Refs #32:

- removed .travis; - fixed gradle build (jdk-17, but java8 compatible; - updated github workflow; - there's no need to build the server using jdk-8 or jdk-11 anymore; - using Spring Boot 2.5.0 (later versions conflicts with old Swagger2 lib)
PathwayCommons · Oct 6, 2022 · 0bc6a8f · 0bc6a8f
1 parent 30073d8
commit 0bc6a8f
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diff --git a/.github/workflows/Build.yml b/.github/workflows/Build.yml
@@ -15,23 +15,22 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-
-    name: Java ${{ matrix.config.java }}
+
+#    env:
+#      _JAVA_OPTIONS: "--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED"
+
+    name: Build with Gradle
 
     strategy:
       fail-fast: false
-      matrix:
-        config:
-          - {java: 8}
-          - {java: 11}
 
     steps:
       - uses: actions/checkout@v2
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: ${{ matrix.config.java }}
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: gradle
       - name: Build with Gradle
         run: |

diff --git a/.travis.yml b/.travis.yml
diff --git a/build.gradle b/build.gradle
@@ -1,6 +1,6 @@
 buildscript {
     ext {
-        springBootVersion = '2.2.6.RELEASE'
+        springBootVersion = '2.5.0'
     }
     repositories {
         maven {
@@ -23,7 +23,7 @@ repositories {
         url "https://oss.sonatype.org/content/groups/public/"
     }
     maven {
-        url "https://www.biopax.org/m2repo/releases/"
+        url "https://jitpack.io"
     }
 }
 
@@ -32,19 +32,18 @@ dependencies {
     implementation 'org.springframework.boot:spring-boot-starter-web'
     runtimeOnly 'org.springframework.boot:spring-boot-devtools'
     testImplementation 'org.springframework.boot:spring-boot-starter-test'
-    implementation 'org.biopax.paxtools:sbgn-converter:5.2.1-SNAPSHOT'
-    implementation 'com.google.code.gson:gson:2.8.2'
-    implementation 'org.apache.commons:commons-collections4:4.1'
+    implementation 'org.biopax.paxtools:sbgn-converter:5.3.0-SNAPSHOT'
+    implementation 'com.google.code.gson:gson:2.9.0'
+    implementation 'org.apache.commons:commons-collections4:4.4'
     implementation 'io.springfox:springfox-swagger2:2.7.0'
     implementation 'io.springfox:springfox-swagger-ui:2.7.0'
 
-    //java 9+ does not have Jax B Dependents
-    implementation 'javax.xml.bind:jaxb-api:2.3.0'
-    implementation 'com.sun.xml.bind:jaxb-core:2.3.0'
-    implementation 'com.sun.xml.bind:jaxb-impl:2.3.0'
+    implementation 'javax.xml.bind:jaxb-api:2.3.1'
+    implementation 'com.sun.xml.bind:jaxb-core:2.3.0.1'
+    implementation 'com.sun.xml.bind:jaxb-impl:2.3.6'
     implementation 'javax.activation:activation:1.1.1'
 }
 
-sourceCompatibility = 1.8
+sourceCompatibility = 8
 group = 'pathwaycommons'
-version =  '0.4.0'
+version =  '0.2.2'
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/src/main/java/factoid/web/Controller.java b/src/main/java/factoid/web/Controller.java
@@ -37,10 +37,7 @@ public class Controller {
     produces = "application/vnd.biopax.rdf+xml"
   )
   public String jsonToBiopax(
-    @ApiParam("Factoid document content (JSON string)") @RequestBody String body
-    //TODO: add url/path options as needed
-//  ,  @ApiParam("test") @RequestParam(required = false) String test
-  ) {
+    @ApiParam("Factoid document content (JSON string)") @RequestBody String body) {
     // Add templates to converter by the reader
     FactoidToBiopax converter = new FactoidToBiopax();
     try {
@@ -107,7 +104,7 @@ public String biopaxToFactoid(
 	  BiopaxToFactoid converter = new BiopaxToFactoid();
 	  try {
 		  InputStream is = new ByteArrayInputStream(body.getBytes(StandardCharsets.UTF_8));
-	      Model model = new SimpleIOHandler().convertFromOWL(is);
+      Model model = new SimpleIOHandler().convertFromOWL(is);
 		  return converter.convert(model).toString();
 	  } catch (IllegalStateException | JsonSyntaxException | JsonIOException e) {
 		  throw new ConverterException(HttpStatus.BAD_REQUEST, e.getMessage());

