Fixes #33 in the validator client. Also bumped Spring version.

biopax-validator-client/src/main/java/org/biopax/validator/BiopaxValidatorClient.java

@@ -12,9 +12,6 @@
 import org.apache.commons.logging.LogFactory;
 import org.apache.http.Header;
 import org.apache.http.HttpEntity;
-import org.apache.http.HttpResponse;
-import org.apache.http.client.ClientProtocolException;
-import org.apache.http.client.ResponseHandler;
 import org.apache.http.client.fluent.Executor;
 import org.apache.http.client.fluent.Request;
 import org.apache.http.entity.ContentType;
@@ -105,13 +102,14 @@ public BiopaxValidatorClient() {
      * @throws IOException
      */
     public void validate(boolean autofix, String profile, RetFormat retFormat, Behavior filterBy,
-    		Integer maxErrs, String biopaxUrl, File[] biopaxFiles, OutputStream out) throws IOException 
+												 Integer maxErrs, String biopaxUrl, List<File> biopaxFiles, OutputStream out) throws IOException
     {
     	MultipartEntityBuilder meb = MultipartEntityBuilder.create();
     	meb.setCharset(Charset.forName("UTF-8"));
 
-    	if(autofix)
-    		meb.addTextBody("autofix", "true");
+    	if(autofix) {
+				meb.addTextBody("autofix", "true");
+			}
 
 		//TODO: add extra options (normalizer.fixDisplayName, normalizer.xmlBase)?
 
@@ -123,18 +121,19 @@ public void validate(boolean autofix, String profile, RetFormat retFormat, Behav
     		meb.addTextBody("filter", filterBy.toString());
     	if(maxErrs != null && maxErrs > 0)
     		meb.addTextBody("maxErrors", maxErrs.toString());
-    	if(biopaxFiles != null && biopaxFiles.length > 0)
-    		for (File f : biopaxFiles) //important: use MULTIPART_FORM_DATA content-type
-    			meb.addBinaryBody("file", f, ContentType.MULTIPART_FORM_DATA, f.getName());
-    	else if(biopaxUrl != null) {
+    	if(biopaxFiles != null) {
+				int i = 0;
+				for (File f : biopaxFiles) { //important: use MULTIPART_FORM_DATA content-type
+					meb.addBinaryBody("file_"+(i++), f, ContentType.MULTIPART_FORM_DATA, f.getName());
+				}
+			} else if(biopaxUrl != null) {
     		meb.addTextBody("url", biopaxUrl);
     	} else {
     		log.error("Nothing to do (no BioPAX data specified)!");
         	return;
     	}
 
     	HttpEntity httpEntity = meb.build();
-//    	if(log.isDebugEnabled()) httpEntity.writeTo(System.err);
     	String content = Executor.newInstance()
     			.execute(Request.Post(url).body(httpEntity))
     				.returnContent().asString();  	
@@ -237,8 +236,7 @@ public static void main(String[] argv) throws IOException
 		}
 
         // collect files
-        Collection<File> files = new HashSet<>();
-
+        List<File> files = new ArrayList<>();
         if (fileOrDir.isDirectory()) {
             // validate all the OWL files in the folder
             FilenameFilter filter = (dir, name) -> (name.endsWith(".owl"));
@@ -254,7 +252,7 @@ public static void main(String[] argv) throws IOException
         if (!files.isEmpty()) {
         	BiopaxValidatorClient val = new BiopaxValidatorClient();
         	val.validate(fix, profile, outf, level, maxErrs, 
-        		null, files.toArray(new File[]{}), new FileOutputStream(output));
+        		null, files, new FileOutputStream(output));
         }
     }
 

biopax-validator-client/src/test/java/BiopaxValidatorClientTest.java

@@ -2,6 +2,7 @@
  *
  */
 import java.io.*;
+import java.util.List;
 
 import jakarta.xml.bind.JAXBException;
 
@@ -12,45 +13,49 @@
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
-// remove @Ignore when biopax.org/biopax-validator/  is available
+/*
+Uncomment when biopax.org/biopax-validator/ is available,
+or run the web app locally (see readme) and this test with -Dbiopax.validator.url=http://localhost:8080/check JVM opt.
+or use client.setUrl in the test case below.
+*/
 @Disabled
 public class BiopaxValidatorClientTest {
 
