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Re: [GUSDEV] PluginError issue
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From: <mro...@cs...> - 2006-10-27 12:21:58
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Steve, I am sorry to be a pain, but I was wondering if you have received any new= s from John concerning the PluginError.pm Thank you Michael > john- > > this GUS user, michael, has downloaded and installed the latest GUS. > > your new PluginError.pm is giving him problems. see below. > > steve > > mro...@cs... wrote: > >>Steve, >> >>Thanks for the phone orientation offer, tomorrow will be great, I am on >> my >>way to a 3 hour class. >> >>In the meantime I run: >> >> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin 9% >> ga GUS::Supported::Plugin::InsertSequenceFeatures >> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >> --fileFormat genbank >> --extDbName "Pseudomonas_aeruginosa" >> --extDbRlsVer "1000" >> --soCvsVersion "1.1.4" >> --commit >> >> >>and got: >> >> Base class package "Error" is empty. >> (Perhaps you need to 'use' the module which defines that package >> first.) >> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> >>I examined the errors by looking in the programs and all errors have >>something in common: >> >> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >> use base qw(Error); #at PluginError.pm line 2 >> >> >>It probably is a stupid mistake on my part, but I can not see >> >>All help will be very much appreciated. >> >> >>Thanks again >> >>Michael >> >> >> >> >> >>>the only documentation is what you get by running the plugin w/ --help >>> >>>i can (try to) answer questions as they come up. >>> >>>it may turn out that the best way to proceed is an orientation by phon= e. >>> >>>steve >>> >>>mro...@cs... wrote: >>> >>> >>> >>>>Steve, >>>> >>>>I am almost ready to insert some bacteria sequences from genebank, an= d >>>> i >>>>have some questions. >>>> >>>>a - i found in the gusdev site the following: >>>> >>>>From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>for those of you who are using the beta version of the ISF plugin: >>>> 1. i will improve its documentation to indicate what it expects to >>>> already be in the database: >>>> - SequenceOntology (InsertSequenceOntology plugin) >>>> - NCBI Taxon (LoadTaxon plugin) >>>> - External database and release (InsertExternalDatabase and >>>> InsertExternalDatabaseRls plugins) >>>> - at least one row in SequenceType so you can say what type = of >>>> sequence you are loading (you can use LoadRow plugin for >>>>this) >>>> >>>> 2. i will improve the error messages so that it better detects the >>>> absence of these, and makes it more clear what to do. >>>> >>>> About loading SO: >>>> 1. can you send the SO term with definition that is too big? >>>> >>>> 2. i understand about the rollback. we have been discussing how t= o >>>> undo a plugin. for now, you need to do it with sql. >>>> >>>> Thanks for helping us make this plugin better. >>>> >>>> steve >>>> >>>>We did a new GUS install two weeks ago and i wonder if this applies t= o >>>>me, >>>>if it does could you tell me where do i find the documentation that y= ou >>>>mention above. >>>> >>>>b - When I do a search in gusdev for "InsertSequenceFeatures" or part= s >>>> of >>>>it, i get very little replies and somotimes none. Is there another wa= y >>>> to >>>>find all documents in gusdev relating to this. >>>> >>>>Thank you >>>> >>>>Michael R >>>> >>>> >>>>-------------------------------------------- >>>> >>>> > |
