From beb4c665ce42b1cfe06cd2c620f0d3aa0c2d2386 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Fri, 7 Apr 2017 13:13:56 -0300
Subject: [PATCH 01/12] json to xml

---
 pom.xml                                       |  7 +++-
 .../gsearch_extensions/JSONToXML.java         | 36 ++++++++++++++++
 .../gsearch_extensions/JSONToXMLTest.java     | 41 +++++++++++++++++++
 3 files changed, 83 insertions(+), 1 deletion(-)
 create mode 100644 src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
 create mode 100644 src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java

diff --git a/pom.xml b/pom.xml
index e13df1c..27cb43e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
   <groupId>ca.discoverygarden</groupId>
   <artifactId>gsearch_extensions</artifactId>
-  <version>0.1.1</version>
+  <version>0.1.2</version>
   <packaging>jar</packaging>
 
 
@@ -35,6 +35,11 @@
     	<artifactId>commons-lang3</artifactId>
     	<version>3.3.2</version>
     </dependency>
+    <dependency>
+      <groupId>org.json</groupId>
+      <artifactId>json</artifactId>
+      <version>20160810</version>
+    </dependency>
   </dependencies>
   
   <build>
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
new file mode 100644
index 0000000..d71e05a
--- /dev/null
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
@@ -0,0 +1,36 @@
+package ca.discoverygarden.gsearch_extensions;
+
+import org.json.JSONObject;
+import org.json.XML;
+
+public class JSONToXML {
+
+  /**
+   * Converts a JSON string to an XML string enclosed in a 'json' tag.
+   *
+   * @param in
+   *   The JSON to convert.
+   *
+   * @return
+   *   XML string.
+   */
+  public static String convertJSONToXML(String in) {
+    return convertJSONToXML(in, "json");
+  }
+
+  /**
+   * Convert a JSON string to an XML string.
+   *
+   * @param in
+   *   The JSON to convert.
+   * @param enclosing_tag
+   *   The tag to enclose the results in.
+   *
+   * @return
+   *   XML string. 
+   */
+  public static String convertJSONToXML(String in, String enclosing_tag) {
+    JSONObject json = new JSONObject(in);
+    return XML.toString(json, enclosing_tag);
+  }
+}
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
new file mode 100644
index 0000000..b992035
--- /dev/null
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
@@ -0,0 +1,41 @@
+package ca.discoverygarden.gsearch_extensions;
+
+import junit.framework.TestCase;
+
+/**
+ * Tests that we can get XML from JSON.
+ */
+public class JSONToXMLTest extends TestCase {
+
+  // Our test JSON we use twice.
+  protected static final String testJson = "{\"thing_1\":{\"subthing_1.1\":\"value_1.1\",\"subthing_1.2\":\"value_1.2\"},\"thing_2\":\"value_2\"}";
+
+  /**
+   * Set up the thingy.
+   */
+  protected void setUp() throws Exception {
+    super.setUp();
+  }
+
+  /**
+   * Tests conversion with the default root element.
+   */
+  public void testDefaultRootElement() {
+    // Should be XML enclosed in a 'json' tag.
+    String dest = "<json><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></json>";
+    String transformed = JSONToXML.convertJSONToXML(testJson);
+
+    assertEquals(dest, transformed);
+  }
+
+  /**
+   * Tests conversion with a custom root element.
+   */
+  public void testCustomRootElement() {
+    // Should be XML enclosed in a 'custom' tag.
+    String dest = "<custom><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></custom>";
+    String transformed = JSONToXML.convertJSONToXML(testJson, "custom");
+
+    assertEquals(dest, transformed);
+  }
+}

From b165ab5f962e39556e2428722a3593797f6299af Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Mon, 10 Apr 2017 17:13:16 -0300
Subject: [PATCH 02/12] json-to-xml

---
 pom.xml                                       | 15 ++++++++++
 .../gsearch_extensions/JSONToXML.java         | 29 +++++++++++++++++++
 2 files changed, 44 insertions(+)

diff --git a/pom.xml b/pom.xml
index 27cb43e..c157363 100644
--- a/pom.xml
+++ b/pom.xml
@@ -40,6 +40,21 @@
       <artifactId>json</artifactId>
       <version>20160810</version>
     </dependency>
+    <dependency>
+        <groupId>javax.xml.parsers</groupId>
+        <artifactId>jaxp-api</artifactId>
+        <version>1.4.5</version>
+    </dependency>
+    <dependency>
+        <groupId>org.w3c</groupId>
+        <artifactId>dom</artifactId>
+        <version>2.3.0-jaxb-1.0.6</version>
+    </dependency>
+    <dependency>
+        <groupId>org.fcrepo</groupId>
+        <artifactId>fcrepo-server</artifactId>
+        <version>3.8.1</version>
+    </dependency>
   </dependencies>
   
   <build>
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
index d71e05a..9f5908d 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
@@ -3,8 +3,18 @@
 import org.json.JSONObject;
 import org.json.XML;
 
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.ParserConfigurationException;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.w3c.dom.Document;
+import java.io.StringReader;
+import java.io.IOException;
+
 public class JSONToXML {
 
+
   /**
    * Converts a JSON string to an XML string enclosed in a 'json' tag.
    *
@@ -33,4 +43,23 @@ public static String convertJSONToXML(String in, String enclosing_tag) {
     JSONObject json = new JSONObject(in);
     return XML.toString(json, enclosing_tag);
   }
+
+  /**
+   * Convert a JSON string to an XML document.
+   *
+   * @param in
+   *   JSON to convert.
+   *
+   * @return
+   *   XML Node.
+   */
+  public static Document convertJSONToDocument(String in) 
+  throws ParserConfigurationException, SAXException, IOException
+  {
+    StringReader xmlStringReader = new StringReader(convertJSONToXML(in));
+
+    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+    DocumentBuilder builder = factory.newDocumentBuilder();
+    return builder.parse(new InputSource(xmlStringReader));
+  }
 }

From c8f56d5e8f37138691999f9823269946a4a63caa Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Mon, 10 Apr 2017 17:18:55 -0300
Subject: [PATCH 03/12] file pls

