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From: Chris S. <sto...@pc...> - 2005-11-22 18:45:31
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Hi Aaron, Don't think that you got an answer to this so here's my perspective. The canonically correct strongly-typed place would be to create a view of NASequence / AASequence that has the desired attributes for a specific purpose (and the view would be named as such). On the other hand if these are overlooked attributes that really should be part of any sequence then we would alter the base NASequence/ AASequence tables. The major argument I would see for weak typed tag values is that there is a long and arbitrary list of such attributes but I'm not convinced that this is the case. Are the examples you gave, attributes needed now? Are there others? Thanks, Chris On Nov 17, 2005, at 10:01 PM, am...@pc... wrote: > > Where is the "canonically correct" place to store simple scalar > attributes that > pertain to an entire sequence (AA and/or NT), e.g.: > > pI (isoelectric point) > codon volatility > codon bias (measured in various ways: CAI, etc) > dinucleotide bias (e.g. Karlin's delta*) > > My non-GUS "gut" instinct is that these should all reside in weakly- > typed > DoTS.(NA/AA)SequenceAttribute tables with very simple tag/value > schemas; but > I'm looking for enlightenment. > > Thanks, > > -Aaron > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Junmin L. <ju...@pc...> - 2005-11-22 15:35:39
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Hi, Amruta, The error you got "Fatal error: Call to undefined function: ora_logon()", means you don't have ORA module installed when you compile the php. Our RAD-SA in cbil here is using ora module against Oracle 10g. We don't have any problem. So looks like Oracle 10g DOES support ORA module. If you still want to use OCI, you might try global replacement the ora functions with corresponding oci functions. If you want me to further look at this problem. Please send me the followings, that may help me quickly solve your problem: 1. configuration string when you compile the php 2. the exact error message you got in php log. Thanks, ---junmin > The problem is not with php compilation; all oci functions are working fine. > Oracle 10g does not support ora_ functions. Hence, to use the > StudyAnnotator, we'll need to migrate the existing code to OCI ie rewrite > the ora_ fuction calls with equivalent oci ones. If you have any simpler > solution for this problem, please let me know. > > If you have a copy of StudyAnnotator with OCI, it will prove helpful as a > starting point/guideline. > > If anyone has an OCI version of StudyAnnotator, we'll appreciate if you can > share the code. > > Thanks, > Amruta > > Quoting Junmin Liu <ju...@pc...>: > >> Hi, Amruta, >> Yes, the OCI is more modern oracle php lib. At one point I migrated the >> code to use OCI, but I had to revert them back due to some reasons I >> cann't >> remember for now. Sorry about that, it could be that I cann't find a way >> to "fetch clob datatype from Oracle using OCI fucntion". >> >> Anyway, could you please check your php config? What is the options you >> use to compile PHP? Do you have the following two options: >> >> --with-oracle=/path/to/oracle/home/dir >> --with-oci8=/path/to/oracle/home/dir >> >> >> ---junmin >> |
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From: Amruta J. <am...@st...> - 2005-11-22 00:57:26
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Hi Junmin, The problem is not with php compilation; all oci functions are working fine. Oracle 10g does not support ora_ functions. Hence, to use the StudyAnnotator, we'll need to migrate the existing code to OCI ie rewrite the ora_ fuction calls with equivalent oci ones. If you have any simpler solution for this problem, please let me know. If you have a copy of StudyAnnotator with OCI, it will prove helpful as a starting point/guideline. If anyone has an OCI version of StudyAnnotator, we'll appreciate if you can share the code. Thanks, Amruta Quoting Junmin Liu <ju...@pc...>: > Hi, Amruta, > Yes, the OCI is more modern oracle php lib. At one point I migrated the > code to use OCI, but I had to revert them back due to some reasons I > cann't > remember for now. Sorry about that, it could be that I cann't find a way > to "fetch clob datatype from Oracle using OCI fucntion". > > Anyway, could you please check your php config? What is the options you > use to compile PHP? Do you have the following two options: > > --with-oracle=/path/to/oracle/home/dir > --with-oci8=/path/to/oracle/home/dir > > > ---junmin > > > > > On Wed, 9 Nov 2005, Amruta Joshi wrote: > > > Hi, > > > > We have installed GUS & have some basic data in it. We are using Oracle > 10g > > (Release 10.1). > > > > I have compiled the Study-Annotator for entering study-related data. > However, > > all the ora_ calls in the php files (likeora_logon, ora_getColumn etc.) > fail. > > I keep getting the error: > > Fatal error: Call to undefined function: ora_logon() > > > > The function ociLogon works just fine. It seems that Oracle 10g > supports only > > OCI calls and not ora_ functions, which means I may have to rewrite > chunks of > > code that use ora_ calls. > > Is there a better alternative to this? > > Is Study-Annotator also made available with the new OCI calls? > > I'm using the Study-Annotator source code from > > http://www.cbil.upenn.edu/downloads/RAD/ > > > > Please reply soon, we need to get this working asap. > > > > thanks, > > Amruta > > > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: > > Tame your development challenges with Apache's Geronimo App Server. > Download > > it for free - -and be entered to win a 42" plasma tv or your very own > > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > |
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From: Steve F. <sfi...@pc...> - 2005-11-19 04:43:50
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ok, well this is now conveniently available in $plugin->getExtDbRlsId(). the flag does matter in the sense that many plugins are *loading* data tagged with an extDbRls. for that, they should standardize on --externalDatabaseSpec. The resources pipeline handles this case elegantly, and, it would be nice if all plugins use it the same way. There are other uses, which are typically for querying. those matter less. steve Jonathan Schug wrote: > Note, by the way that I implemented just such a thing at least 6 > months ago. There are support functions for external database > specifications as follows: > > GUS::PluginMgr::PluginUtilities::ConstraintFunction::CfIsXdbSpec > -- checks to see that the value is in the proper format. I had > chosen name/version or +ddddd for the external_database_release_id > > GUS::PluginMgr::PluginUtilities::ConstraintFunction::ParseXdbSpec > -- parses the value > > GUS::PluginMgr::PluginUtilities::getXdbrIdFromSpec > -- takes a parsed spec and returns the external_database_release_id > > I don't think the name of the flag matters so much, because as > Elisabetta points out, the semantics are not always the same. > > Jonathan > > > > > Jonathan Schug, Ph.D. > > Center for Bioinformatics > Computational Biology and Informatics Lab > University of Pennsylvania > > js...@pc... > (215) 573-3113 voice > (215) 573-3111 fax > > 1413 Blockley Hall, Philadelphia, PA 19014-6021 > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Jonathan S. <js...@pc...> - 2005-11-19 04:31:56
