Migrated to Spring Boot 3.2.4, jakarta servlet, jsp, etc.

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

@@ -37,8 +37,7 @@ public void testClientHtml() throws IOException {
 				() -> Assertions.assertTrue(res.contains("testBiopaxElementIdRule.owl")),
 				() -> Assertions.assertTrue(res.contains("testSyntaxErrors.owl"))
 		);
-//		System.out.println(baos);
-    }
+  }
 
 	@Test
 	public void testClientXml() throws IOException, JAXBException {

biopax-validator-web/pom.xml

@@ -7,7 +7,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.7.18</version>
+    <version>3.2.4</version>
     <relativePath />
   </parent>
 
@@ -282,14 +282,14 @@
       <optional>true</optional>
     </dependency>
     <dependency>
-      <groupId>taglibs</groupId>
-      <artifactId>standard</artifactId>
-      <version>1.1.2</version>
+      <groupId>jakarta.servlet.jsp.jstl</groupId>
+      <artifactId>jakarta.servlet.jsp.jstl-api</artifactId>
+      <version>3.0.0</version>
     </dependency>
     <dependency>
-      <groupId>javax.servlet</groupId>
-      <artifactId>jstl</artifactId>
-      <version>1.2</version>
+      <groupId>org.glassfish.web</groupId>
+      <artifactId>jakarta.servlet.jsp.jstl</artifactId>
+      <version>3.0.1</version>
     </dependency>
     <dependency>
       <groupId>commons-fileupload</groupId>
@@ -340,6 +340,18 @@
       <artifactId>logback-classic</artifactId>
       <scope>runtime</scope>
     </dependency>
+
+    <dependency>
+      <groupId>org.springdoc</groupId>
+      <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
+      <version>2.2.0</version>
+      <exclusions>
+        <exclusion>
+          <groupId>org.yaml</groupId>
+          <artifactId>snakeyaml</artifactId>
+        </exclusion>
+      </exclusions>
+    </dependency>
   </dependencies>
 
 </project>

biopax-validator-web/src/main/java/org/biopax/validator/web/Application.java

@@ -2,8 +2,6 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.context.annotation.Bean;
-import org.springframework.web.multipart.commons.CommonsMultipartResolver;
 import org.springframework.web.servlet.config.annotation.*;
 import org.springframework.web.servlet.view.InternalResourceViewResolver;
 import org.springframework.web.servlet.view.JstlView;
@@ -21,6 +19,10 @@ public static void main(String[] args) {
   @Override
   public void addResourceHandlers(ResourceHandlerRegistry registry) {
     registry.addResourceHandler("/**").addResourceLocations("classpath:/static/");
+    registry.addResourceHandler("/webjars/**")
+        .addResourceLocations("classpath:/META-INF/resources/webjars/");
+    registry.addResourceHandler("swagger-ui.html")
+        .addResourceLocations("classpath:/META-INF/resources/");
   }
 
   @Override
@@ -32,11 +34,4 @@ public void configureViewResolvers(ViewResolverRegistry registry) {
     registry.viewResolver(resolver);
   }
 
-  @Bean(name = "multipartResolver")
-  public CommonsMultipartResolver multipartResolver() {
-    CommonsMultipartResolver multipartResolver = new CommonsMultipartResolver();
-    multipartResolver.setMaxUploadSize(-1);
-    return multipartResolver;
-  }
-
 }

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

@@ -1,23 +1,23 @@
 package org.biopax.validator.web.controller;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.biopax.validator.web.dto.Clue;
 import org.biopax.validator.web.service.Suggester;
 import org.biopax.validator.web.dto.Xref;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.web.bind.annotation.*;
 
-import javax.servlet.http.HttpServletResponse;
 import java.io.IOException;
 
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+import static org.springframework.http.MediaType.*;
 
 @RestController
 public class SuggesterController {
 
   @Autowired
   private Suggester service;
 
