Re: Creating my own dictionaries
Thank you for your reply. Indeed I had to change the java build path but I also had errors due to Lucene version that is deprecated: the constructors 'new IndexWriter(directory, analyzer, true,IndexWriter.MaxFieldLength.LIMITED);' and 'iwriter.optimize();' do not exist in version 4 anymore. So, in CreateLuceneIndexFromDelimitedFile.java, I changed: 1)Line 89: Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_30); by --> Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_40); 2)Line 98: iwriter = new IndexWriter(directory, analyzer, true,IndexWriter.MaxFieldLength.LIMITED); by --> IndexWriterConfig conf = new IndexWriterConfig(Version.LUCENE_40, analyzer); iwriter = new IndexWriter(directory, conf); 3)Line 159: iwriter.optimize(); by --> nothing or TieredMergePolicy.setUseComoundFile(boolean) but I am not certain. Does anyone know more about this problem? Thank you. sources below: https://lucene.apache.org/core/4_0_0/core/org/apache/lucene/index/IndexWriter.html http://lucene.472066.n3.nabble.com/IndexWriter-optimize-is-removed-in-4-0-td4035769.html http://stackoverflow.com/questions/14599297/lucene-migration-from-3-x-to-4-1-0-and-index-optimisation On Tue, Mar 3, 2015 at 4:22 PM, HARPREET KHANDUJA (RIT Student) < hsk5...@rit.edu> wrote: > I am not sure but not setting the classpath to the project could be the > problem. > > > On Tue, Mar 3, 2015 at 5:07 PM, Maite Meseure Hugues < > meseure.ma...@gmail.com> wrote: > > > Hi everyone, > > > > I am currently facing a problem to run The > > CreateLuceneIndexFromDelimitedFile class that allows to get a Lucene > index > > and reads from a pipe-delimited file. the error message is: > > > > Could not find or load main class > > > > > org.apache.ctakes.dictionary.lookup.tools.CreateLuceneIndexFromDelimitedFile > > > > (same thing for > > > > > scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForExampleDrugs.java > > > > > > > scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForSnomedLikeSample.java > > ) > > Does someone know what is the problem? > > Thank you for your time. > > -- > > -- > > Maïté Meseure Hugues > > > -- -- Maïté Meseure Hugues
New cTAKES website
Hello everyone, The new cTAKES website has just gone live: http://ctakes.apache.org/. Enjoy! As always, we would love to have feedback about what is/isn't working or should be included (note: some pages are not complete yet). Also, it would be wonderful if you could fill out this form: https://docs.google.com/forms/d/10ryw42aqkIf2ygjNTa_ To1OgGDZzDqHizVg__Jxyuws/viewform?usp=send_form so that we can get a better sense of the users of cTAKES. Thank you. Enjoy! --- Michelle Chen Massachusetts Institute of Technology Electrical Engineering and Computer Science B.S. '14, M.Eng. '15
Re: New cTAKES website
I think docker containers would be a good idea, though I know UIMA also has an asynchronous scaleout framework already that I haven't yet learned how to use. One of the things I have been thinking about off and on is to try to find a way to set things up so that I can scaleout processing of PHI data over a non-PHI grid compute cluster. My initial thought was to try to use holomorphic encryption, but I wasn't able to find a satisfactory solution. I wonder if there is a containerization model that might work -- I know docker isn't really intended for this kind of thing, but I'm not really familiar with the other models that exist. ᐧ -- Karthik Sarma UCLA Medical Scientist Training Program Class of 20?? Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to the House of Delegates of the American Medical Association ksa...@ksarma.com gchat: ksa...@gmail.com linkedin: www.linkedin.com/in/ksarma On Fri, Mar 6, 2015 at 10:42 AM, Jay Vyas wrote: > Great work Michelle and thanks > I really like the 6 keywords at the bottom. > > Random Idea I got from looking at the sight: We might want to make some > docker containers for beefing up the "portable" section tag line at some > point, if anyone is interested I can help do that ( I use gradle distZip > for this). > > On Mar 6, 2015, at 12:35 PM, Michelle Chen wrote: > > Hello everyone, > > The new cTAKES website has just gone live: http://ctakes.apache.org/. > Enjoy! > > As always, we would love to have feedback about what is/isn't working or > should be included (note: some pages are not complete yet). > > Also, it would be wonderful if you could fill out this form: > https://docs.google.com/forms/d/10ryw42aqkIf2ygjNTa_ > To1OgGDZzDqHizVg__Jxyuws/viewform?usp=send_form so that we can get a > better sense of the users of cTAKES. Thank you. > > Enjoy! > > --- > Michelle Chen > > Massachusetts Institute of Technology > Electrical Engineering and Computer Science > B.S. '14, M.Eng. '15 > >
Is it necessary to put UMLS login into files when passing them with -D to the JVM?
