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 CDM v6.0

Below is the specification document for the OMOP Common Data Model, v6.0. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the forums or the github issue page.

--after regeneration of DDLs link to csv of cdm link to pdf of cdm documentation link to forum on doc page

Changes in v6.0

Latitude and Longitude added to LOCATION
Contract owner field added to PAYER_PLAN_PERIOD
All primary keys were changed to bigint
The name of ADMISSION_SOURCE_CONCEPT_ID was changed to ADMITTED_FROM_CONCEPT_ID in VISIT_OCCURRENCE and VISIT_DETAIL
All Concept_Ids are now mandatory except for UNIT_CONCEPT_ID, VALUE_AS_CONCEPT_ID, and OPERATOR_CONCEPT_ID. If there is no value available then a Concept_Id should be set to 0 instead of NULL.
DEATH table removed and DEATH_DATETIME field added to the PERSON table. Cause of death is stored in the CONDITION_OCCURRENCE
DATETIME fields were made mandatory and date fields were made optional.

tableSpecs <- read.csv("../inst/csv/OMOP_CDMv6.0_Table_Level.csv", stringsAsFactors = FALSE)
cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv6.0_Field_Level.csv", stringsAsFactors = FALSE)

tables <- tableSpecs$cdmTableName

cdmSpecsClean <- cdmSpecs %>%
  dplyr::select(`CDM Table` = cdmTableName,
                `CDM Field` = cdmFieldName,
                `User Guide` = userGuidance,
                `ETL Conventions` = etlConventions,
                `Datatype` = cdmDatatype,
                `Required` = isRequired,
                `Primary Key` = isPrimaryKey,
                `Foreign Key` = isForeignKey,
                `FK Table` = fkTableName,
                `FK Domain` = fkDomain
                )

cdmSpecsClean[is.na(cdmSpecsClean)] <- ""

for(tb in tables) {

  if(tb == 'PERSON'){
    cat("## **Clinical Data Tables**\n\n")
  }

  if(tb == 'LOCATION'){
    cat("## **Health System Data Tables**\n\n")
  }

  if(tb == 'PAYER_PLAN_PERIOD'){
    cat("## **Health Economics Data Tables**\n\n")
  }

  if(tb == 'DRUG_ERA'){
    cat("## **Standardized Derived Elements**\n\n")
  }

  if(tb == 'METADATA'){
    cat("## **Metadata Tables**\n\n")
  }
  if(tb == 'CONCEPT'){
    cat("## **Vocabulary Tables**\n\n")
  }

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

  tableInfo <- subset(tableSpecs, cdmTableName == tb)
  cat("**Table Description**\n\n",tableInfo[,"tableDescription"], "\n\n")

  if(!isTRUE(tableInfo[,"userGuidance"]=="")){
    cat("**User Guide**\n\n",tableInfo[,"userGuidance"],"\n\n")
  }

  if(!isTRUE(tableInfo[,"etlConventions"]=="")){
    cat("**ETL Conventions**\n\n",tableInfo[,"etlConventions"],"\n\n")
  }

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

  print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html") %>% 
           column_spec(1, bold = T) %>%
           column_spec(2, width = "3in", include_thead = T) %>%
           column_spec(3, width = "4in", include_thead = T) %>%
           column_spec(4:9, width = "1in", include_thead = T) %>%
           kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13)) 


  }