From abea644f46b50cdbb38b8d6cf794de347c62dda1 Mon Sep 17 00:00:00 2001
From: Jim Blake <jeb228@cornell.edu>
Date: Fri, 20 Mar 2015 15:34:53 -0400
Subject: [PATCH] Ignore markdown files in RDF directories.

People want to document the RDF directories (such as rdf/abox/filegraph) by adding README.md files
Such files produce either a warning or an exception, depending on the directory and who is reading.
Modify to ignore any file with a .md extension.
---
 .../webapp/servlet/setup/FileGraphSetup.java   |  4 +++-
 .../webapp/servlet/setup/RDFFilesLoader.java   | 18 ++++++++++++------
 .../servlet/setup/UpdateKnowledgeBase.java     |  4 +++-
 3 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java
index bf51f2b85..ef2f03519 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java
@@ -40,8 +40,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
-import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 // This ContextListener must run after the JenaDataSourceSetup ContextListener
@@ -164,6 +164,8 @@ public class FileGraphSetup implements ServletContextListener {
                         model.read( fis, null, "N3" );
                     } else if ( fn.endsWith(".owl") || fn.endsWith(".rdf") || fn.endsWith(".xml") ) {
                         model.read( fis, null, "RDF/XML" );
+                    } else if ( fn.endsWith(".md") ) {
+                    	// Ignore markdown files - documentation.
                     } else {
                         log.warn("Ignoring " + type + " file graph " + p + " because the file extension is unrecognized.");
                     }
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 aa37f3e63..d1d24f7f8 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
@@ -34,7 +34,10 @@ public class RDFFilesLoader {
 	private static final String FIRST_TIME = "firsttime";
 	private static final String EVERY_TIME = "everytime";
 
-	/** Path filter that ignores sub-directories and hidden files. */
+	/**
+	 * Path filter that ignores sub-directories, hidden files, and markdown
+	 * files.
+	 */
 	private static final DirectoryStream.Filter<Path> RDF_FILE_FILTER = new DirectoryStream.Filter<Path>() {
 		@Override
 		public boolean accept(Path p) throws IOException {
@@ -46,6 +49,9 @@ public class RDFFilesLoader {
 						+ p + "' ignored.");
 				return false;
 			}
+			if (p.toString().endsWith(".md")) {
+				return false;
+			}
 			return true;
 		}
 	};
@@ -61,8 +67,8 @@ public class RDFFilesLoader {
 	public static void loadFirstTimeFiles(String modelPath, Model model,
 			boolean firstTime) {
 		if (firstTime) {
-			Set<Path> paths = getPaths(locateHomeDirectory(), RDF,
-					modelPath, FIRST_TIME);
+			Set<Path> paths = getPaths(locateHomeDirectory(), RDF, modelPath,
+					FIRST_TIME);
 			for (Path p : paths) {
 				readOntologyFileIntoModel(p, model);
 			}
@@ -128,8 +134,8 @@ public class RDFFilesLoader {
 	}
 
 	/**
-	 * Find the paths to RDF files in this directory. Sub-directories and hidden
-	 * files are ignored.
+	 * Find the paths to RDF files in this directory. Sub-directories, hidden
+	 * files, and markdown files are ignored.
 	 */
 	private static Set<Path> getPaths(String parentDir, String... strings) {
 		Path dir = Paths.get(parentDir, strings);
@@ -153,7 +159,7 @@ public class RDFFilesLoader {
 
 	private static void readOntologyFileIntoModel(Path p, Model model) {
 		String format = getRdfFormat(p);
-		log.debug("Loading "+ p);
+		log.debug("Loading " + p);
 		try (InputStream stream = new FileInputStream(p.toFile())) {
 			model.read(stream, null, format);
 			log.debug("...successful");
diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
index 28ee0c5f6..8710e50f9 100644
--- a/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
+++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
@@ -532,7 +532,9 @@ public class UpdateKnowledgeBase {
 		try {
 			FileInputStream fis = new FileInputStream(f);
 			try {	
-				if (f.getName().endsWith(".n3")) {
+				if (f.getName().endsWith(".md")) {
+					// Markdown files are documentation - skip.
+				} else if (f.getName().endsWith(".n3")) {
 					om.read(fis, null, "N3");
 				} else {
 					om.read(fis, null, "RDF/XML");