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From: Angel P. <an...@pc...> - 2003-12-11 20:13:18
|
forgot to attach file |
|
From: Angel P. <an...@pc...> - 2003-12-11 20:12:28
|
Hello all folks using WDK classic. I know I spent a good bit of time trying to track down syntax errors (like trailing white space after "\" ) that cause servlet config files to be unparsable, so I committed a smal perl script that does some very basic syntax checking of the config files. The script is attached. Angel |
|
From: Deborah F. P. <pi...@pc...> - 2003-12-11 16:43:14
|
Hi,
I am sorry but I should have looked more closely at your query as I only
addressed one problem.
idSQL should be an sql statement that retrieves the primary keys of the
rows that should be deleted. Here, it would be:
--idSQL "select nrdb_entry_id from dots.nrdbentry where nrdb_entry_id = 3"
I don't think the error you got was caused by using the wrong sql
statement. Try running with this and --verbose and see if you still get an
error.
Debbie
On Thu, 11 Dec 2003, sucheta Tripathy wrote:
> Hi ,
>
> After I tried the query you suggested it gives the following error.
>
> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> (perhaps you
> need to call execute first) [for Statement "delete from DoTS.NRDBEntry
> where nr
> db_entry_id=3"] at /home/apps/gus/gushome/bin/deleteEntries.pl line 51.
> deleting 0 ids from DoTS::NRDBEntry
>
> Sucheta
> > Hi,
> >
> > The sql query should have been --idSQL 'delete from DoTS.NRDBEntry
> > where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry...
> >
> > Debbie
> >
> >
> > On Wed, 10 Dec 2003, sucheta Tripathy wrote:
> >
> >>
> >> Hi,
> >>
> >> I have been trying to use the deleteEntries.pl program to delete some of
> >> the rows inserted into the DoTS::NRDBEntry table.
> >>
> >> First it gave an insufficient privilege error, so when we looked at the
> >> code at line 30, 31, we noticed, it calls the
> >> $gusconfig->getReadOnlyDatabaseLogin(),
> >> $gusconfig->getReadOnlyDatabasePassword()
> >>
> >> which has only readonly privileges (From the .gus.properties file).
> >>
> >> So I changed it to
> >>
> >> $gusconfig->getDatabaseLogin(),
> >> $gusconfig->getDatabasePassword(), at those 2 lines which has read,
> >> write,
> >> delete privileges.
> >>
> >> The options I have used are:
> >>
> >> deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where
> >> nrdb_entry_id=1' --table DoTS::NRDBEntry
> >>
> >> It is throwing the following errors:
> >>
> >> Reading properties from /home/apps/gus/.gus.properties
> >> The login is GUSrw
> >> DBD::Oracle::st execute failed: ORA-00933: SQL command not properly
> >> ended
> >> (DBD E
> >> RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where
> >> nrdb_ent
> >> ry_id=3" with ParamValues: :NRDBEntry=undef] at
> >> /home/apps/gus/gushome/lib/perl/
> >> GUS/ObjRelP/DbiDbHandle.pm line 82.
> >> Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR:
> >> OCIStmtExe
> >> cute)
> >> sql_cmd:
> >> delete from DoTS::NRDBEntry where nrdb_entry_id=3
> >> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> >> (perhaps you
> >> need to call execute first) [for Statement "delete from DoTS::NRDBEntry
> >> where n
> >> rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at
> >> /home/apps/gus/gushome/bi
> >> n/deleteEntries.pl line 51.
> >> deleting ids from DoTS::NRDBEntry
> >>
> >
>
>
>
|
|
From: Steve F. <sfi...@pc...> - 2003-12-11 16:20:17
|
ok, debbie spotted the problem: your SQL is a delete statement. but, it is supposed to be a select statement to select the entries to delete. steve sucheta Tripathy wrote: >Hi Steve, > >I am using the updated DbiDbHandle.pm from the repository. >The query works fine at the SQL prompt. > >Sucheta > > > >>Sucheta- >> >>Thanks for your patience around this. >> >>I have just looked at deleteEntries.pl, on the line where the failure is. >> >>I believe you are still passing it an invalid SQL. The 'nr' is >>suspicious. >> >>Here is a general hint: when you write SQL to pass to a plugin or >>script, it is a good practice to test the SQL first in sqplus or >>whatever interface you use. >> >>That said, the script should give a better message. Can you take a >>look in $PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm, near the top, >>and tell me what CVS version the file is? You may have a slightly old >>one which doesn't have the latest improvements in error handling. >> >>steve >> >> >> >>sucheta Tripathy wrote: >> >> >> >>>Hi , >>> >>>After I tried the query you suggested it gives the following error. >>> >>>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >>>(perhaps you >>>need to call execute first) [for Statement "delete from DoTS.NRDBEntry >>>where nr >>>db_entry_id=3"] at /home/apps/gus/gushome/bin/deleteEntries.pl line 51. >>>deleting ids from DoTS::NRDBEntry >>> >>>Sucheta >>> >>> >>> >>> >>>>Hi, >>>> >>>>The sql query should have been --idSQL 'delete from DoTS.NRDBEntry >>>>where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry... >>>> >>>> Debbie >>>> >>>> >>>>On Wed, 10 Dec 2003, sucheta Tripathy wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hi, >>>>> >>>>>I have been trying to use the deleteEntries.pl program to delete some >>>>>of >>>>>the rows inserted into the DoTS::NRDBEntry table. >>>>> >>>>>First it gave an insufficient privilege error, so when we looked at the >>>>>code at line 30, 31, we noticed, it calls the >>>>>$gusconfig->getReadOnlyDatabaseLogin(), >>>>>$gusconfig->getReadOnlyDatabasePassword() >>>>> >>>>>which has only readonly privileges (From the .gus.properties file). >>>>> >>>>>So I changed it to >>>>> >>>>>$gusconfig->getDatabaseLogin(), >>>>>$gusconfig->getDatabasePassword(), at those 2 lines which has read, >>>>>write, >>>>>delete privileges. >>>>> >>>>>The options I have used are: >>>>> >>>>>deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where >>>>>nrdb_entry_id=1' --table DoTS::NRDBEntry >>>>> >>>>>It is throwing the following errors: >>>>> >>>>>Reading properties from /home/apps/gus/.gus.properties >>>>>The login is GUSrw >>>>>DBD::Oracle::st execute failed: ORA-00933: SQL command not properly >>>>>ended >>>>>(DBD E >>>>>RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where >>>>>nrdb_ent >>>>>ry_id=3" with ParamValues: :NRDBEntry=undef] at >>>>>/home/apps/gus/gushome/lib/perl/ >>>>>GUS/ObjRelP/DbiDbHandle.pm line 82. >>>>>Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR: >>>>>OCIStmtExe >>>>>cute) >>>>>sql_cmd: >>>>>delete from DoTS::NRDBEntry where nrdb_entry_id=3 >>>>>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >>>>>(perhaps you >>>>>need to call execute first) [for Statement "delete from >>>>>DoTS::NRDBEntry >>>>>where n >>>>>rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at >>>>>/home/apps/gus/gushome/bi >>>>>n/deleteEntries.pl line 51. >>>>>deleting ids from DoTS::NRDBEntry >>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >>> >>> > > > > |
|
From: sucheta T. <su...@vb...> - 2003-12-11 16:17:35
|
Thanks, It works now. Sucheta > Hi, > > I am sorry but I should have looked more closely at your query as I only > addressed one problem. > > idSQL should be an sql statement that retrieves the primary keys of the > rows that should be deleted. Here, it would be: > > --idSQL "select nrdb_entry_id from dots.nrdbentry where nrdb_entry_id = 3" > > I don't think the error you got was caused by using the wrong sql > statement. Try running with this and --verbose and see if you still get an > error. > > Debbie > > > > > > > On Thu, 11 Dec 2003, sucheta Tripathy wrote: > >> Hi , >> >> After I tried the query you suggested it gives the following error. >> >> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >> (perhaps you >> need to call execute first) [for Statement "delete from DoTS.NRDBEntry >> where nr >> db_entry_id=3"] at /home/apps/gus/gushome/bin/deleteEntries.pl line 51. >> deleting ids from DoTS::NRDBEntry >> >> Sucheta >> > Hi, >> > >> > The sql query should have been --idSQL 'delete from DoTS.NRDBEntry >> > where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry... >> > >> > Debbie >> > >> > >> > On Wed, 10 Dec 2003, sucheta Tripathy wrote: >> > >> >> >> >> Hi, >> >> >> >> I have been trying to use the deleteEntries.pl program to delete some >> of >> >> the rows inserted into the DoTS::NRDBEntry table. >> >> >> >> First it gave an insufficient privilege error, so when we looked at >> the >> >> code at line 30, 31, we noticed, it calls the >> >> $gusconfig->getReadOnlyDatabaseLogin(), >> >> $gusconfig->getReadOnlyDatabasePassword() >> >> >> >> which has only readonly privileges (From the .gus.properties file). >> >> >> >> So I changed it to >> >> >> >> $gusconfig->getDatabaseLogin(), >> >> $gusconfig->getDatabasePassword(), at those 2 lines which has read, >> >> write, >> >> delete privileges. >> >> >> >> The options I have used are: >> >> >> >> deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where >> >> nrdb_entry_id=1' --table DoTS::NRDBEntry >> >> >> >> It is throwing the following errors: >> >> >> >> Reading properties from /home/apps/gus/.gus.properties >> >> The login is GUSrw >> >> DBD::Oracle::st execute failed: ORA-00933: SQL command not properly >> >> ended >> >> (DBD E >> >> RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry >> where >> >> nrdb_ent >> >> ry_id=3" with ParamValues: :NRDBEntry=undef] at >> >> /home/apps/gus/gushome/lib/perl/ >> >> GUS/ObjRelP/DbiDbHandle.pm line 82. >> >> Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR: >> >> OCIStmtExe >> >> cute) >> >> sql_cmd: >> >> delete from DoTS::NRDBEntry where nrdb_entry_id=3 >> >> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >> >> (perhaps you >> >> need to call execute first) [for Statement "delete from >> DoTS::NRDBEntry >> >> where n >> >> rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at >> >> /home/apps/gus/gushome/bi >> >> n/deleteEntries.pl line 51. >> >> deleting ids from DoTS::NRDBEntry >> >> >> > >> >> >> > -- Sucheta Tripathy Virginia Bioinformatics Institute 1880 pratt drive,Bldg XV Virginia tech. Blacksburg Virginia VA 24061 phone-(540)231-8138 |
|
From: sucheta T. <su...@vb...> - 2003-12-11 16:12:59
|
Hi Steve, I am using the updated DbiDbHandle.pm from the repository. The query works fine at the SQL prompt. Sucheta > Sucheta- > > Thanks for your patience around this. > > I have just looked at deleteEntries.pl, on the line where the failure is. > > I believe you are still passing it an invalid SQL. The 'nr' is > suspicious. > > Here is a general hint: when you write SQL to pass to a plugin or > script, it is a good practice to test the SQL first in sqplus or > whatever interface you use. > > That said, the script should give a better message. Can you take a > look in $PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm, near the top, > and tell me what CVS version the file is? You may have a slightly old > one which doesn't have the latest improvements in error handling. > > steve > > > > sucheta Tripathy wrote: > >>Hi , >> >>After I tried the query you suggested it gives the following error. >> >>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >>(perhaps you >> need to call execute first) [for Statement "delete from DoTS.NRDBEntry >>where nr >>db_entry_id=3"] at /home/apps/gus/gushome/bin/deleteEntries.pl line 51. >>deleting ids from DoTS::NRDBEntry >> >>Sucheta >> >> >>>Hi, >>> >>>The sql query should have been --idSQL 'delete from DoTS.NRDBEntry >>>where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry... >>> >>> Debbie >>> >>> >>>On Wed, 10 Dec 2003, sucheta Tripathy wrote: >>> >>> >>> >>>>Hi, >>>> >>>>I have been trying to use the deleteEntries.pl program to delete some >>>> of >>>>the rows inserted into the DoTS::NRDBEntry table. >>>> >>>>First it gave an insufficient privilege error, so when we looked at the >>>>code at line 30, 31, we noticed, it calls the >>>>$gusconfig->getReadOnlyDatabaseLogin(), >>>>$gusconfig->getReadOnlyDatabasePassword() >>>> >>>>which has only readonly privileges (From the .gus.properties file). >>>> >>>>So I changed it to >>>> >>>>$gusconfig->getDatabaseLogin(), >>>>$gusconfig->getDatabasePassword(), at those 2 lines which has read, >>>>write, >>>>delete privileges. >>>> >>>>The options I have used are: >>>> >>>>deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where >>>>nrdb_entry_id=1' --table DoTS::NRDBEntry >>>> >>>>It is throwing the following errors: >>>> >>>>Reading properties from /home/apps/gus/.gus.properties >>>>The login is GUSrw >>>>DBD::Oracle::st execute failed: ORA-00933: SQL command not properly >>>>ended >>>>(DBD E >>>>RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where >>>>nrdb_ent >>>>ry_id=3" with ParamValues: :NRDBEntry=undef] at >>>>/home/apps/gus/gushome/lib/perl/ >>>>GUS/ObjRelP/DbiDbHandle.pm line 82. >>>>Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR: >>>>OCIStmtExe >>>>cute) >>>> sql_cmd: >>>> delete from DoTS::NRDBEntry where nrdb_entry_id=3 >>>>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >>>>(perhaps you >>>> need to call execute first) [for Statement "delete from >>>> DoTS::NRDBEntry >>>>where n >>>>rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at >>>>/home/apps/gus/gushome/bi >>>>n/deleteEntries.pl line 51. >>>>deleting ids from DoTS::NRDBEntry >>>> >>>> >>>> >> >> >> >> > -- Sucheta Tripathy Virginia Bioinformatics Institute 1880 pratt drive,Bldg XV Virginia tech. Blacksburg Virginia VA 24061 phone-(540)231-8138 |
|
From: Steve F. <sfi...@pc...> - 2003-12-11 15:51:36
|
Sucheta- Thanks for your patience around this. I have just looked at deleteEntries.pl, on the line where the failure is. I believe you are still passing it an invalid SQL. The 'nr' is suspicious. Here is a general hint: when you write SQL to pass to a plugin or script, it is a good practice to test the SQL first in sqplus or whatever interface you use. That said, the script should give a better message. Can you take a look in $PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm, near the top, and tell me what CVS version the file is? You may have a slightly old one which doesn't have the latest improvements in error handling. steve sucheta Tripathy wrote: >Hi , > >After I tried the query you suggested it gives the following error. > >DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >(perhaps you > need to call execute first) [for Statement "delete from DoTS.NRDBEntry >where nr >db_entry_id=3"] at /home/apps/gus/gushome/bin/deleteEntries.pl line 51. >deleting 0 ids from DoTS::NRDBEntry > >Sucheta > > >>Hi, >> >>The sql query should have been --idSQL 'delete from DoTS.NRDBEntry >>where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry... >> >> Debbie >> >> >>On Wed, 10 Dec 2003, sucheta Tripathy wrote: >> >> >> >>>Hi, >>> >>>I have been trying to use the deleteEntries.pl program to delete some of >>>the rows inserted into the DoTS::NRDBEntry table. >>> >>>First it gave an insufficient privilege error, so when we looked at the >>>code at line 30, 31, we noticed, it calls the >>>$gusconfig->getReadOnlyDatabaseLogin(), >>>$gusconfig->getReadOnlyDatabasePassword() >>> >>>which has only readonly privileges (From the .gus.properties file). >>> >>>So I changed it to >>> >>>$gusconfig->getDatabaseLogin(), >>>$gusconfig->getDatabasePassword(), at those 2 lines which has read, >>>write, >>>delete privileges. >>> >>>The options I have used are: >>> >>>deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where >>>nrdb_entry_id=1' --table DoTS::NRDBEntry >>> >>>It is throwing the following errors: >>> >>>Reading properties from /home/apps/gus/.gus.properties >>>The login is GUSrw >>>DBD::Oracle::st execute failed: ORA-00933: SQL command not properly >>>ended >>>(DBD E >>>RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where >>>nrdb_ent >>>ry_id=3" with ParamValues: :NRDBEntry=undef] at >>>/home/apps/gus/gushome/lib/perl/ >>>GUS/ObjRelP/DbiDbHandle.pm line 82. >>>Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR: >>>OCIStmtExe >>>cute) >>> sql_cmd: >>> delete from DoTS::NRDBEntry where nrdb_entry_id=3 >>>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >>>(perhaps you >>> need to call execute first) [for Statement "delete from DoTS::NRDBEntry >>>where n >>>rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at >>>/home/apps/gus/gushome/bi >>>n/deleteEntries.pl line 51. >>>deleting ids from DoTS::NRDBEntry >>> >>> >>> > > > > |
|
From: Steve F. <sfi...@pc...> - 2003-12-11 15:42:43
|
