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From: Jian Lu <jl...@vb...> - 2005-08-18 20:15:09
|
Steve, After further investigation of GO files and comparison of the database, here is the report: GO file information: !autogenerated-by: DAG-Edit version 1.419 rev 3 !saved-by: gocvs !date: Fri Aug 12 21:00:17 PDT 2005 !version: $Revision: 3.306 $ unique GO terms in component.ontology: 1745 unique GO terms in function.ontology: 7902 unique GO terms in process.ontology: 10370 unique GO terms in all three files: 20015 total loaded GO terms: 19395 total missing GO terms: 620 steve wrote: > jian- > > yes, we have used the plugin, but it has been changed a little > recently. can you do a grep on the file to count how many terms there > are in it? have you looked carefully at those entries in the file to > see if there is something that distinguishes them? can you count > how many rows actually are in the database that were put there by that > run of the plugin? > > thanks for your help, > steve > > Jian Lu wrote: > >> Hi group, >> >> I downloaded Gene Ontology version 3.306 >> (component.ontology,function.ontology, process.ontology) and ran >> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS >> database. >> Here is my command: >> >> ga GUS::Supported::Plugin::InsertGeneOntology --filePath >> /home/data/ontology --functionExtDbName 'GO Function' >> --processExtDbName 'GO Process' --componentExtDbName 'GO Component' >> --commit >> >> >> Everything looks fine, no errors. It returned a result as "Created >> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 >> entries in GOSynonym. Skipped 0 total entries". >> >> But when I was doing other data checking, I found there are three GO >> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. >> They do exist on the GO downloaded files. >> Has anyone used this plugin to load GO and checked its completeness? >> Please advise. Thanks. >> >> Jian >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * Testing >> & QA >> Security * Process Improvement & Measurement * >> http://www.sqe.com/bsce5sf >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: steve <sfi...@pc...> - 2005-08-18 19:43:11
|
jian- yes, we have used the plugin, but it has been changed a little recently. can you do a grep on the file to count how many terms there are in it? have you looked carefully at those entries in the file to see if there is something that distinguishes them? can you count how many rows actually are in the database that were put there by that run of the plugin? thanks for your help, steve Jian Lu wrote: > Hi group, > > I downloaded Gene Ontology version 3.306 > (component.ontology,function.ontology, process.ontology) and ran > GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS > database. > Here is my command: > > ga GUS::Supported::Plugin::InsertGeneOntology --filePath > /home/data/ontology --functionExtDbName 'GO Function' > --processExtDbName 'GO Process' --componentExtDbName 'GO Component' > --commit > > > Everything looks fine, no errors. It returned a result as "Created > 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 > entries in GOSynonym. Skipped 0 total entries". > > But when I was doing other data checking, I found there are three GO > terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. > They do exist on the GO downloaded files. > Has anyone used this plugin to load GO and checked its completeness? > Please advise. Thanks. > > Jian > > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing > & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Alberto D. <da...@io...> - 2005-08-18 19:18:28
|
Hi All,
Our problem to use GBParser with some GenBank (should I say GenPept ?)
entries persist... some entries as the one listed below are probably
causing the problem ... Has anybody been faced to this problem while
trying to load that kind of sequence into GUS ? Meaning it has "SecStr"
and "Region" features that are probably not represented in the GUS
tables (such as suggested by Jeetendra)... the error generated by the
GBParser plugin was posted a couple of days ago by Henrique.
Any tips to help to solve this would be greatly appreciated.
Thanks, Alberto
LOCUS 1WCS_A 641 aa linear INV 21-
NOV-2004
DEFINITION Chain A, A Mutant Of Trypanosoma Rangeli Sialidase
Displaying
Trans- Sialidase Activity.
ACCESSION 1WCS_A
VERSION 1WCS_A GI:58177176
DBSOURCE pdb: molecule 1WCS, chain 65, release Nov 21, 2004;
deposition: Nov 21, 2004;
class: Hydrolase;
source: Mol_id: 1; Expression_system: Escherichia Coli;
Expression_system_strain: Bl21; Organism_scientific:
Trypanosoma
Rangeli;
Exp. method: X-Ray Diffraction.
KEYWORDS .
SOURCE Trypanosoma rangeli
ORGANISM Trypanosoma rangeli
Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
Trypanosoma.
REFERENCE 1 (residues 1 to 641)
AUTHORS Paris,G., Ratier,L., Amaya,M.F., Nguyen,T., Alzari,P.M. and
Frasch,A.C.
TITLE A sialidase mutant displaying trans-sialidase activity
JOURNAL J. Mol. Biol. 345 (4), 923-934 (2005)
PUBMED 15588836
REFERENCE 2 (residues 1 to 641)
AUTHORS Paris,G., Ratier,L., Amaya,M.F., Nguyen,T., Alzari,P.M. and
Frasch,C.
TITLE Direct Submission
JOURNAL Submitted (21-NOV-2004)
COMMENT Revision History:
DEC 15 4 Initial Entry.
FEATURES Location/Qualifiers
source 1..641
/organism="Trypanosoma rangeli"
/db_xref="taxon:5698"
Region join(1..40,341..409)
/region_name="Domain 1"
/note="NCBI Domains"
SecStr 7..16
/sec_str_type="sheet"
/note="strand 1"
SecStr 21..26
/sec_str_type="sheet"
/note="strand 2"
SecStr 28..33
/sec_str_type="sheet"
/note="strand 3"
SecStr 36..40
/sec_str_type="sheet"
/note="strand 4"
Region 41..229
/region_name="Domain 2"
/note="NCBI Domains"
SecStr 41..47
/sec_str_type="sheet"
/note="strand 5"
SecStr 48..58
/sec_str_type="sheet"
/note="strand 6"
SecStr 65..75
/sec_str_type="sheet"
/note="strand 7"
SecStr 80..87
/sec_str_type="sheet"
/note="strand 8"
SecStr 95..107
/sec_str_type="sheet"
/note="strand 9"
SecStr 108..119
/sec_str_type="sheet"
/note="strand 10"
SecStr 132..142
/sec_str_type="sheet"
/note="strand 11"
SecStr 143..148
/sec_str_type="sheet"
/note="strand 12"
SecStr 149..159
/sec_str_type="sheet"
/note="strand 13"
SecStr 160..163
/sec_str_type="sheet"
/note="strand 14"
SecStr 169..172
/sec_str_type="sheet"
/note="strand 15"
SecStr 173..176
/sec_str_type="sheet"
/note="strand 16"
SecStr 177..182
/sec_str_type="sheet"
/note="strand 17"
SecStr 183..190
/sec_str_type="sheet"
/note="strand 18"
SecStr 192..203
/sec_str_type="sheet"
/note="strand 19"
SecStr 205..215
/sec_str_type="sheet"
/note="strand 20"
SecStr 221..224
/sec_str_type="sheet"
/note="strand 21"
Region 230..290
/region_name="Domain 3"
/note="NCBI Domains"
SecStr 234..241
/sec_str_type="sheet"
/note="strand 22"
SecStr 242..252
/sec_str_type="sheet"
/note="strand 23"
SecStr 255..261
/sec_str_type="sheet"
/note="strand 24"
SecStr 267..270
/sec_str_type="sheet"
/note="strand 25"
SecStr 286..289
/sec_str_type="sheet"
/note="strand 26"
Region 291..340
/region_name="Domain 4"
/note="NCBI Domains"
SecStr 291..298
/sec_str_type="sheet"
/note="strand 27"
SecStr 301..310
/sec_str_type="sheet"
/note="strand 28"
SecStr 320..327
/sec_str_type="sheet"
/note="strand 29"
SecStr 330..338
/sec_str_type="sheet"
/note="strand 30"
SecStr 343..353
/sec_str_type="sheet"
/note="strand 31"
SecStr 354..365
/sec_str_type="sheet"
/note="strand 32"
SecStr 366..372
/sec_str_type="sheet"
/note="strand 33"
SecStr 373..376
/sec_str_type="sheet"
/note="strand 34"
SecStr 377..397
/sec_str_type="helix"
/note="helix 1"
Bond bond(400,414)
/bond_type="disulfide"
Region 410..641
/region_name="Domain 5"
/note="NCBI Domains"
SecStr 422..428
/sec_str_type="sheet"
/note="strand 35"
SecStr 430..433
/sec_str_type="sheet"
/note="strand 36"
SecStr 434..437
/sec_str_type="sheet"
/note="strand 37"
SecStr 444..448
/sec_str_type="sheet"
/note="strand 38"
SecStr 449..454
/sec_str_type="sheet"
/note="strand 39"
SecStr 455..460
/sec_str_type="sheet"
/note="strand 40"
SecStr 463..467
/sec_str_type="sheet"
/note="strand 41"
SecStr 468..471
/sec_str_type="sheet"
/note="strand 42"
SecStr 485..495
/sec_str_type="sheet"
/note="strand 43"
SecStr 500..505
/sec_str_type="sheet"
/note="strand 44"
SecStr 506..509
/sec_str_type="sheet"
/note="strand 45"
SecStr 518..524
/sec_str_type="sheet"
/note="strand 46"
SecStr 526..533
/sec_str_type="sheet"
/note="strand 47"
SecStr 545..550
/sec_str_type="sheet"
/note="strand 48"
SecStr 551..557
/sec_str_type="sheet"
/note="strand 49"
SecStr 558..565
/sec_str_type="sheet"
/note="strand 50"
SecStr 566..569
/sec_str_type="sheet"
/note="strand 51"
SecStr 572..576
/sec_str_type="sheet"
/note="strand 52"
SecStr 585..591
/sec_str_type="sheet"
/note="strand 53"
SecStr 603..606
/sec_str_type="sheet"
/note="strand 54"
SecStr 607..614
/sec_str_type="sheet"
/note="strand 55"
SecStr 618..626
/sec_str_type="helix"
/note="helix 2"
ORIGIN
1 aaslapgssr velfkrknst vpfeesngti rervvhsfri ptivnvdgvm
vaiadaryet
61 sfdnsfieta vkysvddgat wntqiaikns rassvsrvvd ptvivkgnkl
yilvgsfnkt
121 rnywtqhrdg sdwepllvvg evtksaangk ttatiswgkp vslkplfpae
fdgiltkefv
181 ggvgaaivas ngnlvypvqi admggrvftk imyseddgnt wkfaegrskf
gcsepavlew
241 egkliinnrv dynrrlvyes sdmgktwvea lgtlshvwtn sptsnqpdcq
ssfvavtieg
301 krvmlfthpl nlkgrwmrdr lhlwmtdnqr ifdvgqisig densgyssvl
ykddklyslh
361 eintndvysl vfvrligelq lmksvvrtwk eednhlasic tpvvpatpps
kgacgaavpt
421 aglvgflshs angsvwedvy rcvdanvana ervpnglkfn gvgggavwpv
arqgqtrryq
481 fanyrftlva tvtidelpkg tspllgagle gpgdakllgl sydknrqwrp
lygaapaspt
541 gswelhkkyh vvltmadrqg svyvdgqpla gsgntvvrga tlpdishfyi
ggprskgapt
601 dsrvtvtnvv lynrrlnsse irtlflsqdm igtdggagta a
//
|
|
From: Michael S. <msa...@pc...> - 2005-08-18 18:58:39
|
All,
There are a sufficient number of issue fixes and new feature requests
pending for GUS that thinking about future releases is warranted.
(Note: As you may recall, the App Framework and Schema were separated into
distinct projects/products following the 3.5 release. GusSchema will retain
the 3.x series numbering. GusAppFramework will use 1.x series numbers for
its release following the split.)
_GusSchema 3.5.1_
* Backwards compatible schema changes, such as increasing attribute
precision, creation of tables, addition of subclasses/views.
_GusSchema 3.6_
* Non-Backwards compatible schema changes, such as adding attributes,
deleting tables, etc.
_GusAppFramework 1.0_
* Bug Fixes
* Compatibility Changes
* New Features
*** As part of the planning for these releases, Schema Owners, bug
reporters, and GUS engineers should review the issues in the tracker that
they "own". Every issue should be updated with the appropriate milestone
set. Using GusSchema as an example:
- upcoming patch: version 3.5.1
- following patch: version 3.5.2 or 3.6
- upcoming release: version 3.6
- following release: version 3.7
- near/far future release: > version 3.7
Once completed, a report of issue status for each release will be available:
GusSchema 3.5.1:
https://cbil.upenn.edu/tracker/buglist.cgi?query_format=advanced&short_desc_
type=allwordssubstr&short_desc=&product=GUS+Schema&target_milestone=upcoming
+patch&long_desc_type=allwordssubstr&long_desc=&bug_file_loc_type=allwordssu
bstr&bug_file_loc=&bug_status=UNCONFIRMED&bug_status=NEW&bug_status=ASSIGNED
&bug_status=REOPENED&bug_status=RESOLVED&bug_status=VERIFIED&emailtype1=exac
t&email1=&emailtype2=substring&email2=&bugidtype=include&bug_id=&chfieldfrom
=&chfieldto=Now&chfieldvalue=&cmdtype=doit&order=Importance&field0-0-0=noop&
type0-0-0=noop&value0-0-0=
GusSchema 3.6:
https://cbil.upenn.edu/tracker/buglist.cgi?query_format=advanced&short_desc_
type=allwordssubstr&short_desc=&product=GUS+Schema&target_milestone=upcoming
+release&long_desc_type=allwordssubstr&long_desc=&bug_file_loc_type=allwords
substr&bug_file_loc=&bug_status=UNCONFIRMED&bug_status=NEW&bug_status=ASSIGN
ED&bug_status=REOPENED&bug_status=RESOLVED&bug_status=VERIFIED&emailtype1=ex
act&email1=&emailtype2=substring&email2=&bugidtype=include&bug_id=&chfieldfr
om=&chfieldto=Now&chfieldvalue=&cmdtype=doit&order=Importance&field0-0-0=noo
p&type0-0-0=noop&value0-0-0=
GusAppFramework 1.0
https://cbil.upenn.edu/tracker/buglist.cgi?query_format=advanced&short_desc_
type=allwordssubstr&short_desc=&product=GUS+Application+Framework&target_mil
estone=upcoming+release&long_desc_type=allwordssubstr&long_desc=&bug_file_lo
c_type=allwordssubstr&bug_file_loc=&bug_status=UNCONFIRMED&bug_status=NEW&bu
g_status=ASSIGNED&bug_status=REOPENED&bug_status=RESOLVED&bug_status=VERIFIE
D&emailtype1=exact&email1=&emailtype2=substring&email2=&bugidtype=include&bu
g_id=&chfieldfrom=&chfieldto=Now&chfieldvalue=&cmdtype=doit&order=Importance
&field0-0-0=noop&type0-0-0=noop&value0-0-0=
When all issues from the report have been closed, the product is ready for
release.
Comments/Suggestions?
