From 8232d906513bcdd6023d6cbf0f30757d9aa1cf10 Mon Sep 17 00:00:00 2001
From: Mike McKay <mfmckay@wustl.edu>
Date: Wed, 18 May 2016 00:34:03 -0500
Subject: [PATCH] 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.
---
.../screens/CompressedUploaderPage.java | 32 +
.../turbine/modules/screens/DICOMSCPPage.java | 32 +
.../modules/screens/UploadAssistantPage.java | 24 +
.../modules/screens/UploadOptions.java | 41 ++
src/main/webapp/WEB-INF/tags/page/xnat.tag | 13 +-
.../webapp/WEB-INF/tags/spawner/layout.tag | 13 +-
.../xnat-templates/navigations/DefaultTop.vm | 2 +-
.../screens/CompressedUploaderPage.vm | 579 ++++++++++++++++
.../xnat-templates/screens/DICOMSCPPage.vm | 24 +
.../screens/LaunchUploadApplet.vm | 2 -
.../screens/UploadAssistantPage.vm | 12 +
.../xnat-templates/screens/UploadOptions.vm | 646 ++++++++++++++++++
.../screens/topBar/Upload/Default.vm | 11 +-
13 files changed, 1423 insertions(+), 8 deletions(-)
create mode 100644 src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java
create mode 100644 src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java
create mode 100644 src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java
create mode 100644 src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java
create mode 100644 src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm
create mode 100644 src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm
create mode 100644 src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm
create mode 100644 src/main/webapp/xnat-templates/screens/UploadOptions.vm
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java
new file mode 100644
index 00000000..ab7ac9fe
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/CompressedUploaderPage.java
@@ -0,0 +1,32 @@
+/*
+ * 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);
+ }
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java
new file mode 100644
index 00000000..29b4036e
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/DICOMSCPPage.java
@@ -0,0 +1,32 @@
+/*
+ * 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);
+ }
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java
new file mode 100644
index 00000000..25dbf7a1
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadAssistantPage.java
@@ -0,0 +1,24 @@
+/*
+ * 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
+ }
+
+}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java
new file mode 100644
index 00000000..bf9f2a75
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/UploadOptions.java
@@ -0,0 +1,41 @@
+/*
+ * 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);
+ }
+
+}
diff --git a/src/main/webapp/WEB-INF/tags/page/xnat.tag b/src/main/webapp/WEB-INF/tags/page/xnat.tag
index ea3d6e19..2fd10120 100644
--- a/src/main/webapp/WEB-INF/tags/page/xnat.tag
+++ b/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'));
diff --git a/src/main/webapp/WEB-INF/tags/spawner/layout.tag b/src/main/webapp/WEB-INF/tags/spawner/layout.tag
index 9680c90c..b7875977 100644
--- a/src/main/webapp/WEB-INF/tags/spawner/layout.tag
+++ b/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'));
diff --git a/src/main/webapp/xnat-templates/navigations/DefaultTop.vm b/src/main/webapp/xnat-templates/navigations/DefaultTop.vm
index 4b7abb72..5b4c8152 100644
--- a/src/main/webapp/xnat-templates/navigations/DefaultTop.vm
+++ b/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'));
diff --git a/src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm b/src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm
new file mode 100644
index 00000000..cdb8ad38
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/CompressedUploaderPage.vm
@@ -0,0 +1,579 @@
+<script type="text/javascript">
+ function disableForm(theform) {
+ if (document.getElementById) {
+ document.getElementById('progressBar').style.display = 'block';
+ }
+ else if (document.all) {
+ document.all['progressBar'].style.display = 'block';
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = true;
+ }
+ return true;
+ }
+ else {
+ return true;
+ }
+ }
+
+ function enableForm() {
+ var theform;
+ if (document.getElementById) {
+ theform = document.getElementById('uploadFORM');
+ }
+ else if (document.all) {
+ theform = document.all['uploadFORM'];
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = false;
+ }
+ return true;
+ } else {
+ return true;
+ }
+ }
+</script>
+<script type="text/javascript">
+ var i;
+ var req;
+
+ var uploadCount = 0;
+ var extractCount = 0;
+ var progressBar;
+ var progressPercent;
+ var uploadID = "$uploadID";
+ var started = 0;
+ var extractTimeOut = 300;
+
+ function setUploadProgress(i) {
+ if (i == 0) {
+ document.getElementById("uploadPercent").innerHTML = "";
+ document.getElementById("uploadBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("uploadPercent").innerHTML = parseInt(i) + "%";
+ }
+ else {
+ document.getElementById('preparing').innerHTML = "";
+ }
+ document.getElementById("uploadBar").style.width = pixels + "px";
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ }
+ }
+ }
+
