RE: SimpleServer, instantiating CAS with custom typesystem?
Thanks for your reply, Jens. I admit I had been avoiding setting the text of the CAS to be the entire XML string I get back from the first REST service because it is a massive string and I only want a couple nodes from that xml string to be processed throughout the UIMA pipeline. But I see your point. So then, in this new AE, I retrieve the entire XML string from the CAS, do the zone-information processing from the specific nodes of the XML. I assume it is straightforward to then reset the CAS text to be just this text I have found in the original XML. Specifically, I would use CAS.reset() to empty the CAS of the original (full XML) text, then jCAS.setDocumentText() with the new string of just the relevant text, as well as load all the doc-zone annotations at this point. Is this right? Cheers, Helen -Original Message- From: Jens Grivolla [mailto:j+...@grivolla.net] Sent: Tuesday, February 19, 2013 3:20 AM To: user@uima.apache.org Subject: Re: SimpleServer, instantiating CAS with custom typesystem? Hi, SimpleServer itself is in a way your CR, creating a CAS with the document text you sent. Why do you want to change SimpleServer, it seems that you only want to add annotations to the CAS, not fundamentally change how the CAS is created. It seems to me that it would be far easier to just create an AE that adds those annotations. Then you won't have any typesystem issues either, since the AE would have the appropriate typesystem. HTH, Jens On 02/18/2013 10:37 PM, Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) wrote: I'm stumped: I have a UIMA pipeline that starts with a CollectionReader that - reads XML input (response from a REST service), - identifies a couple of relevant XML nodes - makes document-level annotations from the relevant nodes (title, document body, footnote section) From there, the AnalysisEngine portion of the pipeline has many AEs that I've wrapped into a single AggregateAnalysisEngine. The CollectionReader and the AAE all work correctly in this pipeline. Now I need to transfer this pipeline into a SimpleServer REST service environment. I've created a PEAR of the AAE portion of the pipeline, but I can't include the CollectionReader in this PEAR. First question: It is my understanding the CR cannot be included in the PEAR for the simpleServer, am I correct in this? In order to get those document-zoning annotations of title, body footnote, I have added some methods to the Service.java class in the SimpleServer package that do the XML parsing and then do the adding of these annotations to the JCAS before the AAE is called. The error that is being thrown at this point is this: The server encountered an internal error (JCas type myPackage.DocClass.ArticleMainTitle used in Java code, but was not declared in the XML type descriptor.) that prevented it from fulfilling this request. Second question: Where is Service.java looking for the typesystem xml file to be? I have tried all of the following, with the same error result: - put the typesystem descriptor file, myTSD.xml, in SimpleServer/lib - create a jar containing myTSD.xml, put it into SimpleServer/lib and add that to the build path - (after the two above attempts), in SimpleServer project properties, add lib to the UIMA CDE Property Page - in SimpleServer project properties, in UIMA Type System, point to the myTSD.xml file in lib - put myTSD.xml in SimpeServer/WebContent/WEB-INF/lib - put the jar containing myTSD.xml in the SimpleServer/WebContent/WEB-INF/lib - put myTSD.xml in SimpleServer/WebContent/WEB-INF/resources Final question: When a CAS gets instantiated (or reset, as it does in Service.java), how can I tell it to use a custom typesystem, and where will it look for that typesystem.xml file within the SimpleServer project? Thank you, Helen Johnson
Re: SimpleServer, instantiating CAS with custom typesystem?
