Re: suggestion for default pipelines
It would be nice if uimaFIT provided a Maven plugin to automatically generate descriptors for aggregates. Maybe if we come up with a convention for factories, e.g. a "class with static methods that do not take any parameters and that return descriptors", or "methods that bear a specific Java annotation, e.g. @AutoGenerateDescriptor)" it should be possible to implement such a Maven plugin. Cheers, -- Richard On 16.04.2014, at 05:21, Steven Bethard wrote: > +1. And note that once you have a descriptor, you can generate the > XML, so we should arrange to replace the current XML descriptors with > ones generated automatically from the uimaFIT code. That should reduce > some synchronization problems when the Java code was changed but the > XML descriptor was not. > > Steve > > On Tue, Apr 15, 2014 at 8:52 AM, Miller, Timothy > wrote: >> The discussion in the other thread with Abraham Tom gave me an idea I >> wanted to float to the list. We have been using some UIMAFit pipeline >> builders in the temporal project that maybe could be moved into >> clinical-pipeline. For example, look to this file: >> >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup >> >> with the static methods getPreprocessorAggregateBuilder() and >> getLightweightPreprocessorAggregateBuilder() [no umls]. >> >> So my idea would be to create a class in clinical-pipeline >> (CTakesPipelines) with static methods for some standard pipelines (to >> return AnalysisEngineDescriptions instead of AggregateBuilders?): >> >> getStandardUMLSPipeline() -- builds pipeline currently in >> AggregatePlaintextUMLSProcessor.xml >> getFullPipeline() -- same as above but with SRL, constituency parsing, >> etc., every component in ctakes >> >> We could then potentially merge our entry points -- I think Abraham's >> experience points out that this is currently confusing, as well as >> probably not implemented optimally. For example, either >> ClinicalPipelineWithUmls or BagOfCUIsGenerator would use that static >> method to run a uimafit-style pipeline. Maybe we can slowly deprecate >> our xml descriptors too unless people feel strongly about keeping those >> around. >> >> Another benefit is that the cTAKES API is then trivial -- if you import >> ctakes into your pom file getting a UIMA pipeline is one UimaFit call: >> >> builder.add(CTAKESPipelines.getStandardUMLSPipeline()); >> >> >> I think this would actually be pretty easy to implement, but hoping to >> get some feedback on whether this is a good direction. >> >> Tim
RE: ctakes-vm.apache.org
Hi Andy, Let me know if you're able to ssh -l -v to and...@ctakes-vm.apache.org I believe all you would need to do is run ssh-keygen and then copy your public key to id.apache.org. James: opiekey is only required for sudo access. I see you're able to log in successfully already. Nethertheless, Jan reset opiekey so you can try again if needed. https://issues.apache.org/jira/browse/INFRA-7451 --Pei > -Original Message- > From: andy mcmurry [mailto:mcmurry.a...@gmail.com] > Sent: Monday, April 07, 2014 5:43 PM > To: dev@ctakes.apache.org > Subject: Re: ctakes-vm.apache.org > > On a mac here, also having trouble logging in to the VM. > Looking more into the keys situation. > > On mac, there is this problem: "no support for PKCS#11" > Which I'm working to resolve. > > > > > On Sat, Apr 5, 2014 at 12:15 PM, John Green > wrote: > > > Thanks Pei. > > > > > > > > > > Sure, that would be great, add me. > > > > > > > > > > Jg > > > > -- > > Sent from Mailbox for iPhone > > > > On Fri, Apr 4, 2014 at 10:15 AM, Chen, Pei > > > > > > wrote: > > > > > John, > > > You should have committer rights now... I would suggest opening a > > > Jira > > item just so that it can be tracked. > > > But you should be able create a subdir within > > https://svn.apache.org/repos/asf/ctakes/sandbox and do an svn commit. > > > As a side note: ctakes-vm.apache.org has been created now. John, > > > let > > me know if you would like to added as list of maintainers. > > > We can use that machine to host any of the demo's. > > > It requires passwordless ssh so you'll need to ssh-keygen and save > > > them > > via http://id.apache.org. > > > --Pei > > >> -Original Message- > > >> From: John Green [mailto:john.travis.gr...@gmail.com] > > >> Sent: Thursday, April 03, 2014 6:05 PM > > >> To: dev@ctakes.apache.org > > >> Cc: dev@ctakes.apache.org > > >> Subject: RE: ctakes-vm.apache.org > > >> > > >> Would love to! Ive only submitted those example notes I did though > > >> to a > > jira > > >> ticket. How do I push to the sandbox dir? Any special permissions I > > need? > > >> > > >> > > >> > > >> > > >> JG > > >> > > >> -- > > >> Sent from Mailbox for iPhone > > >> > > >> On Wed, Apr 2, 2014 at 10:51 PM, Chen, Pei > > >> > > >> wrote: > > >> > > >> > John, > > >> > If there are no other objections, you can also put it directly in > > >> > sandbox https://svn.apache.org/repos/asf/ctakes/sandbox/ > > >> > It may make it easier in the future if folks decided to integrate > > >> > into > > >> cTAKES... and possibly save any potential IP/License questions... > > >> > --Pei > > >> > > > >> > From: John Green [john.travis.gr...