Thanks,
Mike
|
|
From: Jian Lu <jl...@vb...> - 2005-08-18 17:58:29
|
Hi Steve, By further investigation of GO data, here is the report: Gene Ontology file info: !autogenerated-by: DAG-Edit version 1.419 rev 3 !saved-by: gocvs !date: Fri Aug 12 21:00:17 PDT 2005 !version: $Revision: 3.306 $ Total unique GO term in component.ontology: 1745 Total unique GO term in function.ontology: 7902 Total unique GO term in process.ontology: 10370 Total unique GO term in three files: 20015 (note: GO:0003673 exists in all three files) By comparing our database SRes.GOTERM Total loaded by GUS plugin: 19395 Surprisingly, there are 620 GO terms unloaded!!! I have attached a file which lists all unqiue GO terms from three original files with flag 'loaded' and 'missing'. Thanks. steve wrote: > jian- > > yes, we have used the plugin, but it has been changed a little > recently. can you do a grep on the file to count how many terms there > are in it? have you looked carefully at those entries in the file to > see if there is something that distinguishes them? can you count > how many rows actually are in the database that were put there by that > run of the plugin? > > thanks for your help, > steve > > Jian Lu wrote: > >> Hi group, >> >> I downloaded Gene Ontology version 3.306 >> (component.ontology,function.ontology, process.ontology) and ran >> GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS >> database. >> Here is my command: >> >> ga GUS::Supported::Plugin::InsertGeneOntology --filePath >> /home/data/ontology --functionExtDbName 'GO Function' >> --processExtDbName 'GO Process' --componentExtDbName 'GO Component' >> --commit >> >> >> Everything looks fine, no errors. It returned a result as "Created >> 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 >> entries in GOSynonym. Skipped 0 total entries". >> >> But when I was doing other data checking, I found there are three GO >> terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. >> They do exist on the GO downloaded files. >> Has anyone used this plugin to load GO and checked its completeness? >> Please advise. Thanks. >> >> Jian >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * Testing >> & QA >> Security * Process Improvement & Measurement * >> http://www.sqe.com/bsce5sf >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Alberto D. <da...@io...> - 2005-08-18 16:56:09
|
Hi All,
Our problem to use GBParser with some GenBank (should I say GenPept ?)
entries persist... some entries as the one listed below are probably
causing the problem ... Has anybody been faced to this problem while
trying to load that kind of sequence into GUS ? Meaning it has "SecStr"
and "Region" features that are probably not represented in the GUS
tables (such as suggested by Jeetendra)... the error generated by the
GBParser plugin was posted a couple of days ago by Henrique.
Any tips to help to solve this would be greatly appreciated.
Thanks, Alberto
LOCUS 1WCS_A 641 aa linear INV 21-
NOV-2004
DEFINITION Chain A, A Mutant Of Trypanosoma Rangeli Sialidase
Displaying
Trans- Sialidase Activity.
ACCESSION 1WCS_A
VERSION 1WCS_A GI:58177176
DBSOURCE pdb: molecule 1WCS, chain 65, release Nov 21, 2004;
deposition: Nov 21, 2004;
class: Hydrolase;
source: Mol_id: 1; Expression_system: Escherichia Coli;
Expression_system_strain: Bl21; Organism_scientific:
Trypanosoma
Rangeli;
Exp. method: X-Ray Diffraction.
KEYWORDS .
SOURCE Trypanosoma rangeli
ORGANISM Trypanosoma rangeli
Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
Trypanosoma.
REFERENCE 1 (residues 1 to 641)
AUTHORS Paris,G., Ratier,L., Amaya,M.F., Nguyen,T., Alzari,P.M. and
Frasch,A.C.
TITLE A sialidase mutant displaying trans-sialidase activity
JOURNAL J. Mol. Biol. 345 (4), 923-934 (2005)
PUBMED 15588836
REFERENCE 2 (residues 1 to 641)
AUTHORS Paris,G., Ratier,L., Amaya,M.F., Nguyen,T., Alzari,P.M. and
Frasch,C.
TITLE Direct Submission
JOURNAL Submitted (21-NOV-2004)
COMMENT Revision History:
DEC 15 4 Initial Entry.
FEATURES Location/Qualifiers
source 1..641
/organism="Trypanosoma rangeli"
/db_xref="taxon:5698"
Region join(1..40,341..409)
/region_name="Domain 1"
/note="NCBI Domains"
SecStr 7..16
/sec_str_type="sheet"
/note="strand 1"
SecStr 21..26
/sec_str_type="sheet"
/note="strand 2"
SecStr 28..33
/sec_str_type="sheet"
/note="strand 3"
SecStr 36..40
/sec_str_type="sheet"
/note="strand 4"
Region 41..229
/region_name="Domain 2"
/note="NCBI Domains"
SecStr 41..47
/sec_str_type="sheet"
/note="strand 5"
SecStr 48..58
/sec_str_type="sheet"
/note="strand 6"
SecStr 65..75
/sec_str_type="sheet"
/note="strand 7"
SecStr 80..87
/sec_str_type="sheet"
/note="strand 8"
SecStr 95..107
/sec_str_type="sheet"
/note="strand 9"
SecStr 108..119
/sec_str_type="sheet"
/note="strand 10"
SecStr 132..142
/sec_str_type="sheet"
/note="strand 11"
SecStr 143..148
/sec_str_type="sheet"
/note="strand 12"
SecStr 149..159
/sec_str_type="sheet"
/note="strand 13"
SecStr 160..163
/sec_str_type="sheet"
/note="strand 14"
SecStr 169..172
/sec_str_type="sheet"
/note="strand 15"
SecStr 173..176
/sec_str_type="sheet"
/note="strand 16"
SecStr 177..182
/sec_str_type="sheet"
/note="strand 17"
SecStr 183..190
/sec_str_type="sheet"
/note="strand 18"
SecStr 192..203
/sec_str_type="sheet"
/note="strand 19"
SecStr 205..215
/sec_str_type="sheet"
/note="strand 20"
SecStr 221..224
/sec_str_type="sheet"
/note="strand 21"
Region 230..290
/region_name="Domain 3"
/note="NCBI Domains"
SecStr 234..241
/sec_str_type="sheet"
/note="strand 22"
SecStr 242..252
/sec_str_type="sheet"
/note="strand 23"
SecStr 255..261
/sec_str_type="sheet"
/note="strand 24"
SecStr 267..270
/sec_str_type="sheet"
/note="strand 25"
SecStr 286..289
/sec_str_type="sheet"
/note="strand 26"
Region 291..340
/region_name="Domain 4"
/note="NCBI Domains"
SecStr 291..298
/sec_str_type="sheet"
/note="strand 27"
SecStr 301..310
/sec_str_type="sheet"
/note="strand 28"
SecStr 320..327
/sec_str_type="sheet"
/note="strand 29"
SecStr 330..338
/sec_str_type="sheet"
/note="strand 30"
SecStr 343..353
/sec_str_type="sheet"
/note="strand 31"
SecStr 354..365
/sec_str_type="sheet"
/note="strand 32"
SecStr 366..372
/sec_str_type="sheet"
/note="strand 33"
SecStr 373..376
/sec_str_type="sheet"
/note="strand 34"
SecStr 377..397
/sec_str_type="helix"
/note="helix 1"
Bond bond(400,414)
/bond_type="disulfide"
Region 410..641
/region_name="Domain 5"
/note="NCBI Domains"
SecStr 422..428
/sec_str_type="sheet"
/note="strand 35"
SecStr 430..433
/sec_str_type="sheet"
/note="strand 36"
SecStr 434..437
/sec_str_type="sheet"
/note="strand 37"
SecStr 444..448
/sec_str_type="sheet"
/note="strand 38"
SecStr 449..454
/sec_str_type="sheet"
/note="strand 39"
SecStr 455..460
/sec_str_type="sheet"
/note="strand 40"
SecStr 463..467
/sec_str_type="sheet"
/note="strand 41"
SecStr 468..471
/sec_str_type="sheet"
/note="strand 42"
SecStr 485..495
/sec_str_type="sheet"
/note="strand 43"
SecStr 500..505
/sec_str_type="sheet"
/note="strand 44"
SecStr 506..509
/sec_str_type="sheet"
/note="strand 45"
SecStr 518..524
/sec_str_type="sheet"
/note="strand 46"
SecStr 526..533
/sec_str_type="sheet"
/note="strand 47"
SecStr 545..550
/sec_str_type="sheet"
/note="strand 48"
SecStr 551..557
/sec_str_type="sheet"
/note="strand 49"
SecStr 558..565
/sec_str_type="sheet"
/note="strand 50"
SecStr 566..569
/sec_str_type="sheet"
/note="strand 51"
SecStr 572..576
/sec_str_type="sheet"
/note="strand 52"
SecStr 585..591
/sec_str_type="sheet"
/note="strand 53"
SecStr 603..606
/sec_str_type="sheet"
/note="strand 54"
SecStr 607..614
/sec_str_type="sheet"
/note="strand 55"
SecStr 618..626
/sec_str_type="helix"
/note="helix 2"
ORIGIN
1 aaslapgssr velfkrknst vpfeesngti rervvhsfri ptivnvdgvm
vaiadaryet
61 sfdnsfieta vkysvddgat wntqiaikns rassvsrvvd ptvivkgnkl
yilvgsfnkt
121 rnywtqhrdg sdwepllvvg evtksaangk ttatiswgkp vslkplfpae
fdgiltkefv
181 ggvgaaivas ngnlvypvqi admggrvftk imyseddgnt wkfaegrskf
gcsepavlew
241 egkliinnrv dynrrlvyes sdmgktwvea lgtlshvwtn sptsnqpdcq
ssfvavtieg
301 krvmlfthpl nlkgrwmrdr lhlwmtdnqr ifdvgqisig densgyssvl
ykddklyslh
361 eintndvysl vfvrligelq lmksvvrtwk eednhlasic tpvvpatpps
kgacgaavpt
421 aglvgflshs angsvwedvy rcvdanvana ervpnglkfn gvgggavwpv
arqgqtrryq
481 fanyrftlva tvtidelpkg tspllgagle gpgdakllgl sydknrqwrp
lygaapaspt
541 gswelhkkyh vvltmadrqg svyvdgqpla gsgntvvrga tlpdishfyi
ggprskgapt
601 dsrvtvtnvv lynrrlnsse irtlflsqdm igtdggagta a
//
|
|
From: Jian Lu <jl...@vb...> - 2005-08-16 19:35:10
|
Hi group, I downloaded Gene Ontology version 3.306 (component.ontology,function.ontology, process.ontology) and ran GUS::Supported::Plugin::InsertGeneOntology to load them into our GUS database. Here is my command: ga GUS::Supported::Plugin::InsertGeneOntology --filePath /home/data/ontology --functionExtDbName 'GO Function' --processExtDbName 'GO Process' --componentExtDbName 'GO Component' --commit Everything looks fine, no errors. It returned a result as "Created 19395 entries in GOTerm, 28145 entries in GORelationship, and 16375 entries in GOSynonym. Skipped 0 total entries". But when I was doing other data checking, I found there are three GO terms that have not been loaded, GO:009387, GO:0005331, GO:0009456. They do exist on the GO downloaded files. Has anyone used this plugin to load GO and checked its completeness? Please advise. Thanks. Jian |
|
From: <fab...@de...> - 2005-08-12 23:11:52
|
-----Mensagem original----- De: Steve Fischer [mailto:sfi...@pc...]=20 Enviada em: sexta-feira, 12 de agosto de 2005 16:29 Para: Fabr=EDcio Assunto: Re: Loading Cap3 results fabricio- can you post this to the gusdev list? i hope that somebody=20 from the AllGenes project will pick it up (i'll encourage them). steve Fabr=EDcio wrote: >Hi Steve, > >I saw in gus mailing list that you created a script to run CAP4 and = load >that result in GUS. I'm thinking in prepare a script to load CAP3 = results, >but as my biological concepts are not very well, I don=92t know yet = what >tables and relations can be explored in GUS Schema to achieve this data >storage.=20 > >Is it possible, for me, to see the script implemented by you? Thus, I = could >reach a better idea about how I could create it.=20 > >Best regards and thanks, > >Fabr=EDcio. > > =20 > --=20 No virus found in this incoming message. Checked by AVG Anti-Virus. Version: 7.0.338 / Virus Database: 267.10.7/70 - Release Date: 11/8/2005 |
|
From: <hen...@gm...> - 2005-08-12 19:41:20
|
Hello everyone,
My name is Henrique and I'll be helping Thiago out with our GUS
implementation around here. Well, we're trying to implement GBParser
plugin, and we achieved some level of success, managing to populate
our databases with nucleotides recently downloaded from Genbank.
However, we're having some problem with protein archives, in Genbank
format. Seems that NCBI made some minor (I couldn't find any major
changes other than its name - GenPept -, and its extension, now .gp)
changes to its format, and I've got the following error while trying
to populate GUS:
$ ga GUS::Community::Plugin::GBParser --file
/home/juca/Tryp_rangeli.gp --db_rel_id 22 --gbRel '148.0' --commit
Fri Aug 12 16:41:35 2005 ARGS algoinvo 1
Fri Aug 12 16:41:35 2005 ARGS comment
Fri Aug 12 16:41:35 2005 ARGS commit 1
Fri Aug 12 16:41:35 2005 ARGS db_rel_id 22
Fri Aug 12 16:41:35 2005 ARGS debug
Fri Aug 12 16:41:35 2005 ARGS div
Fri Aug 12 16:41:35 2005 ARGS failTolerance 100
Fri Aug 12 16:41:35 2005 ARGS file /home/juca/Tryp_rangeli.gp
Fri Aug 12 16:41:35 2005 ARGS gbRel 148.0
Fri Aug 12 16:41:35 2005 ARGS group
Fri Aug 12 16:41:35 2005 ARGS gusconfigfile =20
/usr/local/GUS/gus.properties
Fri Aug 12 16:41:35 2005 ARGS project
Fri Aug 12 16:41:35 2005 ARGS sqlVerbose
Fri Aug 12 16:41:35 2005 ARGS start
Fri Aug 12 16:41:35 2005 ARGS testnumber
Fri Aug 12 16:41:35 2005 ARGS updateAll
Fri Aug 12 16:41:35 2005 ARGS usage
Fri Aug 12 16:41:35 2005 ARGS user
Fri Aug 12 16:41:35 2005 ARGS verbose
Fri Aug 12 16:41:35 2005 ARGS veryVerbose
Fri Aug 12 16:41:35 2005 COMMIT commit on
Fri Aug 12 16:41:35 2005 ALGINVID 21
Fri Aug 12 16:41:35 2005 COMMIT commit on
Maximum number of objects set to 50000
Fri Aug 12 16:41:35 2005 RELEASE 148.0
=20
Fri Aug 12 16:41:35 2005 FILE /home/juca/Tryp_rangeli.gp
=20
VLD CBIL::Bio::GenBank::Locus 1
VLD CBIL::Bio::GenBank::Definition 1
VLD CBIL::Bio::GenBank::Accession 1
VLD CBIL::Bio::GenBank::Version 1
ERR LINE=3D5 unrequireable class Dbsource
ERROR:
Can't locate CBIL/Bio/GenBank/Dbsource.pm in @INC (@INC contains:
/usr/local/GUS/gus_home/lib/perl
/usr/local/GUS/gus_home/lib/perl/5.8.6/i386-linux-thread-multi
/usr/local/GUS/gus_home/lib/perl/5.8.6
/usr/local/GUS/gus_home/lib/perl/i386-linux-thread-multi
/usr/local/GUS/gus_home/lib/perl/5.8.5
/usr/local/GUS/gus_home/lib/perl/5.8.4
/usr/local/GUS/gus_home/lib/perl/5.8.3
/usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5
/usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3
/usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5
/usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3
/usr/lib/perl5/vendor_perl
/usr/lib/perl5/5.8.6/i386-linux-thread-multi /usr/lib/perl5/5.8.6 .)
at (eval 29) line 3, <GEN0> line 87.
