gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] required GenBank information

[Steve F. <sfi...@pc...>]

Terry-

In Chetna's absence, i reviewed the LoadGeneFeaturesFromXML plugin 
(which loads from TIGR xml).

I am not sure why Chetna said that you need Genbank data loaded to run 
the plugin, because it doesn't seem to need that.

Steve

Terry Clark wrote:

>Hi, we are moving on to install required GenBank data into GUS, 
>which I understand comes to play in loading sequence data.
>If someone could send a note about the GenBank files 
>required in GUS for basic operations, that would be most helpful.
>
>cheers,
>Terry 
>
>
>
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Re: [SPAM:08.30/07.00] [Gusdev-gusdev] [question]setup build system

[Steve F. <sfi...@pc...>]

Dear Hee-Jeon-

I am afraid that GUS does not run on Windows.

It runs on Linux.

Steve

=C0=CC=C8=F1=C0=FC wrote:

> Hello!
>
> I'm Korean graduate student.
>
> I do setting up GUS build system.
>
> I use os Windows 2000 (Cannot GUS work on Windows?)
>
> I red 'set up build system' document.
>
> but.. I cannot use ANT!!
>
> bellow error message..
>
> ant -f c:\projects/install/build.xml install -Dproj=3DGUS
> -DtargetDir=3Dc:\gus -Dcom
> p=3D -DprojectsDir=3Dc:\projects -Dappend=3Dtrue -logger
> org.apache.tools.ant.NoBann
> erLogger ']'
>
> Buildfile: c:\projects\install\build.xml
>
> BUILD FAILED
> file:C:/projects/install/build.xml:318: Warning: Could not find file
> C:\projects
> \install\${projectsDir}\install\config\install.prop.sample to copy.
>
> Total time: 1 second
>
> I copied install.prop (<- perl =3D c:\perl\bin\perl.exe ) to c:\gus\con=
fig
>
> I cannot understand error message.
>
> And..
>
> build.pl file..
>
> my $cmd =3D "ant -f $projectHome/install/build.xml $doWhat
> -Dproj=3D$project -DtargetDir=3D$targetDir -Dcomp=3D$component
> -DprojectsDir=3D$projectHome $clean $append $tag -logger
> org.apache.tools.ant.NoBannerLogger | grep ']'";
>
> ANT cannot understand "grep" instruction.
>
> So.. I skip "grep" instruction..
>
> Give me an answer, please.
>
>
>
> (=AA=C5``)=AA=C5~=A2=BD
>
> Hee-Jeon Lee
> Ewha Womans Univ. DB Lab
> E-Mail: kka...@fr... <mailto:kka...@fr...>
>
>
>
>
>
>
>

[Gusdev-gusdev] [question]setup build system

[<kka...@fr...>]

hello!

i'm korean graduate student.

i do setting up gus build system.
i use os windows 2000 (cannot gus work on windows?)

i red 'set up build system' document.
but.. i cannot use ant!!

bellow error message..

ant -f c:\projects/install/build.xml install -dproj=3Dgus -dtargetdir=3Dc=
:\gus -dcom
p=3D -dprojectsdir=3Dc:\projects  -dappend=3Dtrue  -logger org.apache.too=
ls.ant.nobann
erlogger  ']'
buildfile: c:\projects\install\build.xml
build failed
file:c:/projects/install/build.xml:318: warning: could not find file c:\p=
rojects
\install\${projectsdir}\install\config\install.prop.sample to copy.
total time: 1 second

i copied install.prop (<- perl =3D c:\perl\bin\perl.exe ) to c:\gus\confi=
g
i cannot understand error message.

and.. =20
build.pl file..

my $cmd =3D "ant -f $projecthome/install/build.xml $dowhat -dproj=3D$proj=
ect -dtargetdir=3D$targetdir -dcomp=3D$component -dprojectsdir=3D$project=
home $clean $append $tag -logger org.apache.tools.ant.nobannerlogger | gr=
ep ']'";

ant cannot understand "grep" instruction.
so.. i skip "grep" instruction..

give me an answer, please.


  =20
(=AA=C5``)=AA=C5~=A2=BD=20
hee-jeon lee
ewha womans univ. db lab
e-mail: kka...@fr...


FMS =C7=C1=B8=AE=B9=CC=BE=F6 =BC=AD=BA=F1=BD=BA!
http://home.freechal.com/etc/3thousand/MembershipLounge/JoinInfo.asp

[Gusdev-gusdev] required GenBank information

[Terry C. <tw...@cs...>]

Hi, we are moving on to install required GenBank data into GUS, 
which I understand comes to play in loading sequence data.
If someone could send a note about the GenBank files 
required in GUS for basic operations, that would be most helpful.

cheers,
Terry 

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Re: [Gusdev-gusdev] initial GO Files

[Terry C. <tw...@cs...>]

Progress on loading GO here is happening, but ...

Having populated the tables ExternalDatabase and ExternalDatabaseRelease,
and having made the ANCESTOR_GO_TERM_ID in Table SRES.GOTERM nullable, the
LoadGoOntology plugin execution

    ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go 
    --id_file=go03 --function_db_id=4 --component_db_id=5 --process_db_id=6 --verbose
 
breaks (after going some distance) apparently from making a select 
for go_relationship_type_id from the sres.gorelationshiptype table
which is empty. It it necessary to have pre-loaded some enumerated set 
of relationships ?

Can someone help me to determine what could be the matter, a fix possibly? 
Attached is the tail of the output.  
Lines 31 and 32 point to the access to the empty table.

Thanks,

Terry

-- trudgin' across the tundra, mile after mile


4   
5   > ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go03 --function_db_id=4 --component_db_id=5 --process_db_id=6 --verbose
6   
7   
8                ....... many steps ......
9   
10   parsing finished; loading ontology into database
11   executingselect external_database_release_id 
12                  from sres.externalDatabaseRelease
13                  where version = '2.371' and external_database_id = 5
14   
15   
16   prepareAndExecute: select external_database_release_id 
17                  from sres.externalDatabaseRelease
18                  where version = '2.371' and external_database_id = 5 
19   
20   
21   sqlExec: 
22       INSERT INTO SRes.ExternalDatabaseRelease (  group_write, other_read, external_database_release_id, group_read, version, user_read, external_database_id, row_user_id, other_write, modification_date, row_project_id, row_alg_invocation_id, row_group_id, user_write )
23       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ? ) 
24     bindValues (1, 1, 10, 1, 2.371, 1, 5, 1, 0, 1, 22, 1, 1)
25    DbiHandle:sqlExec:insert succeeded 1 row(s)
26   successfully submitted new entry into SRes.ExternalDatabaseReleaseId with primary key of 10
27   making root node for component
28   loading GO Terms into SRes.GOTerm
29   
30   
31   prepareAndExecute: select go_relationship_type_id, name 
32                  from sres.gorelationshiptype 
33   loading hierarchy and synonyms into SRes.GORelationship and SRes.GOSynonym
34   
35   
36   sqlExec: 
37       INSERT INTO SRes.GORelationship (  go_relationship_type_id, go_relationship_id, group_write, other_read, group_read, user_read, row_user_id, other_write, modification_date, row_alg_invocation_id, row_project_id, parent_term_id, child_term_id, row_group_id, user_write )
38       VALUES   (  '', ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, '', '', ?, ? ) 
39     bindValues (1, 1, 1, 1, 1, 1, 0, 22, 1, 1, 1)
40   DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into ("SRES"."GORELATIONSHIP"."PARENT_TERM_ID") (DBD ERROR: OCIStmtExecute) [for statement ``
41       INSERT INTO SRes.GORelationship (  go_relationship_type_id, go_relationship_id, group_write, other_read, group_read, user_read, row_user_id, other_write, modification_date, row_alg_invocation_id, row_project_id, parent_term_id, child_term_id, row_group_id, user_write )
42       VALUES   (  '', ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, '', '', ?, ? ) '' with params: :p5=1, :p8='22', :p10='1', :p2=1, :p3=1, :p6='1', :p1=1, :p7=0, :p4=1, :p9='1', :p11=1]) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
43   
44   
45   sqlExec: 
46       UPDATE  Core.AlgorithmInvocation
47       SET     
48   	modification_date = SYSDATE,
49   	end_time = SYSDATE,
50   	row_alg_invocation_id = ?
51       WHERE   algorithm_invocation_id = ?
52     bindValues (22, 22)
53    DbiHandle:sqlExec:insert succeeded 1 row(s)
54   
55    SQL ERROR!! involving
56    
57       INSERT INTO SRes.GORelationship (  go_relationship_type_id, go_relationship_id, group_write, other_read, group_read, user_read, row_user_id, other_write, modification_date, row_alg_invocation_id, row_project_id, parent_term_id, child_term_id, row_group_id, user_write )
58       VALUES   (  '', ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, '', '', ?, ? )  
59    Values: 1, 1, 1, 1, 1, 1, 0, 22, 1, 1, 1 at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
60   	GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x83515c8)','\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO SRes.GORelationship...') called at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
61   	GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x83515c8)','GUS::ObjRelP::DbiDbHandle::st=HASH(0x8e0362c)','ARRAY(0x8e03614)','\x{a}    INSERT INTO SRes.GORelationship (  go_relationship_type_...') called at /home/gus/run/lib/perl/GUS/ObjRelP/DbiRow.pm line 694
62   	GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c27828)','GUS::Model::SRes::GORelationship','HASH(0x8bc5170)') called at /home/gus/run/lib/perl/GUS/ObjRelP/DbiRow.pm line 641
63   	GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c27828)') called at /home/gus/run/lib/perl/GUS/Model/GusRow.pm line 1677
64   	GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c27828)') called at /home/gus/run/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 270
65   	GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x80699cc)','CBIL::Bio::GeneOntologyParser::Parser=HASH(0x88c6bb8)') called at /home/gus/run/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 125
66   	GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x80699cc)','HASH(0x88c5b7c)') called at /home/gus/run/lib/perl/GUS/PluginMgr/GusApplication.pm line 388
67   	eval {...} called at /home/gus/run/lib/perl/GUS/PluginMgr/GusApplication.pm line 384
68   	GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804c014)','GUS::GOPredict::Plugin::LoadGoOntology') called at /home/gus/run/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
69   	GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804c014)','GUS::GOPredict::Plugin::LoadGoOntology') called at /home/gus/run/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
70   	GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804c014)','ARRAY(0x805f7fc)') called at /home/gus/run/bin/ga line 11
71   












