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From: Steve F. <st...@pc...> - 2003-03-12 15:58:37
|
don't forget to update the 'install' project too... Steve Fischer wrote: > Folks- > > Dave and I have introduced some major new functionality into the build > system: > - compiling Java code > - building the Java object layer > - a new "release" operation, eg, build CBIL release v1-2-0 > > In order for things to work again, please do a cvs update -d in ALL > YOUR PROJECTS. > > As mentioned below, if you are outside CBIL, get the CBIL project from > the download site. > > PSU folks: please bear with us through this process. One of the > problems we are facing now is that our database is down which has > hampered some testing on this. > > Keep me posted, and we'll get this working... > > steve > > Steve Fischer wrote: > >> Folks- >> >> we have released a new version of CBIL. >> >> if you are in CBIL, just do this: >> %cd $PROJECT_HOME/CBIL >> %cvs update -d >> >> if you are outside CBIL, get it from the download site: >> >> http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz >> >> This should solve the problem that Paul and Arnaud are having. >> >> steve >> >> Pjm wrote: >> >>> >>> Okay, I did a cvs update of the install directory and I know get the >>> same problem as Arnaud. See the extra line of debugging I added to >>> the end. Shall I have a go at fixing this? I'm guessing component >>> should just be Bio, not CBIL/Bio... >>> >>> >>> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install >>> -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= >>> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger >>> org.apache.tools.ant.NoBannerLogger | grep ']' >>> >>> [echo] . >>> [echo] Installing CBIL/CBIL/Bio >>> [echo] project = CBIL component = CBIL/Bio >>> >>> >>> Pjm wrote: >>> >>>> >>>> Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs >>>> to look for /nfs/team81/pjm/CVS/CVS-new/GUS/Common. >>>> Arnaud has a similar problem but with a different directory (it >>>> wants CBIL/CBIL/Bio !) >>>> >>>> >>>> >>>> pcs2g[pjm]131: build GUS install -append >>>> >>>> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install >>>> -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= >>>> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger >>>> org.apache.tools.ant.NoBannerLogger | grep ']' >>>> >>>> [echo] . >>>> [echo] Installing CBIL/Bio >>>> [echo] . >>>> [echo] Installing CBIL/CSP >>>> [echo] . >>>> [echo] Installing CBIL/Util >>>> [echo] . >>>> [echo] Installing Common >>>> >>>> BUILD FAILED >>>> file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108: >>>> Component directory /nfs/team81/pjm/CVS/CVS-new/Common not >>>> found. >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.net email is sponsored by:Crypto Challenge is now open! Get >>>> cracking and register here for some mind boggling fun and the >>>> chance of winning an Apple iPod: >>>> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>> >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.net email is sponsored by:Crypto Challenge is now open! Get >>> cracking and register here for some mind boggling fun and the chance >>> of winning an Apple iPod: >>> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >> >> >> > > > |
|
From: Deborah F. P. <pi...@pc...> - 2003-03-12 15:56:04
|
Having followed the directions below and then trying to build I get
errors that vary somewhat:
BUILD FAILED
file:/home/pinney/projects/install/build.xml:114:
Component directory /home/pinney/projects/CSP not found.On Wed, 12
and a similar error but having Bio not found (this was the initial error)
Mar 2003,
Steve
Fischer wrote:
> Folks-
>
> we have released a new version of CBIL.
>
> if you are in CBIL, just do this:
> %cd $PROJECT_HOME/CBIL
> %cvs update -d
>
> if you are outside CBIL, get it from the download site:
>
> http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz
>
> This should solve the problem that Paul and Arnaud are having.
>
> steve
>
> Pjm wrote:
>
> >
> > Okay, I did a cvs update of the install directory and I know get the
> > same problem as Arnaud. See the extra line of debugging I added to the
> > end. Shall I have a go at fixing this? I'm guessing component should
> > just be Bio, not CBIL/Bio...
> >
> >
> > ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install
> > -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp=
> > -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger
> > org.apache.tools.ant.NoBannerLogger | grep ']'
> >
> > [echo] .
> > [echo] Installing CBIL/CBIL/Bio
> > [echo] project = CBIL component = CBIL/Bio
> >
> >
> > Pjm wrote:
> >
> >>
> >> Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs
> >> to look for /nfs/team81/pjm/CVS/CVS-new/GUS/Common.
> >> Arnaud has a similar problem but with a different directory (it wants
> >> CBIL/CBIL/Bio !)
> >>
> >>
> >>
> >> pcs2g[pjm]131: build GUS install -append
> >>
> >> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install
> >> -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp=
> >> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger
> >> org.apache.tools.ant.NoBannerLogger | grep ']'
> >>
> >> [echo] .
> >> [echo] Installing CBIL/Bio
> >> [echo] .
> >> [echo] Installing CBIL/CSP
> >> [echo] .
> >> [echo] Installing CBIL/Util
> >> [echo] .
> >> [echo] Installing Common
> >>
> >> BUILD FAILED
> >> file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108:
> >> Component directory /nfs/team81/pjm/CVS/CVS-new/Common not found.
> >>
> >>
> >>
> >>
> >> -------------------------------------------------------
> >> This SF.net email is sponsored by:Crypto Challenge is now open! Get
> >> cracking and register here for some mind boggling fun and the chance
> >> of winning an Apple iPod:
> >> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> >> _______________________________________________
> >> Gusdev-gusdev mailing list
> >> Gus...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by:Crypto Challenge is now open! Get
> > cracking and register here for some mind boggling fun and the chance
> > of winning an Apple iPod:
> > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by:Crypto Challenge is now open!
