From a39d512fdbb206f71a25680b333222bcb5fc3586 Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:32:49 +0200 Subject: [PATCH 1/7] Revert "Flow types integration for medline and pubmed multipliers." This reverts commit 07707d3837446b21c9620b975058da2185005b96. --- .../jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml | 1 - .../jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml | 1 - 2 files changed, 2 deletions(-) diff --git a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml index 3f6755b..f42c30f 100644 --- a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml +++ b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml @@ -81,7 +81,6 @@ - diff --git a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml index a78d1c5..9ab41c8 100644 --- a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml +++ b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml @@ -81,7 +81,6 @@ - From 9b21b14dbaf11d483bee0f28ec015012fd17a69e Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:33:04 +0200 Subject: [PATCH 2/7] Revert "Still more jUnit fixing." This reverts commit 646813301619ca917012de2e25369ed4fcab7ab2. --- .../de/julielab/jcore/ae/jsbd/TestPipeline.java | 15 +++++++++------ .../biomedical/english/JTBDBiomedEnglishTest.java | 2 +- .../jcore/ae/jtbd/JTBDMedicalGermanTest.java | 2 +- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java b/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java index bfeb4b2..05af114 100644 --- a/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java +++ b/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java @@ -9,13 +9,12 @@ import org.apache.uima.jcas.tcas.Annotation; import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; -import org.junit.jupiter.api.BeforeAll; +import org.junit.Before; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import static org.junit.jupiter.api.Assertions.assertTrue; - +import static org.junit.Assert.assertTrue; public class TestPipeline { @@ -34,16 +33,20 @@ public class TestPipeline { + " Die Patientin wurde insgesamt 14 Tage mit Binotal und Certomycin behandelt." + " Die Klappenfunktion ist echokardiographisch gut, die LV-Funktion mit einer EF von ca. 30 % weiterhin eingeschränkt."; - private static AnalysisEngine entityAnnotator = null; + private XMLInputSource taggerXML = null; + private ResourceSpecifier taggerSpec = null; + private AnalysisEngine entityAnnotator = null; /** * test whether Annotator can be initialized properly from given descriptor */ - @BeforeAll - public static void testInitialize() { + @Before + public void testInitialize() { LOGGER.info("testInitialize()"); try { +// taggerXML = new XMLInputSource(ENTITY_ANNOTATOR_DESC); +// taggerSpec = UIMAFramework.getXMLParser().parseResourceSpecifier(taggerXML); entityAnnotator = AnalysisEngineFactory.createEngine(ENTITY_ANNOTATOR_DESC); } catch (final Exception e) { System.out.println(e); diff --git a/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java b/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java index 66129a5..7920512 100644 --- a/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java +++ b/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java @@ -10,7 +10,7 @@ import org.junit.jupiter.api.Test; import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.Assert.assertTrue; public class JTBDBiomedEnglishTest { @Test diff --git a/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java b/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java index 0d2641a..77d49b8 100644 --- a/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java +++ b/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java @@ -10,7 +10,7 @@ import org.junit.jupiter.api.Test; import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.Assert.assertTrue; public class JTBDMedicalGermanTest { @Test From 040e0f2476f3bd85d4e70c3a7e42d8e21a2bd9d0 Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:33:11 +0200 Subject: [PATCH 3/7] Revert "More jUnit fixing which actually required fixed in jcore-base first." This reverts commit 9a36693db417319b3823a51f5a28ad5fd7206689. --- jcore-jsbd-ae-medical-german/pom.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/jcore-jsbd-ae-medical-german/pom.xml b/jcore-jsbd-ae-medical-german/pom.xml index 4f146a0..2f01afb 100644 --- a/jcore-jsbd-ae-medical-german/pom.xml +++ b/jcore-jsbd-ae-medical-german/pom.xml @@ -19,9 +19,8 @@ - org.apache.maven.plugins maven-assembly-plugin - 3.3.0 + 2.4 jar-with-dependencies From 5d0693f34fe45a327d27941979390cad371d6660 Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:33:17 +0200 Subject: [PATCH 4/7] Revert "More jUnit fixing." This reverts commit 98cf047b0590f97222fe651db84fb8e6fe18ebbe. --- .../jcore/ae/banner/BannerAETest.java | 59 ++++++++++--------- 1 file changed, 31 insertions(+), 28 deletions(-) diff --git a/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java b/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java index 07c9b31..cbda3c4 100644 --- a/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java +++ b/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java @@ -8,6 +8,8 @@ import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import java.util.ArrayList; import java.util.List; @@ -15,35 +17,36 @@ import static org.junit.jupiter.api.Assertions.assertEquals; public class BannerAETest { - @Test - public void testDescriptor() throws Exception { - // just tag a single sentence with a test model that actually used that sentence as training data. - JCas jcas = JCasFactory.createJCas("de.julielab.jcore.types.jcore-morpho-syntax-types", - "de.julielab.jcore.types.jcore-document-meta-types", - "de.julielab.jcore.types.jcore-semantics-biology-types"); - // this is sentence P00055040A0000 from the test BC2GM train data in the jcore-banner-ae project - jcas.setDocumentText( - "Ten out-patients with pustulosis palmaris et plantaris were examined with direct immunofluorescence (IF) technique for deposition of fibrinogen, fibrin or its degradation products (FR-antigen) in affected and unaffected skin, together with heparin-precipitable fraction (HPF), cryoglobulin and total plasma fibrinogen in the blood."); - new Sentence(jcas, 0, jcas.getDocumentText().length()).addToIndexes(); + private final static Logger log = LoggerFactory.getLogger(BannerAETest.class); + @Test + public void testDescriptor() throws Exception { + // just tag a single sentence with a test model that actually used that sentence as training data. + JCas jcas = JCasFactory.createJCas("de.julielab.jcore.types.jcore-morpho-syntax-types", + "de.julielab.jcore.types.jcore-document-meta-types", + "de.julielab.jcore.types.jcore-semantics-biology-types"); + // this is sentence P00055040A0000 from the test BC2GM train data in the jcore-banner-ae project + jcas.setDocumentText( + "Ten out-patients with pustulosis palmaris et plantaris were examined with direct immunofluorescence (IF) technique for deposition of fibrinogen, fibrin or its degradation products (FR-antigen) in affected and unaffected skin, together with heparin-precipitable fraction (HPF), cryoglobulin and total plasma fibrinogen in the blood."); + new Sentence(jcas, 0, jcas.getDocumentText().length()).addToIndexes(); AnalysisEngine bannerAe = null; - bannerAe = AnalysisEngineFactory.createEngine("de.julielab.jcore.ae.banner.desc.jcore-banner-ae-biomedical-english"); - bannerAe.process(jcas); - - // expected result from the GENE.eval.small file: - // P00055040A0000|116 125|fibrinogen - // P00055040A0000|127 132|fibrin - // P00055040A0000|158 167|FR-antigen - // P00055040A0000|243 254|cryoglobulin - // P00055040A0000|269 278|fibrinogen - // However, we ignore the offsets because the eval offsets ignore white spaces - List geneList = new ArrayList<>(JCasUtil.select(jcas, Gene.class)); - assertEquals("fibrinogen", geneList.get(0).getCoveredText()); - assertEquals("fibrin", geneList.get(1).getCoveredText()); - assertEquals("FR-antigen", geneList.get(2).getCoveredText()); - assertEquals("cryoglobulin", geneList.get(3).getCoveredText()); - assertEquals("fibrinogen", geneList.get(4).getCoveredText()); - - } + bannerAe= AnalysisEngineFactory.createEngine("de.julielab.jcore.ae.banner.desc.jcore-banner-ae-biomedical-english"); + bannerAe.process(jcas); + + // expected result from the GENE.eval.small file: + // P00055040A0000|116 125|fibrinogen + // P00055040A0000|127 132|fibrin + // P00055040A0000|158 167|FR-antigen + // P00055040A0000|243 254|cryoglobulin + // P00055040A0000|269 278|fibrinogen + // However, we ignore the offsets because the eval offsets ignore white spaces + List geneList = new ArrayList<>(JCasUtil.select(jcas, Gene.class)); + assertEquals("fibrinogen", geneList.get(0).getCoveredText()); + assertEquals("fibrin", geneList.get(1).getCoveredText()); + assertEquals("FR-antigen", geneList.get(2).getCoveredText()); + assertEquals("cryoglobulin", geneList.get(3).getCoveredText()); + assertEquals("fibrinogen", geneList.get(4).getCoveredText()); + + } } From 14a9b41a11c807488a8fac05d42303579f42d72a Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:33:21 +0200 Subject: [PATCH 5/7] Revert "Fixing jUnit 4 imports." This reverts commit 79e64d5eba90c677defcd25b32854b9165888c7c. --- .../test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java b/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java index fa66d7d..2b4ad67 100644 --- a/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java +++ b/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java @@ -9,15 +9,14 @@ import org.apache.uima.jcas.tcas.Annotation; import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; -import org.junit.jupiter.api.BeforeEach; +import org.junit.Before; import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.io.File; -import static org.junit.jupiter.api.Assertions.assertTrue; - +import static org.junit.Assert.assertTrue; public class TestPipeline { @@ -42,7 +41,7 @@ public class TestPipeline { /** * test whether Annotator can be initialized properly from given descriptor */ - @BeforeEach + @Before public void testInitialize() { LOGGER.info("testInitialize()"); From 86244b8513ffdd56d5849e42dc31adcc34734bc5 Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:33:22 +0200 Subject: [PATCH 6/7] Revert "Resolves #13, #14." This reverts commit b4863c3caca89c6ec9e0277dc19357457b9ffe1e. --- .../jcore-medline-db-multiplier-reader.xml | 2 +- .../desc/jcore-medline-db-multiplier.xml | 28 ------------------- .../desc/jcore-pubmed-db-multiplier.xml | 28 ------------------- 3 files changed, 1 insertion(+), 57 deletions(-) diff --git a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml index 5c4771f..f83f6a6 100644 --- a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml +++ b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml @@ -16,7 +16,7 @@ ResetTable If set to true and the parameter 'Table' is set to a subset table, the subset table will be - reset at the initialization of the reader to be ready for processing of the whole subset. Do not use + reset atthe initialization of the reader to be ready for processing of the whole subset. Do not use when multiple readers read the same subset table. Boolean diff --git a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml index f42c30f..11d99cd 100644 --- a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml +++ b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml @@ -38,34 +38,6 @@ false true - - AddShaHash - For use with AnnotationDefinedFlowController. Possible values: document_text, defaults to 'document_text' and thus doesn't need to be specified manually at the moment. This parameter needs to match the value for the same parameter given to the XMIDBWriter in this pipeline. Then, a comparison between the existing hash in the database and the new hash of the CAS read in this pipeline can be made. In case the hashes match, the CAS skips all component except the DBCheckpointAE to mark the document as processed. - String - false - false - - - DocumentTable - For use with AnnotationDefinedFlowController. String parameter indicating the name of the table where the XMI data and, thus, the hash is stored. The name must be schema qualified. Note that in this component, only the ToVisit annotation is created that determines which components to apply to a CAS with matching (unchanged) hash. The logic to actually control the CAS flow is contained in the AnnotationDefinedFlowController. - String - false - false - - - DocumentTableSchema - For use with AnnotationDefinedFlowController. The name of the schema that the document table - given with the DocumentTable parameter - adheres to. Only the primary key part is required for hash value retrieval. - String - false - false - - - ToVisitKeys - For use with AnnotationDefinedFlowController. The delegate AE keys of the AEs this CAS should still applied on although the hash has not changed. Can be null or empty indicating that no component should be applied to the CAS. This is, however, the task of the AnnotationDefinedFlowController. - String - true - false - diff --git a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml index 9ab41c8..b72256e 100644 --- a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml +++ b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml @@ -38,34 +38,6 @@ false true - - AddShaHash - For use with AnnotationDefinedFlowController. Possible values: document_text, defaults to 'document_text' and thus doesn't need to be specified manually at the moment. This parameter needs to match the