Job request: 1538
- Organisation:
- Bennett Institute
- Workspace:
- surgery-outcomes-full
- ID:
- j3ox3u6siyvhwnry
This page shows the technical details of what happened when the authorised researcher Helen Curtis 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:
-
qtbfedwmvtuqxpfu
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 5000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-04-01 to 2020-04-01 by month"
outputs:
highly_sensitive:
cohort: output/input_2020*.csv
generate_study_population_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-04-01 to 2019-04-01 by month"
outputs:
highly_sensitive:
cohort: output/input_2019*.csv
filter_population_for_matching:
run: python:latest python analysis/filter_population.py
needs: [generate_study_population]
outputs:
highly_sensitive:
filtered_cohort: output/filtered_2020_for_matching.csv
covid_cohort: output/filtered_2020_covid_positive.csv
matching:
run: python:latest python analysis/match_running.py
needs: [generate_study_population, filter_population_for_matching, generate_study_population_2019]
outputs:
moderately_sensitive:
matching_report: output/matching_report_2019.txt
highly_sensitive:
matched_cohort: output/matched_matches_2019.csv
generate_notebook_data_checks:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/data_checks.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
needs: [filter_population_for_matching]
outputs:
moderately_sensitive:
notebook: output/data_checks.html
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/analysis.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
needs: [generate_study_population_2019, filter_population_for_matching, matching]
outputs:
moderately_sensitive:
notebook: output/analysis.html
baseline_char: output/baseline*
counts: output/patient_count*
outcomes_summary: output/summary*
outcomes_detailed: output/detailed*
outcomes_mortality: output/mortality*
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:36
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- surgery-outcomes-full
- Requested by
- Helen Curtis
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 02c6ccf
- Requested actions
-
-
generate_notebook
-
Code comparison
Compare the code used in this Job Request