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From seanfi...@apache.org
Subject svn commit: r1765001 [2/2] - in /ctakes/trunk: ./ ctakes-core/src/main/java/org/apache/ctakes/core/cr/ ctakes-examples-res/ ctakes-examples-res/src/ ctakes-examples-res/src/main/ ctakes-examples-res/src/main/resources/ ctakes-examples-res/src/main/reso...
Date Sat, 15 Oct 2016 00:53:40 GMT
Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,18 @@
+Case description for C-Takes documenting:
+Setting: Outpatient.
+Specialty: Vascular Surgery. 
+Note detail level (1-5): 1.
+Level of abbreviation (Low/Medium/High): High.
+
+HPI/CC: Mrs. X is a 60 yo white female with a PMH significant for HTN, CAD, AFIB, DMtype2
who presents to the clinic today for f/u to r/o a DVT after RLE edema was appreciated on PE
at a f/u apt s/p high saphenous vein ligation and stab phlebectomy of the ipsilateral leg
around Feb of 2010. Patient expresses concern over sutures remaining at the incision sites
as well as a lesion on her L arm that was noted after IV access was attempted by a tech post-op.
+
+ROS: Pt denies cp/sob. Unremarkable otherwise. 
+
+PE: Mrs X is a well appearing woman who appears her stated age. BP-R: 118/76, BP-L: 134/78.
Radial pulses 2+ bilaterally. Could not palpate pedal pulses or pop. pulses bilat., however,
pedal pulses 2 by doppler.
+
+ANC: Right LE duplex indicates no DVT.
+
+A/P: Mrs X is a 60 yo female presenting to clinic for f/u to r/o a DVT s/p a high ligation
of saphenous vein and stab phlebectomy of right leg. Some sutures remained and were removed.
Patient was counceled on hot compress therapy for superficial phlebitis and advised that it
should resolve with time. Given the exclusion of DVT, no further appointments are necessary.
+
+
+

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,5 @@
+Mr. Johnson is presenting signs of a shark bite.  It occurred last week and has caused immense
leg pain.  The pain was so severe that he had begun taking narcotics to relieve it.
+
+The patient also was concerned about a small lesion in his Broca's area and said the lesion
was causing him to lettuce Wednesday baseball applesauce.
+
+After imaging which was inconclusive, the patient was released to go home and treat his pain
himself.
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,2 @@
+Miss. CM is a energetic young woman who has had bouts with sleeplessness for the past year
or so.  She said that her insomnia began with the death of her father who was killed in a
train accident last year.
+Patient is 25 and claims she has smoked for the last five years or so. She used to smoke
about half a pack a day, but for the last month she has been down to about 3-5 cigarettes
a day. She is having trouble stopping altogether.
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,15 @@
+REVIEW OF SYSTEMS:
+General: Has gained about 10 lb in the past 4 yr, no fatigue
+Skin: No rashes or other changes
+Head: See present illness.
+Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
+Ears: Hearing good. No tinnitus, vertigo, infections
+Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
+Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
+Neck: No lumps, goiter, pain
+Breasts: No lumps, pain, discharge.
+Habits:
+Patient claims to have quit smoking about two years ago.
+FAMILY HISTORY
+- Mother died, 67, stroke; had varicose veins, headaches, hypertension
+- Father died, 43, train accident
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,105 @@
+Patient Centered Medicine 2
+Revised: 7/27/99
+DATA BASE: SAMPLE HISTORY
+IDENTIFYING DATA 
+CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
+CHIEF COMPLAINT
+“Bad headaches”
+HISTORY OF PRESENT ILLNESS 
+Patient Perspective
+She thinks her headaches may be like those in the past. However, she now has high blood
+pressure and is concerned because her mother had high blood pressure and died of a
+stroke. She is also concerned that they make her irritable with her family.
+PAST MEDICAL HISTORY
+Significant Childhood Illnesses
+Only measles and chickenpox
+Immunizations
+Last tetanus 1998
+Flu vaccine last November
+Adult Illnesses/Hospitalizations
+- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
+- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
+Patient Centered Medicine 2
+2 Revised: 7/27/99
+Psychiatric Illnesses/Hospitalizations
+None
+Operations
+Tonsillectomy, age 6,
+Appendectomy, age 13
+Injuries/Accidents
+1998 foot laceration, 4 stitches
+Obstetric History
+G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
+Transfusions
+None
+CURRENT HEALTH STATUS
+Medications
+Aspirin for headaches
+Multivitamin 1 per day
+Hydrochlorothiazide 25 mg per day (x 7 years)
+No herbs or supplements
+Allergies/Drug Reactions
+Ampicillin causes rash
+Health Screening
+- Last pap smear 2000, normal.
