Package org.sigpath.action

Controller classes for the Struts model-view-controller (MVC) pattern.

See:
Description

Interface Summary

DBWriteAccess	Indicates that the specified action requires Database write access.
Secure	Indicates that the specified action is available to authenicated users only.
SecureAdmin	Indicates that the specified action is available to the SigPath Administrator only.

Class Summary

ActionRoot	Base class for all Action classes.
ChangeDBStatus	Action for Updating Database Status
CreateModel	Action for Creating a Model for Export.
CreatePathway
DeleteConcentration	Action for Deleting Concentration
DisplayJSP	Action for Displaying any JSP page.
GetConcentration	Action for Retrieving a Concentration Measurement.
GetModel	Action for Retrieving a Model from the Database.
GetSpidRange	Created by IntelliJ IDEA.
Login	Action for Authenticating Users.
PopulateUserData	Action for Populating User Data Form.
RetrieveChemical	Action for Adding a Chemical SPID to the Request.
SaveConcentration	Action for Saving Concentration
SaveUpdatedReaction	Action for Saving an updated Reaction.
SaveXML	Action to save XML import data.
SearchChemicals	Action for Searching Molecules.
SearchModels	Action for Searching Models.
SearchPathways	Action for Searching Pathways.
SearchReactions	Action for Searching Reactions.
SecureAdminDisplayJSP	Action for Displaying JSP Page to SigPath Admin only.
SecureDBWriteDisplayJSP	Action for Displaying any Secure DBWriteAccess required JSP page.
SecureDisplayJSP	Action for Displaying any Secure JSP page.
SetupConcentration	Action for clearing the SpecifyConcentration form and adding a chemical to the request.
SigPathServlet	Controller class for all user requests.
SnoopHTTP	Action for Snooping on the Current HTTP Request.
StoreAffiliation	Action for Storing User Affiliation
StoreConcentration	Action for Storing Concentration
StoreNextPage	Stores the page the user just came from as nextPage in the session.
StoreUserData	Action for Storing User Data
TurnXDebugOn_Off	Action for Turning Live Debugging On/Off.
UIHelper	Provides a number of utilities that help create the Data Submission Wizard
UpdateAffiliation	Action for Updating User Affiliation
UpdateReactionParameters	Action for Updating Reaction Parameters
UpdateUserData	Action for Updating User Data
UploadXML	Action for Uploading an XML document.
ViewDBInfo	Action for Viewing Database/Dictionary Properties.
ViewDetails	Action for Viewing Details of a SigPathEntity.
ViewModelImage
ViewModelImageNone	Action for showing message when the required yFiles library is not available.
ViewModelImageYFiles	Action for Retrieving a Model and Viewing as an Image.
ViewNamedChemicalImageYFiles	Action for Retrieving and Viewing graphics in gif format.
ViewSPEBaseInfo	Action for Viewing a SigPathEntity for editing purposes.

Package org.sigpath.action Description

Controller classes for the Struts model-view-controller (MVC) pattern.

Overview

Controller classes control the overall flow of the web application. In general, a browser request first goes to the generic SigPathServlet, which then forwards the request to the appropriate action class. The action class generally calls one or more database tasks, and passes the results onto a Java Server Page (JSP). HTML formatting is done within the JSP page.

Creating New Actions Classes

All new action classes should extent ActionRoot. Action Root centralizes all live debugging, setting of user messages and exception handling. To create a new action, simply extend ActionRoot and implement the _perform() method. For example:

public class DeleteExternalReference extends ActionRoot {

  protected ActionForward _perform
    (ActionMapping mapping, ActionForm form, HttpServletRequest request,
    HttpServletResponse response, ActionForward actionForward, XDebug xdebug)
    throws Exception {
      xdebug.logMsg(this, "Starting Action:  Delete External Reference");
      ...
  }
}

Warning: The Struts framework will only create one instance of your Action class, and this one object will serve multiple browser requests. Therefore, you must avoid using instance variables within your Action class. Otherwise, you may end up with unpredictable multi-threading issues.

Modifying the struts-config file

Once you have created a new action class, you must register it in the struts-config.xml file. For example:

<action path="/deleteExternalReference"
  type="org.sigpath.action.edit.DeleteExternalReference"
  name="SpecifyExternalReferenceForm"
  input="/editSigPathEntity.action">
  <forward
    name="success"
    path="/editSigPathEntity.action"/>
  </action>

Controlling Access

If you want to restrict access to your action class, you can specify one or more access control interfaces:

• Secure: Indicates that the action is available to authenticated users only.
• SecureAdmin: Indicates that the action is available to the SigPath Administrator only.

For example, to create an action that is available only to the SigPath administrator, you would write the following code:

  public class ChangeDBStatus extends ActionRoot implements SecureAdmin {
    ...
  }

Background Information

• For an overview of the J2EE Model 2 Architecture and the Model-View-Controller pattern, refer to Understanding JavaServer Pages Model 2 architecture
• For an overview of the Struts Framework, refer to the Struts User Guide.
• The Struts documentation is not great. I therefore highly recommend Programming Jakarta Struts (O'Reilly, 2003).