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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>
<br>
~Justin<br>
<br>
<br>
On 10/31/10 6:14 PM, Dan Tenenbaum wrote:
<blockquote
cite="mid:AANLkTimQK2ycv6Gc58Vwq9Tszrb7222jM7Nb-WRkF1zT@mail.gmail.com"
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 moz-do-not-send="true"
href="mailto:dtenenba@fhcrc.org">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 class="h5">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 class="moz-txt-link-abbreviated" href="mailto:email=my@email.address">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>
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