---
 .../gsearch_extensions/FedoraUtils.java       | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java

diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
new file mode 100644
index 0000000..b33f46c
--- /dev/null
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -0,0 +1,38 @@
+package ca.discoverygarden.gsearch_extensions;
+
+import org.apache.log4j.Logger;
+
+import dk.defxws.fedoragsearch.server.GenericOperationsImpl;
+
+import org.fcrepo.client.FedoraClient;
+import org.fcrepo.server.access.FedoraAPIA;
+import org.fcrepo.server.types.gen.Datastream;
+import org.fcrepo.server.types.gen.MIMETypedStream;
+
+/**
+ * Utilities for interfacing with Fedora in ways that GSearch can't.
+ */
+public class FedoraUtils {
+
+  protected static final Logger logger = Logger.getLogger(FedoraUtils.class);
+
+  /**
+   * Gets the raw text of a datastream.
+   */
+  public static String getRawDatastreamText(String pid, String repositoryName, String dsId, String fedoraSoap, String fedoraUser, String fedoraPass, String trustStorePath, String trustStorePass) {
+    dsBuffer = new StringBuffer();
+    FedoraAPIA apia = GenericOperationsImpl.getAPIA(repositoryName, fedoraSoap, fedoraUser, fedoraPass, trustStorePath, trustStorePass);
+    // Get the DS; getDatastreamDissemination could be null.
+    MIMETypedStream dsStream = apia.getDatastreamDissemination(getRealPID(pid), dsId, null);
+    if (dsStream == null) {
+      logger.warn(String.format("Failed to get datastream dissemination of '%s' for '%s'", dsId, pid));
+      return "";
+    }
+    // Get the stream.
+    ds = dsStream.getStream();
+    if (ds == null) {
+      logger.warn(String.format("Failed to get stream from '%s' for '%s'", dsId, pid));
+      return "";
+    }
+  }
+}

From 8e7ea3ded1006fc79a6290c83e2d586d2e66b711 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Mon, 10 Apr 2017 19:24:10 -0300
Subject: [PATCH 04/12] getting text of stuff

---
 pom.xml                                       |  5 +
 .../gsearch_extensions/FedoraUtils.java       | 98 +++++++++++++++----
 .../gsearch_extensions/JSONToXML.java         |  2 +-
 .../gsearch_extensions/FedoraUtilsTest.java   | 33 +++++++
 .../gsearch_extensions/JSONToXMLTest.java     | 18 ++++
 5 files changed, 135 insertions(+), 21 deletions(-)
 create mode 100644 src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java

diff --git a/pom.xml b/pom.xml
index c157363..0396376 100644
--- a/pom.xml
+++ b/pom.xml
@@ -55,6 +55,11 @@
         <artifactId>fcrepo-server</artifactId>
         <version>3.8.1</version>
     </dependency>
+    <dependency>
+        <groupId>org.fcrepo</groupId>
+        <artifactId>fcrepo-client-admin</artifactId>
+        <version>3.8.1</version>
+    </dependency>
   </dependencies>
   
   <build>
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
index b33f46c..85df7ff 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -1,13 +1,14 @@
 package ca.discoverygarden.gsearch_extensions;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
 
-import dk.defxws.fedoragsearch.server.GenericOperationsImpl;
-
-import org.fcrepo.client.FedoraClient;
-import org.fcrepo.server.access.FedoraAPIA;
-import org.fcrepo.server.types.gen.Datastream;
-import org.fcrepo.server.types.gen.MIMETypedStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.ByteArrayInputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
 
 /**
  * Utilities for interfacing with Fedora in ways that GSearch can't.
@@ -16,23 +17,80 @@ public class FedoraUtils {
 
   protected static final Logger logger = Logger.getLogger(FedoraUtils.class);
 
+  /**
+   * Gets an InputStream for a datastream.
+   *
+   * @param pid
+   *   The PID of the object that has the datastream.
+   * @param dsId
+   *   The ID of the datastream to get.
+   * @param fedoraBase
+   *   The base URL of fedora, e.g., localhost:8080/fedora.
+   * @param fedoraUser
+   *   The Fedora username to connect with.
+   * @param fedoraPass
+   *   The Fedora password to connect with.
+   *
+   * @return InputStream
+   *   An InputStream at the constructed dissemination point.
+   */
+  public static InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
+	  URL url;
+	  // Attempt to generate the URL from input.
+	  try {
+		  url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+	      return url.openStream();
+	  }
+	  catch (MalformedURLException e) {
+		  logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
+	  }
+	  catch (IOException e) {
+		  logger.warn(String.format("Failed to open stream: %s", e.getMessage()));
+	  }
+	  return new ByteArrayInputStream("".getBytes());
+  }
+
   /**
    * Gets the raw text of a datastream.
+   *
+   * @param pid
+   *   The PID of the object that has the datastream.
+   * @param dsId
+   *   The ID of the datastream to get.
+   * @param fedoraBase
+   *   The base URL of fedora, e.g., localhost:8080/fedora.
+   * @param fedoraUser
+   *   The Fedora username to connect with.
+   * @param fedoraPass
+   *   The Fedora password to connect with.
+   *
+   * @return String
+   *   The text of the given datastream.
    */
-  public static String getRawDatastreamText(String pid, String repositoryName, String dsId, String fedoraSoap, String fedoraUser, String fedoraPass, String trustStorePath, String trustStorePass) {
-    dsBuffer = new StringBuffer();
-    FedoraAPIA apia = GenericOperationsImpl.getAPIA(repositoryName, fedoraSoap, fedoraUser, fedoraPass, trustStorePath, trustStorePass);
-    // Get the DS; getDatastreamDissemination could be null.
-    MIMETypedStream dsStream = apia.getDatastreamDissemination(getRealPID(pid), dsId, null);
-    if (dsStream == null) {
-      logger.warn(String.format("Failed to get datastream dissemination of '%s' for '%s'", dsId, pid));
+  public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
+	  try {
+	      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+	  	  URLConnection connection = url.openConnection();
+	  	  InputStream dsStream = connection.getInputStream();
+	  	  String encoding = connection.getContentEncoding();
+	  	  encoding = encoding == null ? "UTF=8" : encoding;
+	  	  return IOUtils.toString(dsStream, encoding);
+	  } catch (MalformedURLException e) {
+	      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
+	  } catch (IOException e) {
+		  logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
+	  }
       return "";
-    }
-    // Get the stream.
-    ds = dsStream.getStream();
-    if (ds == null) {
-      logger.warn(String.format("Failed to get stream from '%s' for '%s'", dsId, pid));
-      return "";
-    }
+  }
+
+  /**
+   * Turns some parameters into a datastream dissemination URL.
+   *
+   * @return URL
+   *   A URL object using the given parameters.
+   */
+  protected static URL getDatastreamDisseminationURL(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws MalformedURLException {
+	  String formattedUrl = String.format("http://%s:%s@%s/objects/%s/datastreams/%s/content", fedoraUser, fedoraPass, fedoraBase, pid, dsId);
+	  return new URL(formattedUrl);
   }
 }
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
index 9f5908d..cb8f75a 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
@@ -51,7 +51,7 @@ public static String convertJSONToXML(String in, String enclosing_tag) {
    *   JSON to convert.
    *
    * @return
-   *   XML Node.
+   *   XML Document.
    */
   public static Document convertJSONToDocument(String in) 
   throws ParserConfigurationException, SAXException, IOException
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
new file mode 100644
index 0000000..625fd00
--- /dev/null
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
@@ -0,0 +1,33 @@
+package ca.discoverygarden.gsearch_extensions;
+
+import junit.framework.TestCase;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+public class FedoraUtilsTest extends TestCase {
+
+	/**
+	 * Set that thing up.
+	 */
+	protected void setUp() throws Exception {
+		super.setUp();
+	}
+	
+	/**
+	 * Tests building a URL.
+	 */
+	public void testURLBuild() throws MalformedURLException {
+		String pid = "test:pid";
+		String dsId = "TEST_DSID";
+		String fedoraBase = "localhost:8080/fedora";
+		String fedoraUser = "test_user";
+		String fedoraPass = "test_pass";
+		URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+		
+		assertEquals(url.getPort(), 8080);
+		assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
+		assertEquals(url.getUserInfo(), "test_user:test_pass");
+	}
+
+}
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
index b992035..b0dd71c 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
@@ -2,6 +2,14 @@
 
 import junit.framework.TestCase;
 