On  0, Dave Barkan <db...@pc...> wrote:
> Hey Terry,
> 
> I'm not completely familiar with UpdateGusFromCla, but here are a couple 
> suggestions:
> 
> Specify the table name in SchemaName::TableName format; in this case you 
> would use "SRes::ExternalDatabase" (from what I can tell in the code, it 
> uses the '::' as the delimiter to split on.)
> 
> Also, when running this plugin you don't need to specify any of the 
> overhead columns (eg., user_read, modification_date, etc.).  Simply 
> specifiying 'name', 'lowercase_name' should do the trick (for this table, 
> at least), and the rest of the columns common to all tables will be filled 
> in automatically, in addition to the primary key (external_database_id).
> 
> I'm not aware of any example XML files for the plugin 'UpdateGusFromXML.'  
> Perhaps someone else can help with this?
> 
> Good luck,
> Dave
> 
> 
> On Thu, 3 Jul 2003, Terry Clark wrote:
> 
> > Hi Dave,
> > I had some problems. There is a warning and an error, both puzzling me.
> > The output is below:
> >    command  on line 2
> >    warning on line 144
> >    error looking comment on line 156  
> > 
> > I am stumped. Can you help?
> > 
> > By the way, are there example XML files for using with
> > UpdateGusFromXML.pm available?
> > 
> > 
> > Terry
> > 
> > 
> > 
> > 
> > 1   
> > 2   ga +run GUS::Common::Plugin::UpdateGusFromCla --attrlist="NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE" --valuelist="'GO Function','go function',SYSDATE,1,1,1,1,1,0" --tablename=SRes.ExternalDatabase
> > 3   
> > 4   
> > 5   
> > 6   Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
> > 7   Reading properties from /home/gus/.gus.properties
> > 8   
> > 9   
> > 10   prepareAndExecute:     SELECT *
> > 11         FROM Core.AlgorithmImplementation
> > 12        WHERE executable = 'GUS::Common::Plugin::UpdateGusFromCla'
> > 13          AND cvs_revision    = '1.2'
> > 14   
> > 15    
> > 16   
> > 17   
> > 18   prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
> > 19   
> > 20   RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
> > 21     bindValues (17)
> > 22   
> > 23   
> > 24   prepareAndExecute: select login,user_id from Core.UserInfo 
> > 25   
> > 26   
> > 27   prepareAndExecute: select name,group_id from Core.GroupInfo 
> > 28   
> > 29   
> > 30   prepareAndExecute: select name,project_id from Core.ProjectInfo 
> > 31   
> > 32   
> > 33   sqlExec: 
> > 34       INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
> > 35       VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
> > 36     bindValues (1, 1, 17, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 6, pending)
> > 37    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 38   
> > 39   getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
> > 40     bindValues (17)
> > 41   
> > 42   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > 43     bindValues (2)
> > 44   
> > 45   
> > 46   sqlExec: 
> > 47       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > 48       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > 49     bindValues (206, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 40, 1, 6, 1, 6)
> > 50    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 51   
> > 52   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > 53     bindValues (0)
> > 54   
> > 55   
> > 56   sqlExec: 
> > 57       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 58       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > 59     bindValues (1, 1, 0, 207, 1, 41, 1, 1, 0, 0, 6, 1, 1, 6, NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE, 1)
> > 60    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 61   
> > 62   
> > 63   sqlExec: 
> > 64       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 65       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > 66     bindValues (1, 1, 0, 203, 1, 42, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> > 67    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 68   
> > 69   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > 70     bindValues (4)
> > 71   
> > 72   
> > 73   sqlExec: 
> > 74       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > 75       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > 76     bindValues (210, 1, 1, 0, 0, 1, 1, 0, 1, 1, 43, 1, 6, 1, 6)
> > 77    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 78   
> > 79   
> > 80   sqlExec: 
> > 81       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 82       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > 83     bindValues (1, 1, 0, 211, 1, 44, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> > 84    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 85   
> > 86   
> > 87   sqlExec: 
> > 88       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 89       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > 90     bindValues (1, 1, 0, 201, 1, 45, 1, 1, 0, 0, 6, 1, 1, 6, /home/gus/.gus.properties, 1)
> > 91    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 92   
> > 93   
> > 94   sqlExec: 
> > 95       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 96       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > 97     bindValues (1, 1, 0, 208, 1, 46, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> > 98    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 99   
> > 100   
> > 101   sqlExec: 
> > 102       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > 103       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > 104     bindValues (205, 1, 1, 0, 0, 1, 1, 0, 1, 1, 47, 1, 6, 1, 6)
> > 105    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 106   
> > 107   
> > 108   sqlExec: 
> > 109       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 110       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > 111     bindValues (1, 1, 0, 209, 1, 48, 1, 1, 0, 0, 6, 1, 1, 6, SRes.ExternalDatabase, 1)
> > 112    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 113   
> > 114   
> > 115   sqlExec: 
> > 116       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 117       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > 118     bindValues (1, 1, 0, 202, 1, 49, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> > 119    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 120   
> > 121   
> > 122   sqlExec: 
> > 123       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > 124       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > 125     bindValues (1, 1, 0, 204, 1, 50, 1, 1, 0, 0, 6, 1, 1, 6, 'GO Function','go function',SYSDATE,1,1,1,1,1,0, 1)
> > 126    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 127   Thu Jul  3 12:23:35 2003	ALGINVID	6
> > 128   Thu Jul  3 12:23:35 2003	ARGS	algoinvo	1
> > 129   Thu Jul  3 12:23:35 2003	ARGS	attrlist	NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE
> > 130   Thu Jul  3 12:23:35 2003	ARGS	comment	
> > 131   Thu Jul  3 12:23:35 2003	ARGS	commit	
> > 132   Thu Jul  3 12:23:35 2003	ARGS	debug	
> > 133   Thu Jul  3 12:23:35 2003	ARGS	group	
> > 134   Thu Jul  3 12:23:35 2003	ARGS	gusconfigfile	/home/gus/.gus.properties
> > 135   Thu Jul  3 12:23:35 2003	ARGS	project	
> > 136   Thu Jul  3 12:23:35 2003	ARGS	refresh	
> > 137   Thu Jul  3 12:23:35 2003	ARGS	tablename	SRes.ExternalDatabase
> > 138   Thu Jul  3 12:23:35 2003	ARGS	usage	
> > 139   Thu Jul  3 12:23:35 2003	ARGS	user	
> > 140   Thu Jul  3 12:23:35 2003	ARGS	valuelist	'GO Function','go function',SYSDATE,1,1,1,1,1,0
> > 141   Thu Jul  3 12:23:35 2003	ARGS	verbose	1
> > 142   Thu Jul  3 12:23:35 2003	ARGS	veryVerbose	
> > 143   Thu Jul  3 12:23:35 2003	COMMIT	commit off
> > 144   Warning: Use of "require" without parens is ambiguous at (eval 12) line 1.
> > 145   
> > 146   
> > 147   sqlExec: 
> > 148       UPDATE  Core.AlgorithmInvocation
> > 149       SET     
> > 150   	modification_date = SYSDATE,
> > 151   	end_time = SYSDATE,
> > 152   	row_alg_invocation_id = ?
> > 153       WHERE   algorithm_invocation_id = ?
> > 154     bindValues (6, 6)
> > 155    DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 156   Can't locate object method "new" via package "GUS::Model::SRes.ExternalDatabase" (perhaps you forgot to load "GUS::Model::SRes.ExternalDatabase"?) at /home/gus/run/lib/perl/GUS/Common/Plugin/UpdateGusFromCla.pm line 104.
> > 
> > 
> > 
> > 
> > On  0, Dave Barkan <db...@pc...> wrote:
> > > Hey Terry,
> > > 
> > > Well we just had a conference call where one of the issues that came up 
> > > was the fact that we need to give users of plugins a better idea of what 
> > > needs to be in place before actually running the plugin.  I think this 
> > > qualifies as an example.
> > > 
> > > The problem here is that there needs to be three entries in the 
> > > SRes.ExternalDatabase table representing the three branches of the GO 
> > > Ontology.  The values in the 'name' column of that table should be set to 
> > > 'GO Function', 'GO Component', and 'GO Process' for the respective 
> > > branches (this could really be done better).  We have been inserting these 
> > > entries manually; after you do it once (using updateGusFromXML or 
> > > updateGusFromCla) you don't have to worry about it again when loading 
> > > later releases of the GO Ontology.
> > > 
> > > Additionally, there needs to be an entry in the 
> > > SRes.ExternalDatabaseRelease table representing the current release of 
> > > each branch.  You can enter this manually or create it automatically by 
> > > setting the '--create_release' flag of the plugin.
> > > 
> > > Let me know if there are further issues.  I would suggest running without 
> > > setting --commit initially to make sure everything works and you don't 
> > > insert faulty data.
> > > 
> > > Dave 
> > > 
> > > On Thu, 3 Jul 2003, Terry Clark wrote:
> > > 
> > > > Hi Dave, it went okay for a bit, then I encountered
> > > > what looks to be missing data in an SRES table,
> > > > which is empty but being probed for GO db information.
> > > > I can't find a Plugin to populate this table.
> > > > Here are the details:
> > > > 
> > > > I executed:
> > > > 
> > > > > ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> > > > 
> > > > had a number of successful database reads and inserts (algorithm tables -- the full
> > > > output is attached), but at the end of the output had the following where in line 1,
> > > > the external_database_id (GO id?)  is not available.
> > > >   
> > > > 
> > > > 1 prepareAndExecute: select external_database_release_id
> > > > 2               from sres.externalDatabaseRelease
> > > > 3                where version = '2.371' and external_database_id =
> > > > 4 DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id
> > > > 5               from sres.externalDatabaseRelease
> > > > 6                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > 7 prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> > > > 8
> > > > 9
> > > > 10  sqlExec:
> > > > 11     UPDATE  Core.AlgorithmInvocation
> > > > 12     SET
> > > > 13        modification_date = SYSDATE,
> > > > 14        end_time = SYSDATE,
> > > > 15        row_alg_invocation_id = ?
> > > > 16     WHERE   algorithm_invocation_id = ?
> > > > 17   bindValues (4, 4)
> > > > 18  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 19 Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > 
> > > > 
> > > > The corresponding table is empty
> > > > 
> > > >  SQL> select * from sres.externalDatabaseRelease;
> > > >  no rows selected
> > > > 
> > > > and the empty table consists of 
> > > > 
> > > > SQL> describe sres.externalDatabaseRelease;
> > > >  Name                                                  Null?    Type
> > > >  ----------------------------------------------------- -------- ------------------------------------
> > > >  EXTERNAL_DATABASE_RELEASE_ID                          NOT NULL NUMBER(10)
> > > >  EXTERNAL_DATABASE_ID                                  NOT NULL NUMBER(10)
> > > >  RELEASE_DATE                                                   DATE
> > > >  VERSION                                               NOT NULL VARCHAR2(255)
> > > >  DOWNLOAD_URL                                                   VARCHAR2(255)
> > > >  ID_TYPE                                                        VARCHAR2(255)
> > > >  ID_URL                                                         VARCHAR2(255)
> > > >  SECONDARY_ID_TYPE                                              VARCHAR2(255)
> > > >  SECONDARY_ID_URL                                               VARCHAR2(255)
> > > >  DESCRIPTION                                                    VARCHAR2(4000)
> > > >  FILE_NAME                                                      VARCHAR2(255)
> > > >  FILE_MD5                                                       VARCHAR2(32)
> > > >  BLAST_FILE                                                     VARCHAR2(255)
> > > >  BLAST_FILE_MD5                                                 VARCHAR2(32)
> > > >  MODIFICATION_DATE                                     NOT NULL DATE
> > > >  USER_READ                                             NOT NULL NUMBER(1)
> > > >  USER_WRITE                                            NOT NULL NUMBER(1)
> > > >  GROUP_READ                                            NOT NULL NUMBER(1)
> > > >  GROUP_WRITE                                           NOT NULL NUMBER(1)
> > > >  OTHER_READ                                            NOT NULL NUMBER(1)
> > > >  OTHER_WRITE                                           NOT NULL NUMBER(1)
> > > >  ROW_USER_ID                                           NOT NULL NUMBER(12)
> > > >  ROW_GROUP_ID                                          NOT NULL NUMBER(3)
> > > >  ROW_PROJECT_ID                                        NOT NULL NUMBER(3)
> > > >  ROW_ALG_INVOCATION_ID                                 NOT NULL NUMBER(12)
> > > > 
> > > > SQL> 
> > > > 
> > > >  
> > > > Any ideas?
> > > > 
> > > > 
> > > > Terry
> > > > 
> > > > 
> > > > p.s. Full output is appended.
> > > > 
> > > > 
> > > > On  0, Dave Barkan <db...@pc...> wrote:
> > > > > Hey Terry,
> > > > > 
> > > > > That is the correct plugin.  The files can be found at 
> > > > > 
> > > > > ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
> > > > > 'function.ontology', 'process.ontology', and 'component.ontology' 
> > > > > (corresponding to the three branches of the GO Hierarchy).  Note that 
> > > > > these are not the alternate XML files that the GO people also have 
> > > > > available.
> > > > > 
> > > > > Let me know if you have any complications with the loading process.
> > > > > 
> > > > > On Thu, 3 Jul 2003, Terry Clark wrote:
> > > > > 
> > > > > > Hi, All -
> > > > > > 
> > > > > > I am in the process of loading the GO Ontology into 
> > > > > > GUS to have the necessary GO data for loading the
> > > > > > TIGR Arabidopsis genome into GUS.  Can someone advise
> > > > > > me what GO files I should use?
> > > > > > 
> > > > > > I plan to use the Plugin
> > > > > >   GUS::GOPredict::Plugin::LoadGoOntology
> > > > > > 
> > > > > > 
> > > > > > Thanks in advance for any help,
> > > > > > 
> > > > > > Terry
> > > > > > 
> > > > > > 
> > > > > > 
> > > > > > -------------------------------------------------------
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> > > > > > _______________________________________________
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> > > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > -------------------------------------------------------
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> > > > 
> > > > 
> > > > **************************************************************************************
> > > > 
> > > > THE COMPLETE OUTPUT
> > > > 
> > > >   ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> > > > 
> > > > 
> > > > Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
> > > > Reading properties from /home/gus/.gus.properties
> > > > 
> > > > 
> > > > prepareAndExecute:     SELECT *
> > > >       FROM Core.AlgorithmImplementation
> > > >      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
> > > >        AND cvs_revision    = '1.8'
> > > > 
> > > >  
> > > > 
> > > > 
> > > > prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
> > > > 
> > > > RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
> > > >   bindValues (19)
> > > > 
> > > > 
> > > > prepareAndExecute: select login,user_id from Core.UserInfo 
> > > > 
> > > > 
> > > > prepareAndExecute: select name,group_id from Core.GroupInfo 
> > > > 
> > > > 
> > > > prepareAndExecute: select name,project_id from Core.ProjectInfo 
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
> > > >     VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
> > > >   bindValues (1, 1, 19, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 4, pending)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
> > > >   bindValues (19)
> > > > 
> > > > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > > >   bindValues (2)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (224, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 15, 1, 4, 1, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > > >   bindValues (0)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > > >   bindValues (1, 1, 0, 235, 1, 16, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > > >   bindValues (4)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (232, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 17, 1, 4, 1, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (226, 1, 1, 0, 0, 1, 1, 0, 1, 1, 18, 1, 4, 1, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (1, 1, 0, 236, 1, 19, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/go, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > > >   bindValues (1, 1, 0, 225, 1, 20, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (230, 1, 1, 0, 0, 1, 1, 0, 1, 1, 21, 1, 4, 1, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > > >   bindValues (1, 1, 0, 228, 1, 22, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (1, 1, 0, 229, 1, 23, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/.gus.properties, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (1, 1, 0, 227, 1, 24, 1, 1, 0, 0, 4, 1, 1, 4, go01, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (234, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 25, 1, 4, 1, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > > >   bindValues (233, 1, 1, 0, 0, 1, 1, 0, 1, 1, 26, 1, 4, 1, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > > >   bindValues (1, 1, 0, 237, 1, 27, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > > >   bindValues (1, 1, 0, 231, 1, 28, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > 
> > > > parsing finished; loading ontology into database
> > > > executingselect external_database_release_id 
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.371' and external_database_id = 
> > > > 
> > > > 
> > > > prepareAndExecute: select external_database_release_id 
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.371' and external_database_id =  
> > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id 
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> > > > 
> > > > 
> > > > sqlExec: 
> > > >     UPDATE  Core.AlgorithmInvocation
> > > >     SET     
> > > > 	modification_date = SYSDATE,
> > > > 	end_time = SYSDATE,
> > > > 	row_alg_invocation_id = ?
> > > >     WHERE   algorithm_invocation_id = ?
> > > >   bindValues (4, 4)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > 
> > > > 
> > > > 
> > > > 
> > > 
> > > 
> > > 
> > > -------------------------------------------------------
> > > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
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> > > Download today and enter to win an XBOX or Visual Studio .NET.
> > > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > 
> 
> 
> 
> -------------------------------------------------------
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Re: [Gusdev-gusdev] initial GO Files

[Steve F. <sfi...@pc...>]

Terry-

instead of using UpdateGusFromCla, try the plugin: SubmitRow.  it does 
the same thing, but may be easier to use.

steve

Dave Barkan wrote:

