Re: problem with arguments passed to plugin

From: Dan Tenenbaum <no email>
Date: Sun, 31 Oct 2010 18:31:03 -0700

Yes, thanks for the reminder about Python coding conventions.

I actually violate the conventions for a reason...some of those parameters
are later passed to R methods which have those exact parameter names
(Lpattern, dirPath, etc).
So now in my code I have to change them to all lowercase and then change
them back before passing them to R.

FYI
Dan


On Sun, Oct 31, 2010 at 6:28 PM, Justin Riley <jtriley_at_mit.edu> wrote:

> This is a bug and will be fixed in the github code. However, although
> Python allows variable names like dirPath and Lpattern, a common convention
> in Python is to use all lowercase variable names. Also, multiple words in a
> variable name are often separated with a '_' character rather than
> capitalizing the words. You've used these conventions for most of the plugin
> config and your ShortReadPlugin class except in a few places but using it
> everywhere in your code is good practice.
>
> ~Justin
>
>
>
> On 10/31/10 6:14 PM, Dan Tenenbaum wrote:
>
> Looks like you can't have any uppercase letters in your argument names.
> Dan
>
>
> On Sun, Oct 31, 2010 at 2:56 PM, Dan Tenenbaum <dtenenba_at_fhcrc.org> wrote:
>
>> Hi, I am getting:
>>
>> PluginError: Not enough settings provided for plugin shortreadplugin
>>
>> where I don't think I should.
>>
>> My config:
>>
>> [plugin shortreadplugin]
>> SETUP_CLASS = bioconductor.ShortReadPlugin
>> email=my_at_email.address
>> job_name=myfirsttest
>> output_bucket=my-bucket-name
>> access_key=my_access_key
>> secret_key=my_secret_key
>> dirPath=testsolexaexportfiles
>> _type=SolexaExport
>> pattern=s_3_export.txt
>> Lpattern=None
>> Rpattern=None
>> param=None
>>
>>
>> My plugin constructor signature line:
>> def __init__(self, email, job_name, output_bucket, access_key,
>> secret_key, dirPath, _type, pattern, Lpattern, Rpattern, param):
>>
>> There are 11 parameters passed to the plugin in the config file
>> (excepting SETUP_CLASS). And there are 11 variables expected in the plugin
>> constructor (excepting self).
>>
>> So why is this telling me I am not passing enough settings?
>>
>> Thanks
>> Dan
>>
>>
>>
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>>
>
>
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Received on Sun Oct 31 2010 - 21:31:06 EDT