value for the same parameter given to the XMIDBWriter in this pipeline. Then, a comparison between the existing hash in the database and the new hash of the CAS read in this pipeline can be made. In case the hashes match, the CAS skips all component except the DBCheckpointAE to mark the document as processed. - String - false - false - - - DocumentTable - For use with AnnotationDefinedFlowController. String parameter indicating the name of the table where the XMI data and, thus, the hash is stored. The name must be schema qualified. Note that in this component, only the ToVisit annotation is created that determines which components to apply to a CAS with matching (unchanged) hash. The logic to actually control the CAS flow is contained in the AnnotationDefinedFlowController. - String - false - false - - - DocumentTableSchema - For use with AnnotationDefinedFlowController. The name of the schema that the document table - given with the DocumentTable parameter - adheres to. Only the primary key part is required for hash value retrieval. - String - false - false - - - ToVisitKeys - For use with AnnotationDefinedFlowController. The delegate AE keys of the AEs this CAS should still applied on although the hash has not changed. Can be null or empty indicating that no component should be applied to the CAS. This is, however, the task of the AnnotationDefinedFlowController. - String - true - false - From d7adc952cf03143900b8ae7d91f55d035c210f91 Mon Sep 17 00:00:00 2001 From: khituras Date: Fri, 18 Jun 2021 11:33:23 +0200 Subject: [PATCH 7/7] Revert "Updated to version 2.6.0-SNAPSHOT, switched to jUnit 5." This reverts commit c9a7d73b31a0589f8ff81bd9cb1ebd47a9dda5d4. --- .../component.meta | 2 +- jcore-banner-ae-biomedical-english/pom.xml | 79 ++++--- .../jcore-banner-ae-biomedical-english.xml | 2 +- .../jcore/ae/banner/BannerAETest.java | 4 +- jcore-biosem-ae-bionlp-st09/component.meta | 2 +- jcore-biosem-ae-bionlp-st09/pom.xml | 21 +- .../desc/jcore-biosem-ae-bionlp-st09.xml | 2 +- .../jcore/ae/biosem/bionlpst09/TestData.java | 2 +- .../bionlpst09/TestDifficultDocument.java | 5 +- jcore-biosem-ae-bionlp-st11/component.meta | 2 +- jcore-biosem-ae-bionlp-st11/pom.xml | 21 +- .../desc/jcore-biosem-ae-bionlp-st11.xml | 2 +- .../jcore/ae/biosem/bionlpst11/TestData.java | 2 +- .../bionlpst11/TestDifficultDocument.java | 5 +- jcore-biosem-ae-bionlp-st13/component.meta | 2 +- jcore-biosem-ae-bionlp-st13/pom.xml | 26 +-- .../desc/jcore-biosem-ae-bionlp-st13.xml | 2 +- .../jcore/ae/biosem/bionlpst13/TestData.java | 2 +- .../bionlpst13/TestDifficultDocument.java | 4 +- .../component.meta | 2 +- jcore-jnet-ae-biomedical-english/pom.xml | 65 +++--- .../desc/jcore-jnet-ae-biomedical-english.xml | 2 +- .../julielab/jcore/ae/jnet/TestPipeline.java | 2 +- jcore-jpos-ae-medical-german/component.meta | 2 +- jcore-jpos-ae-medical-german/pom.xml | 21 +- .../desc/jcore-jpos-ae-medical-german.xml | 2 +- .../julielab/jcore/ae/jpos/TestPipeline.java | 2 +- .../component.meta | 2 +- jcore-jsbd-ae-biomedical-english/pom.xml | 199 +++++++++--------- .../desc/jcore-jsbd-ae-biomedical-english.xml | 2 +- .../julielab/jcore/ae/jsbd/TestPipeline.java | 2 +- jcore-jsbd-ae-medical-german/component.meta | 2 +- jcore-jsbd-ae-medical-german/pom.xml | 177 ++++++++-------- .../desc/jcore-jsbd-ae-medical-german.xml | 2 +- .../julielab/jcore/ae/jsbd/TestPipeline.java | 2 +- .../component.meta | 2 +- jcore-jtbd-ae-biomedical-english/pom.xml | 189 ++++++++--------- .../desc/jcore-jtbd-ae-biomedical-english.xml | 2 +- .../english/JTBDBiomedEnglishTest.java | 4 +- jcore-jtbd-ae-medical-german/component.meta | 2 +- jcore-jtbd-ae-medical-german/pom.xml | 187 ++++++++-------- .../desc/jcore-jtbd-ae-medical-german.xml | 2 +- .../jcore/ae/jtbd/JTBDMedicalGermanTest.java | 4 +- .../component.meta | 2 +- .../pom.xml | 63 +++--- .../desc/ApproxGazetteerAnnotatorTest.xml | 2 +- .../lingpipegazetteer/TestDummyGazetteer.java | 2 +- jcore-lingscope-negation-ae/component.meta | 2 +- jcore-lingscope-negation-ae/pom.xml | 21 +- .../desc/jcore-lingscope-negation-ae.xml | 2 +- .../ae/lingscope/LingscopeNegationAeTest.java | 2 +- .../component.meta | 2 +- .../pom.xml | 60 +++--- ...pecies-ae-genera-species-proxies-dicts.xml | 2 +- .../jcore/ae/linnaeus/DescriptorTest.java | 8 +- .../component.meta | 2 +- .../pom.xml | 21 +- ...jcore-linnaeus-species-ae-proxies-dict.xml | 2 +- .../jcore/ae/linnaeus/DescriptorTest.java | 9 +- .../component.meta | 2 +- .../pom.xml | 21 +- ...jcore-linnaeus-species-ae-species-dict.xml | 2 +- .../jcore/ae/linnaeus/DescriptorTest.java | 10 +- jcore-medline-db-reader/component.meta | 2 +- jcore-medline-db-reader/pom.xml | 19 +- .../jcore-medline-db-multiplier-reader.xml | 2 +- .../desc/jcore-medline-db-multiplier.xml | 2 +- .../desc/jcore-medline-db-reader.xml | 2 +- jcore-medline-reader/component.meta | 2 +- jcore-medline-reader/pom.xml | 21 +- .../jcore-medline-citationset-multiplier.xml | 2 +- .../desc/jcore-medline-multiplier-reader.xml | 2 +- .../reader/xml/desc/jcore-medline-reader.xml | 2 +- .../jcore/reader/xml/MedlineReaderTest.java | 7 +- .../component.meta | 2 +- jcore-mstparser-ae-biomedical-english/pom.xml | 21 +- .../jcore-mstparser-ae-biomedical-english.xml | 2 +- .../jcore/ae/mstparser/TestModel.java | 5 +- .../component.meta | 2 +- .../pom.xml | 83 ++++---- ...re-opennlp-chunk-ae-biomedical-english.xml | 2 +- .../chunk/genia/OpenNLPChunkerGeniaTest.java | 6 +- .../component.meta | 2 +- .../pom.xml | 75 +++---- ...e-opennlp-parser-ae-biomedical-english.xml | 2 +- .../ae/opennlp/parser/ParseAnnotatorTest.java | 13 +- .../component.meta | 2 +- .../pom.xml | 139 ++++++------ ...e-opennlp-postag-ae-biomedical-english.xml | 2 +- .../postag/OpenNLPPosTagPennBioIETest.java | 6 +- .../component.meta | 2 +- .../pom.xml | 63 +++--- ...jcore-opennlp-postag-ae-medical-german.xml | 2 +- .../postag/OpenNLPPosTagFraMedTest.java | 6 +- .../component.meta | 2 +- .../pom.xml | 77 ++++--- ...opennlp-sentence-ae-biomedical-english.xml | 2 +- .../ae/opennlp/sentence/TestWorkFlow.java | 2 +- .../component.meta | 2 +- .../pom.xml | 64 +++--- ...ore-opennlp-sentence-ae-medical-german.xml | 2 +- .../sentence/OpenNLPSentenceFraMedTest.java | 2 +- .../component.meta | 2 +- .../pom.xml | 76 ++++--- ...re-opennlp-token-ae-biomedical-english.xml | 2 +- .../BiomedEnglishOpenNlpWrapperTest.java | 4 +- .../component.meta | 2 +- jcore-opennlp-token-ae-medical-german/pom.xml | 63 +++--- .../jcore-opennlp-token-ae-medical-german.xml | 2 +- .../postag/OpenNLPTokenFraMedTest.java | 2 +- jcore-pubmed-db-reader/component.meta | 2 +- jcore-pubmed-db-reader/pom.xml | 26 ++- .../jcore-pubmed-db-multiplier-reader.xml | 2 +- .../desc/jcore-pubmed-db-multiplier.xml | 2 +- .../pubmed-db/desc/jcore-pubmed-db-reader.xml | 2 +- jcore-pubmed-reader/component.meta | 2 +- jcore-pubmed-reader/pom.xml | 8 +- .../jcore-pubmed-articleset-multiplier.xml | 2 +- .../desc/jcore-pubmed-multiplier-reader.xml | 2 +- .../reader/xml/desc/jcore-pubmed-reader.xml | 2 +- .../reader/xml/PubmedMultiplierTest.java | 8 +- .../jcore/reader/xml/PubmedReaderTest.java | 13 +- pom.xml | 7 +- scripts/setProjectVersion.sh | 5 +- travis-deployment/deploy.sh | 2 +- 125 files changed, 1042 insertions(+), 1151 deletions(-) diff --git a/jcore-banner-ae-biomedical-english/component.meta b/jcore-banner-ae-biomedical-english/component.meta index f6b678a..24ff778 100644 --- a/jcore-banner-ae-biomedical-english/component.meta +++ b/jcore-banner-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-banner-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe BANNER AE for Biomedical English" } diff --git a/jcore-banner-ae-biomedical-english/pom.xml b/jcore-banner-ae-biomedical-english/pom.xml index b2fab13..c0d13c5 100644 --- a/jcore-banner-ae-biomedical-english/pom.xml +++ b/jcore-banner-ae-biomedical-english/pom.xml @@ -1,46 +1,39 @@ - + - 4.0.0 - jcore-banner-ae-biomedical-english - jar - JCoRe BANNER AE for Biomedical English - The JCoRe BANNER Gene Tagger wrapper with a model for biomedical english. - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - - - - org.slf4j - slf4j-api - - - de.julielab - jcore-banner-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - - - org.junit.jupiter - junit-jupiter-engine - - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - - JULIE Lab Jena, Germany - http://www.julielab.de - + 4.0.0 + jcore-banner-ae-biomedical-english + jar + JCoRe BANNER AE for Biomedical English + The JCoRe BANNER Gene Tagger wrapper with a model for biomedical english. + + de.julielab + jcore-projects + 2.5.1 + + + + + org.slf4j + slf4j-api + + + de.julielab + jcore-banner-ae + 2.5.0 + + + ch.qos.logback + logback-classic + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + + JULIE Lab Jena, Germany + http://www.julielab.de + diff --git a/jcore-banner-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml b/jcore-banner-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml index ca11783..0a5795d 100644 --- a/jcore-banner-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml +++ b/jcore-banner-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/banner/desc/jcore-banner-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe BANNER AE for Biomedical English This component uses the BANNER named entity recognizer with a model trained on the complete (train and test) dataset of the BioCreative II gene mention challenge. - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java b/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java index cbda3c4..9a35449 100644 --- a/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java +++ b/jcore-banner-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/banner/BannerAETest.java @@ -7,14 +7,14 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.util.ArrayList; import java.util.List; -import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.Assert.assertEquals; public class BannerAETest { private final static Logger log = LoggerFactory.getLogger(BannerAETest.class); diff --git a/jcore-biosem-ae-bionlp-st09/component.meta b/jcore-biosem-ae-bionlp-st09/component.meta index 1bd0d71..a108c6b 100644 --- a/jcore-biosem-ae-bionlp-st09/component.meta +++ b/jcore-biosem-ae-bionlp-st09/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-biosem-ae-bionlp-st09", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe BioSem AE, BioNLP SharedTask 2009" } diff --git a/jcore-biosem-ae-bionlp-st09/pom.xml b/jcore-biosem-ae-bionlp-st09/pom.xml index 121c481..a8b9789 100644 --- a/jcore-biosem-ae-bionlp-st09/pom.xml +++ b/jcore-biosem-ae-bionlp-st09/pom.xml @@ -5,7 +5,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-biosem-ae-bionlp-st09 @@ -17,11 +17,11 @@ de.julielab jcore-biosem-ae - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit ch.qos.logback @@ -34,11 +34,10 @@ ${jcore-types-version} - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-biosem-ae-bionlp-st09 + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-biosem-ae-bionlp-st09 diff --git a/jcore-biosem-ae-bionlp-st09/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st09.xml b/jcore-biosem-ae-bionlp-st09/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st09.xml index 43d4f34..e4b59bd 100644 --- a/jcore-biosem-ae-bionlp-st09/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st09.xml +++ b/jcore-biosem-ae-bionlp-st09/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st09.xml @@ -5,7 +5,7 @@ JCoRe BioSEM Event Annotator - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestData.java b/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestData.java index 10e0134..e91e982 100644 --- a/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestData.java +++ b/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestData.java @@ -5,7 +5,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; public class TestData { @Test diff --git a/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestDifficultDocument.java b/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestDifficultDocument.java index 4830c5a..079126c 100644 --- a/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestDifficultDocument.java +++ b/jcore-biosem-ae-bionlp-st09/src/test/java/de/julielab/jcore/ae/biosem/bionlpst09/TestDifficultDocument.java @@ -8,12 +8,11 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; import java.io.FileInputStream; -import static org.junit.jupiter.api.Assertions.assertTrue; - +import static org.junit.Assert.assertTrue; /** * With 'difficult document' we mean a document that used to make problems with BioSem diff --git a/jcore-biosem-ae-bionlp-st11/component.meta b/jcore-biosem-ae-bionlp-st11/component.meta index 2607f82..8487681 100644 --- a/jcore-biosem-ae-bionlp-st11/component.meta +++ b/jcore-biosem-ae-bionlp-st11/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-biosem-ae-bionlp-st11", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe BioSem AE, BioNLP SharedTask 2011" } diff --git a/jcore-biosem-ae-bionlp-st11/pom.xml b/jcore-biosem-ae-bionlp-st11/pom.xml index 50458e6..12ab4a6 100644 --- a/jcore-biosem-ae-bionlp-st11/pom.xml +++ b/jcore-biosem-ae-bionlp-st11/pom.xml @@ -5,7 +5,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-biosem-ae-bionlp-st11 @@ -17,11 +17,11 @@ de.julielab jcore-biosem-ae - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit ch.qos.logback @@ -34,11 +34,10 @@ ${jcore-types-version} - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-biosem-ae-bionlp-st11 + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-biosem-ae-bionlp-st11 