diff --git a/src/test/java/factoid/converter/BiopaxToFactoidTest.java b/src/test/java/factoid/converter/BiopaxToFactoidTest.java
@@ -1,9 +1,5 @@
 package factoid.converter;
 
-
-import static org.junit.Assert.assertThat;
-import static org.hamcrest.Matchers.*;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
@@ -16,12 +12,14 @@
 import org.biopax.paxtools.io.BioPAXIOHandler;
 import org.biopax.paxtools.io.SimpleIOHandler;
 import org.biopax.paxtools.model.Model;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 import com.google.gson.JsonObject;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 public class BiopaxToFactoidTest {
 
 	@Test
@@ -49,7 +47,7 @@ public void testToJson() throws IOException {
 				}
 			}
 
-			assertThat(entityIds1, is(entityIds2));
+			assertEquals(entityIds1, entityIds2);
 		}
 
 

diff --git a/src/test/java/factoid/converter/FactoidToBiopaxTest.java b/src/test/java/factoid/converter/FactoidToBiopaxTest.java
@@ -13,7 +13,7 @@
 import org.biopax.paxtools.model.*;
 import org.biopax.paxtools.model.level3.*;
 import org.biopax.paxtools.model.level3.Process;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import java.io.ByteArrayInputStream;
 import java.io.FileReader;

diff --git a/src/test/java/factoid/converter/Simplify.java b/src/test/java/factoid/converter/Simplify.java
@@ -32,10 +32,6 @@
 import org.biopax.paxtools.model.level3.ProteinReference;
 import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
 import org.biopax.paxtools.model.level3.TemplateReactionRegulation;
-import org.biopax.paxtools.model.level3.Xref;
-
-import com.google.common.io.Resources;
-import com.sun.xml.bind.v2.model.core.Element;
 
 public class Simplify {
 	public static void main(String[] args) throws FileNotFoundException {

diff --git a/src/test/java/factoid/model/BioPAXModelTest.java b/src/test/java/factoid/model/BioPAXModelTest.java
@@ -1,8 +1,8 @@
 package factoid.model;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -15,7 +15,7 @@
 import org.biopax.paxtools.model.level3.Protein;
 import org.biopax.paxtools.model.level3.ProteinReference;
 import org.biopax.paxtools.model.level3.SmallMoleculeReference;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 public class BioPAXModelTest {
 
@@ -40,21 +40,21 @@ public void addPhysicalEntityTest() throws NoSuchFieldException, SecurityExcepti
 
 		Protein prot1 = model.getOrCreatePhysicalEntity(Protein.class, protName, protRef, modificationTypes, null);
 
-		assertTrue("Protein is added to the model", innerModel.contains(prot1));
-		assertEquals("Protein name is set", prot1.getDisplayName(), protName);
-		assertEquals("Protein reference is set", protRef, prot1.getEntityReference());
-		assertEquals("Protein modification types are set", modificationTypes.size(), prot1.getFeature().size());
-		assertEquals("Protein reference has a new modification", 1, protRef.getEntityFeature().size());
+		assertTrue(innerModel.contains(prot1), "Protein is added to the model");
+		assertEquals(prot1.getDisplayName(), protName, "Protein name is set");
+		assertEquals(protRef, prot1.getEntityReference(), "Protein reference is set");
+		assertEquals(modificationTypes.size(), prot1.getFeature().size(), "Protein modification types are set");
+		assertEquals(1, protRef.getEntityFeature().size(), "Protein reference has a new modification");
 
 		Protein prot2 = model.getOrCreatePhysicalEntity(Protein.class, protName, protRef, modificationTypes, null);
-		assertEquals("No duplication in adding the second Protein with same features", prot1, prot2);
+		assertEquals(prot1, prot2, "No duplication in adding the second Protein with same features");
 