> Get cracking and register here for some mind boggling fun and
> the chance of winning an Apple iPod:
> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Steve F. <st...@pc...> - 2003-03-12 15:55:37
|
Folks- Dave and I have introduced some major new functionality into the build system: - compiling Java code - building the Java object layer - a new "release" operation, eg, build CBIL release v1-2-0 In order for things to work again, please do a cvs update -d in ALL YOUR PROJECTS. As mentioned below, if you are outside CBIL, get the CBIL project from the download site. PSU folks: please bear with us through this process. One of the problems we are facing now is that our database is down which has hampered some testing on this. Keep me posted, and we'll get this working... steve Steve Fischer wrote: > Folks- > > we have released a new version of CBIL. > > if you are in CBIL, just do this: > %cd $PROJECT_HOME/CBIL > %cvs update -d > > if you are outside CBIL, get it from the download site: > > http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz > > This should solve the problem that Paul and Arnaud are having. > > steve > > Pjm wrote: > >> >> Okay, I did a cvs update of the install directory and I know get the >> same problem as Arnaud. See the extra line of debugging I added to >> the end. Shall I have a go at fixing this? I'm guessing component >> should just be Bio, not CBIL/Bio... >> >> >> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install >> -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= >> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger >> org.apache.tools.ant.NoBannerLogger | grep ']' >> >> [echo] . >> [echo] Installing CBIL/CBIL/Bio >> [echo] project = CBIL component = CBIL/Bio >> >> >> Pjm wrote: >> >>> >>> Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs >>> to look for /nfs/team81/pjm/CVS/CVS-new/GUS/Common. >>> Arnaud has a similar problem but with a different directory (it >>> wants CBIL/CBIL/Bio !) >>> >>> >>> >>> pcs2g[pjm]131: build GUS install -append >>> >>> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install >>> -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= >>> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger >>> org.apache.tools.ant.NoBannerLogger | grep ']' >>> >>> [echo] . >>> [echo] Installing CBIL/Bio >>> [echo] . >>> [echo] Installing CBIL/CSP >>> [echo] . >>> [echo] Installing CBIL/Util >>> [echo] . >>> [echo] Installing Common >>> >>> BUILD FAILED >>> file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108: >>> Component directory /nfs/team81/pjm/CVS/CVS-new/Common not >>> found. >>> >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.net email is sponsored by:Crypto Challenge is now open! Get >>> cracking and register here for some mind boggling fun and the chance >>> of winning an Apple iPod: >>> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by:Crypto Challenge is now open! Get >> cracking and register here for some mind boggling fun and the chance >> of winning an Apple iPod: >> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > > |
|
From: Arnaud K. <ax...@sa...> - 2003-03-12 15:47:52
|
Steve
I've downloaded the new CBIL release and did a cvs update. I've got now
this error:
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing GUS/Common
[echo] .
[echo] Installing GUS/DBAdmin
[echo] .
[echo] Installing GUS/GOPredict
[echo] .
[echo] Installing GUS/ObjRelP
[echo] checkJavaObjects: are objects generated ?
${javaObjectsAlreadyGenerated}
[echo] .
[echo] Installing GUS/ObjRelJ
[echo] starting target: javaGeneratedModel
[echo] generating java objects
BUILD FAILED
file:/nfs/team81/axk/cvs/cvs_gus/GUS/build.xml:112: Cannot write to
/nfs/team81/axk/cvs/cvs_gus/GUS/Model/doc/javaGenLog
Total time: 8 seconds
Arnaud
Steve Fischer wrote:
> Folks-
>
> we have released a new version of CBIL.
>
> if you are in CBIL, just do this:
> %cd $PROJECT_HOME/CBIL
> %cvs update -d
>
> if you are outside CBIL, get it from the download site:
>
> http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz
>
> This should solve the problem that Paul and Arnaud are having.
>
> steve
>
|
|
From: Steve F. <st...@pc...> - 2003-03-12 15:19:49
|
Folks- we have released a new version of CBIL. if you are in CBIL, just do this: %cd $PROJECT_HOME/CBIL %cvs update -d if you are outside CBIL, get it from the download site: http://www.cbil.upenn.edu/downloads/CBIL/releases/CBIL_v1-2-0.tar.gz This should solve the problem that Paul and Arnaud are having. steve Pjm wrote: > > Okay, I did a cvs update of the install directory and I know get the > same problem as Arnaud. See the extra line of debugging I added to the > end. Shall I have a go at fixing this? I'm guessing component should > just be Bio, not CBIL/Bio... > > > ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install > -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= > -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger > org.apache.tools.ant.NoBannerLogger | grep ']' > > [echo] . > [echo] Installing CBIL/CBIL/Bio > [echo] project = CBIL component = CBIL/Bio > > > Pjm wrote: > >> >> Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs >> to look for /nfs/team81/pjm/CVS/CVS-new/GUS/Common. >> Arnaud has a similar problem but with a different directory (it wants >> CBIL/CBIL/Bio !) >> >> >> >> pcs2g[pjm]131: build GUS install -append >> >> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install >> -Dproj=GUS -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= >> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger >> org.apache.tools.ant.NoBannerLogger | grep ']' >> >> [echo] . >> [echo] Installing CBIL/Bio >> [echo] . >> [echo] Installing CBIL/CSP >> [echo] . >> [echo] Installing CBIL/Util >> [echo] . >> [echo] Installing Common >> >> BUILD FAILED >> file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108: >> Component directory /nfs/team81/pjm/CVS/CVS-new/Common not found. >> >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by:Crypto Challenge is now open! Get >> cracking and register here for some mind boggling fun and the chance >> of winning an Apple iPod: >> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > > ------------------------------------------------------- > This SF.net email is sponsored by:Crypto Challenge is now open! Get > cracking and register here for some mind boggling fun and the chance > of winning an Apple iPod: > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Dave B. <db...@pc...> - 2003-03-12 15:19:46
|
There have been a few small changes to the way the build system runs, mostly to add the ability to compile java source code. I believe the CBIL/Bio project is failing because it the release that you are working with has not been updated yet to incorporate these changes. Steve is working on getting the next release out and it should be available soon. Not sure why ant is looking for CVS-new/Common when it should be looking for CVS-new/GUS/Common, I'll look into it. Dave On Wed, 12 Mar 2003, Pjm wrote: > > Okay, I did a cvs update of the install directory and I know get the same > problem as Arnaud. See the extra line of debugging I added to the end. Shall I > have a go at fixing this? I'm guessing component should just be Bio, not > CBIL/Bio... > > > ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install -Dproj=GUS > -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= > -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger > org.apache.tools.ant.NoBannerLogger | grep ']' > > [echo] . > [echo] Installing CBIL/CBIL/Bio > [echo] project = CBIL component = CBIL/Bio > > > Pjm wrote: > > > > Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs to > > look for /nfs/team81/pjm/CVS/CVS-new/GUS/Common. > > Arnaud has a similar problem but with a different directory (it wants > > CBIL/CBIL/Bio !) > > > > > > > > pcs2g[pjm]131: build GUS install -append > > > > ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install -Dproj=GUS > > -DtargetDir=/nfs/team81/pjm/GUS -Dcomp= > > -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger > > org.apache.tools.ant.NoBannerLogger | grep ']' > > > > [echo] . > > [echo] Installing CBIL/Bio > > [echo] . > > [echo] Installing CBIL/CSP > > [echo] . > > [echo] Installing CBIL/Util > > [echo] . > > [echo] Installing Common > > > > BUILD FAILED > > file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108: > > Component directory /nfs/team81/pjm/CVS/CVS-new/Common not found. > > > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by:Crypto Challenge is now open! Get > > cracking and register here for some mind boggling fun and the chance of > > winning an Apple iPod: > > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by:Crypto Challenge is now open! > Get cracking and register here for some mind boggling fun and > the chance of winning an Apple iPod: > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Pjm <pj...@sa...> - 2003-03-12 13:59:58
|
Okay, I did a cvs update of the install directory and I know get the same
problem as Arnaud. See the extra line of debugging I added to the end. Shall I
have a go at fixing this? I'm guessing component should just be Bio, not
CBIL/Bio...
ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install -Dproj=GUS
-DtargetDir=/nfs/team81/pjm/GUS -Dcomp=
-DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger
org.apache.tools.ant.NoBannerLogger | grep ']'
[echo] .
[echo] Installing CBIL/CBIL/Bio
[echo] project = CBIL component = CBIL/Bio
Pjm wrote:
>
> Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs to
> look for /nfs/team81/pjm/CVS/CVS-new/GUS/Common.
> Arnaud has a similar problem but with a different directory (it wants
> CBIL/CBIL/Bio !)
>
>
>
> pcs2g[pjm]131: build GUS install -append
>
> ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install -Dproj=GUS
> -DtargetDir=/nfs/team81/pjm/GUS -Dcomp=
> -DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger
> org.apache.tools.ant.NoBannerLogger | grep ']'
>
> [echo] .
> [echo] Installing CBIL/Bio
> [echo] .
> [echo] Installing CBIL/CSP
> [echo] .
> [echo] Installing CBIL/Util
> [echo] .
> [echo] Installing Common
>
> BUILD FAILED
> file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108:
> Component directory /nfs/team81/pjm/CVS/CVS-new/Common not found.
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by:Crypto Challenge is now open! Get
> cracking and register here for some mind boggling fun and the chance of
> winning an Apple iPod:
> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Pjm <pj...@sa...> - 2003-03-12 13:45:58
|
Ant is looking for /nfs/team81/pjm/CVS/CVS-new/Common when it needs to look for
/nfs/team81/pjm/CVS/CVS-new/GUS/Common.
Arnaud has a similar problem but with a different directory (it wants
CBIL/CBIL/Bio !)
pcs2g[pjm]131: build GUS install -append
ant -f /nfs/team81/pjm/CVS/CVS-new/install/build.xml install -Dproj=GUS
-DtargetDir=/nfs/team81/pjm/GUS -Dcomp=
-DprojectsDir=/nfs/team81/pjm/CVS/CVS-new -Dappend=true -logger
org.apache.tools.ant.NoBannerLogger | grep ']'
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing Common
BUILD FAILED
file:/nfs/team81/pjm/CVS/CVS-new/install/build.xml:108:
Component directory /nfs/team81/pjm/CVS/CVS-new/Common not found.
|
|
From: Jonathan C. <cra...@pc...> - 2003-03-11 15:14:33
|
On Tue, 11 Mar 2003, Pjm wrote: > The GUS30 browser eventually comes back with; > > <html><title>allgenes.org | Schema browser | All tables and views</title> > <body BGCOLOR="#ffffff"> > > and nothing else. Any idea whats wrong? Paul- Yes; we're having some Oracle problems and I had to take our development server offline Sunday night for emergency repairs. It should be back in operation in a day or two, but we should also look into changing the schema browser so that it doesn't rely on our development database. Jonathan |
|
From: Pjm <pj...@sa...> - 2003-03-11 14:45:18
|
The GUS30 browser eventually comes back with; <html><title>allgenes.org | Schema browser | All tables and views</title> <body BGCOLOR="#ffffff"> and nothing else. Any idea whats wrong? See; http://www.cbil.upenn.edu/cgi-bin/GUS30/schemaBrowser.pl?db=GUS30 |
|
From: Jonathan C. <cra...@pc...> - 2003-03-11 06:56:16
|
I've committed several files pertaining to the Java object layer; they are all in GUS/ObjRelJ/src/java/org/gusdb/objrelj/. Be warned that this code definitely does *not* compile (and we've modified the build system so that by default it should not try to compile the Java code). However, you can take a look at some of these classes to get some idea where we are headed (see below for some suggestions on where to start with this.) First, a little history; work on the GUS Java object layer was originally started by Sharon Diskin, who had quite a bit of experience with the Perl object layer. As much as possible the Java version of the object layer tries to duplicate the functionality and semantics of the Perl object layer, although we have had to diverge somewhat from that goal in order to allow the Java object layer to be used over RMI. In any case, most of the work on this code has been done by Dave Barkan, who took over when Sharon left to become a full-time Ph.D. student. I've been overseeing the work that Dave has done and, not satisfied that the code was enough of a mess, took it over last week to update the documentation, refactor some of the classes, and make a number of other changes. Needless to say, I am still working on all of this, which is why nothing compiles right now. However, the refactoring and several of the other recent changes are absolutely necessary for the object layer to work correctly, and I don't think it will take too much longer to get everything working again, now that I've finally figured out how the different interfaces should interact (I think.) If you get a chance to look at any of this code before the conference call tomorrow, here's what I'd recommend focusing on: ServerI.java This interface defines the API to the object layer. It allows an application to retrieve "GUSRow" objects from the database, modify them, and then write them back. (Or create entirely new objects and insert them, etc.) GUSRow.java Superclass for all GUS objects. So far each instance of GUSRow should correspond to at most 1 row in a GUS database. GUSTable.java, GUSTableRelation.java, GUSTableAttribute.java Classes used to represent database metadata (i.e., the schema of the various tables.) DatabaseConnectionI.java, RemoteDatabaseConnectionI.java These interfaces describe the same low-level database API, but one is Remote and the other is not, allowing the object layer to be used over RMI if so desired. Note that GUSRow is an abstract class (and GUSTable probably should be too). Subclasses of these classes are generated by a code generator much like the Perl code generator. The Perl and Java code generators are both implemented in Perl and depend on the Perl object layer, and so they reside in GUS/ObjRelP. This will probably make more sense once I get everything working again and can actually show a sample application. The main thing I'm still working on is the refactoring of the code to allow the object layer to be used over RMI. The complication basically results from the fact that the GUSRow objects are passed by value over RMI, not by reference. This means that we can't do anything by side-effect over RMI. However, being able to modify the GUSRow objects by side-effect is a very convenient way of passing information from the object layer back to the application. So what I'm doing is refactoring the classes to properly distinguish the methods that are allowed to use side effects from those that are not. The ones that are not can be accessed over RMI. Let me know if you have any questions; I'll probably be working on this again tomorrow morning. Jonathan |
