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Posted to user@uima.apache.org by Marshall Schor <ms...@schor.com> on 2014/03/01 16:29:59 UTC
Re: UIMA Addons ConceptMapper - where to start
Hi Debbie,
On 2/28/2014 2:35 AM, Debbie Zhang wrote:
> Hi all,
>
>
>
> I would like to learn how to use ConceptMapper in the UIMA Addons. So far,
> what I have done was to add ConceptMapper jar file to my project path and
> attach the doc jar file to the jar file. I have read through the
> documentation came with the package. However, I still don't have a clue how
> to use ConceptMapper in a Java program.
Concept Mapper is a UIMA Annotator - you use it as a component within a UIMA
Pipeline.
There's a quick start for UIMA here:
http://uima.apache.org/documentation.html#getting_started
Hope that Helps! -Marshall
> Can anyone point me to the
> direction? A "Hello World" program would be greatly appreciated. Thank you.
>
>
>
> Regards,
>
>
>
> Debbie
>
>
Re: UIMA Addons ConceptMapper - where to start
Posted by 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
>>>
>>>
>>>
>>>
>
>
>
RE: UIMA Addons ConceptMapper - where to start
Posted by 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
Posted by Marshall Schor <ms...@schor.com>.
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/analysi
>>> 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
Posted by Debbie Zhang <de...@gmail.com>.
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/analysi
> > 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.
Thanks Marshall for your help again - much appreciated!
Regards,
Debbie
Re: UIMA Addons ConceptMapper - where to start
Posted by Marshall Schor <ms...@schor.com>.
On 3/2/2014 1:04 AM, Debbie Zhang wrote:
> Thanks Marshall. I have no problem of following the UIMA getting_started
> tutorial and have successfully created my own applications with my own
> annotators. I think I should ask my question more specifically.
>
> I created a new project called: ConceptMapperTest. I added UIMA nature to
> the project.
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.
> I copied every files under desc and resources folders in the
> downloaded package to the desc and resources folders in the
> ConceptMapperTest project.
This seems not right.
I think the confusion is around "packaging". UIMA provides add-ons as basic
annotators you can add, but also as "PEAR" packages, which have to be
"installed", if you use the PEAR form. See
http://uima.apache.org/d/uimaj-2.5.0/references.html#ugr.ref.pear.installing .
If you're going to use the PEAR packaging form, first "install" the pear package
in some (new) directory. UIMA provides a script to do this, called
runPearInstaller. The installation process creates a UIMA descriptor inside
the install directory that you can then use in your project, for example, as a
delegate in an aggregate.
> 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/analysis_engi
> ne/primitive
> /ConceptMapperOffsetTokenizer.xml)
>
> Therefore, I created all subfolders org/apache/uima/conceptMapper under
> desc, and then put all xml files to there. However, I still have the above
> error when I try to open ConceptMapperOffsetTokenizer.xml and
> OffsetTokenizerMatcher.xml files with "Component Descriptor Editor".
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".
Hope that helps.
-Marshall
>
> Would you please let me know what I did wrong? Thank you very much for your
> help!
>
> Regards,
>
> Debbie
>
>
> -----Original Message-----
> From: Marshall Schor [mailto:msa@schor.com]
> Sent: Sunday, 2 March 2014 2:30 AM
> To: user@uima.apache.org
> Subject: Re: UIMA Addons ConceptMapper - where to start
>
> Hi Debbie,
>
> On 2/28/2014 2:35 AM, Debbie Zhang wrote:
>> Hi all,
>>
>>
>>
>> I would like to learn how to use ConceptMapper in the UIMA Addons. So
>> far, what I have done was to add ConceptMapper jar file to my project
>> path and attach the doc jar file to the jar file. I have read through
>> the documentation came with the package. However, I still don't have
>> a clue how to use ConceptMapper in a Java program.
> Concept Mapper is a UIMA Annotator - you use it as a component within a UIMA
> Pipeline.
> There's a quick start for UIMA here:
> http://uima.apache.org/documentation.html#getting_started
>
> Hope that Helps! -Marshall
>
>> Can anyone point me to the
>> direction? A "Hello World" program would be greatly appreciated. Thank
> you.
>>
>>
>> Regards,
>>
>>
>>
>> Debbie
>>
>>
>
>
>
RE: UIMA Addons ConceptMapper - where to start
Posted by Debbie Zhang <de...@gmail.com>.
Thanks Marshall. I have no problem of following the UIMA getting_started
tutorial and have successfully created my own applications with my own
annotators. I think I should ask my question more specifically.
I created a new project called: ConceptMapperTest. I added UIMA nature to
the project. I copied every files under desc and resources folders in the
downloaded package to the desc and resources folders in the
ConceptMapperTest project. 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/analysis_engi
ne/primitive
/ConceptMapperOffsetTokenizer.xml)
Therefore, I created all subfolders org/apache/uima/conceptMapper under
desc, and then put all xml files to there. However, I still have the above
error when I try to open ConceptMapperOffsetTokenizer.xml and
OffsetTokenizerMatcher.xml files with "Component Descriptor Editor".
Would you please let me know what I did wrong? Thank you very much for your
help!
Regards,
Debbie
-----Original Message-----
From: Marshall Schor [mailto:msa@schor.com]
Sent: Sunday, 2 March 2014 2:30 AM
To: user@uima.apache.org
Subject: Re: UIMA Addons ConceptMapper - where to start
Hi Debbie,
On 2/28/2014 2:35 AM, Debbie Zhang wrote:
> Hi all,
>
>
>
> I would like to learn how to use ConceptMapper in the UIMA Addons. So
> far, what I have done was to add ConceptMapper jar file to my project
> path and attach the doc jar file to the jar file. I have read through
> the documentation came with the package. However, I still don't have
> a clue how to use ConceptMapper in a Java program.
Concept Mapper is a UIMA Annotator - you use it as a component within a UIMA
Pipeline.
There's a quick start for UIMA here:
http://uima.apache.org/documentation.html#getting_started
Hope that Helps! -Marshall
> Can anyone point me to the
> direction? A "Hello World" program would be greatly appreciated. Thank
you.
>
>
>
> Regards,
>
>
>
> Debbie
>
>