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

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Francois,

=20

To follow Alex's thread, I add the CyClone_Core/lib/unix/libunixdomainsocke=
t=2Eso into my $ LD_LIBRARY_PATH. Then got a different error message:

=20

> /opt/local/jdk1.5.0_05/bin/java -jar CyClone_Core_fat-1.0.beta.2006-juill=
et-19-10-12.jar -function:Biocyc2Xsd -orgids:Meta -max:10

Starting Cyclone application :

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

=20

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

2006-08-15 13:32:51,657 INFO [fr.cns.genoscope.nemo.cyclone.application.Bio=
cyc2Xsd] - <managingFunction() - Starting exploring Biocyc ontology to extr=
act a xml schema for cyclone application>

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

2006-08-15 13:32:51,984 INFO [fr.cns.genoscope.nemo.hypercyc.connection.Ser=
verPathwayToolsServices] - <start() - Waiting for PathwayTools server ...>

2281 [Thread-0] INFO  fr.cns.genoscope.nemo.hypercyc.connection.Reader  - r=
ead() - PathwayTools Server started !

2006-08-15 13:32:53,938 INFO [fr.cns.genoscope.nemo.hypercyc.connection.Rea=
der] - <read() - PathwayTools Server started !>

2006-08-15 13:32:53,947 INFO [fr.cns.genoscope.nemo.cyclone.biocyc.ontology=
creation.JavacycFrameOntologyExplorer] - <extractFrameOntology() - start>

2006-08-15 13:32:53,969 INFO [fr.cns.genoscope.nemo.cyclone.biocyc.ontology=
creation.JavacycFrameOntologyExplorer] - <extractFrameOntology(int) - Scree=
ning myOrgcyc=3D Meta>

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

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

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

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethod=
AccessorImpl.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: /data/compbio/projects/CyClone_C=
ore/lib/unix/libunixdomainsocket.so: ld.so.1: /opt/local/jdk1.5.0_05/bin/ja=
va: fatal: /data/compbio/projects/CyClone_Core/lib/unix/libunixdomainsocket=
.so: wrong ELF data format: ELFDATA2LSB

        at java.lang.ClassLoader$NativeLibrary.load(Native Method)

        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1751)

        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1676)

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

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

        at fr.cns.genoscope.nemo.hypercyc.connection.UnixDomainSocket.<clin=
it>(UnixDomainSocket.java:39)

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

        at fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.callFuncAr=
ray(JavacycPlus.java:1548)

=20

Looks like I am using wrong unixdomainsocket.=20

=20

Where can I get the source code and compile it locally?

=20

Thanks very much.

=20

Guanghong Chen

=20

Pioneer Hi-Bred Int'l

=20

________________________________

From: Li, Alex=20
Sent: Tuesday, August 15, 2006 10:59 AM
To: Chen, Guanghong
Cc: Hagen, Tom
Subject: FW: Fwd: oracle section in hyperjaxb2.paths.xml

=20

Here is the error message.

=20

________________________________

From: Li, Alex=20
Sent: Tuesday, August 08, 2006 4:46 PM
To: 'cy...@ge...'
Cc: Hagen, Tom
Subject: RE: Fwd: oracle section in hyperjaxb2.paths.xml

=20

Dear Sir,

=20

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:Bio=
cyc2Xsd -orgids:Meta -max:10

=20

=20

Starting Cyclone application :

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

=20

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

2006-08-08 16:40:24,089 INFO [fr.cns.genoscope.nemo.cyclone.application.Bio=
cyc2Xsd] - <managingFunction() - Starting exploring Biocyc ontology to extr=
act a xml schema for cyclone application>

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

2006-08-08 16:40:25,406 INFO [fr.cns.genoscope.nemo.hypercyc.connection.Ser=
verPathwayToolsServices] - <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.Rea=
der] - <read() - PathwayTools Server started !>

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

2006-08-08 16:41:05,962 INFO [fr.cns.genoscope.nemo.cyclone.biocyc.ontology=
creation.JavacycFrameOntologyExplorer] - <extractFrameOntology(int) - Scree=
ning myOrgcyc=3D Meta>

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

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

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

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethod=
AccessorImpl.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.libr=
ary.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.<clin=
it>(UnixDomainSocket.java:39)

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

        at fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.callFuncAr=
ray(JavacycPlus.java:1548)

        at fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getRootCla=
sses(JavacycPlus.java:685)

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

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

        at fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFra=
meOntologyExplorer.extractFrameOntology(JavacycFrameOntologyExplorer.java:1=
11)

        at fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd.createXsd(B=
iocyc2Xsd.java:107)

        at fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd.managingFun=
ction(Biocyc2Xsd.java:69)

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

        ... 6 more

=20

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)

=20

I tried on sparc/solaris.

=20

Any suggestions?

=20

Alex.

=20

________________________________

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

=20

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,

=20

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

=20

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

=20

Dear Alex,

To solve your problem, I have made a new release of Cyclone which will be d=
isponible at sourceforge in a few hours ( depends on their server charge).
So go to http://sourceforge.net/project/showfiles.php?group_id=3D162756 , a=
nd download the release for Biocyc 10.X ( compatible with biocyc 10.0 and w=
ith 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/soft=
ware/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"/>    =
   =20
		                                </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...> =20

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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