+ function setExtractSummary(jsonobj) {
+ var messages = "";
+ try {
+ var respPos = jsonobj.msgs[0].length - 1;
+ for (i = 0; i <= respPos; i++) {
+ var level = jsonobj.msgs[0][i].status;
+ var message = jsonobj.msgs[0][i].msg;
+ if (level == "COMPLETED") {
+ message = "<tr bgcolor='#CCFFCC'><td>" + message;
+ } else if (level == "PROCESSING") {
+ message = "<tr bgcolor='#CCFFFF'><td>" + message;
+ } else if (level == "WARNING") {
+ message = "<tr bgcolor='#FFCCC'><td>" + message;
+ } else if (level == "FAILED") {
+ message = "<tr bgcolor='#FF99CC'><td>" + message;
+ } else {
+ message = "<tr bgcolor='#CCCCCC'><td>" + message;
+ }
+ messages = messages + message + "</td></tr>";
+ }
+ } catch (e) {
+ }
+ document.getElementById("extractSummary").innerHTML =
+ "<table width='100%' cellpadding='2' cellspacing='0'><tr><th>Extraction / Review summary:</th></tr>" +
+ messages +
+ "</table>";
+ }
+
+ function toggleExtractSummary() {
+ if (document.getElementById("extractSummary").style.display == "none") {
+ document.getElementById("extractSummaryTable").border = "1";
+ document.getElementById("extractSummary").style.display = "block";
+ } else {
+ document.getElementById("extractSummaryTable").border = "0";
+ document.getElementById("extractSummary").style.display = "none";
+ }
+ }
+
+ function setExtractProgress(i) {
+ if (i == 0) {
+ document.getElementById("extractPercent").innerHTML = "";
+ document.getElementById("extractBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("extractPercent").innerHTML = parseInt(i) + "%";
+ }
+ document.getElementById("extractBar").style.width = pixels + "px";
+ }
+ }
+ }
+
+ function evaluateDestination(ele) {
+ if (ele.value == '2') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'true';
+ } else if (ele.value == '1') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'false';
+ } else if (ele.value == '0') {
+ document.getElementById("auto-archive").value = 'false';
+ document.getElementById("quarantine").value = 'false';
+ }
+ }
+
+ var checkProgressFinal = 0;
+
+ function prog(theform) {
+ var imageArchive = document.getElementById("image_archive");
+ if (!imageArchive.value) {
+ xModalMessage('Upload Action', 'Please select an archive to upload.');
+ return false;
+ }
+ if (!(imageArchive.value.endsWith(".gz") || imageArchive.value.endsWith(".tgz") || imageArchive.value.endsWith(".zip"))) {
+ xModalMessage('Upload Action', 'Please select a tar or zip archive to upload.');
+ return false;
+ }
+ if (document.getElementById("project").selectedIndex == 0) {
+ xModalMessage('Upload Action', 'Please select a $displayManager.getSingularDisplayNameForProject().toLowerCase().');
+ return false;
+ }
+ disableForm(theform);
+ document.getElementById("iframe").src = "";
+ started = 0;
+ checkProgressFinal = 0;
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+
+ document.getElementById('preparing').style.display = 'block';
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ setUploadProgress(0);
+ setExtractProgress(0);
+ setExtractSummary("");
+ resetProgress();
+ checkProgress();
+
+ return true;
+ }
+
+ function callback() {
+ if (req.readyState == 4) {
+ if (req.status == 200) {
+ started = 1;
+ // handle response
+ var respDat = YAHOO.lang.JSON.parse(req.responseText);
+ var respPos = respDat.msgs[0].length - 1;
+ var uploadI = 0;
+ var extractI = 0;
+ var statusCount = 0;
+ if (respDat.msgs[0].length > 0) {
+ if (respDat.msgs[0].length > 0) {
+ var level = respDat.msgs[0][respPos].status;
+ var message = respDat.msgs[0][respPos].msg;
+ }
+ }
+
+ if (req.responseText.indexOf("file uploaded") >= 0) {
+ uploadI = 100;
+ }
+ if (req.responseText.indexOf("Successfully uploaded") >= 0) {
+ extractI = 100;
+ }
+ if (req.responseText.indexOf("archiving operation complete") >= 0) {
+ extractI = 100;
+ }
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+
+ //alert("Upload(" + uploadI + "); Extract(" + extractI + ");\r\n" + statusText + "\r\n" + req.responseText);
+
+ if (uploadI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Upload Failed. Please retry at a later time or contact technical support.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (extractI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Extraction/Review Failed. Please verify the integrity of the zipped file and the contained image files.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (uploadI != 100) {
+ //upload complete
+
+ if (uploadCount != 98) {
+ uploadCount = uploadCount + 1;
+ }
+
+ if (uploadCount > 40) {
+ extractTimeOut = 600;
+ }
+ if (uploadCount > 50) {
+ extractTimeOut = 800;
+ }
+ if (uploadCount > 60) {
+ extractTimeOut = 1000;
+ }
+ if (uploadCount > 70) {
+ extractTimeOut = 2000;
+ }
+ if (uploadCount > 80) {
+ extractTimeOut = 3000;
+ }
+ if (uploadCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (uploadCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setUploadProgress(uploadCount);
+ setExtractProgress(0);
+
+ setTimeout("checkProgress();", extractTimeOut);
+ } else if (extractI == 100) {
+ //extract complete
+ setUploadProgress(100);
