On Tue, Feb 25, 2014 at 2:29 PM, John Chilton jmchilton@gmail.com wrote:
On Tue, Feb 25, 2014 at 8:08 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
I've also just tried this for the masking files - but ran into a problem. Here the masks are optional, and I want the default to be no mask:
https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54cd...
This works fine from the user interface perspective:
<param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />
This requires at least one file, although a confusing red error message is given if none is selected:
"History does not include a dataset of the required format / build"
<param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" />
This does not require a file, and defaults to selecting a new dummy entry "Selection is Optional". This is presumably intended as a visual cue - but it means you can do weird things like picking a read file and the dummy entry, or no entries. Neither allows me to proceed, instead on pressing execute I get a red error on a new page:
Error executing tool: 'NoneType' object has no attribute 'file_name'
galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while attempting tool execution: Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1916, in __handle_tool_execute _, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 2424, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py", line 287, in execute data.name = self.get_output_name( output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 26, in params self.wrap_values( self.tool.inputs, params, skip_missing_values=not self.tool.check_values ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 51, in wrap_values name=input.name ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 215, in __init__ list.__init__( self, map( to_wrapper, datasets ) ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 209, in to_wrapper real_path = dataset.file_name AttributeError: 'NoneType' object has no attribute 'file_name'
Any thoughts? Is zero files a little tested corner of the multiple file support?
Yes it is a corner case I personally had not tested. Are you are running something later than the latest dist but not the latest central? It seems like yes. Because I believe Dan has fixed the bug that produces the particular stack trace you are seeing last week - he has probably fixed the other problems you mentioned also? Can you upgrade and let me know, if not let me know and I can take a look a closer look.
This one on TravisCI (which looks like the latest galaxy-central) fails with:
Fatal error: Matched on Error: Error: Ignoring mask file 'None' as it does not exist.
https://travis-ci.org/peterjc/galaxy_blast/builds/19577818
Perhaps I can workaround this in the Cheetah template, but ideally the no-files case would be handled nicely in the framework.
Peter