 		Protein prot3 = model.getOrCreatePhysicalEntity(Protein.class, protName, protRef);
-		assertNotEquals("A new protein is added with no modification", prot1, prot3);
+		assertNotEquals(prot1, prot3, "A new protein is added with no modification");
 
 		Protein prot4 = model.getOrCreatePhysicalEntity(Protein.class, protName, protRef, modificationTypes2, null);
-		assertNotEquals("A new protein is added with with different modifications", prot1, prot4);
-		assertEquals("Protein reference has a new modification", 2, protRef.getEntityFeature().size());
+		assertNotEquals(prot1, prot4, "A new protein is added with with different modifications");
+		assertEquals(2, protRef.getEntityFeature().size(), "Protein reference has a new modification");
 	}
 
 	@Test
@@ -72,41 +72,19 @@ public void addEntityReferenceTest() {
 		XrefModel commonXref = new XrefModel("common-xref", "uniprot");
 
 		ProteinReference protRef1 = model.getOrCreateEntityReference(ProteinReference.class, commonName, commonXref);
-		assertTrue("Protein reference is added to the model", innerModel.contains(protRef1));
-		assertEquals("Protein reference name is set", commonName, protRef1.getDisplayName());
+		assertTrue(innerModel.contains(protRef1), "Protein reference is added to the model");
+		assertEquals(commonName, protRef1.getDisplayName(), "Protein reference name is set");
 
 		ProteinReference protRef2 = model.getOrCreateEntityReference(ProteinReference.class, commonName, commonXref);
-		assertEquals("No duplication in adding second protein modification with same name", protRef1, protRef2);
+		assertEquals(protRef1, protRef2, "No duplication in adding second protein modification with same name");
 
 		SmallMoleculeReference smRef = model.getOrCreateEntityReference(SmallMoleculeReference.class, commonName, commonXref);
-		assertNotEquals("A new small molecule reference is added that has an existing protein reference name", protRef2, smRef);
+		assertNotEquals(protRef2, smRef, "A new small molecule reference is added that has an existing protein reference name");
 
 		ProteinReference protRef3 = model.getOrCreateEntityReference(ProteinReference.class, uniqueName, commonXref);
-		assertNotEquals("A new protein is added with a new name", protRef1, protRef3);
+		assertNotEquals(protRef1, protRef3, "A new protein is added with a new name");
 	}
 
-//	@Test
-//	public void addCellularLocationVocabularyTest() {
-//		
-//		BioPAXModel model = new BioPAXModel();
-//		
-//		// Underlying PAXTools model
-//		Model innerModel = model.getPaxtoolsModel();
-//		
-//		String commonLocationName = "location1";
-//		String uniqueLocationName = "location2";
-//		
-//		CellularLocationVocabulary clv1 = model.getOrCreateCellularLocationVocabulary(commonLocationName);
-//		assertTrue("Cellular location vocabulary is added to the model", innerModel.contains(clv1));
-//		assertEquals("Cellular location vocabulary has the name", 1, clv1.getTerm().size());
-//		
-//		CellularLocationVocabulary clv2 = model.getOrCreateCellularLocationVocabulary(commonLocationName);
-//		assertEquals("No duplication in adding the second cellular location with the same name", clv1, clv2);
-//		
-//		CellularLocationVocabulary clv3 = model.getOrCreateCellularLocationVocabulary(uniqueLocationName);
-//		assertNotEquals("A new cellular location is added with a new name", clv1, clv3);
-//	}
-
 	@Test
 	public void addConversionTest() {
 
@@ -120,10 +98,10 @@ public void addConversionTest() {
 		Protein right = model.addNew(Protein.class);
 
 		Conversion conversion = model.addNewConversion(Conversion.class, left, right, dir);
-		assertTrue("Conversion is added to the model", innerModel.contains(conversion));
-		assertTrue("Coversions left side is set", conversion.getLeft().contains(left));
-		assertTrue("Coversions right side is set", conversion.getRight().contains(right));
-		assertEquals("Conversion direction is set", dir, conversion.getConversionDirection());
+		assertTrue(innerModel.contains(conversion), "Conversion is added to the model");
+		assertTrue(conversion.getLeft().contains(left), "Coversions left side is set");
+		assertTrue(conversion.getRight().contains(right), "Coversions right side is set");
+		assertEquals(dir, conversion.getConversionDirection(), "Conversion direction is set");
 	}
 
