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Posted to dev@ctakes.apache.org by ra...@gmail.com on 2017/10/14 19:10:05 UTC
steps to upgrade to the latest version of umls and snomed
Hello,
As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for dictionary lookup.
Did anyone try to upgrade? What should be the approach to upgrade db scripts to latest umls 2017ab, snomed 2017? Any automation procedure available?
Thanks
Regards
Rajeev
Sent from Mail for Windows 10
RE: steps to upgrade to the latest version of umls and snomed
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Hi Rajeev,
All you got to do is to use latest dictionary generator GUI to generate snomed 2017 scripts. We tried this and loaded to MySQL DB and it works. For more info you can check the recent thread on 'HSQLDB out of memory with custom dictionary' under http://mail-archives.apache.org/mod_mbox/ctakes-dev/201710.mbox/browser
Regards,
Gandhi
-----Original Message-----
From: rajeevxmyemr@gmail.com [mailto:rajeevxmyemr@gmail.com]
Sent: Sunday, October 15, 2017 12:40 AM
To: dev@ctakes.apache.org
Subject: steps to upgrade to the latest version of umls and snomed
Hello,
As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for dictionary lookup.
Did anyone try to upgrade? What should be the approach to upgrade db scripts to latest umls 2017ab, snomed 2017? Any automation procedure available?
Thanks
Regards
Rajeev
Sent from Mail for Windows 10
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: [External] Re: steps to upgrade to the latest version of umls
and snomed
Posted by Sirisha Pulivarthi <Si...@horizonblue.com.INVALID>.
Hi Matthew,
Thanks for the information. I'm connecting to linux from my windows using SSH. It did work in the beginning, but I had to install UMLS under different directory because of space constraints.
I did set DISPLAY and JAVA_OPTIONS as suggested, did not help. I was looking at run_linux.sh which basically looking for lib/jfp-boot.jar which I have.
export DISPLAY=0:hostname
export JAVA_OPTIONS=-Djava.awt.headless=true
Loading MetamorphoSys ...
[Please be patient and wait for MetamorphoSys to begin]
--------------------------------------------
java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have a release_version property.
at gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfiguration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96)
at gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfiguration.open(AbstractPropertyFileConfiguration.java:265)
at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.initialize(StandardConfigurationManager.java:56)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:74)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source)
No protocol specified
Exception in thread "main" java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at java.awt.GraphicsEnvironment.createGE(Unknown Source)
at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(Unknown Source)
at java.awt.Window.initGC(Unknown Source)
at java.awt.Window.init(Unknown Source)
at java.awt.Window.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown Source)
at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown Source)
at javax.swing.JOptionPane.getRootFrame(Unknown Source)
at org.java.plugin.boot.ErrorDialog.showError(Unknown Source)
at org.java.plugin.boot.ErrorDialog.showError(Unknown Source)
at org.java.plugin.boot.BootErrorHandlerGui.handleFatalError(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source)
-----Original Message-----
From: Matthew Vita [mailto:matthewvita48@gmail.com]
Sent: Tuesday, October 17, 2017 1:52 AM
To: dev@ctakes.apache.org
Subject: Re: [External] Re: steps to upgrade to the latest version of umls and snomed
Hi Sirisha,
Sorry to hear you are having troubles. It looks like you are using the correct files from UMLS but may have a UI issue. Please review the following thread:
https://stackoverflow.com/questions/662421/no-x11-display-variable-what-does-it-mean
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Oct 16, 2017 at 12:59 PM, Sirisha Pulivarthi < Sirisha_Pulivarthi@horizonblue.com.invalid> wrote:
> Hi Sean,
> I'm using the same version of nlm files (2017AA-full) that came with
> below download https://www.nlm.nih.gov/research/umls/licensedcontent/
> umlsknowledgesources.html
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Monday, October 16, 2017 3:50 PM
> To: dev@ctakes.apache.org
> Subject: RE: [External] Re: steps to upgrade to the latest version of
> umls and snomed
>
> Hi Sirisha,
>
> Are you trying to use a metamorphosis tool with a different version of
> the nlm files?
> Also, metamorphosis is a gui application. Make sure that you have a
> display:
> > No X11 DISPLAY variable was set, but this program performed an
> > operation
> which requires it.
>
> Sean
>
> -----Original Message-----
> From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@
> horizonblue.com.INVALID]
> Sent: Monday, October 16, 2017 3:44 PM
> To: dev@ctakes.apache.org
> Subject: RE: [External] Re: steps to upgrade to the latest version of
> umls and snomed
>
> Hi Matthew,
>
>
>
> I'm running into below issue while installing UMLS. Do you see any
> issue here?
>
>
>
> total 4637464
>
> drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
>
> drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00
> 2017aa-1-meta.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00
> 2017aa-2-meta.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00
> 2017aa-otherks.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
>
> -rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00
> boot.properties
>
> drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00
> Copyright_Notice.txt
>
> drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
>
> drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
>
> drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
>
> -rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00
> log4j.properties
>
> -rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00
> mmsys.zip
>
> drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00 run_linux.sh
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00
> run_mac.command
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
>
> [spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
>
> --------------------------------------------
>
> Loading MetamorphoSys ...
>
> [Please be patient and wait for MetamorphoSys to begin]
>
> --------------------------------------------
>
> java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have
> a release_version property.
>
> at
> gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfi
> guration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96
> )
>
> at
> gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfigurat
> ion.open(AbstractPropertyFileConfiguration.java:265)
>
> at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.
