XNAT-4209 Added four pages for the different ways of uploading data, in...

XNAT-4209 Added four pages for the different ways of uploading data, in addition to a main page that lists all of them. Also listed the options in a submenu under Upload->Images.

src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java

+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+
+public class CompressedUploaderPage extends SecureScreen {
+
+	@Override
+	protected void doBuildTemplate(RunData data, Context context) throws Exception {
+		final SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMdd_hhmmss");
+		context.put("uploadID", formatter.format(Calendar.getInstance().getTime()));
+		final ArcArchivespecification arc = ArcSpecManager.GetInstance();
+		context.put("arc", arc);
+	}
+
+}

src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java

+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+
+public class DICOMSCPPage extends SecureScreen {
+
+	@Override
+	protected void doBuildTemplate(RunData data, Context context) throws Exception {
+		final SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMdd_hhmmss");
+		context.put("uploadID", formatter.format(Calendar.getInstance().getTime()));
+		final ArcArchivespecification arc = ArcSpecManager.GetInstance();
+		context.put("arc", arc);
+	}
+
+}

src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java

+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+
+public class UploadAssistantPage extends SecureScreen {
+
+	@Override
+	protected void doBuildTemplate(RunData data, Context context) throws Exception {
+		// doesn't currently need any context, just needed to subclass SecureScreen
+	}
+
+}

src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java

+/*
+ * org.nrg.xnat.turbine.modules.screens.ReportIssue
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2014, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ *
+ * Last modified 7/10/13 9:04 PM
+ */
+package org.nrg.xnat.turbine.modules.screens;
+
+import org.apache.turbine.util.RunData;
+import org.apache.velocity.context.Context;
+import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.turbine.modules.screens.SecureScreen;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import org.nrg.xnat.utils.AppletConfig;
+import org.nrg.xnat.utils.XnatHttpUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.nrg.framework.utilities.Reflection;
+import org.nrg.xdat.om.XnatPvisitdata;
+import org.nrg.xdat.turbine.utils.TurbineUtils;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.List;
+
+public class UploadOptions extends SecureScreen {
+
+	@Override
+	protected void doBuildTemplate(RunData data, Context context) throws Exception {
+		final SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMdd_hhmmss");
+		context.put("uploadID", formatter.format(Calendar.getInstance().getTime()));
+		final ArcArchivespecification arc = ArcSpecManager.GetInstance();
+		context.put("arc", arc);
+	}
+
+}

src/main/webapp/WEB-INF/tags/page/xnat.tag

@@ -285,7 +285,16 @@ ${bodyTop}
                     <ul>
                         <!-- Sequence: 10 -->
                         <!-- Upload/Default -->
-                        <li><a href="${SITE_ROOT}/app/template/LaunchUploadApplet.vm">Images</a></li>
+                        <li><a href="${SITE_ROOT}/app/template/UploadOptions.vm">Images</a>
+                            <ul>
+                                <!-- Sequence: 10 -->
+                                <!-- Images -->
+                                <li><a href="${SITE_ROOT}/app/template/LaunchUploadApplet.vm">Upload Applet</a></li>
+                                <li><a href="${SITE_ROOT}/app/template/UploadAssistantPage.vm">Upload Assistant</a></li>
+                                <li><a href="${SITE_ROOT}/app/template/CompressedUploaderPage.vm">Compressed Uploader</a></li>
+                                <li><a href="${SITE_ROOT}/app/template/DICOMSCPPage.vm">DICOM SCP</a></li>
+                            </ul>
+                        </li>
                         <li><a href="${SITE_ROOT}/app/template/XMLUpload.vm">XML</a></li>
                         <li><a href="${SITE_ROOT}/app/template/XDATScreen_uploadCSV.vm">Spreadsheet</a></li>
                         <li><a href="${SITE_ROOT}/app/template/XDATScreen_prearchives.vm">Go to prearchive</a></li>
@@ -507,7 +516,7 @@ ${bodyTop}
                                 li$.find('ul.subnav').each(function(){
                                     var sub$ = $(this);
                                     var offsetL = sub$.closest('ul').outerWidth();
-                                    sub$.css({ 'left': offsetL + -25 })
+                                    sub$.css({ 'left': offsetL + -37 })
                                 });
                                 if (body$.hasClass('applet')) {
                                     coverApplet(li$.find('> ul'));