Agreed. Debbie and I just reviewed the plugin. It is now on GUS::Common component's to-do list to fix this. steve Fidel Salas wrote: >I do not think so. I would expect for the plugin to let the user know >what options are required. That has been the case with other >plugins I have tried. In fact, the protocol I use when trying >plugins is to use as few options as possible and let the plugin >tell me what options are required. > >Fidel > > >Steve Fischer <sfi...@pc...> writes: > > > Does it make sense from the plugin user's perspective for it to have > > this behavior? > > > > steve > > > > Deborah F. Pinney wrote: > > >>>Hi, >>> >>>Regular expressions are needed for this plugin to recognize the source_id, >>>secondary identifier, name, and several other attributes. It doesn't die >>>and give an error when not given these regex because the plugin is not >>>data source specific. When you ran the plugin, it performed normaly >>>by entering the parameter settings and algorithm invocation but as >>>there were no regex defining specific attributes,it processed the >>>file without recoginizing the values it needed to successfully >>>insert into dots.externalnasequence. >>>Debbie On Wed, 10 Dec 2003, Fidel Salas wrote: >>> >>> >>> >>> >>>>Folks, >>>> >>>>I am revisiting an issue with the InsertNewExternalSequences plugin >>>>that was not answered to a post by Sucheta on 11-21-2003. >>>> >>>>I have also tried the InsertNewExternalSequences plugin with similar >>>>results to the ones she reported. The comman issued is: >>>>ga GUS::Common::Plugin::InsertNewExternalSequences \ >>>> --external_database_release_id=138 \ >>>> --table_name=DoTS::ExternalNASequence \ >>>> --sequencefile=soybean-one \ >>>> --debug --sqlVerbose --commit >& soybean-one.out >>>> >>>>The soybean-one file contains: >>>> >>>> >>>> >>>>>psHA001iA02r >>>>> >>>>> >>>>> >>>>TCAGNGCCTNCTTCTGGTCTCCCTGGTGTTGGTCTCCTACGCTGCCCGGTCGGAATCAGCGCTGGGCGGCTGGAGCCCCAT >>>>CAAGGACGTAAACGACAGCCACGTGGCGGAGATCGCCAACTACGCTCTGAGCGAGTACGACAAGCGTTCTGGGGCCAAGCT >>>>CACCCTTGTCAAGGTCGTCAAGGGCGAGACTCAGGTCGTTTCCGGCACCAACTACCGTCTCGTCCTCAAAGCCAAGGATGG >>>>ATCCGCCACGGCCAGTTACGAAGCCATCGTCTGGGAGAAGCCTTGGCTCCATTTCATGAATCTCACTTCCTTCAAACCCCT >>>>TCATTAATCTTAGACCCATACTTTTCTTCACTTTCTCTCTTATCATATTTCATGTGTTAGCTATTCTGTTTTTCTCAATAA >>>>GGTTCCTGTCATGTGCTAATGAATCTCAAATTGTATGTTGGATTATGGATTCCTC >>>> >>>>The plugin finishes and the output file ends with: >>>>output: > sqlExec: output: > UPDATE Core.AlgorithmInvocation >>>>output: > SET output: > modification_date = SYSDATE, >>>>output: > end_time = SYSDATE, >>>>output: > row_alg_invocation_id = ?, >>>>output: > result = ? >>>>output: > WHERE algorithm_invocation_id = ? >>>>output: > bindValues (24971, Run finished: Processed 1, inserted 28 and updated sequences from file soybean-one, 24971) >>>>output: > DbiHandle:sqlExec:insert succeeded 1 row(s) >>>> >>>>Looking through the output file one finds that there were 29 'insert into' statements, >>>>28 into Core.AlgorithmParam and one into Core.AlgorithmInvocation (see below). >>>>There was not a single attempt to insert into the ExternalNASequence table. >>>> >>>>Does anyone know what is going on here? >>>> >>>>Thanks >>>> >>>>Fidel >>>> >>>> >>>>output: 68: 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 ) >>>>output: 429: 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 ) >>>>output: 484: 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 ) >>>>output: 535: 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 ) >>>>output: 590: 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 ) >>>>output: 643: 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 ) >>>>output: 694: 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 ) >>>>output: 745: 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 ) >>>>output: 798: 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 ) >>>>output: 851: 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 ) >>>>output: 904: 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 ) >>>>output: 955: 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 ) >>>>output: 1006: 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 ) >>>>output: 1057: 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 ) >>>>output: 1108: 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 ) >>>>output: 1159: 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 ) >>>>output: 1210: 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 ) >>>>output: 1261: 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 ) >>>>output: 1312: 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 ) >>>>output: 1365: 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 ) >>>>output: 1416: 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 ) >>>>output: 1469: 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 ) >>>>output: 1520: 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 ) >>>>output: 1573: 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 ) >>>>output: 1626: 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 ) >>>>output: 1679: 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 ) >>>>output: 1732: 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 ) >>>>output: 1783: 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 ) >>>>output: 1834: 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 ) >>>> >>>> >>>> >>>>------------------------------------------------------- >>>>This SF.net email is sponsored by: SF.net Giveback Program. >>>>Does SourceForge.net help you be more productive? Does it >>>>help you create better code? SHARE THE LOVE, and help us help >>>>YOU! Click Here: http://sourceforge.net/donate/ >>>>_______________________________________________ >>>>Gusdev-gusdev mailing list >>>>Gus...@li... >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> >>> >>>------------------------------------------------------- >>>This SF.net email is sponsored by: SF.net Giveback Program. >>>Does SourceForge.net help you be more productive? Does it >>>help you create better code? SHARE THE LOVE, and help us help >>>YOU! Click Here: http://sourceforge.net/donate/ >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> |
|
From: sucheta T. <su...@vb...> - 2003-12-11 15:16:40
|
Hi , After I tried the query you suggested it gives the following error. DBD::Oracle::st fetchrow_array failed: ERROR no statement executing (perhaps you need to call execute first) [for Statement "delete from DoTS.NRDBEntry where nr db_entry_id=3"] at /home/apps/gus/gushome/bin/deleteEntries.pl line 51. deleting 0 ids from DoTS::NRDBEntry Sucheta > Hi, > > The sql query should have been --idSQL 'delete from DoTS.NRDBEntry > where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry... > > Debbie > > > On Wed, 10 Dec 2003, sucheta Tripathy wrote: > >> >> Hi, >> >> I have been trying to use the deleteEntries.pl program to delete some of >> the rows inserted into the DoTS::NRDBEntry table. >> >> First it gave an insufficient privilege error, so when we looked at the >> code at line 30, 31, we noticed, it calls the >> $gusconfig->getReadOnlyDatabaseLogin(), >> $gusconfig->getReadOnlyDatabasePassword() >> >> which has only readonly privileges (From the .gus.properties file). >> >> So I changed it to >> >> $gusconfig->getDatabaseLogin(), >> $gusconfig->getDatabasePassword(), at those 2 lines which has read, >> write, >> delete privileges. >> >> The options I have used are: >> >> deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where >> nrdb_entry_id=1' --table DoTS::NRDBEntry >> >> It is throwing the following errors: >> >> Reading properties from /home/apps/gus/.gus.properties >> The login is GUSrw >> DBD::Oracle::st execute failed: ORA-00933: SQL command not properly >> ended >> (DBD E >> RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where >> nrdb_ent >> ry_id=3" with ParamValues: :NRDBEntry=undef] at >> /home/apps/gus/gushome/lib/perl/ >> GUS/ObjRelP/DbiDbHandle.pm line 82. >> Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR: >> OCIStmtExe >> cute) >> sql_cmd: >> delete from DoTS::NRDBEntry where nrdb_entry_id=3 >> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing >> (perhaps you >> need to call execute first) [for Statement "delete from DoTS::NRDBEntry >> where n >> rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at >> /home/apps/gus/gushome/bi >> n/deleteEntries.pl line 51. >> deleting ids from DoTS::NRDBEntry >> > -- Sucheta Tripathy Virginia Bioinformatics Institute 1880 pratt drive,Bldg XV Virginia tech. Blacksburg Virginia VA 24061 phone-(540)231-8138 |
|
From: Fidel S. <fi...@vb...> - 2003-12-11 15:14:05
|
I do not think so. I would expect for the plugin to let the user know
what options are required. That has been the case with other
plugins I have tried. In fact, the protocol I use when trying
plugins is to use as few options as possible and let the plugin
tell me what options are required.
Fidel
Steve Fischer <sfi...@pc...> writes:
> Does it make sense from the plugin user's perspective for it to have
> this behavior?
