Added web services to Neji

BMDSoftware · Oct 26, 2016 · ba67bc7 · ba67bc7
1 parent e2bb9ac
commit ba67bc7
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Showing 289 changed files with 99,595 additions and 2 deletions.
diff --git a/conf/keystore.jks b/conf/keystore.jks
diff --git a/conf/server-configuration.properties b/conf/server-configuration.properties
@@ -0,0 +1,10 @@
+proxy.url =
+proxy.port =
+proxy.username =
+proxy.password =
+
+https.keystore.file = conf/keystore.jks
+https.keystore.password = BMD4key
+
+https.truststore.file = conf/truststore.jks
+https.truststore.password = BMD4key
diff --git a/conf/truststore.jks b/conf/truststore.jks
diff --git a/loginRealm.properties b/loginRealm.properties
@@ -0,0 +1,13 @@
+jdbcdriver = org.sqlite.JDBC
+url = jdbc:sqlite:neji.db
+usertable = users
+usertablekey = id
+usertableuserfield = username
+usertablepasswordfield = pwd
+roletable = roles
+roletablekey = id
+roletablerolefield = role
+userroletable = user_roles
+userroletableuserkey = user_id
+userroletablerolekey = role_id
+cachetime = 300
diff --git a/neji.sh b/neji.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-cp=target/neji-2.0-jar-with-dependencies.jar:$CLASSPATH
+cp=target/neji-2.1.0-SNAPSHOT-jar-with-dependencies.jar:$CLASSPATH
 MEMORY=8G
 JAVA_COMMAND="java -Xmx$MEMORY -Dfile.encoding=UTF-8 -classpath $cp"
 CLASS=pt.ua.tm.neji.cli.Main

diff --git a/nejiTrain.sh b/nejiTrain.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-cp=target/neji-2.0-jar-with-dependencies.jar:$CLASSPATH
+cp=target/neji-2.1.0-SNAPSHOT-jar-with-dependencies.jar:$CLASSPATH
 MEMORY=12G
 JAVA_COMMAND="java -Xmx$MEMORY -Dfile.encoding=UTF-8 -classpath $cp"
 CLASS=pt.ua.tm.neji.train.cli.TrainMain

diff --git a/nejiWeb.sh b/nejiWeb.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+cp=target/neji-2.1.0-SNAPSHOT-server.jar:$CLASSPATH
+MEMORY=6G
+JAVA_COMMAND="java -Xmx$MEMORY -Dfile.encoding=UTF-8 -classpath $cp"
+CLASS=pt.ua.tm.neji.web.cli.WebMain
+
+$JAVA_COMMAND $CLASS $*
diff --git a/pom.xml b/pom.xml
@@ -112,6 +112,9 @@
             <resource>
                 <directory>src/main/resources</directory>
             </resource>
+            <resource>
+                <directory>src/main/resources/webapp</directory>
+            </resource>
         </resources>
         <plugins>
             <plugin>
@@ -235,6 +238,44 @@
                     <forkMode>always</forkMode>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>2.2</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <finalName>${project.build.finalName}-server</finalName>
+                            <transformers>
+                                <!--use transformer to handle merge of META-INF/services - see http://java.net/jira/browse/JERSEY-440?focusedCommentId=14822&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#action_14822-->
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <manifestEntries>
+                                        <Main-Class>pt.ua.tm.neji.web.cli.WebMain</Main-Class>
+                                    </manifestEntries>
+                                </transformer>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+                            </transformers>
+                            <filters>
+                                <!--filter to address "Invalid signature file" issue - see http://stackoverflow.com/a/6743609/589215-->
+                                <filter>
+                                    <artifact>*:*</artifact>
+                                    <excludes>
+                                        <exclude>META-INF/*.SF</exclude>
+                                        <exclude>META-INF/*.DSA</exclude>
+                                        <exclude>META-INF/*.RSA</exclude>
+                                    </excludes>
+                                </filter>
+                            </filters>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 
@@ -377,6 +418,85 @@
             <version>2015</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-webapp</artifactId>
+            <version>8.0.0.RC0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-jsp-2.1</artifactId>
+            <version>7.5.4.v20111024</version>
+        </dependency>
+
+        <dependency>
+            <groupId>javax.servlet</groupId>
+            <artifactId>javax.servlet-api</artifactId>
+            <version>3.0.1</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.mortbay.jetty</groupId>
+            <artifactId>jsp-2.1-glassfish</artifactId>
+            <version>2.1.v20100127</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.sun.jersey</groupId>
+            <artifactId>jersey-server</artifactId>
+            <version>1.9</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.sun.jersey</groupId>
+            <artifactId>jersey-client</artifactId>
+            <version>1.9</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.sun.jersey</groupId>
+            <artifactId>jersey-json</artifactId>
+            <version>1.9</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.sun.jersey.contribs</groupId>
+            <artifactId>jersey-multipart</artifactId>
+            <version>1.9</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.jvnet</groupId>
+                    <artifactId>mimepull</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>org.jvnet.mimepull</groupId>
+            <artifactId>mimepull</artifactId>
+            <version>1.9</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpcore</artifactId>
+            <version>4.4.4</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpclient</artifactId>
+            <version>4.5.1</version>
+        </dependency>
+
+        <!-- SQLite -->
+        <dependency>
+            <groupId>org.xerial</groupId>
+            <artifactId>sqlite-jdbc</artifactId>
+            <version>3.8.10.1</version>
+        </dependency>
+
     </dependencies>   
 
 </project>
diff --git a/src/main/java/pt/ua/tm/neji/web/WebConstants.java b/src/main/java/pt/ua/tm/neji/web/WebConstants.java
@@ -0,0 +1,31 @@
+/*
+ * Copyright (c) 2016 BMD Software and University of Aveiro.
+ *
+ * Neji is a flexible and powerful platform for biomedical information extraction from text.
+ *
+ * This project is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
+ * To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
+ *
+ * This project is a free software, you are free to copy, distribute, change and transmit it.
+ * However, you may not use it for commercial purposes.
+ *
+ * It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
+ * without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ */
+
+package pt.ua.tm.neji.web;
+
+import java.io.File;
+
+/**
+ * Constants to use in the web features.
+ * 
+ * @author André Santos (<a href="mailto:andre.jeronimo@ua.pt">andre.jeronimo@ua.pt</a>)
+ * @version 1.0
+ */
+public class WebConstants {
+
+    public static final String DICTIONARIES_PATH = "resources" + File.separator + "dictionaries" + File.separator;
+    public static final String DICTIONARIES_PRIORITY_PATH = "resources" + File.separator + "dictionaries" + File.separator + "_priority";
+    public static final String MODELS_PATH = "resources" + File.separator + "models" + File.separator;    
+}