|
From: steve f. <sfi...@pc...> - 2003-03-10 19:09:59
|
folks- in anticipation of tuesday's phone conference, we have put together a simple design for separating the layout (structure) of a web site from the content. This is following in the tradition of Jonathan Schug's Perl-based "page generator" which proved enormously useful for PlasmoDB, but is using JSP as the platform this time. it does not cover the specifics of session management. See attached (which i hope survives the OpenOffice to PowerPoint translation). steve |
|
From: Chetna W. <ch...@ar...> - 2003-03-07 16:44:55
|
Hi Jonathan, Thanks for the mail. I was thinking how the script would work without the --commit option and your explanation has clarified that and helped to clear my assumptions. Thanks Chetna > That's not quite true (or at least it shouldn't be); without the --commit > option the plugins will still do all of the same inserts that they would > do with the --commit option. By default these inserts are all performed > in a single transaction and until that transaction is either rolled back > or committed, it is true that *other* transactions won't be able to see the > new rows in TaxonName (or Taxon, actually, since the reference in question > was TaxonName.taxon_id.) However, the plugin itself *should* be able to see > the new rows in Taxon/TaxonName, so long as it doesn't roll the transaction > back and start a new one. The crucial thing to realize is that a table can > appear to be empty in one transaction/session, but not empty in another. > So even though the Taxon table might not contain any rows that have > been committed, it could still contain rows that are visible to the plugin > itself (and that could be used to establish a foreign key constraint from > TaxonName.) The crucial question (I think) is whether the plugin is doing > a commit or rollback between the time it inserts the Taxon rows and the time > it inserts the TaxonName rows. I don't think I've looked at this code but > it should be easy to figure out why it's getting a null taxon_id and it should > be possible to get it to work in no-commit mode. |
|
From: Jonathan C. <cra...@pc...> - 2003-03-07 16:17:30
|
Deborah F. Pinney wrote:
> Several of the attributes in taxon (ncbi_tax_id, parent_id and taxon_id)
> should be indexed or they will cause the plugin to run very slowly at
> several points. That was the reason for the line: $dbh->do("analyze table
> sres.Taxon compute statistics"); However, I suspect the line is not
Doing an analyze table won't help you if it's not properly indexed in the
first place. All it will do is provide the optimizer with up-to-date
statistics that might help it make a better decision about index usage.
Also, if the tables that you're querying from haven't been analyzed at all
then Oracle 8i/9i will revert to using the rule-based optimizer. Anyway,
this is typically something that's handled by the DBA, so removing it from
the plugin sounds like the best idea.
Jonathan
|
|
From: Jonathan C. <cra...@pc...> - 2003-03-07 16:14:05
|
Hi Chetna- > That is because without --commit option the table TaxonName is empty and > thats why the loading stops. Oracle checks that is the specified row That's not quite true (or at least it shouldn't be); without the --commit option the plugins will still do all of the same inserts that they would do with the --commit option. By default these inserts are all performed in a single transaction and until that transaction is either rolled back or committed, it is true that *other* transactions won't be able to see the new rows in TaxonName (or Taxon, actually, since the reference in question was TaxonName.taxon_id.) However, the plugin itself *should* be able to see the new rows in Taxon/TaxonName, so long as it doesn't roll the transaction back and start a new one. The crucial thing to realize is that a table can appear to be empty in one transaction/session, but not empty in another. So even though the Taxon table might not contain any rows that have been committed, it could still contain rows that are visible to the plugin itself (and that could be used to establish a foreign key constraint from TaxonName.) The crucial question (I think) is whether the plugin is doing a commit or rollback between the time it inserts the Taxon rows and the time it inserts the TaxonName rows. I don't think I've looked at this code but it should be easy to figure out why it's getting a null taxon_id and it should be possible to get it to work in no-commit mode. Jonathan -- Jonathan Crabtree Center for Bioinformatics, University of Pennsylvania 1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021 215-573-3115 |
|
From: Deborah F. P. <pi...@pc...> - 2003-03-07 16:12:33
|
Several of the attributes in taxon (ncbi_tax_id, parent_id and taxon_id)
should be indexed or they will cause the plugin to run very slowly at
several points. That was the reason for the line: $dbh->do("analyze table
sres.Taxon compute statistics"); However, I suspect the line is not
accomplishing what I intended because of the permission issue and I
understand that it is platform specific. For those reasons, the line
should be removed (I will remove it now and update cvs).
Debbie
On Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
> Another thing. At some point the code is trying to analyse the
> SRes.TaxonName table. I've got an insufficient privileges error.
>
> I've got two database logins which are used for connecting the database
> from the perl object layer:
> * databaseLogin=GUSrw
> * readOnlyDatabaseLogin=GUSro
>
> I guess the effective login to populate GUS is GUSrw, is that correct?
> Probably a question for you Martin. Does GUSrw have enough privileges to
> execute analyse table statements on any schemas (in particular the SRes
> shema) ?
>
> Arnaud
>
> ---------------------->
> DBD::Oracle::db do failed: ORA-01031: insufficient privileges (DBD
> ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/
> gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm line 304,
> <NODES> line 2.
> <----------------------
>
> line 304: $dbh->do("analyze table sres.TaxonName compute statistics");
>
> Deborah F. Pinney wrote:
>
> >I didn't experience this problem. However, in looking over the
> >LoadTaxon.pm code I noticed that there was still a commented out line
> >that should have been corrected. This line is used only for restarting.
> >I have uncommented it and submitted to cvs. Please update your file.
> >
> > Deborah Pinney
> >
> >
> >
> >
> >
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you feeling lost and
> disoriented. TotalView can help you find your way. Available on major UNIX
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Jonathan C. <cra...@pc...> - 2003-03-07 16:03:19
|
Hi Arnaud-
I agree with Martin about the "EOF on communication channel" error; all
this message means is that something happened to break your connection
to the database. What broke your connection was almost certainly the
server process crashing or shutting down in response to the *other* error
("hostdef extension doesn't exist"). I've never seen this error before
and have no idea what might have caused it. You could try looking at the
trace file dumped by Oracle when the process crashed to see what it was
doing at the time.
As for the problem running the plugin when the --commit flag is not
specified, I'm surprised that it crashes; the foreign key dependencies
should be created just fine in no-commit mode. However, all the inserts
do have to performed within a single transaction, which is then rolled
back before the plugin exits. Maybe the LoadTaxon plugin is doing
something to cause a premature rollback?
Arnaud Kerhornou wrote:
> Another thing. At some point the code is trying to analyse the
> SRes.TaxonName table. I've got an insufficient privileges error.
At the very least the plugin should have an option to let the user
specify whether they want to analyze the table, since not every site
will want to allow regular users the necessary privileges.
Jonathan
--
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115
|
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 15:18:12
|
Another thing. At some point the code is trying to analyse the
SRes.TaxonName table. I've got an insufficient privileges error.
I've got two database logins which are used for connecting the database
from the perl object layer:
* databaseLogin=GUSrw
* readOnlyDatabaseLogin=GUSro
I guess the effective login to populate GUS is GUSrw, is that correct?
Probably a question for you Martin. Does GUSrw have enough privileges to
execute analyse table statements on any schemas (in particular the SRes
shema) ?
Arnaud
---------------------->
DBD::Oracle::db do failed: ORA-01031: insufficient privileges (DBD
ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/
gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm line 304,
<NODES> line 2.
<----------------------
line 304: $dbh->do("analyze table sres.TaxonName compute statistics");
Deborah F. Pinney wrote:
>I didn't experience this problem. However, in looking over the
>LoadTaxon.pm code I noticed that there was still a commented out line
>that should have been corrected. This line is used only for restarting.
>I have uncommented it and submitted to cvs. Please update your file.
>
> Deborah Pinney
>
>
>
>
>
|
|
From: Chetna W. <ch...@ar...> - 2003-03-07 15:06:42
|
Hi,
That is because without --commit option the table TaxonName is empty and
thats why the loading stops. Oracle checks that is the specified row
present in the table TaxonName and only when this check is sucessful it
will allow loading of data into the table under consideration. This way
RDBMS's keep consistency in the database.
Thanks
Chetna
> It's working now. Just noticed something, when the option --commit is
> not specified, the loading stops on the population of the TaxonName
> table, because of the Foreign Key taxon_id integrity not respected.
>
> with '--commit' option it seems to work fine.
>
> ------------->
>
> RetrieveFromDB: select * from SRes.TaxonName where unique_name_variant
> is NULL and name_class = ? and name = ? and
> taxon_id is NULL
> bindValues (synonym, all)
>
>
> sqlExec:
> INSERT INTO SRes.TaxonName ( row_user_id, other_read,
> unique_name_variant, user_write, group_write, name_class, r
> ow_project_id, name, taxon_id, modification_date, user_read,
> row_alg_invocation_id, group_read, other_write, row_group
> _id, taxon_name_id )
> VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1)
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("SRES"."TAXONNAME"."TAXON_ID") (DBD ERROR: OCIStmt
> Execute) at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 137, <NODES> line 2.
>
>
> sqlExec:
> UPDATE Core.AlgorithmInvocation
> SET
> end_time = SYSDATE,
> row_alg_invocation_id = ?,
> modification_date = SYSDATE
> WHERE algorithm_invocation_id = ?
> bindValues (9, 9)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.TaxonName ( row_user_id, other_read,
> unique_name_variant, user_write, group_write, name_class, r
> ow_project_id, name, taxon_id, modification_date, user_read,
> row_alg_invocation_id, group_read, other_write, row_group
> _id, taxon_name_id )
> VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
> Values: 1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1 at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Obj
> RelP/DbiDbHandle.pm line 177, <NODES> line 2.
>
> <--------------------
>
> Arnaud
>
> Deborah F. Pinney wrote:
>
> >I didn't experience this problem. However, in looking over the
> >LoadTaxon.pm code I noticed that there was still a commented out line
> >that should have been corrected. This line is used only for restarting.
> >I have uncommented it and submitted to cvs. Please update your file.
> >
> > Deborah Pinney
> >
> >
> >
> >On
> >Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
> >
> >
> >
> >>Hi
> >>
> >>I've tried to populate the taxonomy files from NCBI into GUS3. it's
> >>working fine until it reaches the last node entry, ie the line 173295 in
> >>the nodes.dmp file.
> >>I now have these 2 errors when populating the nodes file:
> >>
> >> > oerr ora 03113
> >> 03113, 00000, "end-of-file on communication channel"
> >> // *Cause:
> >> // *Action:
> >>
> >> > oerr ora 01041
> >> 01041, 00000, "internal error. hostdef extension doesn't exist"
> >> // *Cause: Pointer to hstdef extension in hstdef is null.
> >> // *Action: Report as a bug
> >>
> >>Have you come across the same problem ?
> >>Any idea about the cause of this 'end-of-file on communication channel'
> >>error ?
> >>
> >>cheers
> >>Arnaud
> >>
> >>./bin/ga GUS::Common::Plugin::LoadTaxon
> >>--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
> >>--names=/nfs/pathsoft/databases/NCBI/names.dmp
> >>--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
> >>
> >>--------------------------->
> >>[...]