>Hey Terry,
>
>I'm not completely familiar with UpdateGusFromCla, but here are a couple 
>suggestions:
>
>Specify the table name in SchemaName::TableName format; in this case you 
>would use "SRes::ExternalDatabase" (from what I can tell in the code, it 
>uses the '::' as the delimiter to split on.)
>
>Also, when running this plugin you don't need to specify any of the 
>overhead columns (eg., user_read, modification_date, etc.).  Simply 
>specifiying 'name', 'lowercase_name' should do the trick (for this table, 
>at least), and the rest of the columns common to all tables will be filled 
>in automatically, in addition to the primary key (external_database_id).
>
>I'm not aware of any example XML files for the plugin 'UpdateGusFromXML.'  
>Perhaps someone else can help with this?
>
>Good luck,
>Dave
>
>
>On Thu, 3 Jul 2003, Terry Clark wrote:
>
>  
>
>>Hi Dave,
>>I had some problems. There is a warning and an error, both puzzling me.
>>The output is below:
>>   command  on line 2
>>   warning on line 144
>>   error looking comment on line 156  
>>
>>I am stumped. Can you help?
>>
>>By the way, are there example XML files for using with
>>UpdateGusFromXML.pm available?
>>
>>
>>Terry
>>
>>
>>
>>
>>1   
>>2   ga +run GUS::Common::Plugin::UpdateGusFromCla --attrlist="NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE" --valuelist="'GO Function','go function',SYSDATE,1,1,1,1,1,0" --tablename=SRes.ExternalDatabase
>>3   
>>4   
>>5   
>>6   Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
>>7   Reading properties from /home/gus/.gus.properties
>>8   
>>9   
>>10   prepareAndExecute:     SELECT *
>>11         FROM Core.AlgorithmImplementation
>>12        WHERE executable = 'GUS::Common::Plugin::UpdateGusFromCla'
>>13          AND cvs_revision    = '1.2'
>>14   
>>15    
>>16   
>>17   
>>18   prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
>>19   
>>20   RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
>>21     bindValues (17)
>>22   
>>23   
>>24   prepareAndExecute: select login,user_id from Core.UserInfo 
>>25   
>>26   
>>27   prepareAndExecute: select name,group_id from Core.GroupInfo 
>>28   
>>29   
>>30   prepareAndExecute: select name,project_id from Core.ProjectInfo 
>>31   
>>32   
>>33   sqlExec: 
>>34       INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
>>35       VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
>>36     bindValues (1, 1, 17, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 6, pending)
>>37    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>38   
>>39   getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
>>40     bindValues (17)
>>41   
>>42   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>>43     bindValues (2)
>>44   
>>45   
>>46   sqlExec: 
>>47       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>48       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>49     bindValues (206, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 40, 1, 6, 1, 6)
>>50    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>51   
>>52   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>>53     bindValues (0)
>>54   
>>55   
>>56   sqlExec: 
>>57       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>58       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>59     bindValues (1, 1, 0, 207, 1, 41, 1, 1, 0, 0, 6, 1, 1, 6, NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE, 1)
>>60    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>61   
>>62   
>>63   sqlExec: 
>>64       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>65       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>66     bindValues (1, 1, 0, 203, 1, 42, 1, 1, 0, 0, 6, 1, 1, 6, 1)
>>67    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>68   
>>69   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>>70     bindValues (4)
>>71   
>>72   
>>73   sqlExec: 
>>74       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>75       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>76     bindValues (210, 1, 1, 0, 0, 1, 1, 0, 1, 1, 43, 1, 6, 1, 6)
>>77    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>78   
>>79   
>>80   sqlExec: 
>>81       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>82       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>83     bindValues (1, 1, 0, 211, 1, 44, 1, 1, 0, 0, 6, 1, 1, 6, 1)
>>84    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>85   
>>86   
>>87   sqlExec: 
>>88       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>89       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>90     bindValues (1, 1, 0, 201, 1, 45, 1, 1, 0, 0, 6, 1, 1, 6, /home/gus/.gus.properties, 1)
>>91    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>92   
>>93   
>>94   sqlExec: 
>>95       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>96       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>97     bindValues (1, 1, 0, 208, 1, 46, 1, 1, 0, 0, 6, 1, 1, 6, 1)
>>98    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>99   
>>100   
>>101   sqlExec: 
>>102       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>103       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>104     bindValues (205, 1, 1, 0, 0, 1, 1, 0, 1, 1, 47, 1, 6, 1, 6)
>>105    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>106   
>>107   
>>108   sqlExec: 
>>109       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>110       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>111     bindValues (1, 1, 0, 209, 1, 48, 1, 1, 0, 0, 6, 1, 1, 6, SRes.ExternalDatabase, 1)
>>112    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>113   
>>114   
>>115   sqlExec: 
>>116       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>117       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>118     bindValues (1, 1, 0, 202, 1, 49, 1, 1, 0, 0, 6, 1, 1, 6, 1)
>>119    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>120   
>>121   
>>122   sqlExec: 
>>123       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>124       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>125     bindValues (1, 1, 0, 204, 1, 50, 1, 1, 0, 0, 6, 1, 1, 6, 'GO Function','go function',SYSDATE,1,1,1,1,1,0, 1)
>>126    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>127   Thu Jul  3 12:23:35 2003	ALGINVID	6
>>128   Thu Jul  3 12:23:35 2003	ARGS	algoinvo	1
>>129   Thu Jul  3 12:23:35 2003	ARGS	attrlist	NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE
>>130   Thu Jul  3 12:23:35 2003	ARGS	comment	
>>131   Thu Jul  3 12:23:35 2003	ARGS	commit	
>>132   Thu Jul  3 12:23:35 2003	ARGS	debug	
>>133   Thu Jul  3 12:23:35 2003	ARGS	group	
>>134   Thu Jul  3 12:23:35 2003	ARGS	gusconfigfile	/home/gus/.gus.properties
>>135   Thu Jul  3 12:23:35 2003	ARGS	project	
>>136   Thu Jul  3 12:23:35 2003	ARGS	refresh	
>>137   Thu Jul  3 12:23:35 2003	ARGS	tablename	SRes.ExternalDatabase
>>138   Thu Jul  3 12:23:35 2003	ARGS	usage	
>>139   Thu Jul  3 12:23:35 2003	ARGS	user	
>>140   Thu Jul  3 12:23:35 2003	ARGS	valuelist	'GO Function','go function',SYSDATE,1,1,1,1,1,0
>>141   Thu Jul  3 12:23:35 2003	ARGS	verbose	1
>>142   Thu Jul  3 12:23:35 2003	ARGS	veryVerbose	
>>143   Thu Jul  3 12:23:35 2003	COMMIT	commit off
>>144   Warning: Use of "require" without parens is ambiguous at (eval 12) line 1.
>>145   
>>146   
>>147   sqlExec: 
>>148       UPDATE  Core.AlgorithmInvocation
>>149       SET     
>>150   	modification_date = SYSDATE,
>>151   	end_time = SYSDATE,
>>152   	row_alg_invocation_id = ?
>>153       WHERE   algorithm_invocation_id = ?
>>154     bindValues (6, 6)
>>155    DbiHandle:sqlExec:insert succeeded 1 row(s)
>>156   Can't locate object method "new" via package "GUS::Model::SRes.ExternalDatabase" (perhaps you forgot to load "GUS::Model::SRes.ExternalDatabase"?) at /home/gus/run/lib/perl/GUS/Common/Plugin/UpdateGusFromCla.pm line 104.
>>
>>
>>
>>
>>On  0, Dave Barkan <db...@pc...> wrote:
>>    
>>
>>>Hey Terry,
>>>
>>>Well we just had a conference call where one of the issues that came up 
>>>was the fact that we need to give users of plugins a better idea of what 
>>>needs to be in place before actually running the plugin.  I think this 
>>>qualifies as an example.
>>>
>>>The problem here is that there needs to be three entries in the 
>>>SRes.ExternalDatabase table representing the three branches of the GO 
>>>Ontology.  The values in the 'name' column of that table should be set to 
>>>'GO Function', 'GO Component', and 'GO Process' for the respective 
>>>branches (this could really be done better).  We have been inserting these 
>>>entries manually; after you do it once (using updateGusFromXML or 
>>>updateGusFromCla) you don't have to worry about it again when loading 
>>>later releases of the GO Ontology.
>>>
>>>Additionally, there needs to be an entry in the 
>>>SRes.ExternalDatabaseRelease table representing the current release of 
>>>each branch.  You can enter this manually or create it automatically by 
>>>setting the '--create_release' flag of the plugin.
>>>
>>>Let me know if there are further issues.  I would suggest running without 
>>>setting --commit initially to make sure everything works and you don't 
>>>insert faulty data.
>>>
>>>Dave 
>>>
>>>On Thu, 3 Jul 2003, Terry Clark wrote:
>>>
>>>      
>>>
>>>>Hi Dave, it went okay for a bit, then I encountered
>>>>what looks to be missing data in an SRES table,
>>>>which is empty but being probed for GO db information.
>>>>I can't find a Plugin to populate this table.
>>>>Here are the details:
>>>>
>>>>I executed:
>>>>
>>>>        
>>>>
>>>>>ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
>>>>>          
>>>>>
>>>>had a number of successful database reads and inserts (algorithm tables -- the full
>>>>output is attached), but at the end of the output had the following where in line 1,
>>>>the external_database_id (GO id?)  is not available.
>>>>  
>>>>
>>>>1 prepareAndExecute: select external_database_release_id
>>>>2               from sres.externalDatabaseRelease
>>>>3                where version = '2.371' and external_database_id =
>>>>4 DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id
>>>>5               from sres.externalDatabaseRelease
>>>>6                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
>>>>7 prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
>>>>8
>>>>9
>>>>10  sqlExec:
>>>>11     UPDATE  Core.AlgorithmInvocation
>>>>12     SET
>>>>13        modification_date = SYSDATE,
>>>>14        end_time = SYSDATE,
>>>>15        row_alg_invocation_id = ?
>>>>16     WHERE   algorithm_invocation_id = ?
>>>>17   bindValues (4, 4)
>>>>18  DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>19 Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
>>>>
>>>>
>>>>The corresponding table is empty
>>>>
>>>> SQL> select * from sres.externalDatabaseRelease;
>>>> no rows selected
>>>>
>>>>and the empty table consists of 
>>>>
>>>>SQL> describe sres.externalDatabaseRelease;
>>>> Name                                                  Null?    Type
>>>> ----------------------------------------------------- -------- ------------------------------------
>>>> EXTERNAL_DATABASE_RELEASE_ID                          NOT NULL NUMBER(10)
>>>> EXTERNAL_DATABASE_ID                                  NOT NULL NUMBER(10)
>>>> RELEASE_DATE                                                   DATE
>>>> VERSION                                               NOT NULL VARCHAR2(255)
>>>> DOWNLOAD_URL                                                   VARCHAR2(255)
>>>> ID_TYPE                                                        VARCHAR2(255)
>>>> ID_URL                                                         VARCHAR2(255)
>>>> SECONDARY_ID_TYPE                                              VARCHAR2(255)
>>>> SECONDARY_ID_URL                                               VARCHAR2(255)
>>>> DESCRIPTION                                                    VARCHAR2(4000)
>>>> FILE_NAME                                                      VARCHAR2(255)
>>>> FILE_MD5                                                       VARCHAR2(32)
>>>> BLAST_FILE                                                     VARCHAR2(255)
>>>> BLAST_FILE_MD5                                                 VARCHAR2(32)
>>>> MODIFICATION_DATE                                     NOT NULL DATE
>>>> USER_READ                                             NOT NULL NUMBER(1)
>>>> USER_WRITE                                            NOT NULL NUMBER(1)
>>>> GROUP_READ                                            NOT NULL NUMBER(1)
>>>> GROUP_WRITE                                           NOT NULL NUMBER(1)
>>>> OTHER_READ                                            NOT NULL NUMBER(1)
>>>> OTHER_WRITE                                           NOT NULL NUMBER(1)
>>>> ROW_USER_ID                                           NOT NULL NUMBER(12)
>>>> ROW_GROUP_ID                                          NOT NULL NUMBER(3)
>>>> ROW_PROJECT_ID                                        NOT NULL NUMBER(3)
>>>> ROW_ALG_INVOCATION_ID                                 NOT NULL NUMBER(12)
>>>>
>>>>SQL> 
>>>>
>>>> 
>>>>Any ideas?
>>>>
>>>>
>>>>Terry
>>>>
>>>>
>>>>p.s. Full output is appended.
>>>>
>>>>
>>>>On  0, Dave Barkan <db...@pc...> wrote:
>>>>        
>>>>
>>>>>Hey Terry,
>>>>>
>>>>>That is the correct plugin.  The files can be found at 
>>>>>
>>>>>ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
>>>>>'function.ontology', 'process.ontology', and 'component.ontology' 
>>>>>(corresponding to the three branches of the GO Hierarchy).  Note that 
>>>>>these are not the alternate XML files that the GO people also have 
>>>>>available.
>>>>>
>>>>>Let me know if you have any complications with the loading process.
>>>>>
>>>>>On Thu, 3 Jul 2003, Terry Clark wrote:
>>>>>
>>>>>          
>>>>>
>>>>>>Hi, All -
>>>>>>
>>>>>>I am in the process of loading the GO Ontology into 
>>>>>>GUS to have the necessary GO data for loading the
>>>>>>TIGR Arabidopsis genome into GUS.  Can someone advise
>>>>>>me what GO files I should use?
>>>>>>
>>>>>>I plan to use the Plugin
>>>>>>  GUS::GOPredict::Plugin::LoadGoOntology
>>>>>>
>>>>>>
>>>>>>Thanks in advance for any help,
>>>>>>
>>>>>>Terry
>>>>>>
>>>>>>
>>>>>>
>>>>>>-------------------------------------------------------
>>>>>>This SF.Net email sponsored by: Free pre-built ASP.NET sites including
>>>>>>Data Reports, E-commerce, Portals, and Forums are available now.
>>>>>>Download today and enter to win an XBOX or Visual Studio .NET.
>>>>>>http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
>>>>>>_______________________________________________
>>>>>>Gusdev-gusdev mailing list
>>>>>>Gus...@li...
>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>            
>>>>>>
>>>>>
>>>>>-------------------------------------------------------
>>>>>This SF.Net email sponsored by: Free pre-built ASP.NET sites including
>>>>>Data Reports, E-commerce, Portals, and Forums are available now.
>>>>>Download today and enter to win an XBOX or Visual Studio .NET.
>>>>>http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>          
>>>>>
>>>>**************************************************************************************
>>>>
>>>>THE COMPLETE OUTPUT
>>>>
>>>>  ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
>>>>
>>>>
>>>>Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
>>>>Reading properties from /home/gus/.gus.properties
>>>>
>>>>
>>>>prepareAndExecute:     SELECT *
>>>>      FROM Core.AlgorithmImplementation
>>>>     WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
>>>>       AND cvs_revision    = '1.8'
>>>>
>>>> 
>>>>
>>>>
>>>>prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
>>>>
>>>>RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
>>>>  bindValues (19)
>>>>
>>>>
>>>>prepareAndExecute: select login,user_id from Core.UserInfo 
>>>>
>>>>
>>>>prepareAndExecute: select name,group_id from Core.GroupInfo 
>>>>
>>>>
>>>>prepareAndExecute: select name,project_id from Core.ProjectInfo 
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
>>>>    VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
>>>>  bindValues (1, 1, 19, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 4, pending)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
>>>>  bindValues (19)
>>>>
>>>>getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>>>>  bindValues (2)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>>>    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (224, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 15, 1, 4, 1, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>>>>  bindValues (0)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>>>  bindValues (1, 1, 0, 235, 1, 16, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>>>>  bindValues (4)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>>>    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (232, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 17, 1, 4, 1, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>>>    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (226, 1, 1, 0, 0, 1, 1, 0, 1, 1, 18, 1, 4, 1, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (1, 1, 0, 236, 1, 19, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/go, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>>>  bindValues (1, 1, 0, 225, 1, 20, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>>>    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (230, 1, 1, 0, 0, 1, 1, 0, 1, 1, 21, 1, 4, 1, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>>>  bindValues (1, 1, 0, 228, 1, 22, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (1, 1, 0, 229, 1, 23, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/.gus.properties, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (1, 1, 0, 227, 1, 24, 1, 1, 0, 0, 4, 1, 1, 4, go01, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>>>    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (234, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 25, 1, 4, 1, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>>>>    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>>>>  bindValues (233, 1, 1, 0, 0, 1, 1, 0, 1, 1, 26, 1, 4, 1, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>>>  bindValues (1, 1, 0, 237, 1, 27, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>
>>>>sqlExec: 
>>>>    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>>>>  bindValues (1, 1, 0, 231, 1, 28, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>
>>>>parsing finished; loading ontology into database
>>>>executingselect external_database_release_id 
>>>>               from sres.externalDatabaseRelease
>>>>               where version = '2.371' and external_database_id = 
>>>>
>>>>
>>>>prepareAndExecute: select external_database_release_id 
>>>>               from sres.externalDatabaseRelease
>>>>               where version = '2.371' and external_database_id =  
>>>>DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id 
>>>>               from sres.externalDatabaseRelease
>>>>               where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
>>>>prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
>>>>
>>>>
>>>>sqlExec: 
>>>>    UPDATE  Core.AlgorithmInvocation
>>>>    SET     
>>>>	modification_date = SYSDATE,
>>>>	end_time = SYSDATE,
>>>>	row_alg_invocation_id = ?
>>>>    WHERE   algorithm_invocation_id = ?
>>>>  bindValues (4, 4)
>>>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>>Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>
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>

