Author: Christian Lopes Date: 2010-02-01 10:22:14 -0800 (Mon, 01 Feb 2010) New Revision: 19088
Modified: cytoscapeweb/trunk/cytoscapeweb/README.txt Log: Updated the README file. Modified: cytoscapeweb/trunk/cytoscapeweb/README.txt =================================================================== --- cytoscapeweb/trunk/cytoscapeweb/README.txt 2010-01-31 16:20:16 UTC (rev 19087) +++ cytoscapeweb/trunk/cytoscapeweb/README.txt 2010-02-01 18:22:14 UTC (rev 19088) @@ -2,11 +2,12 @@ LICENSE AGREEMENT AND DISCLAIMER ================================================================================ -Cytoscape Web is a collaborative effort of the Cytoscape Consortium. -It is available at http://www.cytoscape.org and provided to all users -free of charge. +Cytoscape Web is developed as part of the Cytoscape project, by members of the +Cytoscape Consortium. +It is available at http://www.cytoscape.org and provided to all users +free of charge under the Lesser GNU Public License (LGPL). -Users of Cytoscape Web must first agree to the license agreement +Users of Cytoscape Web must first agree to the license agreement provided in the file "LICENSE.txt". THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, @@ -38,7 +39,7 @@ <script type="text/javascript" src="cytoscapeweb.min.js"></script> </head> -3. Add a div or another HTML container and give it an ID (Cytoscape Web will +3. Add a div or another HTML container and give it an ID (Cytoscape Web will replace its contents with the rendered graph): <body> @@ -66,29 +67,35 @@ -------------------------------------------------------------------------------- -To see other examples and the API documentation, visit +To see other examples and the API documentation, visit http://cytoweb.baderlab.org/documentation. ================================================================================ SOURCE CODE ================================================================================ -- You can browse the Cytoscape Web source code at +- You can browse the Cytoscape Web source code at http://chianti.ucsd.edu/svn/cytoscapeweb -- You can also download the latest source from our Subversion server, by using +- You can also download the latest source from our Subversion server, by using the following command: - + svn checkout http://chianti.ucsd.edu/svn/cytoscapeweb/trunk/cytoscapeweb cytoscapeweb-read-only -- After you download the project from Subversion, you can use Flex Builder or +- After you download the project from Subversion, you can use Flex Builder or Jakarta Ant to build it. ================================================================================ PROJECT SETUP ON FLEX BUILDER ================================================================================ -Requires: Flex Builder 3 or Eclipse + Flex Builder 3 plugin +This option requires Adobe's Flex Builder (or the Flex Builder plugin for +Eclipse). +It is not free, but you can download a 60-day trial from: + http://www.adobe.com/products/flex. + +The Cytoscape Web development team uses Eclipse with the Flex Builder plugin. + 1. Checkout the project from SVN or import it as a Flex project. 2. Setup the Flex Build Path: @@ -104,12 +111,41 @@ * src/CytoscapeWeb.mxml (default) * src/TestRunner.mxml -5. To test it, just right-click src/CytoscapeWeb.mxml and choose: +5. Before running Cytoscape Web with the test page, you need to minify some + JavaScript files. We provided an Ant task for that. + One option is to manually execute the "js minify" Ant task after the + ActionScript code is compiled by the Flex Builder. + But if you are using Eclipse with the Flex Builder plugin, it might be + more convenient to let Eclipse do it automatically after each build. + To allow that, just follow these steps: + 5.1. Open the project Properties panel and select "Builders". + + 5.2. Click "New..." and choose "Ant Builder". + + 5.3. Give it a name (e.g. "JS Minify"), and enter the following parameters: + + - Main tab: + + Buildfile: ${workspace_loc:/cytoscapeweb/build.xml} + Base direectory: ${workspace_loc:/cytoscapeweb} + + - Targets tab: + + Manual Build: js minify + Auto Build: js minify + + 5.4. Click "Apply" and "OK". + + Now, every time the project is built by the Eclipse Flex Builder plugin, + it will also minify the required JavaScript files. + +6. To test Cytoscape Web, just right-click src/CytoscapeWeb.mxml and choose: + Run As >> Flex Application The first time it will open CytoscapeWeb.html in your default browser, but - it does not work. To fix it, right-click CytoscapeWeb.mxml again and select: + it will not work. To fix it, right-click CytoscapeWeb.mxml again and select: Run As >> Run Configurations... @@ -118,8 +154,10 @@ run CytoscapeWeb.mxml again. ================================================================================ -BUILDING IT WITH ANT +BUILDING WITH ANT ================================================================================ +If you do not have Flex Builder, you still can build the project with Jakarta +Ant: 1. Download and install Jakarta Ant. Installation instructions are available at: @@ -130,9 +168,9 @@ http://www.adobe.com/cfusion/entitlement/index.cfm?e=flex3sdk 3. After installing the Flex SDK, create a file called "local.properties" in the - root folder of the Cytoscape Web project (the one that contains "build.xml"). - Open the created properties file with any text editor and add the FLEX_HOME - path, which is the path where you installed the Flex SDK. + root folder of the Cytoscape Web project (the one that contains "build.xml"). + Open the created properties file with any text editor and add the FLEX_HOME + path, which is the location where you just installed the Flex SDK. Example: FLEX_HOME=/Library/flex_sdk_3.5/ @@ -142,7 +180,7 @@ ant build 3. To test it, just open bin/tests.html in a web browser. It will probably not - work if you are doing that directly from the file system, because of the + work if you are doing that directly from the file system, because of the Flash Player security settings. You can change it by going to this web page: http://www.macromedia.com/support/documentation/en/flashplayer/help/settings_manager04.html @@ -151,9 +189,10 @@ that contains the Cytoscape Web project. Now you can open bin/tests.html again. - If you run Cytoscape Web from a Web server, there is no such security issues. + If you run Cytoscape Web from a Web server, there are no such security + issues. - ================================================================================ -Thanks for using Cytoscape Web! +Thank you for using Cytoscape Web! + -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