+- Normal mammogram in 2000.
+- Does breast self-exams monthly
+- Cholesterol = 220 (in 2000)
+Diet, Sleep, Exercise
+- Diet – Low in calcium with little milk or cheese. She frequently eats mid-morning and
+evening snacks that are high in fat. She does follow a low salt diet.
+- Sleep – Generally good, average 7 hr
+- Exercise – “No time”
+Habits
+- Alcohol – Rare drink (wine) only, no history of abuse
+- Drugs – Never tried illegal drugs
+Alternative Therapies
+None
+Patient Centered Medicine 2
+PSYCHOSOCIAL HISTORY
+- 4 yr ago her husband died suddenly of heart attack, leaving little savings and no
+insurance.
+- Lives alone, recently moved to a small apartment to be near daughter
+- Cosmetic saleswoman for 15 years at Sears. Likes her job but feels stressed by demands
+from the new manager
+- Not sexually active since the death of her husband who was her only partner
+- Denies depression
+- Feels safe at work and home
+FAMILY HISTORY
+- Mother died, 67, stroke; had varicose veins, headaches, hypertension
+- Father died, 43, train accident
+- One brother, 56, has high blood pressure, otherwise well
+- One brother, 51, apparently well except for mild arthritis
+- Daughter, 23, “migraine headaches,” otherwise well
+- Son, 21, well
+- Son, 20, well
+REVIEW OF SYSTEMS:
+General: Has gained about 10 lb in the past 4 yr, no fatigue
+Skin: No rashes or other changes
+Head: See present illness.
+Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
+Ears: Hearing good. No tinnitus, vertigo, infections
+Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
+Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
+Neck: No lumps, goiter, pain
+Breasts: No lumps, pain, discharge.
+Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.
+Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.
+Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though
+sometimes has hard stools for 2-3 d when especially tense; no diarrhea or
+bleeding. No pain, jaundice, gallbladder or liver trouble
+Urinary: No frequency, dysuria, hematuria or flank pain
+Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch
+Musculoskeletal: Mild aching low back pain often after a long day’s work; no radiation
+down legs; used to do back exercises, but not now. No other joint pain
+Patient Centered Medicine 2
+Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had
+swollen ankles after prolonged standing for 10 yr; no history of
+phlebitis or leg pain
+Neurological: No fainting, seizures, tremors, weakness, or tingling. Memory good
+Psychiatric: No anxiety or nervousness or depression
+Endocrine: No known thyroid trouble, temperature intolerance. Sweating average. No
+symptoms or history of diabetes
+Hematologic: No easy bleeding. No anemia
+Adapted from Bates’ Guide to Physical Examination and History Taking, Chapter 21, The Patient’s
Record, pp. 722-
+726
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,119 @@
+Patient Centered Medicine 2
+Revised: 7/27/99
+DATA BASE: SAMPLE HISTORY
+IDENTIFYING DATA 
+CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
+CHIEF COMPLAINT
+“Bad headaches”
+HISTORY OF PRESENT ILLNESS (HPI, Problem by problem)
+For about 3 months Mrs. M. has been increasingly troubled by headaches that are rightsided,
+usually throbbing, and can range from mild to moderately severe. Typically her
+headaches are rated at 4 over 10. She recently had a severe headache that she rated 8 over
+10 and missed work because of this headache. This was associated with nausea and
+vomiting. Headaches have increased in frequency and now average once a wk. The
+headaches usually last from 2 to 4 hours. However, the most recent headache, which was
+the most severe, lasted almost 8 hours. During a headache bright lights bother her and she
+just wants to lie down in a dark quiet room and fall asleep. Aspirin provides little relief.
+She has not noticed any association with food or drink. She has no other related symptoms,
+such as fever, dental pain, weakness, numbness or loss of vision. There is no history of
head
+injury or trauma. She remembers having a similar kind of headache with nausea and
+vomiting that began at age 15, recurred through her mid-20s, then diminished to one every
+2 or 3 months and disappeared.
+Patient Perspective
+She thinks her headaches may be like those in the past. However, she now has high blood
+pressure and is concerned because her mother had high blood pressure and died of a
+stroke. She is also concerned that they make her irritable with her family.