Helen, You might also consider using UIMA-AS instead. UIMA-AS allows you to deploy a service (your AAE) that can be remotely accessed by UIMA-AS clients on other machines or in other JVMs for scalable deployments. Each client provides a CollectionReader to supply documents to the service and a Listener to catch return events from the service to know when processing is complete. You can find some additional getting started information about UIMA-AS at the following: http://uima.apache.org/doc-uimaas-what.html Thanks, Thomas Ginter 801-448-7676 thomas.gin...@utah.edu On Feb 19, 2013, at 7:04 AM, Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) heljo...@cisco.com wrote: Thanks for your reply, Jens. I admit I had been avoiding setting the text of the CAS to be the entire XML string I get back from the first REST service because it is a massive string and I only want a couple nodes from that xml string to be processed throughout the UIMA pipeline. But I see your point. So then, in this new AE, I retrieve the entire XML string from the CAS, do the zone-information processing from the specific nodes of the XML. I assume it is straightforward to then reset the CAS text to be just this text I have found in the original XML. Specifically, I would use CAS.reset() to empty the CAS of the original (full XML) text, then jCAS.setDocumentText() with the new string of just the relevant text, as well as load all the doc-zone annotations at this point. Is this right? Cheers, Helen -Original Message- From: Jens Grivolla [mailto:j+...@grivolla.net] Sent: Tuesday, February 19, 2013 3:20 AM To: user@uima.apache.org Subject: Re: SimpleServer, instantiating CAS with custom typesystem? Hi, SimpleServer itself is in a way your CR, creating a CAS with the document text you sent. Why do you want to change SimpleServer, it seems that you only want to add annotations to the CAS, not fundamentally change how the CAS is created. It seems to me that it would be far easier to just create an AE that adds those annotations. Then you won't have any typesystem issues either, since the AE would have the appropriate typesystem. HTH, Jens On 02/18/2013 10:37 PM, Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) wrote: I'm stumped: I have a UIMA pipeline that starts with a CollectionReader that - reads XML input (response from a REST service), - identifies a couple of relevant XML nodes - makes document-level annotations from the relevant nodes (title, document body, footnote section) From there, the AnalysisEngine portion of the pipeline has many AEs that I've wrapped into a single AggregateAnalysisEngine. The CollectionReader and the AAE all work correctly in this pipeline. Now I need to transfer this pipeline into a SimpleServer REST service environment. I've created a PEAR of the AAE portion of the pipeline, but I can't include the CollectionReader in this PEAR. First question: It is my understanding the CR cannot be included in the PEAR for the simpleServer, am I correct in this? In order to get those document-zoning annotations of title, body footnote, I have added some methods to the Service.java class in the SimpleServer package that do the XML parsing and then do the adding of these annotations to the JCAS before the AAE is called. The error that is being thrown at this point is this: The server encountered an internal error (JCas type myPackage.DocClass.ArticleMainTitle used in Java code, but was not declared in the XML type descriptor.) that prevented it from fulfilling this request. Second question: Where is Service.java looking for the typesystem xml file to be? I have tried all of the following, with the same error result: - put the typesystem descriptor file, myTSD.xml, in SimpleServer/lib - create a jar containing myTSD.xml, put it into SimpleServer/lib and add that to the build path - (after the two above attempts), in SimpleServer project properties, add lib to the UIMA CDE Property Page - in SimpleServer project properties, in UIMA Type System, point to the myTSD.xml file in lib - put myTSD.xml in SimpeServer/WebContent/WEB-INF/lib - put the jar containing myTSD.xml in the SimpleServer/WebContent/WEB-INF/lib - put myTSD.xml in SimpleServer/WebContent/WEB-INF/resources Final question: When a CAS gets instantiated (or reset, as it does in Service.java), how can I tell it to use a custom typesystem, and where will it look for that typesystem.xml file within the SimpleServer project? Thank you, Helen Johnson
RE: SimpleServer, instantiating CAS with custom typesystem?
So it turns out I cannot invoke cas.reset() from inside an annotator, nor can I set anew the text to be processed using cas.setDocumentText() once the doc-text has already been set in the SimpleServer Service.java class. What are my options for altering the document text inside an annotator after the SimpleServer Service.java has already set the document text? -Helen -Original Message- From: Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) Sent: Tuesday, February 19, 2013 7:05 AM To: user@uima.apache.org Subject: RE: SimpleServer, instantiating CAS with custom typesystem? Thanks for your reply, Jens. I admit I had been avoiding setting the text of the CAS to be the entire XML string I get back from the first REST service because it is a massive string and I only want a couple nodes from that xml string to be processed throughout the UIMA pipeline. But I see your point. So then, in this new AE, I retrieve the entire XML string from the CAS, do the zone-information processing from the specific nodes of the XML. I assume it is straightforward to then reset the CAS text to be just this text I have found in the original XML. Specifically, I would use CAS.reset() to empty the CAS of the original (full XML) text, then jCAS.setDocumentText() with the new string of just the relevant text, as well as load all the doc-zone annotations at this point. Is this right? Cheers, Helen -Original Message- From: Jens Grivolla [mailto:j+...