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);
+ }
+ }
+}

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);
+ }
+ }
+}

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);
+ }
+ }
+}

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);
+ }
+ }
+}

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);
+ }
+ }
+}

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);
+ }
+ }
+}

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);
+ }
+ }
+}

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);
+ }
+ }
+}