Re: [Gusdev-gusdev] initial GO Files

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

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.