Hi,
I have modified the tool dependency xml file by adding Absolute path to
output file, like below, then my test cases are *passing*:
<tests>
<test>
<param name="input1" value="TCGA-02-0001-01"/>
<param name="input2" value="Project-TSS-Participant"/>
<output name="output" file="path to test-data
directory/barcode-parse-ouput1.txt"/>
</test>
<test>
<param name="input1" value="TCGA-02-0001-01"/>
<param name="input2" value="Project TSS: Participant"/>
<output name="output" file="path to test-data
directory/barcode-parse-ouput2.txt"/>
</test>
<test>
<param name="input1" value="TCGA-02-0001-01"/>
<param name="input2" value="MyBarcodeProjectisTSS"/>
<output name="output" file="path to test-data
directory/barcode-parse-ouput3.txt"/>
</test>
</tests>
Thanks for all your help.
Thanks,
JanakiRam
On Fri, Mar 28, 2014 at 2:39 PM, Janaki Rama Rao Gollapudi <
janakiram.gollap...@india.semanticbits.com> wrote:
> Hi,
>
> I have gone through the resources and able to run the test cases, but some
> how my test cases are failing with below exception
>
> File
> "/home/janakiram/Documents/Galaxy/galaxy-dist/test/base/twilltestcase.py",
> line 192, 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'
>
> My test cases are:
> ..............................
>
> <tests>
>
> <test>
>
> <param name="input1" value="TEST-0001-01"/>
>
> <param name="input2" value="TEST-Sample"/>
>
> <output name="output" file="barcode-parse-ouput1.txt"/>
>
> </test>
>
> <test>
>
> <param name="input1" value="TEST-0001-02"/>
>
> <param name="input2" value="TEST-Sample-New"/>
>
> <output name="output" file="barcode-parse-ouput2.txt"/>
>
> </test>
>
> <test>
>
> <param name="input1" value="TEST-0001-01"/>
>
> <param name="input2" value="MyTestSample"/>
>
> <output name="output" file="barcode-parse-ouput3.txt"/>
>
> </test>
>
> </tests>
> ..............................
>
>
> I put the barcode-parse-ouput1.txt, barcode-parse-ouput2.txt,
> barcode-parse-ouput3.txt files in the "test-data" folder (I also set the
> "tool_dependency_dir" in universe_wsgi.ini). Could you please help me on
> this.
>
> Please find the attached function test case output.
>
> Thanks & Regards,
> G.JanakiRam
>
>
>
> On Thu, Mar 27, 2014 at 7:40 PM, Janaki Rama Rao Gollapudi <
> janakiram.gollap...@india.semanticbits.com> wrote:
>
>> Thank you, I will go through the resources and will reply my results to
>> this email chain.
>>
>> Thanks,
>> JanakiRam
>>
>>
>> On Thu, Mar 27, 2014 at 6:39 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>>
>>> Hello Janaki,
>>>
>>> Thanks for clarifying that you have installed your tools from a Tool
>>> Shed. In this case, functional tests do not use Galaxy's
>>> tool_conf.xml.sample, so changing it will make no difference. For
>>> information about running functional tests on tools installed from the Tool
>>> Shed, see: https://wiki.galaxyproject.org/TestingInstalledTools
>>>
>>> Basically, you'll be doing the following. The functional test framework
>>> is not currently set up to test a specific installed tool using a -id flag.
>>> You'll have to use just the -installed flagg which will end up testing all
>>> installed tools.
>>>
>>>
>>> export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies; sh
>>> run_functional_tests.sh -installed
>>>
>>>
>>> Greg Von Kuster
>>>
>>> On Mar 27, 2014, at 8:58 AM, Janaki Rama Rao Gollapudi <
>>> janakiram.gollap...@india.semanticbits.com> wrote:
>>>
>>> Hi,
>>>
>>> Thanks for reply. I composed a details email for better clarity.
>>>
>>> when run grep command in galaxy home folder ( ./run_functional_tests.sh
>>> -list | grep barcode-parse), I got no results.
