RE: UIMA Addons ConceptMapper - where to start

[Debbie Zhang <de...@gmail.com>]

Marshall, you are right. It is the import problem.

It took me a little while to figure this out. So I think I should share with
others so new users won't have this problem again. 

The main example descriptor in ConceptMapper is: 
desc/analysis_engine/primitive/ConceptMapperOffsetTokenizer.xml

To make it work, apart from copying the descriptor xml files to your desc
folder, you need to do the following:

1. Open the following files using a text editor and delete all elements
inside the import tags
	OffsetTokenizerMatcher.xml
	ConceptMapperOffsetTokenizer.xml

2. Copy a TokenAnnotion.xml from the ConceptMapper package in the source
release to your desc folder

3. Open the above xml files using Component Descriptor Editor and manually
add the deleted items back to using import tag

Regards,

Debbie

> -----Original Message-----
> From: Marshall Schor [mailto:msa@schor.com]
> Sent: Wednesday, 12 March 2014 6:08 AM
> To: user@uima.apache.org
> Subject: Re: UIMA Addons ConceptMapper - where to start
> 
> 
> On 3/4/2014 5:01 AM, Debbie Zhang wrote:
> > Thanks Marshall!
> >
> >> Well, adding the UIMA nature to your project, surprised me a bit.
> >> You would do this if you wanted to package the results of your work
> >> as a PEAR package, after you've finished creating an annotator
> >> pipeline you wish to deliver to others to use.
> > Yes, after creating annotators, we will use IBM Content Analytics to
> > display the results. Therefore, we need to package them as PEAR
> packages.
> >
> >>> I can use "Component Descriptor Editor" to open DictTerm.xml and
> >>> OffsetTokenizer.xml. However, when I use "Component Descriptor
> >> Editor"
> >>> to open ConceptMapperOffsetTokenizer.xml and
> >>> OffsetTokenizerMatcher.xml, I have the following error:
> >>>
> >>> The descriptor has one or more errors. Please fix in the source
> >> editor.
> >>> ResourceInitializationException: An import could not be resolved.
> No
> >>> file with name "org/apache/uima/conceptMapper/DictTerm.xml" was
> >>> found in the class path or data path.
> >>>
> >>
> (Descriptor:file:/C/Work/Java_Workspace/ConceptMapperTest/desc/analys
> >> i
> >>> s_engi
> >>> ne/primitive
> >>> /ConceptMapperOffsetTokenizer.xml)
> >>>
> >> The Component Descriptor Editor needs to be able to find descriptors
> >> that are references.  Descriptors are referenced in two ways: by
> name
> >> and by location.
> >> By location is a relative reference; by name looks things up in the
> >> classpath (in this case in the classpath Eclipse uses for the
> project
> >> containing the descriptor being edited).  See:
> >> http://uima.apache.org/d/uimaj-
> >> 2.5.0/references.html#ugr.ref.xml.component_descriptor.imports
> >>
> >> The simplest thing to do to correct this kind of error is to put the
> >> directory containing the referenced descriptor on Eclipse's source
> >> class path.  (you do this by some menu action - like right clicking
> >> the directory containing the descriptors you want to be able to find,
> >> in the PackageExplorer view of Eclipse, and selecting "Build Path" ->
> >> "add to Build Path".
> > As the uima-an-conceptMapper.jar is in the class path, DictTerm.xml
> > and other descriptors are able to be found by Name. However, due to
> > the file structure in jar file, the file is listed under by-name xml
> > resource as "analysis_engine/primitive/DictTerm.xml" instead of
> > "org/apache/uima/conceptMapper/DictTerm.xml". I think that is how
> that
> > error came from.
> >
> > The reason I want to open these descriptors was I want to see how
> > these descriptors can be used. So I also created a new descriptor
> > "TestConceptMapperDescriptor.xml" and try to use the ConceptMapper
> > annotator here. I am able to import
> analysis_engine.primitive.DictTerm
> > at the "Type System" tab. Under the "Capabilities" tab, I set
> DictTerm
> > as Input and TestConceptMapperDescriptor as Output. This is as far as
> > I can go. I am not sure how to set dictionary to be used by the
> > DictTerm and set the configurations of the parameters.
> >
> > I am not able to import other Descriptors such as OffsetTokenizer.xml
> > with the following errors:
> > An error was caused by adding Import(s); operation cancelled. Please
> > correct the Error and retry.
> > ResourceInitializationException: An object of class
> > Org.apache.uima.resource.metadata.TypeSystemDescription was requested,
> > but the XML input contained an object of class
> > org.apache.uima.analysis_engine.impl.TaeDescription_impl.
> 
> This error probably means the descriptor has an import statement which
> pointed to (I'm guessing) OffsetTokenizer), which is not a type system
> descriptor.
> 
> In the main descriptor (the one with import statements), there are
> multiple xml elements which can contain imports.  Is the import in the
> right spot?  If you can't figure this out, can you post the relevant
> descriptors?
> 
> -Marshall
> >
> >
> > Thanks Marshall for your help again - much appreciated!
> >
> > Regards,
> >
> > Debbie
> >
> >
> >
> >

Re: UIMA Addons ConceptMapper - where to start

[Marshall Schor <ms...@schor.com>]

Hi Debbie,

Thanks for sharing with the community :-)

