Op 26 jan. 2016, om 15:20 heeft Hans-Rudolf Hotz <hrh(a)fmi.ch>
het volgende geschreven:
Hi Matthias
Make sure 'listing' is a list of (displayName,value,boolean)
Though, there might be other errors as well
Regards, Hans-Rudolf
I am not sure, whether this
On 01/26/2016 01:22 PM, Matthias De Smet wrote:
> Hi all,
>
> I’m trying to develop a tool that lets you select a file on the server.
> I’m using the dynamic_options setting to let Galaxy render a dropdown
> list of available file.
>
>
> However, when I try to test the tool in its current form, I get the
> following error:
>
> <pre>
> galaxy.web.framework.decorators ERROR 2016-01-26 13:08:35,649 Uncaught
> exception in exposed API method:
> Traceback (most recent call last):
> File "lib/galaxy/web/framework/decorators.py", line 260, in decorator
> rval = func( self, trans, *args, **kwargs)
> File "lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build
> return tool.to_json(trans, kwd.get('inputs', kwd))
> File "lib/galaxy/tools/__init__.py", line 2602, in to_json
> populate_state(trans, self.inputs, state_inputs, state_errors,
> params.__dict__)
> File "lib/galaxy/tools/__init__.py", line 2471, in populate_state
> state[input.name] = input.get_initial_value(trans, context,
> history=history)
> File "lib/galaxy/tools/parameters/basic.py", line 984, in
> get_initial_value
> value = [ optval for _, optval, selected in options if selected ]
> ValueError: too many values to unpack
> </pre>
>
> My tool xml looks like this:
>
> <pre>
>
> <tool id="archivetolibrary" name="Copy files"
version="0.1.0">
> <description>from the archive to a data library</description>
> <code file="list_files.py"/>
> <command interpreter="bash">
> test.sh > $log
> </command>
> <inputs>
> <param name="archive_source" type="select"
display="radio"
> label="Choose source archive">
> <options from_file="archives.loc">
> <column name="name" index="0"/>
> <column name="value" index="1"/>
> </options>
> </param>
> <param name="query" type="text" label="Search for
files"/>
> <param name="selected_file" type="select"
label="Choose your file"
> dynamic_options="list_files(archive_source,query)"/>
> </inputs>
> <outputs>
> <data name="log" format="txt" label="${tool.name}
on
> ${on_string}"></data>
> </outputs>
> <tests>
> <test>
> </test>
> </tests>
> <help>
> This tool copies data from and archive folder to your history. Keep in
> mind this folder MUST be readable by Galaxy in order for this tool to work.
> </help>
> </tool>
>
> </pre>
>
> and the script called in the “code” tag looks like this
>
> <pre>
> def list_files(dir,query): listing=[]
> for fname in listdir(dir):
> fullpath = path.join(dir, fname) #only select datafiles, not md5
> checksums
> if path.isfile(fullpath) and not fullpath.endswith(".md5"):
> listing.append( fname )
> return listing
> </pre>
>
> This script should return a list with filenames that should be displayed
> in the dropdown list.
>
> I’m tracking Galaxy release 15.10, running on a Ubuntu 14.04.3 server
>
> Thanks for your help!
>
> Matthias
>
>
>
>
>
>
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