Preserve prefix declarations from input ontology.

Author: balhoff

OWLTools-Core/src/main/java/owltools/io/OWLOboGraphsFormat.java

@@ -20,7 +20,7 @@ public String getKey() {
 
 	@Override
 	public boolean isPrefixOWLOntologyFormat() {
-		return true;
+		return false;
 	}
 
 	@Override

OWLTools-Core/src/main/java/owltools/io/OWLOboGraphsYamlFormat.java

@@ -20,7 +20,7 @@ public String getKey() {
 
 	@Override
 	public boolean isPrefixOWLOntologyFormat() {
-		return true;
+		return false;
 	}
 
 	@Override

OWLTools-Oort/src/main/java/owltools/ontologyrelease/OboOntologyReleaseRunner.java

@@ -1752,6 +1752,7 @@ private void saveOntologyInAllFormats(String idspace, String fileNameBase, Strin
 
 	private void write(OWLOntologyManager manager, OWLOntology ont, OWLDocumentFormat format, OutputStream out) throws OWLOntologyStorageException {
 		try {
+			copyPrefixDefinitionsToOutputFormat(ont, format);
 			manager.saveOntology(ont, format, out);
 		} finally {
 			try {
@@ -1763,6 +1764,17 @@ private void write(OWLOntologyManager manager, OWLOntology ont, OWLDocumentForma
 
 	}
 
+	private void copyPrefixDefinitionsToOutputFormat(OWLOntology ont, OWLDocumentFormat format) {
+		OWLDocumentFormat previousFormat = ont.getOWLOntologyManager().getOntologyFormat(ont);
+		if (format != null && format.isPrefixOWLOntologyFormat()
+				&& previousFormat != null
+				&& previousFormat.isPrefixOWLOntologyFormat()) {
+			String defaultNamespace = format.asPrefixOWLOntologyFormat().getDefaultPrefix();
+			format.asPrefixOWLOntologyFormat().copyPrefixesFrom(previousFormat.asPrefixOWLOntologyFormat());
+			format.asPrefixOWLOntologyFormat().setDefaultPrefix(defaultNamespace);
+		}
+	}
+
 	private void saveReasonerReport(String ontologyId,
 			List<String> reasonerReportLines) {
 

OWLTools-Runner/src/main/java/owltools/cli/CommandRunner.java

@@ -3695,6 +3695,7 @@ else if (ofmtname.equals("obo")) {
                             }
                             ofmt = new OBODocumentFormat();
                         }
+                        copyPrefixDefinitionsToOutputFormat(g.getSourceOntology(), ofmt);
                     }
                     else if (opts.nextEq("--prefix")) {
                         opts.info("PREFIX URIBASE","use PREFIX as prefix. Note: specify this sub-arg AFTER -f");
@@ -6637,4 +6638,15 @@ private void showEdges(Set<OWLGraphEdge> edges) {
         }
     }
 
+    private void copyPrefixDefinitionsToOutputFormat(OWLOntology ont, OWLDocumentFormat format) {
+        OWLDocumentFormat previousFormat = ont.getOWLOntologyManager().getOntologyFormat(ont);
+        if (format != null && format.isPrefixOWLOntologyFormat()
+                && previousFormat != null
+                && previousFormat.isPrefixOWLOntologyFormat()) {
+            String defaultNamespace = format.asPrefixOWLOntologyFormat().getDefaultPrefix();
+            format.asPrefixOWLOntologyFormat().copyPrefixesFrom(previousFormat.asPrefixOWLOntologyFormat());
+            format.asPrefixOWLOntologyFormat().setDefaultPrefix(defaultNamespace);
+        }
+    }
+
 }