Here's the final output (if I could just download cTAKES 4.0.1-SNAPSHOT
without having to do the build, that would be fantastic!):
[INFO]
------------------------------------------------------------------------
[INFO] Reactor Summary for Apache cTAKES 4.0.1-SNAPSHOT:
[INFO]
[INFO] Apache cTAKES ...................................... FAILURE [
12.169 s]
[INFO] ctakes-gui-res ..................................... SUCCESS [
3.663 s]
[INFO] Apache cTAKES Resources coreference ................ SUCCESS [
3.055 s]
[INFO] Apache cTAKES Resources temporal ................... SUCCESS [
0.587 s]
[INFO] Apache cTAKES Resources relation-extractor ......... SUCCESS [
0.305 s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res . SUCCESS [
8.437 s]
[INFO] Apache cTAKES Resources core ....................... SUCCESS [
0.362 s]
[INFO] Apache cTAKES common type system ................... SUCCESS [
6.588 s]
[INFO] Apache cTAKES utils ................................ SUCCESS [
1.639 s]
[INFO] Apache cTAKES core ................................. SUCCESS [
7.503 s]
[INFO] Apache cTAKES dictionary lookup fast ............... SUCCESS [
1.065 s]
[INFO] Apache cTAKES document preprocessor ................ SUCCESS [
0.818 s]
[INFO] Apache cTAKES Resources lvg ........................ SUCCESS [01:01
min]
[INFO] Apache cTAKES LVG lexical tools .................... SUCCESS [
2.721 s]
[INFO] Apache cTAKES Resources ne-contexts ................ SUCCESS [
0.223 s]
[INFO] Apache cTAKES named entity contexts ................ SUCCESS [
1.535 s]
[INFO] Apache cTAKES Resources assertion .................. SUCCESS [
1.456 s]
[INFO] Apache cTAKES Resources constituency-parser ........ SUCCESS [
2.099 s]
[INFO] Apache cTAKES Constituency Parser .................. SUCCESS [
0.793 s]
[INFO] Apache cTAKES Resources dependency-parser .......... SUCCESS [
12.839 s]
[INFO] Apache cTAKES Resources pos-tagger ................. SUCCESS [
0.750 s]
[INFO] Apache cTAKES part-of-speech tagger ................ SUCCESS [
2.531 s]
[INFO] Apache cTAKES Dependency Parser .................... SUCCESS [
20.299 s]
[INFO] Apache cTAKES context dependent tokenizer .......... SUCCESS [
1.531 s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ......... SUCCESS [
0.730 s]
[INFO] Apache cTAKES chunker .............................. SUCCESS [
0.710 s]
[INFO] Apache cTAKES Assertion ............................ SUCCESS [
3.114 s]
[INFO] ctakes-clinical-pipeline-res ....................... SUCCESS [
0.307 s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............. SUCCESS [
0.674 s]
[INFO] Apache cTAKES Relation Extractor ................... SUCCESS [
2.564 s]
[INFO] Apache cTAKES Temporal Information Extraction ...... SUCCESS [01:11
min]
[INFO] Apache cTAKES CoReference Resolver ................. SUCCESS [
2.282 s]
[INFO] ctakes-gui ......................................... SUCCESS [
1.681 s]
[INFO] Apache cTAKES fhir support ......................... SUCCESS [
10.391 s]
[INFO] Apache cTAKES Resources dictionary-lookup .......... SUCCESS [
41.824 s]
[INFO] Apache cTAKES dictionary lookup .................... SUCCESS [
0.633 s]
[INFO] Apache cTAKES Resources drug-ner ................... SUCCESS [
0.239 s]
[INFO] Apache cTAKES Drug NER ............................. SUCCESS [
0.898 s]
[INFO] Apache cTAKES Resources side-effect ................ SUCCESS [
0.257 s]
[INFO] Apache cTAKES Side Effects ......................... SUCCESS [
0.549 s]
[INFO] Apache cTAKES Resources smoking-status ............. SUCCESS [
0.263 s]
[INFO] Apache cTAKES Smoking Status ....................... SUCCESS [
0.583 s]
[INFO] Apache cTAKES Resources assertion-zoner ............ SUCCESS [
0.271 s]
[INFO] Apache cTAKES Assertion's zoner .................... SUCCESS [
0.633 s]
[INFO] ctakes-examples-res ................................ SUCCESS [
0.374 s]
[INFO] ctakes-examples .................................... SUCCESS [
0.582 s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ............ SUCCESS [
0.317 s]
[INFO] Apache cTAKES YTEX ................................. SUCCESS [
56.133 s]
[INFO] Apache cTAKES YTEX UIMA ............................ SUCCESS [
53.047 s]
[INFO] Apache cTAKES YTEX Web ............................. SUCCESS [
46.687 s]
[INFO] Apache cTAKES Distribution ......................... SUCCESS [02:00
min]
[INFO] Apache cTAKES Regression-test ...................... SUCCESS [
2.254 s]
[INFO] Apache cTAKES template filler ...................... SUCCESS [
0.749 s]
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 09:58 min
[INFO] Finished at: 2019-09-29T11:15:52-05:00
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal
org.sonarsource.scanner.maven:sonar-maven-plugin:3.6.1.1688:sonar
(default-cli) on project ctakes: You're not authorized to execute any
SonarQube analysis. Please contact your SonarQube administrator. -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute
goal org.sonarsource.scanner.maven:sonar-maven-plugin:3.6.1.1688:sonar
(default-cli) on project ctakes: You're not authorized to execute any
SonarQube analysis. Please contact your SonarQube administrator.
On Sun, Sep 29, 2019 at 11:18 AM 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 ‹
>
--
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 ‹
