Error with test if --galaxy_root is a fresh Galaxy clone #50
Description
$ planemo test --galaxy_root=$HOME/software/galaxy-central ~/software/galaxyproject_tools-devteam/tools/trimmer/trimmer.xml
Testing using galaxy_root /home/nicola/software/galaxy-central
Testing tools with command [type deactivate >/dev/null 2>&1 && deactivate; cd /home/nicola/software/galaxy-central; [ -e .venv ] && . .venv/bin/activate; sh run_tests.sh --report_file /home/nicola/software/galaxyproject_planemo/tool_test_output.html --xunit_report_file /tmp/tmpkUivlK/xunit.xml --structured_data_report_file /home/nicola/software/galaxyproject_planemo/tool_test_output.json functional.test_toolbox]
...
Traceback (most recent call last):
File "./scripts/functional_tests.py", line 547, in <module>
sys.exit( main() )
File "./scripts/functional_tests.py", line 372, in main
app = UniverseApplication( **kwargs )
File "/home/nicola/software/galaxy-central/lib/galaxy/app.py", line 66, in __init__
self._configure_tool_data_tables( from_shed_config=False )
File "/home/nicola/software/galaxy-central/lib/galaxy/config.py", line 739, in _configure_tool_data_tables
from_shed_config=from_shed_config )
File "/home/nicola/software/galaxy-central/lib/galaxy/tools/data/__init__.py", line 77, in load_from_config_file
tree = util.parse_xml( filename )
File "/home/nicola/software/galaxy-central/lib/galaxy/util/__init__.py", line 174, in parse_xml
tree = ElementTree.parse(fname)
File "/home/nicola/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
File "/home/nicola/software/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
IOError: [Errno 2] No such file or directory: './config/shed_tool_data_table_conf.xml'
Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown.
One or more tests failed. See /home/nicola/software/galaxyproject_planemo/tool_test_output.html for detailed breakdown.
Probably scripts/common_startup.sh should be run in the provided galaxy_root , which would create the missing './config/shed_tool_data_table_conf.xml' file.
A similar error is encountered if running ./run_functional_tests.sh in a fresh Galaxy clone, just with a different missing file:
Traceback (most recent call last):
File "./scripts/functional_tests.py", line 547, in <module>
sys.exit( main() )
File "./scripts/functional_tests.py", line 372, in main
app = UniverseApplication( **kwargs )
File "/home/nicola/software/galaxy-central/lib/galaxy/app.py", line 36, in __init__
self.config.check()
File "/home/nicola/software/galaxy-central/lib/galaxy/config.py", line 586, in check
raise ConfigurationError("Tool config file not found: %s" % path )
galaxy.config.ConfigurationError: Tool config file not found: ./config/shed_tool_conf.xml
So maybe this should be better fixed on the Galaxy side.