Cytoscape Wiki|
← Revision 1 as of 2006-04-20 02:04:21 →
Size: 1076
Comment:
|
Size: 2226
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| I have been playing around with using [http://db.apache.org/derby/ Derby] to associate databases with cytoscape networks. Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience. | Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access to relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience. |
| Line 3: | Line 3: |
| ---- | ----- |
| Line 7: | Line 7: |
|
http://db.apache.org/derby/ - Offical Apache Derby site http://db.apache.org/derby/quick_start.html - Useful Quick Start site for newbies [http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Related software] - Reference to OSGi (osgi.jar) * Relevant discussion threads relating to OSGi * [http://mail-archives.apache.org/mod_mbox/db-derby-dev/200512.mbox/%3C001001c602ae$adcdd270$6400a8c0@Apollo%3E thread#1] * [http://mail-archives.apache.org/mod_mbox/incubator-felix-dev/200603.mbox/%3C44061826.7010505@ungoverned.org%3E thread#2] |
* Offical [http://db.apache.org/derby/ Apache Derby] site * Useful [http://db.apache.org/derby/quick_start.html Quick Start] site for newbies * [http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Reference] to OSGi (osgi.jar) * Relevant discussion threads relating to OSGi wrt Derby * [http://mail-archives.apache.org/mod_mbox/db-derby-dev/200512.mbox/%3C001001c602ae$adcdd270$6400a8c0@Apollo%3E thread#1] * [http://mail-archives.apache.org/mod_mbox/incubator-felix-dev/200603.mbox/%3C44061826.7010505@ungoverned.org%3E thread#2] |
| Line 14: | Line 14: |
| == Overview == | == Getting It To Work == |
| Line 16: | Line 16: |
| ...more to come |
1. Like other libraries to be included in a plugin, you have to unjar the classes and include them in your build folder. 1. In order to get my application running, I needed to include both derby.jar and derbytools.jar. Leaving the other out helps keep the size down. These two jars add ~2.3MB. 1. One of the classes in derby.jar throws an exception while the plugin is being loaded by Cytoscape. EmbeddedActivator.class (org.apache.derby.osgi) implements BundleActivator.class which is ''not'' included in the Derby distribution. a. Turns out this class is part of an "optional" OSGi package which is under a proprietary license, not Apache! a. Rather than going down that dark and treacherous road, I simply removed the osgi folder containing only the EmbeddedActivator class and jared the remaining classes along with my plugin. No problems. == Materials == Here is a sinlge jar file containing derby.jar plus derbytools.jar minus the offending class And here is sample code for your build.xml to unjar and include the derby classes in your build file: {{{#!java <unjar overwrite="Yes" dest="${build}"> <fileset dir="${lib.derby}"> <include name="lib/derby-slim.jar"/> </fileset> </unjar> }}} ----- === Comments === |
Derby can serve as an embedded relational database in Java applications. This may be a solution for use cases that need real-time access to relatively stable data, such as gene aliases and annotations. Getting Derby to work within a Cytoscape plugin was not trivial, so I wanted to share that experience.
Important Links
Offical [http://db.apache.org/derby/ Apache Derby] site
Useful [http://db.apache.org/derby/quick_start.html Quick Start] site for newbies
[http://db.apache.org/derby/derby_downloads.html#Software+required+to+build+Derby Reference] to OSGi (osgi.jar)
- Relevant discussion threads relating to OSGi wrt Derby
Getting It To Work
- Like other libraries to be included in a plugin, you have to unjar the classes and include them in your build folder.
- In order to get my application running, I needed to include both derby.jar and derbytools.jar. Leaving the other out helps keep the size down. These two jars add ~2.3MB.
One of the classes in derby.jar throws an exception while the plugin is being loaded by Cytoscape. EmbeddedActivator.class (org.apache.derby.osgi) implements BundleActivator.class which is not included in the Derby distribution.
- Turns out this class is part of an "optional" OSGi package which is under a proprietary license, not Apache!
Rather than going down that dark and treacherous road, I simply removed the osgi folder containing only the EmbeddedActivator class and jared the remaining classes along with my plugin. No problems.
Materials
Here is a sinlge jar file containing derby.jar plus derbytools.jar minus the offending class
And here is sample code for your build.xml to unjar and include the derby classes in your build file:
1 <unjar overwrite="Yes" dest="${build}">
2 <fileset dir="${lib.derby}">
3 <include name="lib/derby-slim.jar"/>
4 </fileset>
5 </unjar>
6