>
> steve
>
> Deborah F. Pinney wrote:
>
>>Hi,
>>
>>Regular expressions are needed for this plugin to recognize the source_id,
>>secondary identifier, name, and several other attributes. It doesn't die
>>and give an error when not given these regex because the plugin is not
>> data source specific. When you ran the plugin, it performed normaly
>> by entering the parameter settings and algorithm invocation but as
>> there were no regex defining specific attributes,it processed the
>> file without recoginizing the values it needed to successfully
>> insert into dots.externalnasequence.
>> Debbie On Wed, 10 Dec 2003, Fidel Salas wrote:
>>
>>
>>>Folks,
>>>
>>>I am revisiting an issue with the InsertNewExternalSequences plugin
>>>that was not answered to a post by Sucheta on 11-21-2003.
>>>
>>>I have also tried the InsertNewExternalSequences plugin with similar
>>>results to the ones she reported. The comman issued is:
>>>ga GUS::Common::Plugin::InsertNewExternalSequences \
>>> --external_database_release_id=138 \
>>> --table_name=DoTS::ExternalNASequence \
>>> --sequencefile=soybean-one \
>>> --debug --sqlVerbose --commit >& soybean-one.out
>>>
>>>The soybean-one file contains:
>>>
>>>>psHA001iA02r
>>>>
>>>TCAGNGCCTNCTTCTGGTCTCCCTGGTGTTGGTCTCCTACGCTGCCCGGTCGGAATCAGCGCTGGGCGGCTGGAGCCCCAT
>>>CAAGGACGTAAACGACAGCCACGTGGCGGAGATCGCCAACTACGCTCTGAGCGAGTACGACAAGCGTTCTGGGGCCAAGCT
>>>CACCCTTGTCAAGGTCGTCAAGGGCGAGACTCAGGTCGTTTCCGGCACCAACTACCGTCTCGTCCTCAAAGCCAAGGATGG
>>>ATCCGCCACGGCCAGTTACGAAGCCATCGTCTGGGAGAAGCCTTGGCTCCATTTCATGAATCTCACTTCCTTCAAACCCCT
>>>TCATTAATCTTAGACCCATACTTTTCTTCACTTTCTCTCTTATCATATTTCATGTGTTAGCTATTCTGTTTTTCTCAATAA
>>>GGTTCCTGTCATGTGCTAATGAATCTCAAATTGTATGTTGGATTATGGATTCCTC
>>>
>>>The plugin finishes and the output file ends with:
>>> output: > sqlExec: output: > UPDATE Core.AlgorithmInvocation
>>> output: > SET output: > modification_date = SYSDATE,
>>>output: > end_time = SYSDATE,
>>>output: > row_alg_invocation_id = ?,
>>>output: > result = ?
>>>output: > WHERE algorithm_invocation_id = ?
>>>output: > bindValues (24971, Run finished: Processed 1, inserted 28 and updated sequences from file soybean-one, 24971)
>>>output: > DbiHandle:sqlExec:insert succeeded 1 row(s)
>>>
>>>Looking through the output file one finds that there were 29 'insert into' statements,
>>>28 into Core.AlgorithmParam and one into Core.AlgorithmInvocation (see below).
>>>There was not a single attempt to insert into the ExternalNASequence table.
>>>
>>>Does anyone know what is going on here?
>>>
>>>Thanks
>>>
>>>Fidel
>>>
>>>
>>>output: 68: 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 )
>>>output: 429: 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 )
>>>output: 484: 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 )
>>>output: 535: 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 )
>>>output: 590: 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 )
>>>output: 643: 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 )
>>>output: 694: 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 )
>>>output: 745: 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 )
>>>output: 798: 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 )
>>>output: 851: 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 )
>>>output: 904: 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 )
>>>output: 955: 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 )
>>>output: 1006: 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 )
>>>output: 1057: 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 )
>>>output: 1108: 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 )
>>>output: 1159: 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 )
>>>output: 1210: 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 )
>>>output: 1261: 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 )
>>>output: 1312: 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 )
>>>output: 1365: 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 )
>>>output: 1416: 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 )
>>>output: 1469: 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 )
>>>output: 1520: 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 )
>>>output: 1573: 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 )
>>>output: 1626: 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 )
>>>output: 1679: 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 )
>>>output: 1732: 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 )
>>>output: 1783: 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 )
>>>output: 1834: 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 )
>>>
>>>
>>>
>>>-------------------------------------------------------
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>>-------------------------------------------------------
>>This SF.net email is sponsored by: SF.net Giveback Program.
>>Does SourceForge.net help you be more productive? Does it
>>help you create better code? SHARE THE LOVE, and help us help
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|
From: Steve F. <sfi...@pc...> - 2003-12-11 15:03:32
|
Does it make sense from the plugin user's perspective for it to have this behavior? steve Deborah F. Pinney wrote: >Hi, > >Regular expressions are needed for this plugin to recognize the source_id, >secondary identifier, name, and several other attributes. It doesn't die >and give an error when not given these regex because the plugin is not >data source specific. When you ran the plugin, it performed normaly >by entering the parameter settings and algorithm invocation but as there >were no regex defining specific attributes,it processed the file >without recoginizing the values it needed to successfully insert into >dots.externalnasequence. > > Debbie > >On Wed, 10 Dec 2003, Fidel Salas wrote: > > > >>Folks, >> >>I am revisiting an issue with the InsertNewExternalSequences plugin >>that was not answered to a post by Sucheta on 11-21-2003. >> >>I have also tried the InsertNewExternalSequences plugin with similar >>results to the ones she reported. The comman issued is: >>ga GUS::Common::Plugin::InsertNewExternalSequences \ >> --external_database_release_id=138 \ >> --table_name=DoTS::ExternalNASequence \ >> --sequencefile=soybean-one \ >> --debug --sqlVerbose --commit >& soybean-one.out >> >>The soybean-one file contains: >> >> >>>psHA001iA02r >>> >>> >>TCAGNGCCTNCTTCTGGTCTCCCTGGTGTTGGTCTCCTACGCTGCCCGGTCGGAATCAGCGCTGGGCGGCTGGAGCCCCAT >>CAAGGACGTAAACGACAGCCACGTGGCGGAGATCGCCAACTACGCTCTGAGCGAGTACGACAAGCGTTCTGGGGCCAAGCT >>CACCCTTGTCAAGGTCGTCAAGGGCGAGACTCAGGTCGTTTCCGGCACCAACTACCGTCTCGTCCTCAAAGCCAAGGATGG >>ATCCGCCACGGCCAGTTACGAAGCCATCGTCTGGGAGAAGCCTTGGCTCCATTTCATGAATCTCACTTCCTTCAAACCCCT >>TCATTAATCTTAGACCCATACTTTTCTTCACTTTCTCTCTTATCATATTTCATGTGTTAGCTATTCTGTTTTTCTCAATAA >>GGTTCCTGTCATGTGCTAATGAATCTCAAATTGTATGTTGGATTATGGATTCCTC >> >>The plugin finishes and the output file ends with: >>output: > sqlExec: >>output: > UPDATE Core.AlgorithmInvocation >>output: > SET >>output: > modification_date = SYSDATE, >>output: > end_time = SYSDATE, >>output: > row_alg_invocation_id = ?, >>output: > result = ? >>output: > WHERE algorithm_invocation_id = ? >>output: > bindValues (24971, Run finished: Processed 1, inserted 28 and updated sequences from file soybean-one, 24971) >>output: > DbiHandle:sqlExec:insert succeeded 1 row(s) >> >>Looking through the output file one finds that there were 29 'insert into' statements, >>28 into Core.AlgorithmParam and one into Core.AlgorithmInvocation (see below). >>There was not a single attempt to insert into the ExternalNASequence table. >> >>Does anyone know what is going on here? >> >>Thanks >> >>Fidel >> >> >>output: 68: 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 ) >>output: 429: 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 ) >>output: 484: 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 ) >>output: 535: 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 ) >>output: 590: 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 ) >>output: 643: 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 ) >>output: 694: 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 ) >>output: 745: 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 ) >>output: 798: 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 ) >>output: 851: 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 ) >>output: 904: 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 ) >>output: 955: 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 ) >>output: 1006: 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 ) >>output: 1057: 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 ) >>output: 1108: 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 ) >>output: 1159: 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 ) >>output: 1210: 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 ) >>output: 1261: 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 ) >>output: 1312: 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 ) >>output: 1365: 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 ) >>output: 1416: 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 ) >>output: 1469: 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 ) >>output: 1520: 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 ) >>output: 1573: 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 ) >>output: 1626: 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 ) >>output: 1679: 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 ) >>output: 1732: 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 ) >>output: 1783: 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 ) >>output: 1834: 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 ) >> >> >> >>------------------------------------------------------- >>This SF.net email is sponsored by: SF.net Giveback Program. >>Does SourceForge.net help you be more productive? Does it >>help you create better code? SHARE THE LOVE, and help us help >>YOU! Click Here: http://sourceforge.net/donate/ >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> > > > >------------------------------------------------------- >This SF.net email is sponsored by: SF.net Giveback Program. >Does SourceForge.net help you be more productive? Does it >help you create better code? SHARE THE LOVE, and help us help >YOU! Click Here: http://sourceforge.net/donate/ >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Pjm <pj...@sa...> - 2003-12-11 14:00:00
