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From: Fidel S. <fi...@vb...> - 2003-12-11 00:00:13
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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 12:43:29
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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: 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: 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 )
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>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
>>>
>>>
>>
>>
>>
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From: Steve F. <sfi...@pc...> - 2003-12-11 15:42:43
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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 >>> >>> >>> |
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