Hi Sean and Joyce,
I'm trying hard to get ytex running as well. I've followed each step you've
outlined but I'm somewhat stuck now.
What I did:
- Tried to compile and run with Java 7 --> not working
- Tried to compile and run with Java 8 --> not working
- Tried to update Spring to 3.2.18.RELEASE in pom.xml
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>3.2.18.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>3.2.18.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>3.2.18.RELEASE</version>
</dependency>
<dependency>
leading to the Exception in thread "main"
java.lang.IncompatibleClassChangeError: class
org.springframework.core.LocalVariableTableParameterNameDiscoverer$ParameterNameDiscoveringVisitor
has interface org.springframework.asm.ClassVisitor as super class
Could you briefly describe what you did to get ytex running? Any help is
greatly appreciated.
Leander
> On 13 Feb 2017, at 17:41, Dunlop, Joyce (HP) <[email protected]> wrote:
>
> Is there anyone on this email list that is using the YTEX web interface?
>
> Thanks for the information Sean!
>
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:[email protected]]
> Sent: Monday, February 13, 2017 10:26 AM
> To: Dunlop, Joyce (HP)
> Cc: [email protected]
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Our main interest in YTEX is the database reader and consumer that it comes
> with. That is probably a smaller subset of its functionality but it was a
> good source for those. We are still working on implementation, but we plan to
> run an annotation pipeline on the new notes we get each day and store the
> resulting annotations in our database. The notes will be read from a
> database, parceled out in chunks to several processes, annotated, and
> consumed by the database consumer.
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:[email protected]]
> Sent: Monday, February 13, 2017 11:17 AM
> To: Mullane, Sean *HS
> Cc: [email protected]
> Subject: RE: YTEX setup notes
>
> Hi Sean,
>
> I will have to check with the VA Researchers to find out what they planned to
> for the ytex web.
> So you don't use YTEX web interface but you do use ytex correct? Could you
> share the steps in a typical process you run for YTEX?
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:[email protected]]
> Sent: Monday, February 13, 2017 7:59 AM
> To: Dunlop, Joyce (HP)
> Cc: [email protected]
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Hi Joyce,
>
> I wound up solving the error by commenting out the bean definition in
> ctakes-ytex-res/src/main/resources/org/apache/ctakes/beans-kernel.xml and
> ctakes-ytex-res/target/classes/org/apache/ctakes/beans-kernel.xml, which
> resolved that error. I think it was deprecated anyway.
>
> I did run into another error where I didn't have LookupDesc_SNOMED.xml in the
> directory path. Added it from the ctakes-src files solved that problem and
> got it working on Java 8 for us.
>
> I haven't tried using the web interface - we don't have any plans to use it.
> Can I ask what you want to use it for? I'm not really familiar with what it
> does.
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:[email protected]]
> Sent: Friday, February 10, 2017 3:57 PM
> To: Mullane, Sean *HS
> Subject: RE: YTEX setup notes
>
> Hi Sean,
>
> We had to change the return type from BagOfWordsExporter to
> WekaBagOfWordsExporter in that file.
>
> From:
> public BagOfWordsExporter getBagOfWordsExporter() {
> return bagOfWordsExporter;
> }
>
> To:
> public WekaBagOfWordsExporter getBagOfWordsExporter() {
> return bagOfWordsExporter;
> }
>
> We have still not be able to get the YTEX web interface to work. The YTEX
> application starts up and we are able to access through the URL:
> http://localhost:8080/semanticSim.jsf - We see 4 tabs but nothing seems
> functional. Is there something we are still missing? We found references to
> rest services - are they called separate from the YTEX UI?
>
> Any clue would be appreciated.
>
> Thanks,
> Joyce
>
> PS: I think there was one other code change to get Java 8 working, so if you
> get another error just shoot it over and I should have the answer.
>
>
>
>
>
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:[email protected]]
> Sent: Monday, February 06, 2017 3:33 PM
> To: Dunlop, Joyce (HP)
> Cc: [email protected]
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Joyce,
>
> I haven't been able to find further documentation. It seems it is somewhat
> out of date and some of the Yale sources have been taken down.
