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From David García <david.garc...@barcelonamedia.org>
Subject Re: [UIMA C++ Framework] making examples
Date Fri, 13 Aug 2010 11:02:36 GMT
  Eddie,

I already tested C++ component with runAECpp tool, but I got the same error.
Maybe I didn't explain my doubt clearly.

In the UIMA C++ SDK examples, for example in MeetingAnnotator, I find 
C++ implementation in /uimacpp/examples/tutorial/src/MeetingAnnotator.cpp
I compile this C++ component. This C++ component also have its 
descriptor in 
/uimacpp/examples/tutorial/descriptors/MeetingAnnotatorCPP.xml.
But, MeetingAnnotator is using, as in its descriptor is specified, next 
types:

org.apache.uima.tutorial.RoomNumber
org.apache.uima.tutorial.TimeAnnot
org.apache.uima.tutorial.DateAnnot
org.apache.uima.tutorial.Meeting

and I don't know where are the files that implement these types. Where 
are they placed? They are not in the examples.

In Java UIMA examples there are the UIMA components implementations, the 
descriptors, and the Java source files with the types. I can't find the 
classes that implement the types in UIMA C++ SDK examples.
For example in /apache-uima/examples/src/org/apache/uima/tutorial/  I 
can find the classes which define the types of the examples.

So my doubt is, where should I place my Java classes defining the types 
that are being used by my C++ UIMA component?
Because this is the error I'm getting. My C++ component can't load the 
types because I suppose the component doesn't know where to find them. I 
haven't setted anywhere where to find the Java classes defining the types.


In MeetingAnnotator component:

     roomNumberT =  
crTypeSystem.getType("org.apache.uima.tutorial.RoomNumber");

How the component is suposed to find the Java class 
org.apache.uima.tutorial.RoomNumber?
I am missing this step, how to 'link' the classes defining the types 
used by the C++ component and the C++ component itself.


