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How to use the 'debug' mode ?

To print all generated SQL and add comments to the generated SQL by Hibernate to the console, edit the file in Cyclone_1.0b>hbm/cyclone>hibernate.properties. Switch to true hibernate.show_sql and hibernate.use_sql_comments.
To print all Cyclone debug information, edit the file in Cyclone_1.0b>src/config>log4j.properties. Switch the parameters to values requested (FATAL, ERROR, DEBUG, INFO,A1)
More on Log4J

How do I solve the Eclipse memory error ?

If you get this error 'Exception in thread "main" java.lang.OutOfMemoryError: Java heap space, you need to add memory to run a Java class. Right click on the class name in the 'Package Explorer'. Select 'RunAS>Run'... In the 'Arguments' tab, enter -Xmx1024M as VM arguments. This will give 1024Mo of memory to Eclipse Virtual Memory.
More on Eclipse

Where can I find more information about the Java functions ?

JavaDoc can be accessed in the directory /doc. Cyclone JavaDoc is also available online.

How to view the object model, XSD ?

With Eclipse, open schema/biocyc.xsd and select the graph view in the biocyc.xsd tab that will open.

How to customize the Cyclone schema ?

Cyclone Platform has been settled with a default schema located at Cyclone_Core/schema/cyclone.xsd. This schema has been extracted by Cyclone from Pathway-Tools 10.0 by querying EcoCyc and MetaCyc.
If it does not match your Pathway-Tools version or your PGDB customized schema, you will need to create a new schema by running the Biocyc2Xsd.createXsd method with your organism for argument. For more information about this procedure, try the function TutorialEx1 located in the file: Cyclone_Core/src/manually-generated/fr.cns.genoscope.nemo.cyclone.application/Tutorial.java .

How to run Cyclone commands in the terminal ?

- To build the XSD schema of a Cyc, type the following command, for example
java -jar Cyclone_1.0b_fat.jar -function:Biocyc2Xsd -orgids:Meta -max:2
It will create a file ./workspace/Cyclone_1.0b/schema/biocyc.xsd
- To build the XML file with the data of a Cyc, type the following command, for example
java -jar Cyclone_1.0b_fat.jar -function:Biocyc2Xml -orgids:Meta -max:100
It will create a file ./workspace/Cyclone_1.0b/samples/Meta-*.xml
The jar archive requires mySQL. To use a distinct database, you will need to make your own .jar. Furthermore, a short selection of functions are available from the jar. We encourage you to add your own functions or use a Java IDE like Eclipse to access all the functions.

How to launch the HQL query interface of Cyclone with JBoss ?

HQL means Object Query Language. You can query and browse Cyclone data using the JBoss interface. This is a really powerful and easier way to query and browse the data than using SQL or SQL browser. Objects underlying Cyclone make it really easier to access data than biowarehouse for example.
- In Eclipse, open the menu Window>Open perspective>Other... and select in the popup window 'Hibernate Console'.
- In the 'Hibernate Configurations' tab (top left panel), right click and select 'Add configuration'
- Enter the following parameters:
Name: Cyclone
Property file: /Cyclone_1.0b/hbm/cyclone/hibernate.properties
Configuration file: Nothing to enter!
Entity resolver: Nothing to enter!
In the 'Mapping file' area, 'Add' all the files in /Cyclone_1.0b/classes/fr/cns/genoscope/nemo/cyclone/db/generated/.
To do so, click on the first file found 'AbbrevName.hbm.xml' and shift click on the last one 'Year.hbm.xml', then click 'Ok'.
In the 'Class path' area, 'add JARs/Dir', all the following files:
/lib/mysql/mysql-connector-java-3.1.10-bin.jar or your favorite rdbms JDBC
/lib/jaxb/*.jar/lib/hyperjaxb2/hyperjaxb2.jarThen click Finish.
Now in the Hibernate Configurations tab, you should see the created configuration Cyclone.
- In this tab, Right click on Cyclone and select menu 'HQL Scratchpad'`
- In the opened tab, write for example: select g.Values from Gene g
You should get the result in the 'Hibernate Query Result' tab on the bottom of the screen instantly.
Some other examples of simple queries: select count(distinct r.FrameId) from GeneralizedReactions r

How to use Cyclone Core with Eclipse ?

This is an optional step. It is required only if you want to use Cyclone within the Eclipse framework.
- Copy or move the Cyclone directory into your eclipse workspace: cp -r ./CyClone_Core /home/user/workspace/Cyclone_Core or mv ./CyClone_Core /home/user/workspace/Cyclone_Core
- Run eclipse: ./eclipse/eclipse &
- Close the Eclipse welcome page if any.
- Select in the Eclipse menu File>Import... and then select 'Existing Projects into Workspace'.
- Next select your root directory (should be /home/user/workspace/CyClone_Core).
- Click the Finish button. Then Eclipse will build the workspace.
- If any error appears, please check that your project is configured for Java 5.0: Right click on Cyclone Project > Java Compiler> Enable project specific settings > Set Compiler compliance level to 5.0
- On the 'Package Explorer' tab on the left of the screen, open CyClone_Core > src/config > cyclone.conf.xml. The file will open in the main tab.
- If not already done, open the property gproot4Server and set it to the command that enables you to start Pathway Tools in server mode.
- Save the file.
- Right-click on cyclone.build.xml and select menu 'Run as>2 Ant Build...'
- In the pop-up window, in the 'Classpath' tab, click on 'User Entries' and 'Add JARs'.
- In the second pop-up window, select Cyclone_core>lib>junit>junit.jar
- Click Apply and Run this will execute the default task described at Architecture-Pipeline
Note: The Ant Build should take between 1 and 10 minutes.
Note: the log may show the error : [junit] test fr.cns.genoscope.cyclone.db.tests.RoundtripTestCase FAILED. This should not have any consequences.

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