I have made some minor changes to DocumentMapperServiceImpl.java to fix this. The bodyLocation attributes now get added via the anno_link table in the database. I created JIRA issue 503 [0] for this issue, per the cTAKES wiki.
Since this is my first time committing a change to the project I'm not sure how to go about it. Is there a tutorial on how to file a pull request I can reference? [0] https://issues.apache.org/jira/browse/CTAKES-503 Thanks, Sean -----Original Message----- From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu] Sent: Wednesday, March 28, 2018 6:54 PM To: 'Finan, Sean'; dev@ctakes.apache.org Subject: RE: consequences of change to typesystem [EXTERNAL] Sean, Glad I asked. I will try either what you suggested or the similar approach of adding some code to handle the bare-annotation-as-feature case similarly to how annotations inside FSArrays are handled. Thanks, Sean -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, March 28, 2018 8:40 AM To: dev@ctakes.apache.org Subject: Re: consequences of change to typesystem [EXTERNAL] Hi Sean, In case nobody else has replied, Yes, this would definitely break a whole lot of things. I am not saying that it is a bad idea, just that the current BinaryTextRelation interface is used as-is in probably a thousand places, and while some refactoring might be trivial I wouldn't bet that it all would be as easy as one would like. I haven't looked at the ytex DBConsumer, but could it possibly be easier to add some code there that would check BinaryTextRelations and create a new FSArray for each? Stick those arrays in the cas immediately before and db write() and you should be able to do what you want without impacting the rest of ctakes. Sean ________________________________________ From: Mullane, Sean *HS <sp...@hscmail.mcc.virginia.edu> Sent: Tuesday, March 27, 2018 6:05 PM To: dev@ctakes.apache.org Subject: consequences of change to typesystem [EXTERNAL] I am trying out a change to the typesystem (explained below). If it works as I hope, I would want to contribute this back to the trunk. Before I invest too much time into this, can anyone tell me if this is likely to break things for other users? I am thinking of this causing problems reading existing annotated corpora, like SHARP. Problem I'm trying to fix: The DBConsumer database writer from YTEX seems to ignore BinaryTextRelation types (e.g. LocationOfTextRelation, used for the bodyLocation feature on annotations like DiseaseDisorderMention). This is because they are not added to the default AnnotationIndex index and are not contained in FSArrays or FSLists inside other annotation types, like the UmlsConcept annotations inside the ontologyConceptArr feature are. It seems that if I were to change the bodyLocation feature to be a FSArray of annotations instead of a bare annotation, the DBConsumer should write it to the output table and add an entry in the anno_link table. Would changing the type of the bodyLocation feature in certain IdentifiedAnnotations break things for others? Thanks, Sean
