Do the updates you mentioned include a way to run a cTAKES pipeline through a GUI? If not, you might want to choose a different name than ctakes-gui for the module
On Fri, Mar 17, 2017 at 11:48 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi James, > I actually do have an expanded version that I was going to check in this > weekend. I will back out your checkin as the new module is just named > "ctakes-gui", having more than the dictionary creator. > Sean > > -----Original Message----- > From: James Masanz [mailto:masanz.ja...@gmail.com] > Sent: Friday, March 17, 2017 8:13 AM > To: dev@ctakes.apache.org > Subject: Re: Trouble with the DictionaryTool > > I checked in the gui under trunk as ctakes-dictionary-gui FYI, I moved > the data directory under resources It runs from source but haven't tested > from a jar yet. > Sean if you make changes, please make them to the trunk version. Thanks. > > On Thu, Mar 16, 2017 at 5:12 PM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Leander, > > > > I thought that I was saving people problems by preselecting English as > > the default ... But you are the second person to request another > language. > > > > I hardcoded the gui to only fetch English synonyms. I will change > > this before it goes into the official release. It is already set up > > for it, but I never exposed the control. > > > > In the class MainPanel line 179 or so has: > > Collections.singletonList( "ENG" ), > > > > I think that umls uses iso 639-2, so you can swap "ENG" with "GER". > > Iso > > 639-3 uses DEU, so just in case one or two vocabularies have switched > > you could catch both with Arrays.asList( "GER", "DEU" ). > > > > That should do it, but let me know if it doesn't work. > > > > Sean > > > > > > -----Original Message----- > > From: Leander Melms [mailto:me...@students.uni-marburg.de] > > Sent: Thursday, March 16, 2017 4:43 PM > > To: dev@ctakes.apache.org > > Subject: Re: Trouble with the DictionaryTool > > > > Sean, > > > > apologies for disturbing again. I'm trying to populate the db with a > > german translation of various sources (such as MesH, DIMDICD, ..). The > > UMLS install succeeded but whenever running the dictionary guy, it > > only fills the db with the english concepts (from RxNorm I think?). > > > > How is the data fetched from the UMLS install? Is it possible to use a > > different language than English? > > > > I had a quick look at the source code but couldn't find out where the > > problem is. Any hints are greatly appreciated. > > > > Leander > > > > > > > On 16 Mar 2017, at 10:50, Leander Melms > > > <me...@students.uni-marburg.de> > > wrote: > > > > > > Sorry, > > > > > > Should have thought before writing again.. I imported the GUI under > > main.java and had to fix the imports. > > > > > > It's working now as expected! > > > > > >> Am 16.03.2017 um 08:37 schrieb Leander Melms < > > me...@students.uni-marburg.de>: > > >> > > >> Hi Sean, > > >> > > >> Thank you for the fast reply! I imported the dictionary gui into > > eclipse (as standalone), added the lib folder to the build path and > > tried to compile with Java 8. Eclipse complained about ~ 200 errors. > > >> > > >> What am I missing here? > > >> > > >> Leander > > >> > > >>> Am 15.03.2017 um 19:16 schrieb Finan, Sean < > > sean.fi...@childrens.harvard.edu>: > > >>> > > >>> Hi Leander. I think that you would be better off using the > > >>> dictionary > > gui. It is also in sandbox, and though it was originally a wrapper > > interface for the cli tool, it has since been the more active project > > with new features and bug fixes. > > >>> > > >>> -----Original Message----- > > >>> From: Leander Melms [mailto:me...@students.uni-marburg.de] > > >>> Sent: Wednesday, March 15, 2017 1:22 PM > > >>> To: dev@ctakes.apache.org > > >>> Subject: Trouble with the DictionaryTool > > >>> > > >>> Hi, > > >>> > > >>> I've followed the instructions found in this mailing list to set > > >>> up > > and run the dictionary tool. I made a quick summary of what I found: > > >>> > > >>> Change the configuration at /data/default/CtakesSources.txt to > > include ICD10 or other extensions; there can be zero or more sources. > > >>> Copy ctakesumls.properties and ctakesumls.script from > > >>> resource/memdbtemplate to a new folder to put the new UMLS DB Run > > >>> DictionaryCreator2 java -cp dictionarytool.jar;lib/* > > >>> org.apache.ctakes.dictionarytool.DictionaryCreator2 > > >>> -umls "/2015AB/META" > > >>> -atui ./data/tiny/CtakesAnatTuis.txt -tui > > >>> ./data/tiny/CtakesSnomedTuis.txt -src > > >>> ./data/tiny/CtakesSources.txt -fd ./data/tiny -db > > >>> jdbc:hsqldb:file:pathTonewDB/snorx2015 > > >>> -tbl CUI_TERMS > > >>> Run CodeMapCreator > > >>> java -cp dictionarytool.jar;lib/* > > >>> org.apache.ctakes.dictionarytool.CodeMapCreator > > >>> -umls "/2015AB/META" > > >>> -atui ./data/tiny/CtakesAnatTuis.txt -db > > >>> jdbc:hsqldb:file:pathTonewDB/snorx2015 > > >>> -fd ./data/tiny > > >>> -tbl CUI_TERMS > > >>> Copy new DB files to new location and create a copy of > > >>> cTakesHsql.xml and update dictionary location > > >>> > > >>> I'm failing at step 3 when running the DictionaryCreator2 with the > > output: > > >>> > > >>> lib/hsqldb.jar: warning: cannot start debugger; debugging mode > > >>> disabled > > >>> lib/hsqldb.jar: line 1: $'PK\003\004': command not found > > >>> lib/hsqldb.jar: line 2: META-INF/ PK: No such file or directory > > >>> lib/hsqldb.jar: line 3: syntax error near unexpected token `(' > > >>> lib/hsqldb.jar: line 3: p < _ xMETA-INF/MANIFEST.MFm Ok! c{ f o > > m {(. \5 uf 5ڙR N 8F+w @ V %m" > > >>> =] / U { D Hc 9eٹ =b tf0 Υ &[ U m g& > > w @ p % )` kQe z{' w ͩ H+. /f՜ Z ] Q S /vHG ٔ e h[ > > -F}PK' > > >>> > > >>> The path should be correctly pointing to the UMLS folder. I'm > > >>> running > > Mac OS Sierra. > > >>> > > >>> Any help is greatly appreciated. > > >>> > > >>> Leander > > >>> > > >>> > > >> > > >> > > > > > > > > > > >