diff --git a/jcore-biosem-ae-bionlp-st11/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st11.xml b/jcore-biosem-ae-bionlp-st11/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st11.xml index a351dac..376e145 100644 --- a/jcore-biosem-ae-bionlp-st11/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st11.xml +++ b/jcore-biosem-ae-bionlp-st11/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st11.xml @@ -5,7 +5,7 @@ JCoRe BioSEM Event Annotator - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestData.java b/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestData.java index 19fb86f..9acf42e 100644 --- a/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestData.java +++ b/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestData.java @@ -5,7 +5,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; public class TestData { @Test diff --git a/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestDifficultDocument.java b/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestDifficultDocument.java index fa4130b..ece5bf5 100644 --- a/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestDifficultDocument.java +++ b/jcore-biosem-ae-bionlp-st11/src/test/java/de/julielab/jcore/ae/biosem/bionlpst11/TestDifficultDocument.java @@ -8,12 +8,11 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; import java.io.FileInputStream; -import static org.junit.jupiter.api.Assertions.assertTrue; - +import static org.junit.Assert.assertTrue; /** * With 'difficult document' we mean a document that used to make problems with BioSem diff --git a/jcore-biosem-ae-bionlp-st13/component.meta b/jcore-biosem-ae-bionlp-st13/component.meta index e10dd4b..5b9597a 100644 --- a/jcore-biosem-ae-bionlp-st13/component.meta +++ b/jcore-biosem-ae-bionlp-st13/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-biosem-ae-bionlp-st13", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe BioSem AE, BioNLP SharedTask 2013" } diff --git a/jcore-biosem-ae-bionlp-st13/pom.xml b/jcore-biosem-ae-bionlp-st13/pom.xml index be95840..8f5090d 100644 --- a/jcore-biosem-ae-bionlp-st13/pom.xml +++ b/jcore-biosem-ae-bionlp-st13/pom.xml @@ -5,7 +5,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-biosem-ae-bionlp-st13 @@ -15,13 +15,13 @@ - org.junit.jupiter - junit-jupiter-engine + junit + junit de.julielab jcore-biosem-ae - ${jcore-version} + 2.5.0 ch.qos.logback @@ -33,17 +33,11 @@ jcore-types ${jcore-types-version} - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-biosem-ae-bionlp-st13 + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-biosem-ae-bionlp-st13 diff --git a/jcore-biosem-ae-bionlp-st13/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st13.xml b/jcore-biosem-ae-bionlp-st13/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st13.xml index 4a9fd37..73c5f9b 100644 --- a/jcore-biosem-ae-bionlp-st13/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st13.xml +++ b/jcore-biosem-ae-bionlp-st13/src/main/resources/de/julielab/jcore/ae/biosem/desc/jcore-biosem-ae-bionlp-st13.xml @@ -5,7 +5,7 @@ JCoRe BioSEM Event Annotator - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestData.java b/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestData.java index 2c498d5..9c5cbc0 100644 --- a/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestData.java +++ b/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestData.java @@ -5,7 +5,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; public class TestData { @Test diff --git a/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestDifficultDocument.java b/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestDifficultDocument.java index 3281f42..7399957 100644 --- a/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestDifficultDocument.java +++ b/jcore-biosem-ae-bionlp-st13/src/test/java/de/julielab/jcore/ae/biosem/bionlpst13/TestDifficultDocument.java @@ -8,11 +8,11 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; import java.io.FileInputStream; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.Assert.assertTrue; /** * With 'difficult document' we mean a document that used to make problems with BioSem diff --git a/jcore-jnet-ae-biomedical-english/component.meta b/jcore-jnet-ae-biomedical-english/component.meta index 8fe02a2..5e5389d 100644 --- a/jcore-jnet-ae-biomedical-english/component.meta +++ b/jcore-jnet-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-jnet-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe JNET AE, Biomedical English" } diff --git a/jcore-jnet-ae-biomedical-english/pom.xml b/jcore-jnet-ae-biomedical-english/pom.xml index 74b69bb..7db3443 100644 --- a/jcore-jnet-ae-biomedical-english/pom.xml +++ b/jcore-jnet-ae-biomedical-english/pom.xml @@ -1,37 +1,32 @@ - - 4.0.0 - jcore-jnet-ae-biomedical-english - JCoRe JNET AE, Biomedical English - This project employs the jcore-jnet-ae (Named Entity Tagger) with a model trained on the PennBioIE - corpus. - - - jcore-projects - 2.6.0-SNAPSHOT - de.julielab - - - - de.julielab - jcore-jnet-ae - ${jcore-version} - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - - JULIE Lab Jena, Germany - http://www.julielab.de - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-jnet-ae-biomedical-english + + 4.0.0 + jcore-jnet-ae-biomedical-english + JCoRe JNET AE, Biomedical English + This project employs the jcore-jnet-ae (Named Entity Tagger) with a model trained on the PennBioIE corpus. + + jcore-projects + 2.5.1 + de.julielab + + + + de.julielab + jcore-jnet-ae + 2.5.0 + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + + JULIE Lab Jena, Germany + http://www.julielab.de + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-jnet-ae-biomedical-english diff --git a/jcore-jnet-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jnet/desc/jcore-jnet-ae-biomedical-english.xml b/jcore-jnet-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jnet/desc/jcore-jnet-ae-biomedical-english.xml index 6908610..11d8f82 100644 --- a/jcore-jnet-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jnet/desc/jcore-jnet-ae-biomedical-english.xml +++ b/jcore-jnet-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jnet/desc/jcore-jnet-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe JNET AE Biomedical English - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-jnet-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jnet/TestPipeline.java b/jcore-jnet-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jnet/TestPipeline.java index effb8ec..1654eea 100644 --- a/jcore-jnet-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jnet/TestPipeline.java +++ b/jcore-jnet-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jnet/TestPipeline.java @@ -4,7 +4,7 @@ import org.apache.uima.analysis_engine.AnalysisEngine; import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; -import org.junit.jupiter.api.Test; +import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/jcore-jpos-ae-medical-german/component.meta b/jcore-jpos-ae-medical-german/component.meta index 4b9cf03..78c9249 100644 --- a/jcore-jpos-ae-medical-german/component.meta +++ b/jcore-jpos-ae-medical-german/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-jpos-ae-medical-german", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe JPOS AE, Medical German" } diff --git a/jcore-jpos-ae-medical-german/pom.xml b/jcore-jpos-ae-medical-german/pom.xml index 544079b..5fb4950 100644 --- a/jcore-jpos-ae-medical-german/pom.xml +++ b/jcore-jpos-ae-medical-german/pom.xml @@ -3,7 +3,7 @@ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 de.julielab 4.0.0 @@ -12,20 +12,19 @@ de.julielab jcore-jpos-ae - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + http://www.julielab.de JULIE Lab, Germany diff --git a/jcore-jpos-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jpos/desc/jcore-jpos-ae-medical-german.xml b/jcore-jpos-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jpos/desc/jcore-jpos-ae-medical-german.xml index f0ea8fd..9222319 100644 --- a/jcore-jpos-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jpos/desc/jcore-jpos-ae-medical-german.xml +++ b/jcore-jpos-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jpos/desc/jcore-jpos-ae-medical-german.xml @@ -6,7 +6,7 @@ JCoRe JPOS AE Medical German - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab diff --git a/jcore-jpos-ae-medical-german/src/test/java/de/julielab/jcore/ae/jpos/TestPipeline.java b/jcore-jpos-ae-medical-german/src/test/java/de/julielab/jcore/ae/jpos/TestPipeline.java index 4e08080..43b3d86 100644 --- a/jcore-jpos-ae-medical-german/src/test/java/de/julielab/jcore/ae/jpos/TestPipeline.java +++ b/jcore-jpos-ae-medical-german/src/test/java/de/julielab/jcore/ae/jpos/TestPipeline.java @@ -4,7 +4,7 @@ import org.apache.uima.analysis_engine.AnalysisEngine; import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; -import org.junit.jupiter.api.Test; +import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/jcore-jsbd-ae-biomedical-english/component.meta b/jcore-jsbd-ae-biomedical-english/component.meta index 3db10be..285bdbb 100644 --- a/jcore-jsbd-ae-biomedical-english/component.meta +++ b/jcore-jsbd-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-jsbd-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Sentence Annotator, Biomedical English" } diff --git a/jcore-jsbd-ae-biomedical-english/pom.xml b/jcore-jsbd-ae-biomedical-english/pom.xml index 364eea6..5007e01 100644 --- a/jcore-jsbd-ae-biomedical-english/pom.xml +++ b/jcore-jsbd-ae-biomedical-english/pom.xml @@ -1,110 +1,101 @@ - + - 4.0.0 - jcore-jsbd-ae-biomedical-english - jar - JCoRe Sentence Annotator, Biomedical English - UIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from - both the GENIA and PennBioIE corpus as well as additional material from MedLine abstracts. - + 4.0.0 + jcore-jsbd-ae-biomedical-english + jar + JCoRe Sentence Annotator, Biomedical English + UIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from both the GENIA and PennBioIE corpus as well as additional material from MedLine abstracts. - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - + + de.julielab + jcore-projects + 2.5.1 + - - - - maven-assembly-plugin - 3.3.0 - - - jar-with-dependencies - - - - de.julielab.jcore.ae.jsbd.SentenceSplitterApplication - - + + + + maven-assembly-plugin + 3.3.0 + + + jar-with-dependencies + + + + de.julielab.jcore.ae.jsbd.SentenceSplitterApplication + + - jsbd-${project.version} - - - - make-assembly - package - - single - - - - - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.apache.maven.plugins - maven-dependency-plugin - [1.0.0,) - - copy-dependencies - - - - - - - - - - - - - - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-jsbd-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - de.julielab - jcore-pmc-reader - ${jcore-version} - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-jsbd-ae-biomedical-english + jsbd-${project.version} + + + + make-assembly + package + + single + + + + + + + + + org.eclipse.m2e + lifecycle-mapping + 1.0.0 + + + + + + org.apache.maven.plugins + maven-dependency-plugin + [1.0.0,) + + copy-dependencies + + + + + + + + + + + + + + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-jsbd-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + de.julielab + jcore-pmc-reader + 2.5.0 + test + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-jsbd-ae-biomedical-english diff --git a/jcore-jsbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-biomedical-english.xml b/jcore-jsbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-biomedical-english.xml index cab769b..a99ce30 100644 --- a/jcore-jsbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-biomedical-english.xml +++ b/jcore-jsbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe Sentence Annotator This is the UIMA Wrapper for the JULIE Sentence Boundary Detector. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java b/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java index 2b4ad67..ec2ac5c 100644 --- a/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java +++ b/jcore-jsbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java @@ -10,7 +10,7 @@ import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; import org.junit.Before; -import org.junit.jupiter.api.Test; +import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/jcore-jsbd-ae-medical-german/component.meta b/jcore-jsbd-ae-medical-german/component.meta index 2741e98..e12b89d 100644 --- a/jcore-jsbd-ae-medical-german/component.meta +++ b/jcore-jsbd-ae-medical-german/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-jsbd-ae-medical-german", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Sentence Annotator, Medical German" } diff --git a/jcore-jsbd-ae-medical-german/pom.xml b/jcore-jsbd-ae-medical-german/pom.xml index 2f01afb..2865e7a 100644 --- a/jcore-jsbd-ae-medical-german/pom.xml +++ b/jcore-jsbd-ae-medical-german/pom.xml @@ -1,99 +1,90 @@ - + - 4.0.0 - jcore-jsbd-ae-medical-german - jar - JCoRe Sentence Annotator, Medical German - UIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from - the confidential FraMed corpus - + 4.0.0 + jcore-jsbd-ae-medical-german + jar + JCoRe Sentence Annotator, Medical German + UIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from the confidential FraMed corpus - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - + + de.julielab + jcore-projects + 2.5.1 + - - - - maven-assembly-plugin - 2.4 - - - jar-with-dependencies - - - - de.julielab.jcore.ae.jsbd.SentenceSplitterApplication - - + + + + maven-assembly-plugin + 2.4 + + + jar-with-dependencies + + + + de.julielab.jcore.ae.jsbd.SentenceSplitterApplication + + - jsbd-${project.version} - - - - make-assembly - package - - single - - - - - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.apache.maven.plugins - maven-dependency-plugin - [1.0.0,) - - copy-dependencies - - - - - - - - - - - - - - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-jsbd-ae - ${jcore-version} - - - org.junit.jupiter - junit-jupiter-engine - - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-jsbd-ae-medical-german + jsbd-${project.version} + + + + make-assembly + package + + single + + + + + + + + + org.eclipse.m2e + lifecycle-mapping + 1.0.0 + + + + + + org.apache.maven.plugins + maven-dependency-plugin + [1.0.0,) + + copy-dependencies + + + + + + + + + + + + + + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-jsbd-ae + 2.5.0 + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-jsbd-ae-medical-german diff --git a/jcore-jsbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-medical-german.xml b/jcore-jsbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-medical-german.xml index 221ca49..9195d96 100644 --- a/jcore-jsbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-medical-german.xml +++ b/jcore-jsbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jsbd/desc/jcore-jsbd-ae-medical-german.xml @@ -6,7 +6,7 @@ JCoRe Sentence Annotator This is the UIMA Wrapper for the JULIE Sentence Boundary Detector. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java b/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java index 05af114..ceb1759 100644 --- a/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java +++ b/jcore-jsbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jsbd/TestPipeline.java @@ -10,7 +10,7 @@ import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; import org.junit.Before; -import org.junit.jupiter.api.Test; +import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/jcore-jtbd-ae-biomedical-english/component.meta b/jcore-jtbd-ae-biomedical-english/component.meta index 9cb2868..2f919db 100644 --- a/jcore-jtbd-ae-biomedical-english/component.meta +++ b/jcore-jtbd-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-jtbd-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Token Annotator, Biomedical English" } diff --git a/jcore-jtbd-ae-biomedical-english/pom.xml b/jcore-jtbd-ae-biomedical-english/pom.xml index 81a5052..58a5019 100644 --- a/jcore-jtbd-ae-biomedical-english/pom.xml +++ b/jcore-jtbd-ae-biomedical-english/pom.xml @@ -1,105 +1,96 @@ - + - 4.0.0 - jcore-jtbd-ae-biomedical-english - jar - UIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on a special biomedical corpus - which consists of data from (manually annotated) material which we took from MedLine abstracts and a modified - version of PennBioIE's underlying tokenization. - + 4.0.0 + jcore-jtbd-ae-biomedical-english + jar + UIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on a special biomedical corpus which consists of data from (manually annotated) material which we took from MedLine abstracts and a modified version of PennBioIE's underlying tokenization. + - - de.julielab - 2.6.0-SNAPSHOT - jcore-projects - + + de.julielab + 2.5.1 + jcore-projects + - - - - org.apache.maven.plugins - maven-assembly-plugin - 3.3.0 - - - jar-with-dependencies - - - - de.julielab.jcore.ae.jtbd.TokenizerApplication - - + + + + maven-assembly-plugin + 2.4 + + + jar-with-dependencies + + + + de.julielab.jcore.ae.jtbd.TokenizerApplication + + - jtbd-${project.version} - - - - make-assembly - package - - single - - - - - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.apache.maven.plugins - maven-dependency-plugin - [1.0.0,) - - copy-dependencies - - - - - - - - - - - - - - JCoRe Token Annotator, Biomedical English - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-jtbd-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-jtbd-ae-biomedical-english + jtbd-${project.version} + + + + make-assembly + package + + single + + + + + + + + + org.eclipse.m2e + lifecycle-mapping + 1.0.0 + + + + + + org.apache.maven.plugins + maven-dependency-plugin + [1.0.0,) + + copy-dependencies + + + + + + + + + + + + + + JCoRe Token Annotator, Biomedical English + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-jtbd-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-jtbd-ae-biomedical-english diff --git a/jcore-jtbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-biomedical-english.xml b/jcore-jtbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-biomedical-english.xml index 9ab9728..d06985b 100644 --- a/jcore-jtbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-biomedical-english.xml +++ b/jcore-jtbd-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe Token Annotator for English in the Biomedical Domain - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java b/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java index 7920512..2683355 100644 --- a/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java +++ b/jcore-jtbd-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/jtbd/biomedical/english/JTBDBiomedEnglishTest.java @@ -7,9 +7,9 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; -import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; public class JTBDBiomedEnglishTest { diff --git a/jcore-jtbd-ae-medical-german/component.meta b/jcore-jtbd-ae-medical-german/component.meta index 7d063a6..d51c28a 100644 --- a/jcore-jtbd-ae-medical-german/component.meta +++ b/jcore-jtbd-ae-medical-german/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-jtbd-ae-medical-german", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Token Annotator, Medical German" } diff --git a/jcore-jtbd-ae-medical-german/pom.xml b/jcore-jtbd-ae-medical-german/pom.xml index c9070e3..5609a82 100644 --- a/jcore-jtbd-ae-medical-german/pom.xml +++ b/jcore-jtbd-ae-medical-german/pom.xml @@ -1,103 +1,96 @@ - + - 4.0.0 - jcore-jtbd-ae-medical-german - jar - UIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on the confidential FraMed - corpus. - + 4.0.0 + jcore-jtbd-ae-medical-german + jar + UIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on the confidential FraMed corpus. + - - de.julielab - 2.6.0-SNAPSHOT - jcore-projects - + + de.julielab + 2.5.1 + jcore-projects + - - - - maven-assembly-plugin - 2.4 - - - jar-with-dependencies - - - - de.julielab.jcore.ae.jtbd.TokenizerApplication - - + + + + maven-assembly-plugin + 2.4 + + + jar-with-dependencies + + + + de.julielab.jcore.ae.jtbd.TokenizerApplication + + - jtbd-${project.version} - - - - make-assembly - package - - single - - - - - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - org.apache.maven.plugins - maven-dependency-plugin - [1.0.0,) - - copy-dependencies - - - - - - - - - - - - - - JCoRe Token Annotator, Medical German - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-jtbd-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-jtbd-ae-medical-german + jtbd-${project.version} + + + + make-assembly + package + + single + + + + + + + + + org.eclipse.m2e + lifecycle-mapping + 1.0.0 + + + + + + org.apache.maven.plugins + maven-dependency-plugin + [1.0.0,) + + copy-dependencies + + + + + + + + + + + + + + JCoRe Token Annotator, Medical German + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-jtbd-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-jtbd-ae-medical-german diff --git a/jcore-jtbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-medical-german.xml b/jcore-jtbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-medical-german.xml index 5cbb935..fdb963d 100644 --- a/jcore-jtbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-medical-german.xml +++ b/jcore-jtbd-ae-medical-german/src/main/resources/de/julielab/jcore/ae/jtbd/desc/jcore-jtbd-ae-medical-german.xml @@ -6,7 +6,7 @@ JCoRe Token Annotator for German in the Medical Domain - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java b/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java index 77d49b8..e7ad37b 100644 --- a/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java +++ b/jcore-jtbd-ae-medical-german/src/test/java/de/julielab/jcore/ae/jtbd/JTBDMedicalGermanTest.java @@ -7,9 +7,9 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; -import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; public class JTBDMedicalGermanTest { diff --git a/jcore-lingpipegazetteer-ae-dummy-implementation/component.meta b/jcore-lingpipegazetteer-ae-dummy-implementation/component.meta index 356dd62..75ed058 100644 --- a/jcore-lingpipegazetteer-ae-dummy-implementation/component.meta +++ b/jcore-lingpipegazetteer-ae-dummy-implementation/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-lingpipegazetteer-ae-dummy-implementation", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Lingpipe Gazetteer Dummy Implementation" } diff --git a/jcore-lingpipegazetteer-ae-dummy-implementation/pom.xml b/jcore-lingpipegazetteer-ae-dummy-implementation/pom.xml index 34baa04..84c7786 100644 --- a/jcore-lingpipegazetteer-ae-dummy-implementation/pom.xml +++ b/jcore-lingpipegazetteer-ae-dummy-implementation/pom.xml @@ -1,35 +1,32 @@ - - 4.0.0 - jcore-lingpipegazetteer-ae-dummy-implementation - - jcore-projects - 2.6.0-SNAPSHOT - de.julielab - - - JULIE Lab, Germany - http://www.julielab.de - - - - de.julielab - jcore-lingpipe-gazetteer-ae - ${jcore-version} - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - JCoRe Lingpipe Gazetteer Dummy Implementation - https://github.com/JULIELab/jcore-projects/tree/master/jcore-lingpipegazetteer-ae-dummy-implementation - This is just a dummy implementation that can be adapted according to ones own need. + + 4.0.0 + jcore-lingpipegazetteer-ae-dummy-implementation + + jcore-projects + 2.5.1 + de.julielab + + + JULIE Lab, Germany + http://www.julielab.de + + + + de.julielab + jcore-lingpipe-gazetteer-ae + 2.5.0 + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + JCoRe Lingpipe Gazetteer Dummy Implementation + https://github.com/JULIELab/jcore-projects/tree/master/jcore-lingpipegazetteer-ae-dummy-implementation + This is just a dummy implementation that can be adapted according to ones own need. diff --git a/jcore-lingpipegazetteer-ae-dummy-implementation/src/main/resources/de/julielab/jcore/ae/lingpipegazetteer/dummy/desc/ApproxGazetteerAnnotatorTest.xml b/jcore-lingpipegazetteer-ae-dummy-implementation/src/main/resources/de/julielab/jcore/ae/lingpipegazetteer/dummy/desc/ApproxGazetteerAnnotatorTest.xml index 44f7a75..cf37134 100644 --- a/jcore-lingpipegazetteer-ae-dummy-implementation/src/main/resources/de/julielab/jcore/ae/lingpipegazetteer/dummy/desc/ApproxGazetteerAnnotatorTest.xml +++ b/jcore-lingpipegazetteer-ae-dummy-implementation/src/main/resources/de/julielab/jcore/ae/lingpipegazetteer/dummy/desc/ApproxGazetteerAnnotatorTest.xml @@ -6,7 +6,7 @@ JCoRe Lingpipe Gazetteer AE Dummy - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-lingpipegazetteer-ae-dummy-implementation/src/test/java/de/julielab/jcore/ae/lingpipegazetteer/TestDummyGazetteer.java b/jcore-lingpipegazetteer-ae-dummy-implementation/src/test/java/de/julielab/jcore/ae/lingpipegazetteer/TestDummyGazetteer.java index d721861..e36a25e 100644 --- a/jcore-lingpipegazetteer-ae-dummy-implementation/src/test/java/de/julielab/jcore/ae/lingpipegazetteer/TestDummyGazetteer.java +++ b/jcore-lingpipegazetteer-ae-dummy-implementation/src/test/java/de/julielab/jcore/ae/lingpipegazetteer/TestDummyGazetteer.java @@ -4,7 +4,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; public class TestDummyGazetteer { @Test diff --git a/jcore-lingscope-negation-ae/component.meta b/jcore-lingscope-negation-ae/component.meta index 1a7e152..bc66156 100644 --- a/jcore-lingscope-negation-ae/component.meta +++ b/jcore-lingscope-negation-ae/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-lingscope-negation-ae", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Lingscope Negation AE" } diff --git a/jcore-lingscope-negation-ae/pom.xml b/jcore-lingscope-negation-ae/pom.xml index 65b3acf..bae29f6 100644 --- a/jcore-lingscope-negation-ae/pom.xml +++ b/jcore-lingscope-negation-ae/pom.xml @@ -9,14 +9,14 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 de.julielab jcore-lingscope-ae - ${jcore-version} + 2.5.0 ch.qos.logback @@ -47,17 +47,16 @@ ${jcore-types-version} - org.junit.jupiter - junit-jupiter-engine + junit + junit - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - JCoRe Lingscope Negation AE + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + JCoRe Lingscope Negation AE JULIE Lab Jena, Germany http://www.julielab.de diff --git a/jcore-lingscope-negation-ae/src/main/resources/de/julielab/jcore/ae/lingscope/desc/jcore-lingscope-negation-ae.xml b/jcore-lingscope-negation-ae/src/main/resources/de/julielab/jcore/ae/lingscope/desc/jcore-lingscope-negation-ae.xml index f703fd8..21e0a2d 100644 --- a/jcore-lingscope-negation-ae/src/main/resources/de/julielab/jcore/ae/lingscope/desc/jcore-lingscope-negation-ae.xml +++ b/jcore-lingscope-negation-ae/src/main/resources/de/julielab/jcore/ae/lingscope/desc/jcore-lingscope-negation-ae.xml @@ -6,7 +6,7 @@ JCoRe Lingscope Negation AE This component runs the jcore-lingscope-ae in negation mode. Please see https://sourceforge.net/p/lingscope/wiki/detailed_instructions/ for information about Lingscope and the models available. To recognize negation cues, the 'negation_models/baseline_cue_all_both.model' is used. We use the baseline model because