Please create a pull request only with the code of ExcelAlex.

Current Semantic Navigation service uses TNTBase to get dependencies. We should use MMT instead.

After doing definition lookup and then trying to update the position/url of the window I get:

Exception in thread "AWT-EventQueue-0" java.lang.IllegalStateException: Not on FX application thread; currentThread = AWT-EventQueue-0
    at com.sun.javafx.tk.Toolkit.checkFxUserThread(Toolkit.java:237)
    at com.sun.javafx.tk.quantum.QuantumToolkit.checkFxUserThread(QuantumToolkit.java:398)
    at javafx.scene.web.WebEngine.checkThread(WebEngine.java:931)
    at javafx.scene.web.WebEngine.load(WebEngine.java:723)
    at info.kwarc.sally.theofx.ui.TheoWindow$3.run(TheoWindow.java:305)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

Looks like TheoFX does not like when the Thread creating a window is not the same as the one updating it. When using complex workflows, I can never warranty that the same thread creating a window will be used. We need to have a solution for this.

Currently all information about workflows comes either from a jboss-drools repository (localhost:8080/drools-guvnor/) or packaged from file Sally.pkg (https://github.com/KWARC/Sally/blob/master/sally_app/src/main/resources/Sally.pkg).
Both sources contain the workflow needed for definition lookup service - which is not good. The workflow should only be part of the sally_def_lookup service.

Sally_app should use reflections to figure out all resources that contain workflow information and load them all.

Create sally_sem_navigation and sally_fency projects services that resamble the structure of sally_def_lookup.

Create BPMN workflows for both services.

CellRange is specified by SheetName, startrow, startcol, endrow, endcol.

Should return a list of { cellrow, cellcol, value, formula }

We need a way for deleting / updating information about blocks relations.

create a new project sally_definition_lookup isolating all the code that Definition Lookup services requires.

TheoFX script injection uses localhost as a source for the scripts. If Sally is running on a different machine than Theo, this will not work. See method injectScripts in info.kwarc.sally.theofx.TheoApp.java

The sally_def_lookup project represents the standalone Definition Lookup service. Right now, the sally_def_lookup project is referenced directly from sally_app (see ProcessMain.java). This dependency should not exist. Sally_app should instead use reflections to look for available services and automatically add them to the pull architecture etc. We already use a reflection framework (https://code.google.com/p/reflections/) and would be very good if it could be used for achieving this task.

Aim: remove sally_def_lookup dependency from sally_app/pom.xml and make definition lookup work.

The pull architecture does not "unregister" Alex clients that have disconnected. And hence even after them disconnecting, one still sees their services being available.

Create a sally_mmt project inside sally that connects to an MMT server and provides utility functions that allows one to:

1. get a list of theories and concepts inside them.
2. get a list of all concepts that any theory that:
   2a) begin with a certain prefix
   2b) contain a certain substring
3. get a list of all concepts that are available in the scope of a certain theory that
   3a) begin with a certain prefix
   3b) contain a certain substring

would be nice 2 and 3 could be somehow combined in a nice way.

ASM Editor needs to be able to assign titles and orderids to blocks/relations. For blocks one could try and do it by creating a "label" and "order" relations. But that would not work for relations any longer.

So I guess we need some other mechanism for that. A key-value properties for blocks and relations could help. Ideas?

.. to use RDF generated by the new ASM.