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From seanfi...@apache.org
Subject svn commit: r1877092 - in /ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core: cr/JCasBuilder.java semantic/SemanticGroup.java semantic/SemanticTui.java
Date Mon, 27 Apr 2020 19:06:09 GMT
Author: seanfinan
Date: Mon Apr 27 19:06:09 2020
New Revision: 1877092

URL: http://svn.apache.org/viewvc?rev=1877092&view=rev
Log:
Refactoring :
Deprecated classes

Added:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java?rev=1877092&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java Mon
Apr 27 19:06:09 2020
@@ -0,0 +1,305 @@
+package org.apache.ctakes.core.cr;
+
+
+import org.apache.ctakes.core.util.doc.DocIdUtil;
+import org.apache.ctakes.core.util.doc.NoteSpecs;
+import org.apache.ctakes.core.util.doc.SourceMetadataUtil;
+import org.apache.ctakes.typesystem.type.structured.*;
+import org.apache.uima.UIMAException;
+import org.apache.uima.fit.factory.JCasFactory;
+import org.apache.uima.jcas.JCas;
+
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+
+/**
+ * Facade to "easily" populate a JCas with creator, patient and note information.
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 9/22/2019
+ * @deprecated Use JCasBuilder in core.util.doc
+ */
+@Deprecated
+final public class JCasBuilder {
+
+   //   For compatibility with sql db : Timestamp format must be yyyy-mm-dd hh:mm:ss[.fffffffff]
+   static private final DateFormat DATE_FORMAT = new SimpleDateFormat( "yyyy-MM-dd hh:mm:ss"
);
+
+   static private final String UNKNOWN_DATE = "UnknownDate";
+   static private final String UNKNOWN_GENDER = "UnknownGender";
+   static private final String UNKNOWN = "Unknown";
+
+
+   private String _institutionId = UNKNOWN;
+   private String _authorSpecialty = UNKNOWN;
+
+   private String _patientId = SourceMetadataUtil.UNKNOWN_PATIENT;
+   private long _patientNum = SourceMetadataUtil.UNKNOWN_PATIENT_NUM;
+
+   private String _firstName = UNKNOWN;
+   private String _middleName = UNKNOWN;
+   private String _lastName = UNKNOWN;
+
+   private String _birthday = UNKNOWN_DATE;
+   private String _deathday = UNKNOWN_DATE;
+   private String _gender = UNKNOWN_GENDER;
+
+
+   private String _instanceId = "";
+   //   private long _instanceNum = -1;
+   private String _encounterId = "";
+//   private int _encounterNum = -1;
+
+   private String _docId = DocIdUtil.NO_DOCUMENT_ID;
+   private String _docIdPrefix = DocIdUtil.NO_DOCUMENT_ID_PREFIX;
+   private String _docType = NoteSpecs.ID_NAME_CLINICAL_NOTE;
+   private String _docSubType = "";
+   private String _docStandard = "";
+   private int _docRevisionNum = 1;
+   private String _docTime = ""; //DATE_FORMAT.format( System.currentTimeMillis() );
+   private String _docPath = "";
+
+
+   private String _docText = "";
+
+   private boolean _overwrite = false;
+
+
+   public JCasBuilder overwrite() {
+      _overwrite = true;
+      return this;
+   }
+
+   public JCasBuilder setInstitutionId( final String institutionId ) {
+      _institutionId = institutionId;
+      return this;
+   }
+
+   public JCasBuilder setAuthorSpecialty( final String authorSpecialty ) {
+      _authorSpecialty = authorSpecialty;
+      return this;
+   }
+
+   public JCasBuilder setPatientId( final String patientId ) {
+      _patientId = patientId;
+      return this;
+   }
+
+   public JCasBuilder setPatientNum( final long patientNum ) {
