Merge 30503bd into e3045b7

monarch-initiative · Feb 9, 2017 · 892d267 · 892d267
2 parents e3045b7 + 30503bd
commit 892d267
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Showing 2 changed files with 107 additions and 89 deletions.
diff --git a/...ervices/src/main/java/org/monarchinitiative/owlsim/services/OwlSimServiceApplication.java b/...ervices/src/main/java/org/monarchinitiative/owlsim/services/OwlSimServiceApplication.java
@@ -48,95 +48,113 @@
 
 public class OwlSimServiceApplication extends Application<ApplicationConfiguration> {
 
-    private Logger LOG = Logger.getLogger(OwlSimServiceApplication.class);
-
-    public static void main(String[] args) throws Exception {
-        new OwlSimServiceApplication().run(args);
-    }
-
-    @Override
-    public String getName() {
-        return "owlsim Web Services";
-    }
-
-    @Override
-    public void initialize(Bootstrap<ApplicationConfiguration> bootstrap) {
-        initializeSwaggger(bootstrap);
-    }
-
-    void initializeSwaggger(Bootstrap<ApplicationConfiguration> bootstrap) {
-        bootstrap.addBundle(new AssetsBundle("/swagger/", "/docs", "index.html"));
+  private Logger LOG = Logger.getLogger(OwlSimServiceApplication.class);
+
+  public static void main(String[] args) throws Exception {
+    new OwlSimServiceApplication().run(args);
+  }
+
+  @Override
+  public String getName() {
+    return "owlsim Web Services";
+  }
+
+  @Override
+  public void initialize(Bootstrap<ApplicationConfiguration> bootstrap) {
+    initializeSwaggger(bootstrap);
+  }
+
+  void initializeSwaggger(Bootstrap<ApplicationConfiguration> bootstrap) {
+    bootstrap.addBundle(new AssetsBundle("/swagger/", "/docs", "index.html"));
+  }
+
+  /***
+   * The context path must be set before configuring swagger
+   * 
+   * @param environment
+   */
+  void configureSwagger(Environment environment) {
+    environment.jersey().register(new ApiListingResource());
+    environment.getObjectMapper().setSerializationInclusion(JsonInclude.Include.NON_NULL);
+
+    BeanConfig config = new BeanConfig();
+
+    // TODO does not work - https://github.com/swagger-api/swagger-core/issues/1594
+    // Info info = new Info();
+    // info.setVersion("1.0.0");
+    // Contact contact = new Contact();
+    // contact.setEmail("contact email");
+    // contact.setName("contact name");
+    // contact.setUrl("http://owlsim3.monarchinitiative.org/api/docs/");
+    // info.setContact(contact);
+    // config.setInfo(info);
+
+    // Manually copy/paste that in the swagger.json to register it to smartAPI
+    // "contact":{
+    // "responsibleDeveloper":"John Do",
+    // "responsibleOrganization":"LBNL",
+    // "url":"http://owlsim3.monarchinitiative.org/api/docs/",
+    // "email":"JohnDo@lbl.gov"
+    // },
+
+    config.setTitle("owlsim - Web Services");
+    config.setVersion("1.0.0");
+    // TODO proper TOS
+    config.setTermsOfServiceUrl("https://github.com/monarch-initiative/owlsim-v3");
+    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, "/*");
+  }
+
+  /***
+   * Configure Jackson parameters
+   * 
+   * @param environment
+   */
+  void configureJackson(Environment environment) {
+    // Some classes from commons-math do not have members to serialized. Ignore those or Jackson
+    // will throw an exception.
+    environment.getObjectMapper().disable(SerializationFeature.FAIL_ON_EMPTY_BEANS);
+  }
+
+  @Override
+  public void run(ApplicationConfiguration configuration, Environment environment)
+      throws Exception {
+    environment.getApplicationContext().setContextPath("/api");
+    configureSwagger(environment);
+    configureJackson(environment);
+    configureCors(environment);
+
+    Concurrency concurrency = Concurrency.CONCURRENT;
+    LOG.info("Creating injector...");
+    Injector i = Guice.createInjector(new OWLAPIImplModule(concurrency), new OWLAPIParsersModule(),
+        new OWLAPIServiceLoaderModule(),
+        new KnowledgeBaseModule(configuration.getOntologyUris(),
+            configuration.getOntologyDataUris(), configuration.getDataTsvs(),
+            configuration.getCuries()),
+        new EnrichmentMapModule(), new MatcherMapModule());
+    LOG.info("BINDINGS =" + i.getAllBindings());
+    // Add resources
+    Set<ClassInfo> resourceClasses = ClassPath.from(getClass().getClassLoader())
+        .getTopLevelClasses("org.monarchinitiative.owlsim.services.resources");
+    for (ClassInfo resourceClass : resourceClasses) {
+      Class<?> c = resourceClass.load();
+      environment.jersey().register(i.getInstance(c));
     }
 
-    /***
-     * The context path must be set before configuring swagger
-     * @param environment
-     */
-    void configureSwagger(Environment environment) {
-        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.setTermsOfServiceUrl("https://github.com/monarch-initiative/owlsim-v3"); // TODO proper TOS
-        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, "/*");
-    }
-
-    /***
-     * Configure Jackson parameters
-     * @param environment
-     */
-    void configureJackson(Environment environment) {
-      // Some classes from commons-math do not have members to serialized. Ignore those or Jackson
-      // will throw an exception.
-      environment.getObjectMapper().disable(SerializationFeature.FAIL_ON_EMPTY_BEANS);
-    }
-
-    @Override
-    public void run(ApplicationConfiguration configuration, Environment environment) throws Exception {
-        environment.getApplicationContext().setContextPath("/api");
-        configureSwagger(environment);
-        configureJackson(environment);
-        configureCors(environment);
-
-        Concurrency concurrency = Concurrency.CONCURRENT;
-        LOG.info("Creating injector...");
-        Injector i = Guice.createInjector(
-                new OWLAPIImplModule(concurrency),
-                new OWLAPIParsersModule(),
-                new OWLAPIServiceLoaderModule(),
-                new KnowledgeBaseModule(
-                        configuration.getOntologyUris(),
-                        configuration.getOntologyDataUris(),
-                        configuration.getDataTsvs(),
-                        configuration.getCuries()
-                        ),
-                        new EnrichmentMapModule(),
-                        new MatcherMapModule());
-        LOG.info("BINDINGS ="+i.getAllBindings());
-        //Add resources
-        Set<ClassInfo> resourceClasses = ClassPath.from(getClass().getClassLoader())
-                .getTopLevelClasses("org.monarchinitiative.owlsim.services.resources");
-        for (ClassInfo resourceClass: resourceClasses) {
-            Class<?> c = resourceClass.load();
-            environment.jersey().register(i.getInstance(c));
-        }
-
-    }
+  }
 
 }
diff --git a/...in/java/org/monarchinitiative/owlsim/services/configuration/ApplicationConfiguration.java b/...in/java/org/monarchinitiative/owlsim/services/configuration/ApplicationConfiguration.java
@@ -1,5 +1,5 @@
 /**
- * Copyright (C) 2014 The SciGraph authors
+ * Copyright (C) 2014 The OwlSim authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.