David

El 12/08/2010 21:03, Eddie Epstein escribió:
> David,
>
> Here are the steps recommended for testing/integrating a new C++ component:
>
> First, test the component using the C++ driver, runAECpp.sh. The
> environment will have to be setup for UIMACPP, and LD_LIBRARY_PATH
> will have to include any additional application libs as well.
> Type runAECpp.sh to get help on use. Note that import by name is note
> supported for this application. This will verify that the c++
> component is working.
>
> Next, try the same test with a Java driver, runAE.sh. The syntax is
> the same, or pretty close to the same. THis will verify the C++
> component is working when accessed thru the JNI.
>
> Finally, starting integrating the c++ component with other components.
>
> Eddie
>
> On Thu, Aug 12, 2010 at 4:57 AM, David García
> <david.garcian@barcelonamedia.org>  wrote:
>>   Hi Eddie,
>>
>> sorry, I fixed that error. It was a problem with the path in UIMACPP_HOME.
>>
>> The error I get is:
>>
>> Caused by: org.apache.uima.uimacpp.UimacppException: null;
>>         org.apache.uima.uimacpp.InternalTafException:
>> Error number  : 1005
>> Recoverable   : No
>> Error         : : typeSystemInit() Error getting Type objects
>>   (1005)
>>         at
>> org.apache.uima.uimacpp.UimacppEngine.throwJTafException(UimacppEngine.java:499)
>>         at
>> org.apache.uima.uimacpp.UimacppEngine.initialize(UimacppEngine.java:262)
>>         at
>> org.apache.uima.uimacpp.UimacppEngine.createJTafTAE(UimacppEngine.java:226)
>>         at
>> org.apache.uima.uimacpp.UimacppAnalysisComponent.initialize(UimacppAnalysisComponent.java:152)
>>         ... 23 more
>>
>>
>> As I told you in a previous mail, I implemented the component in C++,
>> created the proper descriptor file for a C++ component. Then, I created a
>> UIMA Java Eclipse project, and I generated the Type System Definition by
>> clicking on JCasGen button in Type System tab of the Component Descriptor.
>> Next, I generated the pear from this Eclipse Java project, installed it and
>> run the pipeline with the C++ component together with other Java UIMA
>> components.
>>
>> Regards,
>> David
>>
>> El 12/08/2010 10:23, David García escribió:
>>>    Hi Eddie,
>>>
>>> you were right. Now the C++ component is being used by the UIMA pipeline.
>>>
>>> Now, when I launch the UIMA pipeline, I still get a
>>> ResourceInitializationException. The message reads:
>>>
>>> java.lang.UnsatisfiedLinkError: no uima in java.library.path
>>>
>>> Eventually, I have tested the component by implementing it in Java and
>>> reducing its functionality, in order to check if the descriptor was
>>> causing this error.
>>> In Java it works right, but, I got this very same error when, adapting
>>> the descriptor file to Java, I forgot to change tag
>>> <frameworkImplementation>org.apache.uima.cpp</frameworkImplementation>
>>> to
>>>
>>> <annotatorImplementationName>org.barcelonamedia.uima.DeSRAnnotator</annotatorImplementationName>
>>>
>>>
>>> Regards,
>>> David
>>>
>>> El 10/08/2010 13:51, Eddie Epstein escribió:
>>>> Hi David,
>>>>
>>>> The LD_LIBRARY_PATH should only include directories, not specific
>>>> files. Try removing DeSR.so from the path.
>>>>
>>>> Eddie
>>>>
>>>>
>>>> On Tue, Aug 10, 2010 at 5:37 AM, David García
>>>> <david.garcian@barcelonamedia.org>    wrote:
>>>>>    Hi,
>>>>>
>>>>> testing the C++ UIMA annotator I implemented in a UIMA pipeline with
>>>>> other
>>>>> Java UIMA components, I got following error, caused by a
>>>>> ResourceInitializationException:
>>>>>
>>>>>
>>>>> Caused by: org.apache.uima.uimacpp.UimacppException: null;
>>>>>          org.apache.uima.uimacpp.InternalTafException:
>>>>> Error number  : 2001
