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:[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://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, <[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
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