+import java.io.IOException;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
 /**
  * Tests that we can get XML from JSON.
  */
@@ -38,4 +46,14 @@ public void testCustomRootElement() {
 
     assertEquals(dest, transformed);
   }
+  
+  /**
+   * Tests conversion to a Document object.
+   */
+  public void testDocumentConversion() throws ParserConfigurationException, SAXException, IOException {
+	Document transformed = JSONToXML.convertJSONToDocument(testJson);
+	NodeList thingList = transformed.getElementsByTagName("thing_1");
+	
+	assertEquals(thingList.getLength(), 1);
+  }
 }

From 4139f1f636646ef4375234c037920c1eca064840 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Mon, 10 Apr 2017 23:14:43 -0300
Subject: [PATCH 05/12] maybe

---
 pom.xml                                       | 10 ---
 .../gsearch_extensions/FedoraUtils.java       | 61 ++++++++++++++-----
 .../gsearch_extensions/FedoraUtilsTest.java   |  3 +-
 3 files changed, 46 insertions(+), 28 deletions(-)

diff --git a/pom.xml b/pom.xml
index 0396376..9e4e64e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -50,16 +50,6 @@
         <artifactId>dom</artifactId>
         <version>2.3.0-jaxb-1.0.6</version>
     </dependency>
-    <dependency>
-        <groupId>org.fcrepo</groupId>
-        <artifactId>fcrepo-server</artifactId>
-        <version>3.8.1</version>
-    </dependency>
-    <dependency>
-        <groupId>org.fcrepo</groupId>
-        <artifactId>fcrepo-client-admin</artifactId>
-        <version>3.8.1</version>
-    </dependency>
   </dependencies>
   
   <build>
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
index 85df7ff..dc2d583 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -1,6 +1,5 @@
 package ca.discoverygarden.gsearch_extensions;
 
-import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
 
 import java.io.IOException;
@@ -8,7 +7,31 @@
 import java.io.ByteArrayInputStream;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.net.URLConnection;
+import java.net.Authenticator;
+import java.net.PasswordAuthentication;
+import java.util.Scanner;
+
+/**
+ * Authenticator for connecting to Fedora.
+ */
+class FedoraAuthenticator extends Authenticator {
+
+  protected String fedoraUser;
+  protected String fedoraPass;
+
+  public void setCredentials(String username, String password) {
+    fedoraUser = username;
+    fedoraPass = password;
+  }
+
+  /**
+   * Overloaded password authenticator.
+   */
+  protected PasswordAuthentication getPasswordAuthentication() {
+    return new PasswordAuthentication(fedoraUser, fedoraPass.toCharArray());
+  }
+
+}
 
 /**
  * Utilities for interfacing with Fedora in ways that GSearch can't.
@@ -25,7 +48,8 @@ public class FedoraUtils {
    * @param dsId
    *   The ID of the datastream to get.
    * @param fedoraBase
-   *   The base URL of fedora, e.g., localhost:8080/fedora.
+   *   The base URL of fedora, including protocol; e.g., 
+   *   http://localhost:8080/fedora.
    * @param fedoraUser
    *   The Fedora username to connect with.
    * @param fedoraPass
@@ -34,7 +58,7 @@ public class FedoraUtils {
    * @return InputStream
    *   An InputStream at the constructed dissemination point.
    */
-  public static InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
+  public InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
 	  URL url;
 	  // Attempt to generate the URL from input.
 	  try {
@@ -58,7 +82,8 @@ public static InputStream getDatastreamDisseminationInputStream(String pid, Stri
    * @param dsId
    *   The ID of the datastream to get.
    * @param fedoraBase
-   *   The base URL of fedora, e.g., localhost:8080/fedora.
+   *   The base URL of fedora, including protocol; e.g.,
+   *   http://localhost:8080/fedora.
    * @param fedoraUser
    *   The Fedora username to connect with.
    * @param fedoraPass
@@ -67,20 +92,20 @@ public static InputStream getDatastreamDisseminationInputStream(String pid, Stri
    * @return String
    *   The text of the given datastream.
    */
-  public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
+  public String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
 	  try {
 	      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
-	  	  URLConnection connection = url.openConnection();
-	  	  InputStream dsStream = connection.getInputStream();
-	  	  String encoding = connection.getContentEncoding();
-	  	  encoding = encoding == null ? "UTF=8" : encoding;
-	  	  return IOUtils.toString(dsStream, encoding);
+        InputStream dsStream = url.openStream();
+        Scanner scanner = new Scanner(dsStream);
+        String dsString = scanner.hasNext() ? scanner.next() : "";
+        logger.debug(String.format("getRawDatastreamDissemination (pid: %s, DSID: %s): %s", pid, dsId, dsString));
+        return dsString;
 	  } catch (MalformedURLException e) {
 	      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
 	  } catch (IOException e) {
-		  logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
+		    logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
 	  }
-      return "";
+    return "";
   }
 
   /**
@@ -89,8 +114,12 @@ public static String getRawDatastreamDissemination(String pid, String dsId, Stri
    * @return URL
    *   A URL object using the given parameters.
    */
-  protected static URL getDatastreamDisseminationURL(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws MalformedURLException {
-	  String formattedUrl = String.format("http://%s:%s@%s/objects/%s/datastreams/%s/content", fedoraUser, fedoraPass, fedoraBase, pid, dsId);
-	  return new URL(formattedUrl);
+  protected static final URL getDatastreamDisseminationURL(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws MalformedURLException {
+    FedoraAuthenticator auth = new FedoraAuthenticator();
+    auth.setCredentials(fedoraUser, fedoraPass);
+    Authenticator.setDefault(auth);
+    String url = String.format("%s/objects/%s/datastreams/%s/content", fedoraBase, pid, dsId);
+    logger.debug(String.format("Building URL for %s", url));
+	  return new URL(url);
   }
 }
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
index 625fd00..6e09ee4 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
@@ -20,14 +20,13 @@ protected void setUp() throws Exception {
 	public void testURLBuild() throws MalformedURLException {
 		String pid = "test:pid";
 		String dsId = "TEST_DSID";
-		String fedoraBase = "localhost:8080/fedora";
+		String fedoraBase = "http://localhost:8080/fedora";
 		String fedoraUser = "test_user";
 		String fedoraPass = "test_pass";
 		URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
 		
 		assertEquals(url.getPort(), 8080);
 		assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
-		assertEquals(url.getUserInfo(), "test_user:test_pass");
 	}
 