|
Hi Chetna, Terry, I dunno if this has already been answered. Apologies if so. The Pfam-A.full file I used has duplicate entries which is quite normal. In this cut down example you can see two database references to the same protein but the numbers following it are different; # STOCKHOLM 1.0 #=GF ID Acyl_CoA_thio . . #=GF DR PDB; 1c8u A; 147; 281; #=GF DR PDB; 1c8u B; 147; 281; #=GF DR PDB; 1c8u A; 17; 115; #=GF DR PDB; 1c8u B; 17; 115; The numbers are the co-ords on the protein that match up to PF02551. Because the code tries to create another DoTS.DbRefPfamEntry for both of these entries it gives a warning for each. Duplicate reference to db_ref_id 1351 from pfam_entry_id 91 Duplicate reference to db_ref_id 1352 from pfam_entry_id 91 Does this help? Paul. Chetna Warade wrote: > Hello Terry, > > Thanks for the log. I am looking at it and observed > that the pfam_entry_id in your log is a continous > number from the log whereas for me its different. > > Thanks again, > Chetna > > --- Terry Clark <tw...@cs...> wrote: > >>Hi, Chetna, >>I also experienced numerous duplicate entries in the >>pfam load. >>I assumed these were problems with Pfam >>organization, and not >>being a priority to me, I did not track them down; >>but I have >>a not in my log to do so. I've attached my Pfam load >>output >>for comparison. >> >>Terry >> >> >> >>On 0, Chetna Warade <wa...@ya...> wrote: >> >>>Hello Debbie, >>> >>>I am loading (commit) Pfam data in GUS from >> >>scratch. >> >>>I am getting few duplicate errors e.g. >>> >>>Duplicate reference to db_ref_id 621 from >>>pfam_entry_id 1073 >>> >>>Is this behavior okey? If not do you have any idea >>>about fixes for this. >>> >>>Thanks in advance, >>>Chetna >>> > > > > > __________________________________ > Do you Yahoo!? > New Yahoo! Photos - easier uploading and sharing. > http://photos.yahoo.com/ > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Deborah F. P. <pi...@pc...> - 2003-12-11 12:43:29
|
Hi,
Regular expressions are needed for this plugin to recognize the source_id,
secondary identifier, name, and several other attributes. It doesn't die
and give an error when not given these regex because the plugin is not
data source specific. When you ran the plugin, it performed normaly
by entering the parameter settings and algorithm invocation but as there
were no regex defining specific attributes,it processed the file
without recoginizing the values it needed to successfully insert into
dots.externalnasequence.
Debbie
On Wed, 10 Dec 2003, Fidel Salas wrote:
> Folks,
>
> I am revisiting an issue with the InsertNewExternalSequences plugin
> that was not answered to a post by Sucheta on 11-21-2003.
>
> I have also tried the InsertNewExternalSequences plugin with similar
> results to the ones she reported. The comman issued is:
> ga GUS::Common::Plugin::InsertNewExternalSequences \
> --external_database_release_id=138 \
> --table_name=DoTS::ExternalNASequence \
> --sequencefile=soybean-one \
> --debug --sqlVerbose --commit >& soybean-one.out
>
> The soybean-one file contains:
> >psHA001iA02r
> TCAGNGCCTNCTTCTGGTCTCCCTGGTGTTGGTCTCCTACGCTGCCCGGTCGGAATCAGCGCTGGGCGGCTGGAGCCCCAT
> CAAGGACGTAAACGACAGCCACGTGGCGGAGATCGCCAACTACGCTCTGAGCGAGTACGACAAGCGTTCTGGGGCCAAGCT
> CACCCTTGTCAAGGTCGTCAAGGGCGAGACTCAGGTCGTTTCCGGCACCAACTACCGTCTCGTCCTCAAAGCCAAGGATGG
> ATCCGCCACGGCCAGTTACGAAGCCATCGTCTGGGAGAAGCCTTGGCTCCATTTCATGAATCTCACTTCCTTCAAACCCCT
> TCATTAATCTTAGACCCATACTTTTCTTCACTTTCTCTCTTATCATATTTCATGTGTTAGCTATTCTGTTTTTCTCAATAA
> GGTTCCTGTCATGTGCTAATGAATCTCAAATTGTATGTTGGATTATGGATTCCTC
>
> The plugin finishes and the output file ends with:
> output: > sqlExec:
> output: > UPDATE Core.AlgorithmInvocation
> output: > SET
> output: > modification_date = SYSDATE,
> output: > end_time = SYSDATE,
> output: > row_alg_invocation_id = ?,
> output: > result = ?
> output: > WHERE algorithm_invocation_id = ?
> output: > bindValues (24971, Run finished: Processed 1, inserted 28 and updated sequences from file soybean-one, 24971)
> output: > DbiHandle:sqlExec:insert succeeded 1 row(s)
>
> Looking through the output file one finds that there were 29 'insert into' statements,
> 28 into Core.AlgorithmParam and one into Core.AlgorithmInvocation (see below).
> There was not a single attempt to insert into the ExternalNASequence table.
>
> Does anyone know what is going on here?
>
> Thanks
>
> Fidel
>
>
> output: 68: 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 )
> output: 429: 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 )
> output: 484: 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 )
> output: 535: 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 )
> output: 590: 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 )
> output: 643: 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 )
> output: 694: 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 )
> output: 745: 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 )
> output: 798: 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 )
> output: 851: 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 )
> output: 904: 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 )
> output: 955: 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 )
> output: 1006: 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 )
> output: 1057: 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 )
> output: 1108: 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 )
> output: 1159: 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 )
> output: 1210: 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 )
> output: 1261: 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 )
> output: 1312: 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 )
> output: 1365: 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 )
> output: 1416: 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 )
> output: 1469: 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 )
> output: 1520: 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 )
> output: 1573: 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 )
> output: 1626: 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 )
> output: 1679: 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 )
> output: 1732: 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 )
> output: 1783: 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 )
> output: 1834: 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 )
>
>
>
> -------------------------------------------------------
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|
From: Deborah F. P. <pi...@pc...> - 2003-12-11 12:26:25
|
Hi,
The sql query should have been --idSQL 'delete from DoTS.NRDBEntry
where nrdb_entry_id=1' rather than ...DoTS::NRDBEntry...
Debbie
On Wed, 10 Dec 2003, sucheta Tripathy wrote:
>
> Hi,
>
> I have been trying to use the deleteEntries.pl program to delete some of
> the rows inserted into the DoTS::NRDBEntry table.
>
> First it gave an insufficient privilege error, so when we looked at the
> code at line 30, 31, we noticed, it calls the
> $gusconfig->getReadOnlyDatabaseLogin(),
> $gusconfig->getReadOnlyDatabasePassword()
>
> which has only readonly privileges (From the .gus.properties file).
>
> So I changed it to
>
> $gusconfig->getDatabaseLogin(),
> $gusconfig->getDatabasePassword(), at those 2 lines which has read, write,
> delete privileges.
>
> The options I have used are:
>
> deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where
> nrdb_entry_id=1' --table DoTS::NRDBEntry
>
> It is throwing the following errors:
>
> Reading properties from /home/apps/gus/.gus.properties
> The login is GUSrw
> DBD::Oracle::st execute failed: ORA-00933: SQL command not properly ended
> (DBD E
> RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where
> nrdb_ent
> ry_id=3" with ParamValues: :NRDBEntry=undef] at
> /home/apps/gus/gushome/lib/perl/
> GUS/ObjRelP/DbiDbHandle.pm line 82.
> Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR:
> OCIStmtExe
> cute)
> sql_cmd:
> delete from DoTS::NRDBEntry where nrdb_entry_id=3
> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> (perhaps you
> need to call execute first) [for Statement "delete from DoTS::NRDBEntry
> where n
> rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at
> /home/apps/gus/gushome/bi
> n/deleteEntries.pl line 51.
