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. > > *********************************************************** >
