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Posted to commits@ctakes.apache.org by ga...@apache.org on 2018/10/31 11:04:01 UTC
svn commit: r1845321 [26/42] - in /ctakes/trunk/ctakes-web-rest: ./ src/
src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/
src/main/java/org/apache/ctakes/ src/main/java/org/apache/ctakes/rest/
src/main/java/org/apache/ctakes/rest/f...
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml?rev=1845321&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml Wed Oct 31 11:03:43 2018
@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.coreference.types.TypeSystem</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <imports>
+ <import location="Pair.xml"/>
+ <import location="BooleanLabeledFS.xml"/>
+ </imports>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.Markable</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>content</name>
+ <description>The markable instance, i.e., a Named Entity, pronoun Token, etc.</description>
+ <rangeTypeName>uima.tcas.Annotation</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>id</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>anaphoric_prob</name>
+ <description/>
+ <rangeTypeName>uima.cas.Double</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.PronounMarkable</name>
+ <description/>
+ <supertypeName>org.apache.ctakes.coreference.type.Markable</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.NEMarkable</name>
+ <description/>
+ <supertypeName>org.apache.ctakes.coreference.type.Markable</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.DemMarkable</name>
+ <description/>
+ <supertypeName>org.apache.ctakes.coreference.type.Markable</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.MarkablePair</name>
+ <description/>
+ <supertypeName>uima.cas.TOP</supertypeName>
+ <features>
+ <featureDescription>
+ <name>antecedent</name>
+ <description>Proposed antecedent</description>
+ <rangeTypeName>org.apache.ctakes.coreference.type.Markable</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>anaphor</name>
+ <description/>
+ <rangeTypeName>org.apache.ctakes.coreference.type.Markable</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>label</name>
+ <description>Is this pair coreferent?</description>
+ <rangeTypeName>uima.cas.Boolean</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.MarkablePairSet</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>anaphor</name>
+ <description/>
+ <rangeTypeName>org.apache.ctakes.coreference.type.Markable</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>antecedentList</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSList</rangeTypeName>
+ <elementType>org.chboston.cnlp.ctakes.common.BooleanLabeledFS</elementType>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml?rev=1845321&view=auto
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--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml Wed Oct 31 11:03:43 2018
@@ -0,0 +1,88 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>VecInst</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.VecInstance</name>
+ <description/>
+ <supertypeName>uima.cas.TOP</supertypeName>
+ <features>
+ <featureDescription>
+ <name>vector</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>a1</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>a2</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>offset1</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>offset2</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>classifier</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.coreference.type.AnaphoricityVecInstance</name>
+ <description/>
+ <supertypeName>uima.cas.TOP</supertypeName>
+ <features>
+ <featureDescription>
+ <name>vector</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>m</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>offset</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/dependency/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/dependency/README?rev=1845321&view=auto
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--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/dependency/README (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/dependency/README Wed Oct 31 11:03:43 2018
@@ -0,0 +1,26 @@
+#################
+additional models
+#################
+
+There is an additional model available from the ClearTK downloads page:
+
+https://code.google.com/p/clearnlp/
+
+and is called mayo-en-dep-1.3.0.jar. This model is built from
+both the training data and development data from the CoNLL 2009 shared task (see
+links above). This model was provided by Jinho Choi.
+
+#####
+Notes
+#####
+
+- Both models were trained using PennTreebank part-of-speech tags. So, your input part-of-speech
+tags should match the tags used for training this model. The part-of-speech tag for punctuation
+symbols such as "." "," ":" ";" "(" ")" etc. are the symbols themselves (i.e. the part-of-speech tag
+for the token ")" should be ")".) This may be inconsistent with other PTB-derived tagging schemes that
+may use tags such as "COLON" or "RRB". Your part-of-speech tags should be modified to be consistent with
+the tagging scheme used here.
+
+- The dependency labeling scheme produced by the models provided here is separate/different from that of
+the Malt parser models used by ClearTK's wrapper of the Malt parser. You should not assume that
+the wrapper for the Clear Parser can be used interchangeably with the wrapper for the Malt Parser.