=20
STACK TRACE:
at (eval 29) line 3
eval 'require CBIL::Bio::GenBank::Dbsource
;' called at /usr/local/GUS/gus_home/lib/perl/CBIL/Bio/GenBank/Entry.pm lin=
e 39
CBIL::Bio::GenBank::Entry::parse('CBIL::Bio::GenBank::Entry=3DHASH(=
0x9f9fcf4)',
'CBIL::Bio::GenBank::ArrayStream=3DHASH(0x9f9fc88)') called at
/usr/local/GUS/gus_home/lib/perl/CBIL/Bio/GenBank/BaseObject.pm line
13
CBIL::Bio::GenBank::BaseObject::new('CBIL::Bio::GenBank::Entry',
'HASH(0x9f9fcac)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
203
GUS::Community::Plugin::GBParser::processEntry('GUS::Community::Plu=
gin::GBParser=3DHASH(0x91dc570)',
'CBIL::Bio::GenBank::ArrayStream=3DHASH(0x9f9fc88)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
185
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
184
GUS::Community::Plugin::GBParser::run('GUS::Community::Plugin::GBPa=
rser=3DHASH(0x91dc570)',
'HASH(0x9f22cf8)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
469
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
461
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser', 1) called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'ARRAY(0x91a1560)') called at /usr/local/GUS/gus_home/bin/ga line 11
=20
=20
ERR LINE=3D6 unparsed line class: standard.
=20
ERR LINE=3D7 unparsed line created: Nov 1, 1997.
=20
ERR LINE=3D8 unparsed line sequence updated: Nov 1, 1997=
.
=20
ERR LINE=3D9 unparsed line annotation updated: Sep 13, 2=
005.
=20
ERR LINE=3D10 unparsed line xrefs: Z54192.1, CAA90897.1
=20
ERR LINE=3D11 unparsed line xrefs (non-sequence
databases): HSSPQ27709, InterProIPR003299,
=20
ERR LINE=3D12 unparsed line InterProIPR011992,
InterProIPR002048, PfamPF00036, PRINTSPR01362,
=20
ERR LINE=3D13 unparsed line ProDomPD000012,
SMARTSM00054, PROSITEPS00018, PROSITEPS50222
=20
VLD CBIL::Bio::GenBank::Keywords 1
VLD CBIL::Bio::GenBank::Source 1
VLD CBIL::Bio::GenBank::Reference 1
VLD CBIL::Bio::GenBank::Comment 1
RUN 1..204
RUN 1..204
RUN 1..204
RUN 39..74
RUN 52..63
RUN 75..110
RUN 120..155
RUN 133..144
RUN 157..192
RUN 170..181
VLD CBIL::Bio::GenBank::Features 1
VLD CBIL::Bio::GenBank::Origin 1
Fri Aug 12 16:41:35 2005 STATUS N=3D1 ACC=3DQ27052 TOTAL_OBJECTS=
=3D16
=20
ERROR:
Can't open failure file gbparserFailures/1.gb at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
1289, <GEN0> line 87.
=20
STACK TRACE:
at /usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line =
1289
GUS::Community::Plugin::GBParser::handleFailure('GUS::Community::Pl=
ugin::GBParser=3DHASH(0x91dc570)',
'ARRAY(0x9d3d034)', 'CBIL::Util::A=3DHASH(0x9dbbc4c)',
'\x{a}ERROR:\x{a}Can\'t call method "new" on an undefined value at
/us...') called at
/usr/local/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
187
GUS::Community::Plugin::GBParser::run('GUS::Community::Plugin::GBPa=
rser=3DHASH(0x91dc570)',
'HASH(0x9f22cf8)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
469
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
461
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser', 1) called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
380
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
288
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'GUS::Community::Plugin::GBParser') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
197
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x918dc20)',
'ARRAY(0x91a1560)') called at /usr/local/GUS/gus_home/bin/ga line 11
Could I be missing something? I'm pretty much unfamiliar with GUS and
I trying to get the hang of it ;)
Thanks in advance!
--=20
Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
"As soon as you concern yourself with the "good" and "bad" of your fellows,=
=20
you create an opening in your heart for maliciousness to enter. Testing,=20
competing with, and criticizing others weaken and defeat you."
Morihei Ueshiba, O-Sensei (1883-1969)
|
|
From: Chenhong Z. <cz...@da...> - 2005-08-12 14:51:44
|
I forgot to post my reply to Mike on the mailing list yesterday,
after the problem getting solved. I think it may be of a little help
to others later in dealing with similar problems. so here it goes:
thanks a lot Mike. The installation completes. I appreciate your
help very much.
------
so my problem ended up being solved by changing to this line
DbiDsn=dbi:Pg:dbname=myfirst for the DbiDsn setting in gus.config file.
I would also like to thank Sanjeev for responding to my message and
provided a lot of suggestions.
thanks.
chenhong
On Aug 11, 2005, at 12:13 PM, Michael Saffitz wrote:
>
> Ok:
>
> DbiDsn should be:
>
> DbiDsn=dbi:Pg:dbname=myfirst
>
> Try that and see if it works.
>
> --Mike
>
> On 8/11/05 1:12 PM, "Chenhong Zhang" <cz...@da...>
> wrote:
>
>
>> Thanks for the reply Mike. Here is the gus.config, myfirst is the
>> database name
>>
>> dbVendor=postgres
>> dbiDsn=dbi:Pg:myfirst
>> jdbcDsn=jdbc:postgresql://10.101.0.34/myfirst
>>
>> # Login and Password to the RDBMS
>>
>> databaseLogin=postgres
>> databasePassword=**
>>
>> # Username, group, and project info from the relevant Core tables
>>
>> userName=dba
>> group=dba
>> project=Database administration
>>
>> tablespace=GUS
>>
>> ####### install.prop
>>
>> # Path to Perl Executable
>> perl=/usr/bin/perl
>>
>> ####### GUS-PluginMgr.prop
>>
>> # Path to MD5 Executable
>> md5sum=/usr/bin/md5sum
>>
>> ---------------------------------------------------------------------
>> --
>>
>>
>> thanks.
>>
>> chenhong
>>
>>
>>
>>
>> On Aug 11, 2005, at 12:02 PM, Michael Saffitz wrote:
>>
>>
>>>
>>> Hello,
>>>
>>> It looks like your database connection string is improperly
>>> specified. Can
>>> you send the dbiDsn and jdbcDsn settings from your
>>> $PROJECT_HOME/install/gus.config file?
>>>
>>> Thanks,
>>>
>>> Mike
>>>
>>>
>>> On 8/11/05 11:49 AM, "Chenhong Zhang" <cz...@da...>
>>> wrote:
>>>
>>>
>>>
>>>> Hi All,
>>>>
>>>> My database connection problem from yesterday got solved. Thanks to
>>>> Mike Chaplin for the kind help (TCP connection problem). Now I
>>>> got an
>>>> error in generating Perl Objects. The end of this email is the
>>>> output of build.
>>>>
>>>> I browsed through the mailing list for this kind of problem and
>>>> found
>>>> Kumar Sanjeev had similar problem before. Sanjeev, if you happen to
>>>> see this posting, could you lend me some help to solve this
>>>> problem?
>>>> Thanks.
>>>>
>>>>
>>>> here are more config info that might help:
>>>>
>>>> postgres@lnx-bb4:~> which generateGusObjects
>>>> /home/postgres/GUS/gus_home/bin/generateGusObjects
>>>> postgres@lnx-bb4:~> echo $PROJECT_HOME
>>>> /home/postgres/GUS/project_home
>>>> postgres@lnx-bb4:~> echo $GUS_HOME
>>>> /home/postgres/GUS/gus_home
>>>> postgres@lnx-bb4:~> echo $PATH
>>>> /home/postgres/GUS/gus_home/bin:/home/postgres/GUS/project_home/
>>>> install/bin:/home/postgres/bin:/usr/local/bin:/usr/bin:/usr/X11R6/
>>>> bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/sbin:/usr/local/
>>>> pgsql/bin/:/usr/local/ant/bin:.
>>>>
>>>> can someone give me some help on this.
>>>>
>>>> regards,
>>>>
>>>> chenhong zhang
>>>>
>>>> -----output from "build GUS install -append -installDBSchema----
>>>> [echo] Installing GUS/ObjRelP
>>>> [copy] Copying 3 files to /home/postgres/GUS/gus_home/bin
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> ObjRelP
>>>> [copy] Copying 18 files to /home/postgres/GUS/gus_home/lib/
>>>> perl/
>>>> GUS/ObjRelP
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/doc/GUS/
>>>> ObjRelP
>>>> [copy] Copying 3 files to /home/postgres/GUS/gus_home/doc/
>>>> GUS/
>>>> ObjRelP
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/Core
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/DoTS
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/RAD
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/SRes
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/TESS
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/PROT
>>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>>> Model/Study
>>>> [echo] generating Perl Objects
>>>> [exec] GUS::ObjRelP::DbiDbHandle connect
>>>> ('test','postgres',...)
>>>> failed: missing "=" after "test" in connection info string
>>>> [exec] at /home/postgres/GUS/gus_home/lib/perl/GUS/ObjRelP/
>>>> DbiDatabase.pm line 165
>>>> [exec] Can't bless non-reference value at /home/postgres/GUS/
>>>> gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
>>>>
>>>> BUILD FAILED
>>>> /home/postgres/GUS/project_home/install/build.xml:28: The following
>>>> error occurred while executing this line:
>>>> /home/postgres/GUS/project_home/GUS/build.xml:225: exec
>>>> returned: -1
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>>>> Practices
>>>> Agile & Plan-Driven Development * Managing Projects & Teams *
>>>> Testing & QA
>>>> Security * Process Improvement & Measurement * http://www.sqe.com/
>>>> bsce5sf
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>
>>>
>>>
>>>
>
>
>
|
|
From: Michael S. <msa...@pc...> - 2005-08-11 18:48:31
|
As part of the GUS Workshop, we identified the need to update the GUS Schema Browser to allow for the submission of documentation over the web as well as other improvements. A preview release of a new version of the GUS Schema Browser is now available. This release is intended as a stop-gap measure to address immediate needs and update the Schema Browser infrastructure; The Kissinger lab at UGA is working on a future version which will provide additional functionality and views. You may preview the Schema Browser at: http://www.gusdb.org/SchemaBrowser/ Bugs and Feature Requests should be filed at: https://www.cbil.upenn.edu/tracker/enter_bug.cgi?product=SchemaBrowser As this is a preview release, there is still some functionality that has not yet been implemented. Please let me know if you have any questions/comments. Thanks, Mike |
|
From: Michael S. <msa...@pc...> - 2005-08-11 17:14:07
|
Ok:
DbiDsn should be:
DbiDsn=dbi:Pg:dbname=myfirst
Try that and see if it works.
--Mike
On 8/11/05 1:12 PM, "Chenhong Zhang" <cz...@da...> wrote:
> Thanks for the reply Mike. Here is the gus.config, myfirst is the
> database name
>
> dbVendor=postgres
> dbiDsn=dbi:Pg:myfirst
> jdbcDsn=jdbc:postgresql://10.101.0.34/myfirst
>
> # Login and Password to the RDBMS
>
> databaseLogin=postgres
> databasePassword=**
>
> # Username, group, and project info from the relevant Core tables
>
> userName=dba
> group=dba
> project=Database administration
>
> tablespace=GUS
>
> ####### install.prop
>
> # Path to Perl Executable
> perl=/usr/bin/perl
>
> ####### GUS-PluginMgr.prop
>
> # Path to MD5 Executable
> md5sum=/usr/bin/md5sum
>
> -----------------------------------------------------------------------
>
>
> thanks.
>
> chenhong
>
>
>
>
> On Aug 11, 2005, at 12:02 PM, Michael Saffitz wrote:
>
>>
>> Hello,
>>
>> It looks like your database connection string is improperly
>> specified. Can
>> you send the dbiDsn and jdbcDsn settings from your
>> $PROJECT_HOME/install/gus.config file?
>>
>> Thanks,
>>
>> Mike
>>
>>
>> On 8/11/05 11:49 AM, "Chenhong Zhang" <cz...@da...>
>> wrote:
>>
>>
>>> Hi All,
>>>
>>> My database connection problem from yesterday got solved. Thanks to
>>> Mike Chaplin for the kind help (TCP connection problem). Now I got an
>>> error in generating Perl Objects. The end of this email is the
>>> output of build.
>>>
>>> I browsed through the mailing list for this kind of problem and found
>>> Kumar Sanjeev had similar problem before. Sanjeev, if you happen to
>>> see this posting, could you lend me some help to solve this problem?
>>> Thanks.
>>>
>>>
>>> here are more config info that might help:
>>>
>>> postgres@lnx-bb4:~> which generateGusObjects
>>> /home/postgres/GUS/gus_home/bin/generateGusObjects
>>> postgres@lnx-bb4:~> echo $PROJECT_HOME
>>> /home/postgres/GUS/project_home
>>> postgres@lnx-bb4:~> echo $GUS_HOME
>>> /home/postgres/GUS/gus_home
>>> postgres@lnx-bb4:~> echo $PATH
>>> /home/postgres/GUS/gus_home/bin:/home/postgres/GUS/project_home/
>>> install/bin:/home/postgres/bin:/usr/local/bin:/usr/bin:/usr/X11R6/
>>> bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/sbin:/usr/local/
>>> pgsql/bin/:/usr/local/ant/bin:.
>>>
>>> can someone give me some help on this.
>>>
>>> regards,
>>>
>>> chenhong zhang
>>>
>>> -----output from "build GUS install -append -installDBSchema----
>>> [echo] Installing GUS/ObjRelP
>>> [copy] Copying 3 files to /home/postgres/GUS/gus_home/bin
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> ObjRelP
>>> [copy] Copying 18 files to /home/postgres/GUS/gus_home/lib/
>>> perl/
>>> GUS/ObjRelP
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/doc/GUS/ObjRelP
>>> [copy] Copying 3 files to /home/postgres/GUS/gus_home/doc/GUS/
>>> ObjRelP
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/Core
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/DoTS
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/RAD
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/SRes
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/TESS
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/PROT
>>> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
>>> Model/Study
>>> [echo] generating Perl Objects
>>> [exec] GUS::ObjRelP::DbiDbHandle connect('test','postgres',...)
>>> failed: missing "=" after "test" in connection info string
>>> [exec] at /home/postgres/GUS/gus_home/lib/perl/GUS/ObjRelP/
>>> DbiDatabase.pm line 165
>>> [exec] Can't bless non-reference value at /home/postgres/GUS/
>>> gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
>>>
>>> BUILD FAILED
>>> /home/postgres/GUS/project_home/install/build.xml:28: The following
>>> error occurred while executing this line:
>>> /home/postgres/GUS/project_home/GUS/build.xml:225: exec returned: -1
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>>> Practices
>>> Agile & Plan-Driven Development * Managing Projects & Teams *
>>> Testing & QA
>>> Security * Process Improvement & Measurement * http://www.sqe.com/
>>> bsce5sf
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>>
>>
|
|
From: Michael S. <msa...@pc...> - 2005-08-11 17:03:08
|
Hello,
It looks like your database connection string is improperly specified. Can
you send the dbiDsn and jdbcDsn settings from your
$PROJECT_HOME/install/gus.config file?
Thanks,
Mike
On 8/11/05 11:49 AM, "Chenhong Zhang" <cz...@da...> wrote:
> Hi All,
>
> My database connection problem from yesterday got solved. Thanks to
> Mike Chaplin for the kind help (TCP connection problem). Now I got an
> error in generating Perl Objects. The end of this email is the
> output of build.
