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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/12/06 00:34:10 UTC
svn commit: r1643472 - in
/ctakes/branches/sent-detector-newline-fix/ctakes-core: .settings/
resources/launch/ src/main/java/org/apache/ctakes/core/ae/
src/main/java/org/apache/ctakes/core/cr/
Author: tmill
Date: Fri Dec 5 23:34:10 2014
New Revision: 1643472
URL: http://svn.apache.org/r1643472
Log:
Undo accidentally checked-in files not related to sentence issue.
Modified:
ctakes/branches/sent-detector-newline-fix/ctakes-core/.settings/org.eclipse.core.resources.prefs
ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector--train_a_new_model.launch
ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector_annotator.launch
ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/Tokenizer_annotator.launch
ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CPE_GUI--core.launch
ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CVD--core.launch
ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/.settings/org.eclipse.core.resources.prefs
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/.settings/org.eclipse.core.resources.prefs?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/.settings/org.eclipse.core.resources.prefs (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/.settings/org.eclipse.core.resources.prefs Fri Dec 5 23:34:10 2014
@@ -1,4 +1,5 @@
eclipse.preferences.version=1
encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
encoding//src/test/java=UTF-8
encoding/<project>=UTF-8
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector--train_a_new_model.launch
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector--train_a_new_model.launch?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector--train_a_new_model.launch (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector--train_a_new_model.launch Fri Dec 5 23:34:10 2014
@@ -2,7 +2,7 @@
<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
<stringAttribute key="bad_container_name" value="\core\resources\launch\SentenceDetector - argument checking"/>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java"/>
+<listEntry value="/ctakes-core/src/main/java/org/apache/ctakes/ctakes-core/ae/SentenceDetector.java"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
<listEntry value="1"/>
@@ -10,7 +10,7 @@
<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.ctakes.core.ae.SentenceDetector"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="/home/tmill/mnt/rc-pub/resources/corpora/sentence-training/finished/all_finished.train ../ctakes-core-res/src/main/resources/org/apache/ctakes/core/sentdetect/sample_sd.mod 100 5"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="data/test/sample_sd_training_sentences.txt resources/sentdetect/sample_sd.mod 100 5"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-core"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
</launchConfiguration>
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector_annotator.launch
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector_annotator.launch?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector_annotator.launch (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/SentenceDetector_annotator.launch Fri Dec 5 23:34:10 2014
@@ -11,5 +11,5 @@
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-core"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx3g"/>
</launchConfiguration>
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/Tokenizer_annotator.launch
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/Tokenizer_annotator.launch?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/Tokenizer_annotator.launch (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/Tokenizer_annotator.launch Fri Dec 5 23:34:10 2014
@@ -11,5 +11,5 @@
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-core"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx3g"/>
</launchConfiguration>
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CPE_GUI--core.launch
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CPE_GUI--core.launch?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CPE_GUI--core.launch (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CPE_GUI--core.launch Fri Dec 5 23:34:10 2014
@@ -24,5 +24,5 @@
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-core"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx3g"/>
</launchConfiguration>
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CVD--core.launch
