Merge pull request #47 from monarch-initiative/46-swagger-update

swagger update

README.md

@@ -58,6 +58,6 @@ or for some versions of dropwizard:
  * http://localhost:8080/api/docs/
  * http://localhost:8080/api/match/matchers 
 
-Example query using default config (TODO: map URIs to CURIEs)
+Example query using default config:
 
-http://localhost:8080/api/match/jaccard?id=http%3A%2F%2Fx.org%2Fheart-morphology&http%3A%2F%2Fx.org%2Fbrain-morphology
+http://localhost:8080/api/match/jaccard?id=X:heart-morphology&id=X:brain-morphology

owlsim-services/pom.xml

@@ -46,11 +46,11 @@
       <version>${dropwizard.version}</version>
       <scope>test</scope>
     </dependency>
-    <dependency>
-      <groupId>com.wordnik</groupId>
-      <artifactId>swagger-jaxrs_2.10</artifactId>
-      <version>1.3.7</version>
-    </dependency>
+	<dependency>
+	  <groupId>io.swagger</groupId>
+	  <artifactId>swagger-jersey2-jaxrs</artifactId>
+	  <version>1.5.12</version>
+	</dependency>
     <dependency>
       <groupId>net.sf.dozer</groupId>
       <artifactId>dozer</artifactId>

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/OwlSimServiceApplication.java

@@ -15,38 +15,36 @@
  */
 package org.monarchinitiative.owlsim.services;
 
-import io.dropwizard.Application;
-import io.dropwizard.assets.AssetsBundle;
-import io.dropwizard.setup.Bootstrap;
-import io.dropwizard.setup.Environment;
-
+import java.util.EnumSet;
 import java.util.Set;
 
+import javax.servlet.DispatcherType;
+import javax.servlet.FilterRegistration;
+
 import org.apache.log4j.Logger;
+import org.eclipse.jetty.servlets.CrossOriginFilter;
 import org.monarchinitiative.owlsim.compute.enrich.EnrichmentMapModule;
 import org.monarchinitiative.owlsim.compute.matcher.MatcherMapModule;
 import org.monarchinitiative.owlsim.kb.KnowledgeBaseModule;
 import org.monarchinitiative.owlsim.services.configuration.ApplicationConfiguration;
 import org.semanticweb.owlapi.OWLAPIParsersModule;
 import org.semanticweb.owlapi.OWLAPIServiceLoaderModule;
 
-import uk.ac.manchester.cs.owl.owlapi.OWLAPIImplModule;
-import uk.ac.manchester.cs.owl.owlapi.concurrent.Concurrency;
-
+import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.google.common.reflect.ClassPath;
 import com.google.common.reflect.ClassPath.ClassInfo;
 import com.google.inject.Guice;
 import com.google.inject.Injector;
-import com.wordnik.swagger.config.ConfigFactory;
-import com.wordnik.swagger.config.ScannerFactory;
-import com.wordnik.swagger.config.SwaggerConfig;
-import com.wordnik.swagger.jaxrs.config.DefaultJaxrsScanner;
-import com.wordnik.swagger.jaxrs.listing.ApiDeclarationProvider;
-import com.wordnik.swagger.jaxrs.listing.ApiListingResourceJSON;
-import com.wordnik.swagger.jaxrs.listing.ResourceListingProvider;
-import com.wordnik.swagger.jaxrs.reader.DefaultJaxrsApiReader;
-import com.wordnik.swagger.reader.ClassReaders;
+
+import io.dropwizard.Application;
+import io.dropwizard.assets.AssetsBundle;
+import io.dropwizard.setup.Bootstrap;
+import io.dropwizard.setup.Environment;
+import io.swagger.jaxrs.config.BeanConfig;
+import io.swagger.jaxrs.listing.ApiListingResource;
+import uk.ac.manchester.cs.owl.owlapi.OWLAPIImplModule;
+import uk.ac.manchester.cs.owl.owlapi.concurrent.Concurrency;
 
 public class OwlSimServiceApplication extends Application<ApplicationConfiguration> {
 
@@ -75,14 +73,27 @@ void initializeSwaggger(Bootstrap<ApplicationConfiguration> bootstrap) {
      * @param environment
      */
     void configureSwagger(Environment environment) {
-        environment.jersey().register(new ApiListingResourceJSON());
-        environment.jersey().register(new ApiDeclarationProvider());
-        environment.jersey().register(new ResourceListingProvider());
-        ScannerFactory.setScanner(new DefaultJaxrsScanner());
-        ClassReaders.setReader(new DefaultJaxrsApiReader());
-        SwaggerConfig config = ConfigFactory.config();
-        config.setApiVersion("1.0.1");
-        config.setBasePath(".." + environment.getApplicationContext().getContextPath());
+        environment.jersey().register(new ApiListingResource());
+        environment.getObjectMapper().setSerializationInclusion(JsonInclude.Include.NON_NULL);
+
+        BeanConfig config = new BeanConfig();
+        config.setTitle("owlsim - Web Services");
+        config.setVersion("1.0.0");
+        config.setResourcePackage("org.monarchinitiative.owlsim.services.resources");
+        config.setScan(true);
+        config.setBasePath(environment.getApplicationContext().getContextPath());
+    }
+
+    void configureCors(Environment environment) {
+        final FilterRegistration.Dynamic cors = environment.servlets().addFilter("CORS", CrossOriginFilter.class);
+
+        // Configure CORS parameters
+        cors.setInitParameter("allowedOrigins", "*");
+        cors.setInitParameter("allowedHeaders", "X-Requested-With,Content-Type,Accept,Origin");
+        cors.setInitParameter("allowedMethods", "OPTIONS,GET,PUT,POST,DELETE,HEAD");
+
+        // Add URL mapping
+        cors.addMappingForUrlPatterns(EnumSet.allOf(DispatcherType.class), true, "/*");
     }
 
     /***
@@ -100,6 +111,7 @@ public void run(ApplicationConfiguration configuration, Environment environment)
         environment.getApplicationContext().setContextPath("/api");
         configureSwagger(environment);
         configureJackson(environment);
+        configureCors(environment);
 
         Concurrency concurrency = Concurrency.CONCURRENT;
         LOG.info("Creating injector...");

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/AncestorResource.java

@@ -21,9 +21,9 @@
 
 import com.codahale.metrics.annotation.Timed;
 import com.googlecode.javaewah.EWAHCompressedBitmap;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiParam;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
 
 import io.dropwizard.jersey.caching.CacheControl;
 

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/EnrichmentResource.java

@@ -43,9 +43,9 @@
 import org.monarchinitiative.owlsim.services.exceptions.UnknownMatcherException;
 
 import com.codahale.metrics.annotation.Timed;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiParam;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
 
 @Path("/enrichment")
 @Api(value = "/enrichment", description = "enrichment services")

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/MatchResource.java

@@ -27,9 +27,9 @@
 import org.monarchinitiative.owlsim.services.exceptions.UnknownMatcherException;
 
 import com.codahale.metrics.annotation.Timed;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiParam;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
 
 import io.dropwizard.jersey.caching.CacheControl;
 

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/OntologyMatchResource.java

@@ -30,9 +30,9 @@
 import org.monarchinitiative.owlsim.services.exceptions.UnknownMatcherException;
 
 import com.codahale.metrics.annotation.Timed;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiParam;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
 
 import io.dropwizard.jersey.caching.CacheControl;