Merge pull request #26 from hms-dbmi/QA

1.2.2 Release

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>edu.harvard.hms.dbmi.bd2k.irct</groupId>
 	<artifactId>IRCT-RI</artifactId>
-	<version>1.2.1</version>
+	<version>1.2.2</version>
 	<name>INTER-RESOURCE COMMUNICATION TOOL : Resource Interface</name>
 	<description></description>
 	<dependencies>
@@ -43,11 +43,18 @@
 			<artifactId>i2b2-Java-API</artifactId>
 			<version>1.0</version>
 		</dependency>
+
+		<!-- SciDB Java API -->
+		<dependency>
+			<groupId>edu.harvard.hms.dbmi</groupId>
+			<artifactId>SciDB-Java</artifactId>
+			<version>1.0-QA</version>
+		</dependency>
 		<!-- IRCT API -->
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.bd2k.irct</groupId>
 			<artifactId>IRCT-API</artifactId>
-			<version>1.2.1</version>
+			<version>1.2.2</version>
 		</dependency>
 	</dependencies>
 	<build>

src/main/java/edu/harvard/hms/dbmi/bd2k/irct/ri/scidb/SciDBDataType.java

@@ -0,0 +1,141 @@
+package edu.harvard.hms.dbmi.bd2k.irct.ri.scidb;
+
+import java.nio.charset.StandardCharsets;
+import java.util.regex.Pattern;
+
+import javax.json.Json;
+import javax.json.JsonObject;
+import javax.json.JsonObjectBuilder;
+
+import edu.harvard.hms.dbmi.bd2k.irct.model.ontology.DataType;
+import edu.harvard.hms.dbmi.bd2k.irct.model.resource.PrimitiveDataType;
+
+public enum SciDBDataType implements DataType {
+	ARRAY {
+		@Override
+		public String getName() {
+			return "array";
+		}
+
+		@Override
+		public String getDescription() {
+			return "Array";
+		}
+
+		@Override
+		public byte[] toBytes(Object value) {
+			if (value == null) {
+				return new byte[] { (byte) Character.MIN_VALUE };
+			}
+
+			String data = ((String) value).trim();
+			return (data).getBytes(StandardCharsets.UTF_16);
+		}
+
+		@Override
+		public Object fromBytes(byte[] bytes) {
+			if ((bytes.length == 1)
+					&& (bytes[0] == Character.reverseBytes(Character.MIN_VALUE))) {
+				return null;
+			}
+			return new String(bytes, StandardCharsets.UTF_16).trim();
+		}
+	},
+	ATTRIBUTE {
+		@Override
+		public String getName() {
+			return "attribute";
+		}
+
+		@Override
+		public String getDescription() {
+			return "Attribute";
+		}
+
+		@Override
+		public byte[] toBytes(Object value) {
+			if (value == null) {
+				return new byte[] { (byte) Character.MIN_VALUE };
+			}
+
+			String data = ((String) value).trim();
+			return (data).getBytes(StandardCharsets.UTF_16);
+		}
+
+		@Override
+		public Object fromBytes(byte[] bytes) {
+			if ((bytes.length == 1)
+					&& (bytes[0] == Character.reverseBytes(Character.MIN_VALUE))) {
+				return null;
+			}
+			return new String(bytes, StandardCharsets.UTF_16).trim();
+		}
+	},
+	DIMENSION {
+		@Override
+		public String getName() {
+			return "dimension";
+		}
+
+		@Override
+		public String getDescription() {
+			return "DIMENSION";
+		}
+
+		@Override
+		public byte[] toBytes(Object value) {
+			if (value == null) {
+				return new byte[] { (byte) Character.MIN_VALUE };
+			}
+
+			String data = ((String) value).trim();
+			return (data).getBytes(StandardCharsets.UTF_16);
+		}
+
+		@Override
+		public Object fromBytes(byte[] bytes) {
+			if ((bytes.length == 1)
+					&& (bytes[0] == Character.reverseBytes(Character.MIN_VALUE))) {
+				return null;
+			}
+			return new String(bytes, StandardCharsets.UTF_16).trim();
+		}
+	};
+
+	@Override
+	public Pattern getPattern() {
+		return Pattern.compile("^.*$", Pattern.CASE_INSENSITIVE);
+	}
+
+	@Override
+	public DataType typeOf() {
+		return PrimitiveDataType.STRING;
+	}
+
+	@Override
+	public byte[] fromString(String value) {
+		return value.getBytes();
+	}
+
+	@Override
+	public String toString(byte[] bytes) {
+		return new String(bytes);
+	}
+
+	@Override
+	public boolean validate(String value) {
+		return getPattern().matcher(value).matches();
+	}
+
+	@Override
+	public JsonObject toJson() {
+		JsonObjectBuilder build = Json.createObjectBuilder();
+		build.add("name", getName());
+		build.add("pattern", getPattern().toString());
+		build.add("description", getDescription());
+		if (typeOf() != null) {
+			build.add("typeof", typeOf().getName());
+		}
+		return build.build();
+	}
+}