+ setExtractProgress(100);
+
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ if (checkProgressFinal == 0) {
+ checkProgressFinal = 1;
+ //check progress one final time to capture final step summary
+ setTimeout("checkProgress();", 200);
+ }
+ } else {
+ //extract in progress
+ setUploadProgress(100);
+
+ if (extractCount != 98) {
+ extractCount = extractCount + 1;
+ }
+ if (extractCount < 10) {
+ extractTimeOut = 500;
+ }
+ if (extractCount > 10) {
+ extractTimeOut = 100;
+ }
+ if (extractCount > 20) {
+ extractTimeOut = 1500;
+ }
+ if (extractCount > 30) {
+ extractTimeOut = 2000;
+ }
+ if (extractCount > 50) {
+ extractTimeOut = 2800;
+ }
+ if (extractCount > 60) {
+ extractTimeOut = 3300;
+ }
+ if (extractCount > 70) {
+ extractTimeOut = 4000;
+ }
+ if (extractCount > 80) {
+ extractTimeOut = 5000;
+ }
+ if (extractCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (extractCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setExtractProgress(extractCount);
+
+ if (statusCount > 0) {
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ }
+ setTimeout("checkProgress();", extractTimeOut);
+ }
+ }
+ }
+ }
+
+
+ function setCurrentStep(message) {
+ if (message != null && message != undefined) {
+ document.getElementById("current_step").innerHTML = "<A href='' ONCLICK='toggleExtractSummary();return false;'>" + message + "...</A>";
+ }
+ }
+
+ function resetProgress() {
+ var url = "$content.getURI("servlet/AjaxServlet")?remote-class=org.nrg.xnat.ajax.UploadProgress";
+ url = url + "&remote-method=start";
+ url = url + "&ID=" + uploadID;
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.send(null);
+ }
+
+ function checkProgress() {
+ //var url = "$content.getURI("/REST/status/$uploadID")?format=json";
+ var url = "$content.getURI("/REST/status/$uploadID")?format=json&stamp=" + (new Date()).getTime();
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.onreadystatechange = callback;
+ req.send(null);
+ }
+ function makeTheFormGo() {
+ var form = document.getElementById("uploadFORM");
+ prog(form);
+ form.submit();
+ }
+</script>
+
+<table border="0" cellpadding="5" cellspacing="0">
+ <tr>
+ <td>
+ <h4>
+ Compressed upload</h4></td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">Raw image files can be zipped (.zip or .tar.gz) and uploaded using the form. This
+ tool currently supports DICOM and ECAT files. Selecting 'Prearchive' will place your images into a
+ temporary holding space. You will then have the ability to review the details and match the data to the
+ proper $displayManager.getSingularDisplayNameForSubject().toLowerCase() & $displayManager.getSingularDisplayNameForImageSession().toLowerCase() ID. If you are confident the data will be mapped properly, you can directly
+ 'Archive' the files and specify whether the resulting $displayManager.getSingularDisplayNameForImageSession().toLowerCase() should go into a quarantine state.
+ </div>
+ <div class="alert" style="margin:15px 0;max-width:696px;min-width:400px;">
+ The compressed uploader does not yet support splitting PET/MR sessions based on the site-wide or
+ project-specific settings for handling PET/MR data. If you are uploading PET/MR data and need to have
+ the data split into separate PET and MR sessions or created as a PET session rather than a PET/MR
+ session, you should use either the <a href="$link.setPage("LaunchUploadApplet.vm")">upload applet</a> or the
+ DICOM C-STORE receiver as described below.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr id="option1">
+ <td>
+ <input type="hidden" name="popup" value="true"/>
+ <form id="uploadFORM" class="noHide" target="iframe" enctype="multipart/form-data" method="POST"
+ action="$content.getURI("/REST/services/import?http-session-listener=$uploadID&format=html&XNAT_CSRF=$!XNAT_CSRF")">
+ <input type="hidden" name="threshhold" value="51516279"/>
+
+ #if($session)
+ <input type="hidden" name="EXPT_LABEL" value="$!session.getLabel()"/>
+ <input type="hidden" name="SUBJECT_ID" value="$!session.getSubjectData().getLabel()"/>
+ #end
+
+ <table border=0 cellpadding="5" cellspacing="0">
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForProject()</th>
+ <td>
+ #if(!$session)
+ <select id="project" name="project" disabled=true></select>
+ #else
+ <input type="hidden" name="project" id="project"
+ value="$session.getProject()"/>$session.getProject()
+ #end
+ </td>
+ </tr>
+
+ #if($session)
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForImageSession()</th>
+ <td>$!session.getLabel()</td>
+ </tr>
+ #end
+ <tr>
+ <th align="left">Destination</th>
+ <td>
+ <label><input id="pc_0" type='radio' name='prearchive_code' value='0'
+ #if(!$session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Prearchive</label>
+ <label><input id="pc_2" type='radio' name='prearchive_code' value='1'
+ #if($session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Archive</label>
+ #if($session)
+ <input type="hidden" name="overwrite" value="append"/>
+ <input type="hidden" id="auto-archive" name='auto-archive' value='TRUE'/>
+ #else