+      _patientNum = patientNum;
+      return this;
+   }
+
+   public JCasBuilder setFirstName( final String firstName ) {
+      _firstName = firstName;
+      return this;
+   }
+
+   public JCasBuilder setMiddleName( final String middleName ) {
+      _middleName = middleName;
+      return this;
+   }
+
+   public JCasBuilder setLastName( final String lastName ) {
+      _lastName = lastName;
+      return this;
+   }
+
+   public JCasBuilder setBirthDay( final String birthday ) {
+      _birthday = birthday;
+      return this;
+   }
+
+   public JCasBuilder setDeathday( final String deathday ) {
+      _deathday = deathday;
+      return this;
+   }
+
+   public JCasBuilder setGender( final String gender ) {
+      _gender = gender;
+      return this;
+   }
+
+   public JCasBuilder setInstanceId( final String instanceId ) {
+      _instanceId = instanceId;
+      return this;
+   }
+
+   public JCasBuilder setEncounterId( final String encounterId ) {
+      _encounterId = encounterId;
+      return this;
+   }
+
+//   public JCasBuilder setEncounterNum( final int encounterNum ) {
+//      _encounterNum = encounterNum;
+//      return this;
+//   }
+
+   public JCasBuilder setDocId( final String docId ) {
+      _docId = docId;
+      return this;
+   }
+
+   public JCasBuilder setDocIdPrefix( final String docIdPrefix ) {
+      _docIdPrefix = docIdPrefix;
+      return this;
+   }
+
+   public JCasBuilder setDocType( final String docType ) {
+      _docType = docType;
+      return this;
+   }
+
+   public JCasBuilder setDocSubType( final String docSubType ) {
+      _docSubType = docSubType;
+      return this;
+   }
+
+   public JCasBuilder setDocStandard( final String docStandard ) {
+      _docStandard = docStandard;
+      return this;
+   }
+
+   public JCasBuilder setDocRevisionNum( final int docRevisionNum ) {
+      _docRevisionNum = docRevisionNum;
+      return this;
+   }
+
+   public JCasBuilder setDocTime( final String docTime ) {
+      _docTime = docTime;
+      return this;
+   }
+
+   public JCasBuilder setDocPath( final String docPath ) {
+      _docPath = docPath;
+      return this;
+   }
+
+   public JCasBuilder setDocText( final String docText ) {
+      _docText = docText;
+      return this;
+   }
+
+   /**
+    * @return a jcas created from scratch and populated with data added in this builder.
+    * @throws UIMAException is the fresh jcas cannot be created.
+    */
+   public JCas build() throws UIMAException {
+      return populate( JCasFactory.createJCas() );
+   }
+
+   /**
+    * @param jCas ye olde ...
+    * @return a jcas  that has been reset (emptied of previous information) and populated
with data added in this builder.
+    */
+   public JCas rebuild( final JCas jCas ) {
+      jCas.reset();
+      return populate( jCas );
+   }
+
+   private boolean ifWrite( final String value, final String defaultValue ) {
+      return _overwrite || !value.equals( defaultValue );
+   }
+
+   private boolean ifWrite( final int value, final int defaultValue ) {
+      return _overwrite || value != defaultValue;
+   }
+
+   private boolean ifWrite( final long value, final long defaultValue ) {
+      return _overwrite || value != defaultValue;
+   }
+
+
+   /**
+    * @param jCas ye olde ...
+    * @return the given jcas populated with the data added in this builder.
