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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 3000
actions:
generate_study_population:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2019-04-01 to 2019-12-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort: output/input_2019*.csv.gz
generate_study_population_range2:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2020-01-01 to 2020-12-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort: output/input_2020*.csv.gz
generate_study_population_range3:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2021-01-01 to 2021-12-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort: output/input_2021*.csv.gz
generate_study_population_range4:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2022-01-01 to 2022-03-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort: output/input_2022*.csv.gz
generate_study_population_allmedrev:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_allmedrev
--index-date-range "2019-04-01 to 2019-12-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort: output/input_allmedrev_2019*.csv.gz
generate_study_population_allmedrev_range2:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_allmedrev
--index-date-range "2020-01-01 to 2020-12-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort2: output/input_allmedrev_2020*.csv.gz
generate_study_population_allmedrev_range3:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_allmedrev
--index-date-range "2021-01-01 to 2021-12-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort3: output/input_allmedrev_2021*.csv.gz
generate_study_population_allmedrev_range4:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_allmedrev
--index-date-range "2022-01-01 to 2022-03-01 by month"
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort3: output/input_allmedrev_2022*.csv.gz
generate_ethnicity_cohort:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--output-format='csv.gz'
outputs:
highly_sensitive:
cohort: output/input_ethnicity.csv.gz
join_cohorts:
run: >
cohort-joiner:v0.0.44
--lhs output/input_20*.csv.gz
--rhs output/input_ethnicity.csv.gz
--output-dir output/joined
needs: [generate_study_population, generate_study_population_range2, generate_study_population_range3, generate_study_population_range4, generate_ethnicity_cohort]
outputs:
highly_sensitive:
cohort: output/joined/input_20*.csv.gz
join_cohorts_allmedrev:
run: >
cohort-joiner:v0.0.44
--lhs output/input_allmedrev*.csv.gz
--rhs output/input_ethnicity.csv.gz
--output-dir output/joined
needs: [generate_study_population_allmedrev, generate_study_population_allmedrev_range2, generate_study_population_allmedrev_range3, generate_study_population_allmedrev_range4, generate_ethnicity_cohort]
outputs:
highly_sensitive:
cohort: output/joined/input_allmedrev_*.csv.gz
## generate Structured Medication Review Measures and plots
generate_measures_mr_smr:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition
--output-dir=output/joined
needs: [join_cohorts]
outputs:
moderately_sensitive:
mr_measure_csv: output/joined/measure_mr_*_rate.csv
mr12m_measure_csv: output/joined/measure_mr12m_*_rate.csv
smr_measure_csv: output/joined/measure_smr_*_rate.csv
smr12m_measure_csv: output/joined/measure_smr12m_*_rate.csv
generate_measures_all_reviews:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_allmedrev
--output-dir=output/joined
needs: [join_cohorts_allmedrev]
outputs:
moderately_sensitive:
allmedrev_measure_csv: output/joined/measure_allmedrv_*_rate.csv
allmedrev12m_measure_csv: output/joined/measure_allmedrv12m_*_rate.csv
allmedrev_measure_asgrouped_csv: output/joined/measure_allmedrv_*_rate_agestandardgrouped.csv
allmedrev12m_measure_asgrouped_csv: output/joined/measure_allmedrv12m_*_rate_agestandardgrouped.csv
generate_deciles_charts:
run: >
deciles-charts:v0.0.33
--input-files output/joined/measure_*_practice_rate.csv
--output-dir output/joined
config:
show_outer_percentiles: false
tables:
output: true
charts:
output: true
needs: [generate_measures_mr_smr, generate_measures_all_reviews]
outputs:
moderately_sensitive:
deciles_charts: output/joined/deciles_*_*.*
redact_and_round:
run: python:latest python analysis/redact_and_round.py
needs: [generate_measures_mr_smr, generate_codeuse_output, generate_allmedrev_codeuse_output, generate_measures_all_reviews]
outputs:
moderately_sensitive:
cohort: output/redacted/redacted_measure_*.csv
cohort_codeuse: output/redacted/redacted_totalcodeuse*.csv
generate_plots:
run: python:latest python analysis/plots.py
needs: [redact_and_round, generate_deciles_charts]
outputs:
moderately_sensitive:
percent_cohort: output/figures/*_*_rate_percentage.jpeg
perthousand_cohort: output/figures/*_*_rate_perthousand.jpeg
generate_table_1:
run: python:latest python analysis/table_1.py --study_def_paths="output/joined/input_20*.csv.gz" --demographics="age_band,sex,region,imdQ5,ethnicity,learning_disability,care_home_type" --outcome "had_smr"
needs: [join_cohorts]
outputs:
moderately_sensitive:
counts: output/table_1.csv
had_outcome: output/table_1_had_outcome.csv
generate_codeuse_output:
run: python:latest python analysis/code_use_summary.py --study_def_paths="output/joined/input_20*.csv.gz" --codelistfile="user-chriswood-medication-review.csv" --outputfile="codeuse"
needs: [join_cohorts]
outputs:
moderately_sensitive:
code_counts: output/codeuse.csv
total_code_counts: output/totalcodeuse.csv
generate_allmedrev_codeuse_output:
run: python:latest python analysis/code_use_summary.py --study_def_paths="output/joined/input_allmedrev_*.csv.gz" --codelistfile="user-chriswood-all-medication-reviews.csv" --outputfile="codeuse_allmedrev" --totalstart="01/01/2020" --totalend="01/12/2020"
needs: [join_cohorts_allmedrev]
outputs:
moderately_sensitive:
code_counts: output/codeuse_allmedrev.csv
total_code_counts: output/totalcodeuse_allmedrev.csv
run_tests:
run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
outputs:
moderately_sensitive:
log: output/pytest.xml