Sean M, I will try to work through the process this tomorrow.
Thanks! Joyce -----Original Message----- From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu] Sent: Tuesday, January 17, 2017 11:10 AM To: dev@ctakes.apache.org 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:sean.fi...@childrens.harvard.edu] Sent: Tuesday, January 17, 2017 11:57 AM To: dev@ctakes.apache.org 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:joyce.dun...@va.gov] Sent: Tuesday, January 17, 2017 11:25 AM To: dev@ctakes.apache.org 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