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Note, by the way that I implemented just such a thing at least 6 months ago. There are support functions for external database specifications as follows: GUS::PluginMgr::PluginUtilities::ConstraintFunction::CfIsXdbSpec -- checks to see that the value is in the proper format. I had chosen name/version or +ddddd for the external_database_release_id GUS::PluginMgr::PluginUtilities::ConstraintFunction::ParseXdbSpec -- parses the value GUS::PluginMgr::PluginUtilities::getXdbrIdFromSpec -- takes a parsed spec and returns the external_database_release_id I don't think the name of the flag matters so much, because as Elisabetta points out, the semantics are not always the same. Jonathan Jonathan Schug, Ph.D. Center for Bioinformatics Computational Biology and Informatics Lab University of Pennsylvania js...@pc... (215) 573-3113 voice (215) 573-3111 fax 1413 Blockley Hall, Philadelphia, PA 19014-6021 |
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From: Steve F. <sfi...@pc...> - 2005-11-18 18:34:13
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yes, that seems fine. they can take either one value, or they can be list arguments steve Elisabetta Manduchi wrote: > > Note that there are situations in which more than one ExtDbRelId needs > to be passed in to the plugin, for different databases: e.g. RefSeq, > DBTSS, etc. Don't know if the plugins currently in Supported have > examples of this, but there are certainly plugins that we are writing > at CBIL that have this and some of these might one day be moved to > GUS::Supported. > What should the convention be in this case? > I'm currently using things like: > > --refSeqExternalDatabaseSpec > --dbtssExternalDatabaseSpec > > etc. > Elisabetta > > --- > > On Fri, 18 Nov 2005, Steve Fischer wrote: > >> i plan on converting all supported plugins to using >> --externalDatabaseSpec. from there on out it will be a matter of >> people using the convention when they make a new plugin. >> >> >> >> Aaron J. Mackey wrote: >> >>> This is nice candy, but doesn't really solve the problem you've >>> noticed, which is the non-canonicalization of argument names (-- >>> seqTable, --subjectTable, etc. also come to mind). >>> >>> On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote: >>> >>>> I think we should have this as the standard argument: >>>> --externalDatabaseSpec "Genbank|1.0.0" >>> >>> >>> >>> So now we can have --extDbSpec, --externalDatabaseSpecification, and >>> everything in between. >>> >>> -Aaron >>> >>> -- >>> Aaron J. Mackey, Ph.D. >>> Project Manager, ApiDB Bioinformatics Resource Center >>> Penn Genomics Institute, University of Pennsylvania >>> email: am...@pc... >>> office: 215-898-1205 (Biology, 212 Goddard Labs) >>> 215-746-7018 (PCBI, 1428 Blockley Hall) >>> fax: 215-746-6697 (Penn Genomics Institute) >>> postal: Penn Genomics Institute >>> Goddard Labs 212 >>> 415 S. University Avenue >>> Philadelphia, PA 19104-6017 >>> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by the JBoss Inc. Get Certified Today >> Register for a JBoss Training Course. Free Certification Exam >> for All Training Attendees Through End of 2005. For more info visit: >> http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> |
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From: Elisabetta M. <man...@pc...> - 2005-11-18 18:09:57
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Note that there are situations in which more than one ExtDbRelId needs to be passed in to the plugin, for different databases: e.g. RefSeq, DBTSS, etc. Don't know if the plugins currently in Supported have examples of this, but there are certainly plugins that we are writing at CBIL that have this and some of these might one day be moved to GUS::Supported. What should the convention be in this case? I'm currently using things like: --refSeqExternalDatabaseSpec --dbtssExternalDatabaseSpec etc. Elisabetta --- On Fri, 18 Nov 2005, Steve Fischer wrote: > i plan on converting all supported plugins to using > --externalDatabaseSpec. from there on out it will be a matter of people > using the convention when they make a new plugin. > > > > Aaron J. Mackey wrote: > >> This is nice candy, but doesn't really solve the problem you've >> noticed, which is the non-canonicalization of argument names (-- >> seqTable, --subjectTable, etc. also come to mind). >> >> On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote: >> >>> I think we should have this as the standard argument: >>> --externalDatabaseSpec "Genbank|1.0.0" >> >> >> So now we can have --extDbSpec, --externalDatabaseSpecification, and >> everything in between. >> >> -Aaron >> >> -- >> Aaron J. Mackey, Ph.D. >> Project Manager, ApiDB Bioinformatics Resource Center >> Penn Genomics Institute, University of Pennsylvania >> email: am...@pc... >> office: 215-898-1205 (Biology, 212 Goddard Labs) >> 215-746-7018 (PCBI, 1428 Blockley Hall) >> fax: 215-746-6697 (Penn Genomics Institute) >> postal: Penn Genomics Institute >> Goddard Labs 212 >> 415 S. University Avenue >> Philadelphia, PA 19104-6017 >> > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Steve F. <sfi...@pc...> - 2005-11-18 18:02:56
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i plan on converting all supported plugins to using --externalDatabaseSpec. from there on out it will be a matter of people using the convention when they make a new plugin. Aaron J. Mackey wrote: > This is nice candy, but doesn't really solve the problem you've > noticed, which is the non-canonicalization of argument names (-- > seqTable, --subjectTable, etc. also come to mind). > > On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote: > >> I think we should have this as the standard argument: >> --externalDatabaseSpec "Genbank|1.0.0" > > > So now we can have --extDbSpec, --externalDatabaseSpecification, and > everything in between. > > -Aaron > > -- > Aaron J. Mackey, Ph.D. > Project Manager, ApiDB Bioinformatics Resource Center > Penn Genomics Institute, University of Pennsylvania > email: am...@pc... > office: 215-898-1205 (Biology, 212 Goddard Labs) > 215-746-7018 (PCBI, 1428 Blockley Hall) > fax: 215-746-6697 (Penn Genomics Institute) > postal: Penn Genomics Institute > Goddard Labs 212 > 415 S. University Avenue > Philadelphia, PA 19104-6017 > |
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From: Aaron J. M. <am...@pc...> - 2005-11-18 17:41:48
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This is nice candy, but doesn't really solve the problem you've
noticed, which is the non-canonicalization of argument names (--
seqTable, --subjectTable, etc. also come to mind).
On Nov 18, 2005, at 12:30 PM, Steve Fischer wrote:
> I think we should have this as the standard argument:
> --externalDatabaseSpec "Genbank|1.0.0"
So now we can have --extDbSpec, --externalDatabaseSpecification, and
everything in between.
-Aaron
--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email: am...@pc...
office: 215-898-1205 (Biology, 212 Goddard Labs)
215-746-7018 (PCBI, 1428 Blockley Hall)
fax: 215-746-6697 (Penn Genomics Institute)
postal: Penn Genomics Institute
Goddard Labs 212
415 S. University Avenue
Philadelphia, PA 19104-6017
|
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From: Steve F. <sfi...@pc...> - 2005-11-18 17:30:14
|
folks-
there is at least one set of command line args that are used in the
majority of plugins, those that get the name and version of the
externalDatabaseRelease to tag the new data with.
many plugins have different names for these args. here are some:
--externalDatabase and --externalDatabaseVersion
--externalDb and -- externalDbRls
etc.
i'm getting a little tired of having to deal w/ the inconsistency.
i propose that we move to a new convention (slowly but surely). i
propose that plugins be upgraded to this when we get a chance, and, that
we do not provide backward compatibility. it just means a simple
change to any script or pipeline that calls the plugin.