-  @GetMapping(value = "/xref/{db}/{id}/", produces = APPLICATION_JSON_VALUE)
+  @GetMapping(value = "/xref/{db}/{id}/", produces = TEXT_PLAIN_VALUE)
   public String xrefDbId(@PathVariable String db, @PathVariable String id,
                           HttpServletResponse response) throws IOException {
     String uri = null;
@@ -26,7 +26,6 @@ public String xrefDbId(@PathVariable String db, @PathVariable String id,
     } catch (IllegalArgumentException e) {
       response.sendError(400, e.toString());
     }
-
     return uri;
   }
 

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

@@ -5,9 +5,8 @@
 import java.net.MalformedURLException;
 import java.util.*;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.biopax.paxtools.normalizer.Normalizer;
@@ -27,7 +26,7 @@
 import org.springframework.web.multipart.MultipartFile;
 import org.springframework.web.multipart.MultipartHttpServletRequest;
 
-import static org.springframework.http.MediaType.APPLICATION_XML_VALUE;
+import static org.springframework.http.MediaType.*;
 
 @Controller
 public class ValidatorController {
@@ -42,24 +41,24 @@ public ValidatorController(ValidatorAdapter service) {
     this.service = service;
   }
 
-  @RequestMapping(value = {"schema","schema.html"}, method = RequestMethod.GET, produces = APPLICATION_XML_VALUE)
-  @ResponseBody  public String getSchema() {
+  @GetMapping(value = {"schema","schema.html"}, produces = APPLICATION_XML_VALUE)
+  @ResponseBody public String getSchema() {
     return service.getSchema();
   }
 
   //Views (pages)
 
-  @RequestMapping({"/", "home", "home.html"})
+  @GetMapping({"/", "home", "home.html"})
   public String home() {
     return "home";
   }
 
-  @RequestMapping({"ws","ws.html"})
+  @GetMapping({"ws","ws.html"})
   public String ws() {
     return "ws";
   }
 
-  @RequestMapping(value={"check","check.html"}, method=RequestMethod.GET)
+  @GetMapping(value={"check","check.html"})
   public void check(Model model) {
     model.addAttribute("normalizer", new Normalizer());
     //user can edit some of normalizer's options in the 'check' view
@@ -89,18 +88,18 @@ public void check(Model model) {
    * @return results view name (or null if XML or normalized RDF/XML were requested)
    * @throws IOException when data cannot be read from the files or URL, etc.
    */
-  @RequestMapping(value={"check","check.html"}, method=RequestMethod.POST)
+  @PostMapping(value={"check","check.html"},
+      produces = {APPLICATION_XML_VALUE, TEXT_HTML_VALUE, "application/vnd.biopax.rdf+xml"})
   public String check(HttpServletRequest request, HttpServletResponse response,
                       Model mvcModel, Writer writer,
-    @RequestParam(required=false) String url,
-    @RequestParam(required=false) String retDesired,
-    @RequestParam(required=false) Boolean autofix,
-    @RequestParam(required=false) Behavior filter,
-    @RequestParam(required=false) Integer maxErrors,
-    @RequestParam(required=false) String profile,
-    //normalizer!=null when called from the JSP;
-    //but it's usually null when from the validator-client or a web script
-    @ModelAttribute("normalizer") Normalizer normalizer) throws IOException
+                      @RequestParam(required=false) String url,
+                      @RequestParam(required=false) String retDesired,
+                      @RequestParam(required=false) Boolean autofix,
+                      @RequestParam(required=false) Behavior filter,
+                      @RequestParam(required=false) Integer maxErrors,
+                      @RequestParam(required=false) String profile,
+                      //normalizer!=null when called from the JSP (browser); null when called from validator-client or script
+                      @ModelAttribute("normalizer") Normalizer normalizer) throws IOException
   {
     Resource resource; //to validate
     final int lim = (maxErrors != null)? maxErrors.intValue() : 0; //0->no error limit
@@ -110,7 +109,7 @@ public String check(HttpServletRequest request, HttpServletResponse response,
     ValidatorResponse validatorResponse = new ValidatorResponse();
 
     if(url != null && url.length()>0) {
-      log.info("url : " + url);
+      log.info("validate from url : " + url);
 
       try {
         resource = new UrlResource(url);

biopax-validator-web/src/main/java/org/biopax/validator/web/service/ValidatorService.java