+    */
+   public JCas populate( final JCas jCas ) {
+      final Metadata metadata = SourceMetadataUtil.getOrCreateMetadata( jCas );
+
+      if ( ifWrite( _patientId, SourceMetadataUtil.UNKNOWN_PATIENT ) ) {
+         SourceMetadataUtil.setPatientIdentifier( jCas, _patientId );
+      }
+      if ( ifWrite( _patientNum, SourceMetadataUtil.UNKNOWN_PATIENT_NUM ) ) {
+         metadata.setPatientID( _patientNum );
+      }
+
+      final Demographics demographics = new Demographics( jCas );
+      metadata.setDemographics( demographics );
+      if ( ifWrite( _firstName, UNKNOWN ) ) {
+         demographics.setFirstName( _firstName );
+      }
+      if ( ifWrite( _middleName, UNKNOWN ) ) {
+         demographics.setMiddleName( _middleName );
+      }
+      if ( ifWrite( _lastName, UNKNOWN ) ) {
+         demographics.setLastName( _lastName );
+      }
+      if ( ifWrite( _birthday, UNKNOWN_DATE ) ) {
+         demographics.setBirthDate( _birthday );
+      }
+      if ( ifWrite( _deathday, UNKNOWN_DATE ) ) {
+         demographics.setDeathDate( _deathday );
+      }
+      if ( ifWrite( _gender, UNKNOWN_GENDER ) ) {
+         demographics.setGender( _gender );
+      }
+
+      final SourceData sourceData = SourceMetadataUtil.getOrCreateSourceData( jCas );
+      if ( ifWrite( _institutionId, UNKNOWN ) ) {
+         sourceData.setSourceInstitution( _institutionId );
+      }
+      if ( ifWrite( _authorSpecialty, UNKNOWN ) ) {
+         sourceData.setAuthorSpecialty( _authorSpecialty );
+      }
+      if ( ifWrite( _encounterId, "" ) ) {
+         sourceData.setSourceEncounterId( _encounterId );
+      }
+      if ( ifWrite( _instanceId, UNKNOWN ) ) {
+         sourceData.setSourceInstanceId( _instanceId );
+      }
+
+      if ( ifWrite( _docId, DocIdUtil.NO_DOCUMENT_ID ) ) {
+         final DocumentID documentId = new DocumentID( jCas );
+         documentId.setDocumentID( _docId );
+         documentId.addToIndexes();
+      }
+
+      if ( ifWrite( _docIdPrefix, DocIdUtil.NO_DOCUMENT_ID_PREFIX ) ) {
+         final DocumentIdPrefix documentIdPrefix = new DocumentIdPrefix( jCas );
+         documentIdPrefix.setDocumentIdPrefix( _docIdPrefix );
+         documentIdPrefix.addToIndexes();
+      }
+
+      if ( ifWrite( _docType, NoteSpecs.ID_NAME_CLINICAL_NOTE ) ) {
+         sourceData.setNoteTypeCode( _docType );
+      }
+      if ( ifWrite( _docSubType, "" ) ) {
+         sourceData.setNoteSubTypeCode( _docSubType );
+      }
+      if ( ifWrite( _docStandard, "" ) ) {
+         sourceData.setDocumentStandard( _docStandard );
+      }
+
+      if ( ifWrite( _docTime, "" ) ) {
+         sourceData.setSourceRevisionDate( _docTime );
+      }
+      if ( ifWrite( _docRevisionNum, 1 ) ) {
+         sourceData.setSourceRevisionNbr( _docRevisionNum );
+      }
+
+      if ( ifWrite( _docPath, "" ) ) {
+         final DocumentPath documentPath = new DocumentPath( jCas );
+         documentPath.setDocumentPath( _docPath );
+         documentPath.addToIndexes();
+      }
+
+      if ( ifWrite( _docText, "" ) ) {
+         jCas.setDocumentText( _docText );
+      }
+
+      return jCas;
+   }
+
+}

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java?rev=1877092&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