+ <input type="hidden" id="auto-archive" name='auto-archive' value='FALSE'/>
+ #end
+ <input type="hidden" id="quarantine" name='quarantine' value='FALSE'/>
+ </td>
+ </tr>
+ <tr>
+ <th align="left">File</th>
+ <td><input type="file" id="image_archive" name="image_archive" size="60"
+ accept="application/zip, application/x-gzip, application/x-tgz"/></td>
+ </tr>
+ #auditBoxes("3" "" "Standard Upload" "Upload Images")
+ #hideFormJustification()
+ <tr>
+ <td> </td>
+ <td><input id="directButton" type="button" name="eventSubmit_doPerform" value="Begin Upload" onclick="makeTheFormGo();"/>
+ </td>
+ </tr>
+ </table>
+ </form>
+
+<span id="progressBar" style="position:relative; display:none;">
+<div id="ex" style="position:relative;width:468px;background:#eeeeee;border:3px double #000000;">
+ <table width="100%">
+ <tr>
+ <td colspan=2 align="left">
+ <div id="preparing">Loading File... </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="uploadLabel">Upload: </div>
+ </td>
+ <td align="center">
+ <div id="emptyUpload"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="uploadBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="uploadPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="extractLabel">Extract/Review: </div>
+ </td>
+ <td align="center">
+ <div id="emptyExtract"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="extractBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="extractPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 align="center">
+ <div id="current_step"></div>
+ </td>
+ </tr>
+ </table>
+</div>
+<br>
+<table id="extractSummaryTable" border=0 style="border-collapse: collapse;">
+ <tr>
+ <td>
+ <span id="extractSummary"
+ style="position:relative;width:468px;height:100px;display:none;overflow:auto; "></span>
+ </td>
+ </tr>
+</table>
+<br>
+<iframe id="iframe" name="iframe" src="" width="468" height="80" frameborder="0">
+ PROGRESS BAR DISABLED. <br>Try using a more recent web browser.
+</iframe>
+</span>
+ <script type="text/javascript">
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+ </script>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <script type="text/javascript">
+ // Adapted from Sun Java Web Start Auto-Install Demo
+ // http://java.sun.com/developer/technicalArticles/JavaLP/javawebstart/AutoInstallDemo.html
+ var detect = navigator.userAgent.toLowerCase();
+ var windowsIE = (checkPlatform("msie") && checkPlatform("win"));
+
+ function checkPlatform(string) {
+ place = detect.indexOf(string) + 1;
+ thestring = string;
+ return place;
+ }
+ </script>
+</table>
+
+#if(!$session)
+<script type="text/javascript" src="$content.getURI('scripts/subjectAssessorData/proj_tools.js')"></script>
+
+<script type="text/javascript">
+ //load projects
+ window.defaultProject = "$!project";
+
+ window.projectLoader = new ProjectLoader();
+
+ window.projectLoader.onLoadComplete.subscribe(function () {
+ renderProjects(document.getElementById("project"), window.projectLoader.list, window.defaultProject);
+ });
+
+ document.getElementById("project").onchange = function (o) {
+ if (this.selectedIndex > 0) {
+ var s = this.options[this.selectedIndex];
+ var pc = document.getElementById("pc_0");
+ if (pc != undefined && pc != null) {
+ if (s.pc == "4") {
+ if (s.qc == "0") {
+ document.getElementById("pc_2").click();
+ } else {
+ document.getElementById("pc_1").click();
+ }
+ } else {
+ document.getElementById("pc_0").click();
+ }
+ }
+ }
+ };
+
+ window.projectLoader.init();
+
+ function prepApplet(_form) {
+ return true;
+ }
+
+ //build breadcrumb
+ var breadcrumbs = document.getElementById('breadcrumbs');
+
+ if (breadcrumbs != null) {
+ var bread = "";
+ #if($project)
+ bread = bread + "<a href='$link.setAction("DisplayItemAction").addPathInfo("search_element","xnat:projectData").addPathInfo("search_field","xnat:projectData.ID").addPathInfo("search_value","$project")'>$displayManager.getSingularDisplayNameForProject().toUpperCase(): $!project</a>";
+ bread = bread + " > Upload Images";
+ #end
+ breadcrumbs.innerHTML = bread;
+ }
+
+</script>
+#end
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm b/src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm
new file mode 100644
index 00000000..e40241f0
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/DICOMSCPPage.vm
@@ -0,0 +1,24 @@
+<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): $!arc.getDcm_dcmAe()</li>
+ </ul>
+ </td>
+</tr>
+ </table>
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/LaunchUploadApplet.vm b/src/main/webapp/xnat-templates/screens/LaunchUploadApplet.vm
index b41ea47f..b0d56362 100644
--- a/src/main/webapp/xnat-templates/screens/LaunchUploadApplet.vm
+++ b/src/main/webapp/xnat-templates/screens/LaunchUploadApplet.vm
@@ -125,8 +125,6 @@
</div> <!-- end of hideIfProtocol -->
<div id="forProtocolContent" style="display:none"></div>
- <p style="width:500px;margin:20px 0;">Looking for other ways to upload images? <a href="$link.setPage("AlternateImageUpload.vm")">Click here.</a></p>
-
</form>
<script type="text/javascript">