>
> I browsed through the mailing list for this kind of problem and found
> Kumar Sanjeev had similar problem before. Sanjeev, if you happen to
> see this posting, could you lend me some help to solve this problem?
> Thanks.
>
>
> here are more config info that might help:
>
> postgres@lnx-bb4:~> which generateGusObjects
> /home/postgres/GUS/gus_home/bin/generateGusObjects
> postgres@lnx-bb4:~> echo $PROJECT_HOME
> /home/postgres/GUS/project_home
> postgres@lnx-bb4:~> echo $GUS_HOME
> /home/postgres/GUS/gus_home
> postgres@lnx-bb4:~> echo $PATH
> /home/postgres/GUS/gus_home/bin:/home/postgres/GUS/project_home/
> install/bin:/home/postgres/bin:/usr/local/bin:/usr/bin:/usr/X11R6/
> bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/sbin:/usr/local/
> pgsql/bin/:/usr/local/ant/bin:.
>
> can someone give me some help on this.
>
> regards,
>
> chenhong zhang
>
> -----output from "build GUS install -append -installDBSchema----
> [echo] Installing GUS/ObjRelP
> [copy] Copying 3 files to /home/postgres/GUS/gus_home/bin
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> ObjRelP
> [copy] Copying 18 files to /home/postgres/GUS/gus_home/lib/perl/
> GUS/ObjRelP
> [mkdir] Created dir: /home/postgres/GUS/gus_home/doc/GUS/ObjRelP
> [copy] Copying 3 files to /home/postgres/GUS/gus_home/doc/GUS/
> ObjRelP
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/Core
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/DoTS
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/RAD
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/SRes
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/TESS
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/PROT
> [mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
> Model/Study
> [echo] generating Perl Objects
> [exec] GUS::ObjRelP::DbiDbHandle connect('test','postgres',...)
> failed: missing "=" after "test" in connection info string
> [exec] at /home/postgres/GUS/gus_home/lib/perl/GUS/ObjRelP/
> DbiDatabase.pm line 165
> [exec] Can't bless non-reference value at /home/postgres/GUS/
> gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
>
> BUILD FAILED
> /home/postgres/GUS/project_home/install/build.xml:28: The following
> error occurred while executing this line:
> /home/postgres/GUS/project_home/GUS/build.xml:225: exec returned: -1
>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Michael S. <msa...@pc...> - 2005-08-11 17:02:05
|
Hi Josef, You may sign up for an account at: https://www.cbil.upenn.edu/webuser/ You'll probably right-- this isn't documented anywhere. You can file a documentation bug for that if you'd like. --Mike On 8/11/05 12:55 PM, "Josef Jurek" <ju...@cs...> wrote: > > Steve Fischer <sfi...@pc...> writes: >> >> we have given you permission to write to the GUS svn repostitory. your >> username and password are the same as those for the wiki. > > How does one obtain an account to add to the wiki? I searched > the pages but nothing leapt out at me. > > Thanks. > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Josef J. <ju...@cs...> - 2005-08-11 16:55:39
|
Steve Fischer <sfi...@pc...> writes: > > we have given you permission to write to the GUS svn repostitory. your > username and password are the same as those for the wiki. How does one obtain an account to add to the wiki? I searched the pages but nothing leapt out at me. Thanks. |
|
From: Chenhong Z. <cz...@da...> - 2005-08-11 15:49:30
|
Hi All,
My database connection problem from yesterday got solved. Thanks to
Mike Chaplin for the kind help (TCP connection problem). Now I got an
error in generating Perl Objects. The end of this email is the
output of build.
I browsed through the mailing list for this kind of problem and found
Kumar Sanjeev had similar problem before. Sanjeev, if you happen to
see this posting, could you lend me some help to solve this problem?
Thanks.
here are more config info that might help:
postgres@lnx-bb4:~> which generateGusObjects
/home/postgres/GUS/gus_home/bin/generateGusObjects
postgres@lnx-bb4:~> echo $PROJECT_HOME
/home/postgres/GUS/project_home
postgres@lnx-bb4:~> echo $GUS_HOME
/home/postgres/GUS/gus_home
postgres@lnx-bb4:~> echo $PATH
/home/postgres/GUS/gus_home/bin:/home/postgres/GUS/project_home/
install/bin:/home/postgres/bin:/usr/local/bin:/usr/bin:/usr/X11R6/
bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/sbin:/usr/local/
pgsql/bin/:/usr/local/ant/bin:.
can someone give me some help on this.
regards,
chenhong zhang
-----output from "build GUS install -append -installDBSchema----
[echo] Installing GUS/ObjRelP
[copy] Copying 3 files to /home/postgres/GUS/gus_home/bin
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
ObjRelP
[copy] Copying 18 files to /home/postgres/GUS/gus_home/lib/perl/
GUS/ObjRelP
[mkdir] Created dir: /home/postgres/GUS/gus_home/doc/GUS/ObjRelP
[copy] Copying 3 files to /home/postgres/GUS/gus_home/doc/GUS/
ObjRelP
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/Core
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/DoTS
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/RAD
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/SRes
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/TESS
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/PROT
[mkdir] Created dir: /home/postgres/GUS/gus_home/lib/perl/GUS/
Model/Study
[echo] generating Perl Objects
[exec] GUS::ObjRelP::DbiDbHandle connect('test','postgres',...)
failed: missing "=" after "test" in connection info string
[exec] at /home/postgres/GUS/gus_home/lib/perl/GUS/ObjRelP/
DbiDatabase.pm line 165
[exec] Can't bless non-reference value at /home/postgres/GUS/
gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
BUILD FAILED
/home/postgres/GUS/project_home/install/build.xml:28: The following
error occurred while executing this line:
/home/postgres/GUS/project_home/GUS/build.xml:225: exec returned: -1
|
|
From: Steve F. <sfi...@pc...> - 2005-08-10 20:55:32
|
sanjeev- we have given you permission to write to the GUS svn repostitory. your username and password are the same as those for the wiki. follow the instructions in the error message (except use svn instead of cvs. the arguments are the same) please write if you have any trouble with this. steve Kumar, Sanjeev (Contr) wrote: >Hi, > I am having issue in running newly registered plugin. > I have one new plug in which I registered and I tested it , it ran fine. > AFter that I fixed some bug and then tried to run it gave me error saying that plugin has change I need to update it. But when I am trying to update the plug in it is not letting me do so. Errors are listed below : >*************************************** >[oragus35@rdevse02 oragus35]$ ga GUS::Supported::Plugin::LoadPrositeDB >--file /home/oragus35/prosite.dat --commit > >USER ERROR: The md5 checksum of GUS::Supported::Plugin::LoadPrositeDB's >executable file (cvs revision 2943) doesn't match the md5 checksum in >the database for that plugin and revision. IE, the plugin has been >changed but not commited and updated. Please: > - cvs commit the plugin file > - use the build system to install it > - run 'ga +update >GUS::Supported::Plugin::LoadPrositeDB --commit' >Aborting >Issuing rollback() for database handle being DESTROY'd without explicit >disconnect(). >Issuing rollback() for database handle being DESTROY'd without explicit >disconnect(). >[oragus35@rdevse02 oragus35]$ ga +update >GUS::Supported::Plugin::LoadPrositeDB --commit; >Error: GUS::Supported::Plugin::LoadPrositeDB with CVS revision 2943 is >already registered. You don't need to do a +update. > >****************************************************************** >Pl. suggest me what needs to be done. > >Thanks >Sanjeev > > >------------------------------------------------------- >SF.Net email is Sponsored by the Better Software Conference & EXPO >September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices >Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA >Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Chenhong Z. <cz...@da...> - 2005-08-10 20:03:07
|
hi all,
I am installing GUS 3.5 for postgresql database. I got a problem that
says can't connect to the database (output below) . My database
server is running for sure. I think the problem might be in my
configuration file. here is part of the gus.config content:
dbVendor=postgresql
dbiDsn=dbi:Pg:dbname=test
jdbcDsn=jdbc:postgresql://10.101.0.34/test
and here is part of the gus.properties:
userName=dba
group=dba
project=Database administration
dbiDsn=dbi:Pg:dbname=test
could someone give me a help? Thanks very much in advance.
chenhong zhang
-----output from build---------------
postgres@lnx-bb4:~/GUS/project_home/install/bin> sudo build GUS
install -append -installDBSchema
[WritePropertyFiles] log4j:WARN No appenders could be found for
logger (org.gusdb.install.WritePropertyFileTask).
[WritePropertyFiles] log4j:WARN Please initialize the log4j system
properly.
[copy] Copying 1 file to /home/postgres/GUS/gus_home/config
[copy] Copying 1 file to /home/postgres/GUS/gus_home/config
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing CBIL/HQ
[echo] .
[echo] Installing CBIL/ObjectMapper
[concat] No existing files and no nested text, doing nothing
[echo] .
[echo] Installing GUS/Supported
[echo] .
[echo] Installing GUS/Community
[echo] .
[echo] Installing GUS/DBAdmin
[echo] .
[echo] Installing GUS/GOPredict
[echo] .
[echo] Installing GUS/Schema
BUILD FAILED
/home/postgres/GUS/project_home/install/build.xml:28: The following
error occurred while executing this line:
/home/postgres/GUS/project_home/GUS/build.xml:92: Unable to connect
to database
|
|
From: Y. T. G. <yon...@pc...> - 2005-08-10 13:25:29
|
Yeah, I remember working with you trying to switch to it but was not able= =20 to get it to work. I can give it another shot soon. -Thomas On Wed, 10 Aug 2005, Michael Saffitz wrote: > > Thomas, > > This is very similar to an issue we had with the Oracle OCI drivers, whic= h > are much more robust that the thin driver in use around the lab. With ou= r > new servers, I'd like websites to begin to use the OCI drivers, so it may= be > worth our while to test with those as well. > > --Mike > > > > On 8/10/05 8:56 AM, "Y. Thomas Gan" <yon...@pc...> wrote: > >> maybe we need to explicitly register pg drivers. i'll try it. we should >> not have to add the driver jar to tomcat'S CLASSPATH. >> >> -thomas >> >> On Wed, 10 Aug 2005, Steve Fischer wrote: >> >>> is it possibly caused by my having commented out this line in >>> PostegeSQL.java: >>> >>> // DriverManager.registerDriver(new org.postgresql.Driver= ()); >>> >>> it didn't seem to make any difference when running outside of tomcat (s= o >>> i took it out). >>> >>> steve >>> >>> Thiago Satake wrote: >>> >>>> We updated WDK release with postgres and WDKToySite Works well. >>>> >>>> >>>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>> >>>>> >>>> It seems to me that is a tomcat problem,I belive that you must set >>>> $CLASSPATH adding jdbc driver for postgres into >>>> $CATALINA_HOME/bin/setclass.sh..... >>>> as showed bellow: >>>> >>>> >>>>> # Set standard CLASSPATH >>>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc= 3.jar >>>>> >>>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Thiago Seito Stake >>>> >>>> >>>> >>>> >>>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>> >>>> >>>>> Another update on the status of release 1.6: >>>>> >>>>> With tremendous efforts from Steve we were able to get wdkSanityTest >>>>> (including tests for all Questions/Summaries, Queries, and Records) >>>>> passing against both oracle and postgres late last night. >>>>> >>>>> But we are at the last of the last hurdles: the toySite works fine >>>>> with Oracle but does not come up with postgres (as Thiago reported >>>>> earlier). See bug 114: toySite throws 'No suitable driver' SQLExcepti= on at >>>>> start up against postgres (oracle is ok) although sanityTest succeed= s >>>>> (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). >>>>> The ArrayIndexOutOfBounds exception is a result of this. >>>>> >>>>> I am debugging this and will release after it is fixed. >>>>> >>>>> -Thomas >>>>> >>>>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>>>> >>>>> >>>>> >>>>>> just want to give an update on our progress. >>>>>> >>>>>> we are planning a release today or tomorrow. >>>>>> >>>>>> as well as postgres support (tested) it will include a number of oth= er >>>>>> features, including an improved Sanity Test. the test will now test= all >>>>>> Questions in the model XML file as well as all Queries and all Recor= ds. >>>>>> this was needed to thoroughly test postgres. >>>>>> >>>>>> we're working hard to get this release out... >>>>>> >>>>>> steve >>>>>> >>>>>> fab...@de... wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Thiago, >>>>>>> >>>>>>> >>>> >>>> >>>> >>>> >>>>>>> I'm having this problem too. In wdkSummary it seems that the schema= name >>>>>>> is >>>>>>> missing before table names in FROM clause. >>>>>>> >>>>>>> I don't know if this is a Wdk problem or WdkToySite SQL error. >>>>>>> >>>>>>> Can you help us Steve? >>>>>>> >>>>>>> Thanks a lot, >>>>>>> >>>>>>> Fabr=EDcio. >>>>>>> >>>>>>> >>>>>>> Citando Thiago Satake <ma...@gm...>: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> After downloaded WDK from SVN files I run: >>>>>>>> wdkSanityTest -model toyModel >>>>>>>> >>>>>>>> and got this >>>>>>>> >>>>>>>> ***Sanity test summary*** >>>>>>>> 10 queries passed, 4 queries failed >>>>>>>> 1 records passed, 1 records failed >>>>>>>> Sanity Test FAILED >>>>>>>> >>>>>>>> >>>>>>>> and I run: >>>>>>>> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows = 1 20 >>>>>>>> -params NumSeqs 10 ApiTaxon "Neospora caninum" >>>>>>>> >>>>>>>> I got: >>>>>>>> org.gusdb.wdk.model.WdkModelException: >>>>>>>> Failed running query: >>>>>>>> "SELECT * FROM ( select usertest.query_result_4.result_index_colum= n, >>>>>>>> a.assembly_consistency, a.contains_mrna, >>>>>>>> a.number_of_contained_sequences, a.sequence >>>>>>>> from WDKTestAssembly a, WDKTestTaxonName tn , >>>>>>>> usertest.query_result_4 where a.na_sequence_id =3D >>>>>>>> usertest.query_result_4.na_sequence_id and a.taxon= _id >>>>>>>> =3D tn.taxon_id and usertest.query_result_4.result_index_column >= =3D 1 and >>>>>>>> usertest.query_result_4.result_index_column <=3D 20 order by >>>>>>>> usertest.query_result_4.result_index_column ) ORDER BY >>>>>>>> result_index_column" >>>>>>>> >>>>>>>> >>>>>>>> :-( >>>>>>>> >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> Thiago Seito Satake >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 2005/8/5, Steve Fischer <sfi...@pc...>: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Folks- >>>>>>>>> >>>>>>>>> I have made a lot of progress. >>>>>>>>> >>>>>>>>> It is clear that the wdk postgres implementation was never tested= =2E I >>>>>>>>> have fixed many, many things. >>>>>>>>> >>>>>>>>> Here is where I am at so far. i ran: >>>>>>>>> % wdkSanityTest -model toyModel >>>>>>>>> >>>>>>>>> and got this: >>>>>>>>> >>>>>>>>> ***Sanity test summary*** >>>>>>>>> 11 queries passed, 1 queries failed >>>>>>>>> 0 records passed, 2 records failed >>>>>>>>> Sanity Test FAILED >>>>>>>>> >>>>>>>>> tomorrow morning i'll look into the remaining problems >>>>>>>>> >>>>>>>>> steve >>>>>>>>> >>>>>>>>> Thiago Satake wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Thanks a lot, >>>>>>>>>> >>>>>>>>>> Can I help you with something ? >>>>>>>>>> >>>>>>>>>> Thiago Seito Satake >>>>>>>>>> >>>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are prov= ided >>>>>>>>>>> by >>>>>>>>>>> the student's fixes. i am starting now to look at them and mer= ge. >>>>>>>>>>> >>>>>>>>>>> i have a lot of meetings today, so in a little while i'll need = to >>>>>>>>>>> stop >>>>>>>>>>> till tonight >>>>>>>>>>> >>>>>>>>>>> steve >>>>>>>>>>> >>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Ok ........ >>>>>>>>>>>> >>>>>>>>>>>> We can list some problems: >>>>>>>>>>>> 1- we had to change all of perl wdk file ... to set te correct >>>>>>>>>>>> driver >>>>>>>>>>>> to postgres. >>>>>>>>>>>> 2- we had to change testTables files to change the numeric da= ta >>>>>>>>>>>> type >>>>>>>>>>>> ( number > numeric ) >>>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( >>>>>>>>>>>> sequence >>>>>>>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) >>>>>>>>>>>> >>>>>>>>>>>> now we are having problem to use WDKToySite as the log shows: >>>>>>>>>>>> >>>>>>>>>>>> DEBUG: making a QuestionSetForm >>>>>>>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProces= sor >>>>>>>>>>>> processException >>>>>>>>>>>> WARNING: Unhandled Exception thrown: class >>>>>>>>>>>> java.lang.ArrayIndexOutOfBoundsException >>>>>>>>>>>> >>>>>>>>>>>> and other problems ............. >>>>>>>>>>>> >>>>>>>>>>>> Thanks for the help :-) >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> Folks- >>>>>>>>>>>>> >>>>>>>>>>>>> the production uses of wdk so far are in oracle, so we have n= ot put >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> much >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> effort into ensuring the complete functioning of the postgres >>>>>>>>>>>>> module. >>>>>>>>>>>>> >>>>>>>>>>>>> however, a student did successfully use postgres with the wdk= =2E he >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> made >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change = in >>>>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>>>> >>>>>>>>>>>>> I will incorporate those changes today and test it. I hope = to get >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> you >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>>>> >>>>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>>>> >>>>>>>>>>>>> steve >>>>>>>>>>>>> >>>>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> I am having the same problem......... >>>>>>>>>>>>> >>>>>>>>>>>>> Does Someone have the wdk working with postgres database ? >>>>>>>>>>>>> >>>>>>>>>>>>> I would appreciate if someone could help me too !!!!!!!!!!!!!