Problems with database connection
schizzo
I am developing a cytoscape-plugin, that loads some information from a
oracle-database and visualizes it in a graph. Therefore I had to
include the external jar-file ojdbc6.jar into my plugin-project. I
added a classpath variable in the build.xml and everything is working
fine, but only if I start the developer-version of Cytoscape from my
Eclipse-project.
If I try to start the plugin in the "normal" Cytospace_2.6.3-release
(copy the file into the plugin-folder) no database-connection can be
established. Since I want to offer the plugin for some users, that
dont have the experience how to set up an Eclipse-project, I would
like to ask if anybody has an idea, why my plugin isnt working in the
normal release.
Thank you very much!
Peng-Liang Wang
If you add your lib jar in the path for the build.xml, it is only available for compiling, but not on running time. If you plugin depends on a lib jar, an easy way is to include it in your pugin, i.e. unjar the lib and copy all the classes to your plugin.
Peng
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schizzo
thanks for your answer. I extracted the jar-file and put all the class-
files in my plugin, but still I cant get a connection to the database.
Can you tell me in which folder (e. g. the source- or the base-folder)
I have to put the class-files exactly? Do I still need to configure
the classpath or some import-options in Eclipse?
And I have found another problem with loading of cys-files: When I try
to open a cys-file I get the following errors:
java.lang.RuntimeException: java.io.IOException: The AElfred parser
is a SAX2 XMLReader
and on the cytoscape-console:
cytoscape.data.readers.CytoscapeSessionReader[ERROR]: Unable to read
XGMML file: LIFE.xgmml. java.io.IOException: The AElfred parser is a
SAX2 XMLReader java.io.IOException: The AElfred parser is a SAX2
XMLReader java.lang.RuntimeException: java.io.IOException: The AElfred
parser is a SAX2 XMLReader at cytoscape.Cytoscape.createNetwork
(Cytoscape.java:1410) at
cytoscape.data.readers.CytoscapeSessionReader.walkTree
(CytoscapeSessionReader.java:737) at
cytoscape.data.readers.CytoscapeSessionReader.loadCySession
(CytoscapeSessionReader.java:644) at
cytoscape.data.readers.CytoscapeSessionReader.unzipSessionFromURL
(CytoscapeSessionReader.java:481) at
cytoscape.data.readers.CytoscapeSessionReader.read
(CytoscapeSessionReader.java:347) at
cytoscape.actions.OpenSessionTask.run(OpenSessionAction.java:211) at
cytoscape.task.util.TaskWrapper.run(TaskManager.java:160)
thanks for your help.
> > cytoscape-helpd...@googlegroups.com<cytoscape-helpdesk%2Bunsu...@googlegroups.com>
Peng-Liang Wang
You may look at this sample – to include lib in your plugin. http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/tutorial13/
What version of Java are you using? Cytoscape should work with Java 5.
Peng
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schizzo
thanks for the sample, now the database-connection can be established.
GREAT!
Normally I am using the newest update of java 1.6, but now I re-
compiled
the cytospace-sources with jdk_1.5.0_22 and the compliance level for
class-files set to 1.5. Unfortunately I still get the same error when
I
try to load a cys-file:
java.lang.RuntimeException: java.io.IOException: The AElfred parser
is
a SAX2 XMLReader
I am sorry to ask you again, if you have any idea what is going
wrong.
Thanks and merry christmas!
On Dec 22, 6:57 pm, Peng-Liang Wang <penwang2...@gmail.com> wrote:
> You may look at this sample – to include lib in your plugin.http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/tutorial13/
> > <cytoscape-helpdesk%2Bunsu...@googlegroups.com<cytoscape-helpdesk%252Buns...@googlegroups.com>
Peng-Liang Wang
Plugin developer usually doesn’t have to compile Cytoscape from source. All he/she should do is to compile the plugin and copy the plugin to the plugins folder of Cytoscape. It seems you have a lib that conflicts with the cytoscape lib, something related to SAX3 XMLReader.
Hello Peng-Liang,
thanks for the sample, now the database-connection can be established.
GREAT!
Normally I am using the newest update of java 1.6, but now I re-compiled
the cytospace-sources with jdk_1.5.0_22 and the compliance level for
class-files set to 1.5. Unfortunately I still get the same error when I
try to load a cys-file:
java.lang.RuntimeException: java.io.IOException: The AElfred parser is
a SAX2 XMLReader
I am sorry to ask you again, if you have any idea what is going wrong.
Thanks and merry christmas!
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