Re: [Gusdev-gusdev] initial GO Files

[Dave B. <db...@pc...>]

Hey Terry,

I'm not completely familiar with UpdateGusFromCla, but here are a couple 
suggestions:

Specify the table name in SchemaName::TableName format; in this case you 
would use "SRes::ExternalDatabase" (from what I can tell in the code, it 
uses the '::' as the delimiter to split on.)

Also, when running this plugin you don't need to specify any of the 
overhead columns (eg., user_read, modification_date, etc.).  Simply 
specifiying 'name', 'lowercase_name' should do the trick (for this table, 
at least), and the rest of the columns common to all tables will be filled 
in automatically, in addition to the primary key (external_database_id).

I'm not aware of any example XML files for the plugin 'UpdateGusFromXML.'  
Perhaps someone else can help with this?

Good luck,
Dave


On Thu, 3 Jul 2003, Terry Clark wrote:

> Hi Dave,
> I had some problems. There is a warning and an error, both puzzling me.
> The output is below:
>    command  on line 2
>    warning on line 144
>    error looking comment on line 156  
> 
> I am stumped. Can you help?
> 
> By the way, are there example XML files for using with
> UpdateGusFromXML.pm available?
> 
> 
> Terry
> 
> 
> 
> 
> 1   
> 2   ga +run GUS::Common::Plugin::UpdateGusFromCla --attrlist="NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE" --valuelist="'GO Function','go function',SYSDATE,1,1,1,1,1,0" --tablename=SRes.ExternalDatabase
> 3   
> 4   
> 5   
> 6   Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
> 7   Reading properties from /home/gus/.gus.properties
> 8   
> 9   
> 10   prepareAndExecute:     SELECT *
> 11         FROM Core.AlgorithmImplementation
> 12        WHERE executable = 'GUS::Common::Plugin::UpdateGusFromCla'
> 13          AND cvs_revision    = '1.2'
> 14   
> 15    
> 16   
> 17   
> 18   prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
> 19   
> 20   RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
> 21     bindValues (17)
> 22   
> 23   
> 24   prepareAndExecute: select login,user_id from Core.UserInfo 
> 25   
> 26   
> 27   prepareAndExecute: select name,group_id from Core.GroupInfo 
> 28   
> 29   
> 30   prepareAndExecute: select name,project_id from Core.ProjectInfo 
> 31   
> 32   
> 33   sqlExec: 
> 34       INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
> 35       VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
> 36     bindValues (1, 1, 17, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 6, pending)
> 37    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 38   
> 39   getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
> 40     bindValues (17)
> 41   
> 42   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> 43     bindValues (2)
> 44   
> 45   
> 46   sqlExec: 
> 47       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> 48       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> 49     bindValues (206, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 40, 1, 6, 1, 6)
> 50    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 51   
> 52   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> 53     bindValues (0)
> 54   
> 55   
> 56   sqlExec: 
> 57       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 58       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> 59     bindValues (1, 1, 0, 207, 1, 41, 1, 1, 0, 0, 6, 1, 1, 6, NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE, 1)
> 60    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 61   
> 62   
> 63   sqlExec: 
> 64       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 65       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> 66     bindValues (1, 1, 0, 203, 1, 42, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> 67    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 68   
> 69   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> 70     bindValues (4)
> 71   
> 72   
> 73   sqlExec: 
> 74       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> 75       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> 76     bindValues (210, 1, 1, 0, 0, 1, 1, 0, 1, 1, 43, 1, 6, 1, 6)
> 77    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 78   
> 79   
> 80   sqlExec: 
> 81       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 82       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> 83     bindValues (1, 1, 0, 211, 1, 44, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> 84    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 85   
> 86   
> 87   sqlExec: 
> 88       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 89       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> 90     bindValues (1, 1, 0, 201, 1, 45, 1, 1, 0, 0, 6, 1, 1, 6, /home/gus/.gus.properties, 1)
> 91    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 92   
> 93   
> 94   sqlExec: 
> 95       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 96       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> 97     bindValues (1, 1, 0, 208, 1, 46, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> 98    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 99   
> 100   
> 101   sqlExec: 
> 102       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> 103       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> 104     bindValues (205, 1, 1, 0, 0, 1, 1, 0, 1, 1, 47, 1, 6, 1, 6)
> 105    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 106   
> 107   
> 108   sqlExec: 
> 109       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 110       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> 111     bindValues (1, 1, 0, 209, 1, 48, 1, 1, 0, 0, 6, 1, 1, 6, SRes.ExternalDatabase, 1)
> 112    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 113   
> 114   
> 115   sqlExec: 
> 116       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 117       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> 118     bindValues (1, 1, 0, 202, 1, 49, 1, 1, 0, 0, 6, 1, 1, 6, 1)
> 119    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 120   
> 121   
> 122   sqlExec: 
> 123       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> 124       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> 125     bindValues (1, 1, 0, 204, 1, 50, 1, 1, 0, 0, 6, 1, 1, 6, 'GO Function','go function',SYSDATE,1,1,1,1,1,0, 1)
> 126    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 127   Thu Jul  3 12:23:35 2003	ALGINVID	6
> 128   Thu Jul  3 12:23:35 2003	ARGS	algoinvo	1
> 129   Thu Jul  3 12:23:35 2003	ARGS	attrlist	NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE
> 130   Thu Jul  3 12:23:35 2003	ARGS	comment	
> 131   Thu Jul  3 12:23:35 2003	ARGS	commit	
> 132   Thu Jul  3 12:23:35 2003	ARGS	debug	
> 133   Thu Jul  3 12:23:35 2003	ARGS	group	
> 134   Thu Jul  3 12:23:35 2003	ARGS	gusconfigfile	/home/gus/.gus.properties
> 135   Thu Jul  3 12:23:35 2003	ARGS	project	
> 136   Thu Jul  3 12:23:35 2003	ARGS	refresh	
> 137   Thu Jul  3 12:23:35 2003	ARGS	tablename	SRes.ExternalDatabase
> 138   Thu Jul  3 12:23:35 2003	ARGS	usage	
> 139   Thu Jul  3 12:23:35 2003	ARGS	user	
> 140   Thu Jul  3 12:23:35 2003	ARGS	valuelist	'GO Function','go function',SYSDATE,1,1,1,1,1,0
> 141   Thu Jul  3 12:23:35 2003	ARGS	verbose	1
> 142   Thu Jul  3 12:23:35 2003	ARGS	veryVerbose	
> 143   Thu Jul  3 12:23:35 2003	COMMIT	commit off
> 144   Warning: Use of "require" without parens is ambiguous at (eval 12) line 1.
> 145   
> 146   
> 147   sqlExec: 
> 148       UPDATE  Core.AlgorithmInvocation
> 149       SET     
> 150   	modification_date = SYSDATE,
> 151   	end_time = SYSDATE,
> 152   	row_alg_invocation_id = ?
> 153       WHERE   algorithm_invocation_id = ?
> 154     bindValues (6, 6)
> 155    DbiHandle:sqlExec:insert succeeded 1 row(s)
> 156   Can't locate object method "new" via package "GUS::Model::SRes.ExternalDatabase" (perhaps you forgot to load "GUS::Model::SRes.ExternalDatabase"?) at /home/gus/run/lib/perl/GUS/Common/Plugin/UpdateGusFromCla.pm line 104.
> 
> 
> 
> 
> On  0, Dave Barkan <db...@pc...> wrote:
> > Hey Terry,
> > 
> > Well we just had a conference call where one of the issues that came up 
> > was the fact that we need to give users of plugins a better idea of what 
> > needs to be in place before actually running the plugin.  I think this 
> > qualifies as an example.
> > 
> > The problem here is that there needs to be three entries in the 
> > SRes.ExternalDatabase table representing the three branches of the GO 
> > Ontology.  The values in the 'name' column of that table should be set to 
> > 'GO Function', 'GO Component', and 'GO Process' for the respective 
> > branches (this could really be done better).  We have been inserting these 
> > entries manually; after you do it once (using updateGusFromXML or 
> > updateGusFromCla) you don't have to worry about it again when loading 
> > later releases of the GO Ontology.
> > 
> > Additionally, there needs to be an entry in the 
> > SRes.ExternalDatabaseRelease table representing the current release of 
> > each branch.  You can enter this manually or create it automatically by 
> > setting the '--create_release' flag of the plugin.
> > 
> > Let me know if there are further issues.  I would suggest running without 
> > setting --commit initially to make sure everything works and you don't 
> > insert faulty data.
> > 
> > Dave 
> > 
> > On Thu, 3 Jul 2003, Terry Clark wrote:
> > 
> > > Hi Dave, it went okay for a bit, then I encountered
> > > what looks to be missing data in an SRES table,
> > > which is empty but being probed for GO db information.
> > > I can't find a Plugin to populate this table.
> > > Here are the details:
> > > 
> > > I executed:
> > > 
> > > > ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> > > 
> > > had a number of successful database reads and inserts (algorithm tables -- the full
> > > output is attached), but at the end of the output had the following where in line 1,
> > > the external_database_id (GO id?)  is not available.
> > >   
> > > 
> > > 1 prepareAndExecute: select external_database_release_id
> > > 2               from sres.externalDatabaseRelease
> > > 3                where version = '2.371' and external_database_id =
> > > 4 DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id
> > > 5               from sres.externalDatabaseRelease
> > > 6                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > 7 prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> > > 8
> > > 9
> > > 10  sqlExec:
> > > 11     UPDATE  Core.AlgorithmInvocation
> > > 12     SET
> > > 13        modification_date = SYSDATE,
> > > 14        end_time = SYSDATE,
> > > 15        row_alg_invocation_id = ?
> > > 16     WHERE   algorithm_invocation_id = ?
> > > 17   bindValues (4, 4)
> > > 18  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 19 Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > 
> > > 
> > > The corresponding table is empty
> > > 
> > >  SQL> select * from sres.externalDatabaseRelease;
> > >  no rows selected
> > > 
> > > and the empty table consists of 
> > > 
> > > SQL> describe sres.externalDatabaseRelease;
> > >  Name                                                  Null?    Type
> > >  ----------------------------------------------------- -------- ------------------------------------
> > >  EXTERNAL_DATABASE_RELEASE_ID                          NOT NULL NUMBER(10)
> > >  EXTERNAL_DATABASE_ID                                  NOT NULL NUMBER(10)
> > >  RELEASE_DATE                                                   DATE
> > >  VERSION                                               NOT NULL VARCHAR2(255)
> > >  DOWNLOAD_URL                                                   VARCHAR2(255)
> > >  ID_TYPE                                                        VARCHAR2(255)
> > >  ID_URL                                                         VARCHAR2(255)
> > >  SECONDARY_ID_TYPE                                              VARCHAR2(255)
> > >  SECONDARY_ID_URL                                               VARCHAR2(255)
> > >  DESCRIPTION                                                    VARCHAR2(4000)
> > >  FILE_NAME                                                      VARCHAR2(255)
> > >  FILE_MD5                                                       VARCHAR2(32)
> > >  BLAST_FILE                                                     VARCHAR2(255)
> > >  BLAST_FILE_MD5                                                 VARCHAR2(32)
> > >  MODIFICATION_DATE                                     NOT NULL DATE
> > >  USER_READ                                             NOT NULL NUMBER(1)
> > >  USER_WRITE                                            NOT NULL NUMBER(1)
> > >  GROUP_READ                                            NOT NULL NUMBER(1)
> > >  GROUP_WRITE                                           NOT NULL NUMBER(1)
> > >  OTHER_READ                                            NOT NULL NUMBER(1)
> > >  OTHER_WRITE                                           NOT NULL NUMBER(1)
> > >  ROW_USER_ID                                           NOT NULL NUMBER(12)
> > >  ROW_GROUP_ID                                          NOT NULL NUMBER(3)
> > >  ROW_PROJECT_ID                                        NOT NULL NUMBER(3)
> > >  ROW_ALG_INVOCATION_ID                                 NOT NULL NUMBER(12)
> > > 
> > > SQL> 
> > > 
> > >  
> > > Any ideas?
> > > 
> > > 
> > > Terry
> > > 
> > > 
> > > p.s. Full output is appended.
> > > 
> > > 
> > > On  0, Dave Barkan <db...@pc...> wrote:
> > > > Hey Terry,
> > > > 
> > > > That is the correct plugin.  The files can be found at 
> > > > 
> > > > ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
> > > > 'function.ontology', 'process.ontology', and 'component.ontology' 
> > > > (corresponding to the three branches of the GO Hierarchy).  Note that 
> > > > these are not the alternate XML files that the GO people also have 
> > > > available.
> > > > 
> > > > Let me know if you have any complications with the loading process.
> > > > 
> > > > On Thu, 3 Jul 2003, Terry Clark wrote:
> > > > 
> > > > > Hi, All -
> > > > > 
> > > > > I am in the process of loading the GO Ontology into 
> > > > > GUS to have the necessary GO data for loading the
> > > > > TIGR Arabidopsis genome into GUS.  Can someone advise
> > > > > me what GO files I should use?
> > > > > 
> > > > > I plan to use the Plugin
> > > > >   GUS::GOPredict::Plugin::LoadGoOntology
> > > > > 
> > > > > 
> > > > > Thanks in advance for any help,
> > > > > 
> > > > > Terry
> > > > > 
> > > > > 
> > > > > 
> > > > > -------------------------------------------------------
> > > > > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> > > > > Data Reports, E-commerce, Portals, and Forums are available now.
> > > > > Download today and enter to win an XBOX or Visual Studio .NET.
> > > > > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > > > > _______________________________________________
> > > > > Gusdev-gusdev mailing list
> > > > > Gus...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > 
> > > > 
> > > > 
> > > > 
> > > > -------------------------------------------------------
> > > > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> > > > Data Reports, E-commerce, Portals, and Forums are available now.
> > > > Download today and enter to win an XBOX or Visual Studio .NET.
> > > > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > > > _______________________________________________
> > > > Gusdev-gusdev mailing list
> > > > Gus...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > 
> > > 
> > > **************************************************************************************
> > > 
> > > THE COMPLETE OUTPUT
> > > 
> > >   ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> > > 
> > > 
> > > Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
> > > Reading properties from /home/gus/.gus.properties
> > > 
> > > 
> > > prepareAndExecute:     SELECT *
> > >       FROM Core.AlgorithmImplementation
> > >      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
> > >        AND cvs_revision    = '1.8'
> > > 
> > >  
> > > 
> > > 
> > > prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
> > > 
> > > RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
> > >   bindValues (19)
> > > 
> > > 
> > > prepareAndExecute: select login,user_id from Core.UserInfo 
> > > 
> > > 
> > > prepareAndExecute: select name,group_id from Core.GroupInfo 
> > > 
> > > 
> > > prepareAndExecute: select name,project_id from Core.ProjectInfo 
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
> > >     VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
> > >   bindValues (1, 1, 19, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 4, pending)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
> > >   bindValues (19)
> > > 
> > > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > >   bindValues (2)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (224, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 15, 1, 4, 1, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > >   bindValues (0)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > >   bindValues (1, 1, 0, 235, 1, 16, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> > >   bindValues (4)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (232, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 17, 1, 4, 1, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (226, 1, 1, 0, 0, 1, 1, 0, 1, 1, 18, 1, 4, 1, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (1, 1, 0, 236, 1, 19, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/go, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > >   bindValues (1, 1, 0, 225, 1, 20, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (230, 1, 1, 0, 0, 1, 1, 0, 1, 1, 21, 1, 4, 1, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > >   bindValues (1, 1, 0, 228, 1, 22, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (1, 1, 0, 229, 1, 23, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/.gus.properties, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (1, 1, 0, 227, 1, 24, 1, 1, 0, 0, 4, 1, 1, 4, go01, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (234, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 25, 1, 4, 1, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> > >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> > >   bindValues (233, 1, 1, 0, 0, 1, 1, 0, 1, 1, 26, 1, 4, 1, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > >   bindValues (1, 1, 0, 237, 1, 27, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > 
> > > sqlExec: 
> > >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> > >   bindValues (1, 1, 0, 231, 1, 28, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > 
> > > parsing finished; loading ontology into database
> > > executingselect external_database_release_id 
> > >                from sres.externalDatabaseRelease
> > >                where version = '2.371' and external_database_id = 
> > > 
> > > 
> > > prepareAndExecute: select external_database_release_id 
> > >                from sres.externalDatabaseRelease
> > >                where version = '2.371' and external_database_id =  
> > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id 
> > >                from sres.externalDatabaseRelease
> > >                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> > > 
> > > 
> > > sqlExec: 
> > >     UPDATE  Core.AlgorithmInvocation
> > >     SET     
> > > 	modification_date = SYSDATE,
> > > 	end_time = SYSDATE,
> > > 	row_alg_invocation_id = ?
> > >     WHERE   algorithm_invocation_id = ?
> > >   bindValues (4, 4)
> > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > 
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> > Data Reports, E-commerce, Portals, and Forums are available now.
> > Download today and enter to win an XBOX or Visual Studio .NET.
> > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] initial GO Files