(added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java
Mon Apr 27 19:06:09 2020
@@ -0,0 +1,87 @@
+package org.apache.ctakes.core.semantic;
+
+import org.apache.ctakes.typesystem.type.textsem.*;
+import org.apache.uima.jcas.JCas;
+
+import java.util.Collection;
+import java.util.function.Function;
+
+import static org.apache.ctakes.typesystem.type.constants.CONST.*;
+
+/**
+ * @deprecated use SemanticGroup in core.util.annotation
+ */
+@Deprecated
+public enum SemanticGroup {
+   DRUG( NE_TYPE_ID_DRUG, "Drug", MedicationMention.class, MedicationMention::new ),
+   DISORDER( NE_TYPE_ID_DISORDER, "Disorder", DiseaseDisorderMention.class, DiseaseDisorderMention::new
),
+   FINDING( NE_TYPE_ID_FINDING, "Finding", SignSymptomMention.class, SignSymptomMention::new
),
+   PROCEDURE( NE_TYPE_ID_PROCEDURE, "Procedure", ProcedureMention.class, ProcedureMention::new
),
+   ANATOMY( NE_TYPE_ID_ANATOMICAL_SITE, "Anatomy", AnatomicalSiteMention.class, AnatomicalSiteMention::new
),
+   CLINICAL_ATTRIBUTE( NE_TYPE_ID_CLINICAL_ATTRIBUTE, "Attribute", SignSymptomMention.class,
SignSymptomMention::new ),
+   DEVICE( NE_TYPE_ID_DEVICE, "Device", EntityMention.class, EntityMention::new ),
+   LAB( NE_TYPE_ID_LAB, "Lab", LabMention.class, LabMention::new ),
+   PHENOMENON( NE_TYPE_ID_PHENOMENA, "Phenomenon", EventMention.class, EventMention::new
),
+   SUBJECT( NE_TYPE_ID_SUBJECT_MODIFIER, "Subject", SubjectModifier.class, SubjectModifier::new
),
+   TITLE( NE_TYPE_ID_PERSON_TITLE, "Title", PersonTitleAnnotation.class, PersonTitleAnnotation::new
),
+   EVENT( NE_TYPE_ID_GENERIC_EVENT, "Event", EventMention.class, EventMention::new ),
+   ENTITY( NE_TYPE_ID_GENERIC_ENTITY, "Entity", EntityMention.class, EntityMention::new ),
+   TIME( NE_TYPE_ID_TIME_MENTION, "Time", TimeMention.class, TimeAnnotation::new ),
+   MODIFIER( NE_TYPE_ID_GENERIC_MODIFIER, "Modifier", Modifier.class, Modifier::new ),
+   LAB_MODIFIER( NE_TYPE_ID_LAB_VALUE_MODIFIER, "LabModifier", LabValueModifier.class, LabValueModifier::new
),
+   UNKNOWN( NE_TYPE_ID_UNKNOWN, "Unknown", IdentifiedAnnotation.class, IdentifiedAnnotation::new
);
+
+   private final int _code;
+   private final String _name;
+   private final Class<? extends IdentifiedAnnotation> _clazz;
+   private final Function<JCas, ? extends IdentifiedAnnotation> _creator;
+
+   SemanticGroup( final int code, final String name,
+                  final Class<? extends IdentifiedAnnotation> clazz,
+                  final Function<JCas, ? extends IdentifiedAnnotation> creator ) {
+      _code = code;
+      _name = name;
+      _clazz = clazz;
+      _creator = creator;
+   }
+
+   public int getCode() {
+      return _code;
+   }
+
+   public String getName() {
+      return _name;
+   }
+
+   public Class<? extends IdentifiedAnnotation> getCtakesClass() {
+      return _clazz;
+   }
+
+   public Function<JCas, ? extends IdentifiedAnnotation> getCreator() {
+      return _creator;
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticGroup getGroup( final int
code ) {
+      return org.apache.ctakes.core.util.annotation.SemanticGroup.getGroup( code );
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticGroup getGroup( final String
name ) {
