Job request: 292
- The London School of Hygiene & Tropical Medicine
This page shows the technical details of what happened when 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 indicated Requested Actions with the
Pipeline section below, you can infer what
various outputs were written to. Outputs marked as
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
can be requested for release to the public, via a controlled
output review service.
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_th.py --add-ridge 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_model_with_ridge_and_param_1: run: python:latest python analysis/opensafely_age_hh_th.py --add-ridge --starting-parameter=1 needs: [generate_model_data] outputs: moderately_sensitive: log: opensafely_age_hh_with_ridge_and_param_1.log run_model_no_ridge_and_param_1: run: python:latest python analysis/opensafely_age_hh_th.py --starting-parameter=1 needs: [generate_model_data] outputs: moderately_sensitive: log: opensafely_age_hh_without_ridge_and_param_1.log run_all: needs: [ run_model_no_ridge, run_model_with_ridge, run_model_no_ridge_and_param_1, run_model_with_ridge_and_param_1, ] # 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
These timestamps are generated and stored using the UTC timezone on the TPP backend.