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From: Sergi <se...@se...> - 2006-08-21 16:09:13
|
What about Cyclone as a plugin for Cytoscape ? |
|
From: <fle...@ge...> - 2006-08-20 09:00:00
|
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. 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 > > > > 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. 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 > > > > > > 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. 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 > |
|
From: Chen, G. <gua...@pi...> - 2006-08-15 19:20:27
|
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
This communication is for use by the intended recipient and contains=20
information that may be Privileged, confidential or copyrighted under=20
applicable law. If you are not the intended recipient, you are hereby=20
formally notified that any use, copying or distribution of this e-mail,=20
in whole or in part, is strictly prohibited. Please notify the sender by=20
return e-mail and delete this e-mail from your system. Unless explicitly=20
and conspicuously designated as "E-Contract Intended", this e-mail does=20
not constitute a contract offer, a contract amendment, or an acceptance=20
of a contract offer. This e-mail does not constitute a consent to the=20
use of sender's contact information for direct marketing purposes or for=20
transfers of data to third parties.=20
Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean=20
http://www.DuPont.com/corp/email_disclaimer.html=20
=20
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. 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.
=20
Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean
=20
http://www.DuPont.com/corp/email_disclaimer.html
=20
=20
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. 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
|
|
From: Li, A. <al...@pi...> - 2006-08-08 22:12:32
|
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:Biocyc2Xsd -orgids:Meta -max:10
=20
=20
Starting Cyclone application :
******************************
=20
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
=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 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"/> =
=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...> =
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
This communication is for use by the intended recipient and contains=20
information that may be Privileged, confidential or copyrighted under=20
applicable law. If you are not the intended recipient, you are hereby=20
formally notified that any use, copying or distribution of this e-mail,=20
in whole or in part, is strictly prohibited. Please notify the sender by =
return e-mail and delete this e-mail from your system. Unless explicitly =
and conspicuously designated as "E-Contract Intended", this e-mail does=20
not constitute a contract offer, a contract amendment, or an acceptance=20
of a contract offer. This e-mail does not constitute a consent to the=20
use of sender's contact information for direct marketing purposes or for =
transfers of data to third parties.=20
Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean=20
http://www.DuPont.com/corp/email_disclaimer.html=20
=20
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. 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.
=20
Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean
=20
http://www.DuPont.com/corp/email_disclaimer.html
=20
=20
|
|
From: Ludovic C. <co...@bi...> - 2006-07-28 12:52:26
|
Ok, mais pour maintenant j'essaierai ca a la rentree (je m'en vais dans=20 quelques instants). Je t'envoie tout ca a la rentree. Ludovic On Friday 28 July 2006 14:46, Cyclone Support wrote: > Ludovic, > > Donc ce bug est du a un probleme de non respect du standart lisp dans > pathway-tools/biocyc. et donc quand cyclone cherche a introspecter les > slots de l'instance il n'y arrive pas. Il attend un slot de type string > et recoit un slot de type array. > > Le plus simple en premiere approche est que tu m'envoie la frame en > question <ENZRXN2AA-227>. > peux-tu ouvrir le fichier ocelot et rechercher le paragraphe qui > correspond a cette frame et me l'envoyer. > > par ailleurs, est ce que tu as mis en arguments seulement les 2 autres > organismes et est ce que cyclone a =E9t=E9 au bout? > > sinon sur sourceforge, tu trouveras la derniere release de cyclone avec > le correctif entre sur le mot cl=E9 schema. > > Maintenant, que l'email cyclone est bien parametrer, je