[Terry C. <tw...@cs...>]

Hi Dave,
I had some problems. There is a warning and an error, both puzzling me.
The output is below:
   command  on line 2
   warning on line 144
   error looking comment on line 156  

I am stumped. Can you help?

By the way, are there example XML files for using with
UpdateGusFromXML.pm available?


Terry




1   
2   ga +run GUS::Common::Plugin::UpdateGusFromCla --attrlist="NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE" --valuelist="'GO Function','go function',SYSDATE,1,1,1,1,1,0" --tablename=SRes.ExternalDatabase
3   
4   
5   
6   Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
7   Reading properties from /home/gus/.gus.properties
8   
9   
10   prepareAndExecute:     SELECT *
11         FROM Core.AlgorithmImplementation
12        WHERE executable = 'GUS::Common::Plugin::UpdateGusFromCla'
13          AND cvs_revision    = '1.2'
14   
15    
16   
17   
18   prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
19   
20   RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
21     bindValues (17)
22   
23   
24   prepareAndExecute: select login,user_id from Core.UserInfo 
25   
26   
27   prepareAndExecute: select name,group_id from Core.GroupInfo 
28   
29   
30   prepareAndExecute: select name,project_id from Core.ProjectInfo 
31   
32   
33   sqlExec: 
34       INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
35       VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
36     bindValues (1, 1, 17, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 6, pending)
37    DbiHandle:sqlExec:insert succeeded 1 row(s)
38   
39   getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
40     bindValues (17)
41   
42   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
43     bindValues (2)
44   
45   
46   sqlExec: 
47       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
48       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
49     bindValues (206, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 40, 1, 6, 1, 6)
50    DbiHandle:sqlExec:insert succeeded 1 row(s)
51   
52   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
53     bindValues (0)
54   
55   
56   sqlExec: 
57       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
58       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
59     bindValues (1, 1, 0, 207, 1, 41, 1, 1, 0, 0, 6, 1, 1, 6, NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE, 1)
60    DbiHandle:sqlExec:insert succeeded 1 row(s)
61   
62   
63   sqlExec: 
64       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
65       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
66     bindValues (1, 1, 0, 203, 1, 42, 1, 1, 0, 0, 6, 1, 1, 6, 1)
67    DbiHandle:sqlExec:insert succeeded 1 row(s)
68   
69   getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
70     bindValues (4)
71   
72   
73   sqlExec: 
74       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
75       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
76     bindValues (210, 1, 1, 0, 0, 1, 1, 0, 1, 1, 43, 1, 6, 1, 6)
77    DbiHandle:sqlExec:insert succeeded 1 row(s)
78   
79   
80   sqlExec: 
81       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
82       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
83     bindValues (1, 1, 0, 211, 1, 44, 1, 1, 0, 0, 6, 1, 1, 6, 1)
84    DbiHandle:sqlExec:insert succeeded 1 row(s)
85   
86   
87   sqlExec: 
88       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
89       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
90     bindValues (1, 1, 0, 201, 1, 45, 1, 1, 0, 0, 6, 1, 1, 6, /home/gus/.gus.properties, 1)
91    DbiHandle:sqlExec:insert succeeded 1 row(s)
92   
93   
94   sqlExec: 
95       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
96       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
97     bindValues (1, 1, 0, 208, 1, 46, 1, 1, 0, 0, 6, 1, 1, 6, 1)
98    DbiHandle:sqlExec:insert succeeded 1 row(s)
99   
100   
101   sqlExec: 
102       INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
103       VALUES   (  ?, ?, ?, ?, ?, SYSDATE, '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
104     bindValues (205, 1, 1, 0, 0, 1, 1, 0, 1, 1, 47, 1, 6, 1, 6)
105    DbiHandle:sqlExec:insert succeeded 1 row(s)
106   
107   
108   sqlExec: 
109       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
110       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
111     bindValues (1, 1, 0, 209, 1, 48, 1, 1, 0, 0, 6, 1, 1, 6, SRes.ExternalDatabase, 1)
112    DbiHandle:sqlExec:insert succeeded 1 row(s)
113   
114   
115   sqlExec: 
116       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
117       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
118     bindValues (1, 1, 0, 202, 1, 49, 1, 1, 0, 0, 6, 1, 1, 6, 1)
119    DbiHandle:sqlExec:insert succeeded 1 row(s)
120   
121   
122   sqlExec: 
123       INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
124       VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
125     bindValues (1, 1, 0, 204, 1, 50, 1, 1, 0, 0, 6, 1, 1, 6, 'GO Function','go function',SYSDATE,1,1,1,1,1,0, 1)
126    DbiHandle:sqlExec:insert succeeded 1 row(s)
127   Thu Jul  3 12:23:35 2003	ALGINVID	6
128   Thu Jul  3 12:23:35 2003	ARGS	algoinvo	1
129   Thu Jul  3 12:23:35 2003	ARGS	attrlist	NAME,LOWERCASE_NAME,MODIFICATION_DATE,USER_READ,USER_WRITE,GROUP_READ,GROUP_WRITE,OTHER_READ,OTHER_WRITE
130   Thu Jul  3 12:23:35 2003	ARGS	comment	
131   Thu Jul  3 12:23:35 2003	ARGS	commit	
132   Thu Jul  3 12:23:35 2003	ARGS	debug	
133   Thu Jul  3 12:23:35 2003	ARGS	group	
134   Thu Jul  3 12:23:35 2003	ARGS	gusconfigfile	/home/gus/.gus.properties
135   Thu Jul  3 12:23:35 2003	ARGS	project	
136   Thu Jul  3 12:23:35 2003	ARGS	refresh	
137   Thu Jul  3 12:23:35 2003	ARGS	tablename	SRes.ExternalDatabase
138   Thu Jul  3 12:23:35 2003	ARGS	usage	
139   Thu Jul  3 12:23:35 2003	ARGS	user	
140   Thu Jul  3 12:23:35 2003	ARGS	valuelist	'GO Function','go function',SYSDATE,1,1,1,1,1,0
141   Thu Jul  3 12:23:35 2003	ARGS	verbose	1
142   Thu Jul  3 12:23:35 2003	ARGS	veryVerbose	
143   Thu Jul  3 12:23:35 2003	COMMIT	commit off
144   Warning: Use of "require" without parens is ambiguous at (eval 12) line 1.
145   
146   
147   sqlExec: 
148       UPDATE  Core.AlgorithmInvocation
149       SET     
150   	modification_date = SYSDATE,
151   	end_time = SYSDATE,
152   	row_alg_invocation_id = ?
153       WHERE   algorithm_invocation_id = ?
154     bindValues (6, 6)
155    DbiHandle:sqlExec:insert succeeded 1 row(s)
156   Can't locate object method "new" via package "GUS::Model::SRes.ExternalDatabase" (perhaps you forgot to load "GUS::Model::SRes.ExternalDatabase"?) at /home/gus/run/lib/perl/GUS/Common/Plugin/UpdateGusFromCla.pm line 104.




