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project.yaml
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/
project.yaml
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version: "3.0"
expectations:
population_size: 5000
actions:
# Other data
# ----------
# Add actions for other data to this section. Prefix them with a suitable name; place
# scripts in a similarly named sub-directory of the analysis directory; write outputs
# to a similarly named sub-directory of the output directory.
#
# For example, let's call our other data "metrics". We would prefix our actions
# "metrics_"; we would place our scripts in analysis/metrics; we would write outputs
# to output/metrics.
# Metrics data
# ------------
metrics_generate_sro_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_sro_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_sro_2021-12-01.feather
metrics_generate_sro_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_sro_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_sro_2021-06-01.feather
metrics_generate_kids_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_kids_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_kids_2021-12-01.feather
metrics_generate_kids_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_kids_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_kids_2021-06-01.feather
metrics_generate_endpopulation_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_endpopulation_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_endpopulation_2021-12-01.feather
metrics_generate_endpopulation_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_endpopulation_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_endpopulation_2021-06-01.feather
metrics_generate_sro_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_sro --output-dir=output/metrics
needs:
- metrics_generate_sro_dataset_summer
- metrics_generate_sro_dataset_winter
outputs:
highly_sensitive:
measure_csv: output/metrics/mea*.csv
metrics_generate_kids_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_kids --output-dir=output/metrics
needs:
- metrics_generate_kids_dataset_summer
- metrics_generate_kids_dataset_winter
outputs:
highly_sensitive:
measure_csv: output/metrics/me*.csv
metrics_generate_endpopulation_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_endpopulation
--output-dir=output/metrics
needs:
- metrics_generate_endpopulation_dataset_summer
- metrics_generate_endpopulation_dataset_winter
outputs:
highly_sensitive:
measure_csv: output/metrics/m*.csv
metrics_create_seasonal_sro_data:
run: r:latest analysis/metrics/create_seasonal_sro_data.R
needs:
- metrics_generate_sro_measures
outputs:
highly_sensitive:
csv: output/metrics/season_data_*.csv
metrics_create_seasonal_measures:
run: r:latest analysis/metrics/seasonal_measures.R
needs:
- metrics_create_seasonal_sro_data
outputs:
moderately_sensitive:
csv1: output/metrics/*/summer_winter_difference_histogram_data.csv
csv2: output/metrics/*/summer_winter_ratio_histogram_data.csv
png1: output/metrics/*/summer_winter_difference_histogram.png
png2: output/metrics/*/summer_winter_ratio_histogram.png
metrics_run_sro_tests:
run: r:latest analysis/metrics/tests/testthat/run-all.R
needs: [metrics_generate_sro_measures]
outputs:
moderately_sensitive:
log: output/metrics/tests/run-all.log
# Appointments data
# -----------------
appointments_generate_dataset_sql:
run: >
sqlrunner:latest
analysis/appointments/dataset_query.sql
--output output/appointments/dataset_long.csv.gz
--dummy-data-file analysis/appointments/dummy_dataset_long.csv.gz
outputs:
highly_sensitive:
dataset: output/appointments/dataset_long.csv.gz
# appointments_generate_dataset:
# run: >
# databuilder:v0
# generate-dataset
# analysis/appointments/dataset_definition.py
# --output output/appointments/dataset_wide.arrow
# outputs:
# highly_sensitive:
# dataset: output/appointments/dataset_wide.arrow
# appointments_get_freq_na_values:
# run: >
# python:latest
# python
# -m analysis.appointments.get_freq_na_values
# needs: [appointments_generate_dataset]
# outputs:
# moderately_sensitive:
# dataset: output/appointments/freq_na_values.csv
# appointments_reshape_dataset:
# run: >
# python:latest
# python
# -m analysis.appointments.reshape_dataset
# needs: [appointments_generate_dataset]
# outputs:
# highly_sensitive:
# dataset: output/appointments/dataset_long.arrow
# appointments_generate_lead_time_measure_by_booked_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_median_lead_time_measure
# --value-col lead_time_in_days
# --index-cols booked_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_median_lead_time_in_days_by_booked_month.csv
# seasonal_measure: output/appointments/measure_seasonal_median_lead_time_in_days_by_booked_month.csv
# appointments_generate_lead_time_measure_by_start_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_median_lead_time_measure
# --value-col lead_time_in_days
# --index-cols start_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_median_lead_time_in_days_by_start_month.csv
# seasonal_measure: output/appointments/measure_seasonal_median_lead_time_in_days_by_start_month.csv
# appointments_generate_num_appointments_measure_by_start_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_num_appointments_measure
