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From Kannan Thiagarajan <kanna...@gmail.com>
Subject Re: DrugCNP2LookupWindow.xml InvalidXMLException [was RE: export runnable jar issue]
Date Tue, 07 May 2013 17:37:53 GMT
Hello,

Thanks. I had few other issues in my Maven dependencies and launcher files
that caused the issue. Now I'm able to get it to work correctly.

Best Regards
Kannan Thiagarajan



On Tue, May 7, 2013 at 9:27 AM, Masanz, James J. <Masanz.James@mayo.edu>wrote:

>
> After a build, do you end up with TypeSystem.xml in
>
> ctakes-drug-ner-res/target/classes/org/apache/ctakes/drugner/types/
>
> I am not a maven guru but what you described (adding the
> ctakes-drug-ner-res) sounds like it should work.
>
> - James
>
>
> > -----Original Message-----
> > From: dev-return-1577-Masanz.James=mayo.edu@ctakes.apache.org [mailto:
> dev-
> > return-1577-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Kannan
> > Thiagarajan
> > Sent: Monday, May 06, 2013 9:14 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: export runnable jar issue
> >
> > I updated my local "DrugCNP2LookupWindow.xml"  with the latest but the
> > problem persists.
> >
> > Caused by: org.apache.uima.util.InvalidXMLException: An import could not
> > be resolved.  No .xml file with name
> > "org.apache.ctakes.drugner.types.TypeSystem" was found in the class path
> > or data path. (Descriptor:
> > file:/C:/cTAKES_Workspace2/ctakes/ctakes-drug-
> > ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)
> >
> > Please let me know if there are any other files that I need to pull-in.
> >
> > Thanks
> >
> >
> >
> > On Mon, May 6, 2013 at 7:39 PM, Masanz, James J.
> > <Masanz.James@mayo.edu>wrote:
> >
> > >
> > > I just checked in a fix today for this actually.
> > > CTAKES-194
> > > InvalidXMLException: An import could not be resolved.
> > > org.apache.ctakes.drugner.types.Typesystem DrugCNP2LookupWindow.xml
> > > https://issues.apache.org/jira/browse/CTAKES-194
> > >
> > > If you check out the latest you should get the fix. or fix the casing
> > > of TypeSystem so there is a capital S.
> > >
> > > Regards,
> > > James Masanz
> > >
> > > > -----Original Message-----
> > > > From: dev-return-1575-Masanz.James=mayo.edu@ctakes.apache.org[mailto:
> > > dev-
> > > > return-1575-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of
> > > > Kannan Thiagarajan
> > > > Sent: Monday, May 06, 2013 6:12 PM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: export runnable jar issue
> > > >
> > > > Hello,
> > > >
> > > > I'm facing a similar issue not sure if it is related to this.
> > > >
> > > > I created an eclipse/maven project which just contains a pipeline
> > > > that includes many cTAKES components for which I included the Maven
> > > > dependencies. Everything worked out fine until I included the Drug
> > > > NER. I got the following error.
> > > >
> > > > An import could not be resolved.  No .xml file with name
> > > > "org.apache.ctakes.drugner.types.Typesystem" was found in the class
> > > > path or data path. (Descriptor:
> > > > file:/C:/cTAKES_Workspace2/ctakes/ctakes-drug-
> > > > ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)
> > > >
> > > > I tried to add the ctakes-drug-ner-res and it did not resolve the
> > issue.
> > > I
> > > > could workaround this by copying the contents of
> > > ctakes-drug-ner-resources
> > > > project but hate doing so. Maybe this is a maven newbie issue.
> > > >
> > > > Any thoughts?
> > > >
> > > > Thanks
> > > > Kannan
> > > >
> > > >
> > > > On Tue, Apr 23, 2013 at 10:35 AM, Tim Miller <
> > > > timothy.miller@childrens.harvard.edu> wrote:
> > > >
> > > > > It may actually be a maven issue:
> > > > > https://bugs.eclipse.org/bugs/**show_bug.cgi?id=284928<https://bug
> > > > > s.ec lipse.org/bugs/show_bug.cgi?id=284928>
> > > > >
> > > > > I'm a little swamped right now, but I'd like to try setting up a
> > > > > non-maven project with two source folders:
> > > > > src/main/java
> > > > > src/main/resources
> > > > >
> > > > > like ours, and see if this issue persists.
> > > > > Tim
> > > > >
> > > > >
> > > > > On 04/23/2013 11:21 AM, Masanz, James J. wrote:
> > > > >
> > > > >> I'm having the same issue.
> > > > >> I tried just creating a jar instead of a runnable jar and get
the
> > > same.
> > > > >>
> > > > >> Tim, I don't know if it's 1, 2 or 3.
> > > > >>
> > > > >> -- James
> > > > >>
> > > > >>
> > > > >>
> > > > >>  -----Original Message-----
> > > > >>> From: dev-return-1533-
> > > > Masanz.James=m**ayo.edu@ctakes.apache.org<mayo.edu@ctakes.apache.org
> > > >[mail
> > > > to:
> > > > >>> dev-
> > > > >>> return-1533-Masanz.James=mayo.**edu@ctakes.apache.org<mayo.edu@c
> > > > >>> take
> > > > >>> s.apache.org>]
> > > > >>> On Behalf Of Miller,
> > > > >>> Timothy
> > > > >>> Sent: Sunday, April 21, 2013 7:23 AM
> > > > >>> To: dev@ctakes.apache.org
> > > > >>> Subject: export runnable jar issue
> > > > >>>
> > > > >>> I've found it useful to "export runnable jar" to create a
single
> > > > >>> file that can be run with 'java -jar' on a server/cluster
for a
> > > > >>> given run configuration. There is an issue that may be an
> > > > >>> eclipse bug but also may be a ctakes issue.
> > > > >>>
> > > > >>> The issue is that files under src/main/java source folders
> > > > >>> export exactly as expected, while files under src/main/resources
> > > > >>> folders export with the "resources" folder prepended. So
you
> > > > >>> will get the following classpaths in the jar:
> > > > >>>
> > > > >>> org/apache/ctakes/someproject/**SomeCode.class
> > > > >>> resources/org/apache/ctakes/**someproject/some_model.bin
> > > > >>>
> > > > >>> This obviously screws up important classpaths at runtime.
I can
> > > > >>> workaround it, but does anyone have a sense of whether this
> > > > >>> issue
> > > > >>> is:
> > > > >>> 1) Clearly an eclipse issue with nothing we can do except
try to
> > > > >>> notify someone
> > > > >>> 2) An eclipse issue but there is something we're doing wrong
> > > > >>> (like a convention for resources we're not following that
would
> > > > >>> fix this)
> > > > >>> 3) Clearly a ctakes issue
> > > > >>>
> > > > >>> Tim
> > > > >>>
> > > > >>
> > > > >
> > > >
> > > >
> > > > --
> > > > Best Regards
> > > > Kannan Thiagarajan
> > >
> >
> >
> >
> > --
> > Best Regards
> > Kannan Thiagarajan
>



-- 
Best Regards
Kannan Thiagarajan

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