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Downloading using the Java GUI
There are two basic features to the ProteomeCommons.org Tranche network: adding data and getting data. This document describes how to use the Java GUI to download files and how to create hyperlinks that point to Tranche data. For information on how to download Tranche data using a command-line interface or the Java API, consult the developer's guide.
You may download files using a point-and-click program, also referred to as the Java GUI. The Java GUI is intended to be straight-forward and usable by anyone who wants to download files.
The Java GUI may be executed by clicking on the Java WebStart link. If you do not have Java 5 installed, you will be prompted to do so. After execution the application should look similar to the following:
Simply enter the hash string of the file that you'd like to download and click, "Download File(s)", to download the file(s). If you would like to download from a particular server, you may enter the server's URL as an optional parameter. If the file you are requesting is private, you must enter the passphrase. A passphrase can be obtained by contacting the originators of the data. Otherwise, the passphrase field can be left blank. If you would like to download only files that have a certain name or only files of a certain file type, you can enter a regular expression. To download only peaklist files, enter the regular expression "\.pkl". For any other file extensions, simply replace "pkl" in that regular expression with the extension you want to download. For more information on using regular expressions, consult a reference manual. There are many regular expression tutorials available online. We recommend using O'Reilly's Regular Expression Pocket Reference.
It may take a few moments for the data to be found on the network. After this is done, you will be asked to select where to download the data to. The screen will look something like the following:
If you are downloading a project (i.e. a set of files,) you can select a directory in which to place the files and all the files in the project will be downloaded to that directory.
Potential Firewall Issues
The Java GUI is a separate program that runs outside of your web browser. Because of this it may be picked up and blocked by any security tool or firewall program running on your computer. Such programs include ZoneAlarm, Windows Firewall, and others. In order to let the download tool function properly you must opt to let it have access to the internet.
Most users will not experience firewall issues; however, if you do, know that you'll have to either disable the firewall or configure it to let the download tool work. A list of configurations for various firewall programs is provided below. If your particular program isn't listed, please send in information about it so that we may add it to this documentation.
Windows Firewall
Windows Firewall comes automatically installed on most newer versions of Microsoft Windows, including XP Home and XP Professional. If it is running, a popup box will appear asking if you would like to allow "java.exe" to access the internet. Click yes.
Alternatively, you can disable Windows Firewall while using the downloader tool.
ZoneAlarm
ZoneAlarm is a 3rd party firewall program that is commonly installed to help prevent viruses, spyware, and hackers from accessing your computer. If you have ZoneAlarm running it will notify you when the download tool tries to connect to the web. Click the option that tells ZoneAlarm to let the downloader tool have access to the web. You may have to restart the downloader tool after clicking this option.
Alternatively, you can disable ZoneAlarm while using the downloader tool.