= !!!!!! >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> :-) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> Thanks ............. >>>>>>>>>>>>> >>>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Hello all, >>>>>>>>>>>>> >>>>>>>>>>>>> We have a GUS installation running ok and now we're trying to= use >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> 1.5 to >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> manipulating an >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> Oracle database, due to some type columns, sequence using, et= c... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> that >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>>> wdkQuery, >>>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>> >>>>>>>>>>>>> Because of this, we're having a hard work to debug the code a= nd set >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> it to work >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> with the Postgres schema. We would like to know if someone ha= s a >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> working >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>> >>>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>> >>>>>>>>>>>>> -------------------------------------------------------------= --- >>>>>>>>>>>>> This message was sent using IMP, the Internet Messaging Progr= am. >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> WDKDev mailing list >>>>>>>>>>>>> WD...@pc... >>>>>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> -- >>>>>>>> Thiago Seito Satake >>>>>>>> !! Tenha um bom dia !! >>>>>>>> Tel: (041) 990-55422 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> WDKDev mailing list >>>>>>>> WD...@pc... >>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------- >>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>> >>>>>>> >>>>>>> >>>>>> ------------------------------------------------------- >>>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>>>>> Practices >>>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testin= g & QA >>>>>> Security * Process Improvement & Measurement * http://www.sqe.com/bs= ce5sf >>>>>> _______________________________________________ >>>>>> Gusdev-gusdev mailing list >>>>>> Gus...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> -- >>>> Thiago Seito Satake >>>> !! Tenha um bom dia !! >>>> Tel: (041) 990-55422 >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> WDKDev mailing list >>> WD...@pc... >>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>> > > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Michael S. <msa...@pc...> - 2005-08-10 13:19:58
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Thomas, This is very similar to an issue we had with the Oracle OCI drivers, which are much more robust that the thin driver in use around the lab. With our new servers, I'd like websites to begin to use the OCI drivers, so it may b= e worth our while to test with those as well. --Mike On 8/10/05 8:56 AM, "Y. Thomas Gan" <yon...@pc...> wrote: > maybe we need to explicitly register pg drivers. i'll try it. we should > not have to add the driver jar to tomcat'S CLASSPATH. >=20 > -thomas >=20 > On Wed, 10 Aug 2005, Steve Fischer wrote: >=20 >> is it possibly caused by my having commented out this line in >> PostegeSQL.java: >>=20 >> // DriverManager.registerDriver(new org.postgresql.Driver(= )); >>=20 >> it didn't seem to make any difference when running outside of tomcat (so >> i took it out). >>=20 >> steve >>=20 >> Thiago Satake wrote: >>=20 >>> We updated WDK release with postgres and WDKToySite Works well. >>>=20 >>>=20 >>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>=20 >>>>=20 >>> It seems to me that is a tomcat problem,I belive that you must set >>> $CLASSPATH adding jdbc driver for postgres into >>> $CATALINA_HOME/bin/setclass.sh..... >>> as showed bellow: >>>=20 >>>=20 >>>> # Set standard CLASSPATH >>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.j= ar >>>>=20 >>>>=20 >>>=20 >>>=20 >>> Thanks >>>=20 >>>=20 >>>=20 >>> Thiago Seito Stake >>>=20 >>>=20 >>>=20 >>>=20 >>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>=20 >>>=20 >>>> Another update on the status of release 1.6: >>>>=20 >>>> With tremendous efforts from Steve we were able to get wdkSanityTest >>>> (including tests for all Questions/Summaries, Queries, and Records) >>>> passing against both oracle and postgres late last night. >>>>=20 >>>> But we are at the last of the last hurdles: the toySite works fine >>>> with Oracle but does not come up with postgres (as Thiago reported >>>> earlier). See bug 114: toySite throws 'No suitable driver' SQLExceptio= n at >>>> start up against postgres (oracle is ok) although sanityTest succeeds >>>> (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). >>>> The ArrayIndexOutOfBounds exception is a result of this. >>>>=20 >>>> I am debugging this and will release after it is fixed. >>>>=20 >>>> -Thomas >>>>=20 >>>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>>>=20 >>>>=20 >>>>=20 >>>>> just want to give an update on our progress. >>>>>=20 >>>>> we are planning a release today or tomorrow. >>>>>=20 >>>>> as well as postgres support (tested) it will include a number of othe= r >>>>> features, including an improved Sanity Test. the test will now test = all >>>>> Questions in the model XML file as well as all Queries and all Record= s. >>>>> this was needed to thoroughly test postgres. >>>>>=20 >>>>> we're working hard to get this release out... >>>>>=20 >>>>> steve >>>>>=20 >>>>> fab...@de... wrote: >>>>>=20 >>>>>=20 >>>>>=20 >>>>>> Thiago, >>>>>>=20 >>>>>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>>>> I'm having this problem too. In wdkSummary it seems that the schema = name >>>>>> is >>>>>> missing before table names in FROM clause. >>>>>>=20 >>>>>> I don't know if this is a Wdk problem or WdkToySite SQL error. >>>>>>=20 >>>>>> Can you help us Steve? >>>>>>=20 >>>>>> Thanks a lot, >>>>>>=20 >>>>>> Fabr=EDcio. >>>>>>=20 >>>>>>=20 >>>>>> Citando Thiago Satake <ma...@gm...>: >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>> After downloaded WDK from SVN files I run: >>>>>>> wdkSanityTest -model toyModel >>>>>>>=20 >>>>>>> and got this >>>>>>>=20 >>>>>>> ***Sanity test summary*** >>>>>>> 10 queries passed, 4 queries failed >>>>>>> 1 records passed, 1 records failed >>>>>>> Sanity Test FAILED >>>>>>>=20 >>>>>>>=20 >>>>>>> and I run: >>>>>>> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1= 20 >>>>>>> -params NumSeqs 10 ApiTaxon "Neospora caninum" >>>>>>>=20 >>>>>>> I got: >>>>>>> org.gusdb.wdk.model.WdkModelException: >>>>>>> Failed running query: >>>>>>> "SELECT * FROM ( select usertest.query_result_4.result_index_column= , >>>>>>> a.assembly_consistency, a.contains_mrna, >>>>>>> a.number_of_contained_sequences, a.sequence >>>>>>> from WDKTestAssembly a, WDKTestTaxonName tn , >>>>>>> usertest.query_result_4 where a.na_sequence_id =3D >>>>>>> usertest.query_result_4.na_sequence_id and a.taxon_= id >>>>>>> =3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D 1 = and >>>>>>> usertest.query_result_4.result_index_column <=3D 20 order by >>>>>>> usertest.query_result_4.result_index_column ) ORDER BY >>>>>>> result_index_column" >>>>>>>=20 >>>>>>>=20 >>>>>>> :-( >>>>>>>=20 >>>>>>>=20 >>>>>>> Thanks >>>>>>>=20 >>>>>>> Thiago Seito Satake >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>> 2005/8/5, Steve Fischer <sfi...@pc...>: >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>> Folks- >>>>>>>>=20 >>>>>>>> I have made a lot of progress. >>>>>>>>=20 >>>>>>>> It is clear that the wdk postgres implementation was never tested.= I >>>>>>>> have fixed many, many things. >>>>>>>>=20 >>>>>>>> Here is where I am at so far. i ran: >>>>>>>> % wdkSanityTest -model toyModel >>>>>>>>=20 >>>>>>>> and got this: >>>>>>>>=20 >>>>>>>> ***Sanity test summary*** >>>>>>>> 11 queries passed, 1 queries failed >>>>>>>> 0 records passed, 2 records failed >>>>>>>> Sanity Test FAILED >>>>>>>>=20 >>>>>>>> tomorrow morning i'll look into the remaining problems >>>>>>>>=20 >>>>>>>> steve >>>>>>>>=20 >>>>>>>> Thiago Satake wrote: >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>> Thanks a lot, >>>>>>>>>=20 >>>>>>>>> Can I help you with something ? >>>>>>>>>=20 >>>>>>>>> Thiago Seito Satake >>>>>>>>>=20 >>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provi= ded >>>>>>>>>> by >>>>>>>>>> the student's fixes. i am starting now to look at them and merg= e. >>>>>>>>>>=20 >>>>>>>>>> i have a lot of meetings today, so in a little while i'll need t= o >>>>>>>>>> stop >>>>>>>>>> till tonight >>>>>>>>>>=20 >>>>>>>>>> steve >>>>>>>>>>=20 >>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>> Ok ........ >>>>>>>>>>>=20 >>>>>>>>>>> We can list some problems: >>>>>>>>>>> 1- we had to change all of perl wdk file ... to set te correct >>>>>>>>>>> driver >>>>>>>>>>> to postgres. >>>>>>>>>>> 2- we had to change testTables files to change the numeric dat= a >>>>>>>>>>> type >>>>>>>>>>> ( number > numeric ) >>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( >>>>>>>>>>> sequence >>>>>>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) >>>>>>>>>>>=20 >>>>>>>>>>> now we are having problem to use WDKToySite as the log shows: >>>>>>>>>>>=20 >>>>>>>>>>> DEBUG: making a QuestionSetForm >>>>>>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcess= or >>>>>>>>>>> processException >>>>>>>>>>> WARNING: Unhandled Exception thrown: class >>>>>>>>>>> java.lang.ArrayIndexOutOfBoundsException >>>>>>>>>>>=20 >>>>>>>>>>> and other problems ............. >>>>>>>>>>>=20 >>>>>>>>>>> Thanks for the help :-) >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>> Folks- >>>>>>>>>>>>=20 >>>>>>>>>>>> the production uses of wdk so far are in oracle, so we have no= t put >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> much >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> effort into ensuring the complete functioning of the postgres >>>>>>>>>>>> module. >>>>>>>>>>>>=20 >>>>>>>>>>>> however, a student did successfully use postgres with the wdk.= he >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> made >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change i= n >>>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>>>=20 >>>>>>>>>>>> I will incorporate those changes today and test it. I hope t= o get >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> you >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>>>=20 >>>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>>>=20 >>>>>>>>>>>> steve >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> I am having the same problem......... >>>>>>>>>>>>=20 >>>>>>>>>>>> Does Someone have the wdk working with postgres database ? >>>>>>>>>>>>=20 >>>>>>>>>>>> I would appreciate if someone could help me too !!!!!!!!!!!!!!= !!!!! >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> :-) >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> Thanks ............. >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> Hello all, >>>>>>>>>>>>=20 >>>>>>>>>>>> We have a GUS installation running ok and now we're trying to = use >>>>>>>>>>>> WDK >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> 1.5 to >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> manipulating an >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> Oracle database, due to some type columns, sequence using, etc= ... >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> that >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>> wdkQuery, >>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>=20 >>>>>>>>>>>> Because of this, we're having a hard work to debug the code an= d set >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> it to work >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> with the Postgres schema. We would like to know if someone has= a >>>>>>>>>>>> WDK >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> working >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>=20 >>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>=20 >>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>=20 >>>>>>>>>>>> --------------------------------------------------------------= -- >>>>>>>>>>>> This message was sent using IMP, the Internet Messaging Progra= m. >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> WDKDev mailing list >>>>>>>>>>>> WD...@pc... >>>>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>> -- >>>>>>> Thiago Seito Satake >>>>>>> !! Tenha um bom dia !! >>>>>>> Tel: (041) 990-55422 >>>>>>>=20 >>>>>>> _______________________________________________ >>>>>>> WDKDev mailing list >>>>>>> WD...@pc... >>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>> ---------------------------------------------------------------- >>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>> ------------------------------------------------------- >>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>>>> Practices >>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing= & QA >>>>> Security * Process Improvement & Measurement * http://www.sqe.com/bsc= e5sf >>>>> _______________________________________________ >>>>> Gusdev-gusdev mailing list >>>>> Gus...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>=20 >>>>>=20 >>>>>=20 >>>=20 >>>=20 >>> -- >>> Thiago Seito Satake >>> !! Tenha um bom dia !! >>> Tel: (041) 990-55422 >>>=20 >>>=20 >>>=20 >>>=20 >> _______________________________________________ >> WDKDev mailing list >> WD...@pc... >> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>=20 |
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From: Y. T. G. <yon...@pc...> - 2005-08-10 13:03:18
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yes indeed. we need to explicitly register pg drivers (but not oracle=20 drivers). cheers, thomas On Wed, 10 Aug 2005, Y. Thomas Gan wrote: > maybe we need to explicitly register pg drivers. i'll try it. we should n= ot=20 > have to add the driver jar to tomcat'S CLASSPATH. > > -thomas > > On Wed, 10 Aug 2005, Steve Fischer wrote: > >> is it possibly caused by my having commented out this line in >> PostegeSQL.java: >>=20 >> // DriverManager.registerDriver(new org.postgresql.Driver(= )); >>=20 >> it didn't seem to make any difference when running outside of tomcat (so >> i took it out). >>=20 >> steve >>=20 >> Thiago Satake wrote: >>=20 >>> We updated WDK release with postgres and WDKToySite Works well. >>>=20 >>>=20 >>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>=20 >>>>=20 >>> It seems to me that is a tomcat problem,I belive that you must set >>> $CLASSPATH adding jdbc driver for postgres into >>> $CATALINA_HOME/bin/setclass.sh..... >>> as showed bellow: >>>=20 >>>=20 >>>> # Set standard CLASSPATH >>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3= =2Ejar >>>>=20 >>>>=20 >>>=20 >>>=20 >>> Thanks >>>=20 >>>=20 >>>=20 >>> Thiago Seito Stake >>>=20 >>>=20 >>>=20 >>>=20 >>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>=20 >>>=20 >>>> Another update on the status of release 1.6: >>>>=20 >>>> With tremendous efforts from Steve we were able to get wdkSanityTest >>>> (including tests for all Questions/Summaries, Queries, and Records) >>>> passing against both oracle and postgres late last night. >>>>=20 >>>> But we are at the last of the last hurdles: the toySite works fine >>>> with Oracle but does not come up with postgres (as Thiago reported >>>> earlier). See bug 114: toySite throws 'No suitable driver' SQLExceptio= n=20 >>>> at >>>> start up against postgres (oracle is ok) although sanityTest succeeds >>>> (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). >>>> The ArrayIndexOutOfBounds exception is a result of this. >>>>=20 >>>> I am debugging this and will release after it is fixed. >>>>=20 >>>> -Thomas >>>>=20 >>>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>>>=20 >>>>=20 >>>>=20 >>>>> just want to give an update on our progress. >>>>>=20 >>>>> we are planning a release today or tomorrow. >>>>>=20 >>>>> as well as postgres support (tested) it will include a number of othe= r >>>>> features, including an improved Sanity Test. the test will now test = all >>>>> Questions in the model XML file as well as all Queries and all Record= s. >>>>> this was needed to thoroughly test postgres. >>>>>=20 >>>>> we're working hard to get this release out... >>>>>=20 >>>>> steve >>>>>=20 >>>>> fab...@de... wrote: >>>>>=20 >>>>>=20 >>>>>=20 >>>>>> Thiago, >>>>>>=20 >>>>>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>>>> I'm having this problem too. In wdkSummary it seems that the schema= =20 >>>>>> name is >>>>>> missing before table names in FROM clause. >>>>>>=20 >>>>>> I don't know if this is a Wdk problem or WdkToySite SQL error. >>>>>>=20 >>>>>> Can you help us Steve? >>>>>>=20 >>>>>> Thanks a lot, >>>>>>=20 >>>>>> Fabr=EDcio. >>>>>>=20 >>>>>>=20 >>>>>> Citando Thiago Satake <ma...@gm...