[StarCluster] problem with arguments passed to plugin

[Dan Tenenbaum]

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
>>
>>
>>
>> _______________________________________________
>> StarCluster mailing list
>> StarCluster at mit.edu
>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>
>>
>
>
> _______________________________________________
> StarCluster mailing list
> StarCluster at mit.edu
> http://mailman.mit.edu/mailman/listinfo/starcluster
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mit.edu/pipermail/starcluster/attachments/20101031/5d994966/attachment.htm