Job Request: 2466 f44rrjv2rdfsl6ao

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 week ago
Started: 1 week ago
Finished: 1 week 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