This page shows the technical details of what happened when 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 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:
-
4sbadfcqyciyunec
-
- Job identifier:
-
rzebg5dnzvuda65u
-
- Job identifier:
-
ruzgqqh5xerdo7sd
-
- Job identifier:
-
sqf6jbvlno2brype
-
- Job identifier:
-
wso3hgggmizs6acu
-
- Job identifier:
-
2zodsryp7trisley
-
- Job identifier:
-
bg5lhpojjm7yq6al
-
- Job identifier:
-
p3gpkvvgxcb7n3ya
-
- Job identifier:
-
s2sqt2ybd4h5w3is
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 10000
actions:
# convert_codelist:
# run: python:latest python analysis/convert_codelist.py
# outputs:
# highly_sensitive:
# cohort: codelists/opensafely-pulse-oximetry-converted.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-01 to 2021-02-01 by week" --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_*.csv
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
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/input*.csv
generate_study_population_practice_count:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_practice_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_*.csv
generate_measure_ethnicity:
run: python:latest python analysis/generate_measure_ethnicity.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure: output/measure_ethnicity.csv
get_patient_count:
run: python:latest python analysis/get_patients_counts.py
needs: [generate_study_population]
outputs:
moderately_sensitive:
text: output/patient_count.json
create_notebook:
run: python:latest python analysis/create_notebook.py
needs: [get_patient_count, join_ethnicity]
outputs:
moderately_sensitive:
notebook: analysis/SRO_Notebook.ipynb
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/SRO_Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [create_notebook, generate_measures, generate_measure_ethnicity, generate_study_population_practice_count, generate_study_population, join_ethnicity]
outputs:
moderately_sensitive:
notebook: output/SRO_Notebook.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:12:44
These timestamps are generated and stored using the UTC timezone on the backend.
Job information
- Status
-
Failed
Job exited with an error code
- Backend
- TPP
- Workspace
- sro-pulse-oximetry-2
- Requested by
- Louis Fisher
- Branch
- template
- Force run dependencies
- No
- Git commit hash
- 4cf71b3
- Requested actions
-
-
run_all
-