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Posted to dev@ctakes.apache.org by Leander Melms <Me...@students.uni-marburg.de> on 2017/03/15 17:22:03 UTC
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
Re: Trouble with the DictionaryTool
Posted by James Masanz <ma...@gmail.com>.
great! look forward to having that in cTAKES (trunk)
On Fri, Mar 17, 2017 at 12:01 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> yes
>
> -----Original Message-----
> From: James Masanz [mailto:masanz.james@gmail.com]
> Sent: Friday, March 17, 2017 11:57 AM
> To: dev@ctakes.apache.org
> Subject: Re: Trouble with the DictionaryTool
>
> 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.Finan@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.james@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.Finan@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:Melms@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 <
> > > Melms@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.Finan@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:Melms@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
> > > >>>
> > > >>>
> > > >>
> > > >>
> > > >
> > > >
> > >
> > >
> >
>
RE: Trouble with the DictionaryTool
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
yes
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Friday, March 17, 2017 11:57 AM
To: dev@ctakes.apache.org
Subject: Re: Trouble with the DictionaryTool
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.Finan@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.james@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.Finan@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:Melms@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 <
> > Melms@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.Finan@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:Melms@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
> > >>>
> > >>>
> > >>
> > >>
> > >
> > >
> >
> >
>
Re: Trouble with the DictionaryTool
Posted by James Masanz <ma...@gmail.com>.
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.Finan@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.james@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.Finan@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:Melms@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 <
> > Melms@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.Finan@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:Melms@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
> > >>>
> > >>>
> > >>
> > >>
> > >
> > >
> >
> >
>
RE: Trouble with the DictionaryTool
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.james@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.Finan@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:Melms@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 <
> Melms@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.Finan@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:Melms@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
> >>>
> >>>
> >>
> >>
> >
> >
>
>
Re: Trouble with the DictionaryTool
Posted by James Masanz <ma...@gmail.com>.
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.Finan@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:Melms@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 <
> Melms@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.Finan@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:Melms@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
> >>>
> >>>
> >>
> >>
> >
> >
>
>
Re: Trouble with the DictionaryTool
Posted by Leander Melms <Me...@students.uni-marburg.de>.
Thank you so much, this really helped. I have been dealing with this for hours. Solved the issue!
Thanks again
Leander
> On 16 Mar 2017, at 22:12, Finan, Sean <Se...@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:Melms@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 <Se...@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:Melms@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
>>>>
>>>>
>>>
>>>
>>
>>
>
>
RE: Trouble with the DictionaryTool
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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:Melms@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 <Se...@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:Melms@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
>>>
>>>
>>
>>
>
>
Re: Trouble with the DictionaryTool
Posted by Leander Melms <Me...@students.uni-marburg.de>.
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 <Se...@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:Melms@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
>>>
>>>
>>
>>
>
>
Re: Trouble with the DictionaryTool
Posted by Leander Melms <Me...@students.uni-marburg.de>.
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 <Se...@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:Melms@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
>>
>>
>
>
Re: Trouble with the DictionaryTool
Posted by 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 <Se...@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:Melms@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
>
>
RE: Trouble with the DictionaryTool
Posted by "Finan, Sean" <Se...@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:Melms@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