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Re: [Nemo-cyclone-users] Fwd: oracle section in hyperjaxb2.paths.xml
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From: <fle...@ge...> - 2006-08-20 09:00:00
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Dear all, I have just come back from holliday. I think that your analysis of the problem is good. We have never test cyclone on a sparc/solaris o.s. Here the source code for unixdomainsocket, which was designed by the javacyc team for unix system it seems. I will look at it tomorrow at the office, I have no data / program at home to investigate more on the problem. Sincerely Francois > Francois, > > > > To follow Alex's thread, I add the > CyClone_Core/lib/unix/libunixdomainsocket.so into my $ LD_LIBRARY_PATH. > Then got a different error message: > > > >> /opt/local/jdk1.5.0_05/bin/java -jar >> CyClone_Core_fat-1.0.beta.2006-juillet-19-10-12.jar -function:Biocyc2Xsd >> -orgids:Meta -max:10 > > Starting Cyclone application : > > ****************************** > > > > 0 [main] INFO fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd - > managingFunction() - Starting exploring Biocyc ontology to extract a xml > schema for cyclone application > > 2006-08-15 13:32:51,657 INFO > [fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd] - > <managingFunction() - Starting exploring Biocyc ontology to extract a xml > schema for cyclone application> > > 327 [main] INFO > fr.cns.genoscope.nemo.hypercyc.connection.ServerPathwayToolsServices - > start() - Waiting for PathwayTools server ... > > 2006-08-15 13:32:51,984 INFO > [fr.cns.genoscope.nemo.hypercyc.connection.ServerPathwayToolsServices] - > <start() - Waiting for PathwayTools server ...> > > 2281 [Thread-0] INFO fr.cns.genoscope.nemo.hypercyc.connection.Reader - > read() - PathwayTools Server started ! > > 2006-08-15 13:32:53,938 INFO > [fr.cns.genoscope.nemo.hypercyc.connection.Reader] - <read() - > PathwayTools Server started !> > > 2006-08-15 13:32:53,947 INFO > [fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer] > - <extractFrameOntology() - start> > > 2006-08-15 13:32:53,969 INFO > [fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer] > - <extractFrameOntology(int) - Screening myOrgcyc= 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(DelegatingMethodAccessorImpl.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_Core/lib/unix/libunixdomainsocket.so: > ld.so.1: /opt/local/jdk1.5.0_05/bin/java: 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.<clinit>(UnixDomainSocket.java:39) > > at > fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.makeSocket(JavacycPlus.java:96) > > at > fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.callFuncArray(JavacycPlus.java:1548) > > > > Looks like I am using wrong unixdomainsocket. > > > > Where can I get the source code and compile it locally? > > > > Thanks very much. > > > > Guanghong Chen > > > > Pioneer Hi-Bred Int'l > > > > ________________________________ > > From: Li, Alex > Sent: Tuesday, August 15, 2006 10:59 AM > To: Chen, Guanghong > Cc: Hagen, Tom > Subject: FW: Fwd: oracle section in hyperjaxb2.paths.xml > > > > Here is the error message. > > > > ________________________________ > > From: Li, Alex > Sent: Tuesday, August 08, 2006 4:46 PM > To: 'cy...@ge...' > Cc: Hagen, Tom > Subject: RE: Fwd: oracle section in hyperjaxb2.paths.xml > > > > Dear Sir, > > > > 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 > > > > > > Starting Cyclone application : > > ****************************** > > > > 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.JavacycFrameOntologyExplorer] > - <extractFrameOntology() - start> > > 2006-08-08 16:41:05,962 INFO > [fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer] > - <extractFrameOntology(int) - Screening myOrgcyc= 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(DelegatingMethodAccessorImpl.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>(UnixDomainSocket.java:39) > > at > fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.makeSocket(JavacycPlus.java:96) > > at > fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.callFuncArray(JavacycPlus.java:1548) > > at > fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getRootClasses(JavacycPlus.java:685) > > at > fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processAsOrgcyc(JavacycFrameOntologyExplorer.java:172) > > at > fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processOrgcycs(JavacycFrameOntologyExplorer.java:157) > > at > fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.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(Biocyc2Xsd.java:69) > > at > fr.cns.genoscope.nemo.cyclone.application.CycloneTerminal.main(CycloneTerminal.java:63) > > ... 6 more > > > > 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) > > > > I tried on sparc/solaris. > > > > Any suggestions? > > > > Alex. > > > > ________________________________ > > From: Cyclone Support [mailto:cy...@ge...] > Sent: Friday, July 21, 2006 5:09 AM > To: Li, Alex > Subject: Re: Fwd: oracle section in hyperjaxb2.paths.xml > > > > Dear Li, > Sourceforge has released the file this morning. > I have tested it > > * download: ok > * untar ok > * checksum ok > > > Hope it will be fine. > > Francois > > Dear Francios, > > > > I did as you said and got to this page: > > http://sourceforge.net/project/showfiles.php?group_id=162756&package_id=188019&release_id=433503 > > > > But the file size is 0. > > > > Alex. > > > > > > ________________________________ > > From: Cyclone Support [mailto:cy...@ge...] > Sent: Thursday, July 20, 2006 5:10 AM > To: Li, Alex > Cc: Hagen, Tom > Subject: Re: Fwd: oracle section in hyperjaxb2.paths.xml > > > > 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=162756 , > 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="oracledb.path"> > <fileset id="oracledb.fileset" > dir="${hyperjaxb2.lib.dir}/oracle"> > <include name="XXXXXXXXX.jar"/> > </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="hyperjaxb2.db.path"> > <!-- flf --> > <!-- path refid="hsqldb.path"/--> > <!--path refid="mysqldb.path"/--> > <!--path refid="pgsqldb.path"/--> > <!--path refid="sybasedb.path"/--> > <path refid="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 > > > > François, Serge, > > Pouvez-vous répondre à cette requête ? > > Merci d'avance, > > Vincent > > ---------- Forwarded message ---------- > From: Li, Alex <al...@pi...> <mailto:al...@pi...> > Date: 14 juil. 2006 16:51 > Subject: oracle section in hyperjaxb2.paths.xml > To: vs...@ge... > Cc: "Hagen, Tom" <tom...@pi...> <mailto:tom...@pi...> > > > > > > Dear Dr. Schanchter, > > > > I am trying to install Cyclone on our sun server. We have oracle. I > tried to follow the installation section to configurate > huperjaxb2.paths.xml but cannot find the oracle section to uncomment. > I can see hsqldb, pgsqldb, and sybasedb, but not that one for oracle. > > Could you please send me that section? > > > > Thanks in advance. > > > > Alex Li > > Bioinformatics Programmer, > > Pioneer Hi-Bred International > > 515-334-4736 > > > > This communication is for use by the intended recipient and contains > information that may be Privileged, confidential or copyrighted under > applicable law. If you are not the intended recipient, you are hereby > formally notified that any use, copying or distribution of this e-mail, > in whole or in part, is strictly prohibited. Please notify the sender by > return e-mail and delete this e-mail from your system. 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Unless explicitly > and conspicuously designated as "E-Contract Intended", this e-mail does > not constitute a contract offer, a contract amendment, or an acceptance > of a contract offer. This e-mail does not constitute a consent to the > use of sender's contact information for direct marketing purposes or for > transfers of data to third parties. > > Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean > > http://www.DuPont.com/corp/email_disclaimer.html > |