> deleting 0 ids from DoTS::NRDBEntry
>
|
|
From: sucheta T. <su...@vb...> - 2003-12-11 00:23:12
|
Hi, I have been trying to use the deleteEntries.pl program to delete some of the rows inserted into the DoTS::NRDBEntry table. First it gave an insufficient privilege error, so when we looked at the code at line 30, 31, we noticed, it calls the $gusconfig->getReadOnlyDatabaseLogin(), $gusconfig->getReadOnlyDatabasePassword() which has only readonly privileges (From the .gus.properties file). So I changed it to $gusconfig->getDatabaseLogin(), $gusconfig->getDatabasePassword(), at those 2 lines which has read, write, delete privileges. The options I have used are: deleteEntries.pl --idSQL 'delete from DoTS::NRDBEntry where nrdb_entry_id=1' --table DoTS::NRDBEntry It is throwing the following errors: Reading properties from /home/apps/gus/.gus.properties The login is GUSrw DBD::Oracle::st execute failed: ORA-00933: SQL command not properly ended (DBD E RROR: OCIStmtExecute) [for Statement "delete from DoTS::NRDBEntry where nrdb_ent ry_id=3" with ParamValues: :NRDBEntry=undef] at /home/apps/gus/gushome/lib/perl/ GUS/ObjRelP/DbiDbHandle.pm line 82. Execute FAILED: ORA-00933: SQL command not properly ended (DBD ERROR: OCIStmtExe cute) sql_cmd: delete from DoTS::NRDBEntry where nrdb_entry_id=3 DBD::Oracle::st fetchrow_array failed: ERROR no statement executing (perhaps you need to call execute first) [for Statement "delete from DoTS::NRDBEntry where n rdb_entry_id=3" with ParamValues: :NRDBEntry=undef] at /home/apps/gus/gushome/bi n/deleteEntries.pl line 51. deleting 0 ids from DoTS::NRDBEntry -- Sucheta Tripathy Virginia Bioinformatics Institute 1880 pratt drive,Bldg XV Virginia tech. Blacksburg Virginia VA 24061 phone-(540)231-8138 |
|
From: Fidel S. <fi...@vb...> - 2003-12-11 00:00:13
|
Folks, I am revisiting an issue with the InsertNewExternalSequences plugin that was not answered to a post by Sucheta on 11-21-2003. I have also tried the InsertNewExternalSequences plugin with similar results to the ones she reported. The comman issued is: ga GUS::Common::Plugin::InsertNewExternalSequences \ --external_database_release_id=138 \ --table_name=DoTS::ExternalNASequence \ --sequencefile=soybean-one \ --debug --sqlVerbose --commit >& soybean-one.out The soybean-one file contains: >psHA001iA02r TCAGNGCCTNCTTCTGGTCTCCCTGGTGTTGGTCTCCTACGCTGCCCGGTCGGAATCAGCGCTGGGCGGCTGGAGCCCCAT CAAGGACGTAAACGACAGCCACGTGGCGGAGATCGCCAACTACGCTCTGAGCGAGTACGACAAGCGTTCTGGGGCCAAGCT CACCCTTGTCAAGGTCGTCAAGGGCGAGACTCAGGTCGTTTCCGGCACCAACTACCGTCTCGTCCTCAAAGCCAAGGATGG ATCCGCCACGGCCAGTTACGAAGCCATCGTCTGGGAGAAGCCTTGGCTCCATTTCATGAATCTCACTTCCTTCAAACCCCT TCATTAATCTTAGACCCATACTTTTCTTCACTTTCTCTCTTATCATATTTCATGTGTTAGCTATTCTGTTTTTCTCAATAA GGTTCCTGTCATGTGCTAATGAATCTCAAATTGTATGTTGGATTATGGATTCCTC The plugin finishes and the output file ends with: output: > sqlExec: output: > UPDATE Core.AlgorithmInvocation output: > SET output: > modification_date = SYSDATE, output: > end_time = SYSDATE, output: > row_alg_invocation_id = ?, output: > result = ? output: > WHERE algorithm_invocation_id = ? output: > bindValues (24971, Run finished: Processed 1, inserted 28 and updated sequences from file soybean-one, 24971) output: > DbiHandle:sqlExec:insert succeeded 1 row(s) Looking through the output file one finds that there were 29 'insert into' statements, 28 into Core.AlgorithmParam and one into Core.AlgorithmInvocation (see below). There was not a single attempt to insert into the ExternalNASequence table. Does anyone know what is going on here? Thanks Fidel output: 68: 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 ) output: 429: 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 ) output: 484: 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 ) output: 535: 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 ) output: 590: 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 ) output: 643: 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 ) output: 694: 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 ) output: 745: 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 ) output: 798: 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 ) output: 851: 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 ) output: 904: 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 ) output: 955: 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 ) output: 1006: 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 ) output: 1057: 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 ) output: 1108: 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 ) output: 1159: 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 ) output: 1210: 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 ) output: 1261: 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 ) output: 1312: 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 ) output: 1365: 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 ) output: 1416: 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 ) output: 1469: 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 ) output: 1520: 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 ) output: 1573: 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 ) output: 1626: 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 ) output: 1679: 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 ) output: 1732: 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 ) output: 1783: 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 ) output: 1834: 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 ) |
|
From: Fidel S. <fi...@vb...> - 2003-12-10 22:45:02
|
Folks, I have used the GBParser plugin to upload all the mouse chromosomes and ran into a couple of issues (actually, issue 2 I have seen with other data as well). 1. GBParser parsed 2 chromosome files incorrectly. When I run the query: select distinct chromosome, organism from dots.source where organism = 'Mus musculus' chromosomes 11 and 16 are missing from the results. Now, GBParser did not report any errors (gpparserFailures directory was empty after completion and had not been modified since the uploading started) and search for 'fail' or 'error' in the corresponding gbparser ouput files turns up empty. Chromosome info in the input *.gbk files is there (in source features). Searching for 'source' in the gbparser output file again comes up empty. Has anyone uploaded the same kind of chromosome files before? Is what I have just described known to be a bug? 2. GBParser fails on some feature qualifier types: mol_type, locus_tag, and insertion_seq are the ones I have noticed. This is more of a minor issue but also one that needs to be fixed. I do not know how long ago GenBank added these qualifier types but I know new feature and qualifier types have been added for the latest release (138). I am sorry to say I do not have time at the moment to fix these problems with GBParser but I thought everyone should know. Fidel |
|
From: Angel P. <an...@pc...> - 2003-12-09 22:16:35
|
GUSDEV community, I have committed the current state of affairs at CBIL for GUS development as version "3.1" of GUS. You can check out said version by doing: %> cd $GUS_HOME/GUS/Model/schema %> cvs update -r "GUS_3_1" You can see the diff log at GUS/Model/schema/oracle/migrate/gus_3_0_to_3_1.diff to see the files and types of changes that went on. Mainly these were changes in the RAD schema, and there were some doozies, but since I had asked earlier whether anyone was using RAD and no one else was, I figured they were OK. For the rest, I believe that the changes were minor, with the exception of the GO tables, were I will ask Dave to give a synopsis. We will try to release data/schema migration scripts on an as-needed basis, so please email the list for your preference if you can't figure out what the change was. I believe that J.Schug may have some for TESS. I have all the ones for RAD, but they are a mess. Also notice that I added the subdir "GUS/Model/schema/postgresql" for the eventual PostgreSQL release of GUS. Hopefully we can use the SQLFairy (http://sqlfairy.sourceforge.net/) project to do translations of Oracle DDL to PostgreSQL DDL, but I can't say for sure, since I never used it before. Cheers, Angel |
|
From: Terry C. <tw...@cs...> - 2003-12-09 21:32:23
|
