Re: [Gusdev-gusdev] InsertNewExternalSequences Plugin revisited

[Steve F. <sfi...@pc...>]

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 )
>>>>
>>>>
>>>>
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