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Re: [Gusdev-gusdev] initial GO Files
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From: Terry C. <tw...@cs...> - 2003-07-03 22:47:42
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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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> > > > > > Data Reports, E-commerce, Portals, and Forums are available now.
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> > > > > > _______________________________________________
> > > > > > Gusdev-gusdev mailing list
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> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > -------------------------------------------------------
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> > > > > Data Reports, E-commerce, Portals, and Forums are available now.
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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.
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > > -------------------------------------------------------
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> > > _______________________________________________
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> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
>
>
> -------------------------------------------------------
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