> >>
> >>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> >> bindValues (89410)
> >>
> >>sqlExec:
> >> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> >>genetic_code_id, row_project_id, taxon_id, group_r
> >>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> >>modification_date, user_read, row_alg_invocation_id, oth
> >>er_write, ncbi_tax_id, rank )
> >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >> bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
> >> DbiHandle:sqlExec:insert succeeded 1 row(s)
> >>processed ncbi_tax_id : 89410
> >>
> >>^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
> >>communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
> >>team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> >>line 242, <NODES> line 173295.
> >>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> >>(perhaps you need to call execute first) at /nfs/t
> >>eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> >>line 243, <NODES> line 173295.
> >>
> >>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> >> bindValues (110556)
> >>
> >>
> >>sqlExec:
> >> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> >>genetic_code_id, row_project_id, taxon_id, group_r
> >>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> >>modification_date, user_read, row_alg_invocation_id, oth
> >>er_write, ncbi_tax_id, rank )
> >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >> bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
> >> DbiHandle:sqlExec:insert succeeded 1 row(s)
> >>processed ncbi_tax_id : 110556
> >>DBD::Oracle::db prepare failed: Error while trying to retrieve text for
> >>error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
> >>cribe) at
> >>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> >>line 241, <NODES> line 1
> >>73295.
> >>
> >>
> >>sqlExec:
> >> UPDATE Core.AlgorithmInvocation
> >> SET
> >> end_time = SYSDATE,
> >> row_alg_invocation_id = ?,
> >> modification_date = SYSDATE
> >> WHERE algorithm_invocation_id = ?
> >> bindValues (9, 9)
> >> DbiHandle:sqlExec:insert succeeded 1 row(s)
> >>Can't call method "execute" on an undefined value at
> >>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
> >>lugin/LoadTaxon.pm line 242, <NODES> line 173295.
> >><------------------------------------
> >>
> >>
> >>
> >>
> >>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you feeling lost and
> disoriented. TotalView can help you find your way. Available on major UNIX
> and Linux platforms. Try it free. www.etnus.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 14:50:29
|
It's working now. Just noticed something, when the option --commit is
not specified, the loading stops on the population of the TaxonName
table, because of the Foreign Key taxon_id integrity not respected.
with '--commit' option it seems to work fine.
------------->
RetrieveFromDB: select * from SRes.TaxonName where unique_name_variant
is NULL and name_class = ? and name = ? and
taxon_id is NULL
bindValues (synonym, all)
sqlExec:
INSERT INTO SRes.TaxonName ( row_user_id, other_read,
unique_name_variant, user_write, group_write, name_class, r
ow_project_id, name, taxon_id, modification_date, user_read,
row_alg_invocation_id, group_read, other_write, row_group
_id, taxon_name_id )
VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1)
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("SRES"."TAXONNAME"."TAXON_ID") (DBD ERROR: OCIStmt
Execute) at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 137, <NODES> line 2.
sqlExec:
UPDATE Core.AlgorithmInvocation
SET
end_time = SYSDATE,
row_alg_invocation_id = ?,
modification_date = SYSDATE
WHERE algorithm_invocation_id = ?
bindValues (9, 9)
DbiHandle:sqlExec:insert succeeded 1 row(s)
SQL ERROR!! involving
INSERT INTO SRes.TaxonName ( row_user_id, other_read,
unique_name_variant, user_write, group_write, name_class, r
ow_project_id, name, taxon_id, modification_date, user_read,
row_alg_invocation_id, group_read, other_write, row_group
_id, taxon_name_id )
VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
Values: 1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1 at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Obj
RelP/DbiDbHandle.pm line 177, <NODES> line 2.
<--------------------
Arnaud
Deborah F. Pinney wrote:
>I didn't experience this problem. However, in looking over the
>LoadTaxon.pm code I noticed that there was still a commented out line
>that should have been corrected. This line is used only for restarting.
>I have uncommented it and submitted to cvs. Please update your file.
>
> Deborah Pinney
>
>
>
>On
>Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
>
>
>
>>Hi
>>
>>I've tried to populate the taxonomy files from NCBI into GUS3. it's
>>working fine until it reaches the last node entry, ie the line 173295 in
>>the nodes.dmp file.
>>I now have these 2 errors when populating the nodes file:
>>
>> > oerr ora 03113
>> 03113, 00000, "end-of-file on communication channel"
>> // *Cause:
>> // *Action:
>>
>> > oerr ora 01041
>> 01041, 00000, "internal error. hostdef extension doesn't exist"
>> // *Cause: Pointer to hstdef extension in hstdef is null.
>> // *Action: Report as a bug
>>
>>Have you come across the same problem ?
>>Any idea about the cause of this 'end-of-file on communication channel'
>>error ?
>>
>>cheers
>>Arnaud
>>
>>./bin/ga GUS::Common::Plugin::LoadTaxon
>>--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
>>--names=/nfs/pathsoft/databases/NCBI/names.dmp
>>--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
>>
>>--------------------------->
>>[...]
>>
>>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
>> bindValues (89410)
>>
>>sqlExec:
>> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
>>genetic_code_id, row_project_id, taxon_id, group_r
>>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
>>modification_date, user_read, row_alg_invocation_id, oth
>>er_write, ncbi_tax_id, rank )
>> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>> bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>processed ncbi_tax_id : 89410
>>
>>^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
>>communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
>>team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
>>line 242, <NODES> line 173295.
>>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
>>(perhaps you need to call execute first) at /nfs/t
>>eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
>>line 243, <NODES> line 173295.
>>
>>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
>> bindValues (110556)
>>
>>
>>sqlExec:
>> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
>>genetic_code_id, row_project_id, taxon_id, group_r
>>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
>>modification_date, user_read, row_alg_invocation_id, oth
>>er_write, ncbi_tax_id, rank )
>> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>> bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>processed ncbi_tax_id : 110556
>>DBD::Oracle::db prepare failed: Error while trying to retrieve text for
>>error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
>>cribe) at
>>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
>>line 241, <NODES> line 1
>>73295.
