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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 [29/42] - 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/drugner/types/TypeSystem.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml?rev=1845321&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/drugner/types/TypeSystem.xml Wed Oct 31 11:03:43 2018
@@ -0,0 +1,313 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <name>org.apache.ctakes.drugner.types.TypeSystem</name>
+ <description/>
+ <version>1.0</version>
+ <vendor>Mayo Clinic</vendor>
+ <types>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FrequencyAnnotation</name>
+ <description>The frequency determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DurationAnnotation</name>
+ <description>The duration determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.RouteAnnotation</name>
+ <description>The route determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>intakeMethod</name>
+ <description>Means by which the drug was taken.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.SuffixStrengthAnnotation</name>
+ <description>The suffix portion of dosage strength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FractionStrengthAnnotation</name>
+ <description>The fraction portion of dosages strength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.RangeStrengthAnnotation</name>
+ <description>The range portion of dosages stength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DecimalStrengthAnnotation</name>
+ <description>The decimal portion of dosages stength determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation</name>
+ <description>The change status of dosages determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>changeStatus</name>
+ <description>Indicates the drug change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DosagesAnnotation</name>
+ <description>The dosage determination for the Drug NER profile.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.StrengthAnnotation</name>
+ <description>Holds the value representing the unit of the drug dosage.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.StrengthUnitAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FrequencyUnitAnnotation</name>
+ <description>The value represents the unit portion of the drug frequency.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>period</name>
+ <description>The periodic unit used, e.g day, month, hour, etc.</description>
+ <rangeTypeName>uima.cas.Float</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.FormAnnotation</name>
+ <description>The value represents the form portion of the drug mention.</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.SubSectionAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>subSectionBodyBegin</name>
+ <description>Sub-section body begin offset.</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionBodyEnd</name>
+ <description>Sub-section body end offset.</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>status</name>
+ <description>Status of 'possible', 'history of', or 'family history of'.</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionHeaderBegin</name>
+ <description>Begin offset of subSection header</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>subSectionHeaderEnd</name>
+ <description>Ending offset of subsection header</description>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>parentSectionId</name>
+ <description>The section in which the subsection was found.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.DrugMentionAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>status</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>confidence</name>
+ <description>The confidence of the annotation.</description>
+ <rangeTypeName>uima.cas.Float</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequency</name>
+ <description>Frequency refers to how often the patient needs to take the drug. Frequency is divided into frequency number and frequency unit. E.g. twice daily</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequencyBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequencyEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>duration</name>
+ <description>Duration refers to for how long the patient is expected to take the drug. E.g. 'for 2 weeks'
+Strongly encouraged to use bold text</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>durationBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>durationEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>route</name>
+ <description>Medication route refers to the way that a drug is introduced into the body. E.g oral
+Strongly encouraged to use bold text</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>routeBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>routeEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>drugChangeStatus</name>
+ <description>Status refers to the whether the medication is currently being taken or not.</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>dosage</name>
+ <description>Dosage refers to how many of each drug the patient is taking. E.g. 5 mg</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>dosageBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>dosageEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strength</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strengthBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strengthEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>strengthUnit</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>suBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>suEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>form</name>
+ <description>Form refers to the physical appearance of the drug. E.g. cream</description>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>formBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>formEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>frequencyUnit</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>fuBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>fuEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>startDate</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>reason</name>
+ <description/>
+ <rangeTypeName>uima.cas.FSArray</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>changeStatusBegin</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ <featureDescription>
+ <name>changeStatusEnd</name>
+ <description/>
+ <rangeTypeName>uima.cas.Integer</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.drugner.type.ChunkAnnotation</name>
+ <description/>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ <features>
+ <featureDescription>
+ <name>sentenceID</name>
+ <description/>
+ <rangeTypeName>uima.cas.String</rangeTypeName>
+ </featureDescription>
+ </features>
+ </typeDescription>
+ <typeDescription>
+ <name>org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation</name>
+ <description>Similar to LookupWindowAnnotation however, these annotations are restricted to the segments/sections specified in the parameter - sectionOverrideSet - in DrugCNP2LookupWindow</description>
+ <supertypeName>uima.tcas.Annotation</supertypeName>
+ </typeDescription>
+ </types>
+</typeSystemDescription>
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_lemma.voc
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_lemma.voc?rev=1845321&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_lemma.voc (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_lemma.voc Wed Oct 31 11:03:43 2018
@@ -0,0 +1 @@
+1|nonshiny|nonshiny|<adj+adv+noun+verb>
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_norm.voc
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_norm.voc?rev=1845321&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_norm.voc (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/2005_norm.voc Wed Oct 31 11:03:43 2018
@@ -0,0 +1 @@
+1|nonshiny|nonshiny|1|1|l+b|1|
Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.backup
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.backup?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.data
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.data?rev=1845321&view=auto
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Added: ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.properties
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.properties?rev=1845321&view=auto
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--- ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.properties (added)
+++ ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.properties Wed Oct 31 11:03:43 2018
@@ -0,0 +1,36 @@
+#
+# 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.
+#
+
+#HSQL Database Engine 1.8.0.7
+#Sun Dec 21 18:32:22 CST 2008
+hsqldb.script_format=0
+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