@gmail.com] > > >> > Sent: Wednesday, April 02, 2014 6:24 PM > > >> > To: dev@ctakes.apache.org > > >> > Subject: Re: ctakes-vm.apache.org Great! > > >> > Let me clean it up this weekend and ill throw it out onto my github. > > Will > > >> post link soon; nlt cob this weekend. > > >> > JG > > >> > -- > > >> > Sent from Mailbox for iPhone > > >> > On Wed, Apr 2, 2014 at 1:53 PM, andy mcmurry > > >> > > >> > wrote: > > >> >> Yes! Impeccable timing. Where can we find the python source? > > >> >> On Apr 2, 2014 8:33 AM, "John Green" > > >> >> > > >> wrote: > > >> >>> Andy: this is very interesting and exciting. > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> I hacked out a script that makes a visually appealing > > >> >>> representation of the aggregate pipeline in d3js that, at least > > >> >>> for a clinician, is a nice overall summary of the meta data generated > from the pipeline. > > >> >>> Its really no more than a parser of the xml through the type > > >> >>> system spitted out into json, but when I was talking to my > > >> >>> informatics department who didnt know much at all about ctakes, > > >> >>> it was a great visual summary. Its in python. I dont know if > > >> >>> youd want it but it might be worth having the "demo site" spit > > >> >>> out a visually appealing graphic like this automatically. If > > >> >>> not in python it might be worth adapting it to whatever your > > >> >>> using for a platform to spit out the > > json for > > >> the d3js graphic im using. > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> John > > >> >>> > > >> >>> -- > > >> >>> Sent from Mailbox for iPhone > > >> >>> > > >> >>> On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry > > >> >>> > > >> >>> wrote: > > >> >>> > > >> >>> > Yes! I have been working full time on the "apt-get install" > > >> >>> > task specific to medical genetics: > > >> >>> > http://www.ncbi.nlm.nih.gov/medgen > > >> >>> > Right now, millions of $$$ are invested in getting phenotype > > >> >>> > concepts -- indications, diseases, problem lists -- linked to > > >> >>> > patient test results including DNA / RNA / etc. In industry, > > >> >>> > most of the curation work is done manually because platforms > > >> >>> > like cTAKES are not yet immediately > > >> >>> accessible. > > >> >>> > I have wr
RE: Ctakes-data-vis
John, How we use the VM is up to us to decide. For an online demo, We can certainly load up cTAKES and it's resources. If it's a web app, we can prompt the user to enter umls credentials if they choose the umls resources? --Pei > -Original Message- > From: John Green [mailto:john.travis.gr...@gmail.com] > Sent: Sunday, April 13, 2014 9:16 PM > To: dev@ctakes.apache.org > Subject: Re: Ctakes-data-vis > > Great! Ill try and fix that soon. Im back on the wards so time is slim. > > > What are the next steps for the vm? For the demo site? > > > > > Out of curiosity, would this allow resources to stay loaded and a kind of que > be setup? Is there a solution that allows to do this now? That is, the > resources stay loaded in mem, the umls auth stays current, and I could just > pass content as it becomes available? > > > > > Jg > — > Sent from Mailbox for iPhone > > On Sat, Apr 12, 2014 at 2:57 PM, andy mcmurry > wrote: > > > It looks great! The transitions are smooth and the hierarchical > > browsing is straightforward. The only edit I recommend I have is about > > spacing -- The information often exceeds the space of a single page. > > On Sat, Apr 5, 2014 at 12:13 PM, John Green > wrote: > >> Had to refresh my svn skills as its been years. As a result not much > >> cleaning up got done Andy/Pei. The code is solid though and I sent > >> four different ways to view the json up too; collapsable dendrogram > >> is the most useful. > >> > >> > >> The script could easily be re written to iterate through a directory > >> as its in the form of a simple class. Also, it should take command line > >> args. > >> Im out of time this weekend, even for the ten minutes that would > >> take, but I can do both next weekend. > >> > >> > >> Let me know if its useful at all Andy or if you need tweaks on > >> anything to make it useful for whatever demo u have in mind, id be > >> happy to as time permits. > >> > >> > >> Hope to make more significant contributions to this wonderful project > >> sometime in the next year, Jg > >> -- > >> Sent from Mailbox for iPhone
Apache cTAKES Example Application?
