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Added web services to Neji

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andrejeronimo committed Oct 26, 2016
1 parent e2bb9ac commit ba67bc7baa499433a5ce4653194c348ca1e2d15e
Showing with 99,595 additions and 2 deletions.
  1. BIN conf/keystore.jks
  2. +10 −0 conf/server-configuration.properties
  3. BIN conf/truststore.jks
  4. +13 −0 loginRealm.properties
  5. +1 −1 neji.sh
  6. +1 −1 nejiTrain.sh
  7. +7 −0 nejiWeb.sh
  8. +120 −0 pom.xml
  9. +31 −0 src/main/java/pt/ua/tm/neji/web/WebConstants.java
  10. +451 −0 src/main/java/pt/ua/tm/neji/web/annotate/AnnotationResource.java
  11. +100 −0 src/main/java/pt/ua/tm/neji/web/annotate/BecasRequest.java
  12. +64 −0 src/main/java/pt/ua/tm/neji/web/annotate/pubmed/Document.java
  13. +116 −0 src/main/java/pt/ua/tm/neji/web/annotate/pubmed/Pubmed.java
  14. +100 −0 src/main/java/pt/ua/tm/neji/web/annotate/pubmed/PubmedResponse.java
  15. +165 −0 src/main/java/pt/ua/tm/neji/web/annotate/pubmed/PubmedXMLParser.java
  16. +160 −0 src/main/java/pt/ua/tm/neji/web/batch/ServerBatchExecutor.java
  17. +177 −0 src/main/java/pt/ua/tm/neji/web/cli/ServerConfiguration.java
  18. +279 −0 src/main/java/pt/ua/tm/neji/web/cli/WebMain.java
  19. +190 −0 src/main/java/pt/ua/tm/neji/web/database/DatabaseHandler.java
  20. +1,393 −0 src/main/java/pt/ua/tm/neji/web/database/DefaultDatabaseHandler.java
  21. +102 −0 src/main/java/pt/ua/tm/neji/web/manage/Dictionary.java
  22. +264 −0 src/main/java/pt/ua/tm/neji/web/manage/ManageResource.java
  23. +102 −0 src/main/java/pt/ua/tm/neji/web/manage/Model.java
  24. +128 −0 src/main/java/pt/ua/tm/neji/web/processor/ServerProcessor.java
  25. +74 −0 src/main/java/pt/ua/tm/neji/web/server/JSPServlet.java
  26. +997 −0 src/main/java/pt/ua/tm/neji/web/server/Server.java
  27. +238 −0 src/main/java/pt/ua/tm/neji/web/services/Service.java
  28. +226 −0 src/main/java/pt/ua/tm/neji/web/services/ServicesResource.java
  29. +72 −0 src/main/java/pt/ua/tm/neji/web/test/MySSLSocketFactory.java
  30. +106 −0 src/main/java/pt/ua/tm/neji/web/test/TestREST.java
  31. +93 −0 src/main/java/pt/ua/tm/neji/web/util/AddUsers.java
  32. +162 −0 src/main/resources/webapp/WEB-INF/annotate.jsp
  33. +58 −0 src/main/resources/webapp/WEB-INF/becas.jsp
  34. +91 −0 src/main/resources/webapp/WEB-INF/edit_model.jsp
  35. +167 −0 src/main/resources/webapp/WEB-INF/edit_service.jsp
  36. +118 −0 src/main/resources/webapp/WEB-INF/list.jsp
  37. +110 −0 src/main/resources/webapp/WEB-INF/manage.jsp
  38. +87 −0 src/main/resources/webapp/WEB-INF/web.xml
  39. +359 −0 src/main/resources/webapp/admin/help-manage.html
  40. +300 −0 src/main/resources/webapp/admin/resources-dictionaries.html
  41. +348 −0 src/main/resources/webapp/admin/resources-models.html
  42. +404 −0 src/main/resources/webapp/admin/services.html
  43. +207 −0 src/main/resources/webapp/app/app.js
  44. +76 −0 src/main/resources/webapp/app/config.js
  45. +295 −0 src/main/resources/webapp/app/controller.js
  46. +64 −0 src/main/resources/webapp/app/main.js
  47. +44 −0 src/main/resources/webapp/app/models/annotated-pub.js
  48. +539 −0 src/main/resources/webapp/app/models/annotated-text.js
  49. +174 −0 src/main/resources/webapp/app/modules/annotation-service.js
  50. +75 −0 src/main/resources/webapp/app/modules/semantic-groups.js
  51. +40 −0 src/main/resources/webapp/app/modules/syntax-highlight.js
  52. +22 −0 src/main/resources/webapp/app/modules/text-samples.js
  53. +239 −0 src/main/resources/webapp/app/modules/tracker.js
  54. +213 −0 src/main/resources/webapp/app/modules/tutorials.js
  55. +113 −0 src/main/resources/webapp/app/router.js
  56. +10 −0 src/main/resources/webapp/app/templates/alert.html