I think we should have this as the standard argument:
--externalDatabaseSpec "Genbank|1.0.0"
In other words, we introduce a standard representation of a database
name and version of the form:
name|version
The plugin superclass method $self->getExtDbRlsId() will come in two
forms. The first would be new. The second is already supported:
$self->getExtDbRlsId($externalDatabaseSpec)
$self->getExtDbRlsId($externalDatabaseName, $externalDatabaseVersion)
The additional advantage of introducing the standard format of
name|version is that some plugins take two or more extDbRls's on the
command line, and for each one there needs to be parallel args, one for
the name and one for the version. thus, this will simplify many plugin
args.
Unless there are objections, new plugins will use this standard, and old
ones will be upgraded sooner or later.
steve
|
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From: <am...@pc...> - 2005-11-18 03:01:11
|
Where is the "canonically correct" place to store simple scalar attributes that pertain to an entire sequence (AA and/or NT), e.g.: pI (isoelectric point) codon volatility codon bias (measured in various ways: CAI, etc) dinucleotide bias (e.g. Karlin's delta*) My non-GUS "gut" instinct is that these should all reside in weakly-typed DoTS.(NA/AA)SequenceAttribute tables with very simple tag/value schemas; but I'm looking for enlightenment. Thanks, -Aaron |
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From: Y. T. G. <yg...@pc...> - 2005-11-17 22:17:20
|
The underlying imp table, Dots.NaSequenceImp, has a primary key constraint on na_sequence_id Run this query: SELECT table_name, column_name, position FROM all_cons_columns WHERE constraint_name = 'PK_NASEQUENCEIMP' AND owner = 'DOTS'; ... and you get this: NASEQUENCEIMP NA_SEQUENCE_ID 1 -Thomas > -----Original Message----- > From: gus...@li... > [mailto:gus...@li...] On Behalf > Of Aaron J. Mackey > Sent: Thursday, November 17, 2005 4:10 PM > To: Gusdev gusdev-gusdev > Subject: [GUSDEV] na_sequence_id isn't the primary key of > DoTS.NaSequence? > > > FOREIGN KEY (a_na_sequence_id) REFERENCES DoTS.NaSequence > (na_sequence_id), > > * ERROR at line 22: > ORA-02270: no matching unique or primary key for this column-list > > > Does NASequence have a composite primary key with (na_sequence_id, > version) ? How then do NAfeature's enforce constraints without > including version? > > -Aaron > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get > Certified Today Register for a JBoss Training Course. Free > Certification Exam for All Training Attendees Through End of > 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Aaron J. M. <am...@pc...> - 2005-11-17 21:09:51
|
FOREIGN KEY (a_na_sequence_id) REFERENCES DoTS.NaSequence
(na_sequence_id),
*
ERROR at line 22:
ORA-02270: no matching unique or primary key for this column-list
Does NASequence have a composite primary key with (na_sequence_id,
version) ? How then do NAfeature's enforce constraints without
including version?
-Aaron
|
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From: Chris T. <cmt...@gm...> - 2005-11-17 18:30:05
|
I changed jdbc connection string to ws17.itcomplab.missouri.edu:1521<http://ws17.itcomplab.missouri.edu:1521/> :ws17 <http://ws17.itcomplab.missouri.edu/> and get: BUILD FAILED /home/oracle/GUS/project_home/install/build.xml:28: The following error occurred while executing this line: /home/oracle/GUS/project_home/GUS/build.xml:92: Unable to connect to database my db is on the same machine/account I'm running the install script(?) on. Does the jdbc connection string have to deal with this somehow. Do I have t= o have # 1521 port open? Thanks, chris On 11/16/05, Michael Saffitz <msa...@pc...> wrote: > > > Hi Chris, > > That last part of your JDBC connection string should be the SID of > the database-- it looks like you've got the hostname repeated. Hope > this helps. > > --Mike > > On Nov 15, 2005, at 5:08 PM, Chris Topinka wrote: > > > ok. now I get to the point of: > > > > [InstallSchema] SEVERE: Unable to connect to database. > > DSN=3D'jdbc:oracle:thin:@ws17.itcomplab.missouri.edu: > > 1521:ws17.itcomplab.missouri.edu <http://ws17.itcomplab.missouri.edu>' > > [InstallSchema] java.sql.SQLException: Listener refused the > > connection with the following error: > > [InstallSchema] ORA-12505, TNS:listener does not currently know of > > SID given in connect descriptor > > [InstallSchema] The Connection descriptor used by the client was: > > [InstallSchema] ws17.itcomplab.missouri.edu<http://ws17.itcomplab.misso= uri.edu> > : > > 1521:ws17.itcomplab.missouri.edu <http://ws17.itcomplab.missouri.edu> > > > > > > How can I make sure this is set right? > > > > Thanks, > > > > Chris > > > > On 11/15/05, Steve Fischer <sfi...@pc...> wrote: > > $PROJECT_HOME i think > > > > steve > > > > Chris Topinka wrote: > > > > > I run ant cmd from build.pl with --noconfig at cmd line and get: > > > > > > Buildfile: /install/build.xml does not exist! > > > Build failed > > > > > > > > > what variable is setting the path to build.xml? > > > > > > Thanks, > > > > > > Chris > > > > > > On 11/10/05, *Chris Topinka* <cmt...@gm... > > > <mailto:cmt...@gm...>> wrote: > > > > > > when I run ant cmd from cmd line I get: > > > > > > \Exception in thread "main" java.lang.NoClassDefFoundError : > > > org/apache/tools/ant/launch/Launcher > > > > > > does this mean I need certain libraries on my $CLASSPATH? Which > > > ones and where are they? > > > > > > I'm using 2.4.21-15.EL RedHat but have installed my own java and > > > ant because I don't have root. > > > > > > > > > On 11/10/05, *Angel Pizarro* < an...@ma... > > > <mailto: an...@ma...>> wrote: > > > > > > Try: > > > > > > $ build GUS install -append -returnErrStatus - > > installDBSchema > > > > > > This may give you a useful error message. Other than > > that, try > > > un-commenting line line 41 in build.pl to see the ant > > command > > > that is > > > run and try cutting/pasting this command to get even more > > > verbose output > > > from straight from ant. > > > > > > > > > > > > > > > Chris Topinka wrote: > > > > > >> PATH=3D/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/ > > oracle/usr/local/apache-ant-1.6.5/bin:/home/oracle/GUS/gus_home/ > > bin:/home/oracle/GUS/project_home/install/bin:/usr/kerberos/bin:/ > > usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/oracle/product/ > > 9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin > > > > > >> > > >> > > >> this is my $PATH > > >> > > >> which java and which ant now returns the bins that I want and > > >> installed in my home (I don't have root > > > unfortunately). Before which > > >> had old ant and no java. > > >> > > >> Now when I run build it exits immediately with no output. > > >> > > >> What does build require exactly? In what order? > > >> > > >> Is there a simpler way to get the xml schema onto my oracle db? > > >> > > >> Thanks > > >> On 11/8/05, *msa...@pc... > > > <mailto:msa...@pc... > <mailto: > > > msa...@pc... <mailto:msa...@pc...>>* > > >> < msa...@pc... <mailto:msa...@pc...> > > > <mailto:msa...@pc... > > > <mailto: msa...@pc...>>> wrote: > > >> > > >> Hi Chris, > > >> > > >> I would double check your version of Ant. I believe 1.6.2 is > > >> required. Also, > > >> if on Linux, make sure you're using the copy you think > > > you are-- > > >> RedHat for a > > >> while included a non-compatible version of Ant. Do > > > 'which ant' to > > >> display the > > >> version in use. Also, make sure there is no > > > /etc/ant.conf file. > > >> > > >> --Mike > > >> > > >> Quoting Chris Topinka < cmt...@gm... > > > <mailto:cmt...@gm...> > > >> <mailto:cmt...@gm... <mailto: cmt...@gm...