Merge pull request #286 from OHDSI/release-0.10.3

Release 0.10.3

pom.xml

@@ -6,7 +6,7 @@
     <groupId>org.ohdsi</groupId>
     <artifactId>leporidae</artifactId>
     <packaging>pom</packaging>
-    <version>0.10.2</version>
+    <version>0.10.3</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>0.10.2</version>
+        <version>0.10.3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

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

@@ -20,6 +20,7 @@
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVRecord;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -28,6 +29,7 @@
 public class ConceptsMap {
 
     private Map<String, Map<String, List<Concept>>> conceptMap;
+    public String vocabularyVersion;
 
     private ConceptsMap() {
         this.conceptMap = new HashMap<>();
@@ -40,7 +42,9 @@ private ConceptsMap() {
 
     private void load(String filename) throws IOException{
         try (InputStream conceptStream = Database.class.getResourceAsStream(filename)) {
-            for (CSVRecord conceptRow : CSVFormat.RFC4180.withHeader().parse(new InputStreamReader(conceptStream))) {
+            BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(conceptStream));
+            vocabularyVersion = bufferedReader.readLine();
+            for (CSVRecord conceptRow : CSVFormat.RFC4180.withHeader().parse(bufferedReader)) {
                 String omopTableName = conceptRow.get("omop_cdm_table");
                 String omopFieldName = conceptRow.get("omop_cdm_field");
 

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

@@ -55,15 +55,16 @@ public enum CDMVersion {
 	private List<Table>			tables				= new ArrayList<Table>();
 	private static final long	serialVersionUID	= -3912166654601191039L;
 	private String				dbName				= "";
-	private static String		CONCEPT_ID_HINTS_FILE_NAME = "CDMConceptIDHints_v5.0_02-OCT-19.csv";
+	private static final String	CONCEPT_ID_HINTS_FILE_NAME = "CDMConceptIDHints.csv";
+	public String 				conceptIdHintsVocabularyVersion;
 
 	public List<Table> getTables() {
 		return tables;
 	}
 
 	public Table getTableByName(String name) {
 		for (Table table : tables)
-			if (table.getName().toLowerCase().equals(name.toLowerCase()))
+			if (table.getName().equalsIgnoreCase(name))
 				return table;
 		return null;
 	}
@@ -91,7 +92,8 @@ public static Database generateModelFromCSV(InputStream stream, String dbName) {
 
 		Map<String, Table> nameToTable = new HashMap<>();
 		try {
-			ConceptsMap conceptsMap = new ConceptsMap(CONCEPT_ID_HINTS_FILE_NAME);
+			ConceptsMap conceptIdHintsMap = new ConceptsMap(CONCEPT_ID_HINTS_FILE_NAME);
+			database.conceptIdHintsVocabularyVersion = conceptIdHintsMap.vocabularyVersion;
 
 			for (CSVRecord row : CSVFormat.RFC4180.withHeader().parse(new InputStreamReader(stream))) {
 				String tableNameColumn;
@@ -128,7 +130,7 @@ public static Database generateModelFromCSV(InputStream stream, String dbName) {
 				field.setNullable(row.get(isNullableColumn).equals(nullableValue));
 				field.setType(row.get(dataTypeColumn));
 				field.setDescription(row.get(descriptionColumn));
-				field.setConceptIdHints(conceptsMap.get(table.getName(), field.getName()));
+				field.setConceptIdHints(conceptIdHintsMap.get(table.getName(), field.getName()));
 
 				table.getFields().add(field);
 			}

rabbit-core/src/main/java/org/ohdsi/utilities/StringUtilities.java

@@ -871,5 +871,31 @@ public static boolean isDate(String string) {
 		}
 		return false;
 	}
-
+
+	public static int numericOptionToInt(String option) {
+		switch (option) {
+			case "100":
+			case "1 hundred":
+				return 100;
+			case "1,000":
+			case "1 thousand":
+				return 1000;
+			case "10,000":
+			case "10 thousand":
+				return 10000;
+			case "100,000":
+			case "100 thousand":
+				return 100000;
+			case "500,000":
+			case "500 thousand":
+				return 500000;
+			case "1,000,000":
+			case "1 million":
+				return 1000000;
+			case "all":
+				return -1;
+			default:
+				return 0;
+		}
+	}
 }

rabbitinahat/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>leporidae</artifactId>
         <groupId>org.ohdsi</groupId>
-        <version>0.10.2</version>
+        <version>0.10.3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

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

@@ -418,7 +418,9 @@ public void initialise() {
 				table.getColumnModel().getColumn(2).setCellRenderer(rightRenderer);
 			}
 
-			String title = isTargetFieldPanel ? "Concept ID Hints" : "Value Counts";
+			String title = isTargetFieldPanel ?
+					"Concept ID Hints " + ObjectExchange.etl.getTargetDatabase().conceptIdHintsVocabularyVersion
+					: "Value Counts";
 			fieldListPanel.setBorder(BorderFactory.createTitledBorder(title));
 			add(fieldListPanel, BorderLayout.CENTER);
 

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

@@ -49,11 +49,9 @@
 import org.ohdsi.rabbitInAHat.dataModel.Database.CDMVersion;
 import org.ohdsi.rabbitInAHat.dataModel.ETL;
 import org.ohdsi.rabbitInAHat.dataModel.Field;
-import org.ohdsi.rabbitInAHat.dataModel.MappableItem;
 import org.ohdsi.rabbitInAHat.dataModel.StemTableFactory;
 import org.ohdsi.rabbitInAHat.dataModel.Table;
 import org.ohdsi.utilities.Version;
-import org.ohdsi.utilities.collections.Pair;
 
 /**
  * This is the main class for the RabbitInAHat application