it is based on a dictionary which provides a wider coverage than the respective CRF-based cue detection algorithm which is trained on the BioScope corpus. The scope model used is 'negation_models/crf_scope_words_crf_all_both.model'. - 2.6.0-SNAPSHOT + 2.5.1 CueModel diff --git a/jcore-lingscope-negation-ae/src/test/java/de/julielab/jcore/ae/lingscope/LingscopeNegationAeTest.java b/jcore-lingscope-negation-ae/src/test/java/de/julielab/jcore/ae/lingscope/LingscopeNegationAeTest.java index 6eaa85e..cbb9458 100644 --- a/jcore-lingscope-negation-ae/src/test/java/de/julielab/jcore/ae/lingscope/LingscopeNegationAeTest.java +++ b/jcore-lingscope-negation-ae/src/test/java/de/julielab/jcore/ae/lingscope/LingscopeNegationAeTest.java @@ -7,7 +7,7 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; import static org.assertj.core.api.Assertions.assertThat; public class LingscopeNegationAeTest { diff --git a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/component.meta b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/component.meta index d231dcd..9a2f7b0 100644 --- a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/component.meta +++ b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-linnaeus-species-ae-genera-species-proxies-dicts", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Linnaeus Species AE Genera and Species Proxies Dictionaries" } diff --git a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/pom.xml b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/pom.xml index c5fda65..3ca4904 100644 --- a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/pom.xml +++ b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/pom.xml @@ -1,36 +1,26 @@ - - 4.0.0 - jcore-linnaeus-species-ae-genera-species-proxies-dicts - JCoRe Linnaeus Species AE Genera and Species Proxies Dictionaries - This project is a resource for the JCoRe Linnaeus Annotator. The dictionaries contained herein are used - for the recognition of concrete species names in text, e.g. "human", "mouse", "n. - furzeri", "c. elegans" etc as well as species hints, i.e. indirect clues to a species like the - word "patient" which most likely refers to a human. Additionally to such rather clear proxies, this - project also includes a small dictionary containing maximum-frequency-proxies for genus expressions like "Drosophila" - which will be mapped to "D. melanogaster". For the task of only finding concrete species names in - text, there is the project jcore-linnaeus-species-ae-species-dict. - - - - de.julielab - jcore-linnaeus-species-ae-proxies-dict - 2.6.0-SNAPSHOT - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - + + 4.0.0 + jcore-linnaeus-species-ae-genera-species-proxies-dicts + JCoRe Linnaeus Species AE Genera and Species Proxies Dictionaries + This project is a resource for the JCoRe Linnaeus Annotator. The dictionaries contained herein are used for the recognition of concrete species names in text, e.g. "human", "mouse", "n. furzeri", "c. elegans" etc as well as species hints, i.e. indirect clues to a species like the word "patient" which most likely refers to a human. Additionally to such rather clear proxies, this project also includes a small dictionary containing maximum-frequency-proxies for genus expressions like "Drosophila" which will be mapped to "D. melanogaster". For the task of only finding concrete species names in text, there is the project jcore-linnaeus-species-ae-species-dict. + + + de.julielab + jcore-linnaeus-species-ae-proxies-dict + 2.5.1 + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + + de.julielab + jcore-projects + 2.5.1 + diff --git a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-genera-species-proxies-dicts.xml b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-genera-species-proxies-dicts.xml index f7b922d..18904ab 100644 --- a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-genera-species-proxies-dicts.xml +++ b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-genera-species-proxies-dicts.xml @@ -5,7 +5,7 @@ de.julielab.jcore.ae.linnaeus.LinnaeusSpeciesAnnotator JCore LINNAEUS Species AE - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java index 0c0b7ad..33fe06a 100644 --- a/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java +++ b/jcore-linnaeus-species-ae-genera-species-proxies-dicts/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java @@ -4,15 +4,15 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.resource.ResourceInitializationException; import org.apache.uima.util.InvalidXMLException; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; +import org.junit.Ignore; +import org.junit.Test; import java.io.IOException; -import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.Assert.assertNotNull; // The test should be run when something is changed, but it takes too long to run on an automated basis. -@Disabled +@Ignore public class DescriptorTest { @Test public void testDescriptor() throws InvalidXMLException, ResourceInitializationException, IOException { diff --git a/jcore-linnaeus-species-ae-proxies-dict/component.meta b/jcore-linnaeus-species-ae-proxies-dict/component.meta index 4642c1e..0edcd5f 100644 --- a/jcore-linnaeus-species-ae-proxies-dict/component.meta +++ b/jcore-linnaeus-species-ae-proxies-dict/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-linnaeus-species-ae-proxies-dict", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Linnaeus Species AE Proxies Dictionary" } diff --git a/jcore-linnaeus-species-ae-proxies-dict/pom.xml b/jcore-linnaeus-species-ae-proxies-dict/pom.xml index c6e2a24..e5c8498 100644 --- a/jcore-linnaeus-species-ae-proxies-dict/pom.xml +++ b/jcore-linnaeus-species-ae-proxies-dict/pom.xml @@ -4,7 +4,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-linnaeus-species-ae-proxies-dict This project is a resource for the JULES Linnaeus Annotator. The dictionary contained herein is used @@ -18,17 +18,16 @@ de.julielab jcore-linnaeus-species-ae - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + diff --git a/jcore-linnaeus-species-ae-proxies-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-proxies-dict.xml b/jcore-linnaeus-species-ae-proxies-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-proxies-dict.xml index bdc66ed..e0b9e93 100644 --- a/jcore-linnaeus-species-ae-proxies-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-proxies-dict.xml +++ b/jcore-linnaeus-species-ae-proxies-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-proxies-dict.xml @@ -5,7 +5,7 @@ de.julielab.jcore.ae.linnaeus.LinnaeusSpeciesAnnotator JCore LINNAEUS Species AE - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-linnaeus-species-ae-proxies-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java b/jcore-linnaeus-species-ae-proxies-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java index 125d0ae..fafd837 100644 --- a/jcore-linnaeus-species-ae-proxies-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java +++ b/jcore-linnaeus-species-ae-proxies-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java @@ -4,16 +4,15 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.resource.ResourceInitializationException; import org.apache.uima.util.InvalidXMLException; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; +import org.junit.Ignore; +import org.junit.Test; import java.io.IOException; -import static org.junit.jupiter.api.Assertions.assertNotNull; - +import static org.junit.Assert.assertNotNull; // The test should be run when something is changed, but it takes too long to run on an automated basis. -@Disabled +@Ignore public class DescriptorTest { @Test public void testDescriptor() throws InvalidXMLException, ResourceInitializationException, IOException { diff --git a/jcore-linnaeus-species-ae-species-dict/component.meta b/jcore-linnaeus-species-ae-species-dict/component.meta index 80fa3a8..bdd7f7b 100644 --- a/jcore-linnaeus-species-ae-species-dict/component.meta +++ b/jcore-linnaeus-species-ae-species-dict/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-linnaeus-species-ae-species-dict", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Linnaeus Species AE with Species Dictionary" } diff --git a/jcore-linnaeus-species-ae-species-dict/pom.xml b/jcore-linnaeus-species-ae-species-dict/pom.xml index e4e59b2..d4dd210 100644 --- a/jcore-linnaeus-species-ae-species-dict/pom.xml +++ b/jcore-linnaeus-species-ae-species-dict/pom.xml @@ -4,7 +4,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-linnaeus-species-ae-species-dict JCoRe Linnaeus Species AE with Species Dictionary @@ -18,11 +18,11 @@ de.julielab jcore-linnaeus-species-ae - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit ch.qos.logback @@ -30,10 +30,9 @@ test - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + diff --git a/jcore-linnaeus-species-ae-species-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-species-dict.xml b/jcore-linnaeus-species-ae-species-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-species-dict.xml index eb4bbba..7b01f28 100644 --- a/jcore-linnaeus-species-ae-species-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-species-dict.xml +++ b/jcore-linnaeus-species-ae-species-dict/src/main/resources/de/julielab/jcore/ae/linnaeus/desc/jcore-linnaeus-species-ae-species-dict.xml @@ -5,7 +5,7 @@ de.julielab.jcore.ae.linnaeus.LinnaeusSpeciesAnnotator JCore LINNAEUS Species AE - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-linnaeus-species-ae-species-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java b/jcore-linnaeus-species-ae-species-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java index 97710f5..bb0f720 100644 --- a/jcore-linnaeus-species-ae-species-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java +++ b/jcore-linnaeus-species-ae-species-dict/src/test/java/de/julielab/jcore/ae/linnaeus/DescriptorTest.java @@ -6,17 +6,17 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Disabled; -import org.junit.jupiter.api.Test; +import org.junit.Ignore; +import org.junit.Test; import java.util.Collection; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; // The test should be run when something is changed, but it takes too long to run on an automated basis. -@Disabled +@Ignore public class DescriptorTest { @Test public void testDescriptor() throws Exception { diff --git a/jcore-medline-db-reader/component.meta b/jcore-medline-db-reader/component.meta index bd4936e..741ec91 100644 --- a/jcore-medline-db-reader/component.meta +++ b/jcore-medline-db-reader/component.meta @@ -23,7 +23,7 @@ "maven-artifact": { "artifactId": "jcore-medline-db-reader", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe MEDLINE DB Reader" } diff --git a/jcore-medline-db-reader/pom.xml b/jcore-medline-db-reader/pom.xml index bba2ec8..48f3db2 100644 --- a/jcore-medline-db-reader/pom.xml +++ b/jcore-medline-db-reader/pom.xml @@ -5,11 +5,11 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-medline-db-reader JCoRe MEDLINE DB Reader - + An instantiation of the jcore-db-reader that uses the jcore-xml-mapper to retrieve and parse MEDLINE XML from a PostgreSQL database. The XML format of retrieved documents is expected to follow the MEDLINE XML schema @@ -20,20 +20,19 @@ de.julielab jcore-xml-db-reader - ${jcore-version} + 2.5.0 de.julielab jcore-descriptor-creator - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + JULIE Lab, Germany http://www.julielab.de diff --git a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml index f83f6a6..60bf5aa 100644 --- a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml +++ b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier-reader.xml @@ -10,7 +10,7 @@ sent by this reader. The component leverages the corpus storage system (CoStoSys) for this purpose and is part of the Jena Document Information System, JeDIS. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml index 11d99cd..8fcbbe8 100644 --- a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml +++ b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-multiplier.xml @@ -12,7 +12,7 @@ additional database tables and populate the CAS with them via the 'RowMapping' parameter. This component is part of the Jena Document Information System, JeDIS. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-reader.xml b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-reader.xml index 38c0e76..abefc63 100644 --- a/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-reader.xml +++ b/jcore-medline-db-reader/src/main/resources/de/julielab/jcore/reader/medline-db/desc/jcore-medline-db-reader.xml @@ -14,7 +14,7 @@ must be mapped via the 'RowMapping'. This mechanism and this component are part of the Jena Document Information System, JeDIS. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-medline-reader/component.meta b/jcore-medline-reader/component.meta index ff745df..6324fe1 100644 --- a/jcore-medline-reader/component.meta +++ b/jcore-medline-reader/component.meta @@ -23,7 +23,7 @@ "maven-artifact": { "artifactId": "jcore-medline-reader", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe Medline Reader" } diff --git a/jcore-medline-reader/pom.xml b/jcore-medline-reader/pom.xml index 9388256..9e62b72 100644 --- a/jcore-medline-reader/pom.xml +++ b/jcore-medline-reader/pom.xml @@ -5,7 +5,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-medline-reader JCoRe Medline Reader @@ -23,11 +23,11 @@ de.julielab jcore-xml-reader - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit de.julielab @@ -41,13 +41,12 @@ test - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + JULIE Lab, Germany http://www.julielab.de diff --git a/jcore-medline-reader/src/main/resources/de/julielab/jcore/multiplier/xml/desc/jcore-medline-citationset-multiplier.xml b/jcore-medline-reader/src/main/resources/de/julielab/jcore/multiplier/xml/desc/jcore-medline-citationset-multiplier.xml index debbb10..5d67e6c 100644 --- a/jcore-medline-reader/src/main/resources/de/julielab/jcore/multiplier/xml/desc/jcore-medline-citationset-multiplier.xml +++ b/jcore-medline-reader/src/main/resources/de/julielab/jcore/multiplier/xml/desc/jcore-medline-citationset-multiplier.xml @@ -8,7 +8,7 @@ This reader assumes that the input XML format has a MedlineCitationSet element as its root. This format was used for the MEDLINE FTP download until 2016. Since then, the XML format has been changed to a PubmedArticleSet. Use the jcore-pubmed-reader for such files. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab, Germany diff --git a/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-multiplier-reader.xml b/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-multiplier-reader.xml index ad0b5d7..762efac 100644 --- a/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-multiplier-reader.xml +++ b/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-multiplier-reader.xml @@ -6,7 +6,7 @@ JCoRe Medline XML Multiplier Reader Used for MEDLINE XML FTP downloads until 2016. Starting with 2017, the format was changed to PubmedArticleSet. Use the jcore-pubmed-reader for such data. - 2.6.0-SNAPSHOT + 2.5.1 de.julielab.jcore.reader.xml diff --git a/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-reader.xml b/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-reader.xml index 7881e96..ad6ba1b 100644 --- a/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-reader.xml +++ b/jcore-medline-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-medline-reader.xml @@ -5,7 +5,7 @@ JCoRe Medline Reader Leveraging the JCoRe XML Reader, this project employs a Medline-enabled mapping file to map Medline XML documents to CAS instances. The input is a directory of single XML files, each containing exactly one XML MedlineCitation. The XML format is the one used by NCBI when downloading Medline documents in large batches from the NCBI FTP server. However, the component currently expects single documents instead of whole MedlineCitationSets containing sets of MedlineCitations. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab, Germany diff --git a/jcore-medline-reader/src/test/java/de/julielab/jcore/reader/xml/MedlineReaderTest.java b/jcore-medline-reader/src/test/java/de/julielab/jcore/reader/xml/MedlineReaderTest.java index 80ef9b9..557e47c 100644 --- a/jcore-medline-reader/src/test/java/de/julielab/jcore/reader/xml/MedlineReaderTest.java +++ b/jcore-medline-reader/src/test/java/de/julielab/jcore/reader/xml/MedlineReaderTest.java @@ -16,10 +16,9 @@ import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.cas.FSArray; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; - -import static org.junit.jupiter.api.Assertions.*; +import org.junit.Test; +import static org.junit.Assert.*; public class MedlineReaderTest { @Test @@ -148,7 +147,7 @@ public void testVernacularTitle() throws Exception { assertTrue(medlineReader.hasNext()); medlineReader.getNext(jCas.getCas()); - assertFalse(jCas.getDocumentText().isEmpty(), "Document text is empty"); + assertFalse("Document text is empty", jCas.getDocumentText().isEmpty()); final Title title = JCasUtil.selectSingle(jCas, Title.class); assertEquals("document_vernacular", title.getTitleType()); } diff --git a/jcore-mstparser-ae-biomedical-english/component.meta b/jcore-mstparser-ae-biomedical-english/component.meta index a4e9955..74a3b93 100644 --- a/jcore-mstparser-ae-biomedical-english/component.meta +++ b/jcore-mstparser-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-mstparser-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe MST Parser AE, Biomedical English" } diff --git a/jcore-mstparser-ae-biomedical-english/pom.xml b/jcore-mstparser-ae-biomedical-english/pom.xml index 1f7864c..2c2abff 100644 --- a/jcore-mstparser-ae-biomedical-english/pom.xml +++ b/jcore-mstparser-ae-biomedical-english/pom.xml @@ -13,7 +13,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany @@ -23,11 +23,11 @@ de.julielab jcore-mstparser-ae - ${jcore-version} + 2.5.0 - org.junit.jupiter - junit-jupiter-engine + junit + junit org.slf4j @@ -41,10 +41,9 @@ ${jcore-utilities-version} - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + diff --git a/jcore-mstparser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/mstparser/desc/jcore-mstparser-ae-biomedical-english.xml b/jcore-mstparser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/mstparser/desc/jcore-mstparser-ae-biomedical-english.xml index d64583c..0bcef6f 100644 --- a/jcore-mstparser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/mstparser/desc/jcore-mstparser-ae-biomedical-english.xml +++ b/jcore-mstparser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/mstparser/desc/jcore-mstparser-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe MST Parser Annotator specialized package with a model trained on the GENIA conll corpus - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-mstparser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/mstparser/TestModel.java b/jcore-mstparser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/mstparser/TestModel.java index a3da51c..376795e 100644 --- a/jcore-mstparser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/mstparser/TestModel.java +++ b/jcore-mstparser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/mstparser/TestModel.java @@ -11,12 +11,13 @@ import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.cas.FSArray; -import org.junit.jupiter.api.Test; +import org.junit.Test; import javax.naming.NameNotFoundException; import java.util.Collection; -import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; public class TestModel { @Test diff --git a/jcore-opennlp-chunk-ae-biomedical-english/component.meta b/jcore-opennlp-chunk-ae-biomedical-english/component.meta index 2fd0395..69e81fc 100644 --- a/jcore-opennlp-chunk-ae-biomedical-english/component.meta +++ b/jcore-opennlp-chunk-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-chunk-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP Chunker, Biomedical English" } diff --git a/jcore-opennlp-chunk-ae-biomedical-english/pom.xml b/jcore-opennlp-chunk-ae-biomedical-english/pom.xml index 7414966..75acce0 100644 --- a/jcore-opennlp-chunk-ae-biomedical-english/pom.xml +++ b/jcore-opennlp-chunk-ae-biomedical-english/pom.xml @@ -1,47 +1,42 @@ - - 4.0.0 - jcore-opennlp-chunk-ae-biomedical-english - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - JCoRe OpenNLP Chunker, Biomedical English - This project employs the OpenNLP wrapper (jcore-opennlp-chunker-ae) with a model trained on the Genia - corpus. - - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-types - ${jcore-types-version} + + 4.0.0 + jcore-opennlp-chunk-ae-biomedical-english + + de.julielab + jcore-projects + 2.5.1 + + JCoRe OpenNLP Chunker, Biomedical English + This project employs the OpenNLP wrapper (jcore-opennlp-chunker-ae) with a model trained on the Genia corpus. + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-types + ${jcore-types-version} - - de.julielab - jcore-opennlp-chunk-ae - ${jcore-version} - - - org.junit.jupiter - junit-jupiter-engine - - - ch.qos.logback - logback-classic - test - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-chunk-ae-biomedical-english + + de.julielab + jcore-opennlp-chunk-ae + 2.5.0 + + + junit + junit + + ch.qos.logback + logback-classic + test + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-chunk-ae-biomedical-english diff --git a/jcore-opennlp-chunk-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/chunk/desc/jcore-opennlp-chunk-ae-biomedical-english.xml b/jcore-opennlp-chunk-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/chunk/desc/jcore-opennlp-chunk-ae-biomedical-english.xml index 76555af..b1d9cf5 100644 --- a/jcore-opennlp-chunk-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/chunk/desc/jcore-opennlp-chunk-ae-biomedical-english.xml +++ b/jcore-opennlp-chunk-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/chunk/desc/jcore-opennlp-chunk-ae-biomedical-english.xml @@ -8,7 +8,7 @@ JCoRe OpenNLP Chunk AE Biomed English Descriptor for OpenNLP Sentence Splitter using a model trained on Genia Treebank v1 - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-opennlp-chunk-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/chunk/genia/OpenNLPChunkerGeniaTest.java b/jcore-opennlp-chunk-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/chunk/genia/OpenNLPChunkerGeniaTest.java index dc052a1..7f815dc 100644 --- a/jcore-opennlp-chunk-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/chunk/genia/OpenNLPChunkerGeniaTest.java +++ b/jcore-opennlp-chunk-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/chunk/genia/OpenNLPChunkerGeniaTest.java @@ -8,10 +8,10 @@ import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.cas.FSArray; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; public class OpenNLPChunkerGeniaTest { @Test diff --git a/jcore-opennlp-parser-ae-biomedical-english/component.meta b/jcore-opennlp-parser-ae-biomedical-english/component.meta index 409640f..87a31ce 100644 --- a/jcore-opennlp-parser-ae-biomedical-english/component.meta +++ b/jcore-opennlp-parser-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-parser-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP Parser, Biomedical English" } diff --git a/jcore-opennlp-parser-ae-biomedical-english/pom.xml b/jcore-opennlp-parser-ae-biomedical-english/pom.xml index aaa6be6..bf1768e 100644 --- a/jcore-opennlp-parser-ae-biomedical-english/pom.xml +++ b/jcore-opennlp-parser-ae-biomedical-english/pom.xml @@ -1,42 +1,37 @@ - - 4.0.0 - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - jcore-opennlp-parser-ae-biomedical-english - JCoRe OpenNLP Parser, Biomedical English - - - de.julielab - jcore-opennlp-parser-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-parser-ae-biomedical-english - This project employs the OpenNLP wrapper (jcore-opennlp-parser-ae) with a model trained on the Genia - corpus. - - - JULIE Lab Jena, Germany - http://www.julielab.de - + + 4.0.0 + + de.julielab + jcore-projects + 2.5.1 + + jcore-opennlp-parser-ae-biomedical-english + JCoRe OpenNLP Parser, Biomedical English + + + de.julielab + jcore-opennlp-parser-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-parser-ae-biomedical-english + This project employs the OpenNLP wrapper (jcore-opennlp-parser-ae) with a model trained on the Genia corpus. + + JULIE Lab Jena, Germany + http://www.julielab.de + diff --git a/jcore-opennlp-parser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/parser/desc/jcore-opennlp-parser-ae-biomedical-english.xml b/jcore-opennlp-parser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/parser/desc/jcore-opennlp-parser-ae-biomedical-english.xml index 7377879..0f8a1b4 100644 --- a/jcore-opennlp-parser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/parser/desc/jcore-opennlp-parser-ae-biomedical-english.xml +++ b/jcore-opennlp-parser-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/parser/desc/jcore-opennlp-parser-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe OpenNLP Constituency Parser, Genia 2009 -2.6.0-SNAPSHOT +2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-opennlp-parser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/parser/ParseAnnotatorTest.java b/jcore-opennlp-parser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/parser/ParseAnnotatorTest.java index 6fb5563..bf4f3c6 100644 --- a/jcore-opennlp-parser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/parser/ParseAnnotatorTest.java +++ b/jcore-opennlp-parser-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/parser/ParseAnnotatorTest.java @@ -18,6 +18,7 @@ package de.julielab.jcore.ae.opennlp.parser; import de.julielab.jcore.types.*; +import junit.framework.TestCase; import org.apache.uima.UIMAFramework; import org.apache.uima.analysis_engine.AnalysisEngine; import org.apache.uima.jcas.JCas; @@ -25,19 +26,22 @@ import org.apache.uima.resource.ResourceInitializationException; import org.apache.uima.resource.ResourceSpecifier; import org.apache.uima.util.XMLInputSource; -import org.junit.jupiter.api.