>>>: > > >> > > >> > When I run: > > >> > > > >> > build GUS install -append -installDBSchema > > >> > > > >> > I immediately get: > > >> > ant [options] [target [target2 [target3] ...]] > > >> > > > >> > and then 'build' terminates > > >> > > > >> > I couldn't find anything in the list archives with this > > > output. > > >> Is there a > > >> > better way to search for this in the archives for > > > future reference? > > >> > > > >> > I installed Ant myself, so this could very likely be > > > the problem. > > >> > -- > > >> > Christopher M. Topinka > > >> > NLM-BHIRT Predoctoral Fellow in Computer Science > > >> > 113 Life Sciences Center > > >> > University of Missouri > > >> > Columbia, MO 65211 > > >> > (573)-823-0616 > > >> > cmt...@mi... <mailto:cmt...@mi... > > > > <mailto: cmt...@mi... <mailto:cmt...@mi...>> > > >> > > > >> > > >> > > >> > > >> > > >> > > >> > > >> -- > > >> Christopher M. Topinka > > >> NLM-BHIRT Predoctoral Fellow in Computer Science > > >> 113 Life Sciences Center > > >> University of Missouri > > >> Columbia, MO 65211 > > >> (573)-823-0616 > > >> cmt...@mi... <mailto:cmt...@mi...> <mailto: > > > cmt...@mi... <mailto:cmt...@mi...>> > > > > > > > > > > > > -- > > > > > > Angel Pizarro > > > Director, Bioinformatics Facility > > > Institute for Translational Medicine and Therapeutics > > > University of Pennsylvania > > > 806 BRB II/III > > > 421 Curie Blvd. > > > Philadelphia, PA 19104-6160 > > > > > > P: 215-573-3736 > > > F: 215-573-9004 > > > > > > > > > > > > ------------------------------------------------------- > > > SF.Net email is sponsored by: > > > Tame your development challenges with Apache's Geronimo App > > > Server. Download > > > it for free - -and be entered to win a 42" plasma tv or your > > > very own > > > Sony(tm)PSP. Click here to play: > > > http://sourceforge.net/geronimo.php > > > _______________________________________________ > > > Gusdev-gusdev mailing list > > > Gus...@li... > > > <mailto: Gus...@li...> > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > < https://lists.sourceforge.net/lists/listinfo/gusdev- > > gusdev> > > > > > > > > > > > > > > > -- > > > > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... <mailto: cmt...@mi...> > > > > > > > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... <mailto:cmt...@mi...> > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... > > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science 113 Life Sciences Center University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
|
From: Josef J. <ju...@cs...> - 2005-11-16 20:54:21
|
Deborah Pinney <pi...@pc...> writes: > > There is a case here at Cbil, where we need to have the constraint in > place. In that case dots.naentry is used as a book-keeping tool to keep > track of modifications of Genbank entries. This should be the purpose of the *_DATE and *_REL_VER fields, to keep track of the modification of genbank entries. Why would you need anything else? This unique constraint sounds like it was implemented for idiosyncratic reasons by someone at CBIL. I'll bet this field will continue to completely serve your needs if the unique constraint is removed. That the source_id field is provided in many tables to give users at their respective sites the ability to do local bookkeeping is great. Putting a unique constraint on this field for a perceived local bookkeeping need is just a stumbling block that adds a bit of difficulty to the GUS community. So, shall this unique constraint on source_id of AAEntry/NAEntry be eliminated? (We don't have to decide today). Thanks for the response; Josef > I think at one time the > constraint did not apply to dots.aaentry.source_id (I can't swear on > that though). That may have changed for the sake of consistency. > > Josef Jurek wrote: > > >Well, if people do not feel that source_id requires > >an unique constraint in tables AAEntry/NAEntry, > >I propose that these constraints be removed. I can > >of course just remove them in our local gus installations, > >though I would prefer that our local development > >of tools be compatible with canonical GUS. > > > >Another option would be to just include the fields: > > CREATED_DATE DATE > CREATED_REL_VER NUMBER(5) > SEQ_DATE DATE > SEQ_REL_VER NUMBER(5) > ANNOT_DATE DATE > ANNOT_REL_VER NUMBER(5) > >into AASequenceImp/NASequenceImp and eliminate [...] |
|
From: Deborah P. <pi...@pc...> - 2005-11-16 20:29:09
|
There is a case here at Cbil, where we need to have the constraint in place. In that case dots.naentry is used as a book-keeping tool to keep track of modifications of Genbank entries. I think at one time the constraint did not apply to dots.aaentry.source_id (I can't swear on that though). That may have changed for the sake of consistency. Josef Jurek wrote: >Well, if people do not feel that source_id requires >an unique constraint in tables AAEntry/NAEntry, >I propose that these constraints be removed. I can >of course just remove them in our local gus installations, >though I would prefer that our local development >of tools be compatible with canonical GUS. > > >Another option would be to just include the fields: > > CREATED_DATE DATE > CREATED_REL_VER NUMBER(5) > SEQ_DATE DATE > SEQ_REL_VER NUMBER(5) > ANNOT_DATE DATE > ANNOT_REL_VER NUMBER(5) > >into AASequenceImp/NASequenceImp and eliminate >AAEntry/NAEntry. I can see no reason that these >need to be separate tables (though please, someone >correct me if there is a reason) and this would >be an instance of simplifying the schema without >loosing functionality. > >Ideas, anybody? > >Oh, and I still interested if anyone knows why a unique >constraint is presently applied to source_id of >AAEntry/NAEntry. > >Thanks; Josef > > > >Daphne Preuss Laboratory >Molecular Genetics and Cell Biology >The University of Chicago >ju...@cs... > >voice: (773) 834-3985 >fax: (773) 702-6648 > > > > >Josef Jurek <ju...@cs...> writes: > > >>In looking for a place to put ncbi/swissprot entry dates, >>I see that the tables DoTS.AAEntry/DoTS.NAEntry were >>probably made for this purpose. For example, here are >>the dates from a typical swissprot record: >> >> 16-OCT-2001 (Rel. 40, Created) >> 16-OCT-2001 (Rel. 40, Last sequence update) >> 24-JAN-2006 (Rel. 49, Last annotation update) >> >>and here is what the table looks like: >> >> DoTS.AAEntry; >> Name Null? Type >> ------------------- -------- ---------------- >> AA_ENTRY_ID NOT NULL NUMBER(10) >> AA_SEQUENCE_ID NOT NULL NUMBER(10) >> SOURCE_ID NOT NULL VARCHAR2(15) >> STATUS VARCHAR2(12) >> CREATED_DATE DATE >> CREATED_REL_VER NUMBER(5) >> SEQ_DATE DATE >> SEQ_REL_VER NUMBER(5) >> ANNOT_DATE DATE >> ANNOT_REL_VER NUMBER(5) >> >>It looks perfect. >> >> >>HOWEVER, not only is source_id "NOT NULL", it has a unique constraint >>on it. >> >> Every source_id field in this table must be unique. >> >>And though the column source_id is common in tables throughout >>most GUS schemas, >> >> DoTS.AAEntry/DoTS.NAEntry are the only two tables that have >> this unique constraint on source_id. >> >> >>Jeez; what is going on here? What is the intended use for >>this field? I suppose I can put an accession number here, >>but I was already putting accession numbers in >>DoTS.ExternalAASequence. Why would I or anyone want >>to duplicate this? >> >>Please, would someone explain what the intention is here. >> >>Thank you for your help; >> >>Josef >> >> >> >> >> >> > > > > > >------------------------------------------------------- >This SF.Net email is sponsored by the JBoss Inc. Get Certified Today >Register for a JBoss Training Course. Free Certification Exam >for All Training Attendees Through End of 2005. For more info visit: >http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Josef J. <ju...@cs...> - 2005-11-16 20:12:01
|
Well, if people do not feel that source_id requires
an unique constraint in tables AAEntry/NAEntry,
I propose that these constraints be removed. I can
of course just remove them in our local gus installations,
though I would prefer that our local development
of tools be compatible with canonical GUS.
