Yay, with your tip, galaxy direct tests now work with tool_conf.xml AND data 
table in place! 

Galaxy DOC person: please update 
https://wiki.galaxyproject.org/Admin/RunningTests to state that 
tool_conf.xml.sample is NOT used for testing!  It is stated in the run_tests.sh 
help info half way down the page.

Tool wasn't loading on new site because data table it referenced wasn't set up. 

I'll note for galaxy devs that the WARNING is actually fatal i.e. that missing 
data table caused some kind of weird error:

galaxy.tools.toolbox.base INFO 2015-02-27 13:48:48,190 Parsing the tool 
configuration ./config/tool_conf.xml
galaxy.tools.parameters.dynamic_options WARNING 2015-02-27 13:48:48,199 Data 
table named 'blast_reporting_fields' is required by tool but not configured
galaxy.tools.toolbox.base ERROR 2015-02-27 13:48:48,200 Error reading tool from 
path: TESTING/blast_reporting/blast_reporting.xml
Traceback (most recent call last):
  File "...galaxy-dist/lib/galaxy/tools/toolbox/base.py", line 670, in 
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, 
repository_id=repository_id )
  File ".../galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 
608, in column_spec_to_index
    return int( column_spec )
ValueError: invalid literal for int() with base 10: 'type'

Thanks again, Peter!


Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Friday, February 27, 2015 1:39 PM
To: Dooley, Damion
Cc: galaxy-...@lists.bx.psu.edu
Subject: Re: Tool Testing: field inputs that occur inside repeat tag - semi 
> And I run "tests.sh -id blast_reporting" (with Galaxy as owner
> of tool folder):

While the tests used to use tool_conf.xml.sample last year
(or even longer ago?) this was switched to using the main
tool_conf.xml instead. This is much easier for testing what
you actually have installed.

If I've guessed wrong, watch the run_tests.sh output to see
which tools are loaded - and make sure your tool loads OK
(and for example doesn't fail with an XML error or something).

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