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Posted to commits@ctakes.apache.org by se...@apache.org on 2017/03/27 13:46:14 UTC
svn commit: r1788931 - in /ctakes/trunk:
ctakes-core/src/main/java/org/apache/ctakes/core/ae/
ctakes-core/src/main/java/org/apache/ctakes/core/cc/
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/
ctakes-core/src/main/java/org/apach...
Author: seanfinan
Date: Mon Mar 27 13:46:13 2017
New Revision: 1788931
URL: http://svn.apache.org/viewvc?rev=1788931&view=rev
Log:
PipeBitInfo update
Modified:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java
ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java
ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java Mon Mar 27 13:46:13 2017
@@ -20,9 +20,9 @@ import java.io.InputStreamReader;
* @since 10/5/2016
*/
@PipeBitInfo(
- name = "Regex Sectionizer (BSV)",
+ name = "Regex Sectionizer",
description = "Annotates Document Sections by detecting Section Headers using Regular Expressions provided in a Bar-Separated-Value (BSV) File.",
- output = "Segment Annotations."
+ products = { PipeBitInfo.TypeProduct.SECTION }
)
public class BsvRegexSectionizer extends RegexSectionizer {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java Mon Mar 27 13:46:13 2017
@@ -46,7 +46,8 @@ import java.util.regex.Pattern;
@PipeBitInfo(
name = "Segment Annotator (CDA)",
description = "Annotates Document Sections by detecting Section Headers using Regular Expressions provided in a File.",
- output = "Segment Annotations."
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID },
+ products = { PipeBitInfo.TypeProduct.SECTION }
)
public class CDASegmentAnnotator extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java Mon Mar 27 13:46:13 2017
@@ -47,9 +47,7 @@ import java.util.Map;
*/
@PipeBitInfo(
name = "JCas Copy Annotator",
- description = "Copies document text and all annotations into a new JCas.",
- input = "JCas.",
- output = "JCas copy."
+ description = "Copies document text and all annotations into a new JCas."
)
public class CopyAnnotator extends JCasAnnotator_ImplBase {
public static final String PARAM_SOURCE_CLASS = "srcObjClass";
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java Mon Mar 27 13:46:13 2017
@@ -30,7 +30,7 @@ import org.apache.uima.jcas.JCas;
name = "Document ID Printer",
description = "Logs the Document ID to Log4j and Standard Output.",
role = PipeBitInfo.Role.SPECIAL,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class DocumentIdPrinterAnalysisEngine extends JCasAnnotator_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java Mon Mar 27 13:46:13 2017
@@ -40,8 +40,7 @@ import org.apache.uima.resource.Resource
@PipeBitInfo(
name = "Annotation Remover",
description = "Removes annotations of a given type from the JCas.",
- input = PipeBitInfo.POPULATED_JCAS,
- output = "JCas without annotations of the given type."
+ dependencies = { PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class FilterAnnotator extends JCasAnnotator_ImplBase {
// TODO parameterize retainAttrTypeId = DISORDER_ANNOTATIONS = 2
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java Mon Mar 27 13:46:13 2017
@@ -36,7 +36,8 @@ import java.util.stream.Collectors;
@PipeBitInfo(
name = "List Annotator",
description = "Annotates formatted List Sections by detecting them using Regular Expressions provided in an input File.",
- output = "List and ListEntry annotations."
+ dependencies = { PipeBitInfo.TypeProduct.SECTION },
+ products = { PipeBitInfo.TypeProduct.LIST, PipeBitInfo.TypeProduct.LIST_ENTRY }
)
final public class ListAnnotator extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java Mon Mar 27 13:46:13 2017
@@ -22,8 +22,8 @@ import java.util.regex.Pattern;
@PipeBitInfo(
name = "List Sentence Fixer",
description = "Re-annotates Sentences based upon existing List Entries, preventing a Sentence from spanning more than one List Entry.",
- input = "Sentence and List Entry annotations.",
- output = "Adjusted Sentences."
+ dependencies = { PipeBitInfo.TypeProduct.LIST, PipeBitInfo.TypeProduct.LIST_ENTRY,
+ PipeBitInfo.TypeProduct.SENTENCE }
)
final public class ListSentenceFixer extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java Mon Mar 27 13:46:13 2017
@@ -34,8 +34,7 @@ import org.apache.uima.jcas.JCas;
*/
@PipeBitInfo(
name = "Null Annotator",
- description = "Does absolutely nothing.",
- output = PipeBitInfo.NO_OUTPUT
+ description = "Does absolutely nothing."