>>>>> Recoverable   : No
>>>>> Error         : Error loading annotator 'DeSR'.
>>>>> '/usr/local/share/uima/pipelines/DeSR/installed_pears/DeSR/DeSR.so:
>>>>> undefined symbol: _ZTVN4Tanl14MorphExtractorE'
>>>>>     While      : Error loading annotator '???'. '???'
>>>>>    (2001)
>>>>>          at
>>>>>
>>>>> org.apache.uima.uimacpp.UimacppEngine.throwJTafException(UimacppEngine.java:499)
>>>>>          at
>>>>> org.apache.uima.uimacpp.UimacppEngine.initialize(UimacppEngine.java:262)
>>>>>          at
>>>>>
>>>>> org.apache.uima.uimacpp.UimacppEngine.createJTafTAE(UimacppEngine.java:226)
>>>>>          at
>>>>>
>>>>> org.apache.uima.uimacpp.UimacppAnalysisComponent.initialize(UimacppAnalysisComponent.java:152)
>>>>>
>>>>>
>>>>> I have setted all the environment variables required by UIMA SDK:
>>>>>
>>>>> export UIMACPP_HOME=/home/d/uimacpp/uimacpp
>>>>> export PATH=$PATH:$UIMACPP_HOME/bin
>>>>> export LD_LIBRARY_PATH=$UIMACPP_HOME/lib
>>>>> export
>>>>>
>>>>> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/share/uima/pipelines/DeSR/installed_pears/DeSR/DeSR.so
>>>>>
>>>>>
>>>>> It seems the UIMA pipeline can't load the C++ component. Am I doing
>>>>> anything
>>>>> wrong?
>>>>>
>>>>>
>>>>> Regards,
>>>>> David
>>>>>
>>>>> El 06/08/2010 13:24, Eddie Epstein escribió:
>>>>>> Hi David,
>>>>>>
>>>>>> A C++ annotator is intended to be fully interoperable with those
>>>>>> written in Java. That is, it can access feature structures found
in
>>>>>> the CAS and create new FS in the CAS. The type system of the CAS
is
>>>>>> the superset of types defined by all annotators, including any C++
>>>>>> components.
>>>>>>
>>>>>> So yes, you can use eclipse and integrate both java and c++ components.
>>>>>>
>>>>>> Regards,
>>>>>> Eddie
>>>>>>
>>>>>> On Fri, Aug 6, 2010 at 3:35 AM, David García
>>>>>> <david.garcian@barcelonamedia.org>     wrote:
>>>>>>>    Hi Eddie,
>>>>>>>
>>>>>>> this C++ UIMA annotator needs previous Java UIMA annotators
>>>>>>> annotations,
>>>>>>> as
>>>>>>> this C++ UIMA annotator needs them to work with.
>>>>>>> But this types are implemented by means of Java classes, as these
>>>>>>> previous
>>>>>>> UIMA annotators are implemented in Java.
>>>>>>> So my question is whether once I have developed this C++ UIMA
>>>>>>> annotator,
>>>>>>> generated the dynamic library, and composed the pipeline will
work.
>>>>>>>
>>>>>>> Moreover, this C++ UIMA annotator has its own type, which should
be
>>>>>>> implemented, and I neither know if this implementation could
be done
>>>>>>> in
>>>>>>> Java
>>>>>>> or should be in C++.
>>>>>>>
>>>>>>> My idea is to develop the annotator in C++, and afterwards, generate
>>>>>>> its
>>>>>>> own
>>>>>>> type automatically from its descriptor in an Eclipse UIMA Java
>>>>>>> project.
>>>>>>> Is
>>>>>>> this correct?
>>>>>>>
>>>>>>>
>>>>>>> David
>>>>>>>
>>>>>>> El 05/08/2010 14:40, Eddie Epstein escribió:
>>>>>>>> Hi David,
>>>>>>>>
>>>>>>>> Capabilities for any annotator should only declare the input
types
>>>>>>>> needed by that annotator and the output types generated by
that
>>>>>>>> annotator. Why would you need types from other annotators?
>>>>>>>>
>>>>>>>> Eddie
>>>>>>>>
>>>>>>>> On Thu, Aug 5, 2010 at 6:48 AM, David García
>>>>>>>> <david.garcian@barcelonamedia.org>       wrote:
>>>>>>>>>    Hi,
>>>>>>>>>
>>>>>>>>> I have a doubt regarding UIMA C++ annotator.
>>>>>>>>> I'm developing a C++ annotator to be combined within
a UIMA pipeline
>>>>>>>>> with
>>>>>>>>> other Java annotators. The point is this C++ annotator
requires, as
>>>>>>>>> input
>>>>>>>>> capabilities, another Java annotator annotations.
>>>>>>>>> My question is whether it is necessary to translate to
C++ the input