Another option would be to just include the fields:
CREATED_DATE DATE
CREATED_REL_VER NUMBER(5)
SEQ_DATE DATE
SEQ_REL_VER NUMBER(5)
ANNOT_DATE DATE
ANNOT_REL_VER NUMBER(5)
into AASequenceImp/NASequenceImp and eliminate
AAEntry/NAEntry. I can see no reason that these
need to be separate tables (though please, someone
correct me if there is a reason) and this would
be an instance of simplifying the schema without
loosing functionality.
Ideas, anybody?
Oh, and I still interested if anyone knows why a unique
constraint is presently applied to source_id of
AAEntry/NAEntry.
Thanks; Josef
Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...
voice: (773) 834-3985
fax: (773) 702-6648
Josef Jurek <ju...@cs...> writes:
>
>
> In looking for a place to put ncbi/swissprot entry dates,
> I see that the tables DoTS.AAEntry/DoTS.NAEntry were
> probably made for this purpose. For example, here are
> the dates from a typical swissprot record:
>
> 16-OCT-2001 (Rel. 40, Created)
> 16-OCT-2001 (Rel. 40, Last sequence update)
> 24-JAN-2006 (Rel. 49, Last annotation update)
>
> and here is what the table looks like:
>
> DoTS.AAEntry;
> Name Null? Type
> ------------------- -------- ----------------
> AA_ENTRY_ID NOT NULL NUMBER(10)
> AA_SEQUENCE_ID NOT NULL NUMBER(10)
> SOURCE_ID NOT NULL VARCHAR2(15)
> STATUS VARCHAR2(12)
> CREATED_DATE DATE
> CREATED_REL_VER NUMBER(5)
> SEQ_DATE DATE
> SEQ_REL_VER NUMBER(5)
> ANNOT_DATE DATE
> ANNOT_REL_VER NUMBER(5)
>
> It looks perfect.
>
>
> HOWEVER, not only is source_id "NOT NULL", it has a unique constraint
> on it.
>
> Every source_id field in this table must be unique.
>
> And though the column source_id is common in tables throughout
> most GUS schemas,
>
> DoTS.AAEntry/DoTS.NAEntry are the only two tables that have
> this unique constraint on source_id.
>
>
> Jeez; what is going on here? What is the intended use for
> this field? I suppose I can put an accession number here,
> but I was already putting accession numbers in
> DoTS.ExternalAASequence. Why would I or anyone want
> to duplicate this?
>
> Please, would someone explain what the intention is here.
>
> Thank you for your help;
>
> Josef
>
>
>
>
|
|
From: Josef J. <ju...@cs...> - 2005-11-16 17:18:17
|
In looking for a place to put ncbi/swissprot entry dates,
I see that the tables DoTS.AAEntry/DoTS.NAEntry were
probably made for this purpose. For example, here are
the dates from a typical swissprot record:
16-OCT-2001 (Rel. 40, Created)
16-OCT-2001 (Rel. 40, Last sequence update)
24-JAN-2006 (Rel. 49, Last annotation update)
and here is what the table looks like:
DoTS.AAEntry;
Name Null? Type
------------------- -------- ----------------
AA_ENTRY_ID NOT NULL NUMBER(10)
AA_SEQUENCE_ID NOT NULL NUMBER(10)
SOURCE_ID NOT NULL VARCHAR2(15)
STATUS VARCHAR2(12)
CREATED_DATE DATE
CREATED_REL_VER NUMBER(5)
SEQ_DATE DATE
SEQ_REL_VER NUMBER(5)
ANNOT_DATE DATE
ANNOT_REL_VER NUMBER(5)
It looks perfect.
HOWEVER, not only is source_id "NOT NULL", it has a unique constraint
on it.
Every source_id field in this table must be unique.
And though the column source_id is common in tables throughout
most GUS schemas,
DoTS.AAEntry/DoTS.NAEntry are the only two tables that have
this unique constraint on source_id.
Jeez; what is going on here? What is the intended use for
this field? I suppose I can put an accession number here,
but I was already putting accession numbers in
DoTS.ExternalAASequence. Why would I or anyone want
to duplicate this?
Please, would someone explain what the intention is here.
Thank you for your help;
Josef
Josef Jurek, Ph.D.
Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...