We spent some time in the past to make it easier for users to launch the CVD/CPE. But based on the questions/discussions, I think we are passed this stage and a very common use case would be for developers to use cTAKES as a lib, extend a class or two and then, embed it into their existing app. I am proposing a ctakes-web-demo for the sandbox, A simple webapp- war/maven pom.xml that uses the ctakes as a dependency. Have a simple servlet that wires up a pipeline (uimaFIT style), and then dump the CAS as html table. We could even host it on: https://demo-ctakes.apache.org/ It will probably only be a few lines of code, but it may be a good starting point for developers who are more interested in using it as a lib and not necessarily modifying ctakes code. What do folks think? --Pei
errors when run BagOfCUIsGenerator.java
It failed when run BagOfCUIsGenerator.java. The followings are the error information. Thanks for your help. Ying Exception in thread "main" org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" failed. (Descriptor: file:/C:/Users/Ying/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) at org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath(AnalysisEngineFactory.java:147) at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.(BagOfAnnotationsGenerator.java:42) at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.(BagOfAnnotationsGenerator.java:36) at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.(BagOfCUIsGenerator.java:16) at org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:49) Caused by: org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:79) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 18 more Caused by: java.net.ConnectException: Connection timed out: connect at java.net.DualStackPlainSocketImpl.connect0(Native Method) at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) at java.net.AbstractPlainSocketImpl.connect(Unknown Source) at java.net.PlainSocketImpl.connect(Unknown Source) at java.net.SocksSocketImpl.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at sun.security.ssl.SSLSocketImpl.connect(Unknown Source) at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source) at sun.net.NetworkClient.doConnect(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.protocol.https.HttpsClient.(Unknown Source) at sun.net.www.protocol.https.HttpsClient.New(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:93) at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:70) ... 19 more
RE: errors when run BagOfCUIsGenerator.java
Ying, Are you behind a proxy or firewall? If you're trying to use the umls resources, it attempts to make a call to their umls service to validate your credentials. --Pei > -Original Message- > From: Liu, Ying [mailto:l...@advisory.com] > Sent: Wednesday, April 16, 2014 1:13 PM > To: dev@ctakes.apache.org > Subject: errors when run BagOfCUIsGenerator.java > > It failed when run BagOfCUIsGenerator.java. The followings are the error > information. Thanks for your help. > Ying > > > > Exception in thread "main" > org.apache.uima.resource.ResourceInitializationException: Initialization of > annotator class > "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" > failed. (Descriptor: file:/C:/Users/Ying/workspacectakes/ctakes/ctakes- > dictionary- > lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize > AnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize > (PrimitiveAnalysisEngine_impl.java:156) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi > sEngineFactory_impl.java:94) > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > ompositeResourceFactory_impl.java:62) > at > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java: > 269) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework > .java:387) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:25 > 4) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initAS > B(AggregateAnalysisEngine_impl.java:431) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializ > e(AggregateAnalysisEngine_impl.java:185) > at > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analysi > sEngineFactory_impl.java:94) > at > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > ompositeResourceFactory_impl.java:62) > at > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java: > 269) > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework > .java:354) > at > org.uimafit.factory.AnalysisEngineFactory.createAnalysisEngineFromPath(An > alysisEngineFactory.java:147) > at > org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator. >(BagOfAnnotationsGenerator.java:42) > at > org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator. >(BagOfAnnotationsGenerator.java:36) > at > org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.(BagOf > CUIsGenerator.java:16) > at > org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.main(BagOf > CUIsGenerator.java:49) > Caused by: org.apache.uima.resource.ResourceInitializationException > at > org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initi > alize(UmlsDictionaryLookupAnnotator.java:79) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize > AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) > ... 