Wsf merge

Model/pom.xml

@@ -16,23 +16,7 @@
 
     <dependency>
       <groupId>org.gusdb</groupId>
-      <artifactId>wsf-client</artifactId>
-      <exclusions>
-        <exclusion>
-          <groupId>javax.servlet</groupId>
-          <artifactId>javax.servlet-api</artifactId>
-        </exclusion>
-      </exclusions>
-    </dependency>
-
-    <dependency>
-      <groupId>org.gusdb</groupId>
-      <artifactId>wsf-common</artifactId>
-    </dependency>
-
-    <dependency>
-      <groupId>org.gusdb</groupId>
-      <artifactId>wsf-plugin</artifactId>
+      <artifactId>wdk-wsf</artifactId>
     </dependency>
 
     <dependency>

WSF/README.md

@@ -0,0 +1,6 @@
+# WSF
+The [WDK](https://github.com/VEuPathDB/WDK) Web Services Framework: web service architecture to support WDK searches that run a process rather than issue an RDBMS query.
+
+Defines a [plugin API](Plugin/src/main/java/org/gusdb/wsf/plugin/Plugin.java) so that process-based searches can be plugged into the WDK search engine.
+
+This repo will be retired soon, when the plugin functionality will be folded into the WDK directly.

WSF/pom.xml

@@ -0,0 +1,65 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <parent>
+    <groupId>org.gusdb</groupId>
+    <artifactId>wdk</artifactId>
+    <version>1.0.0</version>
+  </parent>
+
+  <name>Web Development Kit - WSF</name>
+  <artifactId>wdk-wsf</artifactId>
+  <packaging>jar</packaging>
+
+  <dependencies>
+
+    <dependency>
+      <groupId>org.gusdb</groupId>
+      <artifactId>fgputil-core</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.gusdb</groupId>
+      <artifactId>fgputil-db</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.gusdb</groupId>
+      <artifactId>fgputil-json</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.glassfish.jersey.core</groupId>
+      <artifactId>jersey-client</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>org.json</groupId>
+      <artifactId>json</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>javax.servlet</groupId>
+      <artifactId>servlet-api</artifactId>
+      <scope>provided</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.apache.logging.log4j</groupId>
+      <artifactId>log4j-core</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.logging.log4j</groupId>
+      <artifactId>log4j-1.2-api</artifactId>
+    </dependency>
+
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <scope>test</scope>
+    </dependency>
+
+  </dependencies>
+
+</project>

WSF/src/main/java/org/gusdb/wsf/client/ClientModelException.java

@@ -0,0 +1,31 @@
+package org.gusdb.wsf.client;
+
+
+/**
+ * @author Jerric
+ */
+public class ClientModelException extends Exception {
+
+  private static final long serialVersionUID = 2L;
+
+  public ClientModelException() {
+    super();
+  }
+
+  public ClientModelException(String message) {
+    super(message);
+  }
+
+  public ClientModelException(Throwable cause) {
+    super(cause);
+  }
+
+  public ClientModelException(String message, Throwable cause) {
+    super(message, cause);
+  }
+
+  public ClientModelException(String message, Throwable cause, boolean enableSuppression,
+      boolean writableStackTrace) {
+    super(message, cause, enableSuppression, writableStackTrace);
+  }
+}

WSF/src/main/java/org/gusdb/wsf/client/ClientRequest.java

@@ -0,0 +1,66 @@
+package org.gusdb.wsf.client;
+
+import org.gusdb.wsf.plugin.PluginRequest;
+import org.json.JSONException;
+import org.json.JSONObject;
+
+/**
+ * @author jerric
+ */
+@SuppressWarnings("hiding")
+public class ClientRequest extends PluginRequest {
+
+  public static final String PLUGIN_KEY = "plugin";
+  public static final String PROJECT_KEY = PluginRequest.PROJECT_KEY;
+  public static final String COLUMNS_ARRAY_KEY = PluginRequest.COLUMNS_ARRAY_KEY;
+  public static final String PARAMETER_MAP_KEY = PluginRequest.PARAMETER_MAP_KEY;
+  public static final String CONTEXT_MAP_KEY = PluginRequest.CONTEXT_MAP_KEY;
+
+  private String pluginClass;
+
+  public ClientRequest() {
+    super();
+  }
+
+  public ClientRequest(ClientRequest request) {
+    super(request);
+    this.pluginClass = request.pluginClass;
+  }
+
+  public ClientRequest(String jsonString) throws ClientModelException {
+    try {
+      JSONObject jsRequest = new JSONObject(jsonString);
+      parseJSON(jsRequest);
+      this.pluginClass = jsRequest.getString(PLUGIN_KEY);
+    }
+    catch (JSONException ex) {
+      throw new ClientModelException(ex);
+    }
+  }
+
+  /**
+   * the full class name of the WSF plugin. The service will instantiate a plugin instance from this class
+   * name, and invoke it.
+   *
+   * @return the pluginClass
+   */
+  public String getPluginClass() {
+    return pluginClass;
+  }
+
+  /**
+   * @param pluginClass
+   *          the pluginClass to set
+   */
+  public void setPluginClass(String pluginClass) {
+    this.pluginClass = pluginClass;
+  }
+
+  @Override
+  protected JSONObject getJSON() throws JSONException {
+    JSONObject jsRequest = super.getJSON();
+    jsRequest.put(PLUGIN_KEY, pluginClass);
+    return jsRequest;
+  }
+
+}