voice: (773) 834-3985
fax: (773) 702-6648
|
|
From: Elisabetta M. <man...@pc...> - 2005-11-16 16:56:33
|
No, currently there is no such alternative or at least no alternative that we have developed at CBIL, as the RADSA is working very well for us. Please see http://www.cbil.upenn.edu/RAD/php/RAD-installation.php?, bullet point 2 for data loading pipeline into RAD. In some special cases (like data coming out of particular software), some of the annotation can be automated via plugins that we provide (precisely the Assay to Quantification or "Module I"), as these particular software packages provide files that can be used to automate part of the process. For other parts, like Module II (annotation about experimental design) and Module III (annotation like biomaterials and protocols), since the info doesn't typically resides in files, but it's in the lab notebook of the person who did the bench work, the Study Annotator provides a suite of webforms to facilitate entering this info. Elisabetta --- On Wed, 16 Nov 2005, Amruta Joshi wrote: > > Is there any alternative software that does the job similar to the > StudyAnnotator (viz. interface for annotating and depositing microarray > data into GUS)? > > thanks, > Amruta > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Amruta J. <am...@st...> - 2005-11-16 16:48:57
|
Is there any alternative software that does the job similar to the StudyAnnotator (viz. interface for annotating and depositing microarray data into GUS)? thanks, Amruta |
|
From: Michael S. <msa...@pc...> - 2005-11-16 14:33:27
|
Hi Chris, That last part of your JDBC connection string should be the SID of the database-- it looks like you've got the hostname repeated. Hope this helps. --Mike On Nov 15, 2005, at 5:08 PM, Chris Topinka wrote: > ok. now I get to the point of: > > [InstallSchema] SEVERE: Unable to connect to database. > DSN='jdbc:oracle:thin:@ws17.itcomplab.missouri.edu: > 1521:ws17.itcomplab.missouri.edu' > [InstallSchema] java.sql.SQLException: Listener refused the > connection with the following error: > [InstallSchema] ORA-12505, TNS:listener does not currently know of > SID given in connect descriptor > [InstallSchema] The Connection descriptor used by the client was: > [InstallSchema] ws17.itcomplab.missouri.edu: > 1521:ws17.itcomplab.missouri.edu > > > How can I make sure this is set right? > > Thanks, > > Chris > > On 11/15/05, Steve Fischer <sfi...@pc...> wrote: > $PROJECT_HOME i think > > steve > > Chris Topinka wrote: > > > I run ant cmd from build.pl with --noconfig at cmd line and get: > > > > Buildfile: /install/build.xml does not exist! > > Build failed > > > > > > what variable is setting the path to build.xml? > > > > Thanks, > > > > Chris > > > > On 11/10/05, *Chris Topinka* <cmt...@gm... > > <mailto:cmt...@gm...>> wrote: > > > > when I run ant cmd from cmd line I get: > > > > \Exception in thread "main" java.lang.NoClassDefFoundError : > > org/apache/tools/ant/launch/Launcher > > > > does this mean I need certain libraries on my $CLASSPATH? Which > > ones and where are they? > > > > I'm using 2.4.21-15.EL RedHat but have installed my own java and > > ant because I don't have root. > > > > > > On 11/10/05, *Angel Pizarro* < an...@ma... > > <mailto: an...@ma...>> wrote: > > > > Try: > > > > $ build GUS install -append -returnErrStatus - > installDBSchema > > > > This may give you a useful error message. Other than > that, try > > un-commenting line line 41 in build.pl to see the ant > command > > that is > > run and try cutting/pasting this command to get even more > > verbose output > > from straight from ant. > > > > > > > > > > Chris Topinka wrote: > > > >> PATH=/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/ > oracle/usr/local/apache-ant-1.6.5/bin:/home/oracle/GUS/gus_home/ > bin:/home/oracle/GUS/project_home/install/bin:/usr/kerberos/bin:/ > usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/oracle/product/ > 9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin > > > >> > >> > >> this is my $PATH > >> > >> which java and which ant now returns the bins that I want and > >> installed in my home (I don't have root > > unfortunately). Before which > >> had old ant and no java. > >> > >> Now when I run build it exits immediately with no output. > >> > >> What does build require exactly? In what order? > >> > >> Is there a simpler way to get the xml schema onto my oracle db? > >> > >> Thanks > >> On 11/8/05, *msa...@pc... > > <mailto:msa...@pc... > <mailto: > > msa...@pc... <mailto:msa...@pc...>>* > >> < msa...@pc... <mailto:msa...@pc...> > > <mailto:msa...@pc... > > <mailto: msa...@pc...>>> wrote: > >> > >> Hi Chris, > >> > >> I would double check your version of Ant. I believe 1.6.2 is > >> required. Also, > >> if on Linux, make sure you're using the copy you think > > you are-- > >> RedHat for a > >> while included a non-compatible version of Ant. Do > > 'which ant' to > >> display the > >> version in use. Also, make sure there is no > > /etc/ant.conf file. > >> > >> --Mike > >> > >> Quoting Chris Topinka < cmt...@gm... > > <mailto:cmt...@gm...> > >> <mailto:cmt...@gm... <mailto: cmt...@gm...>>>: > >> > >> > When I run: > >> > > >> > build GUS install -append -installDBSchema > >> > > >> > I immediately get: > >> > ant [options] [target [target2 [target3] ...]] > >> > > >> > and then 'build' terminates > >> > > >> > I couldn't find anything in the list archives with this > > output. > >> Is there a > >> > better way to search for this in the archives for > > future reference? > >> > > >> > I installed Ant myself, so this could very likely be > > the problem. > >> > -- > >> > Christopher M. Topinka > >> > NLM-BHIRT Predoctoral Fellow in Computer Science > >> > 113 Life Sciences Center > >> > University of Missouri > >> > Columbia, MO 65211 > >> > (573)-823-0616 > >> > cmt...@mi... <mailto:cmt...@mi... > > > <mailto: cmt...@mi... <mailto:cmt...@mi...>> > >> > > >> > >> > >> > >> > >> > >> > >> -- > >> Christopher M. Topinka > >> NLM-BHIRT Predoctoral Fellow in Computer Science > >> 113 Life Sciences Center > >> University of Missouri > >> Columbia, MO 65211 > >> (573)-823-0616 > >> cmt...@mi... <mailto:cmt...@mi...> <mailto: > > cmt...@mi... <mailto:cmt...@mi...>> > > > > > > > > -- > > > > Angel Pizarro > > Director, Bioinformatics Facility > > Institute for Translational Medicine and Therapeutics > > University of Pennsylvania > > 806 BRB II/III > > 421 Curie Blvd. > > Philadelphia, PA 19104-6160 > > > > P: 215-573-3736 > > F: 215-573-9004 > > > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: > > Tame your development challenges with Apache's Geronimo App > > Server. Download > > it for free - -and be entered to win a 42" plasma tv or your > > very own > > Sony(tm)PSP. Click here to play: > > http://sourceforge.net/geronimo.php > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > <mailto: Gus...@li...> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > < https://lists.sourceforge.net/lists/listinfo/gusdev- > gusdev> > > > > > > > > > > -- > > > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... <mailto: cmt...@mi...> > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... <mailto:cmt...@mi...> > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... |
|
From: Chris T. <cmt...@gm...> - 2005-11-16 00:28:38
