Re: [Gusdev-gusdev] initial GO Files

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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
>>>>>>
>>>>>>
>>>>>>
>>>>>>-------------------------------------------------------
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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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