Hi, Chetna, I also experienced numerous duplicate entries in the pfam load. I assumed these were problems with Pfam organization, and not being a priority to me, I did not track them down; but I have a not in my log to do so. I've attached my Pfam load output for comparison. Terry p.s. This is a resend; I had sent the full pfam output a bit ago but it exceeded the unmoderated limit. (Moderator, please feel free to discard that message.) > > On 0, Chetna Warade <wa...@ya...> wrote: > > Hello Debbie, > > > > I am loading (commit) Pfam data in GUS from scratch. > > I am getting few duplicate errors e.g. > > > > Duplicate reference to db_ref_id 621 from > > pfam_entry_id 1073 > > > > Is this behavior okey? If not do you have any idea > > about fixes for this. > > > > Thanks in advance, > > Chetna > > > > > > __________________________________ > > Do you Yahoo!? > > New Yahoo! Photos - easier uploading and sharing. > > http://photos.yahoo.com/ > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: SF.net Giveback Program. > > Does SourceForge.net help you be more productive? Does it > > help you create better code? SHARE THE LOVE, and help us help > > YOU! Click Here: http://sourceforge.net/donate/ > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > Reading properties from /home/gus/run/config/GUS-PluginMgr.prop Reading properties from /home/gus/.gus.properties ImportPfam: COMMIT ****ON**** ImportPfam: reading Pfam release 9.0 from /home/gus/pfam/Pfam-A.full 0: PF00244 1: PF00389 2: PF02826 3: PF00198 4: PF04029 5: PF02834 6: PF03171 7: PF03475 8: PF01612 9: PF00803 10: PF01073 11: PF02829 12: PF00725 13: PF02737 14: PF05902 15: PF02446 16: PF04419 17: PF03061 18: PF01812 19: PF02739 20: PF01367 21: PF05761 22: PF02872 23: PF03491 24: PF02096 25: PF00428 26: PF01591 27: PF00393 28: PF02495 29: PF02294 30: PF00001 31: PF00002 32: PF00003 33: PF01461 34: PF01604 35: PF02949 36: PF01661 37: PF00207 38: PF01835 39: PF02177 40: PF01356 41: PF02137 42: PF00962 43: PF00324 44: PF01490 45: PF00004 Duplicate reference to db_ref_id 538 from pfam_entry_id 46 Duplicate reference to db_ref_id 540 from pfam_entry_id 46 Duplicate reference to db_ref_id 542 from pfam_entry_id 46 Duplicate reference to db_ref_id 543 from pfam_entry_id 46 Duplicate reference to db_ref_id 544 from pfam_entry_id 46 Duplicate reference to db_ref_id 545 from pfam_entry_id 46 Duplicate reference to db_ref_id 546 from pfam_entry_id 46 Duplicate reference to db_ref_id 534 from pfam_entry_id 46 Duplicate reference to db_ref_id 535 from pfam_entry_id 46 Duplicate reference to db_ref_id 536 from pfam_entry_id 46 Duplicate reference to db_ref_id 537 from pfam_entry_id 46 Duplicate reference to db_ref_id 539 from pfam_entry_id 46 Duplicate reference to db_ref_id 541 from pfam_entry_id 46 Duplicate reference to db_ref_id 547 from pfam_entry_id 46 46: PF04326 47: PF00696 48: PF03306 49: PF04611 50: PF05282 51: PF03417 52: PF02496 53: PF00950 54: PF03109 55: PF01061 56: PF00664 57: PF00005 58: PF05270 59: PF03806 60: PF04083 61: PF00561 62: PF02230 63: PF02517 64: PF03992 65: PF00887 66: PF03255 67: PF00871 68: PF02396 69: PF02550 70: PF00583 71: PF00797 72: PF00328 73: PF03767 74: PF05882 75: PF00330 76: PF00694 77: PF01756 78: PF05777 79: PF01648 80: PF00873 81: PF01842 82: PF05058 83: PF00976 84: PF00022 85: PF01064 86: PF01643 87: PF00441 88: PF02770 89: PF02771 90: PF02551 Duplicate reference to db_ref_id 1351 from pfam_entry_id 91 Duplicate reference to db_ref_id 1352 from pfam_entry_id 91 91: PF00698 92: PF02273 93: PF01757 94: PF00708 95: PF01553 96: PF02805 97: PF00928 98: PF01602 99: PF02618 100: PF03352 101: PF02438 102: PF03052 103: PF02703 104: PF01691 105: PF01696 106: PF04623 107: PF04834 108: PF03307 109: PF02440 110: PF02439 111: PF05248 112: PF03376 113: PF04528 114: PF00541 115: PF00608 Duplicate reference to db_ref_id 1467 from pfam_entry_id 116 Duplicate reference to db_ref_id 1468 from pfam_entry_id 116 Duplicate reference to db_ref_id 1469 from pfam_entry_id 116 Duplicate reference to db_ref_id 1470 from pfam_entry_id 116 Duplicate reference to db_ref_id 1471 from pfam_entry_id 116 Duplicate reference to db_ref_id 1472 from pfam_entry_id 116 116: PF04881 117: PF01065 118: PF03678 119: PF02456 120: PF01686 121: PF03955 122: PF03910 123: PF01310 124: PF02459 125: PF03228 126: PF05829 127: PF04439 128: PF01295 129: PF00709 130: PF00106 131: PF00107 132: PF04619 133: PF03257 134: PF00406 135: PF05191 136: PF05221 137: PF00670 138: PF01941 139: PF02675 140: PF03747 141: PF04587 142: PF02039 143: PF01117 144: PF05110 145: PF05775 146: PF03969 147: PF01314 148: PF02730 149: PF02420 Duplicate reference to db_ref_id 2072 from pfam_entry_id 150 Duplicate reference to db_ref_id 2073 from pfam_entry_id 150 Duplicate reference to db_ref_id 2074 from pfam_entry_id 150 Duplicate reference to db_ref_id 2072 from pfam_entry_id 150 Duplicate reference to db_ref_id 2073 from pfam_entry_id 150 Duplicate reference to db_ref_id 2074 from pfam_entry_id 150 Duplicate reference to db_ref_id 2072 from pfam_entry_id 150 Duplicate reference to db_ref_id 2073 from pfam_entry_id 150 Duplicate reference to db_ref_id 2074 from pfam_entry_id 150 Duplicate reference to db_ref_id 2072 from pfam_entry_id 150 Duplicate reference to db_ref_id 2073 from pfam_entry_id 150 Duplicate reference to db_ref_id 2074 from pfam_entry_id 150 Duplicate reference to db_ref_id 2072 from pfam_entry_id 150 Duplicate reference to db_ref_id 2073 from pfam_entry_id 150 Duplicate reference to db_ref_id 2074 from pfam_entry_id 150 Duplicate reference to db_ref_id 2072 from pfam_entry_id 150 Duplicate reference to db_ref_id 2073 from pfam_entry_id 150 Duplicate reference to db_ref_id 2074 from pfam_entry_id 150 150: PF03756 151: PF04671 152: PF05641 153: PF01453 154: PF05039 ... 5721: PF03367 5722: PF00791 5723: PF00569 Loaded 5724 entries and 55160 database references from Pfam release 9.0. Thu Jul 10 11:58:20 2003 RESULT Loaded 5724 entries and 55160 database references from Pfam release 9.0. |
|
From: Chetna W. <wa...@ya...> - 2003-12-09 21:31:39
|
Hello Terry, Thanks for the log. I am looking at it and observed that the pfam_entry_id in your log is a continous number from the log whereas for me its different. Thanks again, Chetna --- Terry Clark <tw...@cs...> wrote: > Hi, Chetna, > I also experienced numerous duplicate entries in the > pfam load. > I assumed these were problems with Pfam > organization, and not > being a priority to me, I did not track them down; > but I have > a not in my log to do so. I've attached my Pfam load > output > for comparison. > > Terry > > > > On 0, Chetna Warade <wa...@ya...> wrote: > > Hello Debbie, > > > > I am loading (commit) Pfam data in GUS from > scratch. > > I am getting few duplicate errors e.g. > > > > Duplicate reference to db_ref_id 621 from > > pfam_entry_id 1073 > > > > Is this behavior okey? If not do you have any idea > > about fixes for this. > > > > Thanks in advance, > > Chetna > > __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ |
|
From: Deborah F. P. <pi...@pc...> - 2003-12-09 20:08:15
|
Hi Chetna,
I am not at all familiar with the pfamentry table so someone else had
better try and handle this question.
Debbie
On Tue, 9 Dec 2003, Chetna Warade
wrote:
> Hello Debbie,
>
> I am loading (commit) Pfam data in GUS from scratch.
> I am getting few duplicate errors e.g.
>
> Duplicate reference to db_ref_id 621 from
> pfam_entry_id 1073
>
> Is this behavior okey? If not do you have any idea
> about fixes for this.
>
> Thanks in advance,
> Chetna
>
>
> __________________________________
> Do you Yahoo!?
> New Yahoo! Photos - easier uploading and sharing.
> http://photos.yahoo.com/
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Chetna W. <wa...@ya...> - 2003-12-09 19:41:55
|
Hello Debbie, I am loading (commit) Pfam data in GUS from scratch. I am getting few duplicate errors e.g. Duplicate reference to db_ref_id 621 from pfam_entry_id 1073 Is this behavior okey? If not do you have any idea about fixes for this. Thanks in advance, Chetna __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ |
|
From: MICHAEL L. <lu...@cs...> - 2003-12-09 14:59:30
|
Hello Everyone:
I have attempted to load data using the loadnrdb plugin and have recieved
errors. I have a few questions to ask concerning the plugin options.