-Marshall
On 9/18/2014 5:56 AM, Debbie Zhang wrote:
> Marshall, you are right. It is the import problem.
>
> It took me a little while to figure this out. So I think I should share with
> others so new users won't have this problem again. 
>
> The main example descriptor in ConceptMapper is: 
> desc/analysis_engine/primitive/ConceptMapperOffsetTokenizer.xml
>
> To make it work, apart from copying the descriptor xml files to your desc
> folder, you need to do the following:
>
> 1. Open the following files using a text editor and delete all elements
> inside the import tags
> 	OffsetTokenizerMatcher.xml
> 	ConceptMapperOffsetTokenizer.xml
>
> 2. Copy a TokenAnnotion.xml from the ConceptMapper package in the source
> release to your desc folder
>
> 3. Open the above xml files using Component Descriptor Editor and manually
> add the deleted items back to using import tag
>
> Regards,
>
> Debbie
>
>> -----Original Message-----
>> From: Marshall Schor [mailto:msa@schor.com]
>> Sent: Wednesday, 12 March 2014 6:08 AM
>> To: user@uima.apache.org
>> Subject: Re: UIMA Addons ConceptMapper - where to start
>>
>>
>> On 3/4/2014 5:01 AM, Debbie Zhang wrote:
>>> Thanks Marshall!
>>>
>>>> Well, adding the UIMA nature to your project, surprised me a bit.
>>>> You would do this if you wanted to package the results of your work
>>>> as a PEAR package, after you've finished creating an annotator
>>>> pipeline you wish to deliver to others to use.
>>> Yes, after creating annotators, we will use IBM Content Analytics to
>>> display the results. Therefore, we need to package them as PEAR
>> packages.
>>>>> I can use "Component Descriptor Editor" to open DictTerm.xml and
>>>>> OffsetTokenizer.xml. However, when I use "Component Descriptor
>>>> Editor"
>>>>> to open ConceptMapperOffsetTokenizer.xml and
>>>>> OffsetTokenizerMatcher.xml, I have the following error:
>>>>>
>>>>> The descriptor has one or more errors. Please fix in the source
>>>> editor.
>>>>> ResourceInitializationException: An import could not be resolved.
>> No
>>>>> file with name "org/apache/uima/conceptMapper/DictTerm.xml" was
>>>>> found in the class path or data path.
>>>>>
>> (Descriptor:file:/C/Work/Java_Workspace/ConceptMapperTest/desc/analys
>>>> i
>>>>> s_engi
>>>>> ne/primitive
>>>>> /ConceptMapperOffsetTokenizer.xml)
>>>>>
>>>> The Component Descriptor Editor needs to be able to find descriptors
>>>> that are references.  Descriptors are referenced in two ways: by
>> name
>>>> and by location.
>>>> By location is a relative reference; by name looks things up in the
>>>> classpath (in this case in the classpath Eclipse uses for the
>> project
>>>> containing the descriptor being edited).  See:
>>>> http://uima.apache.org/d/uimaj-
>>>> 2.5.0/references.html#ugr.ref.xml.component_descriptor.imports
>>>>
>>>> The simplest thing to do to correct this kind of error is to put the
>>>> directory containing the referenced descriptor on Eclipse's source
>>>> class path.  (you do this by some menu action - like right clicking
>>>> the directory containing the descriptors you want to be able to find,
>>>> in the PackageExplorer view of Eclipse, and selecting "Build Path" ->
>>>> "add to Build Path".
>>> As the uima-an-conceptMapper.jar is in the class path, DictTerm.xml
>>> and other descriptors are able to be found by Name. However, due to
>>> the file structure in jar file, the file is listed under by-name xml
>>> resource as "analysis_engine/primitive/DictTerm.xml" instead of
>>> "org/apache/uima/conceptMapper/DictTerm.xml". I think that is how
>> that
>>> error came from.
>>>
>>> The reason I want to open these descriptors was I want to see how
>>> these descriptors can be used. So I also created a new descriptor
>>> "TestConceptMapperDescriptor.xml" and try to use the ConceptMapper
>>> annotator here. I am able to import
>> analysis_engine.primitive.DictTerm
>>> at the "Type System" tab. Under the "Capabilities" tab, I set
>> DictTerm
>>> as Input and TestConceptMapperDescriptor as Output. This is as far as
>>> I can go. I am not sure how to set dictionary to be used by the
>>> DictTerm and set the configurations of the parameters.
>>>
>>> I am not able to import other Descriptors such as OffsetTokenizer.xml
>>> with the following errors:
>>> An error was caused by adding Import(s); operation cancelled. Please
>>> correct the Error and retry.
>>> ResourceInitializationException: An object of class
>>> Org.apache.uima.resource.metadata.TypeSystemDescription was requested,
>>> but the XML input contained an object of class
>>> org.apache.uima.analysis_engine.impl.TaeDescription_impl.
>> This error probably means the descriptor has an import statement which
>> pointed to (I'm guessing) OffsetTokenizer), which is not a type system
>> descriptor.
>>
>> In the main descriptor (the one with import statements), there are
>> multiple xml elements which can contain imports.  Is the import in the
>> right spot?  If you can't figure this out, can you post the relevant
>> descriptors?
>>
>> -Marshall
>>>
>>> Thanks Marshall for your help again - much appreciated!
>>>
>>> Regards,
>>>
>>> Debbie
>>>
>>>
>>>
>>>
>
>
>