In OHDSI/DDLgeneratr: OMOP CDM DDL and Documentation Generator

#todo figure out how to get the document dynamically without specifying the name
library(rmarkdown)
library(knitr)
library(kableExtra)
library(magrittr)
library(dplyr)
library(stringr)

OMOP Common Data Model Documentation

CDM v5.3.1

cdmSpecs <- readxl::read_excel("../docs/OMOP CDMv5.3.1 Specs v0.1.xlsx", sheet = "FIELD LEVEL")
tableSpecs <- readxl::read_excel("../docs/OMOP CDMv5.3.1 Specs v0.1.xlsx", sheet = "TABLE LEVEL")
tables <- tableSpecs$CDM_TABLE

cdmSpecsClean <- cdmSpecs %>%
  dplyr::select(`CDM Table` = CDM_TABLE,
                `CDM Field` = CDM_FIELD,
                `User Guide` = USER_GUIDANCE,
                `ETL Conventions` = ETL_CONVENTIONS,
                `Datatype` = CDM_DATATYPE,
                `Is Required` = IS_REQUIRED,
                `Is Primary Key` = IS_PRIMARY_KEY,
                `Is Foreign Key (FK)` = IS_FOREIGN_KEY,
                `FK Table` = FK_TABLE,
                `FK Domain` = FK_DOMAIN,
                `FK Class` = FK_CLASS
                )

for(tb in tables) {
  cat("###", tb, "{.tabset .tabset-pills} \n\n")

  loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
  loopTable <- subset(loopTable, select = -c(1))

  print(kable(x = loopTable, align = "l", row.names = FALSE) %>% kable_styling(bootstrap_options = c("hover", "condensed", "responsive")))

  }

CDM v6.0

cdmSpecs <- readxl::read_excel("C:/Git/Github/DDLgeneratr_OHDSI/docs/OMOP CDMv6 DQ Checks v0.1.xlsx", sheet = "FIELD LEVEL")
tableSpecs <- readxl::read_excel("C:/Git/Github/DDLgeneratr_OHDSI/docs/OMOP CDMv6 DQ Checks v0.1.xlsx", sheet = "TABLE LEVEL")
tables <- tableSpecs$CDM_TABLE

cdmSpecsClean <- cdmSpecs %>%
  dplyr::select(`CDM Table` = CDM_TABLE,
                `CDM Field` = CDM_FIELD,
                `User Guide` = USER_GUIDANCE,
                `ETL Conventions` = ETL_CONVENTIONS,
                `Datatype` = CDM_DATATYPE,
                `Is Required` = IS_REQUIRED,
                `Is Primary Key` = IS_PRIMARY_KEY,
                `Is Foreign Key (FK)` = IS_FOREIGN_KEY,
                `FK Table` = FK_TABLE,
                `FK Domain` = FK_DOMAIN,
                `FK Class` = FK_CLASS
                )

for(tb in tables) {
  cat("###", tb, "{.tabset .tabset-pills} \n\n")

  loopTable <- subset(cdmSpecsClean, `CDM Table` == tb)
  loopTable <- subset(loopTable, select = -c(1))

  print(kable(x = loopTable, align = "l", row.names = FALSE) %>% kable_styling(bootstrap_options = c("hover", "condensed", "responsive")))

  }