\ No newline at end of file
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/dependency/mayo-en-dep-1.3.0.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/dependency/mayo-en-dep-1.3.0.jar?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/README?rev=1845321&view=auto
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--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/README (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/README Wed Oct 31 11:03:43 2018
@@ -0,0 +1,2 @@
+The file dictionary-1.3.0.jar was obtained directly from the author of
+clearn NLP, Jinho Choi.
\ No newline at end of file
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/dictionary-1.3.1.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/lemmatizer/dictionary-1.3.1.jar?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/pred/mayo-en-pred-1.3.0.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/pred/mayo-en-pred-1.3.0.jar?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/role/mayo-en-role-1.3.0.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/role/mayo-en-role-1.3.0.jar?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/srl/README
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/srl/README?rev=1845321&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/srl/README (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/srl/README Wed Oct 31 11:03:43 2018
@@ -0,0 +1,29 @@
+############################
+mayo-en-srl-1.3.0.jar, ../pred/mayo-en,pred-1.3.0.jar, ../role/mayo-en-role-1.3.0.jar
+############################
+The model mayo-en-srl-1.3.0.jar was provided by Jinho Choi and is trained on the
+development set of the OntoNotes corpus version 4.0. More information about this data can
+be found here:
+http://www.ldc.upenn.edu/Catalog/docs/LDC2011T03/OntoNotes-Release-4.0.pdf
+
+This model produces semantic role labels over a dependency tree. So unlike PropBank,
+predicates and arguments only span the head expression. Knowing the full argument span
+will require traversal of the dependency tree.
+
+#####
+Notes
+#####
+
+- Both models were trained using PennTreebank part-of-speech tags. So, your input part-of-speech
+tags should match the tags used for training this model. The part-of-speech tag for punctuation
+symbols such as "." "," ":" ";" "(" ")" etc. are the symbols themselves (i.e. the part-of-speech tag
+for the token ")" should be ")".) This may be inconsistent with other PTB-derived tagging schemes that
+may use tags such as "COLON" or "RRB". Your part-of-speech tags should be modified to be consistent with
+the tagging scheme used here.
+
+- The models also depend on a dependency tree produced by the ClearNLP dependency parser. This should be
+run prior to running ClearNLP semantic role labeler.
+
+- The dependency labeling scheme produced by the models provided here is separate/different from that of
+the Malt parser models used by ClearTK's wrapper of the Malt parser. You should not assume that
+the wrapper for the Clear Parser can be used interchangeably with the wrapper for the Malt Parser.
\ No newline at end of file
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/srl/mayo-en-srl-1.3.0.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dependency/parser/models/srl/mayo-en-srl-1.3.0.jar?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.properties
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.properties?rev=1845321&view=auto
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--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.properties (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.properties Wed Oct 31 11:03:43 2018
@@ -0,0 +1,17 @@
+#HSQL Database Engine 1.8.0.10
+#Thu Sep 04 09:49:09 EDT 2014
+hsqldb.script_format=1
+runtime.gc_interval=0
+sql.enforce_strict_size=false
+hsqldb.cache_size_scale=8
+readonly=true
+hsqldb.nio_data_file=true
+hsqldb.cache_scale=14
+version=1.8.0
+hsqldb.default_table_type=memory
+hsqldb.cache_file_scale=1
+hsqldb.log_size=200
+modified=no
+hsqldb.cache_version=1.7.0
+hsqldb.original_version=1.8.0
+hsqldb.compatible_version=1.8.0
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml?rev=1845321&view=auto
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--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml Wed Oct 31 11:03:43 2018
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+Licensed to the Apache Software Foundation (ASF) under one
+or more contributor license agreements. See the NOTICE file
+distributed with this work for additional information
+regarding copyright ownership. The ASF licenses this file
+to you under the Apache License, Version 2.0 (the
+"License"); you may not use this file except in compliance
+with the License. You may obtain a copy of the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing,
+software distributed under the License is distributed on an
+"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+KIND, either express or implied. See the License for the
+specific language governing permissions and limitations
+under the License.
