Job request: 7325
- Organisation:
- Bennett Institute
- Workspace:
- bmi-short-data-report
- ID:
- sw4azgh25iunzkbb
This page shows the technical details of what happened when authorised researcher Robin Park 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
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; 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:
-
w43j4zbverztzb7t
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input.feather
preprocess_inputs:
run: python:latest python analysis/preprocess_inputs.py --output-format feather
needs: [generate_study_population]
outputs:
highly_sensitive:
cohort_with_duration: output/data/input_processed.feather
execute_validation_analyses:
run: python:latest python analysis/validation_script.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/phenotype_validation_bmi/tables/*.csv
figures: output/phenotype_validation_bmi/figures/*.png
generate_report_bmi:
run: python:latest jupyter nbconvert /workspace/notebooks/report_bmi.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_validation_analyses]
outputs:
moderately_sensitive:
notebook: output/report_bmi.html
execute_validation_analyses_height:
run: python:latest python analysis/validation_script_height.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/phenotype_validation_height/tables/*.csv
figures: output/phenotype_validation_height/figures/*.png
generate_report_height:
run: python:latest jupyter nbconvert /workspace/notebooks/report_height.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_validation_analyses_height]
outputs:
moderately_sensitive:
notebook: output/report_height.html
execute_validation_analyses_weight:
run: python:latest python analysis/validation_script_weight.py
needs: [preprocess_inputs]
outputs:
moderately_sensitive:
tables: output/phenotype_validation_weight/tables/*.csv
figures: output/phenotype_validation_weight/figures/*.png
generate_report_weight:
run: python:latest jupyter nbconvert /workspace/notebooks/report_weight.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_validation_analyses_weight]
outputs:
moderately_sensitive:
notebook: output/report_weight.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 01:01:53
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- bmi-short-data-report
- Requested by
- Robin Park
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- eb5a346
- Requested actions
-
-
generate_report_bmi
-
Code comparison
Compare the code used in this Job Request