diff --git a/src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm b/src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm
new file mode 100644
index 00000000..20c3dc90
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/UploadAssistantPage.vm
@@ -0,0 +1,12 @@
+<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
diff --git a/src/main/webapp/xnat-templates/screens/UploadOptions.vm b/src/main/webapp/xnat-templates/screens/UploadOptions.vm
new file mode 100644
index 00000000..89b03f05
--- /dev/null
+++ b/src/main/webapp/xnat-templates/screens/UploadOptions.vm
@@ -0,0 +1,646 @@
+<script type="text/javascript">
+ function disableForm(theform) {
+ if (document.getElementById) {
+ document.getElementById('progressBar').style.display = 'block';
+ }
+ else if (document.all) {
+ document.all['progressBar'].style.display = 'block';
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = true;
+ }
+ return true;
+ }
+ else {
+ return true;
+ }
+ }
+
+ function enableForm() {
+ var theform;
+ if (document.getElementById) {
+ theform = document.getElementById('uploadFORM');
+ }
+ else if (document.all) {
+ theform = document.all['uploadFORM'];
+ }
+
+ if (document.all || document.getElementById) {
+ for (i = 0; i < theform.length; i++) {
+ var tempobj = theform.elements[i];
+ if (tempobj.type.toLowerCase() == "submit" || tempobj.type.toLowerCase() == "reset" || tempobj.type.toLowerCase() == "button")
+ tempobj.disabled = false;
+ }
+ return true;
+ } else {
+ return true;
+ }
+ }
+</script>
+<script type="text/javascript">
+ var i;
+ var req;
+
+ var uploadCount = 0;
+ var extractCount = 0;
+ var progressBar;
+ var progressPercent;
+ var uploadID = "$uploadID";
+ var started = 0;
+ var extractTimeOut = 300;
+
+ function setUploadProgress(i) {
+ if (i == 0) {
+ document.getElementById("uploadPercent").innerHTML = "";
+ document.getElementById("uploadBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("uploadPercent").innerHTML = parseInt(i) + "%";
+ }
+ else {
+ document.getElementById('preparing').innerHTML = "";
+ }
+ document.getElementById("uploadBar").style.width = pixels + "px";
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ }
+ }
+ }
+
+ function setExtractSummary(jsonobj) {
+ var messages = "";
+ try {
+ var respPos = jsonobj.msgs[0].length - 1;
+ for (i = 0; i <= respPos; i++) {
+ var level = jsonobj.msgs[0][i].status;
+ var message = jsonobj.msgs[0][i].msg;
+ if (level == "COMPLETED") {
+ message = "<tr bgcolor='#CCFFCC'><td>" + message;
+ } else if (level == "PROCESSING") {
+ message = "<tr bgcolor='#CCFFFF'><td>" + message;
+ } else if (level == "WARNING") {
+ message = "<tr bgcolor='#FFCCC'><td>" + message;
+ } else if (level == "FAILED") {
+ message = "<tr bgcolor='#FF99CC'><td>" + message;
+ } else {
+ message = "<tr bgcolor='#CCCCCC'><td>" + message;
+ }
+ messages = messages + message + "</td></tr>";
+ }
+ } catch (e) {
+ }
+ document.getElementById("extractSummary").innerHTML =
+ "<table width='100%' cellpadding='2' cellspacing='0'><tr><th>Extraction / Review summary:</th></tr>" +
+ messages +
+ "</table>";
+ }
+
+ function toggleExtractSummary() {
+ if (document.getElementById("extractSummary").style.display == "none") {
+ document.getElementById("extractSummaryTable").border = "1";
+ document.getElementById("extractSummary").style.display = "block";
+ } else {
+ document.getElementById("extractSummaryTable").border = "0";
+ document.getElementById("extractSummary").style.display = "none";
+ }
+ }
+
+ function setExtractProgress(i) {
+ if (i == 0) {
+ document.getElementById("extractPercent").innerHTML = "";
+ document.getElementById("extractBar").style.width = 0 + "px";
+ } else {
+ if (i > 100) {
+
+ } else {
+ var pixels = i * 3;
+ if (i > 10) {
+ document.getElementById("extractPercent").innerHTML = parseInt(i) + "%";
+ }
+ document.getElementById("extractBar").style.width = pixels + "px";
+ }
+ }
+ }
+
+ function evaluateDestination(ele) {
+ if (ele.value == '2') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'true';
+ } else if (ele.value == '1') {
+ document.getElementById("auto-archive").value = 'true';
+ document.getElementById("quarantine").value = 'false';
+ } else if (ele.value == '0') {
+ document.getElementById("auto-archive").value = 'false';
+ document.getElementById("quarantine").value = 'false';
+ }
+ }
+
+ var checkProgressFinal = 0;
+
+ function prog(theform) {
+ var imageArchive = document.getElementById("image_archive");
+ if (!imageArchive.value) {
+ xModalMessage('Upload Action', 'Please select an archive to upload.');
+ return false;
+ }
+ if (!(imageArchive.value.endsWith(".gz") || imageArchive.value.endsWith(".tgz") || imageArchive.value.endsWith(".zip"))) {
+ xModalMessage('Upload Action', 'Please select a tar or zip archive to upload.');
+ return false;
+ }
+ if (document.getElementById("project").selectedIndex == 0) {
+ xModalMessage('Upload Action', 'Please select a $displayManager.getSingularDisplayNameForProject().toLowerCase().');
+ return false;
+ }
+ disableForm(theform);
+ document.getElementById("iframe").src = "";
+ started = 0;
+ checkProgressFinal = 0;