>>
>>
>>sqlExec:
>> UPDATE Core.AlgorithmInvocation
>> SET
>> end_time = SYSDATE,
>> row_alg_invocation_id = ?,
>> modification_date = SYSDATE
>> WHERE algorithm_invocation_id = ?
>> bindValues (9, 9)
>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>Can't call method "execute" on an undefined value at
>>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
>>lugin/LoadTaxon.pm line 242, <NODES> line 173295.
>><------------------------------------
>>
>>
>>
>>
>>
|
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 11:59:39
|
I've updated from CVS the files and I'm going to rerun the loading. It'll take a while... Martin Widlake wrote: >Hi Arnaud, > >If the whole file except the last part is processing into the DB OK, > that's right > it >suggest the end of the file is corrupt. > > it looks fine though. >Ora 1041 is an internal error that looks like you have hut an internal >oracle bug, but in fact is often a result of 3113, losing your >connection to the DB. > >I take it 99.99% of what you are processing is getting into the DB? > > no because I haven't commited the loading into the database but should have been in there otherwise. >Martin > > Arnaud >-----Original Message----- >From: Arnaud Kerhornou [mailto:ax...@sa...] >Sent: 07 March 2003 10:57 >To: gusdev-gusdev >Cc: db...@sa... >Subject: Re: LoadTaxon.pm > > >Hi > >I've tried to populate the taxonomy files from NCBI into GUS3. it's >working fine until it reaches the last node entry, ie the line 173295 in > >the nodes.dmp file. >I now have these 2 errors when populating the nodes file: > > > oerr ora 03113 > 03113, 00000, "end-of-file on communication channel" > // *Cause: > // *Action: > > > oerr ora 01041 > 01041, 00000, "internal error. hostdef extension doesn't exist" > // *Cause: Pointer to hstdef extension in hstdef is null. > // *Action: Report as a bug > >Have you come across the same problem ? >Any idea about the cause of this 'end-of-file on communication channel' >error ? > >cheers >Arnaud > >./bin/ga GUS::Common::Plugin::LoadTaxon >--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp >--names=/nfs/pathsoft/databases/NCBI/names.dmp >--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose > >---------------------------> >[...] > >RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ? > bindValues (89410) > >sqlExec: > INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write, >genetic_code_id, row_project_id, taxon_id, group_r >ead, row_group_id, other_read, mitochondrial_genetic_code_id, >modification_date, user_read, row_alg_invocation_id, oth er_write, >ncbi_tax_id, rank ) > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) > bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus) >DbiHandle:sqlExec:insert succeeded 1 row(s) processed ncbi_tax_id : >89410 > >^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on >communication channel (DBD ERROR: OCIStmtExecute) at /nfs/ >team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTa >xon.pm >line 242, <NODES> line 173295. >DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >(perhaps you need to call execute first) at /nfs/t >eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTax >on.pm >line 243, <NODES> line 173295. > >RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ? > bindValues (110556) > > >sqlExec: > INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write, >genetic_code_id, row_project_id, taxon_id, group_r >ead, row_group_id, other_read, mitochondrial_genetic_code_id, >modification_date, user_read, row_alg_invocation_id, oth er_write, >ncbi_tax_id, rank ) > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) > bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, >species) DbiHandle:sqlExec:insert succeeded 1 row(s) processed >ncbi_tax_id : 110556 DBD::Oracle::db prepare failed: Error while trying >to retrieve text for >error ORA-01041 (DBD ERROR: OCIStmtExecute/Des >cribe) at >/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/L >oadTaxon.pm >line 241, <NODES> line 1 >73295. > > >sqlExec: > UPDATE Core.AlgorithmInvocation > SET > end_time = SYSDATE, > row_alg_invocation_id = ?, > modification_date = SYSDATE > WHERE algorithm_invocation_id = ? > bindValues (9, 9) > DbiHandle:sqlExec:insert succeeded 1 row(s) >Can't call method "execute" on an undefined value at >/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P >lugin/LoadTaxon.pm line 242, <NODES> line 173295. ><------------------------------------ > > > -- Arnaud Kerhornou The Wellcome Trust Sanger Institute The Pathogen Sequencing Unit Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Work: +44 (0) 1223 494955 Fax: +44 (0) 1223 494919 |
|
From: Deborah F. P. <pi...@pc...> - 2003-03-07 11:33:08
|
The taxonomy file I loaded was from January 10, 2003. It may be that
there is a problem with the file itself. The problem could exist with the
NCBI file at NCBI or occured when you incompressed it.
Deborah Pinney
|
|
From: Deborah F. P. <pi...@pc...> - 2003-03-07 11:28:45
|
I didn't experience this problem. However, in looking over the
LoadTaxon.pm code I noticed that there was still a commented out line
that should have been corrected. This line is used only for restarting.
I have uncommented it and submitted to cvs. Please update your file.
Deborah Pinney
On
Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
> Hi
>
> I've tried to populate the taxonomy files from NCBI into GUS3. it's
> working fine until it reaches the last node entry, ie the line 173295 in
> the nodes.dmp file.
> I now have these 2 errors when populating the nodes file:
>
> > oerr ora 03113
> 03113, 00000, "end-of-file on communication channel"
> // *Cause:
> // *Action:
>
> > oerr ora 01041
> 01041, 00000, "internal error. hostdef extension doesn't exist"
> // *Cause: Pointer to hstdef extension in hstdef is null.
> // *Action: Report as a bug
>
> Have you come across the same problem ?
> Any idea about the cause of this 'end-of-file on communication channel'
> error ?
>
> cheers
> Arnaud
>
> ./bin/ga GUS::Common::Plugin::LoadTaxon
> --nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
> --names=/nfs/pathsoft/databases/NCBI/names.dmp
> --gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
>
> --------------------------->
> [...]
>
> RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> bindValues (89410)
>
> sqlExec:
> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> genetic_code_id, row_project_id, taxon_id, group_r
> ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> modification_date, user_read, row_alg_invocation_id, oth
> er_write, ncbi_tax_id, rank )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> processed ncbi_tax_id : 89410
>
> ^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
> communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
> team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 242, <NODES> line 173295.
> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> (perhaps you need to call execute first) at /nfs/t
> eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 243, <NODES> line 173295.