Hi, in AggregatePlaintextFastUMLSProcessor.xml of cTAKES it states that: [...] Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS username and password. Similarly, in AggregatePlaintextFastUMLSProcessor.xml from https://issues.apache.org/jira/browse/CTAKES-344 [...] Please update resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml file with your UMLS username and password I am passing my UMLS login and password on startup as arguments, when starting the either CVD/CPE or org.apache.uima.examples.cpe.SimpleRunCPE argumets such as: "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword" In such a case, it is still necessary to modify the file(s) above? Additional question: It seems that the AggregatePlaintextFastUMLSProcessor.xml from https://issues.apache.org/jira/browse/CTAKES-344 has some nice improvements (using DrugNER and default fast pipeline). I just downloaded it from the svn and replaced the old cTAKES 3.2.1 file with this one, and it seems to run just fine and cTAKES does annotations. Can somebody from the devs or users tell me if this manual replacement step is OK and does not break anything that I am not aware of? Many thanks for answers on any of my questions, Tom
RE: Is it necessary to put UMLS login into files when passing them with -D to the JVM?
Hi Tom, > I am passing my UMLS login and password on startup as arguments ... > "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword" That is fine. If I understand correctly you are already running this way without problem. The comments in the .xml files should probably be extended to include mention of the cmd parameters. > [I] downloaded [AggregatePlaintextFastUmlsProcessor.xml] from the svn and > replaced the old cTAKES 3.2.1 ... I think that this should be fine. Java code for each annotator may have changed, but I don't think that any class names (by which annotators are called) have changed. The best way to know for certain is to run it, and if you haven't seen any problems then I think that you are in good shape. Sean -Original Message- From: Tom Devel [mailto:deve...@gmail.com] Sent: Friday, March 06, 2015 3:20 PM To: dev@ctakes.apache.org Subject: Is it necessary to put UMLS login into files when passing them with -D to the JVM? Hi, in AggregatePlaintextFastUMLSProcessor.xml of cTAKES it states that: [...] Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS username and password. Similarly, in AggregatePlaintextFastUMLSProcessor.xml from https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e= [...] Please update resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml file with your UMLS username and password I am passing my UMLS login and password on startup as arguments, when starting the either CVD/CPE or org.apache.uima.examples.cpe.SimpleRunCPE argumets such as: "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword" In such a case, it is still necessary to modify the file(s) above? Additional question: It seems that the AggregatePlaintextFastUMLSProcessor.xml from https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e= has some nice improvements (using DrugNER and default fast pipeline). I just downloaded it from the svn and replaced the old cTAKES 3.2.1 file with this one, and it seems to run just fine and cTAKES does annotations. Can somebody from the devs or users tell me if this manual replacement step is OK and does not break anything that I am not aware of? Many thanks for answers on any of my questions, Tom
Re: Is it necessary to put UMLS login into files when passing them with -D to the JVM?
Sean, On Fri, Mar 6, 2015 at 2:30 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Tom, > > > I am passing my UMLS login and password on startup as arguments ... > "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword" > That is fine. If I understand correctly you are already running this way > without problem. The comments in the .xml files should probably be > extended to include mention of the cmd parameters. > > Yes, I am getting validation output as follows: INFO UmlsUserApprover - UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user xxx has been validated > > [I] downloaded [AggregatePlaintextFastUmlsProcessor.xml] from the svn > and replaced the old cTAKES 3.2.1 ... > I think that this should be fine. Java code for each annotator may have > changed, but I don't think that any class names (by which annotators are > called) have changed. The best way to know for certain is to run it, and > if you haven't seen any problems then I think that you are in good shape. > > It to work without showing any exceptions so far. Thanks, Tom Sean > > -Original Message- > From: Tom Devel [mailto:deve...@gmail.com] > Sent: Friday, March 06, 2015 3:20 PM > To: dev@ctakes.apache.org > Subject: Is it necessary to put UMLS login into files when passing them > with -D to the JVM? > > Hi, > > in AggregatePlaintextFastUMLSProcessor.xml of cTAKES it states that: > > [...] Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS > username and password. > > Similarly, in AggregatePlaintextFastUMLSProcessor.xml from > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e= > > [...] Please update > resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml file > with your UMLS username and password > > I am passing my UMLS login and password on startup as arguments, when > starting the either CVD/CPE or org.apache.uima.examples.cpe.SimpleRunCPE > argumets such as: > > "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword" > > In such a case, it is still necessary to modify the file(s) above? > > Additional question: It seems that the > AggregatePlaintextFastUMLSProcessor.xml from > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D344&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ZOef73O4fpDF9CZPAZHmVyDZDQDa6jKWyTTU1kikj9o&s=7C1osQzBp5-aSIXPeqWPXcafrLDGCeEkR3sfbiJMRDQ&e= > has some nice improvements (using DrugNER and default fast pipeline). I > just downloaded it from the svn and replaced the old cTAKES 3.2.1 file with > this one, and it seems to run just fine and cTAKES does annotations. Can > somebody from the devs or users tell me if this manual replacement step is > OK and does not break anything that I am not aware of? > > Many thanks for answers on any of my questions, Tom >
