You are fast -- I'll update and give it a try! -----Original Message----- From: Peter Klügl [mailto:[email protected]] Sent: Thursday, May 09, 2013 11:30 AM To: [email protected] Subject: Re: Extending TextMarker with new actions
Hi, feature assignments for simple regexp rules are now part of the trunk. RegExpRuleTest.ruta contains an example and the documentation describes the exact syntax. Best, Peter On 08.05.2013 17:56, William Karl Thompson wrote: > Many thanks! > > -----Original Message----- > From: Peter Klügl [mailto:[email protected]] > Sent: Wednesday, May 08, 2013 2:57 AM > To: [email protected] > Subject: Re: Extending TextMarker with new actions > > Hi, > > I will create a feature request and see when I find the time to implement it. > > Best, > > Peter > > On 08.05.2013 04:38, William Karl Thompson wrote: >> Hi Peter, >> >> What you proposed would work fine for what I was trying to do! >> >> Cheers, >> >> Will >> >> -----Original Message----- >> From: Peter Klügl [mailto:[email protected]] >> Sent: Tuesday, May 07, 2013 3:42 AM >> To: [email protected] >> Subject: Re: Extending TextMarker with new actions >> >> Hi, >> >> On 06.05.2013 18:26, William Karl Thompson wrote: >>> Hi Peter, >>> >>> I like the simplified regular expression rule syntax -- very handy. It's >>> almost exactly what I wanted. However, one thing I'm wondering is how to >>> create an annotation with features using such rules. I have in mind >>> something like the following: >>> >>> "(regex string)" -> 1 = CREATE(FooType, "feat" = "bar"); >>> >>> Here's a possible variant of the above that I can imagine would be useful >>> too: >>> >>> "(regex) (string)" -> CREATE(FooType, "feat1" = GROUP(1), >>> "feat2"=GROUP(2)); >>> >>> What are your thoughts on this? >> I think I won't be able to use the existing code of the CREATE action for >> this and it will also be problematic in the grammar without creating a new >> context. >> >> What about something like: >> >> "(regexp) (string)" -> Type1, 1 = Type2 ("feat" = 2); >> >> This will of course not work with numeric feature values, but there isn't an >> auto-cast anyway... >> >> Best, >> >> Peter >> >> >>> Cheers, >>> >>> Will >>> >>> -----Original Message----- >>> From: William Karl Thompson >>> Sent: Thursday, May 02, 2013 1:49 PM >>> To: [email protected] >>> Subject: RE: Extending TextMarker with new actions >>> >>> Vielen Dank, Ich werde es probieren. >>> >>> -----Original Message----- >>> From: Peter Klügl [mailto:[email protected]] >>> Sent: Thursday, May 02, 2013 12:42 PM >>> To: [email protected] >>> Subject: Re: Extending TextMarker with new actions >>> >>> Am 02.05.2013 19:16, schrieb William Karl Thompson: >>>> I see you're way ahead of me! I'll take a look at this -- is it in the >>>> latest on trunk? >>> Yes, and there is also a unit test (if you are interested in some >>> ready-to-work examples): >>> org.apache.uima.ruta.RegExpRuleTest.java(.ruta, >>> .txt) >>> >>> Peter >>> >>>> -----Original Message----- >>>> From: Peter Klügl [mailto:[email protected]] >>>> Sent: Thursday, May 02, 2013 12:14 PM >>>> To: [email protected] >>>> Subject: Re: Extending TextMarker with new actions >>>> >>>> Hi, >>>> >>>> oh, I am afraid I recently added something like that for the 2.0.1 >>>> release, not yet included in the 2.0.0 release. This does not mean >>>> that I would not include the action in UIMA Ruta ;-) >>>> >>>> Here the excerpt of the documentation: >>>> >>>> <section id="ugr.tools.ruta.language.regexprule"> >>>> <title>Simple Rules based on Regular Expressions</title> >>>> <para> >>>> The Ruta language includes, additionally to the normal rules, a >>>> simplified rule syntax for processing regular expressions. >>>> These simple rules consist of two parts separated by >>>> <quote>-></quote>: The left part is the regular expression >>>> (flags: DOTALL and MULTILINE), which may contain capturing groups. >>>> The right part defines, which kind of annotations >>>> should be created for each match of the regular expression. If a >>>> type is given without a group index, then an annotation of that type is >>>> created for the complete regular expression match, which >>>> corresponds to group 0. These simple rules can be restricted to match only >>>> within >>>> certain annotations using the BLOCK construct, and ignore all >>>> filtering settings. >>>> </para> >>>> >>>> <programlisting><![CDATA[ >>>> RegExpRule -> StringExpression "->" GroupAssignment >>>> ("," GroupAssignment)* ";" >>>> GroupAssignment -> TypeExpression | NumberEpxression "=" >>>> TypeExpression ]]></programlisting> >>>> >>>> <para> >>>> The following example contains a simple rule, which is able to >>>> create annotations of two different types. It creates an annotation >>>> of the type <quote>T1</quote> for each match of the complete >>>> regular expression and an annotation >>>> of the type <quote>T2</quote> for each match of the first >>>> capturing group. >>>> </para> >>>> >>>> <programlisting><![CDATA["A(.*?)C" -> T1, 1 = >>>> T2;]]></programlisting> >>>> >>>> >>>> </section> >>>> >>>> >>>> >>>> >>>> Am 02.05.2013 19:06, schrieb William Karl Thompson: >>>>> I forgot to mention, the numeric argument in the proposed MARKREGEXP >>>>> action indicates which capturing group is to be used from regular >>>>> expression to generate the region for the annotation of the specified >>>>> type. >>>>> >>>>> -----Original Message----- >>>>> From: William Karl Thompson >>>>> Sent: Thursday, May 02, 2013 12:02 PM >>>>> To: [email protected] >>>>> Subject: RE: Extending TextMarker with new actions >>>>> >>>>> Peter, >>>>> >>>>> Thanks for helping me to get going on this, it now works like a charm! >>>>> Have been able to generate extensions and have them be recognized by the >>>>> Eclipse IDE as per your instructions. Very nice! >>>>> >>>>> In the process of doing this, I do have an idea for a possibly useful >>>>> action to be added to the current set. The basic idea is implement >>>>> functionality similar to that found in the RegularExpressionAnnotator >>>>> that is one of the UIMA addons: >>>>> >>>>> http://uima.apache.org/sandbox.html#regex.annotator >>>>> >>>>> This allows you to define a set of regular expression matches, and to >>>>> mark an annotation on the region covered by the match, restricted if >>>>> desired by a capturing group within the regular expression. The way I >>>>> implemented it experimentally was like the following: >>>>> >>>>> Sentence{->MARKREGEXP(TypeExpression, "(?i)(ascending colon) >>>>> polyps", 1}; >>>>> NP{PARTOF(FindingsSection)->MARKREGEXP(TypeExpression, >>>>> "(?i)tubular adenoma", 0)}; >>>>> >>>>> The key thing is that the regular expression matching is using the >>>>> equivalent of java.util.regex.Matcher.find(), unlike the current >>>>> implementation of the REGEXP condition, which uses match(): >>>>> >>>>> http://docs.oracle.com/javase/1.5.0/docs/api/java/util/regex/Matcher. >>>>> h >>>>> tml#find() >>>>> >>>>> Anyway, thanks again for your help getting this all working. >>>>> >>>>> Cheers, >>>>> >>>>> Will >>>>> >>>>> ________________________________________ >>>>> From: Peter Klügl [[email protected]] >>>>> Sent: Monday, April 29, 2013 4:20 PM >>>>> To: [email protected] >>>>> Subject: Re: Extending TextMarker with new actions >>>>> >>>>> Hi, >>>>> >>>>> 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. >>>>> >>>>> Best, >>>>> >>>>> Peter >>>>> >>>>> >>>>>> Many thanks, >>>>>> >>>>>> Will >>>>>> >>>>>> -----Original Message----- >>>>>> From: William Karl Thompson >>>>>> Sent: Friday, April 26, 2013 3:40 PM >>>>>> To: [email protected] >>>>>> 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:[email protected]] >>>>>> Sent: Friday, April 26, 2013 4:30 AM >>>>>> To: [email protected] >>>>>> 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 project. >>>>>> >>>>>> 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:[email protected]] >>>>>>> Sent: Thursday, April 25, 2013 10:49 AM >>>>>>> To: [email protected] >>>>>>> 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 >>>>>>>>>