  57. +34 −0 src/main/resources/webapp/app/templates/annotation/controls.html
  58. +14 −0 src/main/resources/webapp/app/templates/annotation/publication.html
  59. +47 −0 src/main/resources/webapp/app/templates/annotation/result.html
  60. +1 −0 src/main/resources/webapp/app/templates/annotation/text.html
  61. +21 −0 src/main/resources/webapp/app/templates/annotation/tooltip.html
  62. +14 −0 src/main/resources/webapp/app/templates/home.html
  63. +161 −0 src/main/resources/webapp/app/templates/layouts/main.html
  64. +19 −0 src/main/resources/webapp/app/templates/pmid-dialog.html
  65. +408 −0 src/main/resources/webapp/app/templates/static/about.html
  66. +1,491 −0 src/main/resources/webapp/app/templates/static/api.html
  67. +50 −0 src/main/resources/webapp/app/templates/static/contact.html
  68. +291 −0 src/main/resources/webapp/app/templates/static/help.html
  69. +614 −0 src/main/resources/webapp/app/templates/static/widget.html
  70. +69 −0 src/main/resources/webapp/app/views/alert.js
  71. +379 −0 src/main/resources/webapp/app/views/annotation/controls.js
  72. +76 −0 src/main/resources/webapp/app/views/annotation/publication.js
  73. +320 −0 src/main/resources/webapp/app/views/annotation/result.js
  74. +57 −0 src/main/resources/webapp/app/views/annotation/text.js
  75. +201 −0 src/main/resources/webapp/app/views/annotation/tooltip.js
  76. +350 −0 src/main/resources/webapp/app/views/home.js
  77. +95 −0 src/main/resources/webapp/app/views/pmid-dialog.js
  78. +88 −0 src/main/resources/webapp/app/views/static.js
  79. +69 −0 src/main/resources/webapp/app/widget.config.js
  80. +192 −0 src/main/resources/webapp/app/widget/app.js
  81. +198 −0 src/main/resources/webapp/app/widget/controller.js
  82. +212 −0 src/main/resources/webapp/app/widget/embed-widget.js
  83. +181 −0 src/main/resources/webapp/app/widget/main.js
  84. +1 −0 src/main/resources/webapp/app/widget/templates/annotation/publication.html
  85. +1 −0 src/main/resources/webapp/app/widget/templates/annotation/text.html
  86. +1 −0 src/main/resources/webapp/app/widget/templates/annotation/tooltip.html
  87. +38 −0 src/main/resources/webapp/app/widget/templates/controls.html
  88. +17 −0 src/main/resources/webapp/app/widget/templates/export.html
  89. +7 −0 src/main/resources/webapp/app/widget/templates/home.html
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  91. +5 −0 src/main/resources/webapp/app/widget/templates/result.html
  92. +230 −0 src/main/resources/webapp/app/widget/views/controls.js
  93. +84 −0 src/main/resources/webapp/app/widget/views/export.js
  94. +52 −0 src/main/resources/webapp/app/widget/views/home.js
  95. +133 −0 src/main/resources/webapp/app/widget/views/result.js
  96. +174 −0 src/main/resources/webapp/assets/css/annotated-text.css
  97. +52 −0 src/main/resources/webapp/assets/css/annotation-controls.css
  98. +79 −0 src/main/resources/webapp/assets/css/annotations.css
  99. +151 −0 src/main/resources/webapp/assets/css/app.css
  100. +13 −0 src/main/resources/webapp/assets/css/becas-widget.css
  101. +23 −0 src/main/resources/webapp/assets/css/becas.css
  102. +1,066 −0 src/main/resources/webapp/assets/css/bootstrap-responsive.css
  103. +4,530 −0 src/main/resources/webapp/assets/css/bootstrap.css
  104. +31 −0 src/main/resources/webapp/assets/css/brand.css
  105. +78 −0 src/main/resources/webapp/assets/css/concept-tree.css
  106. +205 −0 src/main/resources/webapp/assets/css/docs.css
  107. BIN src/main/resources/webapp/assets/css/font/lobster/lobster-webfont.eot
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  109. BIN src/main/resources/webapp/assets/css/font/lobster/lobster-webfont.ttf