>>>>>>>>> capability types defined in Java by the ohter Java annotators,
as
>>>>>>>>> well
>>>>>>>>> as
>>>>>>>>> the C++ annotator types.
>>>>>>>>>
>>>>>>>>> My idea is to develop the C++ annotator, generating the
dynamic
>>>>>>>>> library,
>>>>>>>>> and
>>>>>>>>> afterwards, create an Eclipse UIMA project by using the
proper
>>>>>>>>> descriptor
>>>>>>>>> for the C++ UIMA annotator. Then, in this UIMA project,
include the
>>>>>>>>> Java
>>>>>>>>> types required for the C++ UIMA annotator as well as
its own types.
>>>>>>>>>
>>>>>>>>> Am I wrong, or would it be correct?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> David
>>>>>>>>>
>>>>>>>>> El 22/07/2010 10:02, David García escribió:
>>>>>>>>>>     It was version problem. Now it works.
>>>>>>>>>>
>>>>>>>>>> Thank you Eddie.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> David
>>>>>>>>>>
>>>>>>>>>> El 21/07/2010 20:34, Eddie Epstein escribió:
>>>>>>>>>>> Probably a mismatch between 32 and 64-bit versions.
>>>>>>>>>>>
>>>>>>>>>>> To confirm, use the "file" command on DaveDetector.o
and on
>>>>>>>>>>> uimacpp/lib/libuima.so
>>>>>>>>>>>
>>>>>>>>>>> UIMACPP binary packages come in both flavors
for Linux, so if this
>>>>>>>>>>> is
>>>>>>>>>>> the problem, get the other one.
>>>>>>>>>>>
>>>>>>>>>>> One other solution if your OS is 64-bit and the
uimacpp package is
>>>>>>>>>>> 32-bit: modify uimacpp/lib/base.mak to force
all compiles to be
>>>>>>>>>>> 32-bit.
>>>>>>>>>>>
>>>>>>>>>>> Regards,
>>>>>>>>>>> Eddie
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Jul 21, 2010 at 4:00 AM, David García
>>>>>>>>>>> <david.garcian@barcelonamedia.org>    
     wrote:
>>>>>>>>>>>>     Thanks for your answer Eddie. You are
right, the include
>>>>>>>>>>>> of<memory>
>>>>>>>>>>>> must
>>>>>>>>>>>> be setted before "uima/api.hpp" include.
>>>>>>>>>>>>
>>>>>>>>>>>> Now when I make the DaveDetector example
( make -f
>>>>>>>>>>>> DaveDetector.mak
>>>>>>>>>>>> )
>>>>>>>>>>>> I
>>>>>>>>>>>> get
>>>>>>>>>>>> following error message:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> /usr/bin/ld: skipping incompatible
>>>>>>>>>>>> /home/david.garcian/uimacpp/uimacpp/lib/libuima.so
when searching
>>>>>>>>>>>> for
>>>>>>>>>>>> -luima
>>>>>>>>>>>> /usr/bin/ld: cannot find -luima
>>>>>>>>>>>> collect2: ld returned 1 exit status
>>>>>>>>>>>> make: *** [DaveDetector.so] Error 1
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> It says libuima.so is icompatible. Does it
have anything to do
>>>>>>>>>>>> with
>>>>>>>>>>>> the
>>>>>>>>>>>> version of Linux or gcc?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> David
>>>>>>>>>>>>
>>>>>>>>>>>> El 19/07/2010 15:13, Eddie Epstein escribió:
>>>>>>>>>>>>> If you add the include to DaveDetector.cpp,
it must be before
>>>>>>>>>>>>> the include of uima/api.hpp. A better
way to go would be to
>>>>>>>>>>>>> put the include of<memory>    
       into
>>>>>>>>>>>>> lowlevel_internal_indexes.hpp
>>>>>>>>>>>>>
>>>>>>>>>>>>> Eddie
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Jul 19, 2010 at 3:01 AM, David
García
>>>>>>>>>>>>> <david.garcian@barcelonamedia.org>
           wrote:
>>>>>>>>>>>>>>     Hi Eddie,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I have tried adding "#include<memory>",
but I've got the same
>>>>>>>>>>>>>> error
>>>>>>>>>>>>>> message.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I've also tried using gcc version
4.3.4 and I've also got the
>>>>>>>>>>>>>> same
>>>>>>>>>>>>>> error.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>> David
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> El 16/07/2010 19:44, Eddie Epstein
escribió:
>>>>>>>>>>>>>>> Hi David,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> More recent versions of g++ are
