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The XNAT web application includes a Java-based upload applet that supports uploading DICOM and ECAT data. This uploader guides the user through selecting data files, modifying metadata, and uploading a session to XNAT.

Many web browsers, including Chrome and Safari, have ended support for running embedded Java applets in the browser. If you cannot run XNAT in a supported browser such as Firefox, we recommend installing the Desktop version of the Upload Applet or using another upload method. 

If you are running your XNAT installation using Apache HTTPD as the front-end to Tomcat with SSL, you should read this section about configuring your HTTPD server for SSL to support clients with the Java 7 plugin.

 

Running the upload applet

To launch the XNAT Upload Applet from anywhere in XNAT, go to Upload > Images > Upload Applet in the top navigation.

Select a Project and Subject

All image sessions are treated as subject assessors in XNAT, which means they must be associated with a project and a subject. If you launch the upload applet from a project or subject page, these menus should be preselected. If not, you will need to manually select a project, and then a subject from that project.

If you like, you can add a subject without leaving the context of the uploader by clicking the "Add New Subject" link. A New Subject form will open in a popup.

Your XNAT may require you to specify the Session Date prior to uploading. This setting can be set by an XNAT Admin. See: Site-wide Session Upload and Anonymization Settings.

 

Certificate approval

When the uploader starts, your web browser will most likely warn you that the applet has not been signed by a recognized authority. Allow the applet to run on your computer.

Selecting a project

If you accessed the applet via the form on the Upload Image Sessions page, you will start at the Selecting Data Files step. If instead you accessed it via the button in the top left hand corner of the screen, the uploader window will appear with a list of projects to which you are allowed to add data. There are several action buttons on the bottom right; "Cancel" exits the uploader without uploading any data, "Prev" and "Next" move to the previous and next steps of the upload process, and "Finish" uploads the data. Some of these buttons may be inactive (and grayed out) if the action is not appropriate at the time.

Select a project from the list and click "Next" to continue.

Selecting a subject

Next, a list of subjects in that project will appear.

Select an existing subject, or click the "Create new subject" button to add a new subject.

When a subject has been selected, click "Next" to continue.

Next, you may be prompted to verify the session date. If you launched the applet from the Upload Image Sessions page, you would have already entered the date or indicated that you didn't know the date. But if you launched the applet from the Launch Uploader link in the top left hand corner of the page, you will have to enter the date at this stage before continuing with the upload process. If you do not know the date, you should access the upload applet via Upload->Images and check the "I don't know the date or my session doesn't have a date" checkbox.

Selecting data files

Use the file chooser window to select the directory containing the data you will be uploading. Note for Mac OS X users: if the data are on a removable USB drive or a CD or DVD, use the pop-up menu at the top of the chooser window to navigate up to your computer's top-level directory, then go into Volumes to find your data. When the data directory has been selected, click "Next" to continue.

Reviewing session details

This page includes a summary of the session to be uploaded. If more than one session was found, a list of sessions will be presented and you must select one. At this step, you may also select which scans (DICOM series) to include in the uploaded session. Once you are satisfied with the selection, click "Next" to continue.

Setting data fields

The final page before uploading the data shows the project and subject identifiers and allows you to edit the session name and possibly other metadata, depending on the data type and your configuration. Modify any fields if desired, then press "Finish" to upload the data.

Uploading

The applet will now send the data to XNAT. A progress monitor at the lower left shows how much data has been uploaded, and the expected total size (which may change as data are compressed before sending). Depending on the size of your data and the speed of your network connection, the upload may take seconds to hours.

Success!

When the upload is complete, a confirmation that the upload was successful will be displayed, with a link to the report page of the newly uploaded session. If anything went wrong during the upload, a diagnostic message will be displayed instead.

Configuring Apache HTTPD to Support the Java 7 Plugin

Due to a change in the Java Secure Socket Extension API implementation in Java 7, server name indication is turned on by default in clients using the Java 7 plugin. This means that the server name must be properly configured in the server configuration. Failure to do this will cause these clients to fail with a message like this:

Application Error
ClassNotFoundException
org.nrg.upload.ui.UploadAssistantApplet

The fix for this issue is fairly simple:

  1. Open the httpd.conf file for your Apache HTTPD installation (on most Linux systems, this can be found in /etc/httpd/conf/httpd.conf).
  2. Find the <VirtualHost> entry for your installation.
  3. Somewhere within this entry, add the directive: ServerName server.domain.tld. For example, if your server is foo.bar.edu, it would be ServerName foo.bar.edu.
  4. Save and close the httpd.conf file.
  5. Restart your Apache HTTPD server: service tomcat6 restart. There's no need to restart Tomcat.
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