@@ -36,8 +36,9 @@ public Validation validate(Resource data,
                              Behavior errorLevel, String profile,
                              Normalizer normalizer) throws IOException
   {
+    String dataDescr = data.getDescription();
     Validation validationResult = new Validation(new BiopaxIdentifier(),
-      data.getDescription(), isFix, errorLevel, errMax, profile);
+        dataDescr, isFix, errorLevel, errMax, profile);
     //run the biopax-validator (this updates the validationResult object)
     biopaxValidator.importModel(validationResult, data.getInputStream());
     biopaxValidator.validate(validationResult);

biopax-validator-web/src/main/resources/application.properties

@@ -3,7 +3,8 @@ spring.mvc.view.prefix=/jsp/
 spring.mvc.view.suffix=.jsp
 #spring.mvc.view.view-names:*
 server.error.whitelabel.enabled=false
-#server.servlet.context-path = /
+#server.servlet.context-path = /validate
+
 spring.main.banner-mode=off
 application.message: Hello BioPAX users!
 
@@ -14,11 +15,17 @@ management.endpoint.health.enabled=true
 management.endpoints.web.exposure.include=health
 #management.endpoints.web.exposure.exclude=
 
-#due to migration from spring-boot 2.0 to 2.1
+#due to migration from spring-boot 2.0 to 2.1, then 3.x
 spring.main.allow-bean-definition-overriding=true
 
 #for rest docs
 spring.jackson.serialization.indent-output=true
 
-servlet.multipart.enabled: false
-servlet.multipart.max-file-size: 100MB
+#servlet.multipart.enabled=false
+server.tomcat.max-swallow-size=-1
+spring.servlet.multipart.max-file-size=100MB
+spring.servlet.multipart.max-request-size=10MB
+
+#server.servlet.encoding.charset=UTF-8
+#server.servlet.encoding.enabled=false
+#server.servlet.encoding.force-response=true

biopax-validator-web/src/main/webapp/jsp/ws.jsp

@@ -54,15 +54,14 @@ to save locally and view off-line</li>
 </div>
 
 <div class="row">
-As an example, there is a basic BioPAX validator client module 
-(it connects to the http://www.biopax.org/validator/check), and the
+As an example, there is a BioPAX validator-client library
+(it connects to http://www.biopax.org/validator/check); the
 <a target="_blank" href="https://github.com/BioPAX/validator/tree/master/biopax-validator-client">
-sources are here</a> (see test classes there as well).
+source code is here</a> (see test classes there as well).
 </div>
-
+<br/>
 <div class="row">
-<h3>See also</h3>
-<a target="_blank" href="swagger-ui.html">BioPAX Validator API</a> documentation with examples (OpenAPI/Swagger).
+See also: <a target="_blank" href="swagger-ui.html">OpenAPI/Swagger page</a> (autogenerated, needs work...)
 </div>
 
 <jsp:include page="footer.jsp"/>

biopax-validator-web/src/test/java/org/biopax/validator/web/controller/SuggesterControllerTest.java

@@ -43,12 +43,12 @@ public void before() {
     // valid synonym and valid id
     String anXrefId = "6.1.1.5";
     given(service.xrefDbIdToUri("ec", anXrefId))
-      .willReturn("http://identifiers.org/ec-code/" + anXrefId);
+      .willReturn("http://bioregistry.io/eccode:" + anXrefId);
     // test typo (fixable) name
     given(service.xrefDbIdToUri("ec_code", anXrefId))
-      .willReturn("http://identifiers.org/ec-code/" + anXrefId);
+      .willReturn("http://bioregistry.io/eccode:" + anXrefId);
     given(service.xrefDbIdToUri("Enzyme Nomenclature", anXrefId))
-      .willReturn("http://identifiers.org/ec-code/" + anXrefId);
+      .willReturn("http://bioregistry.io/eccode:" + anXrefId);
     // bad not-fixable name
     given(service.xrefDbIdToUri("foo", anXrefId))
       .willThrow(new IllegalArgumentException("Datatype not found"));
@@ -59,15 +59,14 @@ public void before() {
 