+-->
+
+<!-- New format for the .xml lookup specification. Uses table name and value type/class for Concept Factories. -->
+<lookupSpecification>
+<dictionaries>
+ <dictionary>
+ <name>customDictionaryTerms</name>
+ <implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary</implementationName>
+ <properties>
+<!-- urls for hsqldb memory connections must be file types in hsql 1.8.
+These file urls must be either absolute path or relative to current working directory.
+They cannot be based upon the classpath.
+Though JdbcConnectionFactory will attempt to "find" a db based upon the parent dir of the url
+for the sake of ide ease-of-use, the user should be aware of these hsql limitations.
+-->
+ <property key="jdbcDriver" value="com.mysql.jdbc.Driver"/>
+ <property key="jdbcUrl" value="jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&characterEncoding=utf8&useSSL=false"/>
+ <property key="jdbcUser" value="root"/>
+ <property key="jdbcPass" value="pass"/>
+ <property key="rareWordTable" value="cui_terms"/>
+ <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
+ <property key="umlsVendor" value="NLM-6515182895"/>
+ <property key="umlsUser" value="CHANGE_ME"/>
+ <property key="umlsPass" value="CHANGE_ME"/>
+ </properties>
+ </dictionary>
+</dictionaries>
+
+<conceptFactories>
+ <conceptFactory>
+ <name>customDictionaryConcepts</name>
+ <implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
+ <properties>
+ <property key="jdbcDriver" value="com.mysql.jdbc.Driver"/>
+ <property key="jdbcUrl" value="jdbc:mysql://127.0.0.1:3306/umls?useUnicode=true&characterEncoding=utf8&useSSL=false"/>
+ <property key="jdbcUser" value="root"/>
+ <property key="jdbcPass" value="pass"/>
+ <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
+ <property key="umlsVendor" value="NLM-6515182895"/>
+ <property key="umlsUser" value="CHANGE_ME"/>
+ <property key="umlsPass" value="CHANGE_ME"/>
+ <property key="tuiTable" value="tui"/>
+ <property key="prefTermTable" value="prefTerm"/>
+<!-- Optional tables for optional term info.
+Uncommenting these lines alone may not persist term information;
+persistence depends upon the TermConsumer. -->
+ <property key="rxnormTable" value="long"/>
+ <property key="snomedct_usTable" value="long"/>
+ <property key="mdrTable" value="long"/>
+ </properties>
+ </conceptFactory>
+</conceptFactories>
+
+<!-- Defines what terms and concepts will be used -->
+<dictionaryConceptPairs>
+ <dictionaryConceptPair>
+ <name>customDictionaryPair</name>
+ <dictionaryName>customDictionaryTerms</dictionaryName>
+ <conceptFactoryName>customDictionaryConcepts</conceptFactoryName>
+ </dictionaryConceptPair>
+</dictionaryConceptPairs>
+
+<!-- DefaultTermConsumer will persist all spans.
+PrecisionTermConsumer will only persist only the longest overlapping span of any semantic group.
+SemanticCleanupTermConsumer works as Precision** but also removes signs/sympoms contained within disease/disorder,
+and (just in case) removes any s/s and d/d that are also (exactly) anatomical sites. -->
+<rareWordConsumer>
+ <name>Term Consumer</name>
+ <implementationName>org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer</implementationName>
+ <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer</implementationName>-->
+ <!--<implementationName>org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer</implementationName>-->
+ <properties>
+<!-- Depending upon the consumer, the value of codingScheme may or may not be used. With the packaged consumers,
+codingScheme is a default value used only for cuis that do not have secondary codes (snomed, rxnorm, etc.) -->
+ <property key="codingScheme" value="customDictionary"/>
+ </properties>
+</rareWordConsumer>
+
+</lookupSpecification>
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.lck
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(empty)
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.properties
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.properties?rev=1845321&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.properties (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.properties Wed Oct 31 11:03:43 2018
@@ -0,0 +1,5 @@
+#HSQL Database Engine 2.3.4
+#Tue Apr 04 21:01:14 EDT 2017
+version=2.3.4
+modified=no
+tx_timestamp=0