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https://issues.apache.org/jira/browse/TIKA-1645?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14574545#comment-14574545
]
Chris A. Mattmann commented on TIKA-1645:
-----------------------------------------
OK I got this working by downloading cTAKES 3.2.2.
{noformat}
bash-3.2$ java -classpath
tika-app/target/tika-app-1.10-SNAPSHOT.jar:${CTAKES_HOME}/desc:${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/\*:./config
org.apache.tika.cli.TikaCLI --config=tika-config.xml -m
/Users/mattmann/Downloads/Vose-2013-American_Journal_of_Hematology.pdf
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in
[jar:file:/Users/mattmann/tmp/tika1.9/tika-app/target/tika-app-1.10-SNAPSHOT.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/usr/local/apache-ctakes-3.2.2/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
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].
04 Jun 2015 23:12:40 INFO ClearNLPDependencyParserAE - using Morphy analysis?
true
Loading configuration.
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04 Jun 2015 23:12:50 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
04 Jun 2015 23:12:50 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
04 Jun 2015 23:12:50 INFO ConstituencyParser - Initializing parser...
04 Jun 2015 23:12:52 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
04 Jun 2015 23:12:52 INFO StatusContextAnalyzer - initBoundaryData() called
for ContextInitializer
04 Jun 2015 23:12:52 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
04 Jun 2015 23:12:52 INFO NegationContextAnalyzer - initBoundaryData() called
for ContextInitializer
04 Jun 2015 23:12:53 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
04 Jun 2015 23:12:55 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
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04 Jun 2015 23:12:57 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
04 Jun 2015 23:12:59 INFO JdbcConnectionResourceImpl - Connection established
to: jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/umls
04 Jun 2015 23:12:59 INFO JdbcConnectionResourceImpl - Connection established
to: jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls
04 Jun 2015 23:12:59 INFO JdbcConnectionResourceImpl - Connection established
to: jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls
04 Jun 2015 23:12:59 INFO UmlsDictionaryLookupAnnotator - Parsing descriptor:
/usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
04 Jun 2015 23:12:59 INFO FirstTokenPermLookupInitializerImpl - Exclusion
tagset loaded: [dt, to, rp, ls, pos, md, vbd, vbg, vb, ex, vbp, vbn, pdt, vbz,
wp, wrb, in, wps, pp$, prp$, wdt, prp, pp, cc, cd]
04 Jun 2015 23:12:59 INFO FirstTokenPermLookupInitializerImpl - Exclusion
tagset loaded: [to, dt, rp, ex, vbp, ls, vbn, pdt, wp, vbz, wrb, in, pos, wps,
md, wdt, pp$, vbd, vb, vbg, pp, cc, cd]
04 Jun 2015 23:12:59 INFO UmlsDictionaryLookupAnnotator - Using
ctakes.umlsaddr: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser:
chrismattmann
04 Jun 2015 23:13:00 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
/usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
04 Jun 2015 23:13:00 INFO LvgCmdApiResourceImpl - config file absolute path
=
/usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties
04 Jun 2015 23:13:00 INFO LvgCmdApiResourceImpl - cwd =
/Users/mattmann/tmp/tika1.9
04 Jun 2015 23:13:00 INFO LvgCmdApiResourceImpl - cd
/usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/
04 Jun 2015 23:13:01 INFO LvgCmdApiResourceImpl - cd
/Users/mattmann/tmp/tika1.9
04 Jun 2015 23:13:01 INFO SentenceDetector - Starting processing.
04 Jun 2015 23:13:01 INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
04 Jun 2015 23:13:01 INFO LvgAnnotator - process(JCas)
04 Jun 2015 23:13:05 INFO ContextDependentTokenizerAnnotator - process(JCas)
04 Jun 2015 23:13:07 INFO POSTagger - process(JCas)
04 Jun 2015 23:13:08 INFO Chunker - process(JCas)
04 Jun 2015 23:13:09 INFO ChunkAdjuster - process(JCas)
04 Jun 2015 23:13:09 INFO ChunkAdjuster - process(JCas)
04 Jun 2015 23:13:09 INFO CopyAnnotator - process(JCas)
04 Jun 2015 23:13:09 INFO OverlapAnnotator - process(JCas)
04 Jun 2015 23:13:09 INFO UmlsDictionaryLookupAnnotator - process(JCas)
04 Jun 2015 23:13:54 INFO MaxentParserWrapper - Started processing: null
Couldn't find parse for: � Claim your Certificate.This activity will be
available for CME credit for twelvemonths following its launch date.