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CVD--core.launch?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CVD--core.launch (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/resources/launch/UIMA_CVD--core.launch Fri Dec 5 23:34:10 2014
@@ -13,5 +13,5 @@
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-core"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties" -Xms500M -Xmx500M"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties" -Xms500M -Xmx3g"/>
</launchConfiguration>
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java Fri Dec 5 23:34:10 2014
@@ -36,7 +36,7 @@ public class DocumentIdPrinterAnalysisEn
String documentId = DocumentIDAnnotationUtil.getDocumentID(jcas);
String logMessage = String.format("##### current file document id: \"%s\"", documentId);
logger.info(logMessage);
-// System.out.println(logMessage);
+ System.out.println(logMessage);
}
}
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java Fri Dec 5 23:34:10 2014
@@ -41,7 +41,6 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.refsem.Date;
import org.apache.ctakes.typesystem.type.refsem.Event;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
-import org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag;
import org.apache.ctakes.typesystem.type.refsem.LabReferenceRange;
import org.apache.ctakes.typesystem.type.refsem.LabValue;
import org.apache.ctakes.typesystem.type.refsem.MedicationDosage;
@@ -60,14 +59,10 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.relation.AspectualTextRelation;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation;
-import org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation;
import org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation;
-import org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation;
-import org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation;
import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation;
import org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation;
-import org.apache.ctakes.typesystem.type.relation.PreventsTextRelation;
import org.apache.ctakes.typesystem.type.relation.RelationArgument;
import org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
@@ -83,7 +78,6 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.textsem.GenericModifier;
import org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier;
import org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier;
import org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier;
import org.apache.ctakes.typesystem.type.textsem.LabMention;
@@ -160,7 +154,7 @@ public class SHARPKnowtatorXMLReader ext
/**
* Get the URI that the text in this class was loaded from
*/
- protected URI getTextURI(JCas jCas) {
+ protected URI getTextURI(JCas jCas) throws AnalysisEngineProcessException {
String textPath = JCasUtil.selectSingle(jCas, DocumentID.class).getDocumentID();
if (this.textDirectory != null) {
textPath = this.textDirectory + File.separator + textPath;
@@ -182,18 +176,13 @@ public class SHARPKnowtatorXMLReader ext
* @throws URISyntaxException
*/
protected URI getKnowtatorURI(JCas jCas) throws AnalysisEngineProcessException {
- File textURI = new File(this.getTextURI(jCas));
- String filename = textURI.getName().replace(".txt", "");
-
- File xmlPath = new File(textURI.getParentFile().getParentFile().getParentFile().getParentFile().getParentFile(), "by-document/" + filename + "/" + filename + ".umls.knowtator.xml");
-
-// String xmlURI = textURI.replaceAll("Knowtator[/\\\\]text", "Knowtator_XML") + ".knowtator.xml";
-// File fileTest = new File(URI.create(xmlURI));
-// if(!fileTest.exists()){
-// xmlURI = xmlURI.replace("_XML", " XML");
-// }
-// return URI.create(xmlPath.getAbsolutePath());
- return UriUtils.create("file:" + xmlPath.getAbsolutePath());
+ String textURI = this.getTextURI(jCas).toString();
+ String xmlURI = textURI.replaceAll("Knowtator[/\\\\]text", "Knowtator_XML") + ".knowtator.xml";
+ File fileTest = new File(URI.create(xmlURI));
+ if(!fileTest.exists()){
+ xmlURI = xmlURI.replace("_XML", " XML");
+ }
+ return UriUtils.create(xmlURI);
}
/**
@@ -240,7 +229,6 @@ public class SHARPKnowtatorXMLReader ext
entityRelationTypes.add("location_of");
entityRelationTypes.add("manages/treats");
entityRelationTypes.add("manifestation_of"); // note the misspelling
- entityRelationTypes.add("prevents");
entityRelationTypes.add("result_of");
Set<String> eventRelationTypes = new HashSet<String>();
eventRelationTypes.add("TLINK");
