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