Job request: 329
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- households
- ID:
- vtysw4le6iqaqlyb
This page shows the technical details of what happened when the authorised researcher Kevin Wing 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:
-
a3ynlo47ls5jrayc
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 100000
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: output/hh_analysis_dataset.dta
output_descriptive:
run: stata-mp:latest analysis/02_hh_an_caseFreq_descriptive_plots.do
needs: [prepare_data]
outputs:
moderately_sensitive:
graph1: released_outputs/an_caseFreq_descr_overall_HH_Histogram.svg
graph2: released_outputs/an_caseFreq_descr_overall_HH_HistogramOverlay.svg
log: released_outputs/02_hh_an_caseFreq_descriptive_plots.log
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_0_0_13:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 13 --add-ridge 0.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_0_0_and_seed_13.log
run_model_7_4_13:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 13 --add-ridge 7.4
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_7_4_and_seed_13.log
run_model_20_0_13:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 13 --add-ridge 20.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_20_0_and_seed_13.log
run_model_0_0_15:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 15 --add-ridge 0.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_0_0_and_seed_15.log
run_model_7_4_15:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 15 --add-ridge 7.4
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_7_4_and_seed_15.log
run_model_20_0_15:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 15 --add-ridge 20.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_20_0_and_seed_15.log
run_model_0_0_19:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 19 --add-ridge 0.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_0_0_and_seed_19.log
run_model_7_4_19:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 19 --add-ridge 7.4
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_7_4_and_seed_19.log
run_model_20_0_19:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 19 --add-ridge 20.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_20_0_and_seed_19.log
run_model_0_0_42:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 42 --add-ridge 0.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_0_0_and_seed_42.log
run_model_7_4_42:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 42 --add-ridge 7.4
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_7_4_and_seed_42.log
run_model_20_0_42:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 42 --add-ridge 20.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_20_0_and_seed_42.log
run_model_0_0_56:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 56 --add-ridge 0.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_0_0_and_seed_56.log
run_model_7_4_56:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 56 --add-ridge 7.4
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_7_4_and_seed_56.log
run_model_20_0_56:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 56 --add-ridge 20.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_20_0_and_seed_56.log
run_model_0_0_80:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 80 --add-ridge 0.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_0_0_and_seed_80.log
run_model_7_4_80:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 80 --add-ridge 7.4
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_7_4_and_seed_80.log
run_model_20_0_80:
run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter 80 --add-ridge 20.0
needs: [generate_model_data]
outputs:
moderately_sensitive:
log: opensafely_age_hh_ridge_20_0_and_seed_80.log
run_all:
needs:
[run_model_0_0_13, run_model_7_4_13, run_model_20_0_13, run_model_0_0_15, run_model_7_4_15, run_model_20_0_15, run_model_0_0_19, run_model_7_4_19, run_model_20_0_19, run_model_0_0_42, run_model_7_4_42, run_model_20_0_42, run_model_0_0_56, run_model_7_4_56, run_model_20_0_56, run_model_0_0_80, run_model_7_4_80, run_model_20_0_80]
# 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:
-
Finished:
-
Runtime: 00:00:33
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- households
- Requested by
- Kevin Wing
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 9ceccc3
- Requested actions
-
-
prepare_data
-
Code comparison
Compare the code used in this Job Request