  110. BIN src/main/resources/webapp/assets/css/font/lobster/lobster-webfont.woff
  111. BIN src/main/resources/webapp/assets/css/font/oxygen/Oxygen-Regular.eot
  112. BIN src/main/resources/webapp/assets/css/font/oxygen/Oxygen-Regular.ttf
  113. BIN src/main/resources/webapp/assets/css/font/oxygen/Oxygen-Regular.woff
  114. BIN src/main/resources/webapp/assets/css/font/play/Play-Bold.eot
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  117. BIN src/main/resources/webapp/assets/css/font/play/Play-Regular.eot
  118. BIN src/main/resources/webapp/assets/css/font/play/Play-Regular.ttf
  119. BIN src/main/resources/webapp/assets/css/font/play/Play-Regular.woff
  120. BIN src/main/resources/webapp/assets/css/images/ajax-loader.gif
  121. BIN src/main/resources/webapp/assets/css/images/file.gif
  122. BIN src/main/resources/webapp/assets/css/images/folder-closed.gif
  123. BIN src/main/resources/webapp/assets/css/images/folder.gif
  124. BIN src/main/resources/webapp/assets/css/images/minus.gif
  125. BIN src/main/resources/webapp/assets/css/images/plus.gif
  126. BIN src/main/resources/webapp/assets/css/images/treeview-black-line.gif
  127. BIN src/main/resources/webapp/assets/css/images/treeview-black.gif
  128. BIN src/main/resources/webapp/assets/css/images/treeview-default-line.gif
  129. BIN src/main/resources/webapp/assets/css/images/treeview-default.gif
  130. BIN src/main/resources/webapp/assets/css/images/treeview-famfamfam-line.gif
  131. BIN src/main/resources/webapp/assets/css/images/treeview-famfamfam.gif
  132. BIN src/main/resources/webapp/assets/css/images/treeview-gray-line.gif
  133. BIN src/main/resources/webapp/assets/css/images/treeview-gray.gif
  134. BIN src/main/resources/webapp/assets/css/images/treeview-red-line.gif
  135. BIN src/main/resources/webapp/assets/css/images/treeview-red.gif
  136. +63 −0 src/main/resources/webapp/assets/css/jquery.asmselect.css
  137. +79 −0 src/main/resources/webapp/assets/css/jquery.treeview.css
  138. +480 −0 src/main/resources/webapp/assets/css/neji.css
  139. +1 −0 src/main/resources/webapp/assets/css/pnotify.custom.min.css
  140. +16 −0 src/main/resources/webapp/assets/css/prettify.css
  141. +75 −0 src/main/resources/webapp/assets/css/starter-template.css
  142. +74 −0 src/main/resources/webapp/assets/css/starter-template.css~new_T103-NejiServices
  143. +50 −0 src/main/resources/webapp/assets/css/sunburst.css
  144. +29 −0 src/main/resources/webapp/assets/css/tour.css
  145. +149 −0 src/main/resources/webapp/assets/css/widget.css
  146. BIN src/main/resources/webapp/assets/font/lobster-webfont.eot
  147. +244 −0 src/main/resources/webapp/assets/font/lobster-webfont.svg
  148. BIN src/main/resources/webapp/assets/font/lobster-webfont.ttf
  149. BIN src/main/resources/webapp/assets/font/lobster-webfont.woff
  150. +55 −0 src/main/resources/webapp/assets/html/name.html
  151. BIN src/main/resources/webapp/assets/img/add.png
  152. BIN src/main/resources/webapp/assets/img/annotate.png
  153. BIN src/main/resources/webapp/assets/img/annotating_abstracts.png
  154. BIN src/main/resources/webapp/assets/img/becas-logo.black.png
  155. BIN src/main/resources/webapp/assets/img/becas-logo.png
  156. BIN src/main/resources/webapp/assets/img/becas-logo.small.png
  157. BIN src/main/resources/webapp/assets/img/bg-pattern.png
  158. BIN src/main/resources/webapp/assets/img/bmd.png
  159. BIN src/main/resources/webapp/assets/img/cc_license_80x15.png
  160. BIN src/main/resources/webapp/assets/img/concept_popovers.png
  161. BIN src/main/resources/webapp/assets/img/delete.png
  162. BIN src/main/resources/webapp/assets/img/docs/becas_annotated_abstract.png
  163. BIN src/main/resources/webapp/assets/img/docs/becas_concept_popover.png