> initialize(StandardConfigurationManager.java:56)
>
> at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> startApplication(MetamorphoSysGuiPlugin.java:74)
>
> at org.java.plugin.boot.Boot.boot(Unknown Source)
>
> at org.java.plugin.boot.Boot.main(Unknown Source)
> java.lang.reflect.InvocationTargetException
>
> at java.awt.EventQueue.invokeAndWait(Unknown Source)
>
> at java.awt.EventQueue.invokeAndWait(Unknown Source)
>
> at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
>
> at gov.nih.nlm.umls.swing.SwingToolkit.reportError(
> SwingToolkit.java:273)
>
> at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> startApplication(MetamorphoSysGuiPlugin.java:106)
>
> at org.java.plugin.boot.Boot.boot(Unknown Source)
>
> at org.java.plugin.boot.Boot.main(Unknown Source) Caused by:
> java.awt.HeadlessException:
>
> No X11 DISPLAY variable was set, but this program performed an
> operation which requires it.
>
> at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
>
> at java.awt.Window.<init>(Unknown Source)
>
> at java.awt.Frame.<init>(Unknown Source)
>
> at java.awt.Frame.<init>(Unknown Source)
>
> at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown
> Source)
>
> at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown
> Source)
>
> at javax.swing.JOptionPane.getRootFrame(Unknown Source)
>
> at javax.swing.JOptionPane.getWindowForComponent(Unknown
> Source)
>
> at javax.swing.JOptionPane.createDialog(Unknown Source)
>
> at javax.swing.JOptionPane.createDialog(Unknown Source)
>
> at gov.nih.nlm.umls.swing.SwingToolkit$1.run(
> SwingToolkit.java:255)
>
> at java.awt.event.InvocationEvent.dispatch(Unknown Source)
>
> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>
> at java.awt.EventQueue.access$200(Unknown Source)
>
> at java.awt.EventQueue$3.run(Unknown Source)
>
> at java.awt.EventQueue$3.run(Unknown Source)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
>
> at java.awt.EventQueue.dispatchEvent(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.run(Unknown Source)
> [spulivarthi@emsmnl003d 2017AA-full]$
>
>
>
> -----Original Message-----
>
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
>
> Sent: Saturday, October 14, 2017 4:33 PM
>
> To: dev@ctakes.apache.org
>
> Subject: [External] Re: steps to upgrade to the latest version of umls
> and snomed
>
>
>
> I am on mobile so excuse the short message but you may have luck
> building your own with the latest sources by following this approach
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=GGPg2C_bAdC2Nvjs2INMndNgTOSbpU2yKY9fhE-E6Bs&s=
> Bnj4TNqv9sHM3Vp3KgYjNl1f4V4jFoYWbzH4jepaxsI&e= - obviously the video
> is for ICD10, but the other sources will appear for your selection.
>
>
>
> If you wish to use multiple dictionaries, let me know so you can give
> my cTAKES MySQL script solution a try because HSQLDB has its limits
> with multiple custom dictionaries.
>
>
>
> -m
>
>
>
> On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
>
>
>
> Hello,
>
>
>
> As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for
> dictionary lookup.
>
>
>
> Did anyone try to upgrade? What should be the approach to upgrade db
> scripts to latest umls 2017ab, snomed 2017? Any automation procedure
> available?
>
>
>
>
>
> Thanks
>
> Regards
>
> Rajeev
>
>
>
>
>
> Sent from Mail for Windows 10
>
> ***********************************************************
>
>
>
> This message and any attachments are solely for the intended
> recipient. If you are not the intended recipient, disclosure, copying,
> use, or distribution of the information included in this message is
> prohibited -- please immediately and permanently delete this message.
>
>
>
> ***********************************************************
> ***********************************************************
>
> This message and any attachments are solely for the intended
> recipient. If you are not the intended recipient, disclosure, copying,
> use, or distribution of the information included in this message is
> prohibited -- please immediately and permanently delete this message.
>
> ***********************************************************
>
***********************************************************
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message.
***********************************************************
Re: [External] Re: steps to upgrade to the latest version of umls and snomed
Posted by Matthew Vita <ma...@gmail.com>.
Sirisha,
I'm so happy to hear that you were able to get the dictionary outputted.
Your error logs were beyond my understanding so this is a relief.
Please let me know how the dictionary goes!
Thanks,
Matthew Vita
www.matthewvita.com
On Wed, Oct 18, 2017 at 12:04 PM, Sirisha Pulivarthi <
Sirisha_Pulivarthi@horizonblue.com.invalid> wrote:
> Hi Matthew,
> I was able to create custom dictionary from windows and copy custom
> dictionary to linux where I'm running pipeline.
>
> Thanks
>
> -----Original Message-----
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
> Sent: Tuesday, October 17, 2017 1:52 AM
> To: dev@ctakes.apache.org
> Subject: Re: [External] Re: steps to upgrade to the latest version of umls
> and snomed
>
> Hi Sirisha,
>
> Sorry to hear you are having troubles. It looks like you are using the
> correct files from UMLS but may have a UI issue. Please review the
> following thread:
> https://stackoverflow.com/questions/662421/no-x11-
> display-variable-what-does-it-mean
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Mon, Oct 16, 2017 at 12:59 PM, Sirisha Pulivarthi < Sirisha_Pulivarthi@horizonblue.com.invalid>
> wrote:
>
> > Hi Sean,
> > I'm using the same version of nlm files (2017AA-full) that came with
> > below download https://www.nlm.nih.gov/research/umls/licensedcontent/
> > umlsknowledgesources.html
> >
> >
> > -----Original Message-----
> > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> > Sent: Monday, October 16, 2017 3:50 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: [External] Re: steps to upgrade to the latest version of
> > umls and snomed
> >
> > Hi Sirisha,
> >
> > Are you trying to use a metamorphosis tool with a different version of
> > the nlm files?