>: >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>> After downloaded WDK from SVN files I run: >>>>>>> wdkSanityTest -model toyModel >>>>>>>=20 >>>>>>> and got this >>>>>>>=20 >>>>>>> ***Sanity test summary*** >>>>>>> 10 queries passed, 4 queries failed >>>>>>> 1 records passed, 1 records failed >>>>>>> Sanity Test FAILED >>>>>>>=20 >>>>>>>=20 >>>>>>> and I run: >>>>>>> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1= 20 >>>>>>> -params NumSeqs 10 ApiTaxon "Neospora caninum" >>>>>>>=20 >>>>>>> I got: >>>>>>> org.gusdb.wdk.model.WdkModelException: >>>>>>> Failed running query: >>>>>>> "SELECT * FROM ( select usertest.query_result_4.result_index_column= , >>>>>>> a.assembly_consistency, a.contains_mrna, >>>>>>> a.number_of_contained_sequences, a.sequence >>>>>>> from WDKTestAssembly a, WDKTestTaxonName tn , >>>>>>> usertest.query_result_4 where a.na_sequence_id =3D >>>>>>> usertest.query_result_4.na_sequence_id and a.taxon_= id >>>>>>> =3D tn.taxon_id and usertest.query_result_4.result_index_column >= =3D 1 and >>>>>>> usertest.query_result_4.result_index_column <=3D 20 order by >>>>>>> usertest.query_result_4.result_index_column ) ORDER BY >>>>>>> result_index_column" >>>>>>>=20 >>>>>>>=20 >>>>>>> :-( >>>>>>>=20 >>>>>>>=20 >>>>>>> Thanks >>>>>>>=20 >>>>>>> Thiago Seito Satake >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>> 2005/8/5, Steve Fischer <sfi...@pc...>: >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>> Folks- >>>>>>>>=20 >>>>>>>> I have made a lot of progress. >>>>>>>>=20 >>>>>>>> It is clear that the wdk postgres implementation was never tested.= =20 >>>>>>>> I >>>>>>>> have fixed many, many things. >>>>>>>>=20 >>>>>>>> Here is where I am at so far. i ran: >>>>>>>> % wdkSanityTest -model toyModel >>>>>>>>=20 >>>>>>>> and got this: >>>>>>>>=20 >>>>>>>> ***Sanity test summary*** >>>>>>>> 11 queries passed, 1 queries failed >>>>>>>> 0 records passed, 2 records failed >>>>>>>> Sanity Test FAILED >>>>>>>>=20 >>>>>>>> tomorrow morning i'll look into the remaining problems >>>>>>>>=20 >>>>>>>> steve >>>>>>>>=20 >>>>>>>> Thiago Satake wrote: >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>> Thanks a lot, >>>>>>>>>=20 >>>>>>>>> Can I help you with something ? >>>>>>>>>=20 >>>>>>>>> Thiago Seito Satake >>>>>>>>>=20 >>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provi= ded=20 >>>>>>>>>> by >>>>>>>>>> the student's fixes. i am starting now to look at them and merg= e. >>>>>>>>>>=20 >>>>>>>>>> i have a lot of meetings today, so in a little while i'll need t= o=20 >>>>>>>>>> stop >>>>>>>>>> till tonight >>>>>>>>>>=20 >>>>>>>>>> steve >>>>>>>>>>=20 >>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>> Ok ........ >>>>>>>>>>>=20 >>>>>>>>>>> We can list some problems: >>>>>>>>>>> 1- we had to change all of perl wdk file ... to set te correct= =20 >>>>>>>>>>> driver >>>>>>>>>>> to postgres. >>>>>>>>>>> 2- we had to change testTables files to change the numeric dat= a=20 >>>>>>>>>>> type >>>>>>>>>>> ( number > numeric ) >>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres (=20 >>>>>>>>>>> sequence >>>>>>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) >>>>>>>>>>>=20 >>>>>>>>>>> now we are having problem to use WDKToySite as the log shows: >>>>>>>>>>>=20 >>>>>>>>>>> DEBUG: making a QuestionSetForm >>>>>>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcess= or >>>>>>>>>>> processException >>>>>>>>>>> WARNING: Unhandled Exception thrown: class >>>>>>>>>>> java.lang.ArrayIndexOutOfBoundsException >>>>>>>>>>>=20 >>>>>>>>>>> and other problems ............. >>>>>>>>>>>=20 >>>>>>>>>>> Thanks for the help :-) >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>> Folks- >>>>>>>>>>>>=20 >>>>>>>>>>>> the production uses of wdk so far are in oracle, so we have no= t=20 >>>>>>>>>>>> put >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> much >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> effort into ensuring the complete functioning of the postgres= =20 >>>>>>>>>>>> module. >>>>>>>>>>>>=20 >>>>>>>>>>>> however, a student did successfully use postgres with the wdk.= =20 >>>>>>>>>>>> he >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> made >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change i= n >>>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>>>=20 >>>>>>>>>>>> I will incorporate those changes today and test it. I hope t= o=20 >>>>>>>>>>>> get >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> you >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>>>=20 >>>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>>>=20 >>>>>>>>>>>> steve >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>> I am having the same problem......... >>>>>>>>>>>>>=20 >>>>>>>>>>>>> Does Someone have the wdk working with postgres database ? >>>>>>>>>>>>>=20 >>>>>>>>>>>>> I would appreciate if someone could help me too=20 >>>>>>>>>>>>> !!!!!!!!!!!!!!!!!!! >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>> :-) >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>> Thanks ............. >>>>>>>>>>>>>=20 >>>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Hello all, >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> We have a GUS installation running ok and now we're trying t= o=20 >>>>>>>>>>>>>> use >>>>>>>>>>>>>> WDK >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> 1.5 to >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> manipulating an >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> Oracle database, due to some type columns, sequence using,= =20 >>>>>>>>>>>>>> etc... >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> that >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>>>> wdkQuery, >>>>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Because of this, we're having a hard work to debug the code = and=20 >>>>>>>>>>>>>> set >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> it to work >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> with the Postgres schema. We would like to know if someone h= as=20 >>>>>>>>>>>>>> a >>>>>>>>>>>>>> WDK >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> working >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> ------------------------------------------------------------= ---- >>>>>>>>>>>>>> This message was sent using IMP, the Internet Messaging=20 >>>>>>>>>>>>>> Program. >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> WDKDev mailing list >>>>>>>>>>>>>> WD...@pc... >>>>>>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>> -- >>>>>>> Thiago Seito Satake >>>>>>> !! Tenha um bom dia !! >>>>>>> Tel: (041) 990-55422 >>>>>>>=20 >>>>>>> _______________________________________________ >>>>>>> WDKDev mailing list >>>>>>> WD...@pc... >>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>> ---------------------------------------------------------------- >>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>> ------------------------------------------------------- >>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 >>>>> Practices >>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing= &=20 >>>>> QA >>>>> Security * Process Improvement & Measurement *=20 >>>>> http://www.sqe.com/bsce5sf >>>>> _______________________________________________ >>>>> Gusdev-gusdev mailing list >>>>> Gus...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>=20 >>>>>=20 >>>>>=20 >>>=20 >>>=20 >>> -- >>> Thiago Seito Satake >>> !! Tenha um bom dia !! >>> Tel: (041) 990-55422 >>>=20 >>>=20 >>>=20 >>>=20 >> _______________________________________________ >> WDKDev mailing list >> WD...@pc... >> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > |
|
From: Y. T. G. <yon...@pc...> - 2005-08-10 12:56:53
|
maybe we need to explicitly register pg drivers. i'll try it. we should=20 not have to add the driver jar to tomcat'S CLASSPATH. -thomas On Wed, 10 Aug 2005, Steve Fischer wrote: > is it possibly caused by my having commented out this line in > PostegeSQL.java: > > // DriverManager.registerDriver(new org.postgresql.Driver()= ); > > it didn't seem to make any difference when running outside of tomcat (so > i took it out). > > steve > > Thiago Satake wrote: > >> We updated WDK release with postgres and WDKToySite Works well. >> >> >>> See bug 114: toySite throws 'No suitable driver' SQLException >>> >>> >> It seems to me that is a tomcat problem,I belive that you must set >> $CLASSPATH adding jdbc driver for postgres into >> $CATALINA_HOME/bin/setclass.sh..... >> as showed bellow: >> >> >>> # Set standard CLASSPATH >>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.= jar >>> >>> >> >> >> Thanks >> >> >> >> Thiago Seito Stake >> >> >> >> >> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >> >> >>> Another update on the status of release 1.6: >>> >>> With tremendous efforts from Steve we were able to get wdkSanityTest >>> (including tests for all Questions/Summaries, Queries, and Records) >>> passing against both oracle and postgres late last night. >>> >>> But we are at the last of the last hurdles: the toySite works fine >>> with Oracle but does not come up with postgres (as Thiago reported >>> earlier). See bug 114: toySite throws 'No suitable driver' SQLException= at >>> start up against postgres (oracle is ok) although sanityTest succeeds >>> (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). >>> The ArrayIndexOutOfBounds exception is a result of this. >>> >>> I am debugging this and will release after it is fixed. >>> >>> -Thomas >>> >>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>> >>> >>> >>>> just want to give an update on our progress. >>>> >>>> we are planning a release today or tomorrow. >>>> >>>> as well as postgres support (tested) it will include a number of other >>>> features, including an improved Sanity Test. the test will now test a= ll >>>> Questions in the model XML file as well as all Queries and all Records= =2E >>>> this was needed to thoroughly test postgres. >>>> >>>> we're working hard to get this release out... >>>> >>>> steve >>>> >>>> fab...@de... wrote: >>>> >>>> >>>> >>>>> Thiago, >>>>> >>>>> >> >> >> >> >>>>> I'm having this problem too. In wdkSummary it seems that the schema n= ame is >>>>> missing before table names in FROM clause. >>>>> >>>>> I don't know if this is a Wdk problem or WdkToySite SQL error. >>>>> >>>>> Can you help us Steve? >>>>> >>>>> Thanks a lot, >>>>> >>>>> Fabr=EDcio. >>>>> >>>>> >>>>> Citando Thiago Satake <ma...@gm...>: >>>>> >>>>> >>>>> >>>>> >>>>>> After downloaded WDK from SVN files I run: >>>>>> wdkSanityTest -model toyModel >>>>>> >>>>>> and got this >>>>>> >>>>>> ***Sanity test summary*** >>>>>> 10 queries passed, 4 queries failed >>>>>> 1 records passed, 1 records failed >>>>>> Sanity Test FAILED >>>>>> >>>>>> >>>>>> and I run: >>>>>> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 = 20 >>>>>> -params NumSeqs 10 ApiTaxon "Neospora caninum" >>>>>> >>>>>> I got: >>>>>> org.gusdb.wdk.model.WdkModelException: >>>>>> Failed running query: >>>>>> "SELECT * FROM ( select usertest.query_result_4.result_index_column, >>>>>> a.assembly_consistency, a.contains_mrna, >>>>>> a.number_of_contained_sequences, a.sequence >>>>>> from WDKTestAssembly a, WDKTestTaxonName tn , >>>>>> usertest.query_result_4 where a.na_sequence_id =3D >>>>>> usertest.query_result_4.na_sequence_id and a.taxon_i= d >>>>>> =3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D= 1 and >>>>>> usertest.query_result_4.result_index_column <=3D 20 order by >>>>>> usertest.query_result_4.result_index_column ) ORDER BY >>>>>> result_index_column" >>>>>> >>>>>> >>>>>> :-( >>>>>> >>>>>> >>>>>> Thanks >>>>>> >>>>>> Thiago Seito Satake >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 2005/8/5, Steve Fischer <sfi...@pc...>: >>>>>> >>>>>> >>>>>> >>>>>>> Folks- >>>>>>> >>>>>>> I have made a lot of progress. >>>>>>> >>>>>>> It is clear that the wdk postgres implementation was never tested. = I >>>>>>> have fixed many, many things. >>>>>>> >>>>>>> Here is where I am at so far. i ran: >>>>>>> % wdkSanityTest -model toyModel >>>>>>> >>>>>>> and got this: >>>>>>> >>>>>>> ***Sanity test summary*** >>>>>>> 11 queries passed, 1 queries failed >>>>>>> 0 records passed, 2 records failed >>>>>>> Sanity Test FAILED >>>>>>> >>>>>>> tomorrow morning i'll look into the remaining problems >>>>>>> >>>>>>> steve >>>>>>> >>>>>>> Thiago Satake wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Thanks a lot, >>>>>>>> >>>>>>>> Can I help you with something ? >>>>>>>> >>>>>>>> Thiago Seito Satake >>>>>>>> >>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provid= ed by >>>>>>>>> the student's fixes. i am starting now to look at them and merge= =2E >>>>>>>>> >>>>>>>>> i have a lot of meetings today, so in a little while i'll need to= stop >>>>>>>>> till tonight >>>>>>>>> >>>>>>>>> steve >>>>>>>>> >>>>>>>>> Thiago Satake wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Ok ........ >>>>>>>>>> >>>>>>>>>> We can list some problems: >>>>>>>>>> 1- we had to change all of perl wdk file ... to set te correct d= river >>>>>>>>>> to postgres. >>>>>>>>>> 2- we had to change testTables files to change the numeric data= type >>>>>>>>>> ( number > numeric ) >>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( seq= uence >>>>>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) >>>>>>>>>> >>>>>>>>>> now we are having problem to use WDKToySite as the log shows: >>>>>>>>>> >>>>>>>>>> DEBUG: making a QuestionSetForm >>>>>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcesso= r >>>>>>>>>> processException >>>>>>>>>> WARNING: Unhandled Exception thrown: class >>>>>>>>>> java.lang.ArrayIndexOutOfBoundsException >>>>>>>>>> >>>>>>>>>> and other problems ............. >>>>>>>>>> >>>>>>>>>> Thanks for the help :-) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Folks- >>>>>>>>>>> >>>>>>>>>>> the production uses of wdk so far are in oracle, so we have not= put >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>> much >>>>>> >>>>>> >>>>>> >>>>>>>>>>> effort into ensuring the complete functioning of the postgres m= odule. >>>>>>>>>>> >>>>>>>>>>> however, a student did successfully use postgres with the wdk. = he >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>> made >>>>>> >>>>>> >>>>>> >>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change in >>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>> >>>>>>>>>>> I will incorporate those changes today and test it. I hope to= get >>>>>>>>>>> >>>>>>>>>>> >>>>>> you >>>>>> >>>>>> >>>>>> >>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>> >>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>> >>>>>>>>>>> steve >>>>>>>>>>> >>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> I am having the same problem......... >>>>>>>>>>>> >>>>>>>>>>>> Does Someone have the wdk working with postgres database ? >>>>>>>>>>>> >>>>>>>>>>>> I would appreciate if someone could help me too !!!!!!!!!!!!!!= !!!!! >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>> :-) >>>>>> >>>>>> >>>>>> >>>>>>>>>>>> Thanks ............. >>>>>>>>>>>> >>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> Hello all, >>>>>>>>>>>>> >>>>>>>>>>>>> We have a GUS installation running ok and now we're trying to= use >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> 1.5 to >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> manipulating an >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> Oracle database, due to some type columns, sequence using, et= c... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> that >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>>> wdkQuery, >>>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>> >>>>>>>>>>>>> Because of this, we're having a hard work to debug the code a= nd set >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> it to work >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> with the Postgres schema. We would like to know if someone ha= s a >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> working >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>> >>>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>> >>>>>>>>>>>>> -------------------------------------------------------------= --- >>>>>>>>>>>>> This message was sent using IMP, the Internet Messaging Progr= am. >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> WDKDev mailing list >>>>>>>>>>>>> WD...@pc... >>>>>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> -- >>>>>> Thiago Seito Satake >>>>>> !! Tenha um bom dia !! >>>>>> Tel: (041) 990-55422 >>>>>> >>>>>> _______________________________________________ >>>>>> WDKDev mailing list >>>>>> WD...@pc... >>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>>> >>>> ------------------------------------------------------- >>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Prac= tices >>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing = & QA >>>> Security * Process Improvement & Measurement * http://www.sqe.com/bsce= 5sf >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >> >> >> -- >> Thiago Seito Satake >> !! Tenha um bom dia !! >> Tel: (041) 990-55422 >> >> >> >> > _______________________________________________ > WDKDev mailing list > WD...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > |
|
From: Steve F. <sfi...@pc...> - 2005-08-10 12:52:03
|
is it possibly caused by my having commented out this line in=20
PostegeSQL.java:
=20
// DriverManager.registerDriver(new org.postgresql.Driver(=
));
it didn't seem to make any difference when running outside of tomcat (so=20
i took it out).