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.util.Iterator; -import static org.junit.jupiter.api.Assertions.assertTrue; - -public class ParseAnnotatorTest { +public class ParseAnnotatorTest extends TestCase { private static final Logger LOGGER = LoggerFactory.getLogger(ParseAnnotatorTest.class); private static final String LOGGER_PROPERTIES = "src/test/java/log4j.properties"; + @Override + protected void setUp() throws Exception { + super.setUp(); + // set log4j properties file + // PropertyConfigurator.configure(LOGGER_PROPERTIES); + } String text = "A study on the Prethcamide hydroxylation system in rat hepatic microsomes ."; @@ -64,7 +68,6 @@ public void initCas(JCas jcas) { } } - @Test public void testProcess() { boolean annotationsOK = true; diff --git a/jcore-opennlp-postag-ae-biomedical-english/component.meta b/jcore-opennlp-postag-ae-biomedical-english/component.meta index 2d19a73..698d349 100644 --- a/jcore-opennlp-postag-ae-biomedical-english/component.meta +++ b/jcore-opennlp-postag-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-postag-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP POS Tagger, Biomedical English" } diff --git a/jcore-opennlp-postag-ae-biomedical-english/pom.xml b/jcore-opennlp-postag-ae-biomedical-english/pom.xml index 82329ba..cc24d58 100644 --- a/jcore-opennlp-postag-ae-biomedical-english/pom.xml +++ b/jcore-opennlp-postag-ae-biomedical-english/pom.xml @@ -1,75 +1,70 @@ - + - 4.0.0 - jcore-opennlp-postag-ae-biomedical-english - jar - This project employs the OpenNLP wrapper (jcore-opennlp-postag-ae) with a model trained on the - PennBioIE corpus. - - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - - - - - org.eclipse.m2e - lifecycle-mapping - 1.0.0 - - - - - - - org.apache.maven.plugins - maven-dependency-plugin - [1.0.0,) - - copy-dependencies - - - - - - - - - - - - - - JCoRe OpenNLP POS Tagger, Biomedical English - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-opennlp-postag-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-postag-ae-biomedical-english + 4.0.0 + jcore-opennlp-postag-ae-biomedical-english + jar + This project employs the OpenNLP wrapper (jcore-opennlp-postag-ae) with a model trained on the PennBioIE corpus. + + de.julielab + jcore-projects + 2.5.1 + + + + + + org.eclipse.m2e + lifecycle-mapping + 1.0.0 + + + + + + + org.apache.maven.plugins + maven-dependency-plugin + [1.0.0,) + + copy-dependencies + + + + + + + + + + + + + + JCoRe OpenNLP POS Tagger, Biomedical English + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-opennlp-postag-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-postag-ae-biomedical-english diff --git a/jcore-opennlp-postag-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-biomedical-english.xml b/jcore-opennlp-postag-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-biomedical-english.xml index 2e6083b..dc7ad1d 100644 --- a/jcore-opennlp-postag-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-biomedical-english.xml +++ b/jcore-opennlp-postag-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe OpenNLP POS Tagger - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-opennlp-postag-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagPennBioIETest.java b/jcore-opennlp-postag-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagPennBioIETest.java index 99739b8..d3dfddf 100644 --- a/jcore-opennlp-postag-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagPennBioIETest.java +++ b/jcore-opennlp-postag-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagPennBioIETest.java @@ -8,10 +8,10 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; public class OpenNLPPosTagPennBioIETest { @Test diff --git a/jcore-opennlp-postag-ae-medical-german/component.meta b/jcore-opennlp-postag-ae-medical-german/component.meta index d0fdd38..066d6fe 100644 --- a/jcore-opennlp-postag-ae-medical-german/component.meta +++ b/jcore-opennlp-postag-ae-medical-german/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-postag-ae-medical-german", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP POS Tagger, Medical German" } diff --git a/jcore-opennlp-postag-ae-medical-german/pom.xml b/jcore-opennlp-postag-ae-medical-german/pom.xml index c12f7b5..70e139a 100644 --- a/jcore-opennlp-postag-ae-medical-german/pom.xml +++ b/jcore-opennlp-postag-ae-medical-german/pom.xml @@ -1,35 +1,32 @@ - - 4.0.0 - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - jcore-opennlp-postag-ae-medical-german - JCoRe OpenNLP POS Tagger, Medical German - - - de.julielab - jcore-opennlp-postag-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - This Model was trained on the confidential FraMed corpus. + + 4.0.0 + + de.julielab + jcore-projects + 2.5.1 + + jcore-opennlp-postag-ae-medical-german + JCoRe OpenNLP POS Tagger, Medical German + + + de.julielab + jcore-opennlp-postag-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + This Model was trained on the confidential FraMed corpus. diff --git a/jcore-opennlp-postag-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-medical-german.xml b/jcore-opennlp-postag-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-medical-german.xml index e87bb26..1c483ef 100644 --- a/jcore-opennlp-postag-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-medical-german.xml +++ b/jcore-opennlp-postag-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/postag/desc/jcore-opennlp-postag-ae-medical-german.xml @@ -6,7 +6,7 @@ JCoRe OpenNLP POS Tagger - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-opennlp-postag-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagFraMedTest.java b/jcore-opennlp-postag-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagFraMedTest.java index a43c172..bc0d7d6 100644 --- a/jcore-opennlp-postag-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagFraMedTest.java +++ b/jcore-opennlp-postag-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPPosTagFraMedTest.java @@ -8,10 +8,10 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; +import org.junit.Test; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; public class OpenNLPPosTagFraMedTest { @Test diff --git a/jcore-opennlp-sentence-ae-biomedical-english/component.meta b/jcore-opennlp-sentence-ae-biomedical-english/component.meta index 2565379..d23dc23 100644 --- a/jcore-opennlp-sentence-ae-biomedical-english/component.meta +++ b/jcore-opennlp-sentence-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-sentence-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP Sentence Splitter, Biomedical English" } diff --git a/jcore-opennlp-sentence-ae-biomedical-english/pom.xml b/jcore-opennlp-sentence-ae-biomedical-english/pom.xml index e7e1c3f..ef24de5 100644 --- a/jcore-opennlp-sentence-ae-biomedical-english/pom.xml +++ b/jcore-opennlp-sentence-ae-biomedical-english/pom.xml @@ -1,8 +1,7 @@ - - 4.0.0 - jcore-opennlp-sentence-ae-biomedical-english + + 4.0.0 + jcore-opennlp-sentence-ae-biomedical-english @@ -13,7 +12,7 @@ - + org.apache.maven.plugins @@ -24,7 +23,7 @@ - + @@ -34,40 +33,36 @@ - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - JCoRe OpenNLP Sentence Splitter, Biomedical English - This project employs the UIMA wrapper (jcore-opennlp-sentence-ae) with a model trained on the PennBioIE - and Genia corpora. - - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - org.junit.jupiter - junit-jupiter-engine + + de.julielab + jcore-projects + 2.5.1 + + JCoRe OpenNLP Sentence Splitter, Biomedical English + This project employs the UIMA wrapper (jcore-opennlp-sentence-ae) with a model trained on the PennBioIE and Genia corpora. + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + junit + junit + + de.julielab + jcore-types + ${jcore-types-version} - - de.julielab - jcore-types - ${jcore-types-version} - - - de.julielab - jcore-opennlp-sentence-ae - ${jcore-version} - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-sentence-ae-biomedical-english + + de.julielab + jcore-opennlp-sentence-ae + 2.5.0 + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-sentence-ae-biomedical-english diff --git a/jcore-opennlp-sentence-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-biomedical-english.xml b/jcore-opennlp-sentence-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-biomedical-english.xml index e2c89cc..a5eba03 100644 --- a/jcore-opennlp-sentence-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-biomedical-english.xml +++ b/jcore-opennlp-sentence-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-biomedical-english.xml @@ -6,7 +6,7 @@ JCoRe OpenNLP Sentence Splitter AE Biomed English Descriptor for OpenNLP Sentence Splitter using a model trained on Genia and PennBio -2.6.0-SNAPSHOT +2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-opennlp-sentence-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/sentence/TestWorkFlow.java b/jcore-opennlp-sentence-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/sentence/TestWorkFlow.java index 984461c..0a8bf3b 100644 --- a/jcore-opennlp-sentence-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/sentence/TestWorkFlow.java +++ b/jcore-opennlp-sentence-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/sentence/TestWorkFlow.java @@ -5,7 +5,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; import java.io.IOException; diff --git a/jcore-opennlp-sentence-ae-medical-german/component.meta b/jcore-opennlp-sentence-ae-medical-german/component.meta index 0cf936f..bd0b94c 100644 --- a/jcore-opennlp-sentence-ae-medical-german/component.meta +++ b/jcore-opennlp-sentence-ae-medical-german/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-sentence-ae-medical-german", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP Sentence Segmenter, Medical German" } diff --git a/jcore-opennlp-sentence-ae-medical-german/pom.xml b/jcore-opennlp-sentence-ae-medical-german/pom.xml index bd8266d..46aaf82 100644 --- a/jcore-opennlp-sentence-ae-medical-german/pom.xml +++ b/jcore-opennlp-sentence-ae-medical-german/pom.xml @@ -1,35 +1,33 @@ - - 4.0.0 - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - jcore-opennlp-sentence-ae-medical-german - JCoRe OpenNLP Sentence Segmenter, Medical German - - - org.junit.jupiter - junit-jupiter-engine - - - ch.qos.logback - logback-classic - test - - - de.julielab - jcore-opennlp-sentence-ae - ${jcore-version} - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - This Model was trained on the confidential FraMed corpus. + + 4.0.0 + + de.julielab + jcore-projects + 2.5.1 + + jcore-opennlp-sentence-ae-medical-german + JCoRe OpenNLP Sentence Segmenter, Medical German + + + junit + junit + + + ch.qos.logback + logback-classic + test + + + de.julielab + jcore-opennlp-sentence-ae + 2.5.0 + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + This Model was trained on the confidential FraMed corpus. diff --git a/jcore-opennlp-sentence-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-medical-german.xml b/jcore-opennlp-sentence-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-medical-german.xml index 9f0c854..769db13 100644 --- a/jcore-opennlp-sentence-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-medical-german.xml +++ b/jcore-opennlp-sentence-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/sentence/desc/jcore-opennlp-sentence-ae-medical-german.xml @@ -6,7 +6,7 @@ JCoRe OpenNLP Sentence Segmenter - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-opennlp-sentence-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/sentence/OpenNLPSentenceFraMedTest.java b/jcore-opennlp-sentence-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/sentence/OpenNLPSentenceFraMedTest.java index 2763c73..d1e2c85 100644 --- a/jcore-opennlp-sentence-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/sentence/OpenNLPSentenceFraMedTest.java +++ b/jcore-opennlp-sentence-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/sentence/OpenNLPSentenceFraMedTest.java @@ -4,7 +4,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; public class OpenNLPSentenceFraMedTest { @Test diff --git a/jcore-opennlp-token-ae-biomedical-english/component.meta b/jcore-opennlp-token-ae-biomedical-english/component.meta index 3e5c10b..43befab 100644 --- a/jcore-opennlp-token-ae-biomedical-english/component.meta +++ b/jcore-opennlp-token-ae-biomedical-english/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-token-ae-biomedical-english", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP Token AE, Biomedical English" } diff --git a/jcore-opennlp-token-ae-biomedical-english/pom.xml b/jcore-opennlp-token-ae-biomedical-english/pom.xml index c8dbd1d..ea1be9b 100644 --- a/jcore-opennlp-token-ae-biomedical-english/pom.xml +++ b/jcore-opennlp-token-ae-biomedical-english/pom.xml @@ -1,42 +1,38 @@ - - 4.0.0 - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - jcore-opennlp-token-ae-biomedical-english - JCoRe OpenNLP Token AE, Biomedical English - This project employes the JCoRe OpenNLP tokenizer wrapper with a model trained on the PennBioIE corpus - and data from MedLine abstracts. - - - JULIE Lab Jena, Germany - http://www.julielab.de - - - - de.julielab - jcore-opennlp-token-ae - ${jcore-version} - - - org.junit.jupiter - junit-jupiter-engine - - - ch.qos.logback - logback-classic - test - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-token-ae-biomedical-english + + 4.0.0 + + de.julielab + jcore-projects + 2.5.1 + + jcore-opennlp-token-ae-biomedical-english + JCoRe OpenNLP Token AE, Biomedical English + This project employes the JCoRe OpenNLP tokenizer wrapper with a model trained on the PennBioIE corpus and data from MedLine abstracts. + + JULIE Lab Jena, Germany + http://www.julielab.de + + + + de.julielab + jcore-opennlp-token-ae + 2.5.0 + + + junit + junit + + + ch.qos.logback + logback-classic + test + + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + https://github.com/JULIELab/jcore-projects/tree/master/jcore-opennlp-token-ae-biomedical-english diff --git a/jcore-opennlp-token-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-biomedical-english.xml b/jcore-opennlp-token-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-biomedical-english.xml index 4e96260..43b8e13 100644 --- a/jcore-opennlp-token-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-biomedical-english.xml +++ b/jcore-opennlp-token-ae-biomedical-english/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-biomedical-english.xml @@ -5,7 +5,7 @@ jcore-opennlp-token-ae-biomed-english - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-opennlp-token-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/token/BiomedEnglishOpenNlpWrapperTest.java