> > Also, metamorphosis is a gui application. Make sure that you have a
> > display:
> > > No X11 DISPLAY variable was set, but this program performed an
> > > operation
> > which requires it.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@
> > horizonblue.com.INVALID]
> > Sent: Monday, October 16, 2017 3:44 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: [External] Re: steps to upgrade to the latest version of
> > umls and snomed
> >
> > Hi Matthew,
> >
> >
> >
> > I'm running into below issue while installing UMLS. Do you see any
> > issue here?
> >
> >
> >
> > total 4637464
> >
> > drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
> >
> > drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00
> > 2017aa-1-meta.nlm
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00
> > 2017aa-2-meta.nlm
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00
> > 2017aa-otherks.nlm
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
> >
> > -rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00
> > boot.properties
> >
> > drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00
> > Copyright_Notice.txt
> >
> > drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
> >
> > drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
> >
> > drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
> >
> > -rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00
> > log4j.properties
> >
> > -rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00
> > mmsys.zip
> >
> > drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
> >
> > -rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
> >
> > -rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
> >
> > -rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
> >
> > -rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00
> run_linux.sh
> >
> > -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00
> > run_mac.command
> >
> > -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
> >
> > [spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
> >
> > --------------------------------------------
> >
> > Loading MetamorphoSys ...
> >
> > [Please be patient and wait for MetamorphoSys to begin]
> >
> > --------------------------------------------
> >
> > java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have
> > a release_version property.
> >
> > at
> > gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfi
> > guration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96
> > )
> >
> > at
> > gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfigurat
> > ion.open(AbstractPropertyFileConfiguration.java:265)
> >
> > at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.
> > initialize(StandardConfigurationManager.java:56)
> >
> > at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> > startApplication(MetamorphoSysGuiPlugin.java:74)
> >
> > at org.java.plugin.boot.Boot.boot(Unknown Source)
> >
> > at org.java.plugin.boot.Boot.main(Unknown Source)
> > java.lang.reflect.InvocationTargetException
> >
> > at java.awt.EventQueue.invokeAndWait(Unknown Source)
> >
> > at java.awt.EventQueue.invokeAndWait(Unknown Source)
> >
> > at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
> >
> > at gov.nih.nlm.umls.swing.SwingToolkit.reportError(
> > SwingToolkit.java:273)
> >
> > at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> > startApplication(MetamorphoSysGuiPlugin.java:106)
> >
> > at org.java.plugin.boot.Boot.boot(Unknown Source)
> >
> > at org.java.plugin.boot.Boot.main(Unknown Source) Caused by:
> > java.awt.HeadlessException:
> >
> > No X11 DISPLAY variable was set, but this program performed an
> > operation which requires it.
> >
> > at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
> >
> > at java.awt.Window.<init>(Unknown Source)
> >
> > at java.awt.Frame.<init>(Unknown Source)
> >
> > at java.awt.Frame.<init>(Unknown Source)
> >
> > at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown
> > Source)
> >
> > at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown
> > Source)
> >
> > at javax.swing.JOptionPane.getRootFrame(Unknown Source)
> >
> > at javax.swing.JOptionPane.getWindowForComponent(Unknown
> > Source)
> >
> > at javax.swing.JOptionPane.createDialog(Unknown Source)
> >
> > at javax.swing.JOptionPane.createDialog(Unknown Source)
> >
> > at gov.nih.nlm.umls.swing.SwingToolkit$1.run(
> > SwingToolkit.java:255)
> >
> > at java.awt.event.InvocationEvent.dispatch(Unknown Source)
> >
> > at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
> >
> > at java.awt.EventQueue.access$200(Unknown Source)
> >
> > at java.awt.EventQueue$3.run(Unknown Source)
> >
> > at java.awt.EventQueue$3.run(Unknown Source)
> >
> > at java.security.AccessController.doPrivileged(Native Method)
> >
> > at
> > java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> > Source)
> >
> > at java.awt.EventQueue.dispatchEvent(Unknown Source)
> >
> > at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
> > Source)
> >
> > at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
> > Source)
> >
> > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> > Source)
> >
> > at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> >
> > at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> >
> > at java.awt.EventDispatchThread.run(Unknown Source)
> > [spulivarthi@emsmnl003d 2017AA-full]$
> >
> >
> >
> > -----Original Message-----
> >
> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
> >
> > Sent: Saturday, October 14, 2017 4:33 PM
> >
> > To: dev@ctakes.apache.org
> >
> > Subject: [External] Re: steps to upgrade to the latest version of umls
> > and snomed
> >
> >
> >
> > I am on mobile so excuse the short message but you may have luck
> > building your own with the latest sources by following this approach
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> > youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > pKGd4f7d4gTao&m=GGPg2C_bAdC2Nvjs2INMndNgTOSbpU2yKY9fhE-E6Bs&s=
> > Bnj4TNqv9sHM3Vp3KgYjNl1f4V4jFoYWbzH4jepaxsI&e= - obviously the video
> > is for ICD10, but the other sources will appear for your selection.
> >
> >
> >
> > If you wish to use multiple dictionaries, let me know so you can give
> > my cTAKES MySQL script solution a try because HSQLDB has its limits
> > with multiple custom dictionaries.
> >
> >
> >
> > -m
> >
> >
> >
> > On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
> >
> >
> >
> > Hello,
> >
> >
> >
> > As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for
> > dictionary lookup.