>
> RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> bindValues (110556)
>
>
> sqlExec:
> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> genetic_code_id, row_project_id, taxon_id, group_r
> ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> modification_date, user_read, row_alg_invocation_id, oth
> er_write, ncbi_tax_id, rank )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> processed ncbi_tax_id : 110556
> DBD::Oracle::db prepare failed: Error while trying to retrieve text for
> error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
> cribe) at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 241, <NODES> line 1
> 73295.
>
>
> sqlExec:
> UPDATE Core.AlgorithmInvocation
> SET
> end_time = SYSDATE,
> row_alg_invocation_id = ?,
> modification_date = SYSDATE
> WHERE algorithm_invocation_id = ?
> bindValues (9, 9)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> Can't call method "execute" on an undefined value at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
> lugin/LoadTaxon.pm line 242, <NODES> line 173295.
> <------------------------------------
>
>
>
>
> -------------------------------------------------------
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>
|
|
From: Martin W. <md...@sa...> - 2003-03-07 11:23:24
|
Hi Arnaud,
If the whole file except the last part is processing into the DB OK, it
suggest the end of the file is corrupt.
Ora 1041 is an internal error that looks like you have hut an internal
oracle bug, but in fact is often a result of 3113, losing your
connection to the DB.
I take it 99.99% of what you are processing is getting into the DB?
Martin
-----Original Message-----
From: Arnaud Kerhornou [mailto:ax...@sa...]
Sent: 07 March 2003 10:57
To: gusdev-gusdev
Cc: db...@sa...
Subject: Re: LoadTaxon.pm
Hi
I've tried to populate the taxonomy files from NCBI into GUS3. it's
working fine until it reaches the last node entry, ie the line 173295 in
the nodes.dmp file.
I now have these 2 errors when populating the nodes file:
> oerr ora 03113
03113, 00000, "end-of-file on communication channel"
// *Cause:
// *Action:
> oerr ora 01041
01041, 00000, "internal error. hostdef extension doesn't exist"
// *Cause: Pointer to hstdef extension in hstdef is null.
// *Action: Report as a bug
Have you come across the same problem ?
Any idea about the cause of this 'end-of-file on communication channel'
error ?
cheers
Arnaud
./bin/ga GUS::Common::Plugin::LoadTaxon
--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
--names=/nfs/pathsoft/databases/NCBI/names.dmp
--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
--------------------------->
[...]
RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
bindValues (89410)
sqlExec:
INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
genetic_code_id, row_project_id, taxon_id, group_r
ead, row_group_id, other_read, mitochondrial_genetic_code_id,
modification_date, user_read, row_alg_invocation_id, oth er_write,
ncbi_tax_id, rank )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
DbiHandle:sqlExec:insert succeeded 1 row(s) processed ncbi_tax_id :
89410
^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTa
xon.pm
line 242, <NODES> line 173295.
DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
(perhaps you need to call execute first) at /nfs/t
eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTax
on.pm
line 243, <NODES> line 173295.
RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
bindValues (110556)
sqlExec:
INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
genetic_code_id, row_project_id, taxon_id, group_r
ead, row_group_id, other_read, mitochondrial_genetic_code_id,
modification_date, user_read, row_alg_invocation_id, oth er_write,
ncbi_tax_id, rank )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556,
species) DbiHandle:sqlExec:insert succeeded 1 row(s) processed
ncbi_tax_id : 110556 DBD::Oracle::db prepare failed: Error while trying
to retrieve text for
error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
cribe) at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/L
oadTaxon.pm
line 241, <NODES> line 1
73295.
sqlExec:
UPDATE Core.AlgorithmInvocation
SET
end_time = SYSDATE,
row_alg_invocation_id = ?,
modification_date = SYSDATE
WHERE algorithm_invocation_id = ?
bindValues (9, 9)
DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't call method "execute" on an undefined value at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
lugin/LoadTaxon.pm line 242, <NODES> line 173295.
<------------------------------------
|
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 10:57:23
|
Hi
I've tried to populate the taxonomy files from NCBI into GUS3. it's
working fine until it reaches the last node entry, ie the line 173295 in
the nodes.dmp file.
I now have these 2 errors when populating the nodes file:
> oerr ora 03113
03113, 00000, "end-of-file on communication channel"
// *Cause:
// *Action:
> oerr ora 01041
01041, 00000, "internal error. hostdef extension doesn't exist"
// *Cause: Pointer to hstdef extension in hstdef is null.
// *Action: Report as a bug
Have you come across the same problem ?
Any idea about the cause of this 'end-of-file on communication channel'
error ?
cheers
Arnaud
./bin/ga GUS::Common::Plugin::LoadTaxon
--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
--names=/nfs/pathsoft/databases/NCBI/names.dmp
--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
--------------------------->
[...]
RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
bindValues (89410)
sqlExec:
INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
genetic_code_id, row_project_id, taxon_id, group_r
ead, row_group_id, other_read, mitochondrial_genetic_code_id,
modification_date, user_read, row_alg_invocation_id, oth
er_write, ncbi_tax_id, rank )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
DbiHandle:sqlExec:insert succeeded 1 row(s)
processed ncbi_tax_id : 89410
^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
line 242, <NODES> line 173295.
DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
(perhaps you need to call execute first) at /nfs/t
eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
line 243, <NODES> line 173295.
RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
bindValues (110556)
sqlExec:
INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
genetic_code_id, row_project_id, taxon_id, group_r
ead, row_group_id, other_read, mitochondrial_genetic_code_id,
modification_date, user_read, row_alg_invocation_id, oth
er_write, ncbi_tax_id, rank )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
DbiHandle:sqlExec:insert succeeded 1 row(s)
processed ncbi_tax_id : 110556
DBD::Oracle::db prepare failed: Error while trying to retrieve text for
error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
cribe) at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
line 241, <NODES> line 1
73295.
sqlExec:
UPDATE Core.AlgorithmInvocation
SET
end_time = SYSDATE,
row_alg_invocation_id = ?,
modification_date = SYSDATE
WHERE algorithm_invocation_id = ?
bindValues (9, 9)
DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't call method "execute" on an undefined value at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
lugin/LoadTaxon.pm line 242, <NODES> line 173295.
<------------------------------------
|
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