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From Eric Riebling <e...@cs.cmu.edu>
Subject Re: Getting annotations from CASes 'external' to a pipeline
Date Fri, 16 Mar 2012 18:12:14 GMT
I found out some more about what's going on.  In my pipeline,
for whatever reason, getEmpty(J)Cas() is producing CASes that
have only the base UIMA Types.  No user-defined types are showing
up.  This is not the defined behavior; it should be producing CASes
that have the merged typesystems of the outermost containing
Components.  And there's a lot of them.

I verified that getEmptyCas() does the right thing when in a simple
CPE using tutorial type system and annotators.  So the 'real problem'
is what is weird about the environmental setup of the pipline such
that getEmptyCas() isn't finding the typesystem.

So now I'm debugging what it is about this environment that's different,
that makes getEmptyCas() produce CASes with no user defined types, when
it correctly does so in other environments.

On 3/15/2012 6:50 PM, Eddie Epstein wrote:
> My last note was incorrect. Here is a paraphrase of working code:
>
>    public AbstractCas next() throws AnalysisEngineProcessException {
>      CAS aCAS = getEmptyCAS();
>      try {
>        ByteArrayInputStream casIn = getNextXmiCas();
>        XmiCasDeserializer.deserialize(casIn, aCAS, true); //
> deserialize in a lenient fashion
>        return aCAS;
>      } catch (SAXException e) {
>        throw new AnalysisEngineProcessException(e);
>      } catch (IOException e) {
>        throw new AnalysisEngineProcessException(e);
>      }
> ...
>
>
> On Thu, Mar 15, 2012 at 5:59 PM, Marshall Schor<msa@schor.com>  wrote:
>>
>>
>> On 3/15/2012 4:38 PM, Eddie Epstein wrote:
>>>
>>> Cannot deserialize into a CAS from getEmptyCas().
>>
>> This is not right.  More information soon (ran out of time today). -Marshall
>>
>>> Must use a CAS from
>>> CasCreationUtils.createCas for deserialization, and then use casCopier
>>> to copy to the CAS from getEmptyCas().
>>>
>>> Pick the version of createCas that specifies a typesystem, and use the
>>> typesystem from the pipeline CAS (i.e. the one from getEmptyCas).
>>>
>>> On Thu, Mar 15, 2012 at 2:44 PM, Eric Riebling<er1k@cs.cmu.edu>    wrote:
>>>>
>>>> Thanks, guys.  This is getting me closer to the goal, and explains the
>>>> observed
>>>> behaviors.  Now I'm facing issues when implemented as a CAS Multiplier.
>>>>   I
>>>> try
>>>> creating a new CAS first with getEmptyJCas().
>>>>
>>>> Here are some various strategies and what resulted:
>>>>
>>>>   * create a deserializer with the typesystem from the AE (which
>>>>         includes types in the 'external' CAS to be deserialized)
>>>>   * ues it to deserialize into the empty CAS created with getEmptyJCas()
>>>>
>>>>   ->    The deserialized CAS for some reason has only the base TOP
>>>> typesystem
>>>>   ->    Trying to access an annotation from an index (that should be there)
>>>>     generates the "used in Java code,  but was not declared in the XML
>>>> type
>>>> descriptor"
>>>>         exception
>>>>
>>>>   * same as above, but use CasCopier to try and copy the type system
>>>>         (and everything else) from the CAS in the AE's process() method
>>>>           into the empty CAS
>>>>
>>>>   ->    Attempted to copy a FeatureStructure of type "(my type name)",
which
>>>> is
>>>> not defined in the type system of the destination CAS.
>>>>
>>>> It seems the ONLY way to obtain a CAS (empty or otherwise) that has the
>>>> type
>>>> system able
>>>> to accept the external CAS being deserialized is to use the very CAS
>>>> passed
>>>> into
>>>> the AE's process() method.  Doing so obviously mangles that CAS for the
>>>> rest
>>>> of
>>>> the pipeline.
>>>>
>>>>
>>>> On 3/15/2012 1:50 PM, Marshall Schor wrote:
>>>>>
>>>>>
>>>>> On 3/15/2012 10:38 AM, Eric Riebling wrote:
>>>>>>
>>>>>> I have a pipeline with it's own type system.
>>>>>> I also have deserialized, annotated CASes on disk with a different
type
>>>>>> system.
>>>>>> Suppose I want an Analysis Engine in the pipeline to read in the
>>>>>> deserialized
>>>>>> CASes in order to obtain annotations and 'do things with them'
>>>>>>
>>>>>> I understand some limitations in the UIMA framework prevent this,
but
>>>>>> could it be done by making the first type system include that of
the
>>>>>> CASes to deserialize?
>>>>>
>>>>> Yes, I think so.
>>>>>>
>>>>>>
>>>>>> Also, it would necessitate creating new CASes within the Analysis
>>>>>> Engine.
>>>>>> I could think of several approaches, and have tried some without
>>>>>> success:
>>>>>>
>>>>>> * Create a new, 'temporary' View in the AE's process() method, obtain
a
>>>>>> JCas, obtain it's CAS, and use that to store the deserialized CASes
>>>>>> (seems to mangle the original CAS and break downstream AEs in the
>>>>>> pipeline,
>>>>>> and seems to not be able to find any annotations in the deserialized
>>>>>> CAS)
>>>>>>
>>>>> This won't work. The deserialize method effectively "resets" the CAS
>>>>> before loading it.
>>>>> A view is not a new CAS; it is a new view of the same CAS.
>>>>>
>>>>>> * Use the CAS in the process() method to store the deserialized CASes
>>>>>> (also mangles the original CAS, breaks downstream AEs, but DOES
>>>>>> permit obtaining annotations from the deserialized CASes)
>>>>>
>>>>> Right, deserializing into an existing CAS resets it in flight.
>>>>>>
>>>>>>
>>>>>> * Make the Analysis Engine be a CAS Multiplier, and deserialize into
>>>>>> a CAS created with createEmtpyCas()
>>>>>> (I haven't tried this yet)
>>>>>
>>>>> Yes, this is the way to get a separate CAS instance to deserialize into.
>>>>> It's how Collection Readers do it.
>>>>> -Marshall
>>>>>>
>>>>>>
>>>>>> It's kind of a use case for a hybrid Component that behaves in some
>>>>>> ways
>>>>>> like
>>>>>> an AE (has a process() method), in some ways like XMI Collection
>>>>>> Reader,
>>>>>> and
>>>>>> in some ways like a CAS Multiplier.
>>>>>>
>>>>>> But it's a useful use case! It is also a very bizarre one becuase
you
>>>>>> could
>>>>>> almost think of it as a pipeline within a pipeline, which processes
a
>>>>>> set
>>>>>> of deserialized annotated XMI documents, within a pipeline that
>>>>>> processes
>>>>>> ...
>>>>>> in our case, a Question Answering system with question keyterms,
>>>>>> ranked lists of documents and answer candidates.
>>>>>>
>>
>

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