Question: Problem W/Cheetah, Repeating Dataset Input
0
Jesse Erdmann • 60 wrote:
Hi all,
I'm using the following XML:
...
<inputs>
<param type="data" format="txt" name="seqmeta" label="PAPS.seqmeta"/>
<param type="data" format="txt" name="lib_info" label="Label
Info"/>
<repeat name="to_merge" title="Evaluation Inputs and Results">
<param type="select" name="pmm" label="Mismatch %" help="Maximum
% of mismatch between the construct sequence and the comparison
sequence.">
</param>
<param type="text" name="max_length" label="Max Construct
Length" value="25"/>
<param format="fasta" name="fasta_in" type="data" label="FastA Output"/>
<param format="txt" name="seq_stats" type="data" label="Sequence Stats"/>
</repeat>
</inputs>
...
<configfiles>
<configfile name="file_info">
#for $merge_set in enumerate( $to_merge )
#silent sys.stderr.write($merge_set.__str__()
+ "\n")
#silent
sys.stderr.write($merge_set.fasta_in.__str__())
#end for
</configfile>
</configfiles>
...
And getting the resulting output:
127.0.0.1 - - [07/Apr/2010:15:31:50 -0500] "POST /admin/tool_reload
HTTP/1.1" 200 - "http://localhost:8080/admin/reload_tool" "Mozilla/5.0
(Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316
Firefox/3.6.2"
127.0.0.1 - - [07/Apr/2010:15:31:59 -0500] "POST /tool_runner/index
HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0
(Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316
Firefox/3.6.2"
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,765
RoundRobin queue: user/session did not exist, created new jobqueue for
session = 6
galaxy.jobs DEBUG 2010-04-07 15:32:03,766 job 234 put in policy queue
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,766
RoundRobin queue: retrieving job from job queue for session = 6
galaxy.jobs DEBUG 2010-04-07 15:32:03,766 dispatching job 234 to local
runner
galaxy.jobs DEBUG 2010-04-07 15:32:05,423 job 234 dispatched
(0, {'seq_stats': <galaxy.tools.datasetfilenamewrapper object="" at="" 0x572b390="">, '__index__': 0, 'max_length':
<galaxy.tools.inputvaluewrapper object="" at="" 0x572b8d0="">, 'fasta_in':
<galaxy.tools.datasetfilenamewrapper object="" at="" 0x572b810="">, 'pmm':
<galaxy.tools.selecttoolparameterwrapper object="" at="" 0x572b290="">})
127.0.0.1 - - [07/Apr/2010:15:32:03 -0500] "GET /history HTTP/1.1" 200
- "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh;
U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316
Firefox/3.6.2"
galaxy.jobs.runners.local ERROR 2010-04-07 15:32:07,356 failure
running job 234
Traceback (most recent call last):
File "/Users/jerdmann/Python/galaxy-
central/lib/galaxy/jobs/runners/local.py",
line 55, in run_job
job_wrapper.prepare()
File "/Users/jerdmann/Python/galaxy-
central/lib/galaxy/jobs/__init__.py",
line 386, in prepare
config_filenames = self.tool.build_config_files( param_dict,
self.working_directory )
File "/Users/jerdmann/Python/galaxy-
central/lib/galaxy/tools/__init__.py",
line 1364, in build_config_files
f.write( fill_template( template_text, context=param_dict ) )
File "/Users/jerdmann/Python/galaxy-
central/lib/galaxy/util/template.py",
line 9, in fill_template
return str( Template( source=template_text, searchList=[context] )
)
File "/Users/jerdmann/Python/galaxy-
central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-
ucs2.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File
"cheetah_DynamicallyCompiledCheetahTemplate_1270672326_31_15888.py",
line 86, in respond
NotFound: cannot find 'fasta_in' while searching for
'merge_set.fasta_in'
So, I'm printing the merge_set dictionary and seeing a fasta_in key,
but when I try to use fasta_in it can not be found. I'm assuming this
is probably a syntax oversight on my part, but I'm not seeing it.
--
Jesse Erdmann
Bioinformatics Analyst
Masonic Cancer Center
University of Minnesota
jerdmann@umn.edu
612-626-3123
jesse@jesseerdmann.com
Twitter: http://twitter.com/jesseerdmann
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modified 8.6 years ago
by
Daniel Blankenberg ♦♦ 1.7k
•
written
8.6 years ago by
Jesse Erdmann • 60