 	@Test
@@ -142,10 +120,10 @@ public void addControlTest() {
 
 		Control control = model.addNewControl(Control.class, controller, controlled, controlType);
 
-		assertTrue("Control is added to the model", innerModel.contains(control));
-		assertTrue("Controller is set", control.getController().contains(controller));
-		assertTrue("Controlled is set", control.getControlled().contains(controlled));
-		assertEquals("Control type is set", controlType, control.getControlType());
+		assertTrue(innerModel.contains(control), "Control is added to the model");
+		assertTrue(control.getController().contains(controller), "Controller is set");
+		assertTrue(control.getControlled().contains(controlled), "Controlled is set");
+		assertEquals(controlType, control.getControlType(), "Control type is set");
 	}
 
 }
diff --git a/src/test/java/factoid/web/ControllerT.java b/src/test/java/factoid/web/ControllerT.java
@@ -1,26 +1,24 @@
 package factoid.web;
 
-import org.junit.Test;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.client.TestRestTemplate;
 import org.springframework.context.annotation.Import;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.MediaType;
-import org.springframework.test.context.junit4.SpringRunner;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertThat;
-import static org.hamcrest.Matchers.*;
+import static org.junit.jupiter.api.Assertions.*;
 
 
-@RunWith(SpringRunner.class)
+@ExtendWith(SpringExtension.class)
 @Import(Application.class)
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
 public class ControllerT {
@@ -36,7 +34,7 @@ public void testJsonToBiopax() throws IOException {
     HttpEntity<String> request = new HttpEntity<>(data, headers);
     String res = template.postForObject("/v2/json-to-biopax", request, String.class);
     assertNotNull(res);
-    assertThat(res, containsString("biopax-level3.owl#"));
+    assertTrue(res.contains("biopax-level3.owl#"));
   }
 
   @Test
@@ -47,7 +45,7 @@ public void testJsonToSbgn() throws IOException {
     HttpEntity<String> request = new HttpEntity<>(data, headers);
     String res = template.postForObject("/v2/json-to-sbgn", request, String.class);
     assertNotNull(res);
-    assertThat(res, containsString("http://sbgn.org/libsbgn/"));
+    assertTrue(res.contains("http://sbgn.org/libsbgn/"));
   }
 
   @Test
@@ -58,7 +56,7 @@ public void testBiopaxToSbgn() throws IOException {
     HttpEntity<String> request = new HttpEntity<>(data, headers);
     String res = template.postForObject("/v2/biopax-to-sbgn", request, String.class);
     assertNotNull(res);
-    assertThat(res, containsString("http://sbgn.org/libsbgn/"));
+    assertTrue(res.contains("http://sbgn.org/libsbgn/"));
   }
 
   @Test
@@ -68,8 +66,10 @@ public void testBiopaxToFactoid() throws IOException {
     headers.set("Content-Type", "application/vnd.biopax.rdf+xml");
     HttpEntity<String> request = new HttpEntity<>(data, headers);
     String res = template.postForObject("/v2/biopax-to-json", request, String.class);
-    assertNotNull(res);
-    assertThat(res, containsString("interaction"));
+    assertAll(
+      () -> assertNotNull(res),
+      () -> assertTrue(res.contains("interaction"))
+    );
   }
 
   @Test
@@ -80,7 +80,6 @@ public void testBiopaxUrlToFactoid() throws IOException {
     HttpEntity<String> request = new HttpEntity<>(url, headers);
     String res = template.postForObject("/v2/biopax-url-to-json", request, String.class);
     assertNotNull(res);
-    // this line works fine with unit tests but weirdly blocking the build so commented it out for now.
-//    assertThat(res, containsString("interaction"));
+    assertTrue(res.contains("interaction"));
   }
 }