Re: (Re)introduce myself - James Masanz

[Pei Chen]

Welcome back James!  Good to hear from you again. 
Out of respect for the others in the community who already volunteered to be 
RM, I do not see an need for BCH to override existing volunteers. Unless they 
unable or unwilling.
Would you/others agree? 

Sent from my iPhone

> On Jan 27, 2017, at 2:23 PM, James Masanz  wrote:
> 
> Hi,
> 
> I'm James Masanz -- if you've been on the dev list for more than a couple
> years, you might recognize my name from my previous contributions to
> cTAKES, which include having been a release manager.
> 
> I've joined the Boston Children's Hospital NLP team. I will be devoting
> significant energy to the next release of cTAKES, and I volunteer to be the
> release manager for it.
> 
> My initial thoughts are that we could make the "fast dictionary lookup" be
> the default dictionary lookup, incorporate the dictionary GUI from sandbox,
> and call the release 4.0. I'm also interested in migrating the Wiki away
> from Confluence to Apache's moin-moin instance. I'm sure there are other
> things to include in the next release as well.
> 
> You'll be hearing more from me over the next few weeks as I review the list
> of issues in Jira and get caught up with details of what's been going on
> while I was less active here.
> 
> One thing I would like to track for release candidates would be a list of
> what is tested on which platforms, which could be as simple as a post with
> a matrix of src/bin/other vs. linux/windows/mac, and making sure we have at
> least one volunteer to test the install and run of a pipeline for each
> entry in the table. Future releases might expand on that to include
> tracking multiple pipelines across environments, etc.
> 
> I'm happy I'm returning to being active in the cTAKES community!
> 
> -- James

YTEX setup notes

[Dunlop, Joyce (HP)]

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:joyce.dun...@va.gov] 
Sent: Tuesday, January 17, 2017 12:33 PM
To: dev@ctakes.apache.org
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: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: