Re: [Nemo-cyclone-users] Fwd: oracle section in hyperjaxb2.paths.xml

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Dear Sir,

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Thanks for your help!. I tried again as the installation document says, =
but now I have new error:

java -jar CyClone_Core_fat-1.0.beta.2006-juillet-19-10-12.jar =
-function:Biocyc2Xsd -orgids:Meta -max:10

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Starting Cyclone application :

******************************

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0    [main] INFO  fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd  =
- managingFunction() - Starting exploring Biocyc ontology to extract a =
xml schema for cyclone application

2006-08-08 16:40:24,089 INFO =
[fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd] - =
<managingFunction() - Starting exploring Biocyc ontology to extract a =
xml schema for cyclone application>

1317 [main] INFO  =
fr.cns.genoscope.nemo.hypercyc.connection.ServerPathwayToolsServices  - =
start() - Waiting for PathwayTools server ...

2006-08-08 16:40:25,406 INFO =
[fr.cns.genoscope.nemo.hypercyc.connection.ServerPathwayToolsServices] - =
<start() - Waiting for PathwayTools server ...>

41712 [Thread-0] INFO  fr.cns.genoscope.nemo.hypercyc.connection.Reader  =
- read() - PathwayTools Server started !

2006-08-08 16:41:05,801 INFO =
[fr.cns.genoscope.nemo.hypercyc.connection.Reader] - <read() - =
PathwayTools Server started !>

2006-08-08 16:41:05,810 INFO =
[fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo=
gyExplorer] - <extractFrameOntology() - start>

2006-08-08 16:41:05,962 INFO =
[fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo=
gyExplorer] - <extractFrameOntology(int) - Screening myOrgcyc=3D Meta>

Exception in thread "main" java.lang.reflect.InvocationTargetException

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at =
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java=
:39)

        at =
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorI=
mpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:585)

        at com.simontuffs.onejar.Boot.run(Boot.java:247)

        at com.simontuffs.onejar.Boot.main(Boot.java:105)

Caused by: java.lang.UnsatisfiedLinkError: no unixdomainsocket in =
java.library.path

        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1682)

        at java.lang.Runtime.loadLibrary0(Runtime.java:822)

        at java.lang.System.loadLibrary(System.java:992)

        at =
fr.cns.genoscope.nemo.hypercyc.connection.UnixDomainSocket.<clinit>(UnixD=
omainSocket.java:39)

        at =
fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.makeSocket(JavacycP=
lus.java:96)

        at =
fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.callFuncArray(Javac=
ycPlus.java:1548)

        at =
fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getRootClasses(Java=
cycPlus.java:685)

        at =
fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolog=
yExplorer.processAsOrgcyc(JavacycFrameOntologyExplorer.java:172)

        at =
fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolog=
yExplorer.processOrgcycs(JavacycFrameOntologyExplorer.java:157)

        at =
fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolog=
yExplorer.extractFrameOntology(JavacycFrameOntologyExplorer.java:111)

        at =
fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd.createXsd(Biocyc2Xsd=
.java:107)

        at =
fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd.managingFunction(Bio=
cyc2Xsd.java:69)

        at =
fr.cns.genoscope.nemo.cyclone.application.CycloneTerminal.main(CycloneTer=
minal.java:63)

        ... 6 more

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Here is java version info:

java version "1.5.0_05"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_05-b05)

Java HotSpot(TM) Server VM (build 1.5.0_05-b05, mixed mode)

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I tried on sparc/solaris.

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Any suggestions?

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Alex.

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________________________________

From: Cyclone Support [mailto:cy...@ge...]=20
Sent: Friday, July 21, 2006 5:09 AM
To: Li, Alex
Subject: Re: Fwd: oracle section in hyperjaxb2.paths.xml

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Dear Li,
Sourceforge has released the file this morning.
I have tested it=20

*	download: ok
*	untar ok
*	checksum ok

Hope it will be fine.

Francois

Dear Francios,

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I did as you said and got to this page:

http://sourceforge.net/project/showfiles.php?group_id=3D162756&package_id=
=3D188019&release_id=3D433503

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But the file size is 0.

=20

Alex.

=20

=20

________________________________

From: Cyclone Support [mailto:cy...@ge...]=20
Sent: Thursday, July 20, 2006 5:10 AM
To: Li, Alex
Cc: Hagen, Tom
Subject: Re: Fwd: oracle section in hyperjaxb2.paths.xml

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Dear Alex,

To solve your problem, I have made a new release of Cyclone which will =
be disponible at sourceforge in a few hours ( depends on their server =
charge).
So go to http://sourceforge.net/project/showfiles.php?group_id=3D162756 =
, and download the release for Biocyc 10.X ( compatible with biocyc 10.0 =
and with your oracle configuration )

If your request is urgent, you can follow the procedure:

*	Download Oracle JDBC jar

	*	download jdbc driver for oracle at =
http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/index.html
	*	put it in CyClone_Core/lib/oracle

*	Modify hyperjaxb2.paths.xml by adding the following paragraph to =
declare the variable oracledb.path

	*	<path id=3D"oracledb.path">
		                                <fileset id=3D"oracledb.fileset" =
dir=3D"${hyperjaxb2.lib.dir}/oracle">
		                                    <include name=3D"XXXXXXXXX.jar"/>  =
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		                                </fileset>
		            </path >
	*	XXXX.jar are the name of oracle jdbc driver you have downloaded by =
your own

*	Modify cyclone.build.xml to tell cyclone to use oracle

	*	<path id=3D"hyperjaxb2.db.path">
		        <!-- flf -->
		        <!-- path refid=3D"hsqldb.path"/-->
		        <!--path refid=3D"mysqldb.path"/-->
		        <!--path refid=3D"pgsqldb.path"/-->
		        <!--path refid=3D"sybasedb.path"/-->
		        <path refid=3D"oracledb.path"/>
		        </path>

Hope this will help you,
Tell me if you encounter any other difficulty, we didn't test cyclone =
with oracle, but it should work.

Be sure to write to cy...@ge... which is an alias for =
cyclone developpers, and you will have next time a quicker answer.

Thanks for your interest in Cyclone product.

Francois

Fran=E7ois, Serge,=20

Pouvez-vous r=E9pondre =E0 cette requ=EAte ?=20

Merci d'avance,=20

Vincent=20

---------- Forwarded message ----------=20
From: Li, Alex <al...@pi...> <mailto:al...@pi...> =20
Date: 14 juil. 2006 16:51=20
Subject: oracle section in hyperjaxb2.paths.xml=20
To: vs...@ge...=20
Cc: "Hagen, Tom" <tom...@pi...> <mailto:tom...@pi...>  =

Dear Dr. Schanchter,=20

I am trying to install Cyclone on our sun server. We have oracle. I=20
tried to follow the installation section to configurate=20
huperjaxb2.paths.xml but cannot find the oracle section to uncomment.=20
I can see hsqldb, pgsqldb, and sybasedb, but not that one for oracle.=20

Could you please send me that section?=20

Thanks in advance.=20

Alex Li=20

Bioinformatics Programmer,=20

Pioneer Hi-Bred International=20

515-334-4736=20

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