   @Test
   public void shouldReturnUri() throws Exception {
-    mvc.perform(get("/xref/ec/6.1.1.5/").accept(MediaType.APPLICATION_JSON))
+    mvc.perform(get("/xref/ec/6.1.1.5/").accept(MediaType.TEXT_PLAIN))
       .andDo(print())
       .andExpect(status().isOk())
-      .andExpect(content().contentType(MediaType.APPLICATION_JSON_VALUE))
-      .andExpect(content().string(equalTo("http://identifiers.org/ec-code/6.1.1.5")));
+      .andExpect(content().string(equalTo("http://bioregistry.io/eccode:6.1.1.5")));
 
-    mvc.perform(get("/xref/ec_code/6.1.1.5/").accept(MediaType.APPLICATION_JSON))
+    mvc.perform(get("/xref/ec_code/6.1.1.5/").accept(MediaType.TEXT_PLAIN))
       .andExpect(status().isOk())
-      .andExpect(content().string(equalTo("http://identifiers.org/ec-code/6.1.1.5")));
+      .andExpect(content().string(equalTo("http://bioregistry.io/eccode:6.1.1.5")));
   }
 
   @Test
@@ -106,14 +105,14 @@ public void shouldReturnCheckedXrefs() throws Exception {
     y.setId("foo"); //invalid
     Xref xx = new Xref();
     xx.setDb("ec"); //ok
-    xx.setNamespace("ec-code");
+    xx.setNamespace("eccode");
     xx.setDbOk(true);
     xx.setId("1.1.1.1"); //ok
     xx.setIdOk(true);
     Xref yy = new Xref();
     yy.setDb("ec"); // ok
     yy.setDbOk(true);
-    yy.setNamespace("ec-code");
+    yy.setNamespace("eccode");
     yy.setId("foo"); //invalid
     Clue xyClue = new Clue("some info");
     xyClue.addValue(xx);

biopax-validator/src/main/java/org/biopax/validator/rules/UnificationXrefLimitedRule.java

@@ -67,11 +67,10 @@ void initInternalMaps() {
   }
 
   private void addDbSynonymsTo(Map<Class<? extends BioPAXElement>,Set<String>> map) {
-    for (Map.Entry<Class<? extends BioPAXElement>,Set<String>> entry : map.entrySet()) {
-      Set<String> val = entry.getValue();
-      for (String db : new HashSet<>(val))
-        for (String s : helper.getSynonymsForDbName(db))
-          val.add(s);
+    for (Set<String> val : map.values()) {
+      for (String db : new HashSet<>(val)) {
+        val.addAll(helper.getSynonymsForDbName(db));
+      }
     }
   }
 

pom.xml

@@ -177,7 +177,7 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     <github.global.server>github</github.global.server>
-    <spring-framework.version>5.3.31</spring-framework.version>
+    <spring-framework.version>6.1.5</spring-framework.version>
     <slf4j.version>2.0.11</slf4j.version>
     <agent>${settings.localRepository}/org/springframework/spring-instrument/${spring-framework.version}/spring-instrument-${spring-framework.version}.jar</agent>
     <paxtools.version>6.0.0-SNAPSHOT</paxtools.version>
@@ -484,24 +484,6 @@
         <artifactId>commons-collections</artifactId>
         <version>3.2.2</version>
       </dependency>
-      <dependency>
-        <groupId>taglibs</groupId>
-        <artifactId>standard</artifactId>
-        <version>1.1.2</version>
-        <scope>runtime</scope>
-      </dependency>
-      <dependency>
-        <groupId>javax.servlet</groupId>
-        <artifactId>javax.servlet-api</artifactId>
-        <version>4.0.1</version>
-        <scope>provided</scope>
-      </dependency>
-      <dependency>
-        <groupId>javax.servlet</groupId>
-        <artifactId>jstl</artifactId>
-        <version>1.2</version>
-        <scope>runtime</scope>
-      </dependency>
       <dependency>
         <groupId>commons-fileupload</groupId>
         <artifactId>commons-fileupload</artifactId>