@@ -286,7 +274,6 @@ public class SHARPKnowtatorXMLReader ext
AnatomicalSiteMention mention = new AnatomicalSiteMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_ANATOMICAL_SITE,
@@ -294,8 +281,7 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
KnowtatorAnnotation bodySide = annotationSlots.remove("body_side");
@@ -305,7 +291,6 @@ public class SHARPKnowtatorXMLReader ext
EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_CLINICAL_ATTRIBUTE,
@@ -313,18 +298,12 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
} else if ("Devices".equals(annotation.type)) {
- if(coveringSpan.begin < 0 || coveringSpan.end < 0){
- LOGGER.error(String.format("Device annotation (id=%s) has invalid span [%d,%d]", annotation.id, coveringSpan.begin, coveringSpan.end));
- continue;
- }
EntityMention mention = new EntityMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_DEVICE,
@@ -332,14 +311,12 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
} else if ("Disease_Disorder".equals(annotation.type)) {
DiseaseDisorderMention mention = new DiseaseDisorderMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_DISORDER,
@@ -347,8 +324,7 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
KnowtatorAnnotation alleviatingFactor = annotationSlots.remove("alleviating_factor");
delayedFeatures.add(DelayedRelationFeature.forArg2(
mention,
@@ -400,7 +376,6 @@ public class SHARPKnowtatorXMLReader ext
LabMention mention = new LabMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_LAB,
@@ -408,8 +383,7 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
KnowtatorAnnotation ordinal = annotationSlots.remove("ordinal_interpretation");
delayedFeatures.add(DelayedRelationFeature.forArg1(
mention,
@@ -426,13 +400,11 @@ public class SHARPKnowtatorXMLReader ext
labValue,
ResultOfTextRelation.class,
LabValueModifier.class));
- KnowtatorAnnotation deltaFlag = annotationSlots.remove("delta_flag");
- delayedFeatures.add(new DelayedFeature(mention, "deltaFlag", deltaFlag));
+
} else if ("Medications/Drugs".equals(annotation.type)) {
MedicationMention mention = new MedicationMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_DRUG,
@@ -440,8 +412,7 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
KnowtatorAnnotation allergy = annotationSlots.remove("allergy_indicator");
delayedFeatures.add(new DelayedFeature(mention, "medicationAllergy", allergy));
KnowtatorAnnotation changeStatus = annotationSlots.remove("change_status_model");
@@ -458,8 +429,6 @@ public class SHARPKnowtatorXMLReader ext
delayedFeatures.add(new DelayedFeature(mention, "medicationRoute", route));
KnowtatorAnnotation startDate = annotationSlots.remove("start_date");
delayedFeatures.add(new DelayedFeature(mention, "startDate", startDate));
- KnowtatorAnnotation endDate = annotationSlots.remove("end_date");
- delayedFeatures.add(new DelayedFeature(mention, "endDate", endDate));
KnowtatorAnnotation strength = annotationSlots.remove("strength_model");
delayedFeatures.add(new DelayedFeature(mention, "medicationStrength", strength));
@@ -467,7 +436,6 @@ public class SHARPKnowtatorXMLReader ext
EventMention mention = new EventMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_PHENOMENA,
@@ -475,14 +443,12 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
} else if ("Procedure".equals(annotation.type)) {
ProcedureMention mention = new ProcedureMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_PROCEDURE,
@@ -490,8 +456,7 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
KnowtatorAnnotation bodyLaterality = annotationSlots.remove("body_laterality");
delayedFeatures.add(new DelayedFeature(mention, "bodyLaterality", bodyLaterality));
KnowtatorAnnotation bodyLocation = annotationSlots.remove("body_location");
@@ -512,7 +477,6 @@ public class SHARPKnowtatorXMLReader ext
SignSymptomMention mention = new SignSymptomMention(jCas, coveringSpan.begin, coveringSpan.end);
addIdentifiedAnnotationFeatures(
annotation,
- knowtatorURI,
mention,
jCas,
CONST.NE_TYPE_ID_FINDING,
@@ -520,8 +484,7 @@ public class SHARPKnowtatorXMLReader ext
booleanSlots,
annotationSlots,
idAnnotationMap,
- delayedFeatures,
- delayedRelations);
+ delayedFeatures);
KnowtatorAnnotation alleviatingFactor = annotationSlots.remove("alleviating_factor");
delayedFeatures.add(DelayedRelationFeature.forArg2(
mention,
@@ -882,16 +845,7 @@ public class SHARPKnowtatorXMLReader ext
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
- } else if ("delta_flag_indicator".equals(annotation.type)) {
- String value = stringSlots.remove("delta_flag_normalization");