On  0, Dave Barkan <db...@pc...> wrote:
> Hey Terry,
> 
> Well we just had a conference call where one of the issues that came up 
> was the fact that we need to give users of plugins a better idea of what 
> needs to be in place before actually running the plugin.  I think this 
> qualifies as an example.
> 
> The problem here is that there needs to be three entries in the 
> SRes.ExternalDatabase table representing the three branches of the GO 
> Ontology.  The values in the 'name' column of that table should be set to 
> 'GO Function', 'GO Component', and 'GO Process' for the respective 
> branches (this could really be done better).  We have been inserting these 
> entries manually; after you do it once (using updateGusFromXML or 
> updateGusFromCla) you don't have to worry about it again when loading 
> later releases of the GO Ontology.
> 
> Additionally, there needs to be an entry in the 
> SRes.ExternalDatabaseRelease table representing the current release of 
> each branch.  You can enter this manually or create it automatically by 
> setting the '--create_release' flag of the plugin.
> 
> Let me know if there are further issues.  I would suggest running without 
> setting --commit initially to make sure everything works and you don't 
> insert faulty data.
> 
> Dave 
> 
> On Thu, 3 Jul 2003, Terry Clark wrote:
> 
> > Hi Dave, it went okay for a bit, then I encountered
> > what looks to be missing data in an SRES table,
> > which is empty but being probed for GO db information.
> > I can't find a Plugin to populate this table.
> > Here are the details:
> > 
> > I executed:
> > 
> > > ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> > 
> > had a number of successful database reads and inserts (algorithm tables -- the full
> > output is attached), but at the end of the output had the following where in line 1,
> > the external_database_id (GO id?)  is not available.
> >   
> > 
> > 1 prepareAndExecute: select external_database_release_id
> > 2               from sres.externalDatabaseRelease
> > 3                where version = '2.371' and external_database_id =
> > 4 DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id
> > 5               from sres.externalDatabaseRelease
> > 6                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > 7 prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> > 8
> > 9
> > 10  sqlExec:
> > 11     UPDATE  Core.AlgorithmInvocation
> > 12     SET
> > 13        modification_date = SYSDATE,
> > 14        end_time = SYSDATE,
> > 15        row_alg_invocation_id = ?
> > 16     WHERE   algorithm_invocation_id = ?
> > 17   bindValues (4, 4)
> > 18  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 19 Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > 
> > 
> > The corresponding table is empty
> > 
> >  SQL> select * from sres.externalDatabaseRelease;
> >  no rows selected
> > 
> > and the empty table consists of 
> > 
> > SQL> describe sres.externalDatabaseRelease;
> >  Name                                                  Null?    Type
> >  ----------------------------------------------------- -------- ------------------------------------
> >  EXTERNAL_DATABASE_RELEASE_ID                          NOT NULL NUMBER(10)
> >  EXTERNAL_DATABASE_ID                                  NOT NULL NUMBER(10)
> >  RELEASE_DATE                                                   DATE
> >  VERSION                                               NOT NULL VARCHAR2(255)
> >  DOWNLOAD_URL                                                   VARCHAR2(255)
> >  ID_TYPE                                                        VARCHAR2(255)
> >  ID_URL                                                         VARCHAR2(255)
> >  SECONDARY_ID_TYPE                                              VARCHAR2(255)
> >  SECONDARY_ID_URL                                               VARCHAR2(255)
> >  DESCRIPTION                                                    VARCHAR2(4000)
> >  FILE_NAME                                                      VARCHAR2(255)
> >  FILE_MD5                                                       VARCHAR2(32)
> >  BLAST_FILE                                                     VARCHAR2(255)
> >  BLAST_FILE_MD5                                                 VARCHAR2(32)
> >  MODIFICATION_DATE                                     NOT NULL DATE
> >  USER_READ                                             NOT NULL NUMBER(1)
> >  USER_WRITE                                            NOT NULL NUMBER(1)
> >  GROUP_READ                                            NOT NULL NUMBER(1)
> >  GROUP_WRITE                                           NOT NULL NUMBER(1)
> >  OTHER_READ                                            NOT NULL NUMBER(1)
> >  OTHER_WRITE                                           NOT NULL NUMBER(1)
> >  ROW_USER_ID                                           NOT NULL NUMBER(12)
> >  ROW_GROUP_ID                                          NOT NULL NUMBER(3)
> >  ROW_PROJECT_ID                                        NOT NULL NUMBER(3)
> >  ROW_ALG_INVOCATION_ID                                 NOT NULL NUMBER(12)
> > 
> > SQL> 
> > 
> >  
> > Any ideas?
> > 
> > 
> > Terry
> > 
> > 
> > p.s. Full output is appended.
> > 
> > 
> > On  0, Dave Barkan <db...@pc...> wrote:
> > > Hey Terry,
> > > 
> > > That is the correct plugin.  The files can be found at 
> > > 
> > > ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
> > > 'function.ontology', 'process.ontology', and 'component.ontology' 
> > > (corresponding to the three branches of the GO Hierarchy).  Note that 
> > > these are not the alternate XML files that the GO people also have 
> > > available.
> > > 
> > > Let me know if you have any complications with the loading process.
> > > 
> > > On Thu, 3 Jul 2003, Terry Clark wrote:
> > > 
> > > > Hi, All -
> > > > 
> > > > I am in the process of loading the GO Ontology into 
> > > > GUS to have the necessary GO data for loading the
> > > > TIGR Arabidopsis genome into GUS.  Can someone advise
> > > > me what GO files I should use?
> > > > 
> > > > I plan to use the Plugin
> > > >   GUS::GOPredict::Plugin::LoadGoOntology
> > > > 
> > > > 
> > > > Thanks in advance for any help,
> > > > 
> > > > Terry
> > > > 
> > > > 
> > > > 
> > > > -------------------------------------------------------
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> > > > _______________________________________________
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> > > > Gus...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > 
> > > 
> > > 
> > > 
> > > -------------------------------------------------------
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> > 
> > 
> > **************************************************************************************
> > 
> > THE COMPLETE OUTPUT
> > 
> >   ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> > 
> > 
> > Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
> > Reading properties from /home/gus/.gus.properties
> > 
> > 
> > prepareAndExecute:     SELECT *
> >       FROM Core.AlgorithmImplementation
> >      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
> >        AND cvs_revision    = '1.8'
> > 
> >  
> > 
> > 
> > prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
> > 
> > RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
> >   bindValues (19)
> > 
> > 
> > prepareAndExecute: select login,user_id from Core.UserInfo 
> > 
> > 
> > prepareAndExecute: select name,group_id from Core.GroupInfo 
> > 
> > 
> > prepareAndExecute: select name,project_id from Core.ProjectInfo 
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
> >     VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
> >   bindValues (1, 1, 19, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 4, pending)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
> >   bindValues (19)
> > 
> > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> >   bindValues (2)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (224, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 15, 1, 4, 1, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> >   bindValues (0)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> >   bindValues (1, 1, 0, 235, 1, 16, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
> >   bindValues (4)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (232, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 17, 1, 4, 1, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (226, 1, 1, 0, 0, 1, 1, 0, 1, 1, 18, 1, 4, 1, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (1, 1, 0, 236, 1, 19, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/go, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> >   bindValues (1, 1, 0, 225, 1, 20, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (230, 1, 1, 0, 0, 1, 1, 0, 1, 1, 21, 1, 4, 1, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> >   bindValues (1, 1, 0, 228, 1, 22, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (1, 1, 0, 229, 1, 23, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/.gus.properties, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (1, 1, 0, 227, 1, 24, 1, 1, 0, 0, 4, 1, 1, 4, go01, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (234, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 25, 1, 4, 1, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
> >     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
> >   bindValues (233, 1, 1, 0, 0, 1, 1, 0, 1, 1, 26, 1, 4, 1, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> >   bindValues (1, 1, 0, 237, 1, 27, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > 
> > sqlExec: 
> >     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
> >   bindValues (1, 1, 0, 231, 1, 28, 1, 1, 0, 0, 4, 1, 1, 4, 1)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > 
> > parsing finished; loading ontology into database
> > executingselect external_database_release_id 
> >                from sres.externalDatabaseRelease
> >                where version = '2.371' and external_database_id = 
> > 
> > 
> > prepareAndExecute: select external_database_release_id 
> >                from sres.externalDatabaseRelease
> >                where version = '2.371' and external_database_id =  
> > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id 
> >                from sres.externalDatabaseRelease
> >                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> > 
> > 
> > sqlExec: 
> >     UPDATE  Core.AlgorithmInvocation
> >     SET     
> > 	modification_date = SYSDATE,
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (4, 4)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > 
> > 
> > 
> > 
> 
> 
> 
> -------------------------------------------------------
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Re: [Gusdev-gusdev] initial GO Files

[Dave B. <db...@pc...>]

Hey Terry,

Well we just had a conference call where one of the issues that came up 
was the fact that we need to give users of plugins a better idea of what 
needs to be in place before actually running the plugin.  I think this 
qualifies as an example.

The problem here is that there needs to be three entries in the 
SRes.ExternalDatabase table representing the three branches of the GO 
Ontology.  The values in the 'name' column of that table should be set to 
'GO Function', 'GO Component', and 'GO Process' for the respective 
branches (this could really be done better).  We have been inserting these 
entries manually; after you do it once (using updateGusFromXML or 
updateGusFromCla) you don't have to worry about it again when loading 
later releases of the GO Ontology.

Additionally, there needs to be an entry in the 
SRes.ExternalDatabaseRelease table representing the current release of 
each branch.  You can enter this manually or create it automatically by 
setting the '--create_release' flag of the plugin.

Let me know if there are further issues.  I would suggest running without 
setting --commit initially to make sure everything works and you don't 
insert faulty data.

Dave 

On Thu, 3 Jul 2003, Terry Clark wrote:

> Hi Dave, it went okay for a bit, then I encountered
> what looks to be missing data in an SRES table,
> which is empty but being probed for GO db information.
> I can't find a Plugin to populate this table.
> Here are the details:
> 
> I executed:
> 
> > ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> 
> had a number of successful database reads and inserts (algorithm tables -- the full
> output is attached), but at the end of the output had the following where in line 1,
> the external_database_id (GO id?)  is not available.
>   
> 
> 1 prepareAndExecute: select external_database_release_id
> 2               from sres.externalDatabaseRelease
> 3                where version = '2.371' and external_database_id =
> 4 DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id
> 5               from sres.externalDatabaseRelease
> 6                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> 7 prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> 8
> 9
> 10  sqlExec:
> 11     UPDATE  Core.AlgorithmInvocation
> 12     SET
> 13        modification_date = SYSDATE,
> 14        end_time = SYSDATE,
> 15        row_alg_invocation_id = ?
> 16     WHERE   algorithm_invocation_id = ?
> 17   bindValues (4, 4)
> 18  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 19 Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> 
> 
> The corresponding table is empty
> 
>  SQL> select * from sres.externalDatabaseRelease;
>  no rows selected
> 
> and the empty table consists of 
> 
> SQL> describe sres.externalDatabaseRelease;
>  Name                                                  Null?    Type
>  ----------------------------------------------------- -------- ------------------------------------
>  EXTERNAL_DATABASE_RELEASE_ID                          NOT NULL NUMBER(10)
>  EXTERNAL_DATABASE_ID                                  NOT NULL NUMBER(10)
>  RELEASE_DATE                                                   DATE
>  VERSION                                               NOT NULL VARCHAR2(255)
>  DOWNLOAD_URL                                                   VARCHAR2(255)
>  ID_TYPE                                                        VARCHAR2(255)
>  ID_URL                                                         VARCHAR2(255)
>  SECONDARY_ID_TYPE                                              VARCHAR2(255)
>  SECONDARY_ID_URL                                               VARCHAR2(255)
>  DESCRIPTION                                                    VARCHAR2(4000)
>  FILE_NAME                                                      VARCHAR2(255)
>  FILE_MD5                                                       VARCHAR2(32)
>  BLAST_FILE                                                     VARCHAR2(255)
>  BLAST_FILE_MD5                                                 VARCHAR2(32)
>  MODIFICATION_DATE                                     NOT NULL DATE
>  USER_READ                                             NOT NULL NUMBER(1)
>  USER_WRITE                                            NOT NULL NUMBER(1)
>  GROUP_READ                                            NOT NULL NUMBER(1)
>  GROUP_WRITE                                           NOT NULL NUMBER(1)
>  OTHER_READ                                            NOT NULL NUMBER(1)
>  OTHER_WRITE                                           NOT NULL NUMBER(1)
>  ROW_USER_ID                                           NOT NULL NUMBER(12)
>  ROW_GROUP_ID                                          NOT NULL NUMBER(3)
>  ROW_PROJECT_ID                                        NOT NULL NUMBER(3)
>  ROW_ALG_INVOCATION_ID                                 NOT NULL NUMBER(12)
> 
> SQL> 
> 
>  
> Any ideas?
> 
> 
> Terry
> 
> 
> p.s. Full output is appended.
> 
> 
> On  0, Dave Barkan <db...@pc...> wrote:
> > Hey Terry,
> > 
> > That is the correct plugin.  The files can be found at 
> > 
> > ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
> > 'function.ontology', 'process.ontology', and 'component.ontology' 
> > (corresponding to the three branches of the GO Hierarchy).  Note that 
> > these are not the alternate XML files that the GO people also have 
> > available.
> > 
> > Let me know if you have any complications with the loading process.
> > 
> > On Thu, 3 Jul 2003, Terry Clark wrote:
> > 
> > > Hi, All -
> > > 
> > > I am in the process of loading the GO Ontology into 
> > > GUS to have the necessary GO data for loading the
> > > TIGR Arabidopsis genome into GUS.  Can someone advise
> > > me what GO files I should use?
> > > 
> > > I plan to use the Plugin
> > >   GUS::GOPredict::Plugin::LoadGoOntology
> > > 
> > > 
> > > Thanks in advance for any help,
> > > 
> > > Terry
> > > 
> > > 
> > > 
> > > -------------------------------------------------------
> > > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> > > Data Reports, E-commerce, Portals, and Forums are available now.
> > > Download today and enter to win an XBOX or Visual Studio .NET.
> > > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > 
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> > Data Reports, E-commerce, Portals, and Forums are available now.
> > Download today and enter to win an XBOX or Visual Studio .NET.
> > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> **************************************************************************************
> 
> THE COMPLETE OUTPUT
> 
>   ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit
> 
> 
> Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
> Reading properties from /home/gus/.gus.properties
> 
> 
> prepareAndExecute:     SELECT *
>       FROM Core.AlgorithmImplementation
>      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
>        AND cvs_revision    = '1.8'
> 
>  
> 
> 
> prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 
> 
> RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
>   bindValues (19)
> 
> 
> prepareAndExecute: select login,user_id from Core.UserInfo 
> 
> 
> prepareAndExecute: select name,group_id from Core.GroupInfo 
> 
> 
> prepareAndExecute: select name,project_id from Core.ProjectInfo 
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
>     VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
>   bindValues (1, 1, 19, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 4, pending)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
>   bindValues (19)
> 
> getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>   bindValues (2)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>   bindValues (224, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 15, 1, 4, 1, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>   bindValues (0)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>   bindValues (1, 1, 0, 235, 1, 16, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
>   bindValues (4)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>   bindValues (232, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 17, 1, 4, 1, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>   bindValues (226, 1, 1, 0, 0, 1, 1, 0, 1, 1, 18, 1, 4, 1, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>   bindValues (1, 1, 0, 236, 1, 19, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/go, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>   bindValues (1, 1, 0, 225, 1, 20, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>   bindValues (230, 1, 1, 0, 0, 1, 1, 0, 1, 1, 21, 1, 4, 1, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>   bindValues (1, 1, 0, 228, 1, 22, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>   bindValues (1, 1, 0, 229, 1, 23, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/.gus.properties, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
>   bindValues (1, 1, 0, 227, 1, 24, 1, 1, 0, 0, 4, 1, 1, 4, go01, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>   bindValues (234, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 25, 1, 4, 1, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
>     VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
>   bindValues (233, 1, 1, 0, 0, 1, 1, 0, 1, 1, 26, 1, 4, 1, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>   bindValues (1, 1, 0, 237, 1, 27, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> 
> sqlExec: 
>     INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
>   bindValues (1, 1, 0, 231, 1, 28, 1, 1, 0, 0, 4, 1, 1, 4, 1)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> 
> parsing finished; loading ontology into database
> executingselect external_database_release_id 
>                from sres.externalDatabaseRelease
>                where version = '2.371' and external_database_id = 
> 
> 
> prepareAndExecute: select external_database_release_id 
>                from sres.externalDatabaseRelease
>                where version = '2.371' and external_database_id =  
> DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id 
>                from sres.externalDatabaseRelease
>                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
> 
> 
> sqlExec: 
>     UPDATE  Core.AlgorithmInvocation
>     SET     
> 	modification_date = SYSDATE,
> 	end_time = SYSDATE,
> 	row_alg_invocation_id = ?
>     WHERE   algorithm_invocation_id = ?
>   bindValues (4, 4)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> 
> 
> 
> 

