Trying to do the maven build and getting the following error: "You're not
authorized to execute any SonarQube analysis. Please contact your SonarQube
administrator."
Please advise. I'm under a pretty tight time line to get these files
processed.
Thanks!
Greg--
On Sun, Sep 29, 2019 at 10:56 AM Greg Silverman <g...@umn.edu> wrote:
> Never mind! I see I have to build from source.
>
> Greg--
>
> On Sun, Sep 29, 2019 at 10:44 AM Greg Silverman <g...@umn.edu> wrote:
>
>> Hi Sean,
>> I just ran another set of notes through cTAKES and noticed the following
>> error:
>>
>> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
>> %5p %c{1} - %m%n].
>> log4j: Adding appender named [consoleAppender] to category [root].
>> 29 Sep 2019 15:31:21 ERROR PiperFileReader - Piper File not found:
>> WindowedAttributeCleartkSubPipe
>>
>> Is something missing? This is how my DefaultFastPipeline.piper file looks
>> (NB: I also tried load WindowedAttributeCleartkSubPipe.piper, with similar
>> results)
>>
>> // Commands and parameters to create a default plaintext document
>> processing pipeline with UMLS lookup
>>
>> // Load a simple token processing pipeline from another pipeline file
>> load DefaultTokenizerPipeline.piper
>>
>> // Add non-core annotators
>> add ContextDependentTokenizerAnnotator
>> addDescription POSTagger
>>
>> // Add Chunkers
>> load ChunkerSubPipe.piper
>>
>> // Default fast dictionary lookup
>> add DefaultJCasTermAnnotator
>>
>> // Add Cleartk Entity Attribute annotators
>> // see https://issues.apache.org/jira/browse/CTAKES-449
>> //load AttributeCleartkSubPipe.piper
>> load WindowedAttributeCleartkSubPipe
>>
>>
>> All files seem to have been processed fine, but wondering if something
>> was missed, due to the error. If so, how do I construct the
>> WindowedAttributeCleartkSubPipe.piper file?
>>
>> Thanks very much in advance!
>>
>> Greg--
>>
>>
>> On Tue, Sep 24, 2019 at 7:27 PM Greg Silverman <g...@umn.edu> wrote:
>>
>>> Sweet! That was definitely it! It's flying now (granted, our files are
>>> not in the > 1 mb realm, like it the jira issue - just in the nnn.kb realm,
>>> but still!).
>>>
>>> Mahalo nui loa!
>>>
>>>
>>>
>>> On Tue, Sep 24, 2019 at 6:29 PM Finan, Sean <
>>> sean.fi...@childrens.harvard.edu> wrote:
>>>
>>>> Hi Greg,
>>>>
>>>> Check your log to see what component is taking all the time.
>>>>
>>>> There is a known problem with the cleartk assertion annotators:
>>>>
>>>> https://issues.apache.org/jira/browse/CTAKES-449
>>>>
>>>> A partial fix was made in the "windowed" sub-package of
>>>> ctakes-assertion: org.apache.ctakes.assertion.medfacts.cleartk.windowed.
>>>>
>>>> Each of the normal assertion engines has a replacement in the windowed
>>>> package.
>>>>
>>>> If you are using a piper file that contains "load
>>>> AttributeCleartkSubPipe" as the Default clinical pipeline does, just
>>>> replace it with "load WindowedAttributeCleartkSubPipe".
>>>>
>>>> It isn't a full fix for the problem, and I don't know if it will make
>>>> your processing faster, but you can give it a try.
>>>>
>>>> Sean
>>>>
>>>> ________________________________________
>>>> From: Greg Silverman <g...@umn.edu>
>>>> Sent: Tuesday, September 24, 2019 6:47 PM
>>>> To: dev@ctakes.apache.org
>>>> Subject: Large files taking forever to process [EXTERNAL]
>>>>
>>>> Any suggestions on how to speed up processing large clinical text notes
>>>> approaching 13K lines? This is a very old corpus culled from EPIC notes
>>>> back in 2009. I thought about splitting the notes into smaller chunks,
>>>> but
>>>> then I would have to deal with the offsets when analyzing system output
>>>> against manual annotations that had been done.
>>>>
>>>> As is, I've tried different garbage collection options (this seemed to
>>>> have
>>>> worked well with CLAMP on the same set of notes).
>>>>
>>>> TIA!
>>>>
>>>> Greg--
>>>>
>>>> --
>>>> Greg M. Silverman
>>>> Senior Systems Developer
>>>> NLP/IE <
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__healthinformatics.umn.edu_research_nlpie-2Dgroup&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=kVCVyGR2m-zb7CsPmrrCeBL1N-9Z6tXZOp869xqkcBQ&s=TEirYUPMXTOjZ1PoJMxTXt7M8I5axwQI9zzNrvLmGRo&e=
>>>> >
>>>> Department of Surgery
>>>> University of Minnesota
>>>> g...@umn.edu
>>>>
>>>> › evaluate-it.org ‹
>>>>
>>>
>>>
>>> --
>>> Greg M. Silverman
>>> Senior Systems Developer
>>> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
>>> Department of Surgery
>>> University of Minnesota
>>> g...@umn.edu
>>>
>>> › evaluate-it.org ‹
>>>
>>
>>
>> --
>> Greg M. Silverman
>> Senior Systems Developer
>> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
>> Department of Surgery
>> University of Minnesota
>> g...@umn.edu
>>
>> › evaluate-it.org ‹
>>
>
>
> --
> Greg M. Silverman
> Senior Systems Developer
> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
> Department of Surgery
> University of Minnesota
> g...@umn.edu
>
> › evaluate-it.org ‹
>
--
Greg M. Silverman
Senior Systems Developer
NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group>
Department of Surgery
University of Minnesota
g...@umn.edu
› evaluate-it.org ‹
