RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern
Hi, Great job Matthew !!! Regards, Sandeep From: Matthew Vita [mailto:matthewvit...@gmail.com] Sent: Monday, December 18, 2017 11:53 AM To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane Chesnutt Subject: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern Hi Gandhi, Sean, Tim, Alex, James, Good news, I was able to get MySQL running in the `ctakes-gui` (recall that I am building in a toggle so that folks can create dictionaries using MySQL rather than HSQLDB script files). I found out the source of the issue with bringing in the MySQL dependency. This one definitely took me a while and was super subtle! If you visit /ctakes/ctakes-distribution/src/main/assembly/bin.xml, mysql:*is present because it's a n non-asf compliant dependency used by ytex. Removing the exclude and addingin mysql:mysql-connector-java gets the correct result: /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/lib matthew % ls -lash | grep mysql 3912 -rw-r--r-- 1 matthew staff 1.9M Dec 14 20:23 mysql-connector-java-6.0.6.jar Just for completeness, this is the exact POM entry: mysql mysql-connector-java 6.0.6 Is there anyway we can use MySQL in cTAKES in a way that is compliant with ASF? I wonder if MariaDB or Postgresql would be better because they work with JDBC and are free/open source. Of course, I am biased towards MySQL/MariaDB because the (near) future users of cTAKES Rest Service in the OpenEMR space are going to want MySQL/MariaDB users :). Not a huge deal though. Thanks, Matthew Vita www.matthewvita.com<http://www.matthewvita.com/> This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Use of custom Dictionary Descriptor file
Hi, Is there currently any way to use a custom dictionary descriptor file without making changes to the code or by rebuilding the ctakes-dictionary-lookup-fast jar file. Regards, Sandeep This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: cTAKES Jenkins build is successful. [EXTERNAL]
Hi, Congrats Alex. Great Job. The fix was much needed. Regards, Sandeep -Original Message- From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] Sent: Friday, November 17, 2017 6:49 PM To: Apache cTAKES Dev Subject: Re: cTAKES Jenkins build is successful. [EXTERNAL] Thank you. I realized also why the Java-1.8 job fails: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:1.6:run (generate-test-config) on project ctakes-ytex: An Ant BuildException has occured: The following error occurred while executing this line:[ERROR] /home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex/scripts/build-setup.xml:149: The following error occurred while executing this line:[ERROR] /home/jenkins/jenkins-slave/workspace/cTAKES-trunk-Java-1.8/ctakes-ytex/scripts/data/build.xml:124: java.sql.SQLException: Database lock acquisition failure: lockFile: org.hsqldb.persist.LockFile@72d2ec59[file =/tmp/ctakes-test-hsqldb/ctakes/ctakes.lck, exists=false, locked=false, valid=false, ] method: openRAF reason: java.io.FileNotFoundException: /tmp/ctakes-test-hsqldb/ctakes/ctakes.lck (Permission denied) Being executed on the same machine as the other compiletest job, which finishes faster because it doesn't installs the packages (.jar), it seems there is a race condition caused by the hardcoded " /tmp/ctakes-test-hsqldb/ctakes/ctakes.lck". Will take a look to fix this one too. Alex On Fri, Nov 17, 2017 at 8:04 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Alex, > Great work, > Cheers, > Sean > > -Original Message- > From: Alexandru Zbarcea [mailto:al...@apache.org] > Sent: Thursday, November 16, 2017 7:34 PM > To: Apache cTAKES Dev > Subject: cTAKES Jenkins build is successful. [EXTERNAL] > > Hi, > > The job: > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. > apache.org_view_C_view_Apache-2520cTAKES_job_ctakes-2Dtrunk- > 2Dcompiletest_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU& > r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=ypwu_ > mbOWzqIiU3Kk9TLzvIwmKuQDLan6wsNSjs3f_Y=3ONsDv2KxEEnISqa- > vq6MoaH7BmNHnFlu-qwIOsvBxk= > is successful. > > All tests pass. > > I think this is an important milestone. For quite some time we didn't > have the build as successful :-) > > Alex > This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
Hi Sean, Myself and Gandhi will work on this and try to fix the issues. Regards, Sandeep Hi Gandhi, Many thanks for volunteering. I am slammed with work right now, but if anybody else can also help out ... Sean -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Thursday, November 09, 2017 12:43 AM To: dev@ctakes.apache.org Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL] Hi Sean, I can take it up if someone is willing to guide me on this. Regards, Gandhi -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, November 08, 2017 9:45 PM To: dev@ctakes.apache.org Subject: Disable yTEX and Regression tests on Jenkins Hi all, The Jenkins builds have been failing for about a month now because of internal Jenkins changes and 'unit' tests in the ctakes-Regression and ctakes-yTEX modules. This is holding up the build for all of our primary clinical-pipeline modules. If anybody can take a look at the problems and fix them please respond to this email. Otherwise I would like to create a jira issue and disable them until somebody does have the time to take care of them. If you have a good reason for these tests not being disabled (e.g. we might forget to fix them) please state a case. I do not intend to act unilaterally on this issue. Please respond by midnight Friday, November 10. Thank you, Sean This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law. This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Lab report
Hi Abilash, It can extract unit values and units from the lab report. Regards, Sandeep -Original Message- From: abilash.mat...@cognizant.com [mailto:abilash.mat...@cognizant.com] Sent: Monday, November 13, 2017 4:40 PM To: dev@ctakes.apache.org Subject: Lab report Hi All, Can CTAKES process LAB reports and able to extract key findings from the report? Thanks, Abilash Mathew This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored. This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