Re: [Gusdev-gusdev] initial GO Files

[Terry C. <tw...@cs...>]

Hi Dave, it went okay for a bit, then I encountered
what looks to be missing data in an SRES table,
which is empty but being probed for GO db information.
I can't find a Plugin to populate this table.
Here are the details:

I executed:

> ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit

had a number of successful database reads and inserts (algorithm tables -- the full
output is attached), but at the end of the output had the following where in line 1,
the external_database_id (GO id?)  is not available.
  

1 prepareAndExecute: select external_database_release_id
2               from sres.externalDatabaseRelease
3                where version = '2.371' and external_database_id =
4 DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id
5               from sres.externalDatabaseRelease
6                where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
7 prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr
8
9
10  sqlExec:
11     UPDATE  Core.AlgorithmInvocation
12     SET
13        modification_date = SYSDATE,
14        end_time = SYSDATE,
15        row_alg_invocation_id = ?
16     WHERE   algorithm_invocation_id = ?
17   bindValues (4, 4)
18  DbiHandle:sqlExec:insert succeeded 1 row(s)
19 Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.


The corresponding table is empty

 SQL> select * from sres.externalDatabaseRelease;
 no rows selected

and the empty table consists of 

SQL> describe sres.externalDatabaseRelease;
 Name                                                  Null?    Type
 ----------------------------------------------------- -------- ------------------------------------
 EXTERNAL_DATABASE_RELEASE_ID                          NOT NULL NUMBER(10)
 EXTERNAL_DATABASE_ID                                  NOT NULL NUMBER(10)
 RELEASE_DATE                                                   DATE
 VERSION                                               NOT NULL VARCHAR2(255)
 DOWNLOAD_URL                                                   VARCHAR2(255)
 ID_TYPE                                                        VARCHAR2(255)
 ID_URL                                                         VARCHAR2(255)
 SECONDARY_ID_TYPE                                              VARCHAR2(255)
 SECONDARY_ID_URL                                               VARCHAR2(255)
 DESCRIPTION                                                    VARCHAR2(4000)
 FILE_NAME                                                      VARCHAR2(255)
 FILE_MD5                                                       VARCHAR2(32)
 BLAST_FILE                                                     VARCHAR2(255)
 BLAST_FILE_MD5                                                 VARCHAR2(32)
 MODIFICATION_DATE                                     NOT NULL DATE
 USER_READ                                             NOT NULL NUMBER(1)
 USER_WRITE                                            NOT NULL NUMBER(1)
 GROUP_READ                                            NOT NULL NUMBER(1)
 GROUP_WRITE                                           NOT NULL NUMBER(1)
 OTHER_READ                                            NOT NULL NUMBER(1)
 OTHER_WRITE                                           NOT NULL NUMBER(1)
 ROW_USER_ID                                           NOT NULL NUMBER(12)
 ROW_GROUP_ID                                          NOT NULL NUMBER(3)
 ROW_PROJECT_ID                                        NOT NULL NUMBER(3)
 ROW_ALG_INVOCATION_ID                                 NOT NULL NUMBER(12)

SQL> 

 
Any ideas?


Terry


p.s. Full output is appended.


On  0, Dave Barkan <db...@pc...> wrote:
> Hey Terry,
> 
> That is the correct plugin.  The files can be found at 
> 
> ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
> 'function.ontology', 'process.ontology', and 'component.ontology' 
> (corresponding to the three branches of the GO Hierarchy).  Note that 
> these are not the alternate XML files that the GO people also have 
> available.
> 
> Let me know if you have any complications with the loading process.
> 
> On Thu, 3 Jul 2003, Terry Clark wrote:
> 
> > Hi, All -
> > 
> > I am in the process of loading the GO Ontology into 
> > GUS to have the necessary GO data for loading the
> > TIGR Arabidopsis genome into GUS.  Can someone advise
> > me what GO files I should use?
> > 
> > I plan to use the Plugin
> >   GUS::GOPredict::Plugin::LoadGoOntology
> > 
> > 
> > Thanks in advance for any help,
> > 
> > Terry
> > 
> > 
> > 
> > -------------------------------------------------------
> > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> > Data Reports, E-commerce, Portals, and Forums are available now.
> > Download today and enter to win an XBOX or Visual Studio .NET.
> > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev


**************************************************************************************

THE COMPLETE OUTPUT

  ga +run GUS::GOPredict::Plugin::LoadGoOntology --file_path=/home/gus/go --id_file=go01 --verbose --commit


Reading properties from /home/gus/run/config/GUS-PluginMgr.prop
Reading properties from /home/gus/.gus.properties


prepareAndExecute:     SELECT *
      FROM Core.AlgorithmImplementation
     WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
       AND cvs_revision    = '1.8'

 


prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t, Core.DatabaseInfo d where d.database_id = t.database_id 

RetrieveFromDB: select * from Core.AlgorithmImplementation where  algorithm_implementation_id = ?
  bindValues (19)


prepareAndExecute: select login,user_id from Core.UserInfo 


prepareAndExecute: select name,group_id from Core.GroupInfo 


prepareAndExecute: select name,project_id from Core.ProjectInfo 


sqlExec: 
    INSERT INTO Core.AlgorithmInvocation (  group_read, comment_string, user_read, algorithm_implementation_id, other_write, modification_date, end_time, cpu_time, row_group_id, machine_id, user_write, other_read, group_write, cpus_used, start_time, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id, result )
    VALUES   (  ?, '', ?, ?, ?, SYSDATE, SYSDATE, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) 
  bindValues (1, 1, 19, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 4, pending)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKey where  algorithm_implementation_id = ?
  bindValues (19)

getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
  bindValues (2)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (224, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 15, 1, 4, 1, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
  bindValues (0)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
  bindValues (1, 1, 0, 235, 1, 16, 1, 1, 0, 0, 4, 1, 1, 4, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

getRelations: select * from Core.AlgorithmParamKeyType where  algorithm_param_key_type_id = ?
  bindValues (4)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (232, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 17, 1, 4, 1, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (226, 1, 1, 0, 0, 1, 1, 0, 1, 1, 18, 1, 4, 1, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
  bindValues (1, 1, 0, 236, 1, 19, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/go, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
  bindValues (1, 1, 0, 225, 1, 20, 1, 1, 0, 0, 4, 1, 1, 4, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (230, 1, 1, 0, 0, 1, 1, 0, 1, 1, 21, 1, 4, 1, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
  bindValues (1, 1, 0, 228, 1, 22, 1, 1, 0, 0, 4, 1, 1, 4, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
  bindValues (1, 1, 0, 229, 1, 23, 1, 1, 0, 0, 4, 1, 1, 4, /home/gus/.gus.properties, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ? ) 
  bindValues (1, 1, 0, 227, 1, 24, 1, 1, 0, 0, 4, 1, 1, 4, go01, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, boolean_value, row_group_id, string_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (234, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 25, 1, 4, 1, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  algorithm_param_key_id, group_read, user_read, other_write, order_num, modification_date, row_group_id, string_value, int_value, user_write, is_default, group_write, other_read, algorithm_param_id, row_user_id, row_alg_invocation_id, row_project_id, algorithm_invocation_id )
    VALUES   (  ?, ?, ?, ?, ?, SYSDATE, ?, '', '', ?, ?, ?, ?, ?, ?, ?, ?, ? ) 
  bindValues (233, 1, 1, 0, 0, 1, 1, 0, 1, 1, 26, 1, 4, 1, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
  bindValues (1, 1, 0, 237, 1, 27, 1, 1, 0, 0, 4, 1, 1, 4, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec: 
    INSERT INTO Core.AlgorithmParam (  other_read, group_write, is_default, algorithm_param_key_id, group_read, algorithm_param_id, user_read, row_user_id, other_write, order_num, modification_date, row_alg_invocation_id, row_project_id, row_group_id, algorithm_invocation_id, string_value, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, '', ? ) 
  bindValues (1, 1, 0, 231, 1, 28, 1, 1, 0, 0, 4, 1, 1, 4, 1)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

parsing finished; loading ontology into database
executingselect external_database_release_id 
               from sres.externalDatabaseRelease
               where version = '2.371' and external_database_id = 


prepareAndExecute: select external_database_release_id 
               from sres.externalDatabaseRelease
               where version = '2.371' and external_database_id =  
DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command (DBD ERROR: OCIStmtExecute/Describe) [for statement ``select external_database_release_id 
               from sres.externalDatabaseRelease
               where version = '2.371' and external_database_id = '']) at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
prepareAndExecute FAILED: GUS::ObjRelP::DbiDbHandle=HASH(0x83511c8)->errstr


sqlExec: 
    UPDATE  Core.AlgorithmInvocation
    SET     
	modification_date = SYSDATE,
	end_time = SYSDATE,
	row_alg_invocation_id = ?
    WHERE   algorithm_invocation_id = ?
  bindValues (4, 4)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't call method "execute" without a package or object reference at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.

Re: [Gusdev-gusdev] initial GO Files

[Dave B. <db...@pc...>]

Hey Terry,

That is the correct plugin.  The files can be found at 

ftp://ftp.geneontology.org/pub/go/ontology.  They are named 
'function.ontology', 'process.ontology', and 'component.ontology' 
(corresponding to the three branches of the GO Hierarchy).  Note that 
these are not the alternate XML files that the GO people also have 
available.

Let me know if you have any complications with the loading process.

On Thu, 3 Jul 2003, Terry Clark wrote:

> Hi, All -
> 
> I am in the process of loading the GO Ontology into 
> GUS to have the necessary GO data for loading the
> TIGR Arabidopsis genome into GUS.  Can someone advise
> me what GO files I should use?
> 
> I plan to use the Plugin
>   GUS::GOPredict::Plugin::LoadGoOntology
> 
> 
> Thanks in advance for any help,
> 
> Terry
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

[Gusdev-gusdev] initial GO Files

[Terry C. <tw...@cs...>]

Hi, All -

I am in the process of loading the GO Ontology into 
GUS to have the necessary GO data for loading the
TIGR Arabidopsis genome into GUS.  Can someone advise
me what GO files I should use?

I plan to use the Plugin
  GUS::GOPredict::Plugin::LoadGoOntology


Thanks in advance for any help,

Terry

[Gusdev-gusdev] Bioperl and GUS

[Arnaud K. <ax...@sa...>]

Hi

Sorry for the short delay before the conference call.
Please find attached a review of the current status of the different 
projects within Bioperl and BioSQL.

What I am aiming with this review is to consider the benefits of having 
the GUS system interacting with Bioperl.
One way to consider is to implement the bioperl-db interfaces to make 
GUS as a datasource for the bioperl objects, as it is being done within 
the BioSQL project.

Bear in mind that this survey should be balanced with an equivalent in 
Java, considering GUS as a datasource for Biojava objects.

Arnaud

[Gusdev-gusdev] GUS/build.xml

[Angel P. <an...@pc...>]

folks,
I added the App schema space to the build.xml file for the GUS project 
and committed it to CVS.
The App schema space represents a space where database-bound 
applications can store and retrieve shared data. The difference between 
this and SRes is that no data in other parts of GUS should depend on the 
data in App, but that App data is bound to other data in GUS.

Angel

[Gusdev-gusdev] Change to GUS Perl object layer.

[Jonathan C. <cra...@pc...>]

I've just committed a fix for a long-standing problem in the Perl object
layer.  The object layer (GUS/ObjRelP) was previously hard-coded to
use an Oracle rollback segment ("BIGRBS0", and later "BIGRBS1") that is
specific to CBIL's Oracle instances.  This posed a problem for sites
without a rollback segment of the same name, as well as sites that are
using Oracle 9i's new "AUTO undo management" facility, which eschews
the notion of rollback segments entirely.  In the newly-modified code,
the default behavior is that the object layer will *not* attempt to use
a specific rollback segment at all (relying instead on whatever segment
Oracle assigns it by default.)