te repondrai au > plus vite. > merci pour tout tes commentaires. > Merci pour ta patience, > > Francois > > >Bonjour, > > > >J'ai essaye ce qui suit : > >> o pour etre compatible avec Biocyc 10.0, il faut: > >> + relancer la procedure qui cr=E9e le schema biocyc.xsd > >> # Fonction: Biocyc2Xsd.createXsd(organisms,max) > >> * organims la liste des organismes que tu > >> souhaiteras mettre dans cyclone > >> * max 1000000 : profondeur d'introspection > >> des frames > >> # exemple dans tutorial1 > >> # Resultat un nouveau schema xsd, dans le dossier > >> Cyclone/schema > > > >mais au bout du troisieme organisme, il me renvoie cette erreur (je n'ai > > copie que 2 lignes avant le message d'erreur) : > > > > > >------------------------------------------------------------------------= =2D- > >------------------------------------------------------------------------= =2D- > >---------------------------------------------------------------------- > > 2006-07-17 18:55:25,017 DEBUG > >[fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntol= og > >yExplorer] - <extractFrameOntology(int) - Screening > > baphaps myClass=3D|Enzymatic-Reactions| 11:377> > >2006-07-17 18:55:25,018 DEBUG > >[fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntol= og > >yExplorer] - <extractFrameOntology(int) - myLog=3D2738 ENZRXN2AA-227> > >Exception in thread "main" java.lang.ClassCastException: > > java.util.ArrayList at > >fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getFrameComments(J= av > >acycPlus.java:419) at > >fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getSlotValues(Java= cy > >cPlus.java:151) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processAsInstanceSlot(JavacycFrameOntologyExplorer.java:311) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processAsInstance(JavacycFrameOntologyExplorer.java:279) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processInstances(JavacycFrameOntologyExplorer.java:268) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processAsClass(JavacycFrameOntologyExplorer.java:232) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processClasses(JavacycFrameOntologyExplorer.java:193) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processAsOrgcyc(JavacycFrameOntologyExplorer.java:175) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.processOrgcycs(JavacycFrameOntologyExplorer.java:157) at > >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntolo= gy > >Explorer.extractFrameOntology(JavacycFrameOntologyExplorer.java:111) at > >fr.cns.genoscope.nemo.cyclone.application.Biocyc2Xsd.createXsd(Biocyc2Xs= d. > >java:107) at baobab.createBaobabXsd.main(createBaobabXsd.java:16) > >------------------------------------------------------------------------= =2D- > >------------------------------------------------------------------------= =2D- > >---------------------------------------------------------------------- > > > >Avez vous une idee de ce a quoi ca peut etre du ? > > > >Notes : > >- baobab.createBaobabXsd reprend juste l'exemple 1 du tutorial avec comme > >arguments la liste de mes organismes > >- baphaps est une des pgdbs que j'ai reconstruite. > > > > > >Cordialement, > >LC =2D-=20 =2D-- Ludovic COTTRET Phd student BAOBAB Team (http://biomserv.univ-lyon1.fr/baobab) UMR 5558 Biom=E9trie et Biologie =C9volutive Universit=E9 Claude Bernard, Lyon I 43, Bd du 11 novembre 1918 69622 Villeurbanne cedex =46rance |
|
From: Cyclone S. <cy...@ge...> - 2006-07-28 12:46:32
|
Ludovic, Donc ce bug est du a un probleme de non respect du standart lisp dans pathway-tools/biocyc. et donc quand cyclone cherche a introspecter les slots de l'instance il n'y arrive pas. Il attend un slot de type string et recoit un slot de type array. Le plus simple en premiere approche est que tu m'envoie la frame en question <ENZRXN2AA-227>. peux-tu ouvrir le fichier ocelot et rechercher le paragraphe qui correspond a cette frame et me l'envoyer. par ailleurs, est ce que tu as mis en arguments seulement les 2 autres organismes et est ce que cyclone a été au bout? sinon sur sourceforge, tu trouveras la derniere release de cyclone avec le correctif entre sur le mot clé schema. Maintenant, que l'email cyclone est bien parametrer, je te repondrai au plus vite. merci pour tout tes commentaires. Merci pour ta patience, Francois >Bonjour, > >J'ai essaye ce qui suit : > > > > >> o pour etre compatible avec Biocyc 10.0, il faut: >> + relancer la procedure qui crée le schema biocyc.xsd >> # Fonction: Biocyc2Xsd.createXsd(organisms,max) >> * organims la liste des