WSF/src/main/java/org/gusdb/wsf/client/ClientUserException.java

@@ -0,0 +1,30 @@
+package org.gusdb.wsf.client;
+
+/**
+ * @author Jerric
+ */
+public class ClientUserException extends Exception {
+
+  private static final long serialVersionUID = 2L;
+
+  public ClientUserException() {
+    super();
+  }
+
+  public ClientUserException(String message) {
+    super(message);
+  }
+
+  public ClientUserException(Throwable cause) {
+    super(cause);
+  }
+
+  public ClientUserException(String message, Throwable cause) {
+    super(message, cause);
+  }
+
+  public ClientUserException(String message, Throwable cause,
+    boolean enableSuppression, boolean writableStackTrace) {
+    super(message, cause, enableSuppression, writableStackTrace);
+  }
+}

WSF/src/main/java/org/gusdb/wsf/client/WsfClient.java

@@ -0,0 +1,11 @@
+package org.gusdb.wsf.client;
+
+import org.gusdb.wsf.plugin.DelayedResultException;
+
+public interface WsfClient {
+
+  void setResponseListener(WsfResponseListener listener);
+
+  int invoke(ClientRequest request) throws ClientModelException, ClientUserException, DelayedResultException;
+
+}

WSF/src/main/java/org/gusdb/wsf/client/WsfClientFactory.java

@@ -0,0 +1,10 @@
+package org.gusdb.wsf.client;
+
+import java.net.URI;
+
+public interface WsfClientFactory {
+
+  WsfClient newClient(WsfResponseListener listener);
+
+  WsfClient newClient(WsfResponseListener listener, URI serviceURI);
+}

WSF/src/main/java/org/gusdb/wsf/client/WsfClientFactoryImpl.java

@@ -0,0 +1,20 @@
+package org.gusdb.wsf.client;
+
+import java.net.URI;
+
+public final class WsfClientFactoryImpl implements WsfClientFactory {
+
+  @Override
+  public WsfClient newClient(WsfResponseListener listener) {
+    WsfClient client = new WsfLocalClient();
+    client.setResponseListener(listener);
+    return client;
+  }
+
+  @Override
+  public WsfClient newClient(WsfResponseListener listener, URI serviceURI) {
+    WsfClient client = new WsfRemoteClient(serviceURI);
+    client.setResponseListener(listener);
+    return client;
+  }
+}

WSF/src/main/java/org/gusdb/wsf/client/WsfLocalClient.java

@@ -0,0 +1,76 @@
+package org.gusdb.wsf.client;
+
+import org.gusdb.wsf.plugin.DelayedResultException;
+import org.gusdb.wsf.plugin.PluginExecutor;
+import org.gusdb.wsf.plugin.PluginModelException;
+import org.gusdb.wsf.plugin.PluginResponse;
+import org.gusdb.wsf.plugin.PluginUserException;
+
+/**
+ * @author Jerric
+ */
+public class WsfLocalClient implements WsfClient, PluginResponse {
+
+  private WsfResponseListener listener;
+
+  protected WsfLocalClient() {}
+
+  @Override
+  public void addRow(String[] row) throws PluginModelException, PluginUserException {
+    try {
+      listener.onRowReceived(row);
+    }
+    catch (ClientModelException ex) {
+      throw new PluginModelException(ex);
+    }
+    catch (ClientUserException ex) {
+      throw new PluginUserException(ex);
+    }
+  }
+
+  @Override
+  public void addAttachment(String key, String attachment) throws PluginModelException, PluginUserException {
+    try {
+      listener.onAttachmentReceived(key, attachment);
+    }
+    catch (ClientModelException ex) {
+      throw new PluginModelException(ex);
+    }
+    catch (ClientUserException ex) {
+      throw new PluginUserException(ex);
+    }
+  }
+
+  @Override
+  public void setMessage(String message) throws PluginModelException, PluginUserException {
+    try {
+      listener.onMessageReceived(message);
+    }
+    catch (ClientModelException ex) {
+      throw new PluginModelException(ex);
+    }
+    catch (ClientUserException ex) {
+      throw new PluginUserException(ex);
+    }
+  }
+
+  @Override
+  public void setResponseListener(WsfResponseListener listener) {
+    this.listener = listener;
+  }
+
+  @Override
+  public int invoke(ClientRequest request) throws ClientModelException, ClientUserException, DelayedResultException {
+    PluginExecutor executor = new PluginExecutor();
+    String pluginClassName = request.getPluginClass();
+    try {
+      return executor.execute(pluginClassName, request, this);
+    }
+    catch (PluginModelException ex) {
+      throw new ClientModelException(ex);
+    }
+    catch (PluginUserException ex) {
+      throw new ClientUserException(ex);
+    }
+  }
+}