The two currently implemented commands (WebserverCommand and TestCommand) use different methods to identify the nodes resolved by phyloreferences. In particular, WebserverCommand goes out of its way to ensure that the nodes are (1) not OWL classes and (2) are typed as CDAO:Node, neither of which should be necessary. Given that we're adding a third command to the mix (#52), it would be a good idea to clean this up by replacing both pieces of code with a single method in PhylorefHelper that uses a single method to identify resolved nodes.
The two currently implemented commands (WebserverCommand and TestCommand) use different methods to identify the nodes resolved by phyloreferences. In particular, WebserverCommand goes out of its way to ensure that the nodes are (1) not OWL classes and (2) are typed as CDAO:Node, neither of which should be necessary. Given that we're adding a third command to the mix (#52), it would be a good idea to clean this up by replacing both pieces of code with a single method in PhylorefHelper that uses a single method to identify resolved nodes.
For reference, here is the WebserverCommand implementation of this code is: https://github.com/phyloref/jphyloref/blob/040a9260c1dc4405db48095a340f352bf8db54af/src/main/java/org/phyloref/jphyloref/commands/WebserverCommand.java#L183-L207
And here is the TestCommand implementation:
https://github.com/phyloref/jphyloref/blob/040a9260c1dc4405db48095a340f352bf8db54af/src/main/java/org/phyloref/jphyloref/commands/TestCommand.java#L238-L259