Merge pull request #630 from OHDSI/docs_jan_2024

Docs jan 2024

.github/ISSUE_TEMPLATE/use-case.yaml

@@ -0,0 +1,58 @@
+name: Use Case 
+description: Proposal for a new OHDSI Oncology WG Use Case.
+title: "[Use Case]: <Add your project's name here>"
+labels: ["Use Case"]
+projects: "OHDSI/26"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        # OHDSI Oncology WG Use Case
+        ## Project Deliverable
+        Please provide the following information about your project's deliverable:
+  - type: textarea
+    id: deliverable
+    attributes:
+      label: Description
+      description: "What is your deliverable?"        
+      placeholder: "Give a description of your deliverable here"
+  - type: textarea
+    id: infrastructure
+    attributes:
+      label: Infrastructure
+      description: "Can this be delivered with existing Infrastructure? If no, what needs to be added?"        
+      placeholder: "Can this be delivered with existing infrastructure?"
+  - type: textarea
+    id: timeline
+    attributes:
+      label: Timeline
+      description: "What is your desired timeline for completing this work?"        
+      placeholder: "Explain your desired timeline here"
+  - type: textarea
+    id: credit
+    attributes:
+      label: Credit
+      description: "How would you and your team like to receive credit for this work?"        
+      placeholder: "Can this be delivered with existing infrastructure?"
+  - type: textarea
+    id: support
+    attributes:
+      label: Support
+      description: "What kind of support does your team need from the workgroup?"        
+      placeholder: "Describe the type of support you will need"
+  - type: textarea
+    id: datasets
+    attributes:
+      label: Datasets of Interest
+      description: "Provide a list of datasets (titles, links, descriptions, etc.) that your project is interested in using."
+      placeholder: "List the datasets your project is interested in using"
+  - type: markdown
+    attributes:
+      value: |
+        # Use Case Work Orders
+  - type: textarea
+    id: depends
+    attributes:
+      label: Depends On
+      description: "Work orders that are associated with this Use Case."
+      placeholder: "Issue task list goes here. This can be filled out after "

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)
     }
 

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")