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
>>>
>>
>>
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>
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