- LabDeltaFlagModifier modifier = new LabDeltaFlagModifier(jCas, coveringSpan.begin, coveringSpan.end);
- LabDeltaFlag attribute = new LabDeltaFlag(jCas);
- attribute.setValue(value);
- attribute.addToIndexes();
-// modifier.setValue(value)
- modifier.setNormalizedForm(attribute);
- modifier.addToIndexes();
- idAnnotationMap.put(annotation.id, modifier);
+
} else if ("Value".equals(annotation.type)) {
KnowtatorAnnotation unit = annotationSlots.remove("value_unit");
KnowtatorAnnotation number = annotationSlots.remove("value_number");
@@ -1016,23 +970,18 @@ public class SHARPKnowtatorXMLReader ext
KnowtatorAnnotation unit = annotationSlots.remove("strength_unit");
KnowtatorAnnotation number = annotationSlots.remove("strength_number");
MedicationStrength attribute = new MedicationStrength(jCas);
- int spanStart=text.length()-1,spanEnd=0; // the strength annotation is spanless so we get the modifier span by its components
if (unit != null) {
KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
String unitString = text.substring(unitSpan.begin, unitSpan.end);
attribute.setUnit(unitString);
- if(unitSpan.begin < spanStart) spanStart = unitSpan.begin;
- if(unitSpan.end > spanEnd) spanEnd = unitSpan.end;
}
if (number != null) {
KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
String numberString = text.substring(numberSpan.begin, numberSpan.end);
attribute.setNumber(numberString);
- if(numberSpan.begin < spanStart) spanStart = numberSpan.begin;
- if(numberSpan.end > spanEnd) spanEnd = numberSpan.end;
}
attribute.addToIndexes();
- MedicationStrengthModifier modifier = new MedicationStrengthModifier(jCas, spanStart, spanEnd);
+ MedicationStrengthModifier modifier = new MedicationStrengthModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
@@ -1074,11 +1023,9 @@ public class SHARPKnowtatorXMLReader ext
} else if ("Date".equals(annotation.type)) {
String month = stringSlots.remove("month");
String day = stringSlots.remove("day");
- String year = stringSlots.remove("year");
Date date = new Date(jCas);
date.setMonth(month);
date.setDay(day);
- date.setYear(year);
date.addToIndexes();
TimeMention mention = new TimeMention(jCas, coveringSpan.begin, coveringSpan.end);
mention.setDate(date);
@@ -1139,12 +1086,7 @@ public class SHARPKnowtatorXMLReader ext
// all mentions should be added, so add features that required other annotations
for (DelayedFeature delayedFeature : delayedFeatures) {
- try{
delayedFeature.setValueFrom(idAnnotationMap);
- }catch(Exception e){
- System.err.println("Exception reading input: " + e.getMessage());
- e.printStackTrace(System.err);
- }
}
}
@@ -1158,22 +1100,8 @@ public class SHARPKnowtatorXMLReader ext
return String.format("%s(%s)", ann.getClass().getSimpleName(), result);
}
-// private static void addIdentifiedAnnotationFeatures(
-// KnowtatorAnnotation annotation,
-// final IdentifiedAnnotation mention,
-// JCas jCas,
-// int typeID,
-// Map<String, String> stringSlots,
-// Map<String, Boolean> booleanSlots,
-// Map<String, KnowtatorAnnotation> annotationSlots,
-// Map<String, TOP> idAnnotationMap,
-// List<DelayedFeature> delayedFeatures) {
-// addIdentifiedAnnotationFeatures(annotation, null, mention, jCas, typeID, stringSlots, booleanSlots, annotationSlots, idAnnotationMap, delayedFeatures, null);
-// }
-
private static void addIdentifiedAnnotationFeatures(
KnowtatorAnnotation annotation,
- URI knowtatorURI,
final IdentifiedAnnotation mention,
JCas jCas,
int typeID,
@@ -1181,8 +1109,7 @@ public class SHARPKnowtatorXMLReader ext
Map<String, Boolean> booleanSlots,
Map<String, KnowtatorAnnotation> annotationSlots,
Map<String, TOP> idAnnotationMap,
- List<DelayedFeature> delayedFeatures,
- List<DelayedRelation> delayedRelations) {
+ List<DelayedFeature> delayedFeatures) {
mention.setTypeID(typeID);
mention.setConfidence(1.0f);
mention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);
@@ -1202,15 +1129,6 @@ public class SHARPKnowtatorXMLReader ext
delayedFeatures.add(new DelayedFeatureFromFeature(mention, "historyOf", historyOf));
KnowtatorAnnotation negationIndicator = annotationSlots.remove("negation_indicator_CU");
delayedFeatures.add(new DelayedFeatureFromFeature(mention, "polarity", negationIndicator));
- if(negationIndicator != null){
- DelayedRelation polRel = new DelayedRelation();
- polRel.source = negationIndicator;
- polRel.target = annotation;
- polRel.type = "polarityModifier";
- polRel.sourceFile = knowtatorURI;
- if(delayedRelations != null) delayedRelations.add(polRel);
- }