Couldn't find parse for: Asymptomatic elderly or low-MIPI patients can be
observed without any therapy.When the patients become symptomatic, first line
therapychoices include R-CHOP (6 rituximab maintenance), R-Bendamustine, or a
clinical trial.Initial management of a young symptomatic patientSeveral studies
have suggested that aggressive thera-pies in younger patients with MCL may
improve the out-comes.
04 Jun 2015 23:14:30 INFO MaxentParserWrapper - Done parsing: null
Content-Length: 457115
Content-Type: application/pdf
Creation-Date: 2013-11-20T13:24:11Z
Last-Modified: 2013-11-22T14:13:25Z
Last-Save-Date: 2013-11-22T14:13:25Z
WPS-ARTICLEDOI: 10.1002/ajh.23615
WPS-JOURNALDOI: 10.1002/(ISSN)1096-8652
WPS-PROCLEVEL: 2
X-Parsed-By: org.apache.tika.parser.CompositeParser
X-Parsed-By: org.apache.tika.parser.ctakes.CTAKESParser
X-Parsed-By: org.apache.tika.parser.DefaultParser
X-Parsed-By: org.apache.tika.parser.pdf.PDFParser
access_permission:assemble_document: true
access_permission:can_modify: true
access_permission:can_print: true
access_permission:can_print_degraded: true
access_permission:extract_content: true
access_permission:extract_for_accessibility: true
access_permission:fill_in_form: true
access_permission:modify_annotations: true
created: Wed Nov 20 05:24:11 PST 2013
ctakes:AnatomicalSiteMention: Cell:189:193:C0007634,C1269647
ctakes:AnatomicalSiteMention: Media:432:437:C0162867
ctakes:AnatomicalSiteMention: Media:593:598:C0162867
..
{noformat}
I also made it work for PDF by adding application/pdf to the tika-config.xml.
Great work Giuseppe.With a unit test, this would be perfect to commit!
> Extraction of biomedical information using CTAKESParser
> -------------------------------------------------------
>
> Key: TIKA-1645
> URL: https://issues.apache.org/jira/browse/TIKA-1645
> Project: Tika
> Issue Type: Improvement
> Components: parser
> Reporter: Giuseppe Totaro
> Assignee: Giuseppe Totaro
> Labels: patch
> Fix For: 1.10
>
> Attachments: CTAKESConfig.properties, TIKA-1645.patch,
> TIKA-1645.v02.patch, tika-config.xml
>
>
> As mentioned in [TIKA-1642|https://issues.apache.org/jira/browse/TIKA-1642],
> [CTAKESContentHandler|https://github.com/giuseppetotaro/CTAKESContentHadler]
> is a preliminary work in order to integrate [Apache
> cTAKES|http://ctakes.apache.org/] into Tika allowing users to extract
> biomedical information from clinical text.
> Essentially, this work includes a wrapper for CAS serializers that aim at
> dumping out the identified annotations into XML-based formats.
> You can find in attachment a new patch that includes the CTAKESParser, a new
> parser that decorates the AutoDetectParser and relies on a new version of
> CTAKESContentHandler, based on feedback from
> [TIKA-1642|https://issues.apache.org/jira/browse/TIKA-1642]. This parser
> generates the same output of AutoDetectParser and, in addition, the metadata
> containing the identified clinical annotations detected by cTAKES.
> To perform a cTAKES AnalysisEngine by using Tika CTAKESParser, you need first
> to install the last stable release of cTAKES (3.2.2), following the
> instructions on [User Install
> Guide|https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide].
> Then, you can launch Tika as follows:
> {noformat}
> CTAKES_HOME=/usr/local/apache-ctakes-3.2.2
> java -cp
> tika-app-1.10-SNAPSHOT.jar:${CTAKES_HOME}/desc:${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/*:/path/to/CTAKESConfig
> org.apache.tika.cli.TikaCLI --config=/path/to/tika-config.xml /path/to/input
> {noformat}
> In the example above, {{/path/to/CTAKESConfig}} is the parent directory of
> file {{org/apache/tika/parser/ctakes/CTAKESConfig.properties}} that contains
> the configuration properties to build the cTAKES AnalysisEngine;
> {{tika-config.xml}} is a custom configuration file for Tika that contains the
> mimetypes whose CTAKESParser will perform parsing.
> You can find in attachment an example of both {{CTAKESConfig.properties}} and
> {{tika-config.xml}} to parse ISA-Tab files using cTAKES.
> You need [UMLS credentials|https://uts.nlm.nih.gov/home.html] in order to use
> the UMLS-based components of cTAKES.
> I would really appreciate your feedback.
> Thanks [~selina], [~chrismattmann] and [~lewismc] for supporting me on this
> work.
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