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VFB 1.5 minimum release
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@Robbie1977
Robbie1977 committed Feb 1, 2016
2 parents 57f38b6 + 82629fc commit 562e2cd
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Showing 201 changed files with 28,816 additions and 2,884 deletions.
2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -8,5 +8,5 @@ owlIndRev
google*.html
*.wlz
jdoc/

robots.txt
resources/catalog-v001.xml
Binary file added WEB-INF/lib/Cachefilter2.jar
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100 changes: 82 additions & 18 deletions WEB-INF/web.xml
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@@ -1,13 +1,13 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor
license agreements. See the NOTICE file distributed with this work for additional
information regarding copyright ownership. The ASF licenses this file to
You under the Apache License, Version 2.0 (the "License"); you may not use
this file except in compliance with the License. You may obtain a copy of
the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to in writing, software distributed under the
License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
OF ANY KIND, either express or implied. See the License for the specific
<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor
license agreements. See the NOTICE file distributed with this work for additional
information regarding copyright ownership. The ASF licenses this file to
You under the Apache License, Version 2.0 (the "License"); you may not use
this file except in compliance with the License. You may obtain a copy of
the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to in writing, software distributed under the
License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
OF ANY KIND, either express or implied. See the License for the specific
language governing permissions and limitations under the License. -->

<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
Expand All @@ -18,7 +18,7 @@
VirtualFlyBrain Server -WEBAPP_NAME-
</description>
<display-name>VirtualFlyBrain Server -WEBAPP_NAME-</display-name>

<welcome-file-list>
<welcome-file></welcome-file>
<welcome-file>index.html</welcome-file>
Expand All @@ -41,7 +41,7 @@
<url-pattern>/sitemap2.xml</url-pattern>
</jsp-property-group>
</jsp-config>

<servlet>
<servlet-name>directData</servlet-name>
<servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
Expand Down Expand Up @@ -72,32 +72,32 @@
<servlet-name>directData</servlet-name>
<url-pattern>/jdoc/*</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>directData</servlet-name>
<url-pattern>/logs/*</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>directData</servlet-name>
<url-pattern>/owl/*</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>directData</servlet-name>
<url-pattern>*.log</url-pattern>
</servlet-mapping>
</servlet-mapping>

<servlet-mapping>
<servlet-name>directData</servlet-name>
<url-pattern>*.png</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>directData</servlet-name>
<url-pattern>*.wlz</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>directData</servlet-name>
<url-pattern>*.gz</url-pattern>
Expand All @@ -108,6 +108,16 @@
<url-pattern>*.html</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>springmvc</servlet-name>
<url-pattern>*.json</url-pattern>
</servlet-mapping>

<servlet-mapping>
<servlet-name>springmvc</servlet-name>
<url-pattern>*.xml</url-pattern>
</servlet-mapping>

<listener>
<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
</listener>
Expand All @@ -125,6 +135,60 @@
</param-value>
</context-param>

<filter>
<filter-name>imagesCache</filter-name>
<filter-class>com.samaxes.filter.CacheFilter</filter-class>
<init-param>
<param-name>static</param-name>
<param-value>true</param-value>
</init-param>
<init-param>
<param-name>expirationTime</param-name>
<param-value>2592000</param-value>
</init-param>
</filter>
<filter>
<filter-name>cssCache</filter-name>
<filter-class>com.samaxes.filter.CacheFilter</filter-class>
<init-param>
<param-name>expirationTime</param-name>
<param-value>604800</param-value>
</init-param>
</filter>
<filter>
<filter-name>jsCache</filter-name>
<filter-class>com.samaxes.filter.CacheFilter</filter-class>
<init-param>
<param-name>private</param-name>
<param-value>true</param-value>
</init-param>
<init-param>
<param-name>expirationTime</param-name>
<param-value>2592000</param-value>
</init-param>
</filter>

<filter-mapping>
<filter-name>cssCache</filter-name>
<url-pattern>*.css</url-pattern>
<url-pattern>*.htm</url-pattern>
</filter-mapping>

