The Service Panel provides facilities to manage the various tools available for the building of workflows. It allows the workflow designer to manage service libraries, create instances of a service in the the workflow, and the search for specific services.
Searching for tools
Tools listed in the Service Panel may be searched by using the Filter field. For convenience the text box in the toolbar allows the user to enter a fragment of a service name, e.g. 'blast'. As the user types, all matching services then listed, showing all nodes matching the specified search. This is particularly useful if the user knows exactly what he or she is looking for. The image below shows the search in action which has found Biomart and Biomoby services associated with 'blast':
A search will normally be matched across several service description properties, including the folder path. So a search for say
ensembl will also match all the services within the
ENSEMBL FUNGI 22 folder. You can restrict this search by different service properties by using the form
description:ensembl will only match those services using
ensembl within their description. The possible service properties as of Taverna 2.5 (not all service types support all properties) are:
- name (e.g.
- description (e.g.
- path (e.g.
- type (e.g.
- category (e.g.
- name (e.g.
- local services:
- script (e.g.
- style (e.g.
- external tool
- api consumer
Tools in the Service Panel
Tools in the Service Panel are shown in a hierarchical view. The services are ordered into folders that are defined by service type, such as local services, WSDL-based services, Soaplab, BioMart and BioMoby. Opening these folder nodes will reveal, for example, the operations available from web services:
SoapLab provides services which are categorised by function. The view for a soaplab server shows the top level installation, then child nodes corresponding to the various tool function categories and finally leaf nodes corresponding to actual services:
BioMoby services are located by accessing a central moby repository. In this case the hierarchy is constructed from a root node specifying the repository, then child nodes for each site hosting services and leaf nodes for each individual service:
Adding services to the workflow
The primary function of the service panel is to allow users to create new processors within the current workflow. This can be accomplished either through drag and drop or through the context menus available by right clicking on the nodes in the service panel.
Adding services using drag and drop
Any node representing a service may be incorporated into the workflow by either dragging it from the service selection panel into (1) the Workflow Diagram window or (2) the Workflow Explorer window:
Adding services using menu options
As an alternative, new processors may be created in a workflow by right clicking on the service to be used; this shows the following options:
Populating the Service Panel
The service panel may be populated with different types of services using the Import new services button:
A dialog box will then pop up requesting where metadata about the service to be added into the Service Panel can be obtained. The information that is required depends on the service:
- To add a new BioMoby registry of services, the location of a Moby Central repository will be requested. It uses this repository to determine all available hosts and their services and adds the tree thus created to the service panel.
- Taverna allows the import of pre-prepared Java APIs using its API Consumer functionality. This is used in conjunction with Java libraries augmented with annotations created by the API Consumer tool (see that tool's documentation for more information). This allows the import of existing component systems such as caBIG, BioJava, JUMBO, CDK etc.
- The incorporation of WSDL-based web services into Service Panel requires the location of its Web Service Description Language file on the web. It inspects this file to pull out all appropriate operations and adds them as WSDL based service nodes to the services panel.
- BioMart service allows the user to specify the location online of a Biomart service. By default Taverna will load the public Ensembl+MSD+Vega+DbSNP registry hosted at the EBI and Sanger Institute in the UK.
- Incorporation of Soaplab services involves requesting the user for the root URL of a soaplab server. It interrogates the server to get all available application categories then for each category creates a list of services in that category.