)
public class NullAnnotator extends JCasAnnotator_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java Mon Mar 27 13:46:13 2017
@@ -56,8 +56,7 @@ import java.util.*;
@PipeBitInfo(
name = "Overlap Annotator",
description = "Removes or modifies annotations that overlap.",
- input = PipeBitInfo.POPULATED_JCAS,
- output = "Removed or modified annotations."
+ dependencies = { PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class OverlapAnnotator extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java Mon Mar 27 13:46:13 2017
@@ -29,7 +29,8 @@ import java.util.regex.Pattern;
@PipeBitInfo(
name = "Paragraph Annotator",
description = "Annotates Paragraphs by detecting them using Regular Expressions provided in an input File or by empty text lines.",
- output = "Paragraph annotations."
+ dependencies = { PipeBitInfo.TypeProduct.SECTION },
+ products = { PipeBitInfo.TypeProduct.PARAGRAPH }
)
final public class ParagraphAnnotator extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java Mon Mar 27 13:46:13 2017
@@ -27,8 +27,7 @@ import java.util.stream.Collectors;
@PipeBitInfo(
name = "Paragraph Sentence Fixer",
description = "Re-annotates Sentences based upon existing Paragraphs, preventing a Sentence from spanning more than one Paragraph.",
- input = "Sentence and Paragraph annotations.",
- output = "Adjusted Sentences."
+ dependencies = { PipeBitInfo.TypeProduct.PARAGRAPH, PipeBitInfo.TypeProduct.SENTENCE }
)
final public class ParagraphSentenceFixer extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java Mon Mar 27 13:46:13 2017
@@ -27,9 +27,9 @@ import java.util.stream.Collectors;
* @since 7/20/2016
*/
@PipeBitInfo(
- name = "Regex Sectionizer",
+ name = "Regex Sectionizer (A)",
description = "Annotates Document Sections by detecting Section Headers using Regular Expressions.",
- output = "Segment Annotations."
+ products = { PipeBitInfo.TypeProduct.SECTION }
)
abstract public class RegexSectionizer extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java Mon Mar 27 13:46:13 2017
@@ -59,7 +59,9 @@ import java.util.*;
name = "Knowtator XML Reader",
description = "Reads annotations from Knowtator XML files in a directory.",
role = PipeBitInfo.Role.SPECIAL,
- output = PipeBitInfo.POPULATED_JCAS
+ products = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION, PipeBitInfo.TypeProduct.EVENT,
+ PipeBitInfo.TypeProduct.TIMEX, PipeBitInfo.TypeProduct.LOCATION_RELATION,
+ PipeBitInfo.TypeProduct.DEGREE_RELATION, PipeBitInfo.TypeProduct.TEMPORAL_RELATION }
)
public class SHARPKnowtatorXMLReader extends JCasAnnotator_ImplBase {
static Logger LOGGER = Logger.getLogger(SHARPKnowtatorXMLReader.class);
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java Mon Mar 27 13:46:13 2017
@@ -47,7 +47,7 @@ import java.util.HashMap;
@PipeBitInfo(
name = "Section Annotator",
description = "Annotates Document Sections by detecting Section Headers in template.",
- output = "Segment Annotations."
+ products = { PipeBitInfo.TypeProduct.SECTION }
)
public class SectionSegmentAnnotator extends JCasAnnotator_ImplBase {
private String segmentId;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java Mon Mar 27 13:46:13 2017
@@ -43,7 +43,10 @@ import org.apache.uima.fit.util.JCasUtil
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
import java.nio.charset.Charset;
import java.util.*;
@@ -55,7 +58,8 @@ import java.util.*;
@PipeBitInfo(
name = "Sentence Detector",
description = "Annotates Sentences based upon an OpenNLP model.",
- output = "Sentence annotations."
