Job request: 4836
- Organisation:
- Bennett Institute
- Workspace:
- mechanical-valve-anticoag
- ID:
- drji2cvzikyctrsu
This page shows the technical details of what happened when the authorised researcher Louis Fisher 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:
-
ofime7ox3s5vzk2w
-
- Job identifier:
-
ranweowhwdrz2zto
-
- Job identifier:
-
e7r7ek7cvmyk74sh
-
- Job identifier:
-
sk7wsxpbrqgvoaza
-
- Job identifier:
-
f63opm4bamm2tsvk
-
- Job identifier:
-
lr2diu6xj5xdyhws
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 15000
actions:
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-12-01 by month" --output-dir=output --skip-existing
outputs:
highly_sensitive:
cohort: output/input*.csv
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/in*.csv
patient_count:
run: python:latest python analysis/get_patient_count.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
csv: output/patient_count.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/measure_*_rate.csv
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [join_ethnicity, generate_measures]
outputs:
moderately_sensitive:
notebook: output/notebook.html
figures: output/measure_*.jpeg
total_csv: output/doac_rate_total.csv
csvs: output/current_doac_*.csv
recent_data:
run: python:latest python analysis/recent_data.py
needs: [generate_notebook]
outputs:
moderately_sensitive:
csv: output/doac_rate_total_recent.csv
# # to be run locally
combine:
run: python:latest python analysis/combined_analysis.py
outputs:
moderately_sensitive:
measure_csv: released_outputs/combined_rate.csv
count: released_outputs/count.jpeg
count_with_mean: released_outputs/count_with_mean.jpeg
rate: released_outputs/rate.jpeg
# # to be run locally
generate_report_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report_notebook.ipynb --execute --to html --output-dir=/workspace/released_outputs --ExecutePreprocessor.timeout=86400 --no-input
needs: [combine]
outputs:
moderately_sensitive:
notebook: released_outputs/report_notebook.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 02:28:58
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- mechanical-valve-anticoag
- Requested by
- Louis Fisher
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 5cdf6cd
- Requested actions
-
-
generate_study_population_ethnicity
-
generate_study_population
-
join_ethnicity
-
patient_count
-
generate_measures
-
generate_notebook
-
Code comparison
Compare the code used in this Job Request