> >
> >
> >
> > Did anyone try to upgrade? What should be the approach to upgrade db
> > scripts to latest umls 2017ab, snomed 2017? Any automation procedure
> > available?
> >
> >
> >
> >
> >
> > Thanks
> >
> > Regards
> >
> > Rajeev
> >
> >
> >
> >
> >
> > Sent from Mail for Windows 10
> >
> > ***********************************************************
> >
> >
> >
> > This message and any attachments are solely for the intended
> > recipient. If you are not the intended recipient, disclosure, copying,
> > use, or distribution of the information included in this message is
> > prohibited -- please immediately and permanently delete this message.
> >
> >
> >
> > ***********************************************************
> > ***********************************************************
> >
> > This message and any attachments are solely for the intended
> > recipient. If you are not the intended recipient, disclosure, copying,
> > use, or distribution of the information included in this message is
> > prohibited -- please immediately and permanently delete this message.
> >
> > ***********************************************************
> >
> ***********************************************************
>
> This message and any attachments are solely for the intended recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is prohibited --
> please immediately and permanently delete this message.
>
> ***********************************************************
>
RE: [External] Re: steps to upgrade to the latest version of umls
and snomed
Posted by Sirisha Pulivarthi <Si...@horizonblue.com.INVALID>.
Hi Matthew,
I was able to create custom dictionary from windows and copy custom dictionary to linux where I'm running pipeline.
Thanks
-----Original Message-----
From: Matthew Vita [mailto:matthewvita48@gmail.com]
Sent: Tuesday, October 17, 2017 1:52 AM
To: dev@ctakes.apache.org
Subject: Re: [External] Re: steps to upgrade to the latest version of umls and snomed
Hi Sirisha,
Sorry to hear you are having troubles. It looks like you are using the correct files from UMLS but may have a UI issue. Please review the following thread:
https://stackoverflow.com/questions/662421/no-x11-display-variable-what-does-it-mean
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Oct 16, 2017 at 12:59 PM, Sirisha Pulivarthi < Sirisha_Pulivarthi@horizonblue.com.invalid> wrote:
> Hi Sean,
> I'm using the same version of nlm files (2017AA-full) that came with
> below download https://www.nlm.nih.gov/research/umls/licensedcontent/
> umlsknowledgesources.html
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Monday, October 16, 2017 3:50 PM
> To: dev@ctakes.apache.org
> Subject: RE: [External] Re: steps to upgrade to the latest version of
> umls and snomed
>
> Hi Sirisha,
>
> Are you trying to use a metamorphosis tool with a different version of
> the nlm files?
> Also, metamorphosis is a gui application. Make sure that you have a
> display:
> > No X11 DISPLAY variable was set, but this program performed an
> > operation
> which requires it.
>
> Sean
>
> -----Original Message-----
> From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@
> horizonblue.com.INVALID]
> Sent: Monday, October 16, 2017 3:44 PM
> To: dev@ctakes.apache.org
> Subject: RE: [External] Re: steps to upgrade to the latest version of
> umls and snomed
>
> Hi Matthew,
>
>
>
> I'm running into below issue while installing UMLS. Do you see any
> issue here?
>
>
>
> total 4637464
>
> drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
>
> drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00
> 2017aa-1-meta.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00
> 2017aa-2-meta.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00
> 2017aa-otherks.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
>
> -rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00
> boot.properties
>
> drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00
> Copyright_Notice.txt
>
> drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
>
> drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
>
> drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
>
> -rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00
> log4j.properties
>
> -rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00
> mmsys.zip
>
> drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00 run_linux.sh
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00
> run_mac.command
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
>
> [spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
>
> --------------------------------------------
>
> Loading MetamorphoSys ...
>
> [Please be patient and wait for MetamorphoSys to begin]
>
> --------------------------------------------
>
> java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have
> a release_version property.
>
> at
> gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfi
> guration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96
> )
>
> at
> gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfigurat
> ion.open(AbstractPropertyFileConfiguration.java:265)
>
> at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.
> initialize(StandardConfigurationManager.java:56)
>
> at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> startApplication(MetamorphoSysGuiPlugin.java:74)
>
> at org.java.plugin.boot.Boot.boot(Unknown Source)
>
> at org.java.plugin.boot.Boot.main(Unknown Source)
> java.lang.reflect.InvocationTargetException
>
> at java.awt.EventQueue.invokeAndWait(Unknown Source)
>
> at java.awt.EventQueue.invokeAndWait(Unknown Source)
>
> at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
>
> at gov.nih.nlm.umls.swing.SwingToolkit.reportError(
> SwingToolkit.java:273)
>
> at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> startApplication(MetamorphoSysGuiPlugin.java:106)
>
> at org.java.plugin.boot.Boot.boot(Unknown Source)
>
> at org.java.plugin.boot.Boot.main(Unknown Source) Caused by:
> java.awt.HeadlessException:
>
> No X11 DISPLAY variable was set, but this program performed an
> operation which requires it.
