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Frequently Asked Questions

Soaplab FAQs

  • General
  • Installation and acd files development
  • Deployment and configuration
  • Running the soaplab services

    • Taverna FAQs

  • General
  • Designing workflows
  • Running workflows

    • Panacea registry (Biocatalogue instance) FAQs

  • Registering web services
  • Searching web services

    • For more detailed descriptions of BioCatalogue, myGrid and Taverna services, please click HERE and refer to the "what is....?" series of PDFs.

    Soaplab FAQs

    General

    - I have a command line application. How can I make it a web service?

    There are different solutions. We’re using Soaplab in Panacea.

    - What is Soaplab?

    It’s a software tool to automatically turn command line applications into web services.

    - Where can I get Soaplab?

    Soaplab software and documentation can be found in http://soaplab.sourceforge.net/soaplab2/

    - Which soaplab version is PANACEA using?

    The latest! Now, soaplab2-2.3.2

    - Which web application container / server do I need to use to deploy soaplab web services?

    Apache Tomcat. In Panacea we are using Tomcat 6 or 7. http://tomcat.apache.org

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    Installation and acd files development

    - When I use ant commands I get timeouts when connecting to other sites?

    Probably you’re behind a proxy. Use ant -autoproxy instead of just ant in all your commands.

    - How can I create my ACD files? Follow the instructions in http://soaplab.sourceforge.net/soaplab2/MetadataGuide.html

    - Where do I put my ACD files describing my command line applications? In src/etc/acd/sowa folder in your soaplab2 installation folder.

    - What kind of input parameter should I use for large data?

    In Panacea, we use infile parameters with “comment: default_for_direct”. This way the input data can be provided with a URL (link) or direct data (a stream of characters). Direct data in Spinet web client can be provided directly typing in a text box or by uploading a file with “Browse...” button. Deployment and configuratio

    - How can I create the necessary XML metadata files from ACD files?

    Use ant gen to create metadata from ALL ACD files. In PANACEA we use ant gensowa to only generate XML from files in the SOWA directory (src/etc/acd/sowa).

    - Which protocol should I use: axis1 or jaxws?

    In Panacea, we use axis1 because Taverna workflow editor is not 100% compatible with jaxws.

    - How can I deploy web services?

    Use ant jaxdeploy or ant axis1deploy. In Panacea, we use ant axis1deploy because axis1 is compatible with Taverna.

    - Should I use typed interface?

    Yes. More applications will be able to call your web services. For more information click here: http://soaplab.sourceforge.net/soaplab2/TypedServices.html

    - How can I configure soaplab to create web services with typed interface?

    Set typedinterface.enable = true in your build.properties file.

    - How can I create the WAR file without automatically deploying it?

    Use ant jaxwar or ant axis1war instead of ant jaxdeploy or ant axis1deploy.

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    Running the soaplab services

    - How can I test my soaplab web services?

    An easy way to test them is by using the Spinet web client:http://localhost:8080/soaplab2/ or http://{your_host}:{your_port}/soaplab2

    - How can I run soaplab web services? Which web services clients can I use?

    You can use Taverna workflow editor (http://www.taverna.org.uk/), spinet web client, perl programs like: and there’s more information in http://soaplab.sourceforge.net/soaplab2/ClientsOverview.html

    - What is detailed_status output?

    It indicates the exit status of your command line program. If a program ends correctly its exit status is 0 otherwise its value is 1. Soaplab captures this value and uses detailed_status to show it. If exit status is 1, soaplab will end with an error message.

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    Taverna FAQs

    General

    - Which taverna version are Panacea members using?

    Taverna 2.4

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    Designing workflows

    - Where can I find documentation about Taverna workbench, local processors, etc.?

    http://www.mygrid.org.uk/dev/wiki/display/taverna/Documentation+and+Videos

    - How can I import soaplab web services from a service provider?

    Use soaplab option after “Import new services” button. If the soaplab server you want to use is like http://{host}/soaplab2-axis. Then the address for Taverna is http://{host}/soaplab2-axis/services/ . Don’t forget the final slash (/).

    - I’m trying to add a soaplab server and I get an error message?

    Be sure you add the final slash to the address! http://{host}/soaplab2-axis/services/ . Verify the spinet web client is working.

    - What should I use to connect the inputs and outputs from different soaplab processors: output or output_url?

    In Panacea, we recommend output_url to deal with big files.

    - Can I inspect panacea catalogue from taverna?

    Yes! Go to your Taverna Preferences and configure the Biocatalogue instance you want to use.

    - How can get specific information from an xml data file? Is there a local processor to do that?

    There are two options: 1. use the “Xpath from text” local processor which will require a little xpath knowledge. http://www.mygrid.org.uk/dev/wiki/display/taverna/XPath+From+Text 2. The “Xpath service” from service templates. Really easy to use and no xpath knowledge needed. You may need to update Taverna to be able to use this feature (Advanced menu -> updates). http://www.mygrid.org.uk/dev/wiki/display/taverna/XPath

    - I’m working with some processors which outputs are lists. This is creating a problem of undesired nested lists. How can I solve this?

    You can use “flatten list” local processor to reduce the list one level. http://www.mygrid.org.uk/dev/wiki/display/taverna/Flatten+list

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    Running workflows

    - How can I improve Taverna performance (not web services performance!)?

    Deactivate “in-memory storage” option in “data and provenance” on Taverna Preferences.

    - Can I inspect intermediate results?

    Yes if you have that option activated on “data and provenance” on Taverna Preference.To inspect the results just click on the processor you are interested on the results view.

    - How can I count the execution time?

    In the results view click on the “Progress report” tab you’ll find detailed information about each processor / web service: iterations, Average time / iteration, etc.

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    Panacea registry (Biocatalogue instance) Faqs

    Registering web services

    - How should I register my soaplab2 web services: SOAP(wsdl) or soaplab server?

    You should use soaplab server. The registry will automatically gather all your web services and register them.

    - Is it really necessary to categorize all my web services?

    No, but it’s recommended. Categorization helps users to find your services.

    - Is it important to use tags?

    Yes. Tags are a very versatile and useful tool to annotate web services. With tags users can find web services without being experts. For example, there’s no need to know the category.

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    Searching web services

    - How can I search for web services?

  • The biocatalogue instance has tags, categories, providers, and more parameters to search web services.

  • The “Search” field on the web site can be used with wildcards to make more flexible queries i.e. asterisk (*) or question mark (?). For example crawl* would match crawler and crawling.

    • - Is it possible to know if a service is up and running?

    Yes! Next to every service there’s a “ball” indicating if the service is available. Move your mouse over it to get extra information like “last checked”.

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    For more detailed descriptions of BioCatalogue, myGrid and Taverna services, please click HERE and refer to the "what is....?" series of PDFs.