 	@Test
 	public void testClientHtml() throws IOException {
 		BiopaxValidatorClient client = new BiopaxValidatorClient();
-
-		File[] files = new File[] {
-				new File(getClass().getResource(
-						File.separator + "testBiopaxElementIdRule.owl").getFile())
-		};
-
+		List<File> files = List.of(
+				new File(getClass().getResource(File.separator + "testBiopaxElementIdRule.owl").getFile()),
+				new File(getClass().getResource(File.separator + "testSyntaxErrors.owl").getFile())
+		);
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		client.validate(false, null, RetFormat.HTML, null, null, null, files, baos);
-
-		System.out.println(baos.toString());
+		String res = baos.toString();
+
+		Assertions.assertAll(
+				() -> Assertions.assertTrue(baos.size()>0),
+				() -> Assertions.assertTrue(res.contains("testBiopaxElementIdRule.owl")),
+				() -> Assertions.assertTrue(res.contains("testSyntaxErrors.owl"))
+		);
+//		System.out.println(baos);
     }
 
 	@Test
 	public void testClientXml() throws IOException, JAXBException {
 		BiopaxValidatorClient client = new BiopaxValidatorClient();
-
-		File[] files = new File[] {
-				new File(getClass().getResource(
-					File.separator + "testBiopaxElementIdRule.owl").getFile())
-		};
-
+		List<File> files = List.of(
+				new File(getClass().getResource(File.separator + "testBiopaxElementIdRule.owl").getFile()),
+				new File(getClass().getResource(File.separator + "testSyntaxErrors.owl").getFile())
+		);
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		client.validate(true, null, RetFormat.XML, null, null, null, files, baos);
-
-		//System.out.println(baos.toString());
-
-		Assertions.assertTrue(baos.size()>0);
-
 		ValidatorResponse resp = client.unmarshal(baos.toString());
-
-		Assertions.assertNotNull(resp);
-		Assertions.assertFalse(resp.getValidation().isEmpty());
+
+		Assertions.assertAll(
+			() -> Assertions.assertTrue(baos.size()>0),
+			() -> Assertions.assertNotNull(resp),
+			() -> Assertions.assertEquals(2, resp.getValidation().size())
+		);
 
 		System.out.println(resp.getValidation().get(0).getSummary()
 				+ "; cases: " + resp.getValidation().get(0).getTotalProblemsFound());

biopax-validator-client/src/test/resources/testSyntaxErrors.owl

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
+<owl:Ontology rdf:about="">
+ <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
+</owl:Ontology>
+
+<bp:BioSource rdf:about="biosource_10090">
+ <bp:comment>test: using wrong property name 'taxonXref' (should be 'xref')</bp:comment>
+ <bp:standardName rdf:datatype = "xsd:string">Mus musculus</bp:standardName>
+ <bp:taxonXref rdf:resource="Taxonomy_UnificationXref_10090" />
+ <bp:displayName rdf:datatype = "xsd:string">Mouse</bp:displayName>
+</bp:BioSource>
+
+<bp:UnificationXref rdf:about="Taxonomy_UnificationXref_10090">
+ <bp:db rdf:datatype = "xsd:string">TAXONOMY</bp:db>
+ <bp:id rdf:datatype = "xsd:string">10090</bp:id>
+</bp:UnificationXref>
+
+</rdf:RDF>

biopax-validator-web/pom.xml

@@ -7,7 +7,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.7.15</version>
+    <version>2.7.18</version>
     <relativePath />
   </parent>
 
@@ -96,7 +96,7 @@
   </developers>
 
   <properties>
-<!--    <spring-framework.version>5.3.29</spring-framework.version>--><!-- defined in the parent pom -->
+<!--    <spring-framework.version>5.3.31</spring-framework.version>--><!-- is defined in the parent pom -->
     <start-class>org.biopax.validator.web.Application</start-class>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

biopax-validator-web/src/main/java/org/biopax/validator/web/controller/ValidatorController.java

@@ -127,10 +127,9 @@ public String check(HttpServletRequest request, HttpServletResponse response,
 
     } else if (request instanceof MultipartHttpServletRequest) {
       MultipartHttpServletRequest multiRequest = (MultipartHttpServletRequest) request;
-      Map files = multiRequest.getFileMap();
+      Map<String,MultipartFile> files = multiRequest.getFileMap();
       Assert.state(!files.isEmpty(), "No files to validate");
-      for (Object o : files.values()) {
-        MultipartFile file = (MultipartFile) o;
+      for (MultipartFile file : files.values()) {
         String filename = file.getOriginalFilename();
         // a workaround (for some reason there is always a no-name-file;
         // this might be a javascript isue)