@grivolla.net] Sent: Tuesday, February 19, 2013 3:20 AM To: user@uima.apache.org Subject: Re: SimpleServer, instantiating CAS with custom typesystem? Hi, SimpleServer itself is in a way your CR, creating a CAS with the document text you sent. Why do you want to change SimpleServer, it seems that you only want to add annotations to the CAS, not fundamentally change how the CAS is created. It seems to me that it would be far easier to just create an AE that adds those annotations. Then you won't have any typesystem issues either, since the AE would have the appropriate typesystem. HTH, Jens On 02/18/2013 10:37 PM, Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) wrote: I'm stumped: I have a UIMA pipeline that starts with a CollectionReader that - reads XML input (response from a REST service), - identifies a couple of relevant XML nodes - makes document-level annotations from the relevant nodes (title, document body, footnote section) From there, the AnalysisEngine portion of the pipeline has many AEs that I've wrapped into a single AggregateAnalysisEngine. The CollectionReader and the AAE all work correctly in this pipeline. Now I need to transfer this pipeline into a SimpleServer REST service environment. I've created a PEAR of the AAE portion of the pipeline, but I can't include the CollectionReader in this PEAR. First question: It is my understanding the CR cannot be included in the PEAR for the simpleServer, am I correct in this? In order to get those document-zoning annotations of title, body footnote, I have added some methods to the Service.java class in the SimpleServer package that do the XML parsing and then do the adding of these annotations to the JCAS before the AAE is called. The error that is being thrown at this point is this: The server encountered an internal error (JCas type myPackage.DocClass.ArticleMainTitle used in Java code, but was not declared in the XML type descriptor.) that prevented it from fulfilling this request. Second question: Where is Service.java looking for the typesystem xml file to be? I have tried all of the following, with the same error result: - put the typesystem descriptor file, myTSD.xml, in SimpleServer/lib - create a jar containing myTSD.xml, put it into SimpleServer/lib and add that to the build path - (after the two above attempts), in SimpleServer project properties, add lib to the UIMA CDE Property Page - in SimpleServer project properties, in UIMA Type System, point to the myTSD.xml file in lib - put myTSD.xml in SimpeServer/WebContent/WEB-INF/lib - put the jar containing myTSD.xml in the SimpleServer/WebContent/WEB-INF/lib - put myTSD.xml in SimpleServer/WebContent/WEB-INF/resources Final question: When a CAS gets instantiated (or reset, as it does in Service.java), how can I tell it to use a custom typesystem, and where will it look for that typesystem.xml file within the SimpleServer project? Thank you, Helen Johnson
Re: SimpleServer, instantiating CAS with custom typesystem?
Hi Helen, We use CAS views. Chapter six should help: http://uima.apache.org/d/uimaj-2.4.0/tutorials_and_users_guides.pdf We read the xml into one view and then have an annotator scrape the plain text and put it in another. You can work this so the XML to plaintext code is sofa aware and puts the plain text where your existing code expects it to be without modification. It's been a while since I've looked at this, but I left some notes: http://code.google.com/p/uimafit/wiki/WorkingWithSofaViews Also pay attention to the section called Sofa Incompatibilities between UIMA version 1 and version 2 in the user guide. The uimafit users google group is another good resource. https://groups.google.com/forum/?fromgroups=#!forum/uimafit-users -Chris On 2/19/13 4:43 PM, Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) wrote: So it turns out I cannot invoke cas.reset() from inside an annotator, nor can I set anew the text to be processed using cas.setDocumentText() once the doc-text has already been set in the SimpleServer Service.java class. What are my options for altering the document text inside an annotator after the SimpleServer Service.java has already set the document text? -Helen -Original Message- From: Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) Sent: Tuesday, February 19, 2013 7:05 AM To: user@uima.apache.org Subject: RE: SimpleServer, instantiating CAS with custom typesystem? Thanks for your reply, Jens. I admit I had been avoiding setting the text of the CAS to be the entire XML string I get back from the first REST service because it is a massive string and I only want a couple nodes from that xml string to be processed throughout the UIMA pipeline. But I see your point. So then, in this new AE, I retrieve the entire XML string from the CAS, do the zone-information processing from the specific nodes of the XML. I assume it is straightforward to then reset the CAS text to be just this text I have found in the original XML. Specifically, I would use CAS.reset() to empty the CAS of the original (full XML) text, then jCAS.setDocumentText() with the new string of just the relevant text, as well as load all the doc-zone annotations at this point. Is this right? Cheers, Helen -Original Message- From: Jens Grivolla [mailto:j+...