Re: [GUSDEV] PluginError issue

[<mro...@cs...>]

Steve,

When changes are made to the plugins in GUS (improvements, bugs etc) do
you have "patches" (like in windows programs) that can be applied to GUS,
or how it is handle?

Thanks

Michael R


> 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
>>>>
>>>>
>>>>--------------------------------------------
>>>>
>>>>
>