+PAST MEDICAL HISTORY
+Significant Childhood Illnesses
+Only measles and chickenpox
+Immunizations
+Last tetanus 1998
+Flu vaccine last November
+Adult Illnesses/Hospitalizations
+- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
+- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
+Patient Centered Medicine 2
+2 Revised: 7/27/99
+Psychiatric Illnesses/Hospitalizations
+None
+Operations
+Tonsillectomy, age 6,
+Appendectomy, age 13
+Injuries/Accidents
+1998 foot laceration, 4 stitches
+Obstetric History
+G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
+Transfusions
+None
+CURRENT HEALTH STATUS
+Medications
+Aspirin for headaches
+Multivitamin 1 per day
+Hydrochlorothiazide 25 mg per day (x 7 years)
+No herbs or supplements
+Allergies/Drug Reactions
+Ampicillin causes rash
+Health Screening
+- Last pap smear 2000, normal.
+- Normal mammogram in 2000.
+- Does breast self-exams monthly
+- Cholesterol = 220 (in 2000)
+Diet, Sleep, Exercise
+- Diet – Low in calcium with little milk or cheese. She frequently eats mid-morning and
+evening snacks that are high in fat. She does follow a low salt diet.
+- Sleep – Generally good, average 7 hr
+- Exercise – “No time”
+Habits
+- Tobacco – 1 pack cigs per day from age 18
+- Alcohol – Rare drink (wine) only, no history of abuse
+- Drugs – Never tried illegal drugs
+Alternative Therapies
+None
+Patient Centered Medicine 2
+PSYCHOSOCIAL HISTORY
+- 4 yr ago her husband died suddenly of heart attack, leaving little savings and no
+insurance.
+- Lives alone, recently moved to a small apartment to be near daughter
+- Cosmetic saleswoman for 15 years at Sears. Likes her job but feels stressed by demands
+from the new manager
+- Not sexually active since the death of her husband who was her only partner
+- Denies depression
+- Feels safe at work and home
+FAMILY HISTORY
+- Mother died, 67, stroke; had varicose veins, headaches, hypertension
+- Father died, 43, train accident
+- One brother, 56, has high blood pressure, otherwise well
+- One brother, 51, apparently well except for mild arthritis
+- Daughter, 23, “migraine headaches,” otherwise well
+- Son, 21, well
+- Son, 20, well
+REVIEW OF SYSTEMS:
+General: Has gained about 10 lb in the past 4 yr, no fatigue
+Skin: No rashes or other changes
+Head: See present illness.
+Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
+Ears: Hearing good. No tinnitus, vertigo, infections
+Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
+Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
+Neck: No lumps, goiter, pain
+Breasts: No lumps, pain, discharge.
+Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.
+Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.
+Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though
+sometimes has hard stools for 2-3 d when especially tense; no diarrhea or
+bleeding. No pain, jaundice, gallbladder or liver trouble
+Urinary: No frequency, dysuria, hematuria or flank pain
+Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch
+Musculoskeletal: Mild aching low back pain often after a long day’s work; no radiation
+down legs; used to do back exercises, but not now. No other joint pain
+Patient Centered Medicine 2
+Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had
+swollen ankles after prolonged standing for 10 yr; no history of
+phlebitis or leg pain
+Neurological: No fainting, seizures, tremors, weakness, or tingling. Memory good
+Psychiatric: No anxiety or nervousness or depression
+Endocrine: No known thyroid trouble, temperature intolerance. Sweating average. No
+symptoms or history of diabetes
+Hematologic: No easy bleeding. No anemia
+Adapted from Bates’ Guide to Physical Examination and History Taking, Chapter 21, The Patient’s
Record, pp. 722-
+726
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt
(added)
+++ ctakes/trunk/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,32 @@
+Patient Centered Medicine 2
+Revised: 2/7/10
+DATA BASE: SAMPLE HISTORY
+IDENTIFYING DATA 
+CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
+CHIEF COMPLAINT
+“Insomnia”
+HISTORY OF PRESENT ILLNESS 
+She is also concerned that they make her irritable with her family.  She isn't sleeping well,
since she quit smoking cigs.
+PAST MEDICAL HISTORY
+Significant Childhood Illnesses
+Only measles and chickenpox
+Immunizations
+Last tetanus 1998
+Flu vaccine last November
+Adult Illnesses/Hospitalizations
+- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
+- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
+Patient Centered Medicine 2
+Psychiatric Illnesses/Hospitalizations
+None
+Operations
+Tonsillectomy, age 6,
+Appendectomy, age 13
+Habits
+tobacco : quit.
