Never mind! I see I have to build from source. Greg--
On Sun, Sep 29, 2019 at 10:44 AM Greg Silverman <[email protected]> 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 <[email protected]> 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 < >> [email protected]> 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 <[email protected]> >>> Sent: Tuesday, September 24, 2019 6:47 PM >>> To: [email protected] >>> 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 >>> [email protected] >>> >>> › evaluate-it.org ‹ >>> >> >> >> -- >> Greg M. Silverman >> Senior Systems Developer >> NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group> >> Department of Surgery >> University of Minnesota >> [email protected] >> >> › evaluate-it.org ‹ >> > > > -- > Greg M. Silverman > Senior Systems Developer > NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group> > Department of Surgery > University of Minnesota > [email protected] > > › evaluate-it.org ‹ > -- Greg M. Silverman Senior Systems Developer NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group> Department of Surgery University of Minnesota [email protected] › evaluate-it.org ‹
