Tool test failure - I could use some help...

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Tool test failure - I could use some help...

Dooley, Damion
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
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Re: Tool test failure - I could use some help...

Peter Cock
On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion <[hidden email]> 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
___________________________________________________________
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Re: Tool test failure - I could use some help...

Dooley, Damion
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 = [hidden email]
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 [[hidden email]]
Sent: Thursday, February 12, 2015 3:39 AM
To: Dooley, Damion
Cc: [hidden email]
Subject: Re: [galaxy-dev] Tool test failure - I could use some help...

On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion <[hidden email]> 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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/