 }

From d120095e45631390d910fb7577756309a49cef35 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Tue, 11 Apr 2017 02:07:51 -0300
Subject: [PATCH 06/12] cleanup, documentation

---
 README.md                                     | 170 +++++++++++++-----
 .../gsearch_extensions/FedoraUtils.java       |  34 +++-
 .../gsearch_extensions/JSONToXML.java         |  21 ++-
 .../gsearch_extensions/FedoraUtilsTest.java   |  18 +-
 .../gsearch_extensions/JSONToXMLTest.java     |  25 +--
 5 files changed, 194 insertions(+), 74 deletions(-)

diff --git a/README.md b/README.md
index 5c4e4b4..2938774 100644
--- a/README.md
+++ b/README.md
@@ -1,34 +1,43 @@
-SUMMARY
--------
+# DGI GSearch Extensions
 
-discoverygarden's GSearch extensions
+## Introduction
 
-Currently provides a thin wrapper around the Joda date/time library, in
-order to more reliably transform dates for Solr.
+discoverygarden's GSearch extensions, providing extended functionality available to GSearch XSLTs that would otherwise be extremely difficult or impossible to recreate in XSLT 1.0.
 
-REQUIREMENTS
-------------
+## Requirements
 
-For build:
-- Maven 2/3
+* [Apache Maven](https://maven.apache.org) 2 or 3 to build.
 
-INSTALLATION
-------------
+## Installation
 
-Build the extensions with `mvn package`, and copy the created jar into GSearch's
-lib directory (`$CATALINA_HOME/webapps/fedoragsearch/WEB-INF/lib`).
+Build the extensions with `mvn package`, and copy the created jar into GSearch's lib directory (`$CATALINA_HOME/webapps/fedoragsearch/WEB-INF/lib`).
 
-If you want to include Joda Time manually use gsearch_extensions-0.1.0.jar otherwise use 
-gsearch_extensions-0.1.0-jar-with-dependencies.jar
+If providing package libraries yourself, use gsearch_extensions-0.1.2.jar; otherwise use gsearch_extensions-0.1.2-jar-with-dependencies.jar.
 
-CONFIGURATION
--------------
+## Usage
 
+### Namespacing
 
-USAGE
--------------
+Extensions are available to the java namespace of your XSLT parser. In Xalan, this should be:
+
+`xmlns:java="http://xml.apache.org/xalan/java"`
+
+From there, extension functions can be called at that namespace.
+
+### Functions Available
+
+#### `ca.discoverygarden.gsearch_extensions.JodaAdapter`
+
+##### `transformForSolr($date, $pid, $datastream)`
+
+Attempts to parse dates to a Solr-appropriate format in the following default set and order, assuming UTC if no timezone is provided:
+
+* `M/d/y`, e.g., `7/23/2013` would become `2013-07-23T00:00:00.000Z`
+* `M/d/y H:m`, e.g., `7/23/2013 11:36` would become `2013-07-23T11:36:00.000Z`
+* ISO Date Time, as per [Joda-Time ISODateTimeFormat](http://joda-time.sourceforge.net/apidocs/org/joda/time/format/ISODateTimeFormat.html#dateTimeParser%28%29). Timezone offsets will be transformed off, so `2013-07-23T02:36-03:00` would be transformed to `2013-07-23T11:36:00.000Z`.
+
+For example:
 
-In Xalan, it should be possible to call the code like:
 ```
 <xsl:variable name="date_to_parse">08/13/2013</xsl:variable>
 <xsl:variable xmlns:java="http://xml.apache.org/xalan/java"
@@ -36,37 +45,110 @@ In Xalan, it should be possible to call the code like:
   select="java:ca.discoverygarden.gsearch_extensions.JodaAdapter.transformForSolr($date_to_parse)"/>
 ```
 
-For better logging, one could also call like:
-```
-<xsl:variable xmlns:java="http://xml.apache.org/xalan/java"
-  name="date"
-  select="java:ca.discoverygarden.gsearch_extensions.JodaAdapter.transformForSolr($date_to_parse, $pid, $datastream)"/>
-```
-where `$pid` and `$datastream` are the identifiers of the object and datastream, respectively.
+More parser formats can be added with `addDateParser()`. The list of formats can be reset with `resetParsers()`.
+
+Variable|Description
+--------|-----------
+`$date`|A string date formatted like one of the `JodaAdapter`'s parsers.
+`$pid`|(Optional) The string PID of the object being processed, for potential logging purposes.
+`$datastream`|(Optional; required if `$pid` is given) The string datastream ID of the datastream being processed, for potential logging purposes.
+
+##### `addDateParser($position, $format)`
+
+Adds a parsing format pattern to the list of patterns to attempt when running `transformForSolr()`, optionally at the provided position.
+
+Variable|Description
+--------|-----------
+`$position`|(Optional) An integer position to place the parser format at.
+`$format`|A string format to add to the parser list, e.g., `Y-m-d`.
+
+##### `resetParsers()`
+
+Resets the list of parsers `transformForSolr()` will attempt when converting a date.
+
+#### `ca.discoverygarden.gsearch_extensions.XMLStringUtils`
 
-The three base parsers assume that they are given dates in UTC if no timezone is provided, and are attempted in order:
-- `M/d/y`
-  So `7/23/2013` should result in `2013-07-23T00:00:00.000Z`.
-- `M/d/y H:m`
-  So `7/23/2013 11:36` should result in `2013-07-23T11:36:00.000Z`.
-- ISO Date Time, as per http://joda-time.sourceforge.net/apidocs/org/joda/time/format/ISODateTimeFormat.html#dateTimeParser%28%29
-  Timezone offsets will be transformed off, so `2013-07-23T02:36-03:00` will be transformed to `2013-07-23T11:36:00.000Z`.
+##### `escapeForXML($input, $replacement)`
 