+ dependencies = { PipeBitInfo.TypeProduct.SECTION },
+ products = { PipeBitInfo.TypeProduct.SENTENCE }
)
public class SentenceDetector extends JCasAnnotator_ImplBase {
/**
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java Mon Mar 27 13:46:13 2017
@@ -39,7 +39,7 @@ import org.apache.uima.resource.Resource
@PipeBitInfo(
name = "Single Segment Annotator",
description = "Annotates Document as a single Section.",
- output = "Segment annotation."
+ products = { PipeBitInfo.TypeProduct.SECTION }
)
public class SimpleSegmentAnnotator extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java Mon Mar 27 13:46:13 2017
@@ -41,7 +41,7 @@ import java.io.StringReader;
@PipeBitInfo(
name = "Segment Annotator (Tag)",
description = "Annotates Document Sections by detecting start and end Section Tags.",
- output = "Segment Annotations."
+ products = { PipeBitInfo.TypeProduct.SECTION }
)
public class SimpleSegmentWithTagsAnnotator extends JCasAnnotator_ImplBase {
private String segmentId;
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java Mon Mar 27 13:46:13 2017
@@ -24,8 +24,7 @@ import org.apache.uima.resource.Resource
@PipeBitInfo(
name = "Start or Finish Logger",
description = "Simple Annotator to place before and after other annotators that do not Log their Start and Finish.",
- role = PipeBitInfo.Role.SPECIAL,
- output = PipeBitInfo.NO_OUTPUT
+ role = PipeBitInfo.Role.SPECIAL
)
public class StartFinishLogger extends JCasAnnotator_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java Mon Mar 27 13:46:13 2017
@@ -49,7 +49,8 @@ import java.util.Set;
@PipeBitInfo(
name = "Tokenizer Annotator",
description = "Annotates Document Tokens.",
- output = "Token annotations."
+ dependencies = { PipeBitInfo.TypeProduct.SECTION },
+ products = { PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class TokenizerAnnotator extends JCasAnnotator_ImplBase {
// LOG4J logger based on class name
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java Mon Mar 27 13:46:13 2017
@@ -37,6 +37,8 @@ import org.apache.uima.resource.Resource
import java.util.*;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
+
/**
* UIMA annotator that tokenizes based on Penn Treebank rules.
*
@@ -45,7 +47,8 @@ import java.util.*;
@PipeBitInfo(
name = "Tokenizer Annotator (PTB)",
description = "Annotates Document Penn TreeBank Tokens.",
- output = "Token annotations."
+ dependencies = { SECTION, SENTENCE },
+ products = { BASE_TOKEN }
)
public class TokenizerAnnotatorPTB extends JCasAnnotator_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java Mon Mar 27 13:46:13 2017
@@ -42,8 +42,7 @@ import java.io.OutputStream;
name = "XMI Writer (CasConsumer)",
description = "Writes XMI files with full representation of input text and all extracted information.",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class CasConsumer extends CasConsumer_ImplBase {
// LOG4J logger based on class name
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java Mon Mar 27 13:46:13 2017
@@ -37,8 +37,7 @@ import static org.apache.ctakes.core.con
name = "CUI Count Writer",
description = "Writes a two-column BSV file containing CUIs and their total counts in a document.",
role = PipeBitInfo.Role.WRITER,
- input = "CUI " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
// TODO extend AbstractOutputFileWriter
public class CuiCountFileWriter extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java Mon Mar 27 13:46:13 2017
@@ -24,14 +24,17 @@ import java.io.*;
name = "XMI Writer (Dir Tree)",
description = "Writes XMI files with full representation of input text and all extracted information.",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID },
+ usables = { PipeBitInfo.TypeProduct.DOCUMENT_ID_PREFIX }
)
// TODO Create and extend AbstractInputFileReader a'la the abstract writer
final public class FileTreeXmiWriter extends AbstractOutputFileWriter {
static private final Logger LOGGER = Logger.getLogger( "FileTreeXmiWriter" );
+ /**
+ * {@inheritDoc}
+ */
@Override
public void writeFile( final JCas jCas, final String outputDir,
final String documentId, final String fileName ) throws IOException {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java Mon Mar 27 13:46:13 2017
@@ -46,8 +46,7 @@ import java.io.*;
name = "Document Text Writer",
description = "Writes Text files with original text from the document.",
role = PipeBitInfo.Role.WRITER,
- input = "Document Text.",