+      return org.apache.ctakes.core.util.annotation.SemanticGroup.getGroup( name );
+   }
+
+   static public Collection<org.apache.ctakes.core.util.annotation.SemanticGroup> getGroups(
+         final IdentifiedAnnotation annotation ) {
+      return org.apache.ctakes.core.util.annotation.SemanticGroup.getGroups( annotation );
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticGroup getBestGroup(
+         final IdentifiedAnnotation annotation ) {
+      return org.apache.ctakes.core.util.annotation.SemanticGroup.getBestGroup( getGroups(
annotation ) );
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticGroup getBestGroup(
+         final Collection<org.apache.ctakes.core.util.annotation.SemanticGroup> groups
) {
+      return org.apache.ctakes.core.util.annotation.SemanticGroup.getBestGroup( groups );
+   }
+
+}

Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java?rev=1877092&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
(added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java
Mon Apr 27 19:06:09 2020
@@ -0,0 +1,217 @@
+package org.apache.ctakes.core.semantic;
+
+import org.apache.ctakes.core.util.annotation.SemanticGroup;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.jcas.JCas;
+
+import java.util.Collection;
+import java.util.function.Function;
+
+import static org.apache.ctakes.core.util.annotation.SemanticGroup.*;
+
+/**
+ * @deprecated use SemanticTui in core.util.annotation
+ */
+@Deprecated
+public enum SemanticTui {
+   T116( 116, "Amino Acid, Peptide, or Protein", DRUG ),
+   T020( 20, "Acquired Abnormality", DISORDER ),
+   T052( 52, "Activity", EVENT ),
+   T100( 100, "Age Group", SUBJECT ),
+   T003( 3, "Alga", ENTITY ),
+   T087( 87, "Amino Acid Sequence", DRUG ),
+   T011( 11, "Amphibian", ENTITY ),
+   T190( 190, "Anatomical Abnormality", DISORDER ),
+   T008( 8, "Animal", ENTITY ),
+   T017( 17, "Anatomical Structure", ANATOMY ),
+   T195( 195, "Antibiotic", DRUG ),
+   T194( 194, "Archaeon", ENTITY ),
+   T123( 123, "Biologically Active Substance", DRUG ),
+   T007( 7, "Bacterium", ENTITY ),
+   T031( 31, "Body Substance", FINDING ),
+   T022( 22, "Body System", ANATOMY ),
+   T053( 53, "Behavior", FINDING ),
+   T038( 38, "Biologic Function", PHENOMENON ),
+   T012( 12, "Bird", ENTITY ),
+   T029( 29, "Body Location or Region", ANATOMY ),
+   T091( 91, "Biomedical Occupation or Discipline", TITLE ),
+   T122( 122, "Biomedical or Dental Material", DRUG ),
+   T023( 23, "Body Part, Organ, or Organ Component", ANATOMY ),
+   T030( 30, "Body Space or Junction", ANATOMY ),
+   T118( 118, "Carbohydrate", DRUG ),
+   T026( 26, "Cell Component", ANATOMY ),
+   T043( 43, "Cell Function", FINDING ),
+   T025( 25, "Cell", ANATOMY ),
+   T019( 19, "Congenital Abnormality", DISORDER ),
+   T103( 103, "Chemical", DRUG ),
+   T120( 120, "Chemical Viewed Functionally", DRUG ),
+   T104( 104, "Chemical Viewed Structurally", DRUG ),
+   T185( 185, "Classification", FINDING ),
+   T201( 201, "Clinical Attribute", CLINICAL_ATTRIBUTE ),
+   T200( 200, "Clinical Drug", DRUG ),
+   T077( 77, "Conceptual Entity", FINDING ),
+   T049( 49, "Cell or Molecular Dysfunction", DISORDER ),
+   T088( 88, "Carbohydrate Sequence", DRUG ),
+   T060( 60, "Diagnostic Procedure", PROCEDURE ),