-CUSTOMIZATION
--------------
+Escapes a string for inclusion in XML, for example, in cases where the contents of a plaintext datastream are being provided to Solr.
+
+The list of characters being replaced are based off of the Apache Commons lang3 library's [escapeXML10](https://commons.apache.org/proper/commons-lang/javadocs/api-3.5/org/apache/commons/lang3/StringEscapeUtils.html#escapeXml10-java.lang.String-) list of replaced characters.
+
+Variable|Description
+`$input`|The string to sanitize.
+`$replacement`|(Optional) The string to use when replacing invalid characters; otherwise, invalid characters will be replaced with Unicode U+FFFD (the Unicode replacement character).
+
+#### `ca.discoverygarden.gsearch_extensions.FedoraUtils`
+
+##### `getDatastreamDisseminationInputStream($pid, $dsId, $fedoraBase, $fedoraUser, $fedoraPass)`
+
+Gets the dissemination of a datastream as an InputStream object.
+
+Variable|Description
+--------|-----------
+`$pid`|The PID of the object to get a datastream from.
+`$dsId`|The ID of the datastream to get the dissemination for.
+`$fedoraBase`|The base URL of Fedora, including the protocol; e.g., `http://localhost:8080/fedora`.
+`$fedoraUser`|The username to log into Fedora with.
+`$fedoraPass`|The password for the given username.
+
+##### `getRawDatastreamDissemination($pid, $dsId, $fedoraBase, $fedoraUser, $fedoraPass)`
+
+Gets the dissemination of a datastream as a string. Useful in cases where GSearch refuses to return the text of a datastream, i.e., most cases.
+
+Variable|Description
+--------|-----------
+`$pid`|The PID of the object to get a datastream from.
+`$dsId`|The ID of the datastream to get the dissemination for.
+`$fedoraBase`|The base URL of Fedora, including the protocol; e.g., `http://localhost:8080/fedora`.
+`$fedoraUser`|The username to log into Fedora with.
+`$fedoraPass`|The password for the given username.
+
+#### `ca.discoverygarden.gsearch_extensions.JSONToXML`
+
+##### `convertJSONToXML($input, $enclosing_tag)`
+
+Converts a JSON string to an XML string.
+
+Variable|Description
+--------|-----------
+`$input`|The input JSON string.
+`$enclosing_tag`|(Optional) The top-level element to wrap resultant XML in, to prevent invalid XML from being written. If not provided, defaults to an element called 'json'.
+
+##### `convertJSONToDocument($input, $enclosing_tag)`
+
+Converts a JSON string to an XML Document object.
+
+The resultant document can be interpreted as a Node-Set by Xalan, for example:
+
+```
+<xsl:variable name="some_json">{"something": "has content"}</xsl:variable>
+<xsl:variable
+    xmlns:java="http://xml.apache.org/xalan/java"
+    name="some_xml"
+    select="java:ca.discoverygarden.gsearch_extensions.JSONToXML.convertJSONToDocument($some_json)"/>
+<!-- This will evaluate to "has content". -->
+<xsl:variable name="node" select="$some_xml//something/text()">
+```
 
+Variable|Description
+--------|-----------
+`$input`|The input JSON string.
+`$enclosing_tag|(Optional) The top-level element to wrap resultant XML in, to prevent invalid XML from being written. If not provided, defaults to an element called 'json'.
 
-TROUBLESHOOTING
----------------
+## Troubleshooting/Issues
 
+Having problems or solved a problem? Contact [discoverygarden](http://support.discoverygarden.ca).
 
-F.A.Q.
-------
+## Maintainers/Sponsors
 
+Current maintainers:
 
-CONTACT
--------
+* [discoverygarden](http://www.discoverygarden.ca)
 
+## Development
 
-SPONSORS
---------
+If you would like to contribute to this module, please check out our helpful
+[Documentation for Developers](https://github.com/Islandora/islandora/wiki#wiki-documentation-for-developers)
+info, [Developers](http://islandora.ca/developers) section on Islandora.ca and
+contact [discoverygarden](http://support.discoverygarden.ca).
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
index dc2d583..fb80d23 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -19,6 +19,14 @@ class FedoraAuthenticator extends Authenticator {
   protected String fedoraUser;
   protected String fedoraPass;
 
+  /**
+   * Set the username and password for this authenticator.
+   *
+   * @param username
+   *   The username to set.
+   * @param password
+   *   The password to set.
+   */
   public void setCredentials(String username, String password) {
     fedoraUser = username;
     fedoraPass = password;
@@ -26,6 +34,9 @@ public void setCredentials(String username, String password) {
 
   /**
    * Overloaded password authenticator.
+   *
+   * @return PasswordAuthentication
+   *   Authentication for this authenticator.
    */
   protected PasswordAuthentication getPasswordAuthentication() {
     return new PasswordAuthentication(fedoraUser, fedoraPass.toCharArray());
@@ -58,18 +69,20 @@ public class FedoraUtils {
    * @return InputStream
    *   An InputStream at the constructed dissemination point.
    */
-  public InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
+  public static InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
 	  URL url;
 	  // Attempt to generate the URL from input.
 	  try {
-		  url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+        url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
 	      return url.openStream();
 	  }
+    // On exception, log and return a stream with no content so the caller
+    // doesn't get messed up.
 	  catch (MalformedURLException e) {
-		  logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
+		    logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
 	  }
 	  catch (IOException e) {
-		  logger.warn(String.format("Failed to open stream: %s", e.getMessage()));
+		    logger.warn(String.format("Failed to open stream: %s", e.getMessage()));
 	  }
 	  return new ByteArrayInputStream("".getBytes());
   }
@@ -92,17 +105,22 @@ public InputStream getDatastreamDisseminationInputStream(String pid, String dsId
    * @return String
    *   The text of the given datastream.
    */
-  public String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
+  public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws FileNotFoundException {
 	  try {
 	      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
         InputStream dsStream = url.openStream();
         Scanner scanner = new Scanner(dsStream);
+        // If no content, return an empty string.
         String dsString = scanner.hasNext() ? scanner.next() : "";
         logger.debug(String.format("getRawDatastreamDissemination (pid: %s, DSID: %s): %s", pid, dsId, dsString));
         return dsString;
-	  } catch (MalformedURLException e) {
+	  } 
+    // On exception, log and return an empty string so the caller doesn't get
+    // messed up.
+    catch (MalformedURLException e) {
 	      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
-	  } catch (IOException e) {
+	  }
+    catch (IOException e) {
 		    logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
 	  }
     return "";
@@ -115,9 +133,11 @@ public String getRawDatastreamDissemination(String pid, String dsId, String fedo
    *   A URL object using the given parameters.
    */
   protected static final URL getDatastreamDisseminationURL(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws MalformedURLException {
+    // Set the authenticator.
     FedoraAuthenticator auth = new FedoraAuthenticator();
     auth.setCredentials(fedoraUser, fedoraPass);
     Authenticator.setDefault(auth);
+    // Build the URL.
     String url = String.format("%s/objects/%s/datastreams/%s/content", fedoraBase, pid, dsId);
     logger.debug(String.format("Building URL for %s", url));
 	  return new URL(url);
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
index cb8f75a..ac9f82b 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
@@ -51,12 +51,29 @@ public static String convertJSONToXML(String in, String enclosing_tag) {
    *   JSON to convert.
    *
    * @return
+   *   XML document.
+   */
+  public static Document convertJSONToDocument(String in, String enclosing_tag) 
+  throws ParserConfigurationException, SAXException, IOException
+  {
+    return convertJSONToDocument(in, "json");
+  }
+
+  /**
+   * Convert a JSON string to an XML document.
+   *
+   * @param in
+   *   JSON to convert.
+   * @param enclosing_tag
+   *   The tag to enclose the results in.
+   *
+   * @return
    *   XML Document.
    */
-  public static Document convertJSONToDocument(String in) 
+  public static Document convertJSONToDocument(String in, String enclosing_tag) 
   throws ParserConfigurationException, SAXException, IOException
   {
-    StringReader xmlStringReader = new StringReader(convertJSONToXML(in));
+    StringReader xmlStringReader = new StringReader(convertJSONToXML(in, enclosing_tag));
 