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class FilesInDirectoryCasConsumer extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java Mon Mar 27 13:46:13 2017
@@ -46,8 +46,7 @@ import java.util.*;
name = "HTML Table Writer",
description = "Writes HTML files with a Table representation of extracted information.",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class HtmlTableCasConsumer extends CasConsumer_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java Mon Mar 27 13:46:13 2017
@@ -44,8 +44,7 @@ import java.util.*;
name = "JDBC Writer (Template)",
description = "Stores extracted information and document metadata in a database.",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
public class JdbcWriterTemplate extends AbstractJdbcWriter {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java Mon Mar 27 13:46:13 2017
@@ -49,8 +49,7 @@ import java.io.*;
name = "Document Text Writer (Dir)",
description = "Writes Text files with original text from the document in a specified directory.",
role = PipeBitInfo.Role.WRITER,
- input = "Document Text.",
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class NormalizedFilesInDirectoryCasConsumer extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java Mon Mar 27 13:46:13 2017
@@ -37,8 +37,8 @@ import static org.apache.ctakes.core.con
name = "Sentences Writer",
description = "Writes Text files with original text from the document, sentence by sentence.",
role = PipeBitInfo.Role.WRITER,
- input = "Sentence " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class SentenceTokensPrinter extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java Mon Mar 27 13:46:13 2017
@@ -33,8 +33,7 @@ import static org.apache.ctakes.core.con
name = "Text Span Writer",
description = "Writes BSV files with original text for extracted annotations and their span offsets.",
role = PipeBitInfo.Role.WRITER,
- input = "IdentifiedAnnotation " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
public class TextSpanWriter extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java Mon Mar 27 13:46:13 2017
@@ -44,8 +44,7 @@ import java.util.*;
name = "Word Count Writer",
description = "Writes a two-column BSV file containing Words and their total counts in a document.",
role = PipeBitInfo.Role.WRITER,
- input = "WordToken " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class TokenFreqCasConsumer extends CasConsumer_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java Mon Mar 27 13:46:13 2017
@@ -55,8 +55,7 @@ import java.util.List;
name = "Token Offset Writer",
description = "Writes a two-column BSV file containing Begin and End offsets of tokens in a document.",
role = PipeBitInfo.Role.WRITER,
- input = "BaseToken " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.BASE_TOKEN }
)
public class TokenOffsetsCasConsumer extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java Mon Mar 27 13:46:13 2017
@@ -78,8 +78,7 @@ import java.net.URL;
name = "XMI Writer (CasConsumerCtakes)",
description = "Writes XMI files with full representation of input text and all extracted information.",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class XmiWriterCasConsumerCtakes extends CasConsumer_ImplBase {
/**
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java Mon Mar 27 13:46:13 2017
@@ -11,7 +11,7 @@ import org.apache.uima.resource.Resource
import java.io.IOException;
import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPUTDIR;
-
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
/**
* Writes Document text, pos, semantic types and cuis. Each Sentence starts a new series of pretty text lines.
@@ -29,8 +29,8 @@ import static org.apache.ctakes.core.con
name = "Pretty Text Writer",
description = "Writes text files with document text and simple markups (POS, Semantic Group, CUI, Negation).",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { DOCUMENT_ID, SENTENCE, BASE_TOKEN },
+ usables = { DOCUMENT_ID_PREFIX, IDENTIFIED_ANNOTATION, EVENT, TIMEX, TEMPORAL_RELATION }
)
final public class PrettyTextWriterFit extends AbstractOutputFileWriter {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java Mon Mar 27 13:46:13 2017
@@ -10,6 +10,7 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import static org.apache.ctakes.core.config.ConfigParameterConstants.PARAM_OUTPUTDIR;
+import static org.apache.ctakes.core.pipeline.PipeBitInfo.TypeProduct.*;
/**
* Writes Document text, pos, semantic types and cuis. Each Sentence starts a new series of pretty text lines.