steve
Thiago Satake wrote:
>We updated WDK release with postgres and WDKToySite Works well.
> =20
>
>>See bug 114: toySite throws 'No suitable driver' SQLException
>> =20
>>
>It seems to me that is a tomcat problem,I belive that you must set
>$CLASSPATH adding jdbc driver for postgres into
>$CATALINA_HOME/bin/setclass.sh.....
>as showed bellow:
> =20
>
>># Set standard CLASSPATH
>>CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.=
jar
>> =20
>>
>
>
>Thanks
>
>
>
>Thiago Seito Stake
>
>
>
>
>2005/8/10, Y. Thomas Gan <yon...@pc...>:
> =20
>
>>Another update on the status of release 1.6:
>>
>>With tremendous efforts from Steve we were able to get wdkSanityTest
>>(including tests for all Questions/Summaries, Queries, and Records)
>>passing against both oracle and postgres late last night.
>>
>>But we are at the last of the last hurdles: the toySite works fine
>>with Oracle but does not come up with postgres (as Thiago reported
>>earlier). See bug 114: toySite throws 'No suitable driver' SQLException=
at
>>start up against postgres (oracle is ok) although sanityTest succeeds
>>(https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114).
>>The ArrayIndexOutOfBounds exception is a result of this.
>>
>>I am debugging this and will release after it is fixed.
>>
>>-Thomas
>>
>>On Tue, 9 Aug 2005, Steve Fischer wrote:
>>
>> =20
>>
>>>just want to give an update on our progress.
>>>
>>>we are planning a release today or tomorrow.
>>>
>>>as well as postgres support (tested) it will include a number of other
>>>features, including an improved Sanity Test. the test will now test a=
ll
>>>Questions in the model XML file as well as all Queries and all Records.
>>>this was needed to thoroughly test postgres.
>>>
>>>we're working hard to get this release out...
>>>
>>>steve
>>>
>>>fab...@de... wrote:
>>>
>>> =20
>>>
>>>>Thiago,
>>>> =20
>>>>
>
>
> =20
>
>>>>I'm having this problem too. In wdkSummary it seems that the schema n=
ame is
>>>>missing before table names in FROM clause.
>>>>
>>>>I don't know if this is a Wdk problem or WdkToySite SQL error.
>>>>
>>>>Can you help us Steve?
>>>>
>>>>Thanks a lot,
>>>>
>>>>Fabr=EDcio.
>>>>
>>>>
>>>>Citando Thiago Satake <ma...@gm...>:
>>>>
>>>>
>>>> =20
>>>>
>>>>>After downloaded WDK from SVN files I run:
>>>>>wdkSanityTest -model toyModel
>>>>>
>>>>>and got this
>>>>>
>>>>>***Sanity test summary***
>>>>>10 queries passed, 4 queries failed
>>>>>1 records passed, 1 records failed
>>>>>Sanity Test FAILED
>>>>>
>>>>>
>>>>>and I run:
>>>>>wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 =
20
>>>>>-params NumSeqs 10 ApiTaxon "Neospora caninum"
>>>>>
>>>>>I got:
>>>>>org.gusdb.wdk.model.WdkModelException:
>>>>>Failed running query:
>>>>>"SELECT * FROM ( select usertest.query_result_4.result_index_column,
>>>>>a.assembly_consistency, a.contains_mrna,
>>>>>a.number_of_contained_sequences, a.sequence
>>>>>from WDKTestAssembly a, WDKTestTaxonName tn ,
>>>>>usertest.query_result_4 where a.na_sequence_id =3D
>>>>>usertest.query_result_4.na_sequence_id and a.taxon_i=
d
>>>>>=3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D=
1 and
>>>>>usertest.query_result_4.result_index_column <=3D 20 order by
>>>>>usertest.query_result_4.result_index_column ) ORDER BY
>>>>>result_index_column"
>>>>>
>>>>>
>>>>>:-(
>>>>>
>>>>>
>>>>>Thanks
>>>>>
>>>>>Thiago Seito Satake
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>2005/8/5, Steve Fischer <sfi...@pc...>:
>>>>>
>>>>> =20
>>>>>
>>>>>>Folks-
>>>>>>
>>>>>>I have made a lot of progress.
>>>>>>
>>>>>>It is clear that the wdk postgres implementation was never tested. =
I
>>>>>>have fixed many, many things.
>>>>>>
>>>>>>Here is where I am at so far. i ran:
>>>>>> % wdkSanityTest -model toyModel
>>>>>>
>>>>>>and got this:
>>>>>>
>>>>>>***Sanity test summary***
>>>>>>11 queries passed, 1 queries failed
>>>>>>0 records passed, 2 records failed
>>>>>>Sanity Test FAILED
>>>>>>
>>>>>>tomorrow morning i'll look into the remaining problems
>>>>>>
>>>>>>steve
>>>>>>
>>>>>>Thiago Satake wrote:
>>>>>>
>>>>>>
>>>>>> =20
>>>>>>
>>>>>>>Thanks a lot,
>>>>>>>
>>>>>>>Can I help you with something ?
>>>>>>>
>>>>>>>Thiago Seito Satake
>>>>>>>
>>>>>>>2005/8/4, Steve Fischer <sfi...@pc...>:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> =20
>>>>>>>
>>>>>>>>ok, sorry about this. yes, those all of 1,2,3 i think are provid=
ed by
>>>>>>>>the student's fixes. i am starting now to look at them and merge.
>>>>>>>>
>>>>>>>>i have a lot of meetings today, so in a little while i'll need to=
stop
>>>>>>>>till tonight
>>>>>>>>
>>>>>>>>steve
>>>>>>>>
>>>>>>>>Thiago Satake wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> =20
>>>>>>>>
>>>>>>>>>Ok ........
>>>>>>>>>
>>>>>>>>>We can list some problems:
>>>>>>>>>1- we had to change all of perl wdk file ... to set te correct d=
river
>>>>>>>>>to postgres.
>>>>>>>>>2- we had to change testTables files to change the numeric data=
type
>>>>>>>>>( number > numeric )
>>>>>>>>>3- and now we are changing java file to adapt to Postgres ( seq=
uence
>>>>>>>>>manipulation, Postgres.java - jdbc driver and numeric type )
>>>>>>>>>
>>>>>>>>>now we are having problem to use WDKToySite as the log shows:
>>>>>>>>>
>>>>>>>>>DEBUG: making a QuestionSetForm
>>>>>>>>>Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcesso=
r
>>>>>>>>>processException
>>>>>>>>>WARNING: Unhandled Exception thrown: class
>>>>>>>>>java.lang.ArrayIndexOutOfBoundsException
>>>>>>>>>
>>>>>>>>>and other problems .............
>>>>>>>>>
>>>>>>>>>Thanks for the help :-)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>2005/8/4, Steve Fischer <sfi...@pc...>:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> =20
>>>>>>>>>
>>>>>>>>>>Folks-
>>>>>>>>>>
>>>>>>>>>>the production uses of wdk so far are in oracle, so we have not=
put
>>>>>>>>>>
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>much
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>effort into ensuring the complete functioning of the postgres m=
odule.
>>>>>>>>>>
>>>>>>>>>>however, a student did successfully use postgres with the wdk. =
he
>>>>>>>>>>
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>made
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>improvements in the PostgreSQL.java file, and a small change in
>>>>>>>>>>ResultFactory that are not yet in the release.
>>>>>>>>>>
>>>>>>>>>>I will incorporate those changes today and test it. I hope to=
get
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>you
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>a patch by tomorrow.
>>>>>>>>>>
>>>>>>>>>>can you describe briefly the problems?
>>>>>>>>>>
>>>>>>>>>>steve
>>>>>>>>>>
>>>>>>>>>>Thiago Satake wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>>>>>>>I am having the same problem.........
>>>>>>>>>>>
>>>>>>>>>>>Does Someone have the wdk working with postgres database ?
>>>>>>>>>>>
>>>>>>>>>>>I would appreciate if someone could help me too !!!!!!!!!!!!!!=
!!!!!
>>>>>>>>>>>
>>>>>>>>>>> =20
>>>>>>>>>>>
>>>>>:-)
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>Thanks .............
>>>>>>>>>>>
>>>>>>>>>>>Thiago Seito Satake
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>2005/8/4, fab...@de... <fab...@de...>:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> =20
>>>>>>>>>>>
>>>>>>>>>>>>Hello all,
>>>>>>>>>>>>
>>>>>>>>>>>>We have a GUS installation running ok and now we're trying to=
use
>>>>>>>>>>>>WDK
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>1.5 to
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>explore the postgres schema. We noticed that the WDK code is
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>manipulating an
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>Oracle database, due to some type columns, sequence using, et=
c...
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>that
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>generates many errors when running wdk programs (wdkCache,
>>>>>>>>>>>>wdkQuery,
>>>>>>>>>>>>wdkRecord,...).
>>>>>>>>>>>>
>>>>>>>>>>>>Because of this, we're having a hard work to debug the code a=
nd set
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>it to work
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>with the Postgres schema. We would like to know if someone ha=
s a
>>>>>>>>>>>>WDK
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>working
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>with GUS Postgres perfectly.
>>>>>>>>>>>>
>>>>>>>>>>>>Thanks a lot,
>>>>>>>>>>>>
>>>>>>>>>>>>Fabr=EDcio.
>>>>>>>>>>>>
>>>>>>>>>>>>-------------------------------------------------------------=
---
>>>>>>>>>>>>This message was sent using IMP, the Internet Messaging Progr=
am.
>>>>>>>>>>>>_______________________________________________
>>>>>>>>>>>>WDKDev mailing list
>>>>>>>>>>>>WD...@pc...
>>>>>>>>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> =20
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> =20
>>>>>>>>>
>>>>>>>
>>>>>>> =20
>>>>>>>
>>>>>--
>>>>>Thiago Seito Satake
>>>>>!! Tenha um bom dia !!
>>>>>Tel: (041) 990-55422
>>>>>
>>>>>_______________________________________________
>>>>>WDKDev mailing list
>>>>>WD...@pc...
>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>>>>>
>>>>>
>>>>> =20
>>>>>
>>>>
>>>>
>>>>----------------------------------------------------------------
>>>>This message was sent using IMP, the Internet Messaging Program.
>>>>
>>>> =20
>>>>
>>>-------------------------------------------------------
>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle Prac=
tices
>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing =
& QA
>>>Security * Process Improvement & Measurement * http://www.sqe.com/bsce=
5sf
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>> =20
>>>
>
>
>--
>Thiago Seito Satake
>!! Tenha um bom dia !!