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+
+ document.getElementById('preparing').style.display = 'block';
+ document.getElementById('preparing').innerHTML = "Loading File... ";
+ setUploadProgress(0);
+ setExtractProgress(0);
+ setExtractSummary("");
+ resetProgress();
+ checkProgress();
+
+ return true;
+ }
+
+ function callback() {
+ if (req.readyState == 4) {
+ if (req.status == 200) {
+ started = 1;
+ // handle response
+ var respDat = YAHOO.lang.JSON.parse(req.responseText);
+ var respPos = respDat.msgs[0].length - 1;
+ var uploadI = 0;
+ var extractI = 0;
+ var statusCount = 0;
+ if (respDat.msgs[0].length > 0) {
+ if (respDat.msgs[0].length > 0) {
+ var level = respDat.msgs[0][respPos].status;
+ var message = respDat.msgs[0][respPos].msg;
+ }
+ }
+
+ if (req.responseText.indexOf("file uploaded") >= 0) {
+ uploadI = 100;
+ }
+ if (req.responseText.indexOf("Successfully uploaded") >= 0) {
+ extractI = 100;
+ }
+ if (req.responseText.indexOf("archiving operation complete") >= 0) {
+ extractI = 100;
+ }
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+
+ //alert("Upload(" + uploadI + "); Extract(" + extractI + ");\r\n" + statusText + "\r\n" + req.responseText);
+
+ if (uploadI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Upload Failed. Please retry at a later time or contact technical support.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (extractI == -1) {
+ document.getElementById('preparing').innerHTML = " <font color=red><B>Error: Extraction/Review Failed. Please verify the integrity of the zipped file and the contained image files.</B></font>";
+ document.getElementById('preparing').style.display = 'block';
+ } else if (uploadI != 100) {
+ //upload complete
+
+ if (uploadCount != 98) {
+ uploadCount = uploadCount + 1;
+ }
+
+ if (uploadCount > 40) {
+ extractTimeOut = 600;
+ }
+ if (uploadCount > 50) {
+ extractTimeOut = 800;
+ }
+ if (uploadCount > 60) {
+ extractTimeOut = 1000;
+ }
+ if (uploadCount > 70) {
+ extractTimeOut = 2000;
+ }
+ if (uploadCount > 80) {
+ extractTimeOut = 3000;
+ }
+ if (uploadCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (uploadCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setUploadProgress(uploadCount);
+ setExtractProgress(0);
+
+ setTimeout("checkProgress();", extractTimeOut);
+ } else if (extractI == 100) {
+ //extract complete
+ setUploadProgress(100);
+ setExtractProgress(100);
+
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ if (checkProgressFinal == 0) {
+ checkProgressFinal = 1;
+ //check progress one final time to capture final step summary
+ setTimeout("checkProgress();", 200);
+ }
+ } else {
+ //extract in progress
+ setUploadProgress(100);
+
+ if (extractCount != 98) {
+ extractCount = extractCount + 1;
+ }
+ if (extractCount < 10) {
+ extractTimeOut = 500;
+ }
+ if (extractCount > 10) {
+ extractTimeOut = 100;
+ }
+ if (extractCount > 20) {
+ extractTimeOut = 1500;
+ }
+ if (extractCount > 30) {
+ extractTimeOut = 2000;
+ }
+ if (extractCount > 50) {
+ extractTimeOut = 2800;
+ }
+ if (extractCount > 60) {
+ extractTimeOut = 3300;
+ }
+ if (extractCount > 70) {
+ extractTimeOut = 4000;
+ }
+ if (extractCount > 80) {
+ extractTimeOut = 5000;
+ }
+ if (extractCount > 85) {
+ extractTimeOut = 6000;
+ }
+ if (extractCount > 88) {
+ extractTimeOut = 9000;
+ }
+
+ setExtractProgress(extractCount);
+
+ if (statusCount > 0) {
+ setExtractSummary(respDat);
+ setCurrentStep(message);
+ }
+ setTimeout("checkProgress();", extractTimeOut);
+ }
+ }
+ }
+ }
+
+
+ function setCurrentStep(message) {
+ if (message != null && message != undefined) {
+ document.getElementById("current_step").innerHTML = "<A href='' ONCLICK='toggleExtractSummary();return false;'>" + message + "...</A>";
+ }
+ }
+
+ function resetProgress() {
+ var url = "$content.getURI("servlet/AjaxServlet")?remote-class=org.nrg.xnat.ajax.UploadProgress";
+ url = url + "&remote-method=start";
+ url = url + "&ID=" + uploadID;
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.send(null);
+ }
+
+ function checkProgress() {
+ //var url = "$content.getURI("/REST/status/$uploadID")?format=json";
+ var url = "$content.getURI("/REST/status/$uploadID")?format=json&stamp=" + (new Date()).getTime();
+ if (window.XMLHttpRequest) {
+ req = new XMLHttpRequest();
+ } else if (window.ActiveXObject) {
+ req = new ActiveXObject("Microsoft.XMLHTTP");
+ }
+ req.open("GET", url, true);
+ req.onreadystatechange = callback;
+ req.send(null);
+ }
+ function makeTheFormGo() {
+ var form = document.getElementById("uploadFORM");
+ prog(form);
+ form.submit();
+ }
+</script>
+
+<table border="0" cellpadding="5" cellspacing="0">
+ <tr>
+ <td> </td>
+ </tr>
+ <tr>
+ <td><h3>Options for Uploading $displayManager.getPluralDisplayNameForImageSession()</h3></td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>Option 1: Upload Applet</h4>
+ </td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">DICOM and ECAT files can be uploaded via the Upload Applet. <a href="$link.setPage("LaunchUploadApplet.vm")">Click here</a> to upload using the Upload Applet.