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ok. now I get to the point of: [InstallSchema] SEVERE: Unable to connect to database. DSN=3D' jdbc:oracle:thin:@ws17.itcomplab.missouri.edu:1521<http://jdbc:oracle:thin:= @ws17.itcomplab.missouri.edu:1521> :ws17.itcomplab.missouri.edu <http://ws17.itcomplab.missouri.edu>' [InstallSchema] java.sql.SQLException: Listener refused the connection with the following error: [InstallSchema] ORA-12505, TNS:listener does not currently know of SID give= n in connect descriptor [InstallSchema] The Connection descriptor used by the client was: [InstallSchema] ws17.itcomplab.missouri.edu:1521<http://ws17.itcomplab.missouri.edu:1521> :ws17.itcomplab.missouri.edu <http://ws17.itcomplab.missouri.edu> How can I make sure this is set right? Thanks, Chris On 11/15/05, Steve Fischer <sfi...@pc...> wrote: > > $PROJECT_HOME i think > > steve > > Chris Topinka wrote: > > > I run ant cmd from build.pl with --noconfig at cmd line and get: > > > > Buildfile: /install/build.xml does not exist! > > Build failed > > > > > > what variable is setting the path to build.xml? > > > > Thanks, > > > > Chris > > > > On 11/10/05, *Chris Topinka* <cmt...@gm... > > <mailto:cmt...@gm...>> wrote: > > > > when I run ant cmd from cmd line I get: > > > > \Exception in thread "main" java.lang.NoClassDefFoundError: > > org/apache/tools/ant/launch/Launcher > > > > does this mean I need certain libraries on my $CLASSPATH? Which > > ones and where are they? > > > > I'm using 2.4.21-15.EL RedHat but have installed my own java and > > ant because I don't have root. > > > > > > On 11/10/05, *Angel Pizarro* < an...@ma... > > <mailto:an...@ma...>> wrote: > > > > Try: > > > > $ build GUS install -append -returnErrStatus -installDBSchema > > > > This may give you a useful error message. Other than that, try > > un-commenting line line 41 in build.pl to see the ant command > > that is > > run and try cutting/pasting this command to get even more > > verbose output > > from straight from ant. > > > > > > > > > > Chris Topinka wrote: > > > >> > PATH=3D/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/usr/= local/apache- > ant-1.6.5 > /bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_home/install/= bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/orac= le/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin > > > >> > >> > >> this is my $PATH > >> > >> which java and which ant now returns the bins that I want and > >> installed in my home (I don't have root > > unfortunately). Before which > >> had old ant and no java. > >> > >> Now when I run build it exits immediately with no output. > >> > >> What does build require exactly? In what order? > >> > >> Is there a simpler way to get the xml schema onto my oracle db? > >> > >> Thanks > >> On 11/8/05, *msa...@pc... > > <mailto:msa...@pc...> <mailto: > > msa...@pc... <mailto:msa...@pc...>>* > >> < msa...@pc... <mailto:msa...@pc...> > > <mailto:msa...@pc... > > <mailto:msa...@pc...>>> wrote: > >> > >> Hi Chris, > >> > >> I would double check your version of Ant. I believe 1.6.2 is > >> required. Also, > >> if on Linux, make sure you're using the copy you think > > you are-- > >> RedHat for a > >> while included a non-compatible version of Ant. Do > > 'which ant' to > >> display the > >> version in use. Also, make sure there is no > > /etc/ant.conf file. > >> > >> --Mike > >> > >> Quoting Chris Topinka < cmt...@gm... > > <mailto:cmt...@gm...> > >> <mailto:cmt...@gm... <mailto:cmt...@gm...>>>: > >> > >> > When I run: > >> > > >> > build GUS install -append -installDBSchema > >> > > >> > I immediately get: > >> > ant [options] [target [target2 [target3] ...]] > >> > > >> > and then 'build' terminates > >> > > >> > I couldn't find anything in the list archives with this > > output. > >> Is there a > >> > better way to search for this in the archives for > > future reference? > >> > > >> > I installed Ant myself, so this could very likely be > > the problem. > >> > -- > >> > Christopher M. Topinka > >> > NLM-BHIRT Predoctoral Fellow in Computer Science > >> > 113 Life Sciences Center > >> > University of Missouri > >> > Columbia, MO 65211 > >> > (573)-823-0616 > >> > cmt...@mi... <mailto:cmt...@mi...> > > <mailto: cmt...@mi... <mailto:cmt...@mi...>> > >> > > >> > >> > >> > >> > >> > >> > >> -- > >> Christopher M. Topinka > >> NLM-BHIRT Predoctoral Fellow in Computer Science > >> 113 Life Sciences Center > >> University of Missouri > >> Columbia, MO 65211 > >> (573)-823-0616 > >> cmt...@mi... <mailto:cmt...@mi...> <mailto: > > cmt...@mi... <mailto:cmt...@mi...>> > > > > > > > > -- > > > > Angel Pizarro > > Director, Bioinformatics Facility > > Institute for Translational Medicine and Therapeutics > > University of Pennsylvania > > 806 BRB II/III > > 421 Curie Blvd. > > Philadelphia, PA 19104-6160 > > > > P: 215-573-3736 > > F: 215-573-9004 > > > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: > > Tame your development challenges with Apache's Geronimo App > > Server. Download > > it for free - -and be entered to win a 42" plasma tv or your > > very own > > Sony(tm)PSP. Click here to play: > > http://sourceforge.net/geronimo.php > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > <mailto:Gus...@li...> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > <https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev> > > > > > > > > > > -- > > > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... <mailto:cmt...@mi...> > > > > > > > > > > -- > > Christopher M. Topinka > > NLM-BHIRT Predoctoral Fellow in Computer Science > > 113 Life Sciences Center > > University of Missouri > > Columbia, MO 65211 > > (573)-823-0616 > > cmt...@mi... <mailto:cmt...@mi...> > > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science 113 Life Sciences Center University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Steve F. <sfi...@pc...> - 2005-11-15 21:54:10
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$PROJECT_HOME i think steve Chris Topinka wrote: > I run ant cmd from build.pl with --noconfig at cmd line and get: > > Buildfile: /install/build.xml does not exist! > Build failed > > > what variable is setting the path to build.xml? > > Thanks, > > Chris > > On 11/10/05, *Chris Topinka* <cmt...@gm... > <mailto:cmt...@gm...>> wrote: > > when I run ant cmd from cmd line I get: > > \Exception in thread "main" java.lang.NoClassDefFoundError: > org/apache/tools/ant/launch/Launcher > > does this mean I need certain libraries on my $CLASSPATH? Which > ones and where are they? > > I'm using 2.4.21-15.EL RedHat but have installed my own java and > ant because I don't have root. > > > On 11/10/05, *Angel Pizarro* < an...@ma... > <mailto:an...@ma...>> wrote: > > Try: > > $ build GUS install -append -returnErrStatus -installDBSchema > > This may give you a useful error message. Other than that, try > un-commenting line line 41 in build.pl to see the ant command > that is > run and try cutting/pasting this command to get even more > verbose output > from straight from ant. > > > > > Chris Topinka wrote: > >> PATH=/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/usr/local/apache-ant-1.6.5/bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_home/install/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/opt/oracle/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin > >> >> >> this is my $PATH >> >> which java and which ant now returns the bins that I want and >> installed in my home (I don't have root > unfortunately). Before which >> had old ant and no java. >> >> Now when I run build it exits immediately with no output. >> >> What does build require exactly? In what order? >> >> Is there a simpler way to get the xml schema onto my oracle db? >> >> Thanks >> On 11/8/05, *msa...@pc... > <mailto:msa...@pc...> <mailto: > msa...@pc... <mailto:msa...@pc...>>* >> < msa...@pc... <mailto:msa...@pc...> > <mailto:msa...@pc... > <mailto:msa...@pc...>>> wrote: >> >> Hi Chris, >> >> I would double check your version of Ant. I believe 1.6.2 is >> required. Also, >> if on Linux, make sure you're using the copy you think > you are-- >> RedHat for a >> while included a non-compatible version of Ant. Do > 'which ant' to >> display the >> version in use. Also, make sure there is no > /etc/ant.conf file. >> >> --Mike >> >> Quoting Chris Topinka < cmt...