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     DocumentBuilder builder = factory.newDocumentBuilder();
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
index 6e09ee4..436c870 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
@@ -11,22 +11,22 @@ public class FedoraUtilsTest extends TestCase {
 	 * Set that thing up.
 	 */
 	protected void setUp() throws Exception {
-		super.setUp();
+      super.setUp();
 	}
 	
 	/**
 	 * Tests building a URL.
 	 */
 	public void testURLBuild() throws MalformedURLException {
-		String pid = "test:pid";
-		String dsId = "TEST_DSID";
-		String fedoraBase = "http://localhost:8080/fedora";
-		String fedoraUser = "test_user";
-		String fedoraPass = "test_pass";
-		URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+      String pid = "test:pid";
+      String dsId = "TEST_DSID";
+      String fedoraBase = "http://localhost:8080/fedora";
+      String fedoraUser = "test_user";
+      String fedoraPass = "test_pass";
+      URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
 		
-		assertEquals(url.getPort(), 8080);
-		assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
+      assertEquals(url.getPort(), 8080);
+      assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
 	}
 
 }
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
index b0dd71c..d08b3e8 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
@@ -22,38 +22,39 @@ public class JSONToXMLTest extends TestCase {
    * Set up the thingy.
    */
   protected void setUp() throws Exception {
-    super.setUp();
+      super.setUp();
   }
 
   /**
    * Tests conversion with the default root element.
    */
   public void testDefaultRootElement() {
-    // Should be XML enclosed in a 'json' tag.
-    String dest = "<json><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></json>";
-    String transformed = JSONToXML.convertJSONToXML(testJson);
+      // Should be XML enclosed in a 'json' tag.
+      String dest = "<json><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></json>";
+      String transformed = JSONToXML.convertJSONToXML(testJson);
 
-    assertEquals(dest, transformed);
+      assertEquals(dest, transformed);
   }
 
   /**
    * Tests conversion with a custom root element.
    */
   public void testCustomRootElement() {
-    // Should be XML enclosed in a 'custom' tag.
-    String dest = "<custom><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></custom>";
-    String transformed = JSONToXML.convertJSONToXML(testJson, "custom");
+      // Should be XML enclosed in a 'custom' tag.
+      String dest = "<custom><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></custom>";
+      String transformed = JSONToXML.convertJSONToXML(testJson, "custom");
 
-    assertEquals(dest, transformed);
+      assertEquals(dest, transformed);
   }
   
   /**
    * Tests conversion to a Document object.
    */
   public void testDocumentConversion() throws ParserConfigurationException, SAXException, IOException {
-	Document transformed = JSONToXML.convertJSONToDocument(testJson);
-	NodeList thingList = transformed.getElementsByTagName("thing_1");
+	    Document transformed = JSONToXML.convertJSONToDocument(testJson);
+	    NodeList thingList = transformed.getElementsByTagName("thing_1");
 	
-	assertEquals(thingList.getLength(), 1);
+      // We should have a thing_1 node in our loaded document.
+	    assertEquals(thingList.getLength(), 1);
   }
 }

From e85d4d247afd03ed32ed76547fea75dca0b5484b Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Tue, 11 Apr 2017 02:09:39 -0300
Subject: [PATCH 07/12] tyop

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2938774..598fcb8 100644
--- a/README.md
+++ b/README.md
@@ -134,7 +134,7 @@ The resultant document can be interpreted as a Node-Set by Xalan, for example:
 Variable|Description
 --------|-----------
 `$input`|The input JSON string.
-`$enclosing_tag|(Optional) The top-level element to wrap resultant XML in, to prevent invalid XML from being written. If not provided, defaults to an element called 'json'.
+`$enclosing_tag`|(Optional) The top-level element to wrap resultant XML in, to prevent invalid XML from being written. If not provided, defaults to an element called 'json'.
 
 ## Troubleshooting/Issues
 

From c497936d81354a6784dd02f2238a97767d8eaa9b Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Tue, 11 Apr 2017 10:52:13 -0300
Subject: [PATCH 08/12] travis failing'

---
 .../java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java | 2 +-
 .../java/ca/discoverygarden/gsearch_extensions/JSONToXML.java   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
index fb80d23..dff2eaa 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -105,7 +105,7 @@ public static InputStream getDatastreamDisseminationInputStream(String pid, Stri
    * @return String
    *   The text of the given datastream.
    */
-  public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws FileNotFoundException {
+  public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
 	  try {
 	      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
         InputStream dsStream = url.openStream();
diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
index ac9f82b..5fe9bad 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/JSONToXML.java
@@ -53,7 +53,7 @@ public static String convertJSONToXML(String in, String enclosing_tag) {
    * @return
    *   XML document.
    */
-  public static Document convertJSONToDocument(String in, String enclosing_tag) 
+  public static Document convertJSONToDocument(String in) 
   throws ParserConfigurationException, SAXException, IOException
   {
     return convertJSONToDocument(in, "json");

From 4fd5ab8b79ac439f9bdb5d1fd09f6ed3b44bb33f Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Tue, 11 Apr 2017 12:07:42 -0300
Subject: [PATCH 09/12] accidentally a thing

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 598fcb8..dd4fcb2 100644
--- a/README.md
+++ b/README.md
@@ -75,6 +75,7 @@ Escapes a string for inclusion in XML, for example, in cases where the contents
 The list of characters being replaced are based off of the Apache Commons lang3 library's [escapeXML10](https://commons.apache.org/proper/commons-lang/javadocs/api-3.5/org/apache/commons/lang3/StringEscapeUtils.html#escapeXml10-java.lang.String-) list of replaced characters.
 
 Variable|Description
+--------|-----------
 `$input`|The string to sanitize.
 `$replacement`|(Optional) The string to use when replacing invalid characters; otherwise, invalid characters will be replaced with Unicode U+FFFD (the Unicode replacement character).
 