b/jcore-opennlp-token-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/token/BiomedEnglishOpenNlpWrapperTest.java index d3a3420..c8e03ef 100644 --- a/jcore-opennlp-token-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/token/BiomedEnglishOpenNlpWrapperTest.java +++ b/jcore-opennlp-token-ae-biomedical-english/src/test/java/de/julielab/jcore/ae/opennlp/token/BiomedEnglishOpenNlpWrapperTest.java @@ -7,11 +7,11 @@ import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; import java.util.Collection; -import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.Assert.assertEquals; public class BiomedEnglishOpenNlpWrapperTest { @Test diff --git a/jcore-opennlp-token-ae-medical-german/component.meta b/jcore-opennlp-token-ae-medical-german/component.meta index 8c68f54..975c13a 100644 --- a/jcore-opennlp-token-ae-medical-german/component.meta +++ b/jcore-opennlp-token-ae-medical-german/component.meta @@ -14,7 +14,7 @@ "maven-artifact": { "artifactId": "jcore-opennlp-token-ae-medical-german", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe OpenNLP Tokenizer, Medical German" } diff --git a/jcore-opennlp-token-ae-medical-german/pom.xml b/jcore-opennlp-token-ae-medical-german/pom.xml index 617dbc9..ce1c495 100644 --- a/jcore-opennlp-token-ae-medical-german/pom.xml +++ b/jcore-opennlp-token-ae-medical-german/pom.xml @@ -1,35 +1,32 @@ - - 4.0.0 - - de.julielab - jcore-projects - 2.6.0-SNAPSHOT - - jcore-opennlp-token-ae-medical-german - JCoRe OpenNLP Tokenizer, Medical German - - - de.julielab - jcore-opennlp-token-ae - ${jcore-version} - - - ch.qos.logback - logback-classic - test - - - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - This Model was trained on the confidential FraMed corpus. + + 4.0.0 + + de.julielab + jcore-projects + 2.5.1 + + jcore-opennlp-token-ae-medical-german + JCoRe OpenNLP Tokenizer, Medical German + + + de.julielab + jcore-opennlp-token-ae + 2.5.0 + + + ch.qos.logback + logback-classic + test + + + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + This Model was trained on the confidential FraMed corpus. diff --git a/jcore-opennlp-token-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-medical-german.xml b/jcore-opennlp-token-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-medical-german.xml index a89635e..0a1e6f8 100644 --- a/jcore-opennlp-token-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-medical-german.xml +++ b/jcore-opennlp-token-ae-medical-german/src/main/resources/de/julielab/jcore/ae/opennlp/token/desc/jcore-opennlp-token-ae-medical-german.xml @@ -5,7 +5,7 @@ jcore-opennlp-token-ae-medical-german - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-opennlp-token-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPTokenFraMedTest.java b/jcore-opennlp-token-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPTokenFraMedTest.java index 3c77d98..86cb9d2 100644 --- a/jcore-opennlp-token-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPTokenFraMedTest.java +++ b/jcore-opennlp-token-ae-medical-german/src/test/java/de/julielab/jcore/ae/opennlp/postag/OpenNLPTokenFraMedTest.java @@ -4,7 +4,7 @@ import org.apache.uima.fit.factory.AnalysisEngineFactory; import org.apache.uima.fit.factory.JCasFactory; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; public class OpenNLPTokenFraMedTest { @Test diff --git a/jcore-pubmed-db-reader/component.meta b/jcore-pubmed-db-reader/component.meta index 1825f46..062e1b3 100644 --- a/jcore-pubmed-db-reader/component.meta +++ b/jcore-pubmed-db-reader/component.meta @@ -24,7 +24,7 @@ "maven-artifact": { "artifactId": "jcore-pubmed-db-reader", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe PubMed DB Reader" } diff --git a/jcore-pubmed-db-reader/pom.xml b/jcore-pubmed-db-reader/pom.xml index 49091bb..ed5640b 100644 --- a/jcore-pubmed-db-reader/pom.xml +++ b/jcore-pubmed-db-reader/pom.xml @@ -5,11 +5,11 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-pubmed-db-reader JCoRe PubMed DB Reader - + An instantiation of the jcore-db-reader that uses the jcore-xml-mapper to retrieve and parse PubMed XML from a PostgreSQL database. The XML format of retrieved documents is expected to follow the PubMed/MEDLINE XML schema @@ -20,24 +20,22 @@ de.julielab jcore-xml-db-reader - ${jcore-version} + 2.5.0 de.julielab jcore-descriptor-creator - org.junit.jupiter - junit-jupiter-engine - - - - - BSD-2-Clause - https://opensource.org/licenses/BSD-2-Clause - - - + junit + junit + + + +BSD-2-Clause +https://opensource.org/licenses/BSD-2-Clause + + JULIE Lab, Germany http://www.julielab.de diff --git a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier-reader.xml b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier-reader.xml index e8ef7d5..65a944c 100644 --- a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier-reader.xml +++ b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier-reader.xml @@ -10,7 +10,7 @@ sent by this reader. The component leverages the corpus storage system (CoStoSys) for this purpose and is part of the Jena Document Information System, JeDIS. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml index b72256e..e09e2b6 100644 --- a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml +++ b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-multiplier.xml @@ -12,7 +12,7 @@ additional database tables and populate the CAS with them via the 'RowMapping' parameter. This component is part of the Jena Document Information System, JeDIS. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-reader.xml b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-reader.xml index c39dcb1..b3395c7 100644 --- a/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-reader.xml +++ b/jcore-pubmed-db-reader/src/main/resources/de/julielab/jcore/reader/pubmed-db/desc/jcore-pubmed-db-reader.xml @@ -15,7 +15,7 @@ must be mapped via the 'RowMapping'. This mechanism and this component are part of the Jena Document Information System, JeDIS. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab Jena, Germany diff --git a/jcore-pubmed-reader/component.meta b/jcore-pubmed-reader/component.meta index aa7befb..44450b8 100644 --- a/jcore-pubmed-reader/component.meta +++ b/jcore-pubmed-reader/component.meta @@ -23,7 +23,7 @@ "maven-artifact": { "artifactId": "jcore-pubmed-reader", "groupId": "de.julielab", - "version": "2.6.0-SNAPSHOT" + "version": "2.5.1" }, "name": "JCoRe PubMed Reader" } diff --git a/jcore-pubmed-reader/pom.xml b/jcore-pubmed-reader/pom.xml index 44f8ad5..d179a8b 100644 --- a/jcore-pubmed-reader/pom.xml +++ b/jcore-pubmed-reader/pom.xml @@ -5,7 +5,7 @@ de.julielab jcore-projects - 2.6.0-SNAPSHOT + 2.5.1 jcore-pubmed-reader JCoRe PubMed Reader @@ -17,7 +17,7 @@ de.julielab jcore-xml-reader - ${jcore-version} + 2.5.0 ch.qos.logback @@ -39,8 +39,8 @@ ${jcore-utilities-version} - org.junit.jupiter - junit-jupiter-engine + junit + junit diff --git a/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-articleset-multiplier.xml b/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-articleset-multiplier.xml index dbb0426..de1514b 100644 --- a/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-articleset-multiplier.xml +++ b/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-articleset-multiplier.xml @@ -6,7 +6,7 @@ JCoRe PubMed ArticleSet Multiplier - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab, Germany diff --git a/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-multiplier-reader.xml b/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-multiplier-reader.xml index 7f461cb..74f5f4c 100644 --- a/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-multiplier-reader.xml +++ b/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-multiplier-reader.xml @@ -5,7 +5,7 @@ JCoRe PubMed Reader for ArticleSet Multiplier - 2.6.0-SNAPSHOT + 2.5.1 diff --git a/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-reader.xml b/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-reader.xml index 96ace74..cb70445 100644 --- a/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-reader.xml +++ b/jcore-pubmed-reader/src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-reader.xml @@ -8,7 +8,7 @@ XML documents to CAS instances. The input is a directory of single XML files, each containing exactly one XML PubmedArticle. The XML format is the one used by NCBI when displaying results in PubMed as XML. - 2.6.0-SNAPSHOT + 2.5.1 JULIE Lab, Germany diff --git a/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedMultiplierTest.java b/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedMultiplierTest.java index 0aaec1a..6787188 100644 --- a/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedMultiplierTest.java +++ b/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedMultiplierTest.java @@ -18,7 +18,7 @@ import org.apache.uima.fit.factory.CollectionReaderFactory; import org.apache.uima.fit.util.JCasUtil; import org.apache.uima.jcas.JCas; -import org.junit.jupiter.api.Test; +import org.junit.Test; import org.xml.sax.SAXException; import java.io.IOException; @@ -26,8 +26,8 @@ import java.util.Arrays; import java.util.List; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; /** * Tests the multiplier reader together with the multiplier in a simple CPE. @@ -82,6 +82,8 @@ public void testMultiplier() throws IOException, UIMAException, CpeDescriptorExc assertEquals(177, seenPmids.size()); for (String pmid : seenPmids) assertTrue(pmid.matches("[0-9]+")); + + } public static class TestAe extends JCasAnnotator_ImplBase { diff --git a/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedReaderTest.java b/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedReaderTest.java index 47d93d3..74029e6 100644 --- a/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedReaderTest.java +++ b/jcore-pubmed-reader/src/test/java/de/julielab/jcore/reader/xml/PubmedReaderTest.java @@ -13,10 +13,9 @@ import org.apache.uima.jcas.JCas; import org.apache.uima.jcas.cas.FSArray; import org.apache.uima.jcas.tcas.Annotation; -import org.junit.jupiter.api.Test; - -import static org.junit.jupiter.api.Assertions.*; +import org.junit.Test; +import static org.junit.Assert.*; public class PubmedReaderTest { @Test @@ -27,12 +26,12 @@ public void testPubmedReader() throws Exception { "src/main/resources/de/julielab/jcore/reader/xml/desc/jcore-pubmed-reader.xml"); CollectionReader pubmedReader = CollectionReaderFactory.createReader(pubmedReaderDescription, XMLReader.PARAM_INPUT_FILE, "src/test/resources/pubmedDocs/7723770.xml"); - assertTrue(pubmedReader.hasNext(), "Assertion failure"); + assertTrue("Assertion failure", pubmedReader.hasNext()); pubmedReader.getNext(jCas.getCas()); - assertEquals("7723770", JCasUtil.selectSingle(jCas, Header.class).getDocId(), "Assertion failure"); - assertNotNull(jCas.getDocumentText(), "Assertion failure"); - assertTrue(jCas.getDocumentText().length() > 0, "Assertion failure"); + assertEquals("Assertion failure", "7723770", JCasUtil.selectSingle(jCas, Header.class).getDocId()); + assertNotNull("Assertion failure", jCas.getDocumentText()); + assertTrue("Assertion failure", jCas.getDocumentText().length() > 0); } @Test diff --git a/pom.xml b/pom.xml index 1d00515..69c72f0 100644 --- a/pom.xml +++ b/pom.xml @@ -1,15 +1,14 @@ - + 4.0.0 de.julielab jcore-base - 2.6.0-SNAPSHOT + 2.5.0 jcore-projects pom - 2.6.0-SNAPSHOT + 2.5.1 JCoRe Projects The POM for the JCoRe Projects. diff --git a/scripts/setProjectVersion.sh b/scripts/setProjectVersion.sh index fc1095c..3e85783 100755 --- a/scripts/setProjectVersion.sh +++ b/scripts/setProjectVersion.sh @@ -1,15 +1,14 @@ #!/bin/bash # To executed in the project's root directory. -# The script expects two parameters: The new version to set and whether dependencies to (JULIE Lab) snapshots are allowed. +# The script expectes two parameters: The new version to set and whether dependencies to (JULIE Lab) snapshots are allowed. # This script performs the following actions given a Maven version number: # 1. It sets the version to all parent poms (projects with packaging 'pom') relative to the given root pom (jcore-base or jcore-projects, for example). # 2. It removes all custom tags of the modules so that they inherit the version from their parent. # 3. It updates the inter-module dependencies: -# 3a. It retrieves the version properties from the root POM that have the form 'artifactId-version'. +# 3a. It retrieves the version properties from the root POM that have the form 'artifactId'-version. # 3b. It identifies all dependencies of all modules that refer to another module. # 3c. It sets the dependency version to the given version or to the property associated with the dependency artifact following the convention mentioned in 3a. -set -e if [ ! -f jcore-version-normalizer.jar ]; then wget https://oss.sonatype.org/content/repositories/releases/de/julielab/jcore-version-normalizer/1.1.0/jcore-version-normalizer-1.1.0-jar-with-dependencies.jar -O jcore-version-normalizer.jar diff --git a/travis-deployment/deploy.sh b/travis-deployment/deploy.sh index f06bf59..0812422 100755 --- a/travis-deployment/deploy.sh +++ b/travis-deployment/deploy.sh @@ -32,7 +32,7 @@ if [ "$TRAVIS_PULL_REQUEST" == 'false' ]; then done if [ ! -z "$modulestodeploy" ]; then - echo "Deploying moduls $modulestodeploy" + echo "Deploying moduels $modulestodeploy" mvn deploy -T 1C -B -P sonatype-nexus-deployment --settings travis-deployment/mvnsettings.xml -DskipTests=true -pl $modulestodeploy else echo "Everything up to date, nothing to deploy"