>
> In your feedback on my YTEX setup notes, I'm finding that when I try to run
> YTEX using Java 8 I get an error related to
> org.apache.ctakes.ytex.weka.GramMatrixExporterImpl. When I run it on Java 7 I
> get no errors. You mentioned that upgrading to Spring 3.2 solved an issue for
> you. How did you do that - did you change the Maven build file to pull in the
> newer version or did you do something else to get the newer Spring version?
> I'm hoping that will resolve the Java 8 issue here.
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:[email protected]]
> Sent: Friday, February 03, 2017 4:26 PM
> To: Mullane, Sean *HS
> Cc: [email protected]
> Subject: RE: YTEX setup notes
>
> Sean/others,
>
> Do you by chance have any of the documentation produced by Yale tucked away
> locally?
>
> I see quite a few dead links that seem to go back to demo's and documents on
> cTakes site.
>
> Examples:
> The demo similarity web app is available under
> http://informatics.med.yale.edu/ytex.web;
>
> http://ytex.googlecode.com/svn/trunk/projects/nlm.wsd/doc/YTEX%20Semantic%20Similarity%20Measures.pdf
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Dunlop, Joyce (HP)
> Sent: Monday, January 30, 2017 8:27 PM
> To: 'Mullane, Sean *HS'; [email protected]
> Subject: RE: YTEX setup notes
>
> Sean M,
> This is perfect!
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:[email protected]]
> Sent: Monday, January 30, 2017 3:06 PM
> To: Dunlop, Joyce (HP); [email protected]
> Subject: [EXTERNAL] RE: YTEX setup notes
>
> Joyce,
>
> Thanks for the notes. I'm glad to see you had success using Java 8 - I'll
> have to try that.
>
> To answer your question about table contents, see below for the rowcounts in
> the YTEX tables after in my installation. Apologies in advance for the
> formatting:
>
> tablename tot_cnt
> anno_base 0
> anno_base_sequence 1
> anno_contain 0
> anno_date 0
> anno_link 0
> anno_markable 0
> anno_med_event 0
> anno_mm_acronym 0
> anno_mm_candidate 0
> anno_mm_cuiconcept 0
> anno_mm_negation 0
> anno_mm_utterance 0
> anno_named_entity 0
> anno_ontology_concept 0
> anno_segment 0
> anno_sentence 0
> anno_token 0
> anno_treebank_node 0
> classifier_eval 0
> classifier_eval_ir 0
> classifier_eval_semil 0
> classifier_eval_svm 0
> classifier_instance_eval 0
> classifier_instance_eval_prob 0
> corpus_doc 0
> corpus_label 0
> cv_best_svm 0
> cv_fold 0
> cv_fold_instance 0
> document 0
> feature_eval 0
> feature_parchd 0
> feature_rank 0
> fracture_demo 31
> hibernate_sequences 1
> hotspot 0
> hotspot_instance 0
> hotspot_sentence 0
> kernel_eval 0
> kernel_eval_instance 0
> ref_named_entity_regex 0
> ref_segment_regex 0
> ref_stopword 360
> ref_uima_type 38
> tfidf_doclength 0
> umls_aui_fword 6902003
> v_snomed_fword_lookup 1374810
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:[email protected]]
> Sent: Friday, January 27, 2017 10:12 AM
> To: [email protected]
> Subject: YTEX setup notes
>
> Hi Sean M,
>
> Notes from :
> Step
> -The Needed to add sqljdbc4.jar to CTAKES_HOME/lib probably need to happen
> after -3. Install cTAKES "as usual"
>
> -Java 7 is throwing errors because Spring needs to be upgraded to at least
> 3.2.
> --It looks like Spring was previously upgraded from 2.5 to 3.1, but spring
> context files - xsi:schemaLocation were not previous upgraded and remained
> 2.5.
>
> -We have been able to successful run the script with JAVA 8 after upgrading
> Spring to 3.2.18-Release from the 3.1/2.5 version. We also upgraded the
> version of Jetty.
>
> -Step 7 which I think you list as 8 below to execute the setup script. It
> looks like it has mostly been successful but I do have a few errors at the
> bottom related to the database password we chose which had an & (AMP)
> character is being parsed on the & character.