>
> at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
>
> at java.awt.Window.<init>(Unknown Source)
>
> at java.awt.Frame.<init>(Unknown Source)
>
> at java.awt.Frame.<init>(Unknown Source)
>
> at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown
> Source)
>
> at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown
> Source)
>
> at javax.swing.JOptionPane.getRootFrame(Unknown Source)
>
> at javax.swing.JOptionPane.getWindowForComponent(Unknown
> Source)
>
> at javax.swing.JOptionPane.createDialog(Unknown Source)
>
> at javax.swing.JOptionPane.createDialog(Unknown Source)
>
> at gov.nih.nlm.umls.swing.SwingToolkit$1.run(
> SwingToolkit.java:255)
>
> at java.awt.event.InvocationEvent.dispatch(Unknown Source)
>
> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>
> at java.awt.EventQueue.access$200(Unknown Source)
>
> at java.awt.EventQueue$3.run(Unknown Source)
>
> at java.awt.EventQueue$3.run(Unknown Source)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at
> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
>
> at java.awt.EventQueue.dispatchEvent(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.run(Unknown Source)
> [spulivarthi@emsmnl003d 2017AA-full]$
>
>
>
> -----Original Message-----
>
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
>
> Sent: Saturday, October 14, 2017 4:33 PM
>
> To: dev@ctakes.apache.org
>
> Subject: [External] Re: steps to upgrade to the latest version of umls
> and snomed
>
>
>
> I am on mobile so excuse the short message but you may have luck
> building your own with the latest sources by following this approach
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=GGPg2C_bAdC2Nvjs2INMndNgTOSbpU2yKY9fhE-E6Bs&s=
> Bnj4TNqv9sHM3Vp3KgYjNl1f4V4jFoYWbzH4jepaxsI&e= - obviously the video
> is for ICD10, but the other sources will appear for your selection.
>
>
>
> If you wish to use multiple dictionaries, let me know so you can give
> my cTAKES MySQL script solution a try because HSQLDB has its limits
> with multiple custom dictionaries.
>
>
>
> -m
>
>
>
> On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
>
>
>
> Hello,
>
>
>
> As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for
> dictionary lookup.
>
>
>
> Did anyone try to upgrade? What should be the approach to upgrade db
> scripts to latest umls 2017ab, snomed 2017? Any automation procedure
> available?
>
>
>
>
>
> Thanks
>
> Regards
>
> Rajeev
>
>
>
>
>
> Sent from Mail for Windows 10
>
> ***********************************************************
>
>
>
> This message and any attachments are solely for the intended
> recipient. If you are not the intended recipient, disclosure, copying,
> use, or distribution of the information included in this message is
> prohibited -- please immediately and permanently delete this message.
>
>
>
> ***********************************************************
> ***********************************************************
>
> This message and any attachments are solely for the intended
> recipient. If you are not the intended recipient, disclosure, copying,
> use, or distribution of the information included in this message is
> prohibited -- please immediately and permanently delete this message.
>
> ***********************************************************
>
***********************************************************
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message.
***********************************************************
Re: [External] Re: steps to upgrade to the latest version of umls and snomed
Posted by Matthew Vita <ma...@gmail.com>.
Hi Sirisha,
Sorry to hear you are having troubles. It looks like you are using the
correct files from UMLS but may have a UI issue. Please review the
following thread:
https://stackoverflow.com/questions/662421/no-x11-display-variable-what-does-it-mean
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Oct 16, 2017 at 12:59 PM, Sirisha Pulivarthi <
Sirisha_Pulivarthi@horizonblue.com.invalid> wrote:
> Hi Sean,
> I'm using the same version of nlm files (2017AA-full) that came with below
> download
> https://www.nlm.nih.gov/research/umls/licensedcontent/
> umlsknowledgesources.html
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Monday, October 16, 2017 3:50 PM
> To: dev@ctakes.apache.org
> Subject: RE: [External] Re: steps to upgrade to the latest version of umls
> and snomed
>
> Hi Sirisha,
>
> Are you trying to use a metamorphosis tool with a different version of the
> nlm files?
> Also, metamorphosis is a gui application. Make sure that you have a
> display:
> > No X11 DISPLAY variable was set, but this program performed an operation
> which requires it.
>
> Sean
>
> -----Original Message-----
> From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@
> horizonblue.com.INVALID]
> Sent: Monday, October 16, 2017 3:44 PM
> To: dev@ctakes.apache.org
> Subject: RE: [External] Re: steps to upgrade to the latest version of umls
> and snomed
>
> Hi Matthew,
>
>
>
> I'm running into below issue while installing UMLS. Do you see any issue
> here?
>
>
>
> total 4637464
>
> drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
>
> drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00
> 2017aa-1-meta.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00
> 2017aa-2-meta.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00
> 2017aa-otherks.nlm
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
>
> -rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00
> boot.properties
>
> drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00
> Copyright_Notice.txt
>
> drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
>
> drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
>
> drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
>
> -rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00
> log4j.properties
>
> -rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00 mmsys.zip
>
> drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
>
> -rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00 run_linux.sh
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00
> run_mac.command
>
> -rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
>
> [spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
>
> --------------------------------------------
>
> Loading MetamorphoSys ...
>
> [Please be patient and wait for MetamorphoSys to begin]
>
> --------------------------------------------
>
> java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have a
> release_version property.
>
> at gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfi
> guration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96)
>
> at gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfigurat
> ion.open(AbstractPropertyFileConfiguration.java:265)
>
> at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.
> initialize(StandardConfigurationManager.java:56)
>
> at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> startApplication(MetamorphoSysGuiPlugin.java:74)
>
> at org.java.plugin.boot.Boot.boot(Unknown Source)
>
> at org.java.plugin.boot.Boot.main(Unknown Source)
> java.lang.reflect.InvocationTargetException
>
> at java.awt.EventQueue.invokeAndWait(Unknown Source)
>
> at java.awt.EventQueue.invokeAndWait(Unknown Source)
>
> at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
>
> at gov.nih.nlm.umls.swing.SwingToolkit.reportError(
> SwingToolkit.java:273)
>
> at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.