@@ -25,8 +26,8 @@ import static org.apache.ctakes.core.con
name = "Pretty Text Writer (UIMA)",
description = "Writes text files with document text and simple markups (POS, Semantic Group, CUI, Negation).",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { DOCUMENT_ID, SENTENCE, BASE_TOKEN },
+ usables = { IDENTIFIED_ANNOTATION, EVENT, TIMEX, TEMPORAL_RELATION }
)
final public class PrettyTextWriterUima extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java Mon Mar 27 13:46:13 2017
@@ -30,8 +30,8 @@ import static org.apache.ctakes.core.con
name = "Property Text Writer",
description = "Writes text files with lists of annotations and properties (POS, Semantic Group, CUI, Negation).",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
public class PropertyTextWriterFit extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java Mon Mar 27 13:46:13 2017
@@ -25,8 +25,8 @@ import static org.apache.ctakes.core.con
name = "Property Text Writer (UIMA)",
description = "Writes text files with lists of annotations and properties (POS, Semantic Group, CUI, Negation).",
role = PipeBitInfo.Role.WRITER,
- input = PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.SENTENCE,
+ PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
public class PropertyTextWriterUima extends CasConsumer_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java Mon Mar 27 13:46:13 2017
@@ -12,6 +12,15 @@ final public class ConfigParameterConsta
/**
* Name of configuration parameter that can be set to the path of
+ * a Piper file.
+ */
+ static public final String PARAM_PIPER = "Piper";
+ static public final String OPTION_PIPER = "-p";
+ static public final String DESC_PIPER = "Location of a Piper File.";
+
+
+ /**
+ * Name of configuration parameter that can be set to the path of
* a directory containing input files.
*/
static public final String PARAM_INPUTDIR = "InputDirectory";
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java Mon Mar 27 13:46:13 2017
@@ -38,7 +38,7 @@ import java.util.List;
name = "Files in Dir Tree Reader",
description = "Reads document texts from text files in a directory tree.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.DOCUMENT_ID_PREFIX }
)
final public class FileTreeReader extends JCasCollectionReader_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java Mon Mar 27 13:46:13 2017
@@ -57,7 +57,7 @@ import java.io.IOException;
name = "Files in Dir Cycle Reader",
description = "Reads document texts from text files in a directory, repeating for a number of iterations.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class FilesInDirectoryCollectionCyclicalReads extends FilesInDirectoryCollectionReader
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java Mon Mar 27 13:46:13 2017
@@ -63,7 +63,7 @@ import java.util.List;
name = "Files in Dir Reader",
description = "Reads document texts from text files in a directory.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class FilesInDirectoryCollectionReader extends CollectionReader_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java Mon Mar 27 13:46:13 2017
@@ -45,7 +45,7 @@ import java.util.StringTokenizer;
name = "JDBC Collection Reader",
description = "Reads document texts from database text fields.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class JdbcCollectionReader extends CollectionReader_ImplBase
{
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java Mon Mar 27 13:46:13 2017
@@ -56,7 +56,7 @@ import java.util.List;
name = "Lines in File Reader",
description = "Reads a document texts from a single text file, treating each line as a document.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class LinesFromFileCollectionReader extends CollectionReader_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java Mon Mar 27 13:46:13 2017
@@ -26,7 +26,7 @@ import java.io.IOException;
name = "Lucene Field Reader",
description = "Reads document texts from Lucene text fields.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class LuceneCollectionReader extends CasCollectionReader_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java Mon Mar 27 13:46:13 2017
@@ -41,7 +41,7 @@ import java.util.List;
name = "Text Files Reader",
description = "Reads document texts from text files specified in a provided list.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.NEW_JCAS