+ </div>
+ </tr>
+
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>Option 2: 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>
+
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>
+ Option 3: Compressed upload</h4></td>
+ </tr>
+ <tr>
+ <td valign="top" align="left">
+ <div style="width:500px">Raw image files can be zipped (.zip or .tar.gz) and uploaded using the form. This
+ tool currently supports DICOM and ECAT files. Selecting 'Prearchive' will place your images into a
+ temporary holding space. You will then have the ability to review the details and match the data to the
+ proper $displayManager.getSingularDisplayNameForSubject().toLowerCase() & $displayManager.getSingularDisplayNameForImageSession().toLowerCase() ID. If you are confident the data will be mapped properly, you can directly
+ 'Archive' the files and specify whether the resulting $displayManager.getSingularDisplayNameForImageSession().toLowerCase() should go into a quarantine state.
+ </div>
+ <div class="alert" style="margin:15px 0;max-width:696px;min-width:400px;">
+ The compressed uploader does not yet support splitting PET/MR sessions based on the site-wide or
+ project-specific settings for handling PET/MR data. If you are uploading PET/MR data and need to have
+ the data split into separate PET and MR sessions or created as a PET session rather than a PET/MR
+ session, you should use either the <a href="$link.setPage("LaunchUploadApplet.vm")">upload applet</a> or the
+ DICOM C-STORE receiver as described below.
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr id="option3">
+ <td>
+ <input type="hidden" name="popup" value="true"/>
+ <form id="uploadFORM" class="noHide" target="iframe" enctype="multipart/form-data" method="POST"
+ action="$content.getURI("/REST/services/import?http-session-listener=$uploadID&format=html&XNAT_CSRF=$!XNAT_CSRF")">
+ <input type="hidden" name="threshhold" value="51516279"/>
+
+ #if($session)
+ <input type="hidden" name="EXPT_LABEL" value="$!session.getLabel()"/>
+ <input type="hidden" name="SUBJECT_ID" value="$!session.getSubjectData().getLabel()"/>
+ #end
+
+ <table border=0 cellpadding="5" cellspacing="0">
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForProject()</th>
+ <td>
+ #if(!$session)
+ <select id="project" name="project" disabled=true></select>
+ #else
+ <input type="hidden" name="project" id="project"
+ value="$session.getProject()"/>$session.getProject()
+ #end
+ </td>
+ </tr>
+
+ #if($session)
+ <tr>
+ <th align="left">$displayManager.getSingularDisplayNameForImageSession()</th>
+ <td>$!session.getLabel()</td>
+ </tr>
+ #end
+ <tr>
+ <th align="left">Destination</th>
+ <td>
+ <label><input id="pc_0" type='radio' name='prearchive_code' value='0'
+ #if(!$session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Prearchive</label>
+ <label><input id="pc_2" type='radio' name='prearchive_code' value='1'
+ #if($session)CHECKED#end onchange="evaluateDestination(this)"/>
+ Archive</label>
+ #if($session)
+ <input type="hidden" name="overwrite" value="append"/>
+ <input type="hidden" id="auto-archive" name='auto-archive' value='TRUE'/>
+ #else
+ <input type="hidden" id="auto-archive" name='auto-archive' value='FALSE'/>
+ #end
+ <input type="hidden" id="quarantine" name='quarantine' value='FALSE'/>
+ </td>
+ </tr>
+ <tr>
+ <th align="left">File</th>
+ <td><input type="file" id="image_archive" name="image_archive" size="60"
+ accept="application/zip, application/x-gzip, application/x-tgz"/></td>
+ </tr>
+ #auditBoxes("3" "" "Standard Upload" "Upload Images")
+ #hideFormJustification()
+ <tr>
+ <td> </td>
+ <td><input id="directButton" type="button" name="eventSubmit_doPerform" value="Begin Upload" onclick="makeTheFormGo();"/>
+ </td>
+ </tr>
+ </table>
+ </form>
+
+<span id="progressBar" style="position:relative; display:none;">
+<div id="ex" style="position:relative;width:468px;background:#eeeeee;border:3px double #000000;">
+ <table width="100%">
+ <tr>
+ <td colspan=2 align="left">
+ <div id="preparing">Loading File... </div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="uploadLabel">Upload: </div>