+Injuries/Accidents
+1998 foot laceration, 4 stitches
+Obstetric History
+G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
+Transfusions
+None

Modified: ctakes/trunk/ctakes-examples/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/pom.xml?rev=1765001&r1=1765000&r2=1765001&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/pom.xml (original)
+++ ctakes/trunk/ctakes-examples/pom.xml Sat Oct 15 00:53:39 2016
@@ -34,5 +34,9 @@
       <groupId>org.apache.ctakes</groupId>
       <artifactId>ctakes-clinical-pipeline</artifactId>
     </dependency>
+     <dependency>
+        <groupId>org.apache.ctakes</groupId>
+        <artifactId>ctakes-examples-res</artifactId>
+     </dependency>
   </dependencies>
 </project>
\ No newline at end of file

Added: ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java?rev=1765001&view=auto
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java
(added)
+++ ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/DirNotesBuildPipeRunner.java
Sat Oct 15 00:53:39 2016
@@ -0,0 +1,72 @@
+package org.apache.ctakes.examples.pipeline;
+
+import org.apache.ctakes.assertion.medfacts.cleartk.*;
+import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
+import org.apache.ctakes.core.ae.SentenceDetector;
+import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
+import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
+import org.apache.ctakes.core.pipeline.EntityCollector;
+import org.apache.ctakes.core.pipeline.PipelineBuilder;
+import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
+import org.apache.ctakes.postagger.POSTagger;
+import org.apache.log4j.Logger;
+import org.apache.uima.UIMAException;
+
+import java.io.IOException;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 10/12/2016
+ */
+final public class DirNotesBuildPipeRunner {
+
+   static private final Logger LOGGER = Logger.getLogger( "DirNotesBuildPipeRunner" );
+
+   static private final String INPUT_DIR = "org/apache/ctakes/examples/notes";
+
+   private DirNotesBuildPipeRunner() {
+   }
+
+   /**
+    * @param args an output directory for xmi files or none if xmi files are not wanted
+    */
+   public static void main( final String... args ) {
+      try {
+         PipelineBuilder builder = new PipelineBuilder();
+         builder
+               // Read files from a directory
+               .readFiles( INPUT_DIR )
+               // Add a simple pre-defined existing pipeline for Tokenization.
+               // Equivalent of ClinicalPipelineFactory.getTokenProcessingPipeline()
+               .add( SimpleSegmentAnnotator.class )
+               .add( SentenceDetector.class )
+               .add( TokenizerAnnotatorPTB.class )
+               .add( ContextDependentTokenizerAnnotator.class )
+               // The POSTagger has a -complex- startup, but it can create its own description
to handle it
+               .addDescription( POSTagger.createAnnotatorDescription() )
+               // Add the Dependency parser for use by cleartk
+               .addDescription( ClearNLPDependencyParserAE.createAnnotatorDescription() )
+               // Add the cleartk attribute engines
+               .addDescription( PolarityCleartkAnalysisEngine.createAnnotatorDescription()
)
+               .addDescription( UncertaintyCleartkAnalysisEngine.createAnnotatorDescription()
)
+               .addDescription( HistoryCleartkAnalysisEngine.createAnnotatorDescription()
)
+               .addDescription( ConditionalCleartkAnalysisEngine.createAnnotatorDescription()
)
+               .addDescription( GenericCleartkAnalysisEngine.createAnnotatorDescription()
)
+               .addDescription( SubjectCleartkAnalysisEngine.createAnnotatorDescription()
)
+               // Collect discovered entities for post-run information
+               .collectEntities();
+         if ( args.length > 0 ) {
+            // Example to save the Aggregate descriptor to an xml file for external use such
as the UIMA CVD
+            builder.writeXMIs( args[ 0 ] );
+         }
+         // Run the pipeline with specified text
+         builder.run();
+         //Print out the IdentifiedAnnotation objects
+         LOGGER.info( "\n" + EntityCollector.getInstance().toString() );
+      } catch ( IOException | UIMAException multE ) {
+         LOGGER.error( multE.getMessage() );
+      }
+   }
+
+}

Modified: ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/pom.xml?rev=1765001&r1=1765000&r2=1765001&view=diff
==============================================================================
--- ctakes/trunk/pom.xml (original)
+++ ctakes/trunk/pom.xml Sat Oct 15 00:53:39 2016
@@ -131,6 +131,7 @@
 		<module>ctakes-ne-contexts-res</module>
 		<module>ctakes-template-filler</module>
 		<module>ctakes-examples</module>
+		<module>ctakes-examples-res</module>
 		<module>ctakes-ytex-res</module>
 		<module>ctakes-ytex</module>
 		<module>ctakes-ytex-uima</module>
@@ -143,6 +144,13 @@
 			<!-- cTAKES module versions -->
 			<dependency>
 				<groupId>org.apache.ctakes</groupId>
+				<artifactId>
+					ctakes-examples-res
+				</artifactId>
+				<version>${ctakes.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.ctakes</groupId>
 				<artifactId>ctakes-type-system</artifactId>
 				<version>${ctakes.version}</version>
 			</dependency>



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