src/main/webapp/WEB-INF/tags/spawner/layout.tag

@@ -326,7 +326,16 @@
                 <ul>
                     <!-- Sequence: 10 -->
                     <!-- Upload/Default -->
-                    <li><a href="/app/template/LaunchUploadApplet.vm">Images</a></li>
+                    <li><a href="/app/template/UploadOptions.vm">Images</a>
+                        <ul>
+                            <!-- Sequence: 10 -->
+                            <!-- Images -->
+                            <li><a href="/app/template/LaunchUploadApplet.vm">Upload Applet</a></li>
+                            <li><a href="/app/template/UploadAssistantPage.vm">Upload Assistant</a></li>
+                            <li><a href="/app/template/CompressedUploaderPage.vm">Compressed Uploader</a></li>
+                            <li><a href="/app/template/DICOMSCPPage.vm">DICOM SCP</a></li>
+                        </ul>
+                    </li>
                     <li><a href="/app/template/XMLUpload.vm">XML</a></li>
                     <li><a href="/app/template/XDATScreen_uploadCSV.vm">Spreadsheet</a></li>
                     <li><a href="/app/template/XDATScreen_prearchives.vm">Go to prearchive</a></li>
@@ -535,7 +544,7 @@
                         li$.find('ul.subnav').each(function () {
                             var sub$ = $(this);
                             var offsetL = sub$.closest('ul').outerWidth();
-                            sub$.css({'left': offsetL + -25})
+                            sub$.css({'left': offsetL + -37})
                         });
                         if (body$.hasClass('applet')) {
                             coverApplet(li$.find('> ul'));

src/main/webapp/xnat-templates/navigations/DefaultTop.vm

@@ -200,7 +200,7 @@
                     li$.find('ul.subnav').each(function(){
                         var sub$ = $(this);
                         var offsetL = sub$.closest('ul').outerWidth();
-                        sub$.css({ 'left': offsetL + -25 })
+                        sub$.css({ 'left': offsetL + -37 })
                     });
                     if (body$.hasClass('applet')) {
                         coverApplet(li$.find('> ul'));

src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm

+<table>
+<tr>
+    <td>
+        <h4>DICOM C-STORE Service Class User</h4>
+    </td>
+</tr>
+<tr>
+    <td valign="top" align="left">
+        <div style="width:500px">Any DICOM C-STORE SCU, including scanner consoles or DICOM applications like
+            <a href="http://www.osirix-viewer.com">OsiriX</a> or <a href="http://nrg.wustl.edu/software/dicom-browser">DicomBrowser</a>,
+            can send files directly to this server.
+        </div>
+</tr>
+<tr id="option4">
+    <td>
+        <br><b>DICOM C-STORE receiver (SCP) Specifications</b>
+        <ul>
+            <li>Host Name: $!arc.getDcm_dcmHost()</li>
+            <li>Port: $!arc.getDcm_dcmPort()</li>
+            <li>AE Title(s): $!arc.getDcm_dcmAe()</li>
+        </ul>
+    </td>
+</tr>
+    </table>
\ No newline at end of file

src/main/webapp/xnat-templates/screens/LaunchUploadApplet.vm

@@ -125,8 +125,6 @@
  </div> <!-- end of hideIfProtocol -->
 <div id="forProtocolContent" style="display:none"></div>
 
-    <p style="width:500px;margin:20px 0;">Looking for other ways to upload images? <a href="$link.setPage("AlternateImageUpload.vm")">Click here.</a></p>
-
 </form>
 
 <script type="text/javascript">

src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm

+<table>
+        <tr>
+            <td>
+                <h4>Download Upload Assistant application</h4>
+            </td>
+        </tr>
+        <tr>
+            <td valign="top" align="left">
+                <div style="width:500px">You can download the XNAT Upload Assistant application and use it to upload your session. If the Upload Applet does not work for you, you might want to try this. <a href="https://bitbucket.org/xnatdev/upload-assistant/downloads">Click here</a> to find the appropriate version of the XNAT Upload Assistant application for your operating system.
+                </div>
+        </tr>
+</table>
\ No newline at end of file

src/main/webapp/xnat-templates/screens/topBar/Upload/Default.vm

 <!-- Sequence: 10 -->
 <!-- Upload/Default -->
-    <li><a href="$link.setPage("LaunchUploadApplet.vm")">Images</a></li>
+    <li><a href="$link.setPage("UploadOptions.vm")">Images</a>
+        <ul>
+            <!-- Sequence: 10 -->
+            <!-- Images -->
+            <li><a href="$link.setPage("LaunchUploadApplet.vm")">Upload Applet</a></li>
+            <li><a href="$link.setPage("UploadAssistantPage.vm")">Upload Assistant</a></li>
+            <li><a href="$link.setPage("CompressedUploaderPage.vm")">Compressed Uploader</a></li>
+            <li><a href="$link.setPage("DICOMSCPPage.vm")">DICOM SCP</a></li>
+        </ul>
+    </li>
     <li><a href="$link.setPage("XMLUpload.vm")">XML</a></li>
     <li><a href="$link.setPage("XDATScreen_uploadCSV.vm")">Spreadsheet</a></li>
     <li><a href="$link.setPage("XDATScreen_prearchives.vm")">Go to prearchive</a></li>