Fix/ignore some bugs due to spotbugs upgrade

Author: adrienlauer

cli/src/main/java/org/seedstack/seed/cli/CliConfig.java

@@ -17,6 +17,11 @@ public String getDefaultCommand() {
         return defaultCommand;
     }
 
+    public CliConfig setDefaultCommand(String defaultCommand) {
+        this.defaultCommand = defaultCommand;
+        return this;
+    }
+
     public boolean hasDefaultCommand() {
         return defaultCommand != null && !defaultCommand.isEmpty();
     }

core/src/main/java/org/seedstack/seed/core/internal/crypto/PBKDF2HashingService.java

@@ -7,22 +7,24 @@
  */
 package org.seedstack.seed.core.internal.crypto;
 
+import org.seedstack.seed.SeedException;
+import org.seedstack.seed.crypto.Hash;
+import org.seedstack.seed.crypto.HashingService;
+
+import javax.crypto.SecretKeyFactory;
+import javax.crypto.spec.PBEKeySpec;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.security.SecureRandom;
 import java.security.spec.InvalidKeySpecException;
-import javax.crypto.SecretKeyFactory;
-import javax.crypto.spec.PBEKeySpec;
-import org.seedstack.seed.SeedException;
-import org.seedstack.seed.crypto.Hash;
-import org.seedstack.seed.crypto.HashingService;
 
 class PBKDF2HashingService implements HashingService {
     private static final String PBKDF2_ALGORITHM = "PBKDF2WithHmacSHA1";
 
     private static final int SALT_BYTE_SIZE = 24;
     private static final int HASH_BYTE_SIZE = 24;
     private static final int PBKDF2_ITERATIONS = 1000;
+    private static final SecureRandom random = new SecureRandom();
 
     @Override
     public Hash createHash(String toHash) {
@@ -31,8 +33,6 @@ public Hash createHash(String toHash) {
 
     @Override
     public Hash createHash(char[] toHash) {
-        // Generate a random salt
-        SecureRandom random = new SecureRandom();
         byte[] salt = new byte[SALT_BYTE_SIZE];
         random.nextBytes(salt);
 

core/src/main/java/org/seedstack/seed/core/internal/diagnostic/DiagnosticPlugin.java

@@ -76,8 +76,10 @@ public Object nativeUnitModule() {
 
     @Override
     public void start(Context context) {
-        for (Map.Entry<String, DiagnosticInfoCollector> entry : diagnosticInfoCollectors.entrySet()) {
-            diagnosticManager.registerDiagnosticInfoCollector(entry.getKey(), entry.getValue());
+        if (diagnosticInfoCollectors != null && diagnosticManager != null) {
+            for (Map.Entry<String, DiagnosticInfoCollector> entry : diagnosticInfoCollectors.entrySet()) {
+                diagnosticManager.registerDiagnosticInfoCollector(entry.getKey(), entry.getValue());
+            }
         }
     }
 }

core/src/main/java/org/seedstack/seed/core/internal/guice/BindingUtils.java

@@ -11,6 +11,12 @@
 import com.google.inject.Key;
 import com.google.inject.TypeLiteral;
 import com.google.inject.util.Types;
+import org.seedstack.seed.SeedException;
+import org.seedstack.seed.core.internal.CoreErrorCode;
+import org.seedstack.shed.reflect.AnnotationPredicates;
+import org.seedstack.shed.reflect.Annotations;
+
+import javax.inject.Qualifier;
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Modifier;
 import java.lang.reflect.Type;
@@ -21,11 +27,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import javax.inject.Qualifier;
-import org.seedstack.seed.SeedException;
-import org.seedstack.seed.core.internal.CoreErrorCode;
-import org.seedstack.shed.reflect.AnnotationPredicates;
-import org.seedstack.shed.reflect.Annotations;
 
 /**
  * Utilities for Guice bindings.
@@ -76,7 +77,7 @@ private BindingUtils() {
      */
     @SuppressWarnings({"unchecked", "rawtypes"})
     public static <T> Map<Key<T>, Class<? extends T>> resolveBindingDefinitions(Class<T> injecteeClass,
-            Class<? extends T> firstImplClass, Class<? extends T>... restImplClasses) {
+                                                                                Class<? extends T> firstImplClass, Class<? extends T>... restImplClasses) {
         Map<Key<T>, Class<? extends T>> typeLiterals = new HashMap<>();
         List<Class<? extends T>> subClasses = new ArrayList<>();
 
@@ -89,13 +90,7 @@ public static <T> Map<Key<T>, Class<? extends T>> resolveBindingDefinitions(Clas
 
         for (Class<? extends T> subClass : subClasses) {
             if (isBindable(subClass)) {
-                Type resolvedType = TypeToken.of(subClass).getSupertype((Class) injecteeClass).getType();
-                TypeLiteral<T> parentTypeLiteral;
-                if (resolvedType == null) {
-                    parentTypeLiteral = TypeLiteral.get(injecteeClass);
-                } else {
-                    parentTypeLiteral = (TypeLiteral<T>) TypeLiteral.get(resolvedType);
-                }
+                TypeLiteral<T> parentTypeLiteral = (TypeLiteral<T>) TypeLiteral.get(TypeToken.of(subClass).getSupertype(injecteeClass).getType());
 