From 2b7da068072a07739e239fdd0aacbbfe37d28450 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Tue, 11 Apr 2017 16:33:08 -0300
Subject: [PATCH 10/12] eclipse how could u

---
 .../gsearch_extensions/FedoraUtils.java       | 54 +++++++++----------
 .../gsearch_extensions/FedoraUtilsTest.java   | 42 +++++++--------
 .../gsearch_extensions/JSONToXMLTest.java     | 30 +++++------
 3 files changed, 63 insertions(+), 63 deletions(-)

diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
index dff2eaa..ed05778 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -70,21 +70,21 @@ public class FedoraUtils {
    *   An InputStream at the constructed dissemination point.
    */
   public static InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
-	  URL url;
-	  // Attempt to generate the URL from input.
-	  try {
-        url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
-	      return url.openStream();
-	  }
+    URL url;
+    // Attempt to generate the URL from input.
+    try {
+      url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+      return url.openStream();
+    }
     // On exception, log and return a stream with no content so the caller
     // doesn't get messed up.
-	  catch (MalformedURLException e) {
-		    logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
-	  }
-	  catch (IOException e) {
-		    logger.warn(String.format("Failed to open stream: %s", e.getMessage()));
-	  }
-	  return new ByteArrayInputStream("".getBytes());
+    catch (MalformedURLException e) {
+      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
+    }
+    catch (IOException e) {
+      logger.warn(String.format("Failed to open stream: %s", e.getMessage()));
+    }
+    return new ByteArrayInputStream("".getBytes());
   }
 
   /**
@@ -106,23 +106,23 @@ public static InputStream getDatastreamDisseminationInputStream(String pid, Stri
    *   The text of the given datastream.
    */
   public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
-	  try {
-	      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
-        InputStream dsStream = url.openStream();
-        Scanner scanner = new Scanner(dsStream);
-        // If no content, return an empty string.
-        String dsString = scanner.hasNext() ? scanner.next() : "";
-        logger.debug(String.format("getRawDatastreamDissemination (pid: %s, DSID: %s): %s", pid, dsId, dsString));
-        return dsString;
-	  } 
+    try {
+      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+      InputStream dsStream = url.openStream();
+      Scanner scanner = new Scanner(dsStream);
+      // If no content, return an empty string.
+      String dsString = scanner.hasNext() ? scanner.next() : "";
+      logger.debug(String.format("getRawDatastreamDissemination (pid: %s, DSID: %s): %s", pid, dsId, dsString));
+      return dsString;
+    } 
     // On exception, log and return an empty string so the caller doesn't get
     // messed up.
     catch (MalformedURLException e) {
-	      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
-	  }
+      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
+    }
     catch (IOException e) {
-		    logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
-	  }
+      logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
+    }
     return "";
   }
 
@@ -140,6 +140,6 @@ protected static final URL getDatastreamDisseminationURL(String pid, String dsId
     // Build the URL.
     String url = String.format("%s/objects/%s/datastreams/%s/content", fedoraBase, pid, dsId);
     logger.debug(String.format("Building URL for %s", url));
-	  return new URL(url);
+    return new URL(url);
   }
 }
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
index 436c870..39f2cde 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
@@ -7,26 +7,26 @@
 
 public class FedoraUtilsTest extends TestCase {
 
-	/**
-	 * Set that thing up.
-	 */
-	protected void setUp() throws Exception {
-      super.setUp();
-	}
-	
-	/**
-	 * Tests building a URL.
-	 */
-	public void testURLBuild() throws MalformedURLException {
-      String pid = "test:pid";
-      String dsId = "TEST_DSID";
-      String fedoraBase = "http://localhost:8080/fedora";
-      String fedoraUser = "test_user";
-      String fedoraPass = "test_pass";
-      URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
-		
-      assertEquals(url.getPort(), 8080);
-      assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
-	}
+  /**
+   * Set that thing up.
+   */
+  protected void setUp() throws Exception {
+    super.setUp();
+  }
+
+  /**
+   * Tests building a URL.
+   */
+  public void testURLBuild() throws MalformedURLException {
+    String pid = "test:pid";
+    String dsId = "TEST_DSID";
+    String fedoraBase = "http://localhost:8080/fedora";
+    String fedoraUser = "test_user";
+    String fedoraPass = "test_pass";
+    URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+
+    assertEquals(url.getPort(), 8080);
+    assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
+  }
 
 }
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
index d08b3e8..ca4b677 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
@@ -22,39 +22,39 @@ public class JSONToXMLTest extends TestCase {
    * Set up the thingy.
    */
   protected void setUp() throws Exception {
-      super.setUp();
+    super.setUp();
   }
 
   /**
    * Tests conversion with the default root element.
    */
   public void testDefaultRootElement() {
-      // Should be XML enclosed in a 'json' tag.
-      String dest = "<json><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></json>";
-      String transformed = JSONToXML.convertJSONToXML(testJson);
+    // Should be XML enclosed in a 'json' tag.
+    String dest = "<json><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></json>";
+    String transformed = JSONToXML.convertJSONToXML(testJson);
 
-      assertEquals(dest, transformed);
+    assertEquals(dest, transformed);
   }
 
   /**
    * Tests conversion with a custom root element.
    */
   public void testCustomRootElement() {
-      // Should be XML enclosed in a 'custom' tag.
-      String dest = "<custom><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></custom>";
-      String transformed = JSONToXML.convertJSONToXML(testJson, "custom");
+    // Should be XML enclosed in a 'custom' tag.
+    String dest = "<custom><thing_1><subthing_1.2>value_1.2</subthing_1.2><subthing_1.1>value_1.1</subthing_1.1></thing_1><thing_2>value_2</thing_2></custom>";
+    String transformed = JSONToXML.convertJSONToXML(testJson, "custom");
 
-      assertEquals(dest, transformed);
+    assertEquals(dest, transformed);
   }
-  
+
   /**
    * Tests conversion to a Document object.
    */
   public void testDocumentConversion() throws ParserConfigurationException, SAXException, IOException {
-	    Document transformed = JSONToXML.convertJSONToDocument(testJson);
-	    NodeList thingList = transformed.getElementsByTagName("thing_1");
-	
-      // We should have a thing_1 node in our loaded document.
-	    assertEquals(thingList.getLength(), 1);
+    Document transformed = JSONToXML.convertJSONToDocument(testJson);
+    NodeList thingList = transformed.getElementsByTagName("thing_1");
+
+    // We should have a thing_1 node in our loaded document.
+    assertEquals(thingList.getLength(), 1);
   }
 }

From a465083d0e14624a8325d41e24137fbce22ee630 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Wed, 12 Apr 2017 14:35:36 -0300
Subject: [PATCH 11/12] fixies

---
 .../gsearch_extensions/FedoraUtils.java       | 98 +++++++++----------
 .../gsearch_extensions/FedoraUtilsTest.java   | 11 +--
 .../gsearch_extensions/JSONToXMLTest.java     |  7 --
 3 files changed, 46 insertions(+), 70 deletions(-)

diff --git a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
index ed05778..95ee178 100644
--- a/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
+++ b/src/main/java/ca/discoverygarden/gsearch_extensions/FedoraUtils.java
@@ -12,44 +12,44 @@
 import java.util.Scanner;
 
 /**
- * Authenticator for connecting to Fedora.
+ * Utilities for interfacing with Fedora in ways that GSearch can't.
  */
-class FedoraAuthenticator extends Authenticator {
+public class FedoraUtils {
 
-  protected String fedoraUser;
-  protected String fedoraPass;
+  protected static final Logger logger = Logger.getLogger(FedoraUtils.class);
 
   /**
-   * Set the username and password for this authenticator.
-   *
-   * @param username
-   *   The username to set.
-   * @param password
-   *   The password to set.
+   * Authenticator for connecting to Fedora.
    */
-  public void setCredentials(String username, String password) {
-    fedoraUser = username;
-    fedoraPass = password;
-  }
+  static class FedoraAuthenticator extends Authenticator {
 
