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Re: [Gusdev-gusdev] InsertNewExternalSequences Plugin revisited
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From: Steve F. <sfi...@pc...> - 2003-12-11 15:03:32
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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 > > |
