Tool test failure - I could use some help...
I was trying to track down why an attempt to test my tool is eventually failing with: "ValueError: No such test TestForTool_ffp_phylogeny" In my case the tool code is located in a Galaxy's tool shed folder, so I'm guessing that might have something to do with it? Has someone come up with a thorough checklist on issues around this? Tool xml file header: <tool id="ffp_phylogeny" name="Feature Frequency Profile Phylogeny" version="0.1.00"> Using John Chilton's ready made sqlite db (though our live server uses a postgres one)
export GALAXY_TEST_DB_TEMPLATE=tmp/db_gx_rev_0120.sqlite
Command line (recent Update tag latest_2015.01.13 for changeset 0cb6cec4ee57):
run_tests.sh -id ffp_phylogeny
begins the process alright. *********************************** My galaxy-dist/tool_shed.xml.sample where I understand references to the tool are supposed to go (and I confirmed the tool file absolute path): <?xml version="1.0"?> <toolbox tool_path="../shed_tools"> <section id="bccdc_tools" name="BCCDC Tools" version=""> <tool file="/usr/local/galaxy/production1/shed_tools/salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/eb1924fbd3ba/ffp_phylogeny/ffp_phylogeny.xml" guid="salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00"> <tool_shed>salk.bccdc.med.ubc.ca/toolshed</tool_shed> <repository_name>ffp_phylogeny</repository_name> <repository_owner>ddooley</repository_owner> <installed_changeset_revision>eb1924fbd3ba</installed_changeset_revision> <id>salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00</id> <version>0.1.00</version> </tool> <tool file="salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/e9ebe2959300/versioned_data/versioned_data.xml" guid="salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00"> <tool_shed>salk.bccdc.med.ubc.ca/toolshed</tool_shed> <repository_name>versioned_data</repository_name> <repository_owner>damion</repository_owner> <installed_changeset_revision>e9ebe2959300</installed_changeset_revision> <id>salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00</id> <version>0.1.00</version> </tool> </toolbox> Thanks for any pointers! Soon as tests fly, I'll be contributing the tools up to the test tooshed. Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
I was trying to track down why an attempt to test my tool is eventually failing with:
"ValueError: No such test TestForTool_ffp_phylogeny"
There are at least two reasons that can happen. (a) The tool wasn't loaded by the test framework. (b) Your tool was loaded, but no <test> and <tests> tags were recognised. My first set would be to check the test log output to see which tools were loaded, and if your tool was mentioned. Peter
Hi, Thanks for the tips, Peter. Hmm. No amount of playing with my galaxy-dist/tool_conf.xml.sample file is enabling the tool to be found by run_tests.sh . In the run_functional_tests.html I see: File "/usr/lib64/python2.6/unittest.py", line 278, in run testMethod() File "/usr/local/galaxy/production1/galaxy-dist/eggs/nose-0.11.1-py2.6.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_ffp_phylogeny In the run_tests.sh stdout I see galaxy.jobs WARNING 2015-02-12 15:26:56,326 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/tmp8_2Kiq/functional_tests_wsgi.ini" instead ... galaxy.tools INFO 2015-02-12 15:26:59,958 Parsing the tool configuration ./config/migrated_tools_conf.xml galaxy.tools DEBUG 2015-02-12 15:26:59,959 Loading section: BCCDC Tools galaxy.tools DEBUG 2015-02-12 15:26:59,989 Loaded tool id: salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00, version: 0.1.00 into tool panel.... galaxy.tools DEBUG 2015-02-12 15:27:00,018 Loaded tool id: salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00, version: 0.1.00 into tool panel.... galaxy.tools DEBUG 2015-02-12 15:27:00,108 Loaded tool id: salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/select_subsets/bccdcSelectSubsets/1.0.0, version: 1.0.0 into tool panel.... ... ====================================================================== ERROR: Failure: ValueError (No such test TestForTool_ffp_phylogeny) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/galaxy/production1/galaxy-dist/eggs/nose-0.11.1-py2.6.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_ffp_phylogeny ---------------------------------------------------------------------- Ran 1 test in 0.002s Now investigating that "/tmp/tmp8_2Kiq/functional_tests_wsgi.ini" file I SEE A STRANGE THING - the prefix shows "/galaxy" whereas I'm testing on a /galaxylab prefix install. There is a /galaxy prefix ALREADY as another galaxy install on our server. Is this relevant/irrelevant? [galaxy_amqp] [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [server:main] use_threadpool = True use = egg:Paste#http threadpool_kill_thread_limit = 10800 [app:main] use_nglims = False database_connection = sqlite:////tmp/tmp1OhjFo/tmpQTWBB8/database/universe.sqlite new_file_path = /tmp/tmp1OhjFo/tmpQTWBB8/new_files_path_XuJDZT job_queue_workers = 5 ... tool_config_file = None job_working_directory = /tmp/tmp1OhjFo/tmpQTWBB8/job_working_directory_bsFveu tool_path = tools tool_data_table_config_path = None user_library_import_dir = /usr/local/galaxy/production1/galaxy-dist/test-data/users galaxy_data_manager_data_path = /tmp/tmp1OhjFo/data_manager_test_tmpHUW6pF/data_manager_tool-datafebj6D file_path = /tmp/tmp1OhjFo/tmpQTWBB8/database/files datatype_converters_config_file = datatype_converters_conf.xml.sample database_auto_migrate = True ... allow_user_creation = True use_heartbeat = False allow_library_path_paste = True api_allow_run_as = test@bx.psu.edu test_conf = test.conf ... debug = True library_import_dir = /usr/local/galaxy/production1/galaxy-dist/test-data running_functional_tests = True So the last thing I'd say is does anyone have comments about whether or not to use this "/job_conf.xml" file for a test setup? I haven't the slightest about how it should be configured. I see John Chilton's example files in the /config/ subfolder. Regards, Damion 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.cock@googlemail.com] Sent: Thursday, February 12, 2015 3:39 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool test failure - I could use some help... On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
I was trying to track down why an attempt to test my tool is eventually failing with:
"ValueError: No such test TestForTool_ffp_phylogeny"
There are at least two reasons that can happen. (a) The tool wasn't loaded by the test framework. (b) Your tool was loaded, but no <test> and <tests> tags were recognised. My first set would be to check the test log output to see which tools were loaded, and if your tool was mentioned. Peter
participants (2)
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Dooley, Damion -
Peter Cock