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:[email protected]] Sent: Tuesday, October 17, 2017 1:52 AM To: [email protected] 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 < [email protected]> 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:[email protected]] > Sent: Monday, October 16, 2017 3:50 PM > To: [email protected] > 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: [email protected] > 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:[email protected]] > > Sent: Saturday, October 14, 2017 4:33 PM > > To: [email protected] > > 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, <[email protected]> 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. ***********************************************************