+ </td>
+ <td align="center">
+ <div id="emptyUpload"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="uploadBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="uploadPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td> </td>
+ </tr>
+ <tr>
+ <td>
+ <div id="extractLabel">Extract/Review: </div>
+ </td>
+ <td align="center">
+ <div id="emptyExtract"
+ style="background-color:#cccccc;border:1px solid black;height:22px;width:300px;padding:0;"
+ align="left">
+ <div id="extractBar"
+ style="position:relative;top:0;left:0;background-color:#333333;height:22px;width:0;padding-top:5px;padding:0;">
+ <div id="extractPercent"
+ style="position:relative;top:0;left:0;color:#f0ffff;height:22px;text-align:center;font:bold;padding:0;padding-top:5px;">
+ </div>
+ </div>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 align="center">
+ <div id="current_step"></div>
+ </td>
+ </tr>
+ </table>
+</div>
+<br>
+<table id="extractSummaryTable" border=0 style="border-collapse: collapse;">
+ <tr>
+ <td>
+ <span id="extractSummary"
+ style="position:relative;width:468px;height:100px;display:none;overflow:auto; "></span>
+ </td>
+ </tr>
+</table>
+<br>
+<iframe id="iframe" name="iframe" src="" width="468" height="80" frameborder="0">
+ PROGRESS BAR DISABLED. <br>Try using a more recent web browser.
+</iframe>
+</span>
+ <script type="text/javascript">
+ progressBar = document.getElementById("uploadBar");
+ progressPercent = document.getElementById("uploadPercent");
+ </script>
+ </td>
+ </tr>
+
+
+ <tr>
+ <td>
+ <hr/>
+ <h4>Option 4: 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): $!arc.getDcm_dcmAe()</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <hr/>
+ </td>
+ </tr>
+ <script type="text/javascript">
+ // Adapted from Sun Java Web Start Auto-Install Demo
+ // http://java.sun.com/developer/technicalArticles/JavaLP/javawebstart/AutoInstallDemo.html
+ var detect = navigator.userAgent.toLowerCase();
+ var windowsIE = (checkPlatform("msie") && checkPlatform("win"));
+
+ function checkPlatform(string) {
+ place = detect.indexOf(string) + 1;
+ thestring = string;
+ return place;
+ }
+ </script>
+</table>
+
+#if(!$session)
+<script type="text/javascript" src="$content.getURI('scripts/subjectAssessorData/proj_tools.js')"></script>
+
+<script type="text/javascript">
+ //load projects
+ window.defaultProject = "$!project";
+
+ window.projectLoader = new ProjectLoader();
+
+ window.projectLoader.onLoadComplete.subscribe(function () {
+ renderProjects(document.getElementById("project"), window.projectLoader.list, window.defaultProject);
+ });
+
+ document.getElementById("project").onchange = function (o) {
+ if (this.selectedIndex > 0) {
+ var s = this.options[this.selectedIndex];
+ var pc = document.getElementById("pc_0");
+ if (pc != undefined && pc != null) {
+ if (s.pc == "4") {
+ if (s.qc == "0") {
+ document.getElementById("pc_2").click();
+ } else {
+ document.getElementById("pc_1").click();
+ }
+ } else {
+ document.getElementById("pc_0").click();
+ }
+ }
+ }
+ };
+
+ window.projectLoader.init();
+
+ function prepApplet(_form) {
+ return true;
+ }
+
+ //build breadcrumb
+ var breadcrumbs = document.getElementById('breadcrumbs');
+
+ if (breadcrumbs != null) {
+ var bread = "";
+ #if($project)
+ bread = bread + "<a href='$link.setAction("DisplayItemAction").addPathInfo("search_element","xnat:projectData").addPathInfo("search_field","xnat:projectData.ID").addPathInfo("search_value","$project")'>$displayManager.getSingularDisplayNameForProject().toUpperCase(): $!project</a>";
+ bread = bread + " > Upload Images";
+ #end
+ breadcrumbs.innerHTML = bread;
+ }
+
+</script>
+#end
\ No newline at end of file
diff --git a/src/main/webapp/xnat-templates/screens/topBar/Upload/Default.vm b/src/main/webapp/xnat-templates/screens/topBar/Upload/Default.vm
index ce743b31..012965a5 100644
--- a/src/main/webapp/xnat-templates/screens/topBar/Upload/Default.vm
+++ b/src/main/webapp/xnat-templates/screens/topBar/Upload/Default.vm
@@ -1,6 +1,15 @@
<!-- Sequence: 10 -->
<!-- Upload/Default -->
- <li><a href="$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>
--
GitLab