+   T056( 56, "Daily or Recreational Activity", FINDING ),
+   T047( 47, "Disease or Syndrome", DISORDER ),
+   T203( 203, "Drug Delivery Device", DEVICE ),
+   T065( 65, "Educational Activity", PROCEDURE ),
+   T069( 69, "Environmental Effect of Humans", PHENOMENON ),
+   T111( 111, "Eicosanoid", ENTITY ),
+   T196( 196, "Element, Ion, or Isotope", DRUG ),
+   T050( 50, "Experimental Model of Disease", DISORDER ),
+   T018( 18, "Embryonic Structure", ANATOMY ),
+   T071( 71, "Entity", ENTITY ),
+   T126( 126, "Enzyme", DRUG ),
+   T051( 51, "Event", EVENT ),
+   T099( 99, "Family Group", SUBJECT ),
+   T021( 21, "Fully Formed Anatomical Structure", ANATOMY ),
+   T013( 13, "Fish", ENTITY ),
+   T033( 33, "Finding", FINDING ),
+   T004( 4, "Fungus", ENTITY ),
+   T168( 168, "Food", DRUG ),
+   T169( 169, "Functional Concept", FINDING ),
+   // double-check
+   T045( 45, "Genetic Function", FINDING ),
+   T083( 83, "Geographic Area", ENTITY ),
+   T028( 28, "Gene or Genome", FINDING ),
+   T064( 64, "Governmental or Regulatory Activity", EVENT ),
+   T102( 102, "Group Attribute", SUBJECT ),
+   T096( 96, "Group", SUBJECT ),
+   T068( 68, "Human-caused Phenomenon or Process", PHENOMENON ),
+   T093( 93, "Health Care Related Organization", ENTITY ),
+   T058( 58, "Health Care Activity", PROCEDURE ),
+   T131( 131, "Hazardous or Poisonous Substance", DRUG ),
+   T125( 125, "Hormone", DRUG ),
+   T016( 16, "Human", SUBJECT ),
+   T078( 78, "Idea or Concept", FINDING ),
+   T129( 129, "Immunologic Factor", DRUG ),
+   T055( 55, "Individual Behavior", FINDING ),
+   T197( 197, "Inorganic Chemical", DRUG ),
+   T037( 37, "Injury or Poisoning", DISORDER ),
+   T170( 170, "Intellectual Product", FINDING ),
+   // double-check
+   T009( 9, "Invertebrate", ENTITY ),
+   T130( 130, "Indicator, Reagent, or Diagnostic Aid", DRUG ),
+   T171( 171, "Language", ENTITY ),
+   T059( 59, "Laboratory Procedure", PROCEDURE ),
+   T034( 34, "Laboratory or Test Result", LAB ),
+   T119( 119, "Lipid", DRUG ),
+   T015( 15, "Mammal", ENTITY ),
+   T063( 63, "Molecular Biology Research Technique", PROCEDURE ),
+   T066( 66, "Machine Activity", PROCEDURE ),
+   T074( 74, "Medical Device", DEVICE ),
+   T041( 41, "Mental Process", FINDING ),
+   T073( 73, "Manufactured Object", DEVICE ),
+   T048( 48, "Mental or Behavioral Dysfunction", DISORDER ),
+   T044( 44, "Molecular Function", FINDING ),
+   T085( 85, "Molecular Sequence", FINDING ),
+   T191( 191, "Neoplastic Process", DISORDER ),
+   T114( 114, "Nucleic Acid, Nucleoside, or Nucleotide", DRUG ),
+   T070( 70, "Natural Phenomenon or Process", PHENOMENON ),
+   T124( 124, "Neuroreactive Substance or Biogenic Amine", DRUG ),
+   T086( 86, "Nucleotide Sequence", FINDING ),
+   T057( 57, "Occupational Activity", EVENT ),
+   T090( 90, "Occupation or Discipline", SUBJECT ),
+   T115( 115, "Organophosphorous Compound", DRUG ),
+   T109( 109, "Organic Chemical", DRUG ),
+   T032( 32, "Organism Attribute", SUBJECT ),
+   T040( 40, "Organism Function", FINDING ),
+   T001( 1, "Organism", ENTITY ),
+   T092( 92, "Organization", ENTITY ),
+   T042( 42, "Organ or Tissue Function", FINDING ),
+   T046( 46, "Pathologic Function", FINDING ),