18 more > Caused by: java.net.ConnectException: Connection timed out: connect > at java.net.DualStackPlainSocketImpl.connect0(Native Method) > at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) > at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) > at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) > at java.net.AbstractPlainSocketImpl.connect(Unknown Source) > at java.net.PlainSocketImpl.connect(Unknown Source) > at java.net.SocksSocketImpl.connect(Unknown Source) > at java.net.Socket.connect(Unknown Source) > at sun.security.ssl.SSLSocketImpl.connect(Unknown Source) > at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source) > at sun.net.NetworkClient.doConnect(Unknown Source) > at sun.net.www.http.HttpClient.openServer(Unknown Source) > at sun.net.www.http.HttpClient.openServer(Unknown Source) > at sun.net.www.protocol.https.HttpsClient.(Unknown Source) > at sun.net.www.protocol.https.HttpsClient.New(Unknown Source) > at > sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNew > HttpClient(Unknown Source) > at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown > Source) > at > sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect( > Unknown Source) > at > sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknow > n Source) > at > sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Un > known Source) > at > org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isV > alidUMLSUser(UmlsDicti
RE: errors when run BagOfCUIsGenerator.java
Try to open https://uts-ws.nlm.nih.gov
If that works then try
https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser and see if you get a
message like
"This XML file does not appear to have any style information associated with
it. The document tree is shown below."
If that works and you are comfortable with the code, try with
umlsaddr : https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser
vendor : NLM-6515182895
/**
* @param umlsaddr -
* @param vendor -
* @param username -
* @param password -
* @return true if the server at umlsaddr approves of the vendor, user,
password combination
*/
public static boolean isValidUMLSUser( final String umlsaddr, final String
vendor,
final String username, final String
password ) {
String data;
try {
data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "=" +
URLEncoder.encode( vendor, "UTF-8" );
data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "=" +
URLEncoder.encode( username, "UTF-8" );
data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "=" +
URLEncoder.encode( password, "UTF-8" );
} catch ( UnsupportedEncodingException unseE ) {
LOGGER.error( "Could not encode URL for " + username + " with vendor
license " + vendor );
return false;
}
try {
final URL url = new URL( umlsaddr );
final URLConnection connection = url.openConnection();
connection.setDoOutput( true );
final OutputStreamWriter writer = new OutputStreamWriter(
connection.getOutputStream() );
writer.write( data );
writer.flush();
boolean result = false;
final BufferedReader reader = new BufferedReader( new
InputStreamReader( connection.getInputStream() ) );
String line;
while ( (line = reader.readLine()) != null ) {
final String trimline = line.trim();
if ( trimline.isEmpty() ) {
break;
}
result = trimline.equalsIgnoreCase( "true" );
}
writer.close();
reader.close();
return result;
} catch ( IOException ioE ) {
LOGGER.error( ioE.getMessage() );
return false;
}
}
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Wednesday, April 16, 2014 1:25 PM
To: dev@ctakes.apache.org
Subject: RE: errors when run BagOfCUIsGenerator.java
Ying,
Are you behind a proxy or firewall?
If you're trying to use the umls resources, it attempts to make a call to their
umls service to validate your credentials.
--Pei
> -Original Message-
> From: Liu, Ying [mailto:l...@advisory.com]
> Sent: Wednesday, April 16, 2014 1:13 PM
> To: dev@ctakes.apache.org
> Subject: errors when run BagOfCUIsGenerator.java
>
> It failed when run BagOfCUIsGenerator.java. The followings are the
> error information. Thanks for your help.
> Ying
>
>
>
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
> failed. (Descriptor:
> file:/C:/Users/Ying/workspacectakes/ctakes/ctakes-
> dictionary-
> lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> ialize
> AnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> ialize
> (PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> i
> sEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> ompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> 269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> .java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:
> 25
> 4)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> AS
> B(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> ializ
> eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> ializ
> e(AggregateAnalysisEngine_impl.java:185)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> i
> sEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> ompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> 269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> .java:354)
> at
> org.uimafit.
RE: errors when run BagOfCUIsGenerator.java
Sorry bother the email list. The problem is caused by my VPN connection. I
connected to VPN and it didn't allow me to access any other website. So, my
UMLS username and password didn't get through.