always getting stricter.
>>>>>>>>>>>>>>> Try adding
>>>>>>>>>>>>>>> #include<memory>
>>>>>>>>>>>>>>> to DaveDetector.cpp.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> A goal for uimacpp annotators
is that they be portable,
>>>>>>>>>>>>>>> meaning
>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>> the annotator code and any non-standard
dependencies could be
>>>>>>>>>>>>>>> packaged
>>>>>>>>>>>>>>> together, and installed anyplace
on a target system.
>>>>>>>>>>>>>>> LD_LIBRARY_PATH
>>>>>>>>>>>>>>> is very useful for this.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The alternative is to install
uimacpp and it's dependencies in
>>>>>>>>>>>>>>> some
>>>>>>>>>>>>>>> standard system directory, but
this would require root access.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>>> Eddie
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Thu, Jul 15, 2010 at 8:04
AM, David García
>>>>>>>>>>>>>>> <david.garcian@barcelonamedia.org>
             wrote:
>>>>>>>>>>>>>>>>     Hi all,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I am trying to use uimacpp,
Linux version, but I have got
>>>>>>>>>>>>>>>> problems
>>>>>>>>>>>>>>>> making
>>>>>>>>>>>>>>>> C++ examples.
>>>>>>>>>>>>>>>> I follow README instructions,
and when I do:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> make -f DaveDetector.mak
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I get following error:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> /uimacpp/include/uima/lowlevel_internal_indexes.hpp:
In
>>>>>>>>>>>>>>>> member
>>>>>>>>>>>>>>>> function
>>>>>>>>>>>>>>>> ‘virtual void
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> uima::lowlevel::internal::CachedCompositeIndex<T>::clearAndFillCache()’:
>>>>>>>>>>>>>>>> /uimacpp/include/uima/lowlevel_internal_indexes.hpp:348:
>>>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>>>> ‘auto_ptr’
>>>>>>>>>>>>>>>> was not declared in this
scope
>>>>>>>>>>>>>>>> /uimacpp/include/uima/lowlevel_internal_indexes.hpp:348:
>>>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>>>> expected
>>>>>>>>>>>>>>>> primary-expression before
‘>’ token
>>>>>>>>>>>>>>>> /uimacpp/include/uima/lowlevel_internal_indexes.hpp:348:
>>>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>>>> there
>>>>>>>>>>>>>>>> are
>>>>>>>>>>>>>>>> no
>>>>>>>>>>>>>>>> arguments to ‘apit’ that
depend on a template parameter, so a
>>>>>>>>>>>>>>>> declaration
>>>>>>>>>>>>>>>> of
>>>>>>>>>>>>>>>> ‘apit’ must be available
>>>>>>>>>>>>>>>> /uimacpp/include/uima/lowlevel_internal_indexes.hpp:348:
>>>>>>>>>>>>>>>> note:
>>>>>>>>>>>>>>>> (if
>>>>>>>>>>>>>>>> you
>>>>>>>>>>>>>>>> use
>>>>>>>>>>>>>>>> ‘-fpermissive’, G++ will
accept your code, but allowing the
>>>>>>>>>>>>>>>> use
>>>>>>>>>>>>>>>> of
>>>>>>>>>>>>>>>> an
>>>>>>>>>>>>>>>> undeclared name is deprecated)
>>>>>>>>>>>>>>>> /uimacpp/include/uima/lowlevel_internal_indexes.hpp:349:
>>>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>>>> ‘apit’
>>>>>>>>>>>>>>>> was
>>>>>>>>>>>>>>>> not declared in this scope
>>>>>>>>>>>>>>>> make: *** [DaveDetector.o]
Error 1
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I am using gcc version 4.4.1
(Ubuntu 4.4.1-4ubuntu9).
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Am I doing something wrong?
>>>>>>>>>>>>>>>> I have also found that it
is not a good practise to use
>>>>>>>>>>>>>>>> LD_LIBRARY_PATH
>>>>>>>>>>>>>>>> env
>>>>>>>>>>>>>>>> variable. Is this correct?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks in advanced,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> David
>>>>>>>>>>>>>>>>

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