+   T072( 72, "Physical Object", ENTITY ),
+   T067( 67, "Phenomenon or Process", PHENOMENON ),
+   T039( 39, "Physiologic Function", FINDING ),
+   T121( 121, "Pharmacologic Substance", DRUG ),
+   T002( 2, "Plant", ENTITY ),
+   T101( 101, "Patient or Disabled Group", SUBJECT ),
+   T098( 98, "Population Group", SUBJECT ),
+   T097( 97, "Professional or Occupational Group", SUBJECT ),
+   T094( 94, "Professional Society", ENTITY ),
+   T080( 80, "Qualitative Concept", MODIFIER ),
+   T081( 81, "Quantitative Concept", LAB_MODIFIER ),
+   T192( 192, "Receptor", FINDING ),
+   T014( 14, "Reptile", ENTITY ),
+   T062( 62, "Research Activity", PROCEDURE ),
+   T075( 75, "Research Device", DEVICE ),
+   T006( 6, "Rickettsia or Chlamydia", DISORDER ),
+   T089( 89, "Regulation or Law", ENTITY ),
+   T167( 167, "Substance", DRUG ),
+   // Double-check
+   T095( 95, "Self-help or Relief Organization", ENTITY ),
+   T054( 54, "Social Behavior", FINDING ),
+   T184( 184, "Sign or Symptom", FINDING ),
+   T082( 82, "Spatial Concept", MODIFIER ),
+   T110( 110, "Steroid", DRUG ),
+   T024( 24, "Tissue", ANATOMY ),
+   T079( 79, "Temporal Concept", TIME ),
+   T061( 61, "Therapeutic or Preventive Procedure", PROCEDURE ),
+   T005( 5, "Virus", DISORDER ),
+   T127( 127, "Vitamin", DRUG ),
+   T010( 10, "Vertebrate", ENTITY ),
+   UNKNOWN( 0, "Unknown", SemanticGroup.UNKNOWN );
+
+   private final int _code;
+   private final String _name;
+   private final SemanticGroup _group;
+
+   SemanticTui( final int code, final String name, final SemanticGroup group ) {
+      _code = code;
+      _name = name;
+      _group = group;
+   }
+
+   public int getCode() {
+      return _code;
+   }
+
+   public String getSemanticType() {
+      return _name;
+   }
+
+   public SemanticGroup getGroup() {
+      return _group;
+   }
+
+   public int getGroupCode() {
+      return _group.getCode();
+   }
+
+   public String getGroupName() {
+      return _group.getName();
+   }
+
+   public Class<? extends IdentifiedAnnotation> getCtakesClass() {
+      return _group.getCtakesClass();
+   }
+
+   public Function<JCas, ? extends IdentifiedAnnotation> getCreator() {
+      return _group.getCreator();
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticTui getTui( final String
semanticType ) {
+      return org.apache.ctakes.core.util.annotation.SemanticTui.getTui( semanticType );
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticTui getTui( final int code
) {
+      return org.apache.ctakes.core.util.annotation.SemanticTui.getTui( code );
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticTui getTuiFromCode( final
String tuiCode ) {
+      return org.apache.ctakes.core.util.annotation.SemanticTui.getTuiFromCode( tuiCode );
+   }
+
+   static public Collection<org.apache.ctakes.core.util.annotation.SemanticTui> getTuis(
+         final IdentifiedAnnotation annotation ) {
+      return org.apache.ctakes.core.util.annotation.SemanticTui.getTuis( annotation );
+   }
+
+   static public org.apache.ctakes.core.util.annotation.SemanticTui getTui( final UmlsConcept
umlsConcept ) {
+      return org.apache.ctakes.core.util.annotation.SemanticTui.getTui( umlsConcept );
+   }
+
+}



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