Change messages to System.err

Move to version 2.3.1
SynBioDex · Jan 28, 2018 · 8a4f758 · 8a4f758
1 parent 15cdfc1
commit 8a4f758
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Showing 5 changed files with 10 additions and 11 deletions.
diff --git a/core2/pom.xml b/core2/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.sbolstandard</groupId>
 		<artifactId>libSBOLj-parent</artifactId>
-		<version>2.3.0</version>
+		<version>2.3.1</version>
 	</parent>
 
 	<artifactId>libSBOLj</artifactId>

diff --git a/core2/src/main/java/org/sbolstandard/core2/Annotation.java b/core2/src/main/java/org/sbolstandard/core2/Annotation.java
@@ -133,7 +133,7 @@ public Annotation(QName qName, QName nestedQName, URI nestedURI, List<Annotation
 		if (value.getName().getNamespaceURI().equals(Sbol2Terms.sbol2.getNamespaceURI()) ||
 				value.getName().getNamespaceURI().equals(Sbol1Terms.sbol1.getNamespaceURI())) {
 			if (value.getName().equals(Sbol2Terms.Identified.timeStamp)) {
-				System.out.println("Warning: sbol:timeStamp is deprecated");
+				System.err.println("Warning: sbol:timeStamp is deprecated");
 			}
 		}
 		setQName(value.getName());

diff --git a/core2/src/main/java/org/sbolstandard/core2/SBOLReader.java b/core2/src/main/java/org/sbolstandard/core2/SBOLReader.java
@@ -1243,7 +1243,6 @@ else if (namedProperty.getName().equals(Sbol1Terms.DNAComponent.annotations))
 						component_displayId = instantiatedDef.getDisplayId();
 						instantiatedComponents.add(instantiatedDef.getDisplayId());
 					} else {
-						//System.out.println("Repeated: " + instantiatedDef.getDisplayId());
 						component_num++;
 					}
 
@@ -3504,7 +3503,7 @@ else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access))
 				}
 				String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
 				if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
-					System.out.println("Warning: namespace for access types should be http://sbols.org/v2#");
+					System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
 					accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
 				}
 				try {
@@ -5403,7 +5402,7 @@ else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapsTo))
 			}
 			else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapping))
 			{
-				System.out.println("Warning: tag should be sbol:mapTo, not sbol:mapping.");
+				System.err.println("Warning: tag should be sbol:mapTo, not sbol:mapping.");
 				if (namedProperty.getValue() instanceof NestedDocument) {
 					mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()),true));
 				}
@@ -5579,7 +5578,7 @@ else if (namedProperty.getName().equals(Sbol2Terms.MapsTo.refinement))
 				}
 				String refinementStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
 				if (!refinementStr.startsWith("http://sbols.org/v2#")) {
-					System.out.println("Warning: namespace for refinement types should be http://sbols.org/v2#");
+					System.err.println("Warning: namespace for refinement types should be http://sbols.org/v2#");
 					refinementStr = "http://sbols.org/v2#" + refinementStr;
 				}
 				try {
@@ -5996,7 +5995,7 @@ else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access))
 				}
 				String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
 				if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
-					System.out.println("Warning: namespace for access types should be http://sbols.org/v2#");
+					System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
 					accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
 				}
 				try {
@@ -6014,7 +6013,7 @@ else if (namedProperty.getName().equals(Sbol2Terms.FunctionalComponent.direction
 				}
 				String directionTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
 				if (directionTypeStr.startsWith("http://www.sbolstandard.org/")) {
-					System.out.println("Warning: namespace for direction types should be http://sbols.org/v2#");
+					System.err.println("Warning: namespace for direction types should be http://sbols.org/v2#");
 					directionTypeStr = directionTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
 					directionTypeStr = directionTypeStr.replace("input","in");
 					directionTypeStr = directionTypeStr.replace("output","out");

diff --git a/examples/pom.xml b/examples/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.sbolstandard</groupId>
         <artifactId>libSBOLj-parent</artifactId>
-         <version>2.3.0</version>
+         <version>2.3.1</version>
     </parent>
 
     <packaging>jar</packaging>
@@ -18,7 +18,7 @@
         <dependency>
             <groupId>${project.parent.groupId}</groupId>
             <artifactId>libSBOLj</artifactId>
-            <version>2.3.0</version>
+            <version>2.3.1</version>
         </dependency>
 
         <!-- test dependencies -->

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.sbolstandard</groupId>
     <artifactId>libSBOLj-parent</artifactId>
-    <version>2.3.0</version>
+    <version>2.3.1</version>
     <packaging>pom</packaging>
     <name>libSBOLj-parent</name>
     <description>Implementation of the SBOL 2.2.0 data standard.</description>