Job request: 2148
- Organisation:
- Bennett Institute
- Workspace:
- mechanical-valve-anticoag
- ID:
- usokekfwh4og367l
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:
-
dvsypz3k3z75kxjd
-
- Job identifier:
-
xdxwv5dflxccl3ai
-
- Job identifier:
-
ezvjdvzgfpxagwvb
-
- Job identifier:
-
xcsqeszeqshqmhsl
-
- Job identifier:
-
gqp6tgogfy3ajqte
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 15000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-01 to 2021-04-01 by month" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_*.csv
get_patient_count:
run: python:latest python analysis/get_patient_count.py
needs: [generate_study_population]
outputs:
moderately_sensitive:
patient_count: output/patient_count.json
valve_code_counts: output/patient_valve_codes.json
doac_valve_code_counts: output/patient_doac_valve_codes.json
recent_doac_valve_code_counts: output/recent_patient_doac_valve_codes.json
generate_study_population_demographics:
run: cohortextractor:latest generate_cohort --study-definition study_definition_demographics
outputs:
highly_sensitive:
cohort: output/input_demographics.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measure_*.csv
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/measures_notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_study_population, generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/measures_notebook.html
# measures_csv: output/measures_dropped.csv
# csv: output/check.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: [generate_study_population, generate_study_population_demographics,generate_measures, get_patient_count]
outputs:
moderately_sensitive:
notebook: output/notebook.html
figures: output/measure_*.jpeg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:15
These timestamps are generated and stored using the UTC timezone on the EMIS backend.
Job information
- Status
-
Failed
- Backend
- EMIS
- Workspace
- mechanical-valve-anticoag
- Requested by
- Louis Fisher
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- d7c1109
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request
- No previous Job Request available for comparison