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https://issues.apache.org/jira/browse/TIKA-1645?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14573782#comment-14573782
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Chris A. Mattmann commented on TIKA-1645:
-----------------------------------------
Hey Giuseppe:
I tried out your latest patch. It didn't seem to work maybe there is something
I'm doing wrong here.
{noformat}
[chipotle:~/tmp/tika1.9] mattmann% java -classpath
tika-app/target/tika-app-1.10-SNAPSHOT.jar:${CTAKES_HOME}/desc:${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/\*:.
org.apache.tika.cli.TikaCLI --config=tika-config.xml -m
gist5a56f8815bbb7374fddd-069bf364fb0a178a9321cc67b6e14b38d80c2446/i_Investigation.txt
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-3.2.1/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: 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].
Content-Length: 8128
Content-Type: application/x-isatab-investigation
X-Parsed-By: org.apache.tika.parser.EmptyParser
resourceName: i_Investigation.txt
{noformat}
I'm using your tika-config.xml attached to this issue. I changed the
CTAKESConfig.properties to look like:
{noformat}
aeDescriptorPath=/usr/local/apache-ctakes-3.2.1/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
text=false
annotationProps=BEGIN,END,ONTOLOGY_CONCEPT_ARR
separatorChar=:
metadata=Study Title,Study Description
UMLSUser=<OMITTED>
UMLPass=<OMITTED>
{noformat}
I downloaded:
https://gist.github.com/5a56f8815bbb7374fddd/download
Per your instructions offline, and then tried the above command to parse. Any
idea?
My $CTAKES_HOME is:
{noformat}
[chipotle:~/tmp/tika1.9] mattmann% echo $CTAKES_HOME
/usr/local/apache-ctakes-3.2.1
[chipotle:~/tmp/tika1.9] mattmann% ls $CTAKES_HOME
LICENSE NOTICE README RELEASE_NOTES.html
bin/ config/ desc/ lib/
resources/
[chipotle:~/tmp/tika1.9] mattmann%
{noformat}
I am using Apache cTAKES 3.2.1.
I also noticed the * jar classpath include didn't work for me it gives me this
error:
{noformat}
[chipotle:~/tmp/tika1.9] mattmann% java -cp
tika-app/target/tika-app-1.10-SNAPSHOT.jar:${CTAKES_HOME}/desc:${CTAKES_HOME}/resources:${CTAKES_HOME}/lib/*
org.apache.tika.cli.TikaCLI
java: No match.
{noformat}
> 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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