Job request: 285
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- households
- ID:
- zieoz7n4qwmimhqm
This page shows the technical details of what happened when the authorised researcher Seb Bacon 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:
-
wewlh5s2gnrdmmuo-manually-set
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 1000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort
outputs:
highly_sensitive:
cohort: output/input.csv
prepare_data:
run: stata-mp:latest analysis/01_hh_cr_analysis_dataset.do
needs: [generate_cohort]
outputs:
highly_sensitive:
allvars: hh_analysis_dataset.dta
descriptive_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/opensafely_eda_test_notebook.ipynb --execute --to html --output-dir=/workspace --ExecutePreprocessor.timeout=86400
needs: [prepare_data]
outputs:
moderately_sensitive:
notebook: opensafely_eda_test_notebook.html
ages: analysis/ages.png
hhsize: analysis/hh_sizes.png
cases: analysis/hh_cases_*.png
vo_test:
run: python:latest python analysis/fit_vo.py 20
needs: []
outputs:
moderately_sensitive:
vo: vo.txt
generate_model_data:
run: python:latest python analysis/generate_model_data.py
needs: [prepare_data]
outputs:
moderately_sensitive:
log: generate_model_data.log
timeseries: output/case_series.pickle
agecats: output/age_categories_series.pickle
run_model_with_ridge:
run: python:latest python analysis/opensafely_age_hh.py increase_nll
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_with_ridge.log
run_model_no_ridge:
run: python:latest python analysis/opensafely_age_hh_th.py
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_without_ridge.log
run_all:
needs: [run_model_no_ridge]
# In order to be valid this action needs to define a run commmand and some
# output. We don't really care what these are but the below does the trick.
# In a future release of the platform, this special action won't need to be
# defined at all.
run: cohortextractor:latest --version
outputs:
moderately_sensitive:
whatever: project.yaml
Timeline
-
Created:
-
Started:
-
Runtime:
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- households
- Requested by
- Seb Bacon
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- fd97279
- Requested actions
-
-
run_model_no_ridge
-
Code comparison
Compare the code used in this Job Request