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From William Karl Thompson <...@northwestern.edu>
Subject RE: Extending TextMarker with new actions
Date Tue, 30 Apr 2013 03:17:44 GMT
Thanks very much for the tips -- I did notice the name change! I think I'll wait a couple of
days until that series of updates has percolated through the code base, and you've had a chance
to validate the update site.

Best regards,


-----Original Message-----
From: Peter Klügl [mailto:pkluegl@uni-wuerzburg.de] 
Sent: Monday, April 29, 2013 4:21 PM
To: user@uima.apache.org
Subject: Re: Extending TextMarker with new actions


Am 29.04.2013 20:22, schrieb William Karl Thompson:
> Hi Peter,
> I've updated and built the TextMarker projects, but now I'm spinning my wheels a bit
trying to install the updated TextMarker Workbench feature from the projects. Could you give
me a tip on how to do that? This isn't something I've ever done before, and I'm not having
much success at the moment.

There are different ways. You could either just build the jars and put them in the dropins
folder of your eclipse installation (with no textmarker installed) - not really recommended.
Or, you could build the update site, which can be used to install the feature and plugins.
The pom of the update site project (was textmarker-eclipse-update-site) has two important
properties: item-maven-release-version and item-eclipse-release-version. If you want to build
an update site using the SNAPSHOT artifacts, then you need to adapt these values, e.g., to
2.0.1-SNAPSHOT and 2.0.1.SNAPSHOT. The normal process is to install everything and then package
the update site.

You have also to include your extensions somehow, e.g., by extending the update site (and
feature) or by copying the built plugin to the dropins folder.

When I try new stuff, I always start an Eclipse Application using my textmarker workspace.
Here, no installation is needed. I could also build a textmarker update site with the fixed
extensions for you, but unfortunately not before Thursday.

I am currently in the process of renaming all textmarker projects (the new name is UIMA Ruta).
You have to be careful which revision you are using to build the projects right now, because
I wasn't able to finish the renaming today, and I haven't tested the new update site yet.
The renaming started with revision 1477012. Sorry for the bad timing.



> Many thanks,
> Will
> -----Original Message-----
> From: William Karl Thompson
> Sent: Friday, April 26, 2013 3:40 PM
> To: user@uima.apache.org
> Subject: RE: Extending TextMarker with new actions
> Hi Peter,
> Thanks very much, I will try this out!
> Best,
> Will
> -----Original Message-----
> From: Peter Klügl [mailto:pkluegl@uni-wuerzburg.de]
> Sent: Friday, April 26, 2013 4:30 AM
> To: user@uima.apache.org
> Subject: Re: Extending TextMarker with new actions
> Hi,
> On 25.04.2013 19:16, William Karl Thompson wrote:
>> Hi Peter,
>>   Many thanks! I was just about to try it out before reading your latest email. Should
I check out the latest trunk version from the svn repository tomorrow?
> I fixed most problems and committed the changes together with two 
> example projects (in
> https://svn.apache.org/repos/asf/uima/sandbox/textmarker/trunk/example-projects):
> textmarker-ep-example-extensions contains two parts: the implementation of an action
(ExampleAction) and the integration in the ide. That's the reason, why it is a maven eclipse-plugin
> ExtensionsExample is a simple textmarker project, which uses the extension.
> The syntax check in the Workbench is not yet correctly integrated. It will take a while
until I will be able to write the documentation for the extensions. Just let me know, if any
problems occur.
> Best,
> Peter
> Btw: I am also involved in a project about information extraction in 
> clinical texts. That's a quite active area ;-)
>> In terms of feature requests, I appreciate your willingness to consider extensions.
My strategy will be to try accomplishing a few tasks first, to see what can be abstracted
that is of sufficient generality. As background info, I am creating some NLP applications
for clinical text using cTAKES, and I think TextMarker is a nice option to have for rule-based
alternatives to certain tasks (like relating two annotations to each other, DiseaseDisorder
and AnatomicalLocation in the same sentence). The current cTAKES relation extractor is based
on machine learning, and requires an annotated corpus for training, whereas sometimes it's
just easier to create a set of rules.
>> Cheers,
>> Will
>> -----Original Message-----
>> From: Peter Klügl [mailto:pkluegl@uni-wuerzburg.de]
>> Sent: Thursday, April 25, 2013 10:49 AM
>> To: user@uima.apache.org
>> Subject: Re: Extending TextMarker with new actions
>> Hi,
>> I checked the language extensions and unfortunately they do not work right now. There
are some small bugs, but they will be fixed tomorrow.
>> Best,
>> Peter
>> Am 25.04.2013 11:37, schrieb Peter Klügl:
>>> Hi,
>>> Am 25.04.2013 03:29, schrieb William Karl Thompson:
>>>> Hello,
>>>> (My apologies, I mistakenly sent this to the dev list initially)
>>>> I'm very interested in using the TextMarker project, but the 
>>>> current set of action types doesn't quite do what I need. I found 
>>>> references to an extension mechanism, have also found the 
>>>> ITextMarkerActionExtension interface in the source code. I also 
>>>> found the antlr grammar and lexer files where the TextMarker 
>>>> language is defined, which appears to be where new action type 
>>>> names are to be added. So I surmise the steps to add new actions is 
>>>> to
>>>> 1.       Add the desired action signature to the antlr grammar
>>>> 2.       Define an implementation of ITextMarkerActionExtension that
>>>> implements the functionality.
>>>> Is there an easier way to do this? My concern is that I need to 
>>>> modify TextMarker source files (the grammar and lexer files), which 
>>>> would be overwritten on any updated version of TextMarker.
>>> This should be possible without changing any textmarker code.
>>> There is a generic parsing rule in the grammar, which creates an 
>>> external action using the set of ITextMarkerExtension mentioned in 
>>> the descriptor (parameter: additionalExtensions). There is no 
>>> default syntax check since the possible arguments are of course not 
>>> yet known by the engine. Syntax checks need to be implemented in the 
>>> ITextMarkerActionExtension.createAction(), which throws an 
>>> ANTLRException. The arguments of the action are delegated to this 
>>> method, which return the action implementation, so there will 
>>> probably many casts and "if instanceOf" checks. Language constructs 
>>> like assignments ("feature" = Type) known by the CREATE action, are 
>>> not yet supported.
>>> Unfortunately, there is no automatic integration in the workbench yet.
>>> You have to modify the BasicEngine (add the extension) in the 
>>> textmarker project yourself. The implemenatation of the extension 
>>> needs of course then also be available to the workbench.
>>> I haven't used the language extensions since 2009 (it was a wordnet
>>> integration) and they are not yet covered by unit tests. So, there 
>>> are maybe some bugs due to the changes after the contribution to 
>>> Apache UIMA. However, I will check the functionality, add a test 
>>> case and extend the documentation.
>>> Concerning the list of available actions: You are of course also 
>>> welcome to create feature requests for new actions. The current set 
>>> of actions is mainly based on my own requirements and I will gladly 
>>> add new reasonable/generic actions (within the limits of my available time).
>>> Best,
>>> Peter
>>>> Thanks!
>>>> Will Thompson

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