> startApplication(MetamorphoSysGuiPlugin.java:106)
>
> at org.java.plugin.boot.Boot.boot(Unknown Source)
>
> at org.java.plugin.boot.Boot.main(Unknown Source) Caused by:
> java.awt.HeadlessException:
>
> No X11 DISPLAY variable was set, but this program performed an operation
> which requires it.
>
> at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
>
> at java.awt.Window.<init>(Unknown Source)
>
> at java.awt.Frame.<init>(Unknown Source)
>
> at java.awt.Frame.<init>(Unknown Source)
>
> at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown
> Source)
>
> at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown Source)
>
> at javax.swing.JOptionPane.getRootFrame(Unknown Source)
>
> at javax.swing.JOptionPane.getWindowForComponent(Unknown Source)
>
> at javax.swing.JOptionPane.createDialog(Unknown Source)
>
> at javax.swing.JOptionPane.createDialog(Unknown Source)
>
> at gov.nih.nlm.umls.swing.SwingToolkit$1.run(
> SwingToolkit.java:255)
>
> at java.awt.event.InvocationEvent.dispatch(Unknown Source)
>
> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>
> at java.awt.EventQueue.access$200(Unknown Source)
>
> at java.awt.EventQueue$3.run(Unknown Source)
>
> at java.awt.EventQueue$3.run(Unknown Source)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
> Source)
>
> at java.awt.EventQueue.dispatchEvent(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.run(Unknown Source)
> [spulivarthi@emsmnl003d 2017AA-full]$
>
>
>
> -----Original Message-----
>
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
>
> Sent: Saturday, October 14, 2017 4:33 PM
>
> To: dev@ctakes.apache.org
>
> Subject: [External] Re: steps to upgrade to the latest version of umls and
> snomed
>
>
>
> I am on mobile so excuse the short message but you may have luck building
> your own with the latest sources by following this approach
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=GGPg2C_bAdC2Nvjs2INMndNgTOSbpU2yKY9fhE-E6Bs&s=
> Bnj4TNqv9sHM3Vp3KgYjNl1f4V4jFoYWbzH4jepaxsI&e= - obviously the video is
> for ICD10, but the other sources will appear for your selection.
>
>
>
> If you wish to use multiple dictionaries, let me know so you can give my
> cTAKES MySQL script solution a try because HSQLDB has its limits with
> multiple custom dictionaries.
>
>
>
> -m
>
>
>
> On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
>
>
>
> Hello,
>
>
>
> As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for
> dictionary lookup.
>
>
>
> Did anyone try to upgrade? What should be the approach to upgrade db
> scripts to latest umls 2017ab, snomed 2017? Any automation procedure
> available?
>
>
>
>
>
> Thanks
>
> Regards
>
> Rajeev
>
>
>
>
>
> Sent from Mail for Windows 10
>
> ***********************************************************
>
>
>
> This message and any attachments are solely for the intended recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is prohibited --
> please immediately and permanently delete this message.
>
>
>
> ***********************************************************
> ***********************************************************
>
> This message and any attachments are solely for the intended recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is prohibited --
> please immediately and permanently delete this message.
>
> ***********************************************************
>
RE: [External] Re: steps to upgrade to the latest version of umls
and snomed
Posted by Sirisha Pulivarthi <Si...@horizonblue.com.INVALID>.
Hi Sean,
I'm using the same version of nlm files (2017AA-full) that came with below download
https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Monday, October 16, 2017 3:50 PM
To: dev@ctakes.apache.org
Subject: RE: [External] Re: steps to upgrade to the latest version of umls and snomed
Hi Sirisha,
Are you trying to use a metamorphosis tool with a different version of the nlm files?
Also, metamorphosis is a gui application. Make sure that you have a display:
> No X11 DISPLAY variable was set, but this program performed an operation which requires it.
Sean
-----Original Message-----
From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@horizonblue.com.INVALID]
Sent: Monday, October 16, 2017 3:44 PM
To: dev@ctakes.apache.org
Subject: RE: [External] Re: steps to upgrade to the latest version of umls and snomed
Hi Matthew,
I'm running into below issue while installing UMLS. Do you see any issue here?
total 4637464
drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
-rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00 2017aa-1-meta.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00 2017aa-2-meta.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
-rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
-rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00 2017aa-otherks.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
-rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00 boot.properties
drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
-rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00 Copyright_Notice.txt
drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
-rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00 log4j.properties
-rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00 mmsys.zip
drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
-rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
-rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
-rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
-rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
-rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00 run_linux.sh
-rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.command
-rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
[spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
--------------------------------------------
Loading MetamorphoSys ...
[Please be patient and wait for MetamorphoSys to begin]
--------------------------------------------
java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have a release_version property.
at gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfiguration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96)
at gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfiguration.open(AbstractPropertyFileConfiguration.java:265)
at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.initialize(StandardConfigurationManager.java:56)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:74)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source) java.lang.reflect.InvocationTargetException
at java.awt.EventQueue.invokeAndWait(Unknown Source)
at java.awt.EventQueue.invokeAndWait(Unknown Source)
at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
at gov.nih.nlm.umls.swing.SwingToolkit.reportError(SwingToolkit.java:273)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:106)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source) Caused by: java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
at java.awt.Window.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown Source)
at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown Source)
at javax.swing.JOptionPane.getRootFrame(Unknown Source)
at javax.swing.JOptionPane.getWindowForComponent(Unknown Source)
at javax.swing.JOptionPane.createDialog(Unknown Source)
at javax.swing.JOptionPane.createDialog(Unknown Source)
at gov.nih.nlm.umls.swing.SwingToolkit$1.run(SwingToolkit.java:255)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source) [spulivarthi@emsmnl003d 2017AA-full]$
-----Original Message-----
From: Matthew Vita [mailto:matthewvita48@gmail.com]
Sent: Saturday, October 14, 2017 4:33 PM
To: dev@ctakes.apache.org
Subject: [External] Re: steps to upgrade to the latest version of umls and snomed
I am on mobile so excuse the short message but you may have luck building your own with the latest sources by following this approach https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GGPg2C_bAdC2Nvjs2INMndNgTOSbpU2yKY9fhE-E6Bs&s=Bnj4TNqv9sHM3Vp3KgYjNl1f4V4jFoYWbzH4jepaxsI&e= - obviously the video is for ICD10, but the other sources will appear for your selection.