>>> What I did was:
>>>
>>> - Implemented a custom tool (It has one python script and tool
>>> definition file. These files are located in
>>> ../tools/Mytools/customToolName/)
>>> - Then run the ToolShed in my local which is running on port 9009 (I
>>> have)
>>> - Created a new repository in the ToolShed (which is running on
>>> 9009) and uploaded .py and .xml files in to it
>>> - Now I run the galaxy (running on port 8080) and browse the my
>>> custom tool from my local galaxy and install the custom tool successfully
>>> - And "shed_tool_conf.xml" file updated with new section:
>>> -
>>> - <section id="mTools" name="MyTools" version="">
>>> - <tool
>>>
>>> file="xxx.xx.x.xx/repos/janakiram-t1/barcode_parse_1/b6a60d02b1a2/barcode_parse_1/barcode-
>>> parse.xml"
>>>
>>> guid="xxx.xx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0">
>>> - <tool_shed>xxx.xxx.x.xx:9009</tool_shed>
>>> - <repository_name>barcode_parse_1</repository_name>
>>> - <repository_owner>janakiram-t1</repository_owner>
>>> -
>>>
>>> <installed_changeset_revision>b6a60d02b1a2</installed_changeset_revision>
>>> -
>>>
>>> <id>xxx.xxx.x.xx:9009/repos/janakiram-t1/barcode_parse_1/barcode-parse/1.0.0</id>
>>> - <version>1.0.0</version>
>>> - </tool>
>>> - </section>
>>>
>>> - My tool definition file look likes below:
>>> -
>>> - <tool id="barcode-parse" name="Barcode parse">
>>> - <description>some description</description>
>>> - <command interpreter="python">barcode-parse.py $input1
>>> $input2 $output</command>
>>> - <inputs>
>>> - <param format="input" name="input1" type="text"
>>> size="50" label="barcode" help="Enter barcode">
>>> - <validator type="empty_field" message="please enter barcode"/>
>>> - </param>
>>> - <param format="input" name="input2" type="text" size="50"
>>> label="Expected format" help="Enter format to parse barcode">
>>> - <validator type="empty_field" message="please enter expected
>>> format barcode"/>
>>> - </param>
>>> - </inputs>
>>> - <outputs>
>>> - <data format="txt" name="output" />
>>> - </outputs>
>>> - <tests>
>>> - <test>
>>> - <param name="input1"
>>> value="test-01-sample-test-02-sampl1-test-03-sample3"/>
>>> - <param name="input2" value="name-id"/>
>>> - <output name="output" file="barcode-parse.txt"/>
>>> - </test>
>>> - </tests>
>>> - <help>
>>> - Parse the barcode into expected format
>>> - </help>
>>> - </tool>
>>> -
>>>
>>> As galaxy using tool_conf.xml.sample, this file has no section for my
>>> custom tool. I have added a section manually like below:
>>>
>>> <section name="MyTools" id="mTools">
>>> <tool file="myTools/barcode-parse/barcode-parse.xml" />
>>> </section>
>>>
>>> Then my tool id found when I run the grep command. After that Then I run
>>> the below command to run the test cases:
>>>
>>> sh run_functional_tests.sh -id barcode-parse
>>>
>>> But I got below out put (from the run_functional_tests.html)
>>>
>>>
>>> AttributeError: 'module' object has no attribute
>>> 'test_toolbox:TestForTool_barcode-parse'
>>>
>>>
>>> Am I doing anything wrong.
>>>
>>> Thanks,
>>> JanakiRam
>>>
>>>
>>> On Thu, Mar 27, 2014 at 6:16 PM, Greg Von Kuster <g...@bx.psu.edu>wrote:
>>>
>>>> As Janaki replied below, see:
>>>> http://wiki.galaxyproject.org/Admin/RunningTests?action=show&redirect=Admin%2FRunning+Tests
>>>>
>>>> On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi <
>>>> janakiram.gollap...@india.semanticbits.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I have added tests to tool dependency xml, but how should I run these
>>>> tests, can you please help me to run test cases.
>>>>
>>>> .....................
>>>> <tests>
>>>> <test>
>>>> <param name="input1" value="some string"/>
>>>> <param name="input2" value="expected format"/>
>>>> <output name="output" file="output.txt"/>
>>>> </test>
>>>> </tests>
>>>> ......................
>>>>
>>>>
>>>> Thanks,
>>>> G.JanakiRam
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Mar 27, 2014 at 3:27 PM, Janaki Rama Rao Gollapudi <
>>>> janakiram.gollap...@india.semanticbits.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I found below resources:
>>>>>
>>>>> - Running
>>>>> test<https://wiki.galaxyproject.org/Admin/RunningTests?action=show&redirect=Admin%2FRunning+Tests>
>>>>> - Writing Functional
>>>>> tests<https://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests>
>>>>>
>>>>>
>>>>> Thanks,
>>>>> JanakiRam
>>>>>
>>>>>
>>>>> On Thu, Mar 27, 2014 at 2:53 PM, Janaki Rama Rao Gollapudi <
>>>>> janakiram.gollap...@india.semanticbits.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have implemented a custom tool which will parse a given string in
>>>>>> to expected format. Installed this custom tool into galaxy and was able
>>>>>> to
>>>>>> run successfully.
>>>>>>
>>>>>> I would like to add test cases to this tool, can you please provide
>>>>>> me resources to write test cases for this custom tool.
>>>>>>
>>>>>> Is this tool need functional, unit, integration test cases ? I am not
>>>>>> sure about which test cases needed for this tool.
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> JanakiRam
>>>>>>
>>>>>
>>>>>
>>>> ___________________________________________________________
>>>> 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:
>>>> http://lists.bx.psu.edu/
>>>>
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>>>> http://galaxyproject.org/search/mailinglists/
>>>>
>>>>
>>>>
>>>
>>>
>>
>
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