                 Optional<Annotation> qualifier = Annotations.on(subClass)
                         .traversingSuperclasses()
@@ -127,7 +122,7 @@ public static <T> Map<Key<T>, Class<? extends T>> resolveBindingDefinitions(Clas
      */
     @SuppressWarnings("unchecked")
     public static <T> Map<Key<T>, Class<? extends T>> resolveBindingDefinitions(Class<T> injecteeClass,
-            Collection<Class<? extends T>> implClasses) {
+                                                                                Collection<Class<? extends T>> implClasses) {
         if (implClasses != null && !implClasses.isEmpty()) {
             return resolveBindingDefinitions(injecteeClass, null, implClasses.toArray(new Class[implClasses.size()]));
         }
@@ -157,7 +152,7 @@ public static boolean isBindable(Class<?> subClass) {
      */
     @SuppressWarnings("unchecked")
     public static <T> Key<T> resolveKey(Class<T> injecteeClass, Class<? extends T> genericImplClass,
-            Type... typeVariableClasses) {
+                                        Type... typeVariableClasses) {
         Optional<Annotation> qualifier = Annotations.on(genericImplClass)
                 .findAll()
                 .filter(AnnotationPredicates.annotationAnnotatedWith(Qualifier.class, false))

pom.xml

@@ -41,9 +41,6 @@
         <tomcat.version>7.0.86</tomcat.version>
 
         <compatibility.version>3.1.0</compatibility.version>
-
-        <!-- TODO remove the limitation to TLSv1.2 below once built on JDK 12 -->
-        <itArgLine>-Djdk.tls.client.protocols="TLSv1,TLSv1.1,TLSv1.2"</itArgLine>
     </properties>
 
     <modules>

rest/core/src/main/java/org/seedstack/seed/rest/internal/RestPlugin.java

@@ -12,6 +12,7 @@
 import com.fasterxml.jackson.jaxrs.json.JacksonJaxbJsonProvider;
 import com.fasterxml.jackson.jaxrs.json.JacksonJsonProvider;
 import com.google.inject.AbstractModule;
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import io.nuun.kernel.api.plugin.InitState;
 import io.nuun.kernel.api.plugin.context.InitContext;
 import io.nuun.kernel.api.plugin.request.ClasspathScanRequest;
@@ -47,6 +48,7 @@
 import java.util.Set;
 import java.util.function.Predicate;
 
+@SuppressFBWarnings(value = "UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR", justification = "Fields init are following plugin lifecycle")
 public class RestPlugin extends AbstractSeedPlugin implements RestProvider {
     private static final Logger LOGGER = LoggerFactory.getLogger(RestPlugin.class);
     private final Map<Variant, Class<? extends RootResource>> rootResourcesByVariant = new HashMap<>();

security/core/src/main/java/org/seedstack/seed/security/internal/ShiroRealmAdapter.java

@@ -7,6 +7,7 @@
  */
 package org.seedstack.seed.security.internal;
 
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import org.apache.shiro.authc.AuthenticationException;
 import org.apache.shiro.authc.AuthenticationInfo;
 import org.apache.shiro.authc.AuthenticationToken;
@@ -34,6 +35,7 @@
 import java.util.List;
 import java.util.Set;
 
+@SuppressFBWarnings(value = "UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR", justification = "Field cannot be set in constructor due to injection")
 class ShiroRealmAdapter extends AuthorizingRealm {
     private static final Logger LOGGER = LoggerFactory.getLogger(ShiroRealmAdapter.class);
     private Realm realm;
@@ -45,8 +47,8 @@ public AuthorizationInfo getAuthorizationInfo(PrincipalCollection principals) {
         return super.getAuthorizationInfo(principals);
     }
 
-    @SuppressWarnings("unchecked")
     @Override
+    @SuppressWarnings("unchecked")
     protected AuthorizationInfo doGetAuthorizationInfo(PrincipalCollection principals) {
         SeedAuthorizationInfo authzInfo = new SeedAuthorizationInfo();
         PrincipalProvider<?> idPrincipal = (PrincipalProvider<?>) principals.getPrimaryPrincipal();

web/core/src/main/java/org/seedstack/seed/web/internal/WebPlugin.java

@@ -38,6 +38,7 @@
 /**
  * This plugin provides support for servlet-based Web applications.
  */
+@SuppressFBWarnings(value = "UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR", justification = "Fields init are following plugin lifecycle")
 public class WebPlugin extends AbstractSeedPlugin {
     private static final Logger LOGGER = LoggerFactory.getLogger(WebPlugin.class);
     private static final String WEB_INF_LIB = "/WEB-INF/lib";

web/core/src/main/java/org/seedstack/seed/web/internal/diagnostic/WebDiagnosticPlugin.java

@@ -8,6 +8,7 @@
 package org.seedstack.seed.web.internal.diagnostic;
 
 import com.google.common.collect.Lists;
+import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
 import io.nuun.kernel.api.plugin.InitState;
 import io.nuun.kernel.api.plugin.context.InitContext;
 import java.util.List;
@@ -24,6 +25,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@SuppressFBWarnings(value = "UWF_FIELD_NOT_INITIALIZED_IN_CONSTRUCTOR", justification = "Fields init are following plugin lifecycle")
 public class WebDiagnosticPlugin extends AbstractSeedPlugin implements WebProvider {
     private static final Logger LOGGER = LoggerFactory.getLogger(WebDiagnosticPlugin.class);
     private DiagnosticManager diagnosticManager;

web/core/src/main/java/org/seedstack/seed/web/internal/scan/tomcat/JndiJarInputDir.java

@@ -75,7 +75,9 @@ protected Vfs.File computeNext() {
     @Override
     public void close() {
         try {
-            jarInputStream.close();
+            if (jarInputStream != null) {
+                jarInputStream.close();
+            }
         } catch (IOException e) {
             LOGGER.warn("Unable to close JAR at {}", url.toExternalForm(), e);
         }