com.eldrix.iort.impl.cdm — com.eldrix/iort 0.1.52

cdm clj

(cdm)

(cdm v)

Returns information from the registry about a specific CDM version, or the default if omitted. For example,

(cdm "5.4")

=> {:id "5.4" :fields "OMOP_CDMv5.4_Field_Level.csv" :tables "OMOP_CDMv5.4_Table_Level.csv"}

cdm-version-by-id clj

column-title->kw clj

(column-title->kw s)

Convert column title to a keyword. Almost all columns are camelCase, but they've added a column 'unique DQ identifiers' which we convert.

default-cdm-version clj

model-structures* clj

(model-structures* {:keys [cdmVersion schemas] :as config})

parse-int clj

(parse-int x)

parse-model clj

(parse-model m)

parse-str clj

(parse-str x)

parse-yes-no clj

(parse-yes-no x)

parsers clj

read-csv clj

(read-csv f)

supported-cdm-versions clj

Registry of supported versions.

with-model-structures clj

(with-model-structures {:keys [cdmModel] :as config})

Updates the configuration with OMOP model structures using key :cdmModel. For convenience, returns its argument if cdmModel already defined. The model specification is a map of CDM table name to the table definition. Each definition is a close representation of the source Table_Level.csv but with an additional key ':cdmFields' with data from Field_Level.csv for that table. Some source data are parsed such as 'NA' to 'null', and 'Yes' and 'No' to boolean.