Re: [Gusdev-gusdev] initial GO Files

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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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> 
> **************************************************************************************
> 
> 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.
> 
> 
> 
> 