If you wish to use multiple dictionaries, let me know so you can give my cTAKES MySQL script solution a try because HSQLDB has its limits with multiple custom dictionaries.
-m
On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
Hello,
As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for dictionary lookup.
Did anyone try to upgrade? What should be the approach to upgrade db scripts to latest umls 2017ab, snomed 2017? Any automation procedure available?
Thanks
Regards
Rajeev
Sent from Mail for Windows 10
***********************************************************
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message.
***********************************************************
***********************************************************
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message.
***********************************************************
RE: [External] Re: steps to upgrade to the latest version of umls and
snomed
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sirisha,
Are you trying to use a metamorphosis tool with a different version of the nlm files?
Also, metamorphosis is a gui application. Make sure that you have a display:
> No X11 DISPLAY variable was set, but this program performed an operation which requires it.
Sean
-----Original Message-----
From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@horizonblue.com.INVALID]
Sent: Monday, October 16, 2017 3:44 PM
To: dev@ctakes.apache.org
Subject: RE: [External] Re: steps to upgrade to the latest version of umls and snomed
Hi Matthew,
I'm running into below issue while installing UMLS. Do you see any issue here?
total 4637464
drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
-rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00 2017aa-1-meta.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00 2017aa-2-meta.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
-rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
-rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00 2017aa-otherks.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
-rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00 boot.properties
drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
-rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00 Copyright_Notice.txt
drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
-rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00 log4j.properties
-rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00 mmsys.zip
drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
-rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
-rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
-rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
-rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
-rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00 run_linux.sh
-rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.command
-rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
[spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
--------------------------------------------
Loading MetamorphoSys ...
[Please be patient and wait for MetamorphoSys to begin]
--------------------------------------------
java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have a release_version property.
at gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfiguration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96)
at gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfiguration.open(AbstractPropertyFileConfiguration.java:265)
at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.initialize(StandardConfigurationManager.java:56)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:74)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source) java.lang.reflect.InvocationTargetException
at java.awt.EventQueue.invokeAndWait(Unknown Source)
at java.awt.EventQueue.invokeAndWait(Unknown Source)
at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
at gov.nih.nlm.umls.swing.SwingToolkit.reportError(SwingToolkit.java:273)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:106)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source) Caused by: java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
at java.awt.Window.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown Source)
at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown Source)
at javax.swing.JOptionPane.getRootFrame(Unknown Source)
at javax.swing.JOptionPane.getWindowForComponent(Unknown Source)
at javax.swing.JOptionPane.createDialog(Unknown Source)
at javax.swing.JOptionPane.createDialog(Unknown Source)
at gov.nih.nlm.umls.swing.SwingToolkit$1.run(SwingToolkit.java:255)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source) [spulivarthi@emsmnl003d 2017AA-full]$
-----Original Message-----
From: Matthew Vita [mailto:matthewvita48@gmail.com]
Sent: Saturday, October 14, 2017 4:33 PM
To: dev@ctakes.apache.org
Subject: [External] Re: steps to upgrade to the latest version of umls and snomed
I am on mobile so excuse the short message but you may have luck building your own with the latest sources by following this approach https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GGPg2C_bAdC2Nvjs2INMndNgTOSbpU2yKY9fhE-E6Bs&s=Bnj4TNqv9sHM3Vp3KgYjNl1f4V4jFoYWbzH4jepaxsI&e= - obviously the video is for ICD10, but the other sources will appear for your selection.
If you wish to use multiple dictionaries, let me know so you can give my cTAKES MySQL script solution a try because HSQLDB has its limits with multiple custom dictionaries.
-m
On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
Hello,
As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for dictionary lookup.
Did anyone try to upgrade? What should be the approach to upgrade db scripts to latest umls 2017ab, snomed 2017? Any automation procedure available?
Thanks
Regards
Rajeev
Sent from Mail for Windows 10
***********************************************************
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message.
***********************************************************
RE: [External] Re: steps to upgrade to the latest version of umls
and snomed
Posted by Sirisha Pulivarthi <Si...@horizonblue.com.INVALID>.
Hi Matthew,
I'm running into below issue while installing UMLS. Do you see any issue here?
total 4637464
drwxr-xr-x 7 spulivarthi spulivarthi 4096 Oct 16 15:28 .
drwxrwxrwx 18 root root 4096 Oct 16 15:25 ..