The implication for users not at CBIL should be that the following
annoying (but non-fatal) error messages should go away (and the similar
warnings that appear when an Oracle instance supports rollback segments
but doesn't have one called "BIGRBS1"):

DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation in Automatic Undo 
mode
+(DBD ERROR: OCIStmtExecute) [for statement ``set transaction use rollback segment BIGRBS1''])
+at /home/gus/run/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.

The implication for users at CBIL is that--if you want to continue using
BIGRBS1 as your default rollback segment--you must add the following line
to your $GUS_CONFIG_FILE (after getting the updated code from CVS, of
course):

oracleDefaultRollbackSegment=BIGRBS1

I've done some brief tests and it appears to work OK.  Perl object layer
programmers should note that DbiDatabase now has an extra optional parameter
that specifies the rollback segment to use (if any).  If this parameter is
undefined, the empty string, or =~ /^none$/i, the object layer will not attempt
to run any "set transaction use rollback segment" commands.  Let me know if
you encounter any problems.

Jonathan

Re: [Gusdev-gusdev] gene table needs taxon_id?

[Arnaud K. <ax...@sa...>]

Might be worth to investigate.
Especially I think it can happen that a gene entry might not be attached 
to any genomic sequence, but such a gene should be attached to an organism.

Also I've been working on speeding up the queries and I noticed that 
replacing the index on NASEQUENCEIMP.taxon_id by a bitmap index makes 
the queries MUCH faster.

I think it's worth replacing in the file, dots-indexes.sql :
=> create index @oracle_dots@.NASEQUENCEIMP_IND16 on 
@oracle_dots@.NASEQUENCEIMP (TAXON_ID)  TABLESPACE 
@oracle_dotsIndexTablespace@;
By:
=> create bitmap index @oracle_dots@.NASEQUENCEIMP_IND16 on 
@oracle_dots@.NASEQUENCEIMP (TAXON_ID)  TABLESPACE 
@oracle_dotsIndexTablespace@;

Arnaud

---------------------------------
Benchmark - Bear in mind I've used the gusdev schema

*** With Bitmap index:

select count (g.name)
from gene g, ExternalNaSequence ena, Taxon t, GeneFeature gf, 
GeneSequence gs
where t.taxon_id = 150
and t.taxon_id = ena.taxon_id
and ena.na_sequence_id = gf.na_sequence_id
and gf.na_feature_id = gs.na_feature_id
and gs.gene_id = g.gene_id;

COUNT(G.NAME)
-------------
     4957

Elapsed: 00:00:02.76

*** Without:

select count (g.name)
from gene g, ExternalNaSequence ena, Taxon t, GeneFeature gf, 
GeneSequence gs
where t.scientific_name = 'Schizosaccharomyces pombe'
and t.taxon_id = ena.taxon_id
and ena.na_sequence_id = gf.na_sequence_id
and gf.na_feature_id = gs.na_feature_id
and gs.gene_id = g.gene_id;

COUNT(G.NAME)
-------------
     4957

Elapsed: 00:00:12.06

Steve Fischer wrote:

> folks-
>
> i think that we might want to add taxon_id to Gene.
>
> As it stands now i believe that you need to go through RNA, 
> RNAInstance, RNAFeature, NASequence to find this out.
>
> Steve
>

[Gusdev-gusdev] gene table needs taxon_id?

[Steve F. <sfi...@pc...>]

folks-

i think that we might want to add taxon_id to Gene.

As it stands now i believe that you need to go through RNA, RNAInstance, 
RNAFeature, NASequence to find this out.

Steve

Re: [Gusdev-gusdev] RAD3 Schema Question

[Angel P. <an...@pc...>]

Paul Boutros wrote:

>Hi again all,
>
>One more question about the RAD3 schema, if I may:
>
>The BioMaterialImp table has three main views:
>- BioSource	==> raw sample
>- BioSample	==> treated sample
>- LabeledExtract	==> labeled sample
>
>How can I relate the bio_material_id of a BioSource with those of its 
>BioSamples and LabeledExtracts?  The treatment table appears to detail the 
>treatments performed on a BioSource, but not what the resulting BioSample is 
>called.
>  
>
It follows the same mechanism as does the MAGE model. Namely, a 
Treatment will have a set of BioMaterialMeasurements, which in turn 
point back to BioMaterialImp.
Thus for a BioSample that was a result of a pooling of a couple of  
BioSources and subsequently labeled, you would have:

BioSource (mouse 1)  id= b1
BioSource  (mouse 2) id =b2
BioSample (sample1 ) id= b3
Treatement (pool) id = t1  bio_material_id = b3
BioMaterialMeasurement id = bm1   treatment_id = t1, bio_material_id = b1
BioMaterialMeasurement id = bm2   treatment_id = t1, bio_material_id = b2
LabeledExtract (lex 1) id = b4
Treatment (label) id = t2 bio_material_id = b4
BioMaterialMeasurement id = bm3   treatment_id = t2, bio_material_id = b3

And don't forget about the FK's to Protocol and LabelMethod for that 
appropriate BioMaterials.

I'll leave your examples as homework for yourself ;) see what you can do 
using the above shorthand and I'll tell you if it is correct.

Angel


>Let me specify the biological case, in case I'm being unclear.  We have animals 
>(BioSources) that are sacrificed, and the resulting tissues handled in 
>different ways (BioSamples), then labeled (LabeledExtracts) and run on arrays.  
>I'm struggling to see how to relate a particular BioSource to all the 
>BioSamples that have been derived from it.  The same idea could correspond to, 
>for instance, taking different tissues from the same animal.
>
>Thanks in advance for any suggestions/explanations -- very much appreciated.
>Paul
>
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>
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[Gusdev-gusdev] RAD3 Schema Question

[Paul B. <pcb...@en...>]

Hi again all,

One more question about the RAD3 schema, if I may:

The BioMaterialImp table has three main views:
- BioSource	==> raw sample
- BioSample	==> treated sample
- LabeledExtract	==> labeled sample

How can I relate the bio_material_id of a BioSource with those of its 
BioSamples and LabeledExtracts?  The treatment table appears to detail the 
treatments performed on a BioSource, but not what the resulting BioSample is 
called.

Let me specify the biological case, in case I'm being unclear.  We have animals 
(BioSources) that are sacrificed, and the resulting tissues handled in 
different ways (BioSamples), then labeled (LabeledExtracts) and run on arrays.  
I'm struggling to see how to relate a particular BioSource to all the 
BioSamples that have been derived from it.  The same idea could correspond to, 
for instance, taking different tissues from the same animal.

Thanks in advance for any suggestions/explanations -- very much appreciated.
Paul

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Re: [Gusdev-gusdev] plug-in insertion question....

[Angel P. <an...@pc...>]

Steve Fischer wrote:

 > michael-
 >
 > try do() instead of execute().
 >
 > steve

Steve, this doesn't help very much. What mike is doing should work. Does
the object layer turn the autocommit option on query handles to off by
default? If so then a simple "$dbh->commit();" should do the trick. Also
if this is the case $dbh->do() wouldn't work either since it would still
need a commit.

Angel

 >
 > MICHAEL LUCHTAN wrote:
 >
 >> Hello all-
 >> In keeping with the spirit of only interacting with the gus database
 >> through perl modules (and in attempting to automate a repetitive
 >> task), I
 >> was trying to insert some things in the database by writing a plugin.  I
 >> use the gusconfig file to log into the data base like so:
 >> my $gusconfig= GUS::Common::GusConfig->new("$ARGV[1]");
 >> my $db= GUS::ObjRelP::DbiDatabase->new($gusconfig->getDbiDsn(),
 >>                                        $gusconfig->getDatabaseLogin(),
 >>                                        $gusconfig->getDatabasePassword,
 >>                                        1,0,1,
 >>                                        $gusconfig->getCoreSchemaName);
 >>
 >> And can read the database easily by commands like:
 >> $dbh= $db->getQueryHandle();
 >> $stmt= $dbh->prepare("select MAX(external_database_id) from
 >> sres.externaldatabase");
 >> $stmt->execute();
 >>
 >> But when I attempt to insert things in the database using the same
 >> paradigm, nothing gets inserted.  Foor example, the following code
 >> segment
 >> does NOT result in anything being inserted into the database:
 >>     $dbh= $db->getQueryHandle();
 >>        $stmt= $dbh->prepare("insert into sres.externaldatabase
 >> values($maxID, '$ucAbb', '$lcAbb', SYSDATE,1,1,1,1,1,0,6,3,2,1)");
 >>        $stmt->execute();
 >>
 >> But if I do the equivalent thing at an sql*plus prompt, using the same
 >> login information as was gotten from the gusconfiguration file, I am
 >> allowed to do an insertion.  Am I missing a commit option somewhere?
 >> Any helo would be appreciated.
 >>
 >>
 >> Michael Luchtan
 >> http://www.cs.uga.edu/~luchtan
 >>
 >>
 >>
 >>
 >> -------------------------------------------------------
 >> This SF.net email is sponsored by:  Etnus, makers of TotalView, The best
 >> thread debugger on the planet. Designed with thread debugging features
 >> you've never dreamed of, try TotalView 6 free at www.etnus.com.
 >> _______________________________________________
 >> Gusdev-gusdev mailing list
 >> Gus...@li...
 >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
 >>
 >>
 >
 >
 >
 >
 > -------------------------------------------------------
 > This SF.net email is sponsored by:  Etnus, makers of TotalView, The best
 > thread debugger on the planet. Designed with thread debugging features
 > you've never dreamed of, try TotalView 6 free at www.etnus.com.
 > _______________________________________________
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 > Gus...@li...
 > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] plug-in insertion question....

[Steve F. <st...@pc...>]

michael-

try do() instead of execute().

steve

MICHAEL LUCHTAN wrote:

>Hello all-
>In keeping with the spirit of only interacting with the gus database
>through perl modules (and in attempting to automate a repetitive task), I
>was trying to insert some things in the database by writing a plugin.  I
>use the gusconfig file to log into the data base like so:
>my $gusconfig= GUS::Common::GusConfig->new("$ARGV[1]");
>my $db= GUS::ObjRelP::DbiDatabase->new($gusconfig->getDbiDsn(),
>                                        $gusconfig->getDatabaseLogin(),
>                                        $gusconfig->getDatabasePassword,
>                                        1,0,1,
>                                        $gusconfig->getCoreSchemaName);
>
>And can read the database easily by commands like:
>$dbh= $db->getQueryHandle();
>$stmt= $dbh->prepare("select MAX(external_database_id) from
>sres.externaldatabase");
>$stmt->execute();
>
>But when I attempt to insert things in the database using the same
>paradigm, nothing gets inserted.  Foor example, the following code segment
>does NOT result in anything being inserted into the database:
>	$dbh= $db->getQueryHandle();
>        $stmt= $dbh->prepare("insert into sres.externaldatabase
>values($maxID, '$ucAbb', '$lcAbb', SYSDATE,1,1,1,1,1,0,6,3,2,1)");
>        $stmt->execute();
>
>But if I do the equivalent thing at an sql*plus prompt, using the same
>login information as was gotten from the gusconfiguration file, I am
>allowed to do an insertion.  Am I missing a commit option somewhere?
>Any helo would be appreciated.
>
>
> Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by:  Etnus, makers of TotalView, The best
>thread debugger on the planet. Designed with thread debugging features
>you've never dreamed of, try TotalView 6 free at www.etnus.com.
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] plug-in insertion question....

[MICHAEL L. <lu...@cs...>]

Hello all-
In keeping with the spirit of only interacting with the gus database
through perl modules (and in attempting to automate a repetitive task), I
was trying to insert some things in the database by writing a plugin.  I
use the gusconfig file to log into the data base like so:
my $gusconfig= GUS::Common::GusConfig->new("$ARGV[1]");
my $db= GUS::ObjRelP::DbiDatabase->new($gusconfig->getDbiDsn(),
                                        $gusconfig->getDatabaseLogin(),
                                        $gusconfig->getDatabasePassword,
                                        1,0,1,
                                        $gusconfig->getCoreSchemaName);

And can read the database easily by commands like:
$dbh= $db->getQueryHandle();
$stmt= $dbh->prepare("select MAX(external_database_id) from
sres.externaldatabase");
$stmt->execute();

But when I attempt to insert things in the database using the same
paradigm, nothing gets inserted.  Foor example, the following code segment
does NOT result in anything being inserted into the database:
	$dbh= $db->getQueryHandle();
        $stmt= $dbh->prepare("insert into sres.externaldatabase
values($maxID, '$ucAbb', '$lcAbb', SYSDATE,1,1,1,1,1,0,6,3,2,1)");
        $stmt->execute();

But if I do the equivalent thing at an sql*plus prompt, using the same
login information as was gotten from the gusconfiguration file, I am
allowed to do an insertion.  Am I missing a commit option somewhere?
Any helo would be appreciated.


 Michael Luchtan
http://www.cs.uga.edu/~luchtan

[Gusdev-gusdev] new feature: gusreport

[Steve F. <sfi...@pc...>]

folks-

i have checked into CVS a new GUS feature, gusreport.

gusreport prints tab-delimited reports on gus entities.  so far it has 
been configured to support gene and transcript reports, but can be 
configured to report on anything you would like.

the basic idea is that you paste together into one report columns that 
rely on a bunch of different queries.  so, the report you make can be 
much more powerful than what is possible with a single query.  

a "guru" (possibly you) sets up the configuration of a report for others 
to use (i have begun this for genes and transcripts).
a "user" calls gusreport, providing an sql query that designates the 
set, say, of genes to report and a list of supported columns to include

the guru can always define new columns to add to the configuration.

To install gusreport:
  - get the latest CVS version of GUS
  - build GUS install -append
  - rehash

to get help, just run gushome with no args.

steve