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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject DrugCNP2LookupWindow.xml InvalidXMLException [was RE: export runnable jar issue]
Date Tue, 07 May 2013 14:27:04 GMT

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

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