resp_*.eps
# 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/line_mortality_*.eps
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 01:50:28
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
- Rohini Mathur
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 7757094
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request