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config.yml
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global:
schema: "mimic_v5"
version: "5"
scopes:
- demographics
- demographics_historical
- features
- condition
- drugs
- drug_era
- milenial_features
- cohortpatients
- bulk_features
- bulk_drugs
- bulk_condition
- bulk_demographic
- bulk_procedure
- migration_feature_tables
demographics:
Template: "demographics.sql.tmpl"
Filename: "demographics.sql"
Limit: "LIMIT ?"
Cond: "year <= 2016 and year >= 2000"
Table: "table"
demographics_historical:
Template: "demographics.sql.tmpl"
Filename: "demographics.historical.sql"
Limit: ""
Cond: "year <= 2000 and year >= 1900"
Table: "table"
features:
Template: features.sql.tmpl
Filename: features.sql
condition:
Template: condition.sql.tmpl
Filename: condition.sql
drugs:
Template: drugs.sql.tmpl
Filename: drugs.sql
drug_era:
Template: drug_era.sql.tmpl
Filename: drug_era.sql
milenial_features:
Template: constrained_features.sql.tmpl
Filename: milenial_features.sql
Constraint: WHERE PT.year_of_birth > 1980
Persontable: person
migration_feature_tables:
Template: sql/migration.tmpl
Filename: migration/feature_tables.sql
Results_schema: results_mimic
Concept_schema: mimic_v5
cohortpatients:
Template: selectwhere.sql.templ
Filename: cohortpatients.sql
Schema: results_mimic
Table: cohort
Fields: "subject_id as person_id,
cohort_start_date as start_date,
cohort_end_date as end_date,
cohort_definition_id as concept_id,
'cohort_id' as type,
1 as value"
Whereclause: "cohort_definition_id = $1"
bulk_features:
Template: bulk.sql.tmpl
Filename: bulkfeatures.sql
Table: features
Fields: "(job_id, person_id, cohort_start_date, cohort_end_date, concept_id, value, type)"
Select: "select ?, person_id, cohort_start_date, cohort_end_date, 'drugs'"
bulk_drugs:
Template: plp.sql.template
Filename: bulk_drugs.sql
Targettable: drug_era
Concept: drug
Cohorttable: "results_mimic.cohort"
Whereclause: "WHERE cohort_definition_id= $1 and ( cohort_end_date > drug_era_start_date ) and not (drug_era_end_date < cohort_start_date)"
bulk_condition:
Template: plp.sql.template
Filename: bulk_condition.sql
Targettable: condition_era
Concept: condition
Cohorttable: "results_mimic.cohort"
Whereclause: "WHERE cohort_definition_id= $1 and ( cohort_end_date > condition_era_start_date ) -- and not (condition_era_end_date < cohort_start_date)"
# historical_Whereclause: "WHERE cohort_definition_id= $1 and ( cohort_end_date > condition_era_start_date ) and (condition_era_end_date < cohort_start_date)"
bulk_procedure:
Template: plp.sql.template
Filename: bulk_procedure.sql
Targettable: procedure_occurrence
Concept: procedure
Datefield : "procedure_date"
Cohorttable: "results_mimic.cohort"
Whereclause: "WHERE cohort_definition_id= $1"
bulk_demographic:
Template: demographics_omop.sql.tmpl
Filename: bulk_demographics.sql
Targettable: person
Concept: demographic
Cohorttable: "results_mimic.cohort"
Whereclause: "WHERE cohort_definition_id= $1"
Gender: true
Race: true