Merge branch 'sas-labels'

.gitignore

@@ -4,10 +4,14 @@ dist/
 /Error.txt
 /.gitignore
 /Error1.txt
-/ScanReport.xlsx
 /.classpath
 target/
 *.iml
 .idea/
+
+/ScanReport.xlsx
 *ScanReport*
 *swp
+tmp/*
+Try*
+/examples/

README.md

@@ -1,13 +1,16 @@
-![alt text](https://github.com/OHDSI/WhiteRabbit/blob/master/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit64.png) WhiteRabbit
+![WR logo](https://github.com/OHDSI/WhiteRabbit/blob/master/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit64.png) White Rabbit 
+===========
+
+![RiaH logo](https://github.com/OHDSI/WhiteRabbit/blob/master/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat64.png) Rabbit in a Hat
 ===========
 
 Introduction
 ========
-WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. 
+**WhiteRabbit** is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with **RabbitInAHat**, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. 
 
 Features
 ========
-- Can scan databases in SQL Server, Oracle, PostgreSQL, MySQL, MS Access, Amazon RedShift, and CSV files
+- Can scan databases in SQL Server, Oracle, PostgreSQL, MySQL, MS Access, Amazon RedShift, Google BigQuery, SAS files and CSV files
 - The scan report contains information on tables, fields, and frequency distributions of values
 - Cutoff on the minimum frequency of values to protect patient privacy
 - WhiteRabbit can be run with a graphical user interface or from the command prompt
@@ -58,6 +61,20 @@ Rabbit-In-A-Hat
 
 Note: on releases earlier than version 0.8.0, open the respective `WhiteRabbit.jar` or `RabbitInAHat.jar` files instead.
 
+Example in- and output
+========
+The file `examples.zip` contains a set of input and output examples for White Rabbit and Rabbit in a Hat.
+These are used for testing of the main White Rabbit and Rabbit in a Hat features. An overview is given in below table.
+
+| Folder         | Description                                                                                                                                                                                                                                                                                                                                              |
+|:---------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `wr_input_csv` | csv files to test scanning on different data types and long table names.                                                                                                                                                                                                                                                                                 |
+| `wr_input_sas` | sas7bdat files to test sas input                                                                                                                                                                                                                                                                                                                         |
+| `wr_output`    | Scan reports created from files in `wr_input_csv`, `wr_input_sas` and [native a Synthea database loaded in Postgres](https://github.com/ohdsi/ETL-Synthea). All with default scan options.<br> This folder also includes fake data generated from the csv scan report. The csv scan report is used to test the opening a Scan Report in Rabbit in a Hat. |
+| `riah_input`   | An example mapping file used to create the Rabbit in a Hat outputs.                                                                                                                                                                                                                                                                                      |
+| `riah_output`  | All export formats created by Rabbit in a Hat: as word, html, markdown, sql skeleton and the R TestFramework.<br> These are all generated from `riah_input/riah_mapping_example.gz`.                                                                                                                                                                     |
+
+
 Getting Involved
 =============
 * User guide and Help: <a href="http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:whiterabbit">WhiteRabbit Wiki</a>

iniFileExamples/WhiteRabbit.ini

@@ -1,4 +1,5 @@
-WORKING_FOLDER = /users/joe                   # Path to the folder where all output will be written 
+# Usage: dist/bin/whiteRabbit -ini <ini_file_path>
+WORKING_FOLDER = /users/joe                   # Path to the folder where all output will be written
 DATA_TYPE = PostgreSQL                        # "Delimited text files", "MySQL", "Oracle", "SQL Server", "PostgreSQL", "MS Access", or "Redshift"
 SERVER_LOCATION = 127.0.0.1/data_base_name    # Name or address of the server. For Postgres, add the database name 
 USER_NAME = joe                               # User name for the database 

pom.xml

@@ -6,7 +6,7 @@
     <groupId>org.ohdsi</groupId>
     <artifactId>leporidae</artifactId>
     <packaging>pom</packaging>
-    <version>0.8.0-SNAPSHOT</version>
+    <version>0.9.0</version>
     <modules>
         <module>rabbitinahat</module>
         <module>whiterabbit</module>

rabbit-core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>leporidae</artifactId>
         <groupId>org.ohdsi</groupId>
-        <version>0.8.0-SNAPSHOT</version>
+        <version>0.9.0</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Database.java

@@ -100,7 +100,6 @@ public static Database generateModelFromCSV(InputStream stream, String dbName) {
 					dataTypeColumn = "type";
 					descriptionColumn = "description";
 				}
-				System.out.println(row.toString());
 				Table table = nameToTable.get(row.get(tableNameColumn).toLowerCase());
 
 				if (table == null) {

rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Table.java

@@ -40,6 +40,7 @@ public Table(Table table) {
 		db = table.db;
 		name = table.name;
 		rowCount = table.rowCount;
+		rowsCheckedCount = table.rowsCheckedCount;
 		comment = table.comment;
 		fields = new ArrayList<Field>(table.fields);
 		isStem = table.isStem;

rabbitinahat/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>leporidae</artifactId>
         <groupId>org.ohdsi</groupId>
-        <version>0.8.0-SNAPSHOT</version>
+        <version>0.9.0</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLMarkupDocumentGenerator.java

@@ -68,9 +68,13 @@ void generate(String fileName, DocumentType documentType) {
 		}
 
 		for (Table targetTable : etl.getTargetDatabase().getTables()) {
-			if (addTargetTableSection(targetTable)) {
+			boolean targetTableHasMapping = addTargetTableSection(targetTable);
+
+			if (targetTableHasMapping) {
 				document.write(targetTable.getName());
 				targetTablesWritten.add(targetTable.getName());
+			} else {
+				document.reset();
 			};
 		}
 
@@ -214,6 +218,8 @@ private interface MarkupDocument {
 		void addTable(List<Row> rows);
 
 		void write(String targetName);
+
+		void reset();
 	}
 
 	private static class MarkdownDocument implements MarkupDocument {
@@ -287,8 +293,11 @@ public void write(String targetName) {
 			} catch (IOException e) {
 				e.printStackTrace();
 			}
+			this.reset();
+		}
 
-			// Reset
+		@Override
+		public void reset() {
 			lines = new ArrayList<>();
 		}
 
@@ -390,7 +399,11 @@ public void write(String targetName) {
 				e.printStackTrace();
 			}
 
-			// Reset
+			this.reset();
+		}
+
+		@Override
+		public void reset() {
 			lines = new ArrayList<>();
 		}