Hi Arron,
I'm sorry that didn't work. I normally run using a dozen different methods
depending upon my needs. No real silver bullet ...
The easiest way to run the fast clinical pipeline from a command line, is:
1. Check out trunk
2. Build with mvn package
you may need to specify -DskipTests
3. Unzip the appropriate zip for your system in ctakes-distribution/target/
On a command in the unzipped ctakes root directory, run:
bin/runClinicalPipeline –i inputDirectory –-xmiOut outputDirectory --user
umlsUsername --pass umlsPassword
Note the double dashes for --xmiOut --user and --pass. Yours truly gave a live
demo and forgot to double-dash :^)
Anyway, that will run the clinical pipeline on a directory tree of plaintext
files in the specified inputDirectory, and write an identical directory tree of
.xmi files in the outputDirectory. I haven't tested it for about a week, but
last I did it worked just fine.
On that note, thank you for pointing out that there is a problem going through
such a should-be-simple workflow. It is something that we should remedy before
the 3.2.3 release. If you notice any other hardships with the software please
let the community know.
Thanks,
Sean
-----Original Message-----
From: Arron Lacey [mailto:[email protected]]
Sent: Sunday, January 22, 2017 9:36 AM
To: [email protected]
Subject: RE: Cannot load XMIWriterCasConsumer.xml with CPE.sh
Thanks very much Sean. Didn't work unfortunately - but I am curious if you
don't personally use the CPE, how to you batch process documents?
I would like to just run the AggregatePlaintextFastUMLSProcessor.xml on all
files in a given directory - perhaps with *some* control over the output
filenames.
Thanks,
Arron.
On Fri, 20 Jan, 2017 at 4:38 PM, Finan, Sean <[email protected]>
wrote:
> Hi Arron Lacey,
>
> That particular cas consumer java class is a uimafit-paradigm
> implementation, and from my memory the CPE gui does not play well with
> Uimafit. I could be wrong - I never use the cpe anymore.
>
> You might be able to get things working by changing line #23 in the
> .xml file from
>
> <implementationName>org.apache.ctakes.core.cc.XmiWriterCasConsumerCtak
> es</implementationName>
>
> To
> <implementationName>org.apache.uima.tools.components.XmiWriterCasConsu
> mer</implementationName>
>
> As far as I know the ctakes version is the same as the uima version
> but with better output file naming and a uimafit framing.
>
> Again, I'm not certain that the problem is cpe : uimafit
> incompatibility. If somebody else out there knows better then please
> speak up.
>
> Good luck,
> Sean
>
> -----Original Message-----
> From: Arron Lacey [mailto:[email protected]]
> Sent: Friday, January 20, 2017 11:13 AM
> To: [email protected]
> Subject: Cannot load XMIWriterCasConsumer.xml with CPE.sh
>
> Hi - I am trying to use the CPI to output results using the CAS
> Consumer: __XmiWriterCasConsumer.xml
>
>
> but here is the error message I am getting:
>
>> org.apache.uima.resource.ResourceInitializationException
>> CausedBy: org.apache.uima.resource.ResourceConfigurationException
>> CausedBy: java.lang.Exception: The component XMI Writer CAS Consumer
>> cannot be created (Thread name: Thread-4)
>
> My setup is using:
>
> Collection Reader
>>
>> desc/ctakes-core/desc/collection_reader/FilesInDirectoryCollectionRea
>> der.xml
>
> Analysis Engine
>>
>> desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintext
>> FastUMLSProcessor.xml
>
> CAS Consumer
>> desc/ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml
>
> I can get the normal XML writer to work, so I would like to ask what I
> need to do to my pipeline to use the XMI Writer?
>
> Thanks very much,
>
> Arron Lacey.