+ products = PipeBitInfo.TypeProduct.DOCUMENT_ID
)
public class TextReader extends JCasCollectionReader_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java Mon Mar 27 13:46:13 2017
@@ -44,7 +44,7 @@ import java.util.List;
name = "XMI Files Reader",
description = "Reads document texts and annotations from XMI files specified in a provided list.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.POPULATED_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class XMIReader extends JCasCollectionReader_ImplBase {
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java Mon Mar 27 13:46:13 2017
@@ -42,7 +42,7 @@ import java.util.ArrayList;
name = "XMI in Dir Reader",
description = "Reads document texts and annotations from XMI files in a directory.",
role = PipeBitInfo.Role.READER,
- output = PipeBitInfo.POPULATED_JCAS
+ products = { PipeBitInfo.TypeProduct.DOCUMENT_ID }
)
public class XmiCollectionReaderCtakes extends CollectionReader_ImplBase {
/**
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java Mon Mar 27 13:46:13 2017
@@ -125,8 +125,7 @@ public enum CuiCollector {
name = "CUI Collector",
description = "Collects all CUIs generated during a run.",
role = PipeBitInfo.Role.SPECIAL,
- input = "CUI " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
static public final class CuiCollectorEngine extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java Mon Mar 27 13:46:13 2017
@@ -132,8 +132,7 @@ public enum EntityCollector {
name = "Entity Collector",
description = "Collects information on entities generated during a run.",
role = PipeBitInfo.Role.SPECIAL,
- input = "IdentifiedAnnotation " + PipeBitInfo.POPULATED_JCAS,
- output = PipeBitInfo.NO_OUTPUT
+ dependencies = { PipeBitInfo.TypeProduct.DOCUMENT_ID, PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION }
)
static public final class EntityCollectorEngine extends JCasAnnotator_ImplBase {
@Override
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java Mon Mar 27 13:46:13 2017
@@ -1,6 +1,21 @@
package org.apache.ctakes.core.pipeline;
+import org.apache.ctakes.typesystem.type.refsem.Event;
+import org.apache.ctakes.typesystem.type.relation.*;
+import org.apache.ctakes.typesystem.type.structured.DocumentID;
+import org.apache.ctakes.typesystem.type.structured.DocumentIdPrefix;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textsem.Markable;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.ctakes.typesystem.type.textspan.ListEntry;
+import org.apache.ctakes.typesystem.type.textspan.Paragraph;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.jcas.cas.TOP;
+
import java.lang.annotation.*;
/**
@@ -20,12 +35,54 @@ public @interface PipeBitInfo {
READER, ANNOTATOR, WRITER, SPECIAL
}
- String NO_INPUT = "No Required Input.";
- String NO_OUTPUT = "No Produced Output.";
String NO_PARAMETERS = "No Parameters.";
- String NO_DEPENDENCIES = "No Dependencies.";
- String NEW_JCAS = "New JCas.";
- String POPULATED_JCAS = "Populated JCas.";
+ TypeProduct[] NO_TYPE_PRODUCTS = new TypeProduct[ 0 ];
+
+
+ /**
+ * Using an enum allows us to use a TypeSystem equivalent in the annotation
+ */
+ enum TypeProduct {
+ TOP( TOP.class ),
+ DOCUMENT_ID( DocumentID.class ),
+ DOCUMENT_ID_PREFIX( DocumentIdPrefix.class ),
+ SECTION( Segment.class ),
+ SENTENCE( Sentence.class ),
+ PARAGRAPH( Paragraph.class ),
+ LIST( org.apache.ctakes.typesystem.type.textspan.List.class ),
+ LIST_ENTRY( ListEntry.class ),
+ BASE_TOKEN( BaseToken.class ),
+ CHUNK( Chunk.class ),
+ IDENTIFIED_ANNOTATION( IdentifiedAnnotation.class ),
+ EVENT( Event.class ),
+ TIMEX( TimeMention.class ),
+ GENERIC_RELATION( BinaryTextRelation.class ),
+ LOCATION_RELATION( LocationOfTextRelation.class ),
+ DEGREE_RELATION( DegreeOfTextRelation.class ),
+ TEMPORAL_RELATION( TemporalTextRelation.class ),
+ MARKABLE( Markable.class ),
+ COREFERENCE_RELATION( CoreferenceRelation.class );
+
+ final Class<? extends TOP> _classType;
+
+ TypeProduct( final Class<? extends TOP> classType ) {
+ _classType = classType;
+ }
+
+ @Override
+ public String toString() {
+ return _classType.getSimpleName();
+ }
+
+ static public TypeProduct getForClass( Class<? extends TOP> classType ) {
+ for ( TypeProduct typeProduct : TypeProduct.values() ) {
+ if ( typeProduct._classType.equals( classType ) ) {
+ return typeProduct;
+ }
+ }
+ return TOP;
+ }
+ }
/**