-  /**
-   * Overloaded password authenticator.
-   *
-   * @return PasswordAuthentication
-   *   Authentication for this authenticator.
-   */
-  protected PasswordAuthentication getPasswordAuthentication() {
-    return new PasswordAuthentication(fedoraUser, fedoraPass.toCharArray());
-  }
+    protected String fedoraUser;
+    protected String fedoraPass;
 
-}
+    /**
+     * Constructor; sets the username and password for this authenticator.
+     *
+     * @param username
+     *   The username to set.
+     * @param password
+     *   The password to set.
+     */
+    FedoraAuthenticator(String username, String password) {
+      fedoraUser = username;
+      fedoraPass = password;
+    }
 
-/**
- * Utilities for interfacing with Fedora in ways that GSearch can't.
- */
-public class FedoraUtils {
+    /**
+     * Overloaded password authenticator.
+     *
+     * @return PasswordAuthentication
+     *   Authentication for this authenticator.
+     */
+    protected PasswordAuthentication getPasswordAuthentication() {
+      return new PasswordAuthentication(fedoraUser, fedoraPass.toCharArray());
+    }
 
-  protected static final Logger logger = Logger.getLogger(FedoraUtils.class);
+  }
 
   /**
    * Gets an InputStream for a datastream.
@@ -70,10 +70,12 @@ public class FedoraUtils {
    *   An InputStream at the constructed dissemination point.
    */
   public static InputStream getDatastreamDisseminationInputStream(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
-    URL url;
+    // Set the authenticator.
+    FedoraAuthenticator auth = new FedoraAuthenticator(fedoraUser, fedoraPass);
+    Authenticator.setDefault(auth);
     // Attempt to generate the URL from input.
     try {
-      url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase);
       return url.openStream();
     }
     // On exception, log and return a stream with no content so the caller
@@ -106,24 +108,16 @@ public static InputStream getDatastreamDisseminationInputStream(String pid, Stri
    *   The text of the given datastream.
    */
   public static String getRawDatastreamDissemination(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) {
-    try {
-      URL url = getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
-      InputStream dsStream = url.openStream();
-      Scanner scanner = new Scanner(dsStream);
-      // If no content, return an empty string.
-      String dsString = scanner.hasNext() ? scanner.next() : "";
+    InputStream dsStream = getDatastreamDisseminationInputStream(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+    // Scan the InputStream, delimited by the start of string marker, so the
+    // whole string gets scanned.
+    Scanner scanner = new Scanner(dsStream).useDelimiter("\\A");
+    // If no content, return an empty string.
+    String dsString = scanner.hasNext() ? scanner.next() : "";
+    if (logger.isDebugEnabled()) {
       logger.debug(String.format("getRawDatastreamDissemination (pid: %s, DSID: %s): %s", pid, dsId, dsString));
-      return dsString;
-    } 
-    // On exception, log and return an empty string so the caller doesn't get
-    // messed up.
-    catch (MalformedURLException e) {
-      logger.warn(String.format("Attempt to generate URL for datastream dissemination failed: %s", e.getMessage()));
-    }
-    catch (IOException e) {
-      logger.warn(String.format("Failed to open connection to datastream dissemination: %s", e.getMessage()));
     }
-    return "";
+    return dsString;
   }
 
   /**
@@ -132,14 +126,12 @@ public static String getRawDatastreamDissemination(String pid, String dsId, Stri
    * @return URL
    *   A URL object using the given parameters.
    */
-  protected static final URL getDatastreamDisseminationURL(String pid, String dsId, String fedoraBase, String fedoraUser, String fedoraPass) throws MalformedURLException {
-    // Set the authenticator.
-    FedoraAuthenticator auth = new FedoraAuthenticator();
-    auth.setCredentials(fedoraUser, fedoraPass);
-    Authenticator.setDefault(auth);
+  protected static final URL getDatastreamDisseminationURL(String pid, String dsId, String fedoraBase) throws MalformedURLException {
     // Build the URL.
     String url = String.format("%s/objects/%s/datastreams/%s/content", fedoraBase, pid, dsId);
-    logger.debug(String.format("Building URL for %s", url));
+    if (logger.isDebugEnabled()) {
+      logger.debug(String.format("Building URL for %s", url));
+    }
     return new URL(url);
   }
 }
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
index 39f2cde..f8aa4ea 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/FedoraUtilsTest.java
@@ -7,13 +7,6 @@
 
 public class FedoraUtilsTest extends TestCase {
 
-  /**
-   * Set that thing up.
-   */
-  protected void setUp() throws Exception {
-    super.setUp();
-  }
-
   /**
    * Tests building a URL.
    */
@@ -21,9 +14,7 @@ public void testURLBuild() throws MalformedURLException {
     String pid = "test:pid";
     String dsId = "TEST_DSID";
     String fedoraBase = "http://localhost:8080/fedora";
-    String fedoraUser = "test_user";
-    String fedoraPass = "test_pass";
-    URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase, fedoraUser, fedoraPass);
+    URL url = FedoraUtils.getDatastreamDisseminationURL(pid, dsId, fedoraBase);
 
     assertEquals(url.getPort(), 8080);
     assertEquals(url.getPath(), "/fedora/objects/test:pid/datastreams/TEST_DSID/content");
diff --git a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
index ca4b677..8d33e20 100644
--- a/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
+++ b/src/test/java/ca/discoverygarden/gsearch_extensions/JSONToXMLTest.java
@@ -18,13 +18,6 @@ public class JSONToXMLTest extends TestCase {
   // Our test JSON we use twice.
   protected static final String testJson = "{\"thing_1\":{\"subthing_1.1\":\"value_1.1\",\"subthing_1.2\":\"value_1.2\"},\"thing_2\":\"value_2\"}";
 
-  /**
-   * Set up the thingy.
-   */
-  protected void setUp() throws Exception {
-    super.setUp();
-  }
-
   /**
    * Tests conversion with the default root element.
    */

From a60e81dc4bdfa9f80912e8d180c28965b9005be0 Mon Sep 17 00:00:00 2001
From: qadan <daitken@discoverygarden.ca>
Date: Wed, 12 Apr 2017 17:34:42 -0300
Subject: [PATCH 12/12] rely on the jar in gsearch

---
 pom.xml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/pom.xml b/pom.xml
index 9e4e64e..6d79e48 100644
--- a/pom.xml
+++ b/pom.xml
@@ -41,14 +41,10 @@
       <version>20160810</version>
     </dependency>
     <dependency>
-        <groupId>javax.xml.parsers</groupId>
-        <artifactId>jaxp-api</artifactId>
-        <version>1.4.5</version>
-    </dependency>
-    <dependency>
-        <groupId>org.w3c</groupId>
-        <artifactId>dom</artifactId>
-        <version>2.3.0-jaxb-1.0.6</version>
+        <groupId>dom4j</groupId>
+        <artifactId>dom4j</artifactId>
+        <version>1.6.1</version>
+        <scope>provided</scope>
     </dependency>
   </dependencies>