using multiple PEAR components in dynamically built pipelines

["Chavan, Girish" <ch...@upmc.edu>]

Hi All,

I am trying to build a system where users will be able to build
pipelines using any of the installed PEAR components and then save them
for later use. From searching the mailing lists it has become apparent
that you can use a PEAR component as an analysis engine. 

Now, Looking at the SimpleRunCPE.java, and SimpleRunCPM.java code I can
come up with two strategies to do this...

Strategy 1: Create a CPE descriptor file based on the user selections of
the PEAR components to be used and then build a CPE using the CPE
descriptor similar to how it is done in SimpleRunCPE. 

My question here is, can you specify a PEAR component descriptor file as
a CasProcessor in the CPE descriptor file?

Strategy 2: Create an Aggregate Analysis Engine descriptor that has the
user selected PEAR components. Then specify that as the Analysis Engine,
similar to how it is done in the SimpleRunCPM..java code.

Again, can I use the PEAR descriptor file in the same fashion as I would
use a TAE descriptor file in an Aggregate AE descriptor?

Another alternative is to build the CPE programmatically, and add the
PEAR components as CasProcessors programmatically. Basically do what the
SImpleRunCPE might be doing behind the curtain
(UIMAFramework.produceCollectionProcessingEngine() is a good place to
look I presume)

However the first two strategies are preferable as I would like the
ability for users to build these pipelines in one session and then load
and run them later in another session. For that I need to persist their
selections in some form, and Id rather use a standard CPE descriptor or
Aggregate AE descriptor file rather than introduce my own xml format.

I hope I could put my point across clearly. Is anyone doing anything
similar? Has anyone used multiple PEAR components in the same pipeline? 

Any help would be much appreciated.

Kind Regards,

Girish Chavan
Dept. of Biomedical Informatics,
University of Pittsburgh

Re: using multiple PEAR components in dynamically built pipelines

[Michael Baessler <mb...@michael-baessler.de>]

It is also possible to use a pear descriptor as a CasProcessor 
descriptor in a CPE.

-- Michael

Marshall Schor wrote:
> Hi Girish -
>
> As I recall, you can only use a pear descriptor as a delegate of a 
> containing aggregate.  The person who knows the most about this is 
> away this week, so probably the definitive answer will come next week :-)
>
> -Marshall
>
> Chavan, Girish wrote:
>> Hi All,
>>
>> I am trying to build a system where users will be able to build
>> pipelines using any of the installed PEAR components and then save them
>> for later use. From searching the mailing lists it has become apparent
>> that you can use a PEAR component as an analysis engine.
>> Now, Looking at the SimpleRunCPE.java, and SimpleRunCPM.java code I can
>> come up with two strategies to do this...
>>
>> Strategy 1: Create a CPE descriptor file based on the user selections of
>> the PEAR components to be used and then build a CPE using the CPE
>> descriptor similar to how it is done in SimpleRunCPE.
>> My question here is, can you specify a PEAR component descriptor file as
>> a CasProcessor in the CPE descriptor file?
>>
>> Strategy 2: Create an Aggregate Analysis Engine descriptor that has the
>> user selected PEAR components. Then specify that as the Analysis Engine,
>> similar to how it is done in the SimpleRunCPM..java code.
>>
>> Again, can I use the PEAR descriptor file in the same fashion as I would
>> use a TAE descriptor file in an Aggregate AE descriptor?
>>
>> Another alternative is to build the CPE programmatically, and add the
>> PEAR components as CasProcessors programmatically. Basically do what the
>> SImpleRunCPE might be doing behind the curtain
>> (UIMAFramework.produceCollectionProcessingEngine() is a good place to
>> look I presume)
>>
>> However the first two strategies are preferable as I would like the
>> ability for users to build these pipelines in one session and then load
>> and run them later in another session. For that I need to persist their
>> selections in some form, and Id rather use a standard CPE descriptor or
>> Aggregate AE descriptor file rather than introduce my own xml format.
>>
>> I hope I could put my point across clearly. Is anyone doing anything
>> similar? Has anyone used multiple PEAR components in the same pipeline?
>> Any help would be much appreciated.
>>
>> Kind Regards,
>>
>> Girish Chavan
>> Dept. of Biomedical Informatics,
>> University of Pittsburgh
>>
>>
>>
>>   
>

Re: using multiple PEAR components in dynamically built pipelines

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

Hi Girish -

As I recall, you can only use a pear descriptor as a delegate of a 
containing aggregate.  The person who knows the most about this is away 
this week, so probably the definitive answer will come next week :-)

-Marshall

Chavan, Girish wrote:
> Hi All,
>
> I am trying to build a system where users will be able to build
> pipelines using any of the installed PEAR components and then save them
> for later use. From searching the mailing lists it has become apparent
> that you can use a PEAR component as an analysis engine. 
>
> Now, Looking at the SimpleRunCPE.java, and SimpleRunCPM.java code I can
> come up with two strategies to do this...
>
> Strategy 1: Create a CPE descriptor file based on the user selections of
> the PEAR components to be used and then build a CPE using the CPE
> descriptor similar to how it is done in SimpleRunCPE. 
>
> My question here is, can you specify a PEAR component descriptor file as
> a CasProcessor in the CPE descriptor file?
>
> Strategy 2: Create an Aggregate Analysis Engine descriptor that has the
> user selected PEAR components. Then specify that as the Analysis Engine,
> similar to how it is done in the SimpleRunCPM..java code.
>
> Again, can I use the PEAR descriptor file in the same fashion as I would
> use a TAE descriptor file in an Aggregate AE descriptor?
>
> Another alternative is to build the CPE programmatically, and add the
> PEAR components as CasProcessors programmatically. Basically do what the
> SImpleRunCPE might be doing behind the curtain
> (UIMAFramework.produceCollectionProcessingEngine() is a good place to
> look I presume)
>
> However the first two strategies are preferable as I would like the
> ability for users to build these pipelines in one session and then load
> and run them later in another session. For that I need to persist their
> selections in some form, and Id rather use a standard CPE descriptor or
> Aggregate AE descriptor file rather than introduce my own xml format.
>
> I hope I could put my point across clearly. Is anyone doing anything
> similar? Has anyone used multiple PEAR components in the same pipeline? 
>
> Any help would be much appreciated.
>
> Kind Regards,
>
> Girish Chavan
> Dept. of Biomedical Informatics,
> University of Pittsburgh
>
>
>
>