Ok, no problem, I really didn't notice. Really sorry about that. I'll be careful from now on. Thanks for the add in the changeset but I suspect the problem should be fixed somewhere else, I mean upstream since the value variable doesn't receive the appropriate stuff. I didn't quite get where it comes from though. Looking forward to seeing you in Lunteren :) Regards, L-A Le 24/05/2011 11:38, Nate Coraor a écrit :
Thanks! This has been fixed in changeset 5594:2f84c42a548a.
Also, if I could ask for a minor thing to assist us with list maintenance: when starting a new thread on the list, please create a brand new email to galaxy-dev rather than replying to an existing message. Replying includes headers that reference the message you replied to, which means it threads with the original thread in mail readers and the list archive.
Thanks, --nate
Louise-Amélie Schmitt wrote:
Yeah, and I fixed it... somehow.
In the lib/galaxy/web/form_builder.py I added the import on string_as_bool from galaxy.util, then I modified the code as follows:
126 @staticmethod 127 def is_checked( value ): 128 if value == True: 129 return True 130 # This may look strange upon initial inspection, but see the comments in the get_html() method 131 # above for clarification. Basically, if value is not True, then it will always be a list with 132 # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 133 # checked, then value will be only the hidden field. 134 if isinstance(value, basestring): 135 return string_as_bool( value ) 136 return isinstance( value, list ) and len( value ) == 2
(see l.134 and 135) The value variable actually contained something else than True or a list, namely the string "true". Now it seems to work fine.
Cheers, L-A
Le 23/05/2011 18:26, Peter Cock a écrit :
2011/5/23 Louise-Amélie Schmitt<louise-amelie.schmitt@embl.de>:
@ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the "yes" and the "true" values to no avail.
@ Leandro: Yes I already saw that ...
But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work.
To give an example, here is one of the lines of my tool XML file: <param name="SQA" type="boolean" label="Run SolexaQA" checked="true" /> This checkbox remains unchecked at tool opening.
As far as I know, some people managed to get it working and I'd like to know how.
Any suggestion? I think you've found a bug :(
I found two working examples, "Filter out low complexity regions (with DUST)" parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and the scaffolding parameter in sr_assembly/velvetg.xml - however they are both within a conditional parameter section (only shown in advanced mode).
Have a look at sr_mapping/bwa_color_wrapper.xml which has a "Suppress the header in the output SAM file" boolean which should be checked by default:
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
It's not working on http://usegalaxy.org - the box isn't checked.
If you can verify that, please file an issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new
Peter
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