-// delayedFeatures.add(DelayedRelationFeature.forArg2(mention, "polarityModifier", negationIndicator, BinaryTextRelation.class, PolarityModifier.class));
KnowtatorAnnotation subject = annotationSlots.remove("subject_CU");
delayedFeatures.add(new DelayedFeatureFromFeature(mention, "subject", subject) {
@Override
@@ -1367,26 +1285,15 @@ public class SHARPKnowtatorXMLReader ext
// add the relation to the CAS
BinaryTextRelation relation = null;
- if(this.annotation == null){
- relation = new BinaryTextRelation(jCas);
- } else if ("affects".equals(this.annotation.type)) {
+ if ("affects".equals(this.annotation.type)) {
this.assertTypes(sourceMention, EventMention.class, targetMention, IdentifiedAnnotation.class);
relation = new AffectsTextRelation(jCas);
} else if ("complicates/disrupts".equals(this.annotation.type)) {
this.assertTypes(sourceMention, EventMention.class, targetMention, EventMention.class);
relation = new ComplicatesDisruptsTextRelation(jCas);
- } else if ("contraindicates".equals(this.annotation.type)) {
- this.assertTypes(sourceMention, IdentifiedAnnotation.class, targetMention, EventMention.class);
- relation = new ContraindicatesTextRelation(jCas);
} else if ("degree_of".equals(this.annotation.type)) {
this.assertTypes(sourceMention, EventMention.class, targetMention, Modifier.class);
relation = new DegreeOfTextRelation(jCas);
- } else if ("diagnoses".equals(this.annotation.type)) {
- this.assertTypes(sourceMention, EventMention.class, targetMention, IdentifiedAnnotation.class);
- relation = new DiagnosesTextRelation(jCas);
- } else if ("indicates".equals(this.annotation.type)) {
- this.assertTypes(sourceMention, EventMention.class, targetMention, EventMention.class);
- relation = new IndicatesTextRelation(jCas);
} else if ("location_of".equals(this.annotation.type)) {
if (!(targetMention instanceof AnatomicalSiteMention) && (sourceMention instanceof AnatomicalSiteMention)) {
// fix reversed arguments in manual annotations
@@ -1407,15 +1314,9 @@ public class SHARPKnowtatorXMLReader ext
this.assertTypes(sourceMention, EventMention.class, targetMention, EventMention.class);
relation = new ManifestationOfTextRelation(jCas);
relation.setCategory("manifestation_of"); // fix typo in Knowtator type system
- } else if ("prevents".equals(this.annotation.type)) {
- this.assertTypes(sourceMention, EventMention.class, targetMention, EventMention.class);
- relation = new PreventsTextRelation(jCas);
} else if ("result_of".equals(this.annotation.type)) {
this.assertTypes(sourceMention, EventMention.class, targetMention, IdentifiedAnnotation.class);
relation = new ResultOfTextRelation(jCas);
-// } else if ("prevents".equals(this.annotation.type)) {
-// this.assertTypes(sourceMention, expectedSourceClass, targetMention, expectedTargetClass);
-// relation = new PreventsTextRelation(jCas);
} else if ("TLINK".equals(this.annotation.type)) {
relation = new TemporalTextRelation(jCas);
relation.setCategory(this.type);
@@ -1428,11 +1329,7 @@ public class SHARPKnowtatorXMLReader ext
// set the relation cateory (if not already set)
if (relation.getCategory() == null) {
- if(this.type != null){
- relation.setCategory(this.type);
- }else{
- relation.setCategory(this.annotation.type);
- }
+ relation.setCategory(this.annotation.type);
}
// link the relation to its arguments and add it to the CAS
@@ -1447,7 +1344,7 @@ public class SHARPKnowtatorXMLReader ext
relation.addToIndexes();
// add the relation to the map so it can be used in features of other annotations
- if(this.annotation != null) idAnnotationMap.put(this.annotation.id, relation);
+ idAnnotationMap.put(this.annotation.id, relation);
}
private void assertTypes(Annotation sourceMention, Class<? extends Annotation> expectedSourceClass, Annotation targetMention, Class<? extends Annotation> expectedTargetClass) {
Modified: ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java?rev=1643472&r1=1643471&r2=1643472&view=diff
==============================================================================
--- ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java (original)
+++ ctakes/branches/sent-detector-newline-fix/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java Fri Dec 5 23:34:10 2014
@@ -138,7 +138,7 @@ public class FilesInDirectoryCollectionR
File[] files = directory.listFiles();
for (int i = 0; i < files.length; i++)
{
- if (!files[i].isDirectory() && hasValidExtension(files[i]) && !files[i].isHidden())
+ if (!files[i].isDirectory() && hasValidExtension(files[i]))
{
iv_files.add(files[i]);
}