interproscan-web
Used in:
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency>
<groupId>uk.ac.ebi.interpro.scan</groupId>
<artifactId>interproscan-web</artifactId>
<version>5.36-75.0</version>
</dependency><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/maven-v4_0_0.xsd">
<parent>
<artifactId>interproscan</artifactId>
<groupId>uk.ac.ebi.interpro.scan</groupId>
<version>5.36-75.0</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>interproscan-web</artifactId>
<!--Default packaging is JAR, but the WAR file is build at the same time by simply running the MAVEN install goal-->
<packaging>jar</packaging>
<name>InterProScan Web</name>
<version>5.36-75.0</version>
<description>InterProScan Web</description>
<url>http://www.ebi.ac.uk/interpro/</url>
<properties>
<jetty.version>9.3.6.v20151106</jetty.version>
</properties>
<dependencies>
<!-- i5 model -->
<dependency>
<groupId>uk.ac.ebi.interpro.scan</groupId>
<artifactId>interproscan-model</artifactId>
<version>5.36-75.0</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.interpro.scan</groupId>
<artifactId>interproscan-business</artifactId>
<version>5.36-75.0</version>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${spring.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
<version>${spring.version}</version>
</dependency>
<!-- Spring Security -->
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>${spring.security.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-config</artifactId>
<version>${spring.security.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-web</artifactId>
<version>${spring.security.version}</version>
</dependency>
<!-- Servlet -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>${javax.servlet.api.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.servlet.jsp</groupId>
<artifactId>jsp-api</artifactId>
<version>2.1</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<!-- HttpClient -->
<dependency>
<groupId>commons-httpclient</groupId>
<artifactId>commons-httpclient</artifactId>
<version>3.1</version>
</dependency>
<!--Packages to use embedded Jetty server-->
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<version>${jetty.version}</version>
</dependency>
<!---->
<dependency>
<groupId>net.sourceforge.htmlunit</groupId>
<artifactId>htmlunit</artifactId>
<version>2.19</version>
</dependency>
<dependency>
<groupId>net.sf.ehcache</groupId>
<artifactId>ehcache-core</artifactId>
<version>2.6.11</version>
</dependency>
<dependency>
<groupId>org.freemarker</groupId>
<artifactId>freemarker</artifactId>
<version>2.3.18</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<excludes>
<exclude>interpro-