Yes, thanks for the reminder about Python coding conventions.<div><br></div><div>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).</div>
<div>So now in my code I have to change them to all lowercase and then change them back before passing them to R.</div><div><br></div><div>FYI</div><div>Dan</div><div><br><br><div class="gmail_quote">On Sun, Oct 31, 2010 at 6:28 PM, Justin Riley <span dir="ltr"><<a href="mailto:jtriley@mit.edu">jtriley@mit.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">
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.<br><font color="#888888">
<br>
~Justin</font><div><div></div><div class="h5"><br>
<br>
<br>
On 10/31/10 6:14 PM, Dan Tenenbaum wrote:
<blockquote type="cite">Looks like you can't have any uppercase letters in
your argument names.
<div>Dan</div>
<div><br>
<br>
<div class="gmail_quote">On Sun, Oct 31, 2010 at 2:56 PM, Dan
Tenenbaum <span dir="ltr"><<a href="mailto:dtenenba@fhcrc.org" target="_blank">dtenenba@fhcrc.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div>
<div>Hi, I am getting:
<div><br>
</div>
<div>
<div>PluginError: Not enough settings provided for
plugin shortreadplugin</div>
<div><br>
</div>
</div>
<div>where I don't think I should.</div>
<div><br>
</div>
<div>My config:</div>
<div>
<br>
</div>
<div>
<div>[plugin shortreadplugin]</div>
<div>SETUP_CLASS = bioconductor.ShortReadPlugin</div>
<div><a href="mailto:email=my@email.address" target="_blank">email=my@email.address</a></div>
<div>job_name=myfirsttest</div>
<div>output_bucket=my-bucket-name</div>
<div>access_key=my_access_key</div>
<div>secret_key=my_secret_key</div>
<div>dirPath=testsolexaexportfiles</div>
<div>_type=SolexaExport</div>
<div>pattern=s_3_export.txt</div>
<div>Lpattern=None</div>
<div>Rpattern=None</div>
<div>param=None</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>My plugin constructor signature line:</div>
<div> def __init__(self, email, job_name,
output_bucket, access_key, secret_key, dirPath, _type,
pattern, Lpattern, Rpattern, param):</div>
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>So why is this telling me I am not passing enough
settings?</div>
<div><br>
</div>
<div>Thanks</div>
<div>Dan</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
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<br>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div></div></div>
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<br></blockquote></div><br></div>