Release 1.0.1.

JULIELab · Oct 19, 2020 · 2132db5 · 2132db5
1 parent 6a0ec0a
commit 2132db5
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Showing 5 changed files with 3 additions and 13 deletions.
diff --git a/gene-name-mapping-ae/gene-name-mapping-ae.iml b/gene-name-mapping-ae/gene-name-mapping-ae.iml
@@ -37,11 +37,6 @@
     <orderEntry type="library" name="Maven: tw.edu.ntu.csie:libsvm:3.17" level="project" />
     <orderEntry type="library" name="Maven: de.julielab:jcore-types:2.4.0" level="project" />
     <orderEntry type="library" name="Maven: org.apache.uima:uimaj-core:2.10.3" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: javax.xml.bind:jaxb-api:2.3.1" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: javax.activation:javax.activation-api:1.2.0" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: com.sun.xml.bind:jaxb-core:2.3.0.1" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: com.sun.xml.bind:jaxb-impl:2.3.1" level="project" />
-    <orderEntry type="library" name="Maven: javax.annotation:javax.annotation-api:1.3.2" level="project" />
     <orderEntry type="library" name="Maven: org.apache.uima:uimafit-core:2.4.0" level="project" />
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     <orderEntry type="library" name="Maven: commons-logging:commons-logging-api:1.1" level="project" />

diff --git a/gene-name-mapping-ae/src/main/java/de/julielab/jules/ae/genemapping/QueryGenerator.java b/gene-name-mapping-ae/src/main/java/de/julielab/jules/ae/genemapping/QueryGenerator.java
@@ -49,7 +49,7 @@ public static BooleanQuery makeDisjunctiveQuery(String searchString, String fiel
         String[] tokens = searchString.split(" ");
 
         Builder disjunctiveQuery = new BooleanQuery.Builder();
-        for (int i = 0; i < tokens.length; i++) {
+        for (int i = 0; i < tokens.length && i < 1024; i++) {
             Query q = new TermQuery(new Term(field, tokens[i]));
             disjunctiveQuery.add(q, BooleanClause.Occur.SHOULD);
         }

diff --git a/...ping-ae/src/main/java/de/julielab/jules/ae/genemapping/genemodel/GeneDocumentFactory.java b/...ping-ae/src/main/java/de/julielab/jules/ae/genemapping/genemodel/GeneDocumentFactory.java
@@ -76,7 +76,7 @@ public GeneDocument createGeneDocument(JCas jCas, Map<String, Matcher> entityMap
         Title documentTitle = null;
         final Collection<Title> titles = JCasUtil.select(jCas, Title.class);
         if (titles != null) {
-            final Optional<Title> titleOpt = titles.stream().filter(t -> t.getTitleType().equals("document")).findAny();
+            final Optional<Title> titleOpt = titles.stream().filter(t -> t.getTitleType() != null).filter(t -> t.getTitleType().equals("document")).findAny();
             if (titleOpt.isPresent()) {
                 documentTitle = titleOpt.get();
                 doc.setDocumentTitle(documentTitle.getCoveredText());

diff --git a/gene-name-mapping-resource-creation/gene-name-mapping-resource-creation.iml b/gene-name-mapping-resource-creation/gene-name-mapping-resource-creation.iml
@@ -14,11 +14,6 @@
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     <orderEntry type="library" name="Maven: org.apache.uima:uimaj-core:2.10.3" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: javax.xml.bind:jaxb-api:2.3.1" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: javax.activation:javax.activation-api:1.2.0" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: com.sun.xml.bind:jaxb-core:2.3.0.1" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: com.sun.xml.bind:jaxb-impl:2.3.1" level="project" />
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     <orderEntry type="library" name="Maven: commons-logging:commons-logging-api:1.1" level="project" />

diff --git a/pom.xml b/pom.xml
@@ -17,7 +17,7 @@
 		<module>gene-name-mapping-ae</module>
 		<module>gene-name-mapping-resource-creation</module>
 	</modules>
-	<version>1.0.1-SNAPSHOT</version>
+	<version>1.0.1</version>
 	<dependencyManagement>
 		<dependencies>
 			<dependency>