[galaxy-dev] problems with 'Profile Annotations' tool UI
Hi
we are looking into different methods to display dynamic contents in the
tool user interface.
To start, we looked at the 'Operate on Genomic Intervals:Profile
Annotations' tool. We turned it on in a local installation (May 20,
8c11dd28a3cf release), but we struggled to get the interface to work.
On 'http://main.g2.bx.psu.edu/', the tables to choose from are only
displayed if there is a history item with: format: bed, database: hg18.
But in our local test installation, we don't get the list of tables, no
matter whether we have a ('hg18') bed file in our history or not. It
looks like as if the 'from_file=annotation_profiler_options.xml'
statement in the annotation_profiler.xml is ignored.
I know, the file 'annotation_profiler_options.xml' is read, since I get
an error during restart, if I provide invalid xml.
Is there anything else, I have to enable, in order to get this interface
to work? Currently, I don't care about the tools functionality, I just
want the (cool) interface to work.
Thank you very much for your help.
Regards, Hans
PS: this question is connected to Tim's question yesterday - I just
should have sent mine first - sorry.
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[galaxy-dev] format=input
Hi everyone,
I'm facing a little problem ...
I have the following input :
param name=input type=data format=sff,fasta,fastq label=454
reads /
param name=qual_file type=data format=qual optional=true
label=Quality reads file (if input is a fasta) /
and the following output:
data name=output format=input label=${tool.name} on ${on_string}:
cleaned reads/
data name=out_qual format=qual label=${tool.name} on ${on_string}:
cleaned reads
filterqual_file != None/filter
/data
If I provide the tool a sff file, the output is sff, if I only provide a
fasta file and no qual file the output will be a fasta.
However if I provide a fasta+qual the output will be considered as qual
file even if it's a fasta file.
I don't get how it can mark my output file as a qual file knowing it's
not a valid input file format.
Any ideas ?
thx,
Jerome
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Re: [galaxy-dev] checkboxes bug fix
Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] CSV import of Sample information Error
Joe, Thanks very much for the example csv file. I've fixed this issue in change set 5668:81a5c317d909, which should be available in the distribution within the next few weeks. If you don't want to wait, you can update from our development repo at https://bitbucket.org/galaxy/galaxy-central/wiki/Home. Greg Von Kuster On Jun 7, 2011, at 6:21 PM, Joe Cruz wrote: For my sample forms I have fields for Sample type, concentration, run type, and read length. I greatly appreciate your help Greg. If you have any other questions let me know. Thanks, Joe On Tue, Jun 7, 2011 at 2:56 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Joe, Can you send me your csv file? Thanks! On Jun 7, 2011, at 10:45 AM, Joe Cruz wrote: Hello Everyone, I wanted to ask if anyone has experience successfully importing sample information through a csv file. I know there is an issue already created for csv file import, which I left a comment earlier: https://bitbucket.org/galaxy/galaxy-central/issue/398/csv-import-of-sample-information-is-broken#comment-510683\ but my bug doesn't seem to deal with an 'Invalid Request ID' as the issue above states. This is the error I get: URL: http://localhost/requests_common/add_samples?cntrller=requestsid=a65cf3ca8eb85be3 File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 829 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 1109 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/add_samples.mako.py', line 164 in render_body __M_writer(unicode(render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header ))) File '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/common.mako.py', line 749 in render_render_samples_grid sample_widget_history = sample_widget[ 'history' ] KeyError: 'history' I greatly appreciate your help and patience. Thanks, joe ___ Please keep all replies on the list by using reply all in your mail client. To manage your
Re: [galaxy-dev] galaxy-dev] format=input
On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnson johns...@umn.edu wrote: I added an attribute format_source (analogous to metadata_source) to the data tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Where is the code to handle this? Maybe I missed the commit with all the recent activity. What happens if both format and format_source are given? I would hope an error - which means the wiki is misleading in that format is listed as required. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] galaxy-dev] format=input
It went into galaxy-central: $ hg log -pr 5082 changeset: 5082:a86e1fa82a89 user:Kanwei Li kan...@gmail.com date:Thu Feb 17 15:35:07 2011 -0500 summary: Add a format_source attribute to the ToolConfig output data element [JJ Johnson]. Closes #470 diff -r 885f04ae671e -r a86e1fa82a89 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Feb 17 14:48:53 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Feb 17 15:35:07 2011 -0500 @@ -249,10 +249,11 @@ (format, metadata_source, parent) -def __init__( self, name, format=None, metadata_source=None, +def __init__( self, name, format=None, format_source=None, metadata_source=None, parent=None, label=None, filters = None, actions = None ): self.name = name self.format = format +self.format_source = format_source self.metadata_source = metadata_source self.parent = parent self.label = label @@ -559,6 +560,7 @@ output = ToolOutput( data_elem.get(name) ) output.format = data_elem.get(format, data) output.change_format = data_elem.findall(change_format) +output.format_source = data_elem.get(format_source, None) output.metadata_source = data_elem.get(metadata_source, ) output.parent = data_elem.get(parent, None) output.label = util.xml_text( data_elem, label ) diff -r 885f04ae671e -r a86e1fa82a89 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Thu Feb 17 14:48:53 2011 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Thu Feb 17 15:35:07 2011 -0500 @@ -244,6 +244,12 @@ ext = output.format if ext == input: ext = input_ext +if output.format_source is not None and output.format_source in inp_data: +try: +ext = inp_data[output.format_source].ext +except Exception, e: +pass + #process change_format tags if output.change_format: if params is None: And I should have put an example in: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax On 6/8/11 3:32 PM, Peter Cock wrote: On Wed, Jun 8, 2011 at 9:26 PM, Jim Johnsonjohns...@umn.edu wrote: I added an attribute format_source (analogous to metadata_source) to thedata tag to deal with that kind of issue: see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Where is the code to handle this? Maybe I missed the commit with all the recent activity. What happens if both format and format_source are given? I would hope an error - which means the wiki is misleading in that format is listed as required. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