@gm... > <mailto:cmt...@gm...> >> <mailto:cmt...@gm... <mailto:cmt...@gm...>>>: >> >> > When I run: >> > >> > build GUS install -append -installDBSchema >> > >> > I immediately get: >> > ant [options] [target [target2 [target3] ...]] >> > >> > and then 'build' terminates >> > >> > I couldn't find anything in the list archives with this > output. >> Is there a >> > better way to search for this in the archives for > future reference? >> > >> > I installed Ant myself, so this could very likely be > the problem. >> > -- >> > Christopher M. Topinka >> > NLM-BHIRT Predoctoral Fellow in Computer Science >> > 113 Life Sciences Center >> > University of Missouri >> > Columbia, MO 65211 >> > (573)-823-0616 >> > cmt...@mi... <mailto:cmt...@mi...> > <mailto: cmt...@mi... <mailto:cmt...@mi...>> >> > >> >> >> >> >> >> >> -- >> Christopher M. Topinka >> NLM-BHIRT Predoctoral Fellow in Computer Science >> 113 Life Sciences Center >> University of Missouri >> Columbia, MO 65211 >> (573)-823-0616 >> cmt...@mi... <mailto:cmt...@mi...> <mailto: > cmt...@mi... <mailto:cmt...@mi...>> > > > > -- > > Angel Pizarro > Director, Bioinformatics Facility > Institute for Translational Medicine and Therapeutics > University of Pennsylvania > 806 BRB II/III > 421 Curie Blvd. > Philadelphia, PA 19104-6160 > > P: 215-573-3736 > F: 215-573-9004 > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App > Server. Download > it for free - -and be entered to win a 42" plasma tv or your > very own > Sony(tm)PSP. Click here to play: > http://sourceforge.net/geronimo.php > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > <mailto:Gus...@li...> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > <https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev> > > > > > -- > > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... <mailto:cmt...@mi...> > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... <mailto:cmt...@mi...> |
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From: Chris T. <cmt...@gm...> - 2005-11-15 21:50:58
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I run ant cmd from build.pl with --noconfig at cmd line and get: Buildfile: /install/build.xml does not exist! Build failed what variable is setting the path to build.xml? Thanks, Chris On 11/10/05, Chris Topinka <cmt...@gm...> wrote: > > when I run ant cmd from cmd line I get: > > \Exception in thread "main" java.lang.NoClassDefFoundError: > org/apache/tools/ant/launch/Launcher > > does this mean I need certain libraries on my $CLASSPATH? Which ones and > where are they? > > I'm using 2.4.21-15.EL RedHat but have installed my own java and antbecau= se I don't have root. > > On 11/10/05, Angel Pizarro < an...@ma...> wrote: > > > > Try: > > > > $ build GUS install -append -returnErrStatus -installDBSchema > > > > This may give you a useful error message. Other than that, try > > un-commenting line line 41 in build.pl to see the ant command that is > > run and try cutting/pasting this command to get even more verbose outpu= t > > from straight from ant. > > > > > > > > > > Chris Topinka wrote: > > > > > > > PATH=3D/home/oracle/usr/local/SunWappserver/jdk/jre/bin:/home/oracle/us= r/local/apache- > > ant-1.6.5/bin:/home/oracle/GUS/gus_home/bin:/home/oracle/GUS/project_ho= me/install/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bi= n:/opt/oracle/product/9.2.0/bin:/sbin:/usr/local/java/bin:/home/oracle/bin > > > > > > > > > > > this is my $PATH > > > > > > which java and which ant now returns the bins that I want and > > > installed in my home (I don't have root unfortunately). Before which > > > had old ant and no java. > > > > > > Now when I run build it exits immediately with no output. > > > > > > What does build require exactly? In what order? > > > > > > Is there a simpler way to get the xml schema onto my oracle db? > > > > > > Thanks > > > On 11/8/05, *msa...@pc... <mailto:msa...@pc...>= * > > > < msa...@pc... <mailto:msa...@pc...>> wrote: > > > > > > Hi Chris, > > > > > > I would double check your version of Ant. I believe 1.6.2 is > > > required. Also, > > > if on Linux, make sure you're using the copy you think you are-- > > > RedHat for a > > > while included a non-compatible version of Ant. Do 'which ant' to > > > display the > > > version in use. Also, make sure there is no /etc/ant.conf file. > > > > > > --Mike > > > > > > Quoting Chris Topinka <cmt...@gm... > > > <mailto:cmt...@gm...>>: > > > > > > > When I run: > > > > > > > > build GUS install -append -installDBSchema > > > > > > > > I immediately get: > > > > ant [options] [target [target2 [target3] ...]] > > > > > > > > and then 'build' terminates > > > > > > > > I couldn't find anything in the list archives with this output. > > > Is there a > > > > better way to search for this in the archives for future reference? > > > > > > > > I installed Ant myself, so this could very likely be the problem. > > > > -- > > > > Christopher M. Topinka > > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > > 113 Life Sciences Center > > > > University of Missouri > > > > Columbia, MO 65211 > > > > (573)-823-0616 > > > > cmt...@mi... <mailto:cmt...@mi...> > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > Christopher M. Topinka > > > NLM-BHIRT Predoctoral Fellow in Computer Science > > > 113 Life Sciences Center > > > University of Missouri > > > Columbia, MO 65211 > > > (573)-823-0616 > > > cmt...@mi... <mailto:cmt...@mi...> > > > > > > > > -- > > > > Angel Pizarro > > Director, Bioinformatics Facility > > Institute for Translational Medicine and Therapeutics > > University of Pennsylvania > > 806 BRB II/III > > 421 Curie Blvd. > > Philadelphia, PA 19104-6160 > > > > P: 215-573-3736 > > F: 215-573-9004 > > > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: > > Tame your development challenges with Apache's Geronimo App Server. > > Download > > it for free - -and be entered to win a 42" plasma tv or your very own > > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > -- > Christopher M. Topinka > NLM-BHIRT Predoctoral Fellow in Computer Science > 113 Life Sciences Center > University of Missouri > Columbia, MO 65211 > (573)-823-0616 > cmt...@mi... > -- Christopher M. Topinka NLM-BHIRT Predoctoral Fellow in Computer Science 113 Life Sciences Center University of Missouri Columbia, MO 65211 (573)-823-0616 cmt...@mi... |
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From: Elisabetta M. <man...@pc...> - 2005-11-15 20:30:32
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Hi Juan, sorry, I should have clarified this in the announcement. There are some plugins that have been updated or added to the list of plugins from the GUS 3.5 release. So you want to use the trunk of the GUS svn repository to this end. If you go to http://www.gusdb.org/download.php you'll see in the section "Source Repository" a command that will enable you to check out the trunk in way that will automatically set up your $GUS_HOME, $PROJECT_HOME, etc. For any plugin referred to by the RAD/RADSA documentation you'll want to get the code from this svn repository. Elisabetta --- On Tue, 15 Nov 2005, Juan Carlos Perin wrote: > Upon attempting to setup today's release, I'm having some trouble loading > the bootstrap ontologies. I'm following the instructions to load > ontolRelTypeTerms.txt using > > GUS::Supported::Plugin::InsertOntologyRelationshipType > > First thing I found was that this plugin is actually in GUS::Community for > me, I'm not sure if that changed recently. Then, when I do run it with > --help to see its usage, or with any flags, I get: > > Can't locate object method "new" via package > "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1. > > Am I missing something obvious? > > Juan > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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