Re: [Gusdev-gusdev] initial GO Files

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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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