<filter-mapping>
<filter-name>jsCache</filter-name>
<url-pattern>*.js</url-pattern>
<url-pattern>*.jso</url-pattern>
<url-pattern>*.json</url-pattern>
</filter-mapping>

<filter-mapping>
<filter-name>imagesCache</filter-name>
<url-pattern>*.png</url-pattern>
<url-pattern>*.gif</url-pattern>
<url-pattern>*.jpg</url-pattern>
<url-pattern>*.ico</url-pattern>
</filter-mapping>

<filter>
<filter-name>charsetFilter</filter-name>
<filter-class>uk.ac.ed.vfb.servlets.CharsetEncodingFilter</filter-class>
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18 changes: 5 additions & 13 deletions build.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -80,13 +80,10 @@
<pathelement location="./src/uk/ac/ed/vfb/dao/db/pojo/GeneQueryResultSetExtractor.java"/>
<pathelement location="./src/uk/ac/ed/vfb/dao/db/pojo/PubQueryResultSetExtractor.java"/>
<pathelement location="./src/uk/ac/ed/vfb/dao/db/pojo/ThirdPartyQueryResultSetExtractor.java"/>
<pathelement location="./src/uk/ac/ed/vfb/dao/db/pojo/UserBeanQueryResultSetExtractor.java"/>
<pathelement location="./src/uk/ac/ed/vfb/dao/security/UserManagerDAO.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/OntBean.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/OntBeanIndividual.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/PubBean.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/ThirdPartyBean.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/security/UserBean.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/tree/OntNode.java"/>
<pathelement location="./src/uk/ac/ed/vfb/model/tree/OntTreeManager.java"/>
<pathelement location="./src/uk/ac/ed/vfb/ont_query/model/Argument.java"/>
Expand All @@ -100,7 +97,6 @@
<pathelement location="./src/uk/ac/ed/vfb/service/OntBeanManager.java"/>
<pathelement location="./src/uk/ac/ed/vfb/service/PubBeanManager.java"/>
<pathelement location="./src/uk/ac/ed/vfb/service/ThirdPartyBeanManager.java"/>
<pathelement location="./src/uk/ac/ed/vfb/service/UserManager.java"/>
<pathelement location="./src/uk/ac/ed/vfb/servlets/CharsetEncodingFilter.java"/>
<pathelement location="./src/uk/ac/ed/vfb/servlets/ServletUtil.java"/>
<pathelement location="./src/uk/ac/ed/vfb/tags/TrimToWhiteSpace.java"/>
Expand All @@ -117,16 +113,13 @@
<pathelement location="./src/uk/ac/ed/vfb/web/JsonController.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/OntBeanController.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/OntBeanListController.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/UserController.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/UserValidator.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/WebQueryUtils.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/csvviewer/CsvGeneView.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/csvviewer/CsvOntView.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/csvviewer/CsvQueryView.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/csvviewer/CsvViewer.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/exception/SessionExpiredException.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/exception/StackExistsException.java"/>
<pathelement location="./src/uk/ac/ed/vfb/web/exception/UserPermissionsException.java"/>
<pathelement location="./src/uk/ac/ebi/brain/core/Brain.java"/>
<pathelement location="./src/uk/ac/ebi/brain/error/BadNameException.java"/>
<pathelement location="./src/uk/ac/ebi/brain/error/BadPrefixException.java"/>
Expand Down Expand Up @@ -161,13 +154,13 @@
</fileset>
</copy>
</target>

<target name="clean">
<delete dir="build"/>
</target>
<target depends="jdoc-clean, init, compile, copy, jdoc, clean" name="build"/>

<target depends="init, compile, copy, clean" name="build"/>

<target depends="init" name="compile">
<echo message="${ant.project.name}: ${ant.file}"/>
<javac debug="true" debuglevel="${debuglevel}" destdir="build" includeantruntime="false" source="${source}" target="${target}">
Expand All @@ -181,7 +174,7 @@
</copy>
</target>
<target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/>

<!-- Generate javadocs for current project into doc -->
<target name="jdoc-clean">
<delete dir="jdoc"/>
Expand All @@ -193,4 +186,3 @@
</target>

</project>

10 changes: 10 additions & 0 deletions css/bootstrap-colorpicker.min.css
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