Hi Greg, Can you check you pom.xml and see if you have enabled any
sonarqube related profile Iin build?
On Sunday, September 29, 2019, Greg Silverman <g...@umn.edu> wrote:
> 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 ‹
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