  164. BIN src/main/resources/webapp/assets/img/docs/becas_concept_tree.png
  165. BIN src/main/resources/webapp/assets/img/docs/becas_export_button.png
  166. BIN src/main/resources/webapp/assets/img/docs/becas_homepage.png
  167. BIN src/main/resources/webapp/assets/img/docs/becas_pmid_dialog.png
  168. BIN src/main/resources/webapp/assets/img/docs/becas_widget_sample.png
  169. BIN src/main/resources/webapp/assets/img/edit.png
  170. BIN src/main/resources/webapp/assets/img/exporting_results.png
  171. BIN src/main/resources/webapp/assets/img/favicon.ico
  172. BIN src/main/resources/webapp/assets/img/glyphicons-halflings-white.png
  173. BIN src/main/resources/webapp/assets/img/glyphicons-halflings.png
  174. BIN src/main/resources/webapp/assets/img/loader.gif
  175. BIN src/main/resources/webapp/assets/img/loader.mini.gif
  176. BIN src/main/resources/webapp/assets/img/neji-logo.medium.png
  177. BIN src/main/resources/webapp/assets/img/neji-logo.png
  178. BIN src/main/resources/webapp/assets/img/og-app-1.png
  179. BIN src/main/resources/webapp/assets/img/og-app-2.png
  180. BIN src/main/resources/webapp/assets/img/sponsors/compete.png
  181. BIN src/main/resources/webapp/assets/img/sponsors/ieeta.png
  182. BIN src/main/resources/webapp/assets/img/sponsors/qren.png
  183. BIN src/main/resources/webapp/assets/img/sponsors/ua-bioinformatics.png
  184. BIN src/main/resources/webapp/assets/img/sponsors/ua.png
  185. BIN src/main/resources/webapp/assets/img/sponsors/ue.png
  186. BIN src/main/resources/webapp/assets/img/the_input_interface.png
  187. BIN src/main/resources/webapp/assets/img/the_output_interface.png
  188. +1 −0 src/main/resources/webapp/assets/js/becas-widget.js
  189. +2,041 −0 src/main/resources/webapp/assets/js/becas.js
  190. +7 −0 src/main/resources/webapp/assets/js/bootstrap-confirmation.min.js
  191. +86 −0 src/main/resources/webapp/assets/js/common.js
  192. +23 −0 src/main/resources/webapp/assets/js/edit.js
  193. +4,131 −0 src/main/resources/webapp/assets/js/handlebars-v3.0.3.js
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  225. +846 −0 src/main/resources/webapp/assets/js/services.js
  226. BIN src/main/resources/webapp/assets/src/becas_annotated_abstract.psd
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  286. +303 −0 src/main/resources/webapp/index.html
  287. +62 −0 src/main/resources/webapp/logon.html
  288. +54 −0 src/main/resources/webapp/logonError.html
  289. +24 −0 src/main/resources/webapp/run
BIN +2.2 KB conf/keystore.jks
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@@ -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
BIN +964 Bytes conf/truststore.jks
Binary file not shown.
@@ -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
@@ -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 $cp"
CLASS=pt.ua.tm.neji.cli.Main
@@ -1,5 +1,5 @@
#!/bin/bash
cp=target/neji-2.0-jar-with-dependencies.jar:$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 $cp"
CLASS=pt.ua.tm.neji.train.cli.TrainMain
@@ -0,0 +1,7 @@
#!/bin/bash
cp=target/neji-2.1.0-SNAPSHOT-server.jar:$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 $*
120 pom.xml
@@ -112,6 +112,9 @@
<resource>
<directory>src/main/resources</directory>
</resource>
<resource>
<directory>src/main/resources/webapp</directory>
</resource>
</resources>
<plugins>
<plugin>
@@ -235,6 +238,44 @@
<forkMode>always</forkMode>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.2</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<finalName>${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>
@@ -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;
}
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