Job Request: 2466 f44rrjv2rdfsl6ao

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 Service Restoration Observatory 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.

State

State is inferred from the related Jobs
Status: failed

Config

Backend: tpp
Workspace: sro-measures (master)
Creator: LFISHER7
Force run dependencies?: False
Git Commit Hash: 22ae183
Requested Actions:
  • get_population_count

Timings

Created: 1 month, 3 weeks ago
Started: 1 month, 3 weeks ago
Finished: 1 month, 3 weeks ago
Runtime: 01:27:35

Pipeline

version: '3.0'

expectations:
population_size: 1000


actions:

generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_*.feather

get_patient_count:
run: python:latest python analysis/get_patients_counts.py
needs: [generate_study_population]
outputs:
moderately_sensitive:
text: output/patient_count.json


generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather

join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/input*.feather

generate_study_population_practice_count:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_practice_count.feather

get_practice_count:
run: python:latest python analysis/get_practice_count.py
needs: [generate_study_population_practice_count]
outputs:
moderately_sensitive:
text: output/practice_count.json

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_measures_demographics:
run: python:latest python analysis/calculate_measures.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure: output/combined_measure_*.csv


generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_measures, get_practice_count, get_patient_count]
outputs:
moderately_sensitive:
notebook: output/sentinel_measures.html


generate_notebook_demographics:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_demographics.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_measures, generate_measures_demographics]
outputs:
moderately_sensitive:
notebook: output/sentinel_measures_demographics.html

get_population_count:
run: python:latest python analysis/population_counts.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
text: output/*_count.csv

demographic_changes:
run: python:latest python notebooks/demographic_change.py
needs: [generate_measures_demographics]
outputs:
moderately_sensitive:
csv: output/demographics_differences.csv
csv_sorted: output/demographics_differences_sorted.csv


# run_tests:
# run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
# outputs:
# moderately_sensitive:
# log: output/pytest.xml

Jobs

ID Status Action
vcdcvbx57ee23qhl failed get_population_count View