Diff for "Pluginwebsite"

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About this document

This is an official Request for Comment (RFC) for Add your text here.

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Status

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Proposal

Cytoscape plugins are mainly developed by third parties to add extra functionality to Cytoscape. Many plugin authors are willing to share the plugins they developed. Cytoscape maintains a long list of plugins at Cytoscape website at (http://cytoscape.org/plugins2.php) and the list is growing over time.

Right now, if a user wants to install a plugin, he/she can only do it manually. (1) Look at the Cytoscape website or the plugin website he/she knows. (2) Download the plugin, (3) Install the plugin into the Cytoscape. To manage the plugins (add/delete/update), user needs to keep track of each plugins manually and must know where the Cytoscape plugins are placed (in a designated directory).

The goal of this project is to provide a “Plugin manager” at Cytoscape to automate the the plugin installation process, so the users will have GUIs to manage their plugins (add/delete/update). The GUIs will integrate Cytoscape, plugin website, and installation process together and user even don’t need to know what the designated Cytoscape plugin directory is. We also note that “Firefox” and “Eclipse” already have such practice to add their add-ons.

This project should include three components: (1) plugin database (2) plugin web site (3) plugin manager

Use Cases

Load a plugin “BiNGO” into Cytoscape with Plugin_Manager.

1. Launch Cytoscape, click menu “Plugins”, click submenu “Import/update plugins”.

2. A dialog with title “Plugin manager” shows up. All the plugins installed are listed in the JTable. There are three buttons at the right side of JTable, “Get plugins”, “Uninstall” and “Find Updates”.

3. Click the button “Get plugins”. A new dialog with title “Plugin List” pops up, which list all the plugins available (Retrieved dynamically from “CyPluginDB”). In the dialog, there is a JTree, which list five categories of Cytoscape plugins (“Functional Enrichment plugins”, “Analysis plugins”, “Network and Attribute I/O Plugins”, “Network Inference Plugins”). Click the tree node “Functional Enrichment plugins” expands the node, which list all the plugins belong to this category.

4. Click “BiNGO”, a new dialog with title “Add BiNGO Plugin” show up, which gives detail description of the plugin. A plugin may have several versions for download. Each radio button represents plugin versions that are compatible with the current Cytoscape version. There are three buttons at the end of the page, “Install”, “Use once”, “Cancel”. – If multiple versions are compatible might the user expect a description for each one so they can tell which one they want? If not offering the most recent version by default may make more sense.

5. Selected the version of plugin, click “Install” button will initiate the installation process. (License agreement dialog and progress bar) If “Use once” is clicked, the plugin will be load into memory only, not persist in disk.

6. After Installation is completed, an info dialog will inform the user that the plugin is installed.

Data flow diagram

attachment:DataFlowDiagram.png

Note: The web site may be built with PHP and MySQL. Cytoscape will have different versions. Plugins will also have different versions. Different versions may not compatible each other. Therefore a dynamic web site with database as back-end is desirable to retrieve plugins, which are compatible with current Cyoscape version.

Plugin database

Host: chianti.ucsd.edu Database name: CyPluginDB

* Current Design:

attachment:CyPluginDB_Schema.png

Plugin webpages

Host: cytoscape.org

1. Main page, which lists all the plugins. Same as usual, but data source will be from CyPluginDB. If the DB is updated, this page will be updated automatically.

• pluginList.php

2. Pages for each plugin

getPlugin.php parameters: PluginName

Plugin data management

1. Plugin author submit plugin to Cytoscape pluginSubmit.php (Web form)

Title: Submit Plugin to Cytoscape (File_upload) Authors: xxx Plugin_Name: textField Plugin_version: textField Release Date: May 2, 2005 Institution: textField Jar File: textField Verified to work in Cytoscape version: 2.3, 2.4 (checkboxes) Plugin URL: XXXXXXX.com

Submit button, cancel button

2. Load plugin to CyPluginDB after validation pluginLoading.py (web form, password required to upload, DB admin only) (ToDo: ScreenShot)

Plugin Manager

Implementation Plan

• Plugin database

  • “CyPluginDB” (PluginList,Plugins,PluginAuthors)

• Web pages
  • (1) pluginList.php (2) getPlugin.php (3) submitPlugin.php (4) loadingPlugin.php
• Java class

  • (1) PluginManagerDialog.java (2) PluginListDialog.java (3) PluginLoadingDialog.java (4) GetAllPluginFromDB.java (5) GetPluginInfoFromDB.java (6) DownloadPluginFromDB.java

Deferred Items

Open Issues

Backward Compatibility

Expected growth and plan for growth

References

Comments

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