* @return Human-readable name of the Reader, Annotator, or Writer
@@ -43,23 +100,24 @@ public @interface PipeBitInfo {
String description();
/**
- * @return Human-readable description of the input of the Reader, Annotator, or Writer
+ * @return Human-readable names of Configuration Parameters
*/
- String input() default NO_INPUT;
+ String[] parameters() default { NO_PARAMETERS };
/**
- * @return Human-readable description of the output of the Reader, Annotator, or Writer
+ * @return array of typesystem type dependencies of the Reader, Annotator, or Writer
*/
- String output();
+ TypeProduct[] dependencies() default {};
/**
- * @return Human-readable names of Configuration Parameters
+ * @return array of usable but not required typesystem types of the Reader, Annotator, or Writer
*/
- String[] parameters() default { NO_PARAMETERS };
+ TypeProduct[] usables() default {};
/**
- * @return Human-readable array of dependencies of the Reader, Annotator, or Writer
+ * @return array of typesystem type products of the Reader, Annotator, or Writer
*/
- String[] dependencies() default { NO_DEPENDENCIES };
+ TypeProduct[] products() default {};
+
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java Mon Mar 27 13:46:13 2017
@@ -12,6 +12,7 @@ import java.lang.reflect.Field;
import java.util.*;
import java.util.stream.Collectors;
+
/**
* @author SPF , chip-nlp
* @version %I%
@@ -157,33 +158,36 @@ final public class PipeBitInfoUtil {
* {@inheritDoc}
*/
@Override
- public String input() {
- return "Unknown Inputs.";
+ public String[] parameters() {
+ final Collection<String> parameters = getParameterDescriptions( _pipeBitClass );
+ return parameters.toArray( new String[ parameters.size() ] );
}
/**
* {@inheritDoc}
*/
@Override
- public String output() {
- return "Unknown Outputs.";
+ public TypeProduct[] dependencies() {
+ if ( CollectionReader_ImplBase.class.isAssignableFrom( _pipeBitClass ) ) {
+ return NO_TYPE_PRODUCTS;
+ }
+ return new TypeProduct[] { TypeProduct.SECTION, TypeProduct.BASE_TOKEN };
}
/**
* {@inheritDoc}
*/
@Override
- public String[] parameters() {
- final Collection<String> parameters = getParameterDescriptions( _pipeBitClass );
- return parameters.toArray( new String[ parameters.size() ] );
+ public TypeProduct[] usables() {
+ return NO_TYPE_PRODUCTS;
}
/**
* {@inheritDoc}
*/
@Override
- public String[] dependencies() {
- return new String[] { "Unknown Dependencies." };
+ public TypeProduct[] products() {
+ return NO_TYPE_PRODUCTS;
}
/**
Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java Mon Mar 27 13:46:13 2017
@@ -41,7 +41,8 @@ import java.util.List;
@PipeBitInfo(
name = "Dictionary Lookup (Default)",
description = "Annotates clinically-relevant terms. Terms must match dictionary entries exactly.",
- output = "Clinically-relevant Terms and their unique concept identifiers."
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.BASE_TOKEN },
+ products = PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION
)
final public class DefaultJCasTermAnnotator extends AbstractJCasTermAnnotator {
Modified: ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java Mon Mar 27 13:46:13 2017
@@ -47,7 +47,8 @@ import java.util.List;
@PipeBitInfo(
name = "Dictionary Lookup (Default)",
description = "Annotates clinically-relevant terms. Terms can overlap dictionary entries.",
- output = "Clinically-relevant Terms and their unique concept identifiers."
+ dependencies = { PipeBitInfo.TypeProduct.SENTENCE, PipeBitInfo.TypeProduct.BASE_TOKEN },
+ products = PipeBitInfo.TypeProduct.IDENTIFIED_ANNOTATION
)
final public class OverlapJCasTermAnnotator extends AbstractJCasTermAnnotator {
Modified: ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java?rev=1788931&r1=1788930&r2=1788931&view=diff
==============================================================================
--- ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java (original)
+++ ctakes/trunk/ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java Mon Mar 27 13:46:13 2017
@@ -23,8 +23,7 @@ import java.io.IOException;
@PipeBitInfo(
name = "Thread-Safe LVG",
description = "Annotates Lexical Variants for terms with attempted thread safety.",
- input = "WordTokens.",
- output = "Lexical Variants stored in existing WordTokens."
+ dependencies = PipeBitInfo.TypeProduct.BASE_TOKEN
)
final public class ThreadSafeLvg extends JCasAnnotator_ImplBase {