naaccr xml bug fix

- fixed bug where database schema was hardwired within function - ndp_schema now a required parameter in functions
OHDSI · Jan 11, 2024 · 7176cf1 · 7176cf1
1 parent 6371e06
commit 7176cf1
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Showing 2 changed files with 18 additions and 3 deletions.
diff --git a/NaaccrParser/R/parse_NAACCR.R b/NaaccrParser/R/parse_NAACCR.R
@@ -3,6 +3,7 @@
 # main function for parsing fixed-width data
 NAACCR_to_db <- function(file_path
                          ,record_id_prefix = NULL
+                         ,ndp_schema
                          ,connectionDetails){
 
 
@@ -148,7 +149,7 @@ NAACCR_to_db <- function(file_path
 
         DatabaseConnector::insertTable(connection = conn,
                                        tableName = "naaccr_data_points",
-                                       databaseSchema = "NAACCR_OMOP.dbo",
+                                       databaseSchema = ndp_schema,
                                        data = tmp_df,
                                        dropTableIfExists = FALSE,
                                        createTable = FALSE,
@@ -196,6 +197,7 @@ assign_person_id <- function(connectionDetails
 # main function for parsing XML
 parse_XML_to_DB <- function(file_path
                              ,record_id_prefix = NULL
+                             ,ndp_schema
                              ,connectionDetails){
 
   if(is.null(file_path)){
@@ -420,7 +422,7 @@ parse_XML_to_DB <- function(file_path
 
     DatabaseConnector::insertTable(connection = conn,
                                    tableName = "naaccr_data_points",
-                                   databaseSchema = "NAACCR_OMOP.dbo",
+                                   databaseSchema = ndp_schema,
                                    data = res,
                                    dropTableIfExists = FALSE,
                                    createTable = FALSE,
@@ -439,6 +441,7 @@ parse_XML_to_DB <- function(file_path
 # umbrella function to parse directory of source files
 # can be either fixed width or XML
 parse_directory <- function(dir_path
+                            ,ndp_schema
                             ,connectionDetails){
 
 
@@ -456,10 +459,12 @@ parse_directory <- function(dir_path
     if(fext == "XML"){
       parse_XML_to_DB(file_path = curr_file
                       ,record_id_prefix = NULL
+                      ,ndp_schema = ndp_schema
                       ,connectionDetails = connectionDetails)
     }else{
       NAACCR_to_db(file_path = curr_file
                    ,record_id_prefix = NULL
+                   ,ndp_schema = ndp_schema
                    ,connectionDetails = connectionDetails)
     }
 

diff --git a/NaaccrParser/README.md b/NaaccrParser/README.md
@@ -43,13 +43,21 @@ connectionDetails <- createConnectionDetails(
 
 ```
 
+Specify the database schema where the NAACCR_DATA_POINTS table exists. 
+
+```r
+ndp_schema <- 'NAACCR_OMOP.dbo'
+
+```
+
 There are separate functions for parsing and ingesting fixed-width source files (v16-18) as well as for XML formatted source files (v20+). If you have a collection of files in the same directory you can leverage an umbrella function that parses all files, regardless of version. 
 
 ### Option 1: (directory specific)
 
 Parse and ingest **all NAACCR files within a specified directory**
 ```r
 parse_directory(dir_path = dir_path # folder containing NAACCR files
+                ,ndp_schema = ndp_schema
                 ,connectionDetails = connectionDetails)
 
 ```
@@ -63,6 +71,7 @@ Parse and ingest a **fixed-width file**:
 # Import data  into database
 NAACCR_to_db(file_path = "path_to_data/naaccr_file.csv"
              , record_id_prefix = record_id_prefix  # optional
+             , ndp_schema = ndp_schema
              , connectionDetails = connectionDetails)
 ```
 
@@ -73,6 +82,7 @@ Parse and ingest a **XML file**:
 # Import data  into database
 parse_XML_to_DB(file_path = file_path
                 ,record_id_prefix = NULL  # optional
+                ,ndp_schema = ndp_schema
                 ,connectionDetails = connectionDetails)
 ```
 
@@ -82,7 +92,7 @@ At this point the data exists in your database without person_id assigned. This
 
 ```r
 assign_person_id(connectionDetails = connectionDetails
-                ,ndp_schema = 'NAACCR_OMOP.dbo'
+                ,ndp_schema = ndp_schema
                 ,person_map_schema = 'OMOP_COMMON.dbo'
                 ,person_map_table = 'person_map'
                 ,person_map_field = "MRN")