# --index-cols start_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_num_appointments_by_start_month.csv
# seasonal_measure: output/appointments/measure_seasonal_num_appointments_by_start_month.csv
# appointments_generate_num_appointments_measure_by_booked_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_num_appointments_measure
# --index-cols booked_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_num_appointments_by_booked_month.csv
# seasonal_measure: output/appointments/measure_seasonal_num_appointments_by_booked_month.csv
# appointments_generate_num_unique_patients_measure_by_booked_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_num_unique_patients_measure
# --unique-col patient_id
# --index-cols booked_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_num_unique_patients_by_booked_month.csv
# seasonal_measure: output/appointments/measure_seasonal_num_unique_patients_by_booked_month.csv
# appointments_generate_num_unique_patients_measure_by_start_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_num_unique_patients_measure
# --unique-col patient_id
# --index-cols start_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_num_unique_patients_by_start_month.csv
# seasonal_measure: output/appointments/measure_seasonal_num_unique_patients_by_start_month.csv
# appointments_generate_proportion_same_day_lead_time_measure_by_booked_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_proportion_lead_time_measure
# --value-col lead_time_in_days
# --value-threshold 0
# --index-cols booked_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_proportion_lead_time_in_days_within_0days_by_booked_month.csv
# seasonal_measure: output/appointments/measure_seasonal_proportion_lead_time_in_days_within_0days_by_booked_month.csv
# appointments_generate_proportion_same_day_lead_time_measure_by_start_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_proportion_lead_time_measure
# --value-col lead_time_in_days
# --value-threshold 0
# --index-cols start_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_proportion_lead_time_in_days_within_0days_by_start_month.csv
# seasonal_measure: output/appointments/measure_seasonal_proportion_lead_time_in_days_within_0days_by_start_month.csv
# appointments_generate_proportion_two_day_lead_time_measure_by_booked_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_proportion_lead_time_measure
# --value-col lead_time_in_days
# --value-threshold 2
# --index-cols booked_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_proportion_lead_time_in_days_within_2days_by_booked_month.csv
# seasonal_measure: output/appointments/measure_seasonal_proportion_lead_time_in_days_within_2days_by_booked_month.csv
# appointments_generate_proportion_two_day_lead_time_measure_by_start_month:
# run: >
# python:latest
# python
# -m analysis.appointments.generate_proportion_lead_time_measure
# --value-col lead_time_in_days
# --value-threshold 2
# --index-cols start_month practice
# needs: [appointments_generate_dataset_sql]
# outputs:
# moderately_sensitive:
# monthly_measure: output/appointments/measure_monthly_proportion_lead_time_in_days_within_2days_by_start_month.csv
# seasonal_measure: output/appointments/measure_seasonal_proportion_lead_time_in_days_within_2days_by_start_month.csv
appointments_generate_monthly_measures_by_booked_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_monthly_measures
--value-thresholds 0 2
--index-cols booked_month practice
needs: [appointments_generate_dataset_sql]
outputs:
moderately_sensitive:
monthly_measure: output/appointments/measure_monthly_*_by_booked_month.csv
appointments_generate_monthly_measures_by_start_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_monthly_measures
--value-thresholds 0 2
--index-cols start_month practice
needs: [appointments_generate_dataset_sql]
outputs:
moderately_sensitive:
monthly_measure: output/appointments/measure_monthly_*_by_start_month.csv
appointments_generate_seasonal_summaries_by_start_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_seasonal_summaries
--value-thresholds 0 2
--index-cols start_month practice
needs: [appointments_generate_dataset_sql]
outputs:
moderately_sensitive:
monthly_measure: output/appointments/measure_seasonal_*_by_start_month.csv
appointments_generate_seasonal_summaries_by_booked_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_seasonal_summaries
--value-thresholds 0 2
--index-cols booked_month practice
needs: [appointments_generate_dataset_sql]
outputs:
moderately_sensitive:
monthly_measure: output/appointments/measure_seasonal_*_by_booked_month.csv
appointments_generate_deciles_charts:
run: >
deciles-charts:v0.0.33
--input-files output/appointments/measure_monthly_*.csv
--output-dir output/appointments
config:
show_outer_percentiles: true
needs:
- appointments_generate_monthly_measures_by_booked_month
- appointments_generate_monthly_measures_by_start_month
outputs:
moderately_sensitive:
deciles_charts: output/appointments/deciles_chart_*.png
deciles_tables: output/appointments/deciles_table_*.csv
run_tests:
run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
outputs:
moderately_sensitive:
log: output/pytest.xml