Thanks,
Ying
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Wednesday, April 16, 2014 10:30 AM
To: dev@ctakes.apache.org
Subject: RE: errors when run BagOfCUIsGenerator.java
Try to open https://uts-ws.nlm.nih.gov
If that works then try
https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser and see if you get a
message like
"This XML file does not appear to have any style information associated with
it. The document tree is shown below."
If that works and you are comfortable with the code, try with
umlsaddr : https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser
vendor : NLM-6515182895
/**
* @param umlsaddr -
* @param vendor -
* @param username -
* @param password -
* @return true if the server at umlsaddr approves of the vendor, user,
password combination
*/
public static boolean isValidUMLSUser( final String umlsaddr, final String
vendor,
final String username, final String
password ) {
String data;
try {
data = URLEncoder.encode( "licenseCode", "UTF-8" ) + "=" +
URLEncoder.encode( vendor, "UTF-8" );
data += "&" + URLEncoder.encode( "user", "UTF-8" ) + "=" +
URLEncoder.encode( username, "UTF-8" );
data += "&" + URLEncoder.encode( "password", "UTF-8" ) + "=" +
URLEncoder.encode( password, "UTF-8" );
} catch ( UnsupportedEncodingException unseE ) {
LOGGER.error( "Could not encode URL for " + username + " with vendor
license " + vendor );
return false;
}
try {
final URL url = new URL( umlsaddr );
final URLConnection connection = url.openConnection();
connection.setDoOutput( true );
final OutputStreamWriter writer = new OutputStreamWriter(
connection.getOutputStream() );
writer.write( data );
writer.flush();
boolean result = false;
final BufferedReader reader = new BufferedReader( new
InputStreamReader( connection.getInputStream() ) );
String line;
while ( (line = reader.readLine()) != null ) {
final String trimline = line.trim();
if ( trimline.isEmpty() ) {
break;
}
result = trimline.equalsIgnoreCase( "true" );
}
writer.close();
reader.close();
return result;
} catch ( IOException ioE ) {
LOGGER.error( ioE.getMessage() );
return false;
}
}
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Wednesday, April 16, 2014 1:25 PM
To: dev@ctakes.apache.org
Subject: RE: errors when run BagOfCUIsGenerator.java
Ying,
Are you behind a proxy or firewall?
If you're trying to use the umls resources, it attempts to make a call to their
umls service to validate your credentials.
--Pei
> -Original Message-
> From: Liu, Ying [mailto:l...@advisory.com]
> Sent: Wednesday, April 16, 2014 1:13 PM
> To: dev@ctakes.apache.org
> Subject: errors when run BagOfCUIsGenerator.java
>
> It failed when run BagOfCUIsGenerator.java. The followings are the
> error information. Thanks for your help.
> Ying
>
>
>
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException:
> Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
> failed. (Descriptor:
> file:/C:/Users/Ying/workspacectakes/ctakes/ctakes-
> dictionary-
> lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> ialize
> AnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> ialize
> (PrimitiveAnalysisEngine_impl.java:156)
> at
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> i
> sEngineFactory_impl.java:94)
> at
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> ompositeResourceFactory_impl.java:62)
> at
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> 269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> .java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:
> 25
> 4)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> AS
> B(AggregateAnalysisEngine_impl.java:431)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> ializ
> eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> ializ
> e(AggregateAnalysisEngine_impl.java:185)
> at
> o
Re: Apache cTAKES Example Application?
Lowering the barrier to entry = worth the effort Notice the NCBO users mailing list has solid routine comments and discussion about the VM "appliance" they distribute. On Wed, Apr 16, 2014 at 9:37 AM, Pei Chen wrote: > We spent some time in the past to make it easier for users to launch the > CVD/CPE. > But based on the questions/discussions, I think we are passed this stage > and a very common use case would be for developers to use cTAKES as a lib, > extend a class or two and then, embed it into their existing app. > > I am proposing a ctakes-web-demo for the sandbox, > A simple webapp- war/maven pom.xml that uses the ctakes as a dependency. > Have a simple servlet that wires up a pipeline (uimaFIT style), and then > dump the CAS as html table. We could even host it on: > https://demo-ctakes.apache.org/ > > It will probably only be a few lines of code, but it may be a good starting > point for developers who are more interested in using it as a lib and not > necessarily modifying ctakes code. > > > What do folks think? > > --Pei >