organismes que tu >> souhaiteras mettre dans cyclone >> * max 1000000 : profondeur d'introspection >> des frames >> # exemple dans tutorial1 >> # Resultat un nouveau schema xsd, dans le dossier >> Cyclone/schema >> >> > >mais au bout du troisieme organisme, il me renvoie cette erreur (je n'ai copie >que 2 lignes avant le message d'erreur) : > > >-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >2006-07-17 18:55:25,017 DEBUG >[fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer] - ><extractFrameOntology(int) - Screening baphaps myClass=|Enzymatic-Reactions| >11:377> >2006-07-17 18:55:25,018 DEBUG >[fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer] - ><extractFrameOntology(int) - myLog=2738 ENZRXN2AA-227> >Exception in thread "main" java.lang.ClassCastException: java.util.ArrayList > at >fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getFrameComments(JavacycPlus.java:419) > at >fr.cns.genoscope.nemo.hypercyc.connection.JavacycPlus.getSlotValues(JavacycPlus.java:151) > at >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processAsInstanceSlot(JavacycFrameOntologyExplorer.java:311) > at >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processAsInstance(JavacycFrameOntologyExplorer.java:279) > at >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processInstances(JavacycFrameOntologyExplorer.java:268) > at >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processAsClass(JavacycFrameOntologyExplorer.java:232) > at >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processClasses(JavacycFrameOntologyExplorer.java:193) > at >fr.cns.genoscope.nemo.cyclone.biocyc.ontologycreation.JavacycFrameOntologyExplorer.processAsOrgcyc(JavacycFrameOntologyExplorer.java:175) > 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 baobab.createBaobabXsd.main(createBaobabXsd.java:16) >-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > >Avez vous une idee de ce a quoi ca peut etre du ? > >Notes : >- baobab.createBaobabXsd reprend juste l'exemple 1 du tutorial avec comme >arguments la liste de mes organismes >- baphaps est une des pgdbs que j'ai reconstruite. > > >Cordialement, >LC > > > > |
|
From: Ludovic C. <co...@bi...> - 2006-07-28 12:27:35
|
Bien recu ! On Friday 28 July 2006 13:25, Cyclone Support wrote: > Ludovic, > voici un test d'envoi d'email avec une nouvelle adresse. > peux-tu me dire si tu as bien recu cet email, > > merci > > Francois =2D-=20 =2D-- Ludovic COTTRET Phd student BAOBAB Team (http://biomserv.univ-lyon1.fr/baobab) UMR 5558 Biom=E9trie et Biologie =C9volutive Universit=E9 Claude Bernard, Lyon I 43, Bd du 11 novembre 1918 69622 Villeurbanne cedex =46rance |
|
From: Cyclone S. <cy...@ge...> - 2006-07-28 11:25:47
|
Ludovic, voici un test d'envoi d'email avec une nouvelle adresse. peux-tu me dire si tu as bien recu cet email, merci Francois |
|
From: Cyclone S. <cy...@ge...> - 2006-07-21 10:09:29
|
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
> <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
> o download jdbc driver for oracle at
> http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/index.html
> o put it in CyClone_Core/lib/oracle
> * Modify hyperjaxb2.paths.xml by adding the following paragraph to
> declare the variable oracledb.path
> o <path id="oracledb.path">
> <fileset
> id="oracledb.fileset" dir="${hyperjaxb2.lib.dir}/oracle">
> <include
> name="XXXXXXXXX.jar"/>
> </fileset>
> </path >
> o 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
> o <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...
> <mailto: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... <mailto: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. Unless explicitly
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> 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
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> transfers of data to third parties.
>
> Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean
>
> http://www.DuPont.com/corp/email_disclaimer.html
>
>
>
>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. 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
>
>
|
|
From: Cyclone S. <cy...@ge...> - 2006-07-21 08:32:55
|
|
From: Francois Le F. <fl...@gm...> - 2006-07-21 07:59:02
|
--
----------------------------------------------------------------
Francois Le Fevre
Management Informatics Biotechnology
France, Paris
|
|
From: Francois Le F. <fle...@ge...> - 2006-04-21 08:07:12
|
Welcome to the Cyclone mailling list. Francois |
1 message has been excluded from this view by a project administrator.
