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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: uimafit and cleartk upgrades
Date Thu, 18 Sep 2014 15:12:19 GMT
For Uimafit the biggest change is the namespace. There were also some
minor changes to method names of the factory methods for readers and
aes. The JCasIterable changed and now the JCasIterator is more like what
the JCasIterable used to be.

ConfigurationParameters now have mandatory=true by default. There were
one or two places where I had to specify mandatory=false to allow for
this to compile.

XWriter and XWriterFileNamer were removed. There is a new utility class
called CasIoUtil and there is also still a ctakes class called
XmiWriterCasConsumerCtakes. CasIoUtil is a simple standalone utility
class -- has methods that take an already processed JCas and a File to
write to. XmiWriterCasConsumerCtakes is a consumer that goes on the end
of a pipeline (similar to XWriter).

Anyone interested in more detail on these issues can check out this link
which I used to do the upgrade:

Cleartk changed many package names. The common feature interface
SimpleFeatureExtractor was changed to FeatureExtractor1 (meaning, takes
1 argument). There is also now FeatureExtractor2 which takes 2
arguments, suitable for things like relation classification.

Class names were standardized to prefer camel case conventions over
library naming conventions (LibSVM => LibSvm, LIBLINEAR => LibLinear).

There were some other similar things but I think those were the ones
that concerned ctakes the most.


On 09/18/2014 10:37 AM, Dligach, Dmitriy wrote:
> Tim, thank you very much for working on this upgrade. I know it was a pretty serious
> Question: were there any particular changes in uimafit/cleartk that we should be aware
of? Any major deviation from the way we typically used uimafit/cleartk?
> Dima
> On Sep 16, 2014, at 15:02, Miller, Timothy <Timothy.Miller@childrens.harvard.edu>
>> This mega-revision is now checked in. Jenkins will let me know if there
>> are any major issues with compiling, but please feedback to the list if
>> there is anything more subtle that was a mistake and we can try to work
>> through it.
>> Thanks
>> Tim
>> On 09/11/2014 03:41 PM, Miller, Timothy wrote:
>>> Just wanted to send a heads up to the list/community that I am working
>>> on upgrading ctakes to use most recent versions of Uimafit (2.1) and
>>> Cleartk (2.0). This will allow us to keep up with namespace changes in
>>> uimafit and new machine learning methods being used in cleartk (that we
>>> are also contributing to). However, this will entail a lot of small
>>> changes across the codebase, so I thought it would be good to give a bit
>>> of a warning. Specifically if anyone else has any large unchecked-in
>>> changes to the code svn may throw some conflicts at you.
>>> Tim

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