Hi everyone,
I'm running into a bit of trouble with running functional tests on tool wrappers for rseqc that I am writing (testing according to the wiki pagehttp://wiki.galaxyproject.org/TestingInstalledTools). The tools are listed in shed_tool_conf.xml. Though I'm working with ~15 tool wrappers, I'm attaching the error for read_quality.py, which is recurring for each of the other tools I'm writing. I'm attaching the link to the xml wrapper for read_qualityhttps://gist.github.com/nkav/abae3a22c1e4c881c2d8to show you how I write the tests.
Here is the specific error message (this was the same message returned for the 12 other rseqc tools I had wrapped):
====================================================================== ERROR: test_tool_000000 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/nilesh/rseqc_dev2/read_quality/1.0.0 ) Read Quality ( testtoolshed.g2.bx.psu.edu/repos/nilesh/rseqc_dev2/read_quality/1.0.0 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nilesh/galaxy-dist/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/home/nilesh/galaxy-dist/test/functional/test_toolbox.py", line 43, in do_it shed_tool_id=shed_tool_id ) File "/home/nilesh/galaxy-dist/test/base/twilltestcase.py", line 204, in upload_file filename = self.get_filename( filename, shed_tool_id=shed_tool_id ) File "/home/nilesh/galaxy-dist/test/base/twilltestcase.py", line 179, in get_filename return os.path.abspath( os.path.join( file_dir, filename ) ) File "/usr/lib/python2.7/posixpath.py", line 77, in join elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith' -------------------- >> begin captured stdout << ---------------------
form 'login' contains the following controls ( note the values )
--------------------- >> end captured stdout << ----------------------
I'm using the latest version of Galaxy and the RSeQC package, and the tool dependencies for rseqc install correctly after downloading from the test tool shed. Am I forgetting to do something here? Thanks so much for your help.