I entered the following command:
[luchtan@mkiwi luchtan]$ ga GUS::Common::Plugin::LoadNRDB
--temp_login=luchtan
--sourceDB=1:gb,2:emb,3:dbj,4:pir,5:prf,6:sp,7:pdb,8:pat,9:bbs,
10:gnl,11:ref,12:lcl,13:genpept,14:tpe --temp_password=xxxxxxx
--dbi_str="dbi:Oracle:host=xx.xxx.xxx.xx;sid=XXXXX"
--gitax=/home/luchtan
/GUS/loadNRDB/gi_taxid_prot.dmp
--nrdb=/opt/app/oracle/db_storage/data/downloadNRDB/downloadNRDB/nr.Z
--extDbRelId=15 --plugin --delete --verb
ose --maketemp --commit
With the proceeding output:
Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
Mon Dec 8 17:28:08 2003 ***COMMIT ON***
There are 14 entries in the source database hash
Mon Dec 8 17:28:42 2003 There are 3233042 gi to taxon_id pairs
Mon Dec 8 17:28:47 2003 2000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 17:28:50 2003 4000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 17:28:53 2003 5000 sets have been processed
and put in the NRDBTemp table
.
.
.
Mon Dec 8 19:01:59 2003 2956000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 19:02:00 2003 2957000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 19:02:03 2003 2958396 total entries have been made
into the NRDBTemp table
Mon Dec 8 19:02:11 2003 2958395 entries in temp table
Submitted set number:1
Submitted set number:2
Submitted set number:3
Submitted set number:4
Submitted set number:5
Submitted set number:6
.
.
.
Submitted set number:3478
Submitted set number:3479
DBD::Oracle::st execute failed: ORA-00942: table or view does not exist
(DBD ERROR: OCIStmtExecute) at /var/local/gus_home/lib/perl/GUS/ObjRel
P/DbiDbHandle.pm line 145, <NRDB> line 19198.
SQL ERROR!! involving
Values: 6805 at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8645bf4)',
'^J SQL ERROR!! involving^J ^J Values: 6805') called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8645bf4)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x41386b68)', 'ARR
AY(0x849384c)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1798
GUS::Model::GusRow::version('GUS::Model::DoTS::NRDBEntry=HASH(0x87dcb28)')
called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1665
GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x87dcb28)',
undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/G
usRow.pm line 1764
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x878fa6c)',
'GUS::Model::DoTS::NRDBEntry') calle
d at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x878fa6c)')
called at /var/local/gus_home/lib/perl/G
US/Model/GusRow.pm line 1684
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x878fa6c)')
called at /var/local/gus_home/lib/perl/GUS/Common/P
lugin/LoadNRDB.pm line 332
GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x81069d8)',
'HASH(0x85810c0)', 'HASH
(0x857ea9c)', 15) called at
/var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x81069d8)',
'HASH(0x87dd904)') called at /var/local/gus_home/l
ib/perl/GUS/PluginMgr/GusApplication.pm line 430
eval {...} called at
/var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)',
'GUS::Common::Plugin::LoadNRDB') cal
led at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
283
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)',
'GUS::Common::Plugin::LoadNRDB') called
at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)',
'ARRAY(0x8102dbc)') called at /var/local
/gus_home/bin/ga line 11
write error onstdout: Broken pipe
-----------------------------------------------------------------------------------------------
And that's that.
So something's wrong, but before I get too deep into debugging, I would
like to know what kind of data has been entered already into the database,
and if there is a way to remove it. I would like to run the same with a
--sqlVerbose, but I'm not sure how the plugin will react with the data
already present.
What does the --delete option do? I was under the impression that it
deleted the temp table, or so I was told. The --help reveals this:
--delete!
hint: option to run delete portion
type: boolean
So what is the delete portion?
Supposing that the data has been entered correctly up to a certain point,
I would assume that either
--plugin!
hint: choice of whether to run the remainder of the plug_in
type: boolean
--restart=i
hint: for restarting the interrupted plugin(use with plugin
option), use number from last set number in log
type: int
or
--restart_temp_table!
hint: indicates temp table insertion should be restarted
because table already exits
type: boolean
are the options that I should provide. It is not plainly clear to me.
Is my assumption that I would specify --restart=3479 for this case
correct?
Any help is much appreciated!
Michael Luchtan
http://www.cs.uga.edu/~luchtan
-------------------------------------------------------------------------
" The two basic topics that fascinate me are "What is reality?" and "What
constitutes the authentic human being?"" ---Philip K. Dick
-------------------------------------------------------------------------
|
|
From: Deborah F. P. <pi...@pc...> - 2003-12-08 13:15:32
|
Hi Sucheta,
I was referring to LoadNRDB.pm
Debbie
On Sun, 7 Dec 2003, sucheta Tripathy wrote:
> Hi Debbie,
>
> I also got the same error as Chetna.
>
> Which file do I need to update from the CVS?
>
> Sucheta
>
>
> > Hi Chetna,
> >
> > The external_db_rel_id attribute holds the sres.externaldatabaserelease id
> > for each of the source databases that are found in the defline of nr
> > protein db records.
> >
> > I have modified the plugin and submitted it to cvs because we are now
> > maintaining two versions of the ncbi nr protein database. If you update
> > the new command line should be similar to the following:
> >
> >
> >
> > --temp_login $temp_login --sourceDB $sourceDB --temp_password
> > $temp_password --dbi_str $dbi_str --gitax $gitax --nrdb
> > $nrdb --extDbRelId $nrdbReleaseId --maketemp --plugin --delete
> >
> > $temp_login = pinney
> > $temp_password = xxxxxx
> > $sourceDB =
> > 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,
> > 7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe
> > $dbi_str = dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld
> > $nrdbReleaseId = 7484
> > etc.
> >
> > The previous version took the name of the source database and retrieved
> > the external_database_release_id while this version is given the id. I
> > think this is better because you don't have to run the risk of mistyping
> > the name and allows you to maintain more than one version of nrdb. It
> > still requires that you enter a row into sres.externaldatabase and
> > sres.externaldatabaserelease for each of the source db in the NCBI files
> > (see the README file at NCBI). (We have a couple extra here - if you can
> > query our db, you can get their descriptions). The ids can be permanent so
> > you don't have to come up with the command line and new ids every time.
> >
> > You also need to have a separate NRDB external_database_release_id for
> > NRDB on the whole and this will be put into dots.externalaasequence. We
> > also don't change this id, rather we update information in the
> > sres.externaldatabaserelease table row.
> >
> > Debbie
> >
> > On Fri, 5 Dec 2003, Chetna Warade wrote:
> >
> >> Hello,
> >>
> >> I tried with --maketemp and I am getting:
> >>
> >> DBD::Oracle::st execute failed: ORA-01400: cannot
> >> insert NULL into
> >> ("CHETNA"."NRDBTEMP"."EXTERNAL_DB_REL_I
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: sucheta T. <su...@vb...> - 2003-12-08 00:27:27
|
Hi Debbie, I also got the same error as Chetna. Which file do I need to update from the CVS? Sucheta > Hi Chetna, > > The external_db_rel_id attribute holds the sres.externaldatabaserelease id > for each of the source databases that are found in the defline of nr > protein db records. > > I have modified the plugin and submitted it to cvs because we are now > maintaining two versions of the ncbi nr protein database. If you update > the new command line should be similar to the following: > > > > --temp_login $temp_login --sourceDB $sourceDB --temp_password > $temp_password --dbi_str $dbi_str --gitax $gitax --nrdb > $nrdb --extDbRelId $nrdbReleaseId --maketemp --plugin --delete > > $temp_login = pinney > $temp_password = xxxxxx > $sourceDB = > 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat, > 7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe > $dbi_str = dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld > $nrdbReleaseId = 7484 > etc. > > The previous version took the name of the source database and retrieved > the external_database_release_id while this version is given the id. I > think this is better because you don't have to run the risk of mistyping > the name and allows you to maintain more than one version of nrdb. It > still requires that you enter a row into sres.externaldatabase and > sres.externaldatabaserelease for each of the source db in the NCBI files > (see the README file at NCBI). (We have a couple extra here - if you can > query our db, you can get their descriptions). The ids can be permanent so > you don't have to come up with the command line and new ids every time. > > You also need to have a separate NRDB external_database_release_id for > NRDB on the whole and this will be put into dots.externalaasequence. We > also don't change this id, rather we update information in the > sres.externaldatabaserelease table row. > > Debbie > > On Fri, 5 Dec 2003, Chetna Warade wrote: > >> Hello, >> >> I tried with --maketemp and I am getting: >> >> DBD::Oracle::st execute failed: ORA-01400: cannot >> insert NULL into >> ("CHETNA"."NRDBTEMP"."EXTERNAL_DB_REL_I |
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