From 1c475a56612b23206b3f64d82839e1bb0bbb9731 Mon Sep 17 00:00:00 2001
From: j2blake <jeb228@cornell.edu>
Date: Wed, 21 Aug 2013 15:08:48 -0400
Subject: [PATCH] VIVO-248 Tweak some issues with file paths and Application
 Model init.

---
 .../servlet/setup/ContentModelSetup.java      | 22 ++++++++++++++-----
 .../webapp/servlet/setup/RDFFilesLoader.java  | 18 +++++++++------
 2 files changed, 28 insertions(+), 12 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java
index 02ec7bf8d..3ad2addca 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java
@@ -82,11 +82,9 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
 
 
         if (isFirstStartup()) {
+        	initializeApplicationMetadata(ctx, applicationMetadataModel);
         	RDFFilesLoader.loadFirstTimeFiles(ctx, "abox", baseABoxModel, true);
         	RDFFilesLoader.loadFirstTimeFiles(ctx, "tbox", baseTBoxModel, true);
-
-        	RDFFilesLoader.loadFirstTimeFiles(ctx, "applicationMetadata", applicationMetadataModel, true);
-        	setPortalUriOnFirstTime(applicationMetadataModel, ctx);
         } else {
         	checkForNamespaceMismatch( applicationMetadataModel, ctx );
         }
@@ -171,13 +169,27 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
 
     /* ===================================================================== */
 
+	/**
+	 * We need to read the RDF files and change the Portal from a blank node to
+	 * one with a URI in the default namespace.
+	 * 
+	 * Do this before adding the data to the RDFService-backed model, to avoid
+	 * warnings about editing a blank node.
+	 */
+	private void initializeApplicationMetadata(ServletContext ctx,
+			OntModel applicationMetadataModel) {
+		OntModel temporaryAMModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
+    	RDFFilesLoader.loadFirstTimeFiles(ctx, "applicationMetadata", temporaryAMModel, true);
+    	setPortalUriOnFirstTime(temporaryAMModel, ctx);
+    	applicationMetadataModel.add(temporaryAMModel);
+	}
+
 	/**
 	 * If we are loading the application metadata for the first time, set the
 	 * URI of the Portal based on the default namespace.
 	 */
 	private void setPortalUriOnFirstTime(OntModel model, ServletContext ctx) {
-		// currently, only a single portal is permitted in the initialization
-		// data
+		// Only a single portal is permitted in the initialization data
 		Resource portalResource = null;
 		ClosableIterator<Resource> portalResIt = model
 				.listSubjectsWithProperty(RDF.type,
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java
index 0fc145d7b..cbd0f8c3d 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java
@@ -33,6 +33,7 @@ public class RDFFilesLoader {
 
 	private static final String PROPERTY_VITRO_HOME = "vitro.home";
 	private static final String DEFAULT_RDF_FORMAT = "RDF/XML";
+	private static final String RDF_FILES = "rdffiles";
 	private static final String FIRST_TIME = "firsttime";
 	private static final String EVERY_TIME = "everytime";
 
@@ -63,11 +64,14 @@ public class RDFFilesLoader {
 	public static void loadFirstTimeFiles(ServletContext ctx, String modelPath,
 			Model model, boolean firstTime) {
 		if (firstTime) {
-			Set<Path> paths = getPaths(locateHomeDirectory(ctx), modelPath,
-					FIRST_TIME);
+			Set<Path> paths = getPaths(locateHomeDirectory(ctx), RDF_FILES,
+					modelPath, FIRST_TIME);
 			for (Path p : paths) {
 				readOntologyFileIntoModel(p, model);
 			}
+		} else {
+			log.debug("Not loading first time files on '" + modelPath
+					+ "', firstTime=false");
 		}
 	}
 
@@ -83,8 +87,8 @@ public class RDFFilesLoader {
 			OntModel model) {
 		OntModel everytimeModel = ModelFactory
 				.createOntologyModel(OntModelSpec.OWL_MEM);
-		Set<Path> paths = getPaths(locateHomeDirectory(ctx), modelPath,
-				EVERY_TIME);
+		Set<Path> paths = getPaths(locateHomeDirectory(ctx), RDF_FILES,
+				modelPath, EVERY_TIME);
 		for (Path p : paths) {
 			readOntologyFileIntoModel(p, everytimeModel);
 		}
@@ -144,13 +148,13 @@ public class RDFFilesLoader {
 
 	private static void readOntologyFileIntoModel(Path p, Model model) {
 		String format = getRdfFormat(p);
-		log.info("Loading ontology file at " + p + " as format " + format);
+		log.info("Loading file at " + p + " as " + format);
 		try (InputStream stream = new FileInputStream(p.toFile())) {
 			model.read(stream, null, format);
 			log.debug("...successful");
 		} catch (Exception e) {
-			log.warn("Could not load RDF file '" + p
-					+ "'. Check that it contains valid " + format + " data.", e);
+			log.warn("Could not load file '" + p + "' as " + format
+					+ ". Check that it contains valid data.", e);
 		}
 	}