diff --git a/gene-name-mapping-ae/gene-name-mapping-ae.iml b/gene-name-mapping-ae/gene-name-mapping-ae.iml index 65f56e0..91107f2 100644 --- a/gene-name-mapping-ae/gene-name-mapping-ae.iml +++ b/gene-name-mapping-ae/gene-name-mapping-ae.iml @@ -37,11 +37,6 @@ - - - - - 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 index a2a596d..5b655c5 100644 --- 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/gene-name-mapping-ae/src/main/java/de/julielab/jules/ae/genemapping/genemodel/GeneDocumentFactory.java b/gene-name-mapping-ae/src/main/java/de/julielab/jules/ae/genemapping/genemodel/GeneDocumentFactory.java index f319e1b..59f992a 100644 --- a/gene-name-mapping-ae/src/main/java/de/julielab/jules/ae/genemapping/genemodel/GeneDocumentFactory.java +++ b/gene-name-mapping-ae/src/main/java/de/julielab/jules/ae/genemapping/genemodel/GeneDocumentFactory.java @@ -76,7 +76,7 @@ public GeneDocument createGeneDocument(JCas jCas, Map entityMap Title documentTitle = null; final Collection 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 index 5b17db4..cc2f332 100644 --- 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 @@ <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.7.25" 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" /> <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.6" level="project" /> <orderEntry type="library" name="Maven: commons-logging:commons-logging-api:1.1" level="project" /> diff --git a/pom.xml b/pom.xml index 99207be..1b7cb4e 100644 --- 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>