-rw-rw-r-- 1 spulivarthi spulivarthi 1680762375 May 8 05:00 2017aa-1-meta.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 1556169544 May 8 05:00 2017aa-2-meta.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 213 May 8 05:00 2017AA.CHK
-rw-rw-r-- 1 spulivarthi spulivarthi 343 May 8 05:00 2017AA.MD5
-rw-rw-r-- 1 spulivarthi spulivarthi 1252951377 May 8 05:00 2017aa-otherks.nlm
-rw-rw-r-- 1 spulivarthi spulivarthi 23 May 8 05:00 Autorun.inf
-rw-r--r-- 1 spulivarthi spulivarthi 830 May 8 05:00 boot.properties
drwxr-xr-x 5 spulivarthi spulivarthi 63 May 8 05:00 config
-rw-rw-r-- 1 spulivarthi spulivarthi 8862 May 8 05:00 Copyright_Notice.txt
drwxr-xr-x 2 spulivarthi spulivarthi 122 May 8 05:00 etc
drwxr-xr-x 6 spulivarthi spulivarthi 64 May 8 05:00 jre
drwxr-xr-x 2 spulivarthi spulivarthi 85 May 8 05:00 lib
-rw-r--r-- 1 spulivarthi spulivarthi 794 May 8 05:00 log4j.properties
-rwxrwxrwx 1 spulivarthi spulivarthi 258793451 May 8 05:00 mmsys.zip
drwxr-xr-x 18 spulivarthi spulivarthi 4096 May 8 05:00 plugins
-rw-rw-r-- 1 spulivarthi spulivarthi 4137 May 8 05:00 README.txt
-rw-rw-r-- 1 spulivarthi spulivarthi 300 May 8 05:00 release.dat
-rwxrwxr-x 1 spulivarthi spulivarthi 547 May 8 05:00 run64.bat
-rwxrwxr-x 1 spulivarthi spulivarthi 545 May 8 05:00 run.bat
-rwxrwxr-x 1 spulivarthi spulivarthi 540 May 8 05:00 run_linux.sh
-rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.command
-rwxrwxr-x 1 spulivarthi spulivarthi 858 May 8 05:00 run_mac.sh
[spulivarthi@emsmnl003d 2017AA-full]$ ./run_linux.sh
--------------------------------------------
Loading MetamorphoSys ...
[Please be patient and wait for MetamorphoSys to begin]
--------------------------------------------
java.io.IOException: /home/spulivarthi/.mmsys/mmsys.prop does not have a release_version property.
at gov.nih.nlm.umls.mmsys.config.PropertyFileMetamorphoSysConfiguration.loadProperties(PropertyFileMetamorphoSysConfiguration.java:96)
at gov.nih.nlm.umls.mmsys.config.AbstractPropertyFileConfiguration.open(AbstractPropertyFileConfiguration.java:265)
at gov.nih.nlm.umls.mmsys.config.StandardConfigurationManager.initialize(StandardConfigurationManager.java:56)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:74)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source) java.lang.reflect.InvocationTargetException
at java.awt.EventQueue.invokeAndWait(Unknown Source)
at java.awt.EventQueue.invokeAndWait(Unknown Source)
at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
at gov.nih.nlm.umls.swing.SwingToolkit.reportError(SwingToolkit.java:273)
at gov.nih.nlm.umls.mmsys.gui.MetamorphoSysGuiPlugin.startApplication(MetamorphoSysGuiPlugin.java:106)
at org.java.plugin.boot.Boot.boot(Unknown Source)
at org.java.plugin.boot.Boot.main(Unknown Source) Caused by: java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
at java.awt.Window.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at java.awt.Frame.<init>(Unknown Source)
at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(Unknown Source)
at javax.swing.SwingUtilities.getSharedOwnerFrame(Unknown Source)
at javax.swing.JOptionPane.getRootFrame(Unknown Source)
at javax.swing.JOptionPane.getWindowForComponent(Unknown Source)
at javax.swing.JOptionPane.createDialog(Unknown Source)
at javax.swing.JOptionPane.createDialog(Unknown Source)
at gov.nih.nlm.umls.swing.SwingToolkit$1.run(SwingToolkit.java:255)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source) [spulivarthi@emsmnl003d 2017AA-full]$
-----Original Message-----
From: Matthew Vita [mailto:matthewvita48@gmail.com]
Sent: Saturday, October 14, 2017 4:33 PM
To: dev@ctakes.apache.org
Subject: [External] Re: steps to upgrade to the latest version of umls and snomed
I am on mobile so excuse the short message but you may have luck building your own with the latest sources by following this approach https://www.youtube.com/watch?v=4aOnafv-NQs - obviously the video is for ICD10, but the other sources will appear for your selection.
If you wish to use multiple dictionaries, let me know so you can give my cTAKES MySQL script solution a try because HSQLDB has its limits with multiple custom dictionaries.
-m
On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
Hello,
As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for dictionary lookup.
Did anyone try to upgrade? What should be the approach to upgrade db scripts to latest umls 2017ab, snomed 2017? Any automation procedure available?
Thanks
Regards
Rajeev
Sent from Mail for Windows 10
***********************************************************
This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message.
***********************************************************
Re: steps to upgrade to the latest version of umls and snomed
Posted by Matthew Vita <ma...@gmail.com>.
I am on mobile so excuse the short message but you may have luck building
your own with the latest sources by following this approach
https://www.youtube.com/watch?v=4aOnafv-NQs - obviously the video is for
ICD10, but the other sources will appear for your selection.
If you wish to use multiple dictionaries, let me know so you can give my
cTAKES MySQL script solution a try because HSQLDB has its limits with
multiple custom dictionaries.
-m
On Oct 14, 2017 12:10 PM, <ra...@gmail.com> wrote:
Hello,
As we understand, ctakes 4.0.0 is using umls2011ab and snomed 2016 for
dictionary lookup.
Did anyone try to upgrade? What should be the approach to upgrade db
scripts to latest umls 2017ab, snomed 2017? Any automation procedure
available?
Thanks
Regards
Rajeev
Sent from Mail for Windows 10