>
> 3 tables that are showing errors related to the amp characters:
> -ref_uima_type.xml
> -fracture_demo.xml
> -stopword.xml
>
> 2 tables are the only table will significant record counts:
> -umls_aui_fword
> -v_snomed_fword_lookup
>
> 2 other table seem to have one row inserted.
>
> The question I have is when this step completes how many of the tables should
> have data?
>
> Thanks again.
> Joyce
>
>
>
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:[email protected]]
> Sent: Tuesday, January 17, 2017 12:33 PM
> To: [email protected]
> Subject: [EXTERNAL] RE: New to CTAKES
>
> Sean M,
>
> I will try to work through the process this tomorrow.
>
> Thanks!
>
> Joyce
>
> -----Original Message-----
> From: Mullane, Sean *HS [mailto:[email protected]]
> Sent: Tuesday, January 17, 2017 11:10 AM
> To: [email protected]
> Subject: [EXTERNAL] RE: New to CTAKES
>
> Joyce,
>
> This may help, here are some notes I put together when installing YTEX in our
> Windows/SQL Server test environment. I didn't build from source here, this is
> just installation (including UMLS). I'm working on writing up these
> instructions more thoroughly so if you use this please let me know if you
> find any points of improvement.
>
> Requirements and steps to set up YTEX
> These notes refer to the installation instructions at
> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
> 1. They suggest installing UMLS in our database
> Follow instructions here to install UMLS:
> https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
> -http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is
> useful when installing from .zip file. The mmsys.zip file needs to be
> unzipped to access the run64.bat file but also needs to be present as a .zip
> file for the run64.bat file to read from.
> 2. Create a database user and schema for use with YTEX 3. Load UMLS into
> database
> -Needed to create ytex.properties file from examples files in the
> developer/source version of cTAKES
> -Needed to change path in ctakes.profile to match version name of
> CTAKES_HOME directory
> -Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to
> C:\Program Files\Java\jre_Version\bin
> -Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
> -Need to change table definitions as follows to install UMLS-2016AB:
> MRCONSO.CODE varchar(75) -- was varchar(50)
> MRDEF.DEF varchar(max) -- was varchar(4000)
> MRSAB.VSAB varchar(24) -- was varchar(20)
> MRSAT.ATN varchar(64) -- was varchar(50)
> MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES
> "as usual"
> 4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your
> installation.
> -I believe this step is deprecated - skip to step 6 5. Unzip YTEX
> Resources (Optional - UTS login required)
> -I believe this step is deprecated - skip to step 6
> -may be needed for concept graphs and dictionary lookup table for NER
> 6. Fix the path references in shell script to match your environment 7.
> Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and
> specify database connection parameters.
> 8. Execute the setup script
> -Need to use Java 7 - Java 8 errors out
> -If SQL errors encountered, appenders can be added to log4j.xml to
> collect SQL queries
>
> Sean
>
> -----Original Message-----
> From: Finan, Sean [mailto:[email protected]]
> Sent: Tuesday, January 17, 2017 11:57 AM
> To: [email protected]
> Subject: RE: New to CTAKES
>
> Hi Joyce,
>
> If you are building from source then you should not need to manually download
> the resources. Maven should be doing it for you. Well, that is the behavior
> of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
>
> Otherwise, I think that if the latest was the 3.2.1.1 then that is probably
> the most appropriate for the 3.2.2 release if you want all of the resources.
>
> As for building and deploying ytex, I don't have any advice. Perhaps some
> ytex power-user out there can help.
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:[email protected]]
> Sent: Tuesday, January 17, 2017 11:25 AM
> To: [email protected]
> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
> Subject: New to CTAKES
>
> Good Morning,
>
> I am trying to set up a development environment using the source release of
> 3.2.2.
>
> Reading though the documentation on
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e=
> .
>
> Merge the version-matching resources ZIP file from
> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e=
> into your ctakes-dictionary-lookup-res project.
>
> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e=
> > is available for download. Is there a 3.2.2 version of the resources?
>
> After reading some of the posts from the email box, and reading the
> documentation on the site above. It looks like the documentation may be
> somewhat dated and not fulling integrated for YTEX.
>
> Would you have any recommendations in advance on how to set up a build
> process for deployment and YTEX database from scratch?
>
> Thanks,
> Joyce
>
>
>
>
>
>
>
>
>
>
>
>