>Tel: (041) 990-55422
>
>
> =20
>
|
|
From: Thiago S. <ma...@gm...> - 2005-08-10 12:39:12
|
We updated WDK release with postgres and WDKToySite Works well. >See bug 114: toySite throws 'No suitable driver' SQLException It seems to me that is a tomcat problem,I belive that you must set $CLASSPATH adding jdbc driver for postgres into $CATALINA_HOME/bin/setclass.sh..... as showed bellow: ># Set standard CLASSPATH >CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.jar Thanks Thiago Seito Stake 2005/8/10, Y. Thomas Gan <yon...@pc...>: > Another update on the status of release 1.6: > > With tremendous efforts from Steve we were able to get wdkSanityTest > (including tests for all Questions/Summaries, Queries, and Records) > passing against both oracle and postgres late last night. > > But we are at the last of the last hurdles: the toySite works fine > with Oracle but does not come up with postgres (as Thiago reported > earlier). See bug 114: toySite throws 'No suitable driver' SQLException a= t > start up against postgres (oracle is ok) although sanityTest succeeds > (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). > The ArrayIndexOutOfBounds exception is a result of this. > > I am debugging this and will release after it is fixed. > > -Thomas > > On Tue, 9 Aug 2005, Steve Fischer wrote: > > > just want to give an update on our progress. > > > > we are planning a release today or tomorrow. > > > > as well as postgres support (tested) it will include a number of other > > features, including an improved Sanity Test. the test will now test al= l > > Questions in the model XML file as well as all Queries and all Records. > > this was needed to thoroughly test postgres. > > > > we're working hard to get this release out... > > > > steve > > > > fab...@de... wrote: > > > >> Thiago, > >> > >> I'm having this problem too. In wdkSummary it seems that the schema na= me is > >> missing before table names in FROM clause. > >> > >> I don't know if this is a Wdk problem or WdkToySite SQL error. > >> > >> Can you help us Steve? > >> > >> Thanks a lot, > >> > >> Fabr=EDcio. > >> > >> > >> Citando Thiago Satake <ma...@gm...>: > >> > >> > >>> After downloaded WDK from SVN files I run: > >>> wdkSanityTest -model toyModel > >>> > >>> and got this > >>> > >>> ***Sanity test summary*** > >>> 10 queries passed, 4 queries failed > >>> 1 records passed, 1 records failed > >>> Sanity Test FAILED > >>> > >>> > >>> and I run: > >>> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 2= 0 > >>> -params NumSeqs 10 ApiTaxon "Neospora caninum" > >>> > >>> I got: > >>> org.gusdb.wdk.model.WdkModelException: > >>> Failed running query: > >>> "SELECT * FROM ( select usertest.query_result_4.result_index_column, > >>> a.assembly_consistency, a.contains_mrna, > >>> a.number_of_contained_sequences, a.sequence > >>> from WDKTestAssembly a, WDKTestTaxonName tn , > >>> usertest.query_result_4 where a.na_sequence_id =3D > >>> usertest.query_result_4.na_sequence_id and a.taxon_id > >>> =3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D = 1 and > >>> usertest.query_result_4.result_index_column <=3D 20 order by > >>> usertest.query_result_4.result_index_column ) ORDER BY > >>> result_index_column" > >>> > >>> > >>> :-( > >>> > >>> > >>> Thanks > >>> > >>> Thiago Seito Satake > >>> > >>> > >>> > >>> > >>> > >>> > >>> 2005/8/5, Steve Fischer <sfi...@pc...>: > >>> > >>>> Folks- > >>>> > >>>> I have made a lot of progress. > >>>> > >>>> It is clear that the wdk postgres implementation was never tested. = I > >>>> have fixed many, many things. > >>>> > >>>> Here is where I am at so far. i ran: > >>>> % wdkSanityTest -model toyModel > >>>> > >>>> and got this: > >>>> > >>>> ***Sanity test summary*** > >>>> 11 queries passed, 1 queries failed > >>>> 0 records passed, 2 records failed > >>>> Sanity Test FAILED > >>>> > >>>> tomorrow morning i'll look into the remaining problems > >>>> > >>>> steve > >>>> > >>>> Thiago Satake wrote: > >>>> > >>>> > >>>>> Thanks a lot, > >>>>> > >>>>> Can I help you with something ? > >>>>> > >>>>> Thiago Seito Satake > >>>>> > >>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: > >>>>> > >>>>> > >>>>> > >>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provide= d by > >>>>>> the student's fixes. i am starting now to look at them and merge. > >>>>>> > >>>>>> i have a lot of meetings today, so in a little while i'll need to = stop > >>>>>> till tonight > >>>>>> > >>>>>> steve > >>>>>> > >>>>>> Thiago Satake wrote: > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>>> Ok ........ > >>>>>>> > >>>>>>> We can list some problems: > >>>>>>> 1- we had to change all of perl wdk file ... to set te correct dr= iver > >>>>>>> to postgres. > >>>>>>> 2- we had to change testTables files to change the numeric data = type > >>>>>>> ( number > numeric ) > >>>>>>> 3- and now we are changing java file to adapt to Postgres ( sequ= ence > >>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) > >>>>>>> > >>>>>>> now we are having problem to use WDKToySite as the log shows: > >>>>>>> > >>>>>>> DEBUG: making a QuestionSetForm > >>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcessor > >>>>>>> processException > >>>>>>> WARNING: Unhandled Exception thrown: class > >>>>>>> java.lang.ArrayIndexOutOfBoundsException > >>>>>>> > >>>>>>> and other problems ............. > >>>>>>> > >>>>>>> Thanks for the help :-) > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>>> Folks- > >>>>>>>> > >>>>>>>> the production uses of wdk so far are in oracle, so we have not = put > >>>>>>>> > >>> much > >>> > >>>>>>>> effort into ensuring the complete functioning of the postgres mo= dule. > >>>>>>>> > >>>>>>>> however, a student did successfully use postgres with the wdk. = he > >>>>>>>> > >>> made > >>> > >>>>>>>> improvements in the PostgreSQL.java file, and a small change in > >>>>>>>> ResultFactory that are not yet in the release. > >>>>>>>> > >>>>>>>> I will incorporate those changes today and test it. I hope to = get > >>> you > >>> > >>>>>>>> a patch by tomorrow. > >>>>>>>> > >>>>>>>> can you describe briefly the problems? > >>>>>>>> > >>>>>>>> steve > >>>>>>>> > >>>>>>>> Thiago Satake wrote: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>> I am having the same problem......... > >>>>>>>>> > >>>>>>>>> Does Someone have the wdk working with postgres database ? > >>>>>>>>> > >>>>>>>>> I would appreciate if someone could help me too !!!!!!!!!!!!!!!= !!!! > >>>>>>>>> > >>> :-) > >>> > >>>>>>>>> Thanks ............. > >>>>>>>>> > >>>>>>>>> Thiago Seito Satake > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>>> Hello all, > >>>>>>>>>> > >>>>>>>>>> We have a GUS installation running ok and now we're trying to = use > >>>>>>>>>> WDK > >>>>>>>>>> > >>> 1.5 to > >>> > >>>>>>>>>> explore the postgres schema. We noticed that the WDK code is > >>>>>>>>>> > >>> manipulating an > >>> > >>>>>>>>>> Oracle database, due to some type columns, sequence using, etc= ... > >>>>>>>>>> > >>> that > >>> > >>>>>>>>>> generates many errors when running wdk programs (wdkCache, > >>>>>>>>>> wdkQuery, > >>>>>>>>>> wdkRecord,...). > >>>>>>>>>> > >>>>>>>>>> Because of this, we're having a hard work to debug the code an= d set > >>>>>>>>>> > >>> it to work > >>> > >>>>>>>>>> with the Postgres schema. We would like to know if someone has= a > >>>>>>>>>> WDK > >>>>>>>>>> > >>> working > >>> > >>>>>>>>>> with GUS Postgres perfectly. > >>>>>>>>>> > >>>>>>>>>> Thanks a lot, > >>>>>>>>>> > >>>>>>>>>> Fabr=EDcio. > >>>>>>>>>> > >>>>>>>>>> --------------------------------------------------------------= -- > >>>>>>>>>> This message was sent using IMP, the Internet Messaging Progra= m. > >>>>>>>>>> _______________________________________________ > >>>>>>>>>> WDKDev mailing list > >>>>>>>>>> WD...@pc... > >>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>> > >>>>> > >>>>> > >>> -- > >>> Thiago Seito Satake > >>> !! Tenha um bom dia !! > >>> Tel: (041) 990-55422 > >>> > >>> _______________________________________________ > >>> WDKDev mailing list > >>> WD...@pc... > >>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > >>> > >>> > >> > >> > >> > >> > >> ---------------------------------------------------------------- > >> This message was sent using IMP, the Internet Messaging Program. > >> > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices > > Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA > > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
|
From: Y. T. G. <yon...@pc...> - 2005-08-10 11:52:57
|
Another update on the status of release 1.6: With tremendous efforts from Steve we were able to get wdkSanityTest=20 (including tests for all Questions/Summaries, Queries, and Records)=20 passing against both oracle and postgres late last night. But we are at the last of the last hurdles: the toySite works fine=20 with Oracle but does not come up with postgres (as Thiago reported=20 earlier). See bug 114: toySite throws 'No suitable driver' SQLException at= =20 start up against postgres (oracle is ok) although sanityTest succeeds=20 (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). The ArrayIndexOutOfBounds exception is a result of this. I am debugging this and will release after it is fixed. -Thomas On Tue, 9 Aug 2005, Steve Fischer wrote: > just want to give an update on our progress. > > we are planning a release today or tomorrow. > > as well as postgres support (tested) it will include a number of other=20 > features, including an improved Sanity Test. the test will now test all= =20 > Questions in the model XML file as well as all Queries and all Records.= =20 > this was needed to thoroughly test postgres. > > we're working hard to get this release out... > > steve > > fab...@de... wrote: > >> Thiago, >>=20 >> I'm having this problem too. In wdkSummary it seems that the schema name= is >> missing before table names in FROM clause. >>=20 >> I don't know if this is a Wdk problem or WdkToySite SQL error. >>=20 >> Can you help us Steve? >>=20 >> Thanks a lot, >>=20 >> Fabr=EDcio. >>=20 >>=20 >> Citando Thiago Satake <ma...@gm...>: >>=20 >>=20 >>> After downloaded WDK from SVN files I run: >>> wdkSanityTest -model toyModel >>>=20 >>> and got this >>>=20 >>> ***Sanity test summary*** >>> 10 queries passed, 4 queries failed >>> 1 records passed, 1 records failed >>> Sanity Test FAILED >>>=20 >>>=20 >>> and I run: >>> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 20 >>> -params NumSeqs 10 ApiTaxon "Neospora caninum" >>>=20 >>> I got:=20 >>> org.gusdb.wdk.model.WdkModelException: >>> Failed running query: >>> "SELECT * FROM ( select usertest.query_result_4.result_index_column,=20 >>> a.assembly_consistency, a.contains_mrna,=20 >>> a.number_of_contained_sequences, a.sequence=20 >>> from WDKTestAssembly a, WDKTestTaxonName tn ,=20 >>> usertest.query_result_4 where a.na_sequence_id =3D >>> usertest.query_result_4.na_sequence_id and a.taxon_id >>> =3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D 1 = and >>> usertest.query_result_4.result_index_column <=3D 20 order by >>> usertest.query_result_4.result_index_column ) ORDER BY >>> result_index_column" >>>=20 >>>=20 >>> :-( >>>=20 >>>=20 >>> Thanks >>>=20 >>> Thiago Seito Satake >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>> 2005/8/5, Steve Fischer <sfi...@pc...>: >>>=20 >>>> Folks- >>>>=20 >>>> I have made a lot of progress. >>>>=20 >>>> It is clear that the wdk postgres implementation was never tested. = I >>>> have fixed many, many things. >>>>=20 >>>> Here is where I am at so far. i ran: >>>> % wdkSanityTest -model toyModel >>>>=20 >>>> and got this: >>>>=20 >>>> ***Sanity test summary*** >>>> 11 queries passed, 1 queries failed >>>> 0 records passed, 2 records failed >>>> Sanity Test FAILED >>>>=20 >>>> tomorrow morning i'll look into the remaining problems >>>>=20 >>>> steve >>>>=20 >>>> Thiago Satake wrote: >>>>=20 >>>>=20 >>>>> Thanks a lot, >>>>>=20 >>>>> Can I help you with something ? >>>>>=20 >>>>> Thiago Seito Satake >>>>>=20 >>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>=20 >>>>>=20 >>>>>=20 >>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provided = by >>>>>> the student's fixes. i am starting now to look at them and merge. >>>>>>=20 >>>>>> i have a lot of meetings today, so in a little while i'll need to st= op >>>>>> till tonight >>>>>>=20 >>>>>> steve >>>>>>=20 >>>>>> Thiago Satake wrote: >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>> Ok ........ >>>>>>>=20 >>>>>>> We can list some problems: >>>>>>> 1- we had to change all of perl wdk file ... to set te correct driv= er >>>>>>> to postgres. >>>>>>> 2- we had to change testTables files to change the numeric data ty= pe >>>>>>> ( number > numeric ) >>>>>>> 3- and now we are changing java file to adapt to Postgres ( sequen= ce >>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) >>>>>>>=20 >>>>>>> now we are having problem to use WDKToySite as the log shows: >>>>>>>=20 >>>>>>> DEBUG: making a QuestionSetForm >>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcessor >>>>>>> processException >>>>>>> WARNING: Unhandled Exception thrown: class >>>>>>> java.lang.ArrayIndexOutOfBoundsException >>>>>>>=20 >>>>>>> and other problems ............. >>>>>>>=20 >>>>>>> Thanks for the help :-) >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>> Folks- >>>>>>>>=20 >>>>>>>> the production uses of wdk so far are in oracle, so we have not pu= t >>>>>>>>=20 >>> much >>>=20 >>>>>>>> effort into ensuring the complete functioning of the postgres modu= le. >>>>>>>>=20 >>>>>>>> however, a student did successfully use postgres with the wdk. he >>>>>>>>=20 >>> made >>>=20 >>>>>>>> improvements in the PostgreSQL.java file, and a small change in >>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>=20 >>>>>>>> I will incorporate those changes today and test it. I hope to ge= t=20 >>> you >>>=20 >>>>>>>> a patch by tomorrow. >>>>>>>>=20 >>>>>>>> can you describe briefly the problems? >>>>>>>>=20 >>>>>>>> steve >>>>>>>>=20 >>>>>>>> Thiago Satake wrote: >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>> I am having the same problem......... >>>>>>>>>=20 >>>>>>>>> Does Someone have the wdk working with postgres database ? >>>>>>>>>=20 >>>>>>>>> I would appreciate if someone could help me too !!!!!!!!!!!!!!!!!= !! >>>>>>>>>=20 >>> :-) >>>=20 >>>>>>>>> Thanks ............. >>>>>>>>>=20 >>>>>>>>> Thiago Seito Satake >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>> Hello all, >>>>>>>>>>=20 >>>>>>>>>> We have a GUS installation running ok and now we're trying to us= e=20 >>>>>>>>>> WDK >>>>>>>>>>=20 >>> 1.5 to >>>=20 >>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>=20 >>> manipulating an >>>=20 >>>>>>>>>> Oracle database, due to some type columns, sequence using, etc..= =2E >>>>>>>>>>=20 >>> that >>>=20 >>>>>>>>>> generates many errors when running wdk programs (wdkCache,=20 >>>>>>>>>> wdkQuery, >>>>>>>>>> wdkRecord,...). >>>>>>>>>>=20 >>>>>>>>>> Because of this, we're having a hard work to debug the code and = set >>>>>>>>>>=20 >>> it to work >>>=20 >>>>>>>>>> with the Postgres schema. We would like to know if someone has a= =20 >>>>>>>>>> WDK >>>>>>>>>>=20 >>> working >>>=20 >>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>=20 >>>>>>>>>> Thanks a lot, >>>>>>>>>>=20 >>>>>>>>>> Fabr=EDcio. >>>>>>>>>>=20 >>>>>>>>>> ---------------------------------------------------------------- >>>>>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>>>>> _______________________________________________ >>>>>>>>>> WDKDev mailing list >>>>>>>>>> WD...@pc... >>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>=20 >>>>>=20 >>>>>=20 >>> --=20 >>> Thiago Seito Satake >>> !! Tenha um bom dia !! >>> Tel: (041) 990-55422 >>>=20 >>> _______________________________________________ >>> WDKDev mailing list >>> WD...@pc... >>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>=20 >>>=20 >>=20 >>=20 >>=20 >>=20 >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >>=20 > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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