@grivolla.net] Sent: Tuesday, February 19, 2013 3:20 AM To: user@uima.apache.org Subject: Re: SimpleServer, instantiating CAS with custom typesystem? Hi, SimpleServer itself is in a way your CR, creating a CAS with the document text you sent. Why do you want to change SimpleServer, it seems that you only want to add annotations to the CAS, not fundamentally change how the CAS is created. It seems to me that it would be far easier to just create an AE that adds those annotations. Then you won't have any typesystem issues either, since the AE would have the appropriate typesystem. HTH, Jens On 02/18/2013 10:37 PM, Helen Johnson -X (heljohns - Infobahn Softworld Inc at Cisco) wrote: I'm stumped: I have a UIMA pipeline that starts with a CollectionReader that - reads XML input (response from a REST service), - identifies a couple of relevant XML nodes - makes document-level annotations from the relevant nodes (title, document body, footnote section) From there, the AnalysisEngine portion of the pipeline has many AEs that I've wrapped into a single AggregateAnalysisEngine. The CollectionReader and the AAE all work correctly in this pipeline. Now I need to transfer this pipeline into a SimpleServer REST service environment. I've created a PEAR of the AAE portion of the pipeline, but I can't include the CollectionReader in this PEAR. First question: It is my understanding the CR cannot be included in the PEAR for the simpleServer, am I correct in this? In order to get those document-zoning annotations of title, body footnote, I have added some methods to the Service.java class in the SimpleServer package that do the XML parsing and then do the adding of these annotations to the JCAS before the AAE is called. The error that is being thrown at this point is this: The server encountered an internal error (JCas type myPackage.DocClass.ArticleMainTitle used in Java code, but was not declared in the XML type descriptor.) that prevented it from fulfilling this request. Second question: Where is Service.java looking for the typesystem xml file to be? I have tried all of the following, with the same error result: - put the typesystem descriptor file, myTSD.xml, in SimpleServer/lib - create a jar containing myTSD.xml, put it into SimpleServer/lib and add that to the build path - (after the two above attempts), in SimpleServer project properties, add lib to the UIMA CDE Property Page - in SimpleServer project properties, in UIMA Type System, point to the myTSD.xml file in lib - put myTSD.xml in SimpeServer/WebContent
SimpleServer, instantiating CAS with custom typesystem?
I'm stumped: I have a UIMA pipeline that starts with a CollectionReader that - reads XML input (response from a REST service), - identifies a couple of relevant XML nodes - makes document-level annotations from the relevant nodes (title, document body, footnote section) From there, the AnalysisEngine portion of the pipeline has many AEs that I've wrapped into a single AggregateAnalysisEngine. The CollectionReader and the AAE all work correctly in this pipeline. Now I need to transfer this pipeline into a SimpleServer REST service environment. I've created a PEAR of the AAE portion of the pipeline, but I can't include the CollectionReader in this PEAR. First question: It is my understanding the CR cannot be included in the PEAR for the simpleServer, am I correct in this? In order to get those document-zoning annotations of title, body footnote, I have added some methods to the Service.java class in the SimpleServer package that do the XML parsing and then do the adding of these annotations to the JCAS before the AAE is called. The error that is being thrown at this point is this: The server encountered an internal error (JCas type myPackage.DocClass.ArticleMainTitle used in Java code, but was not declared in the XML type descriptor.) that prevented it from fulfilling this request. Second question: Where is Service.java looking for the typesystem xml file to be? I have tried all of the following, with the same error result: - put the typesystem descriptor file, myTSD.xml, in SimpleServer/lib - create a jar containing myTSD.xml, put it into SimpleServer/lib and add that to the build path - (after the two above attempts), in SimpleServer project properties, add lib to the UIMA CDE Property Page - in SimpleServer project properties, in UIMA Type System, point to the myTSD.xml file in lib - put myTSD.xml in SimpeServer/WebContent/WEB-INF/lib - put the jar containing myTSD.xml in the SimpleServer/WebContent/WEB-INF/lib - put myTSD.xml in SimpleServer/WebContent/WEB-INF/resources Final question: When a CAS gets instantiated (or reset, as it does in Service.java), how can I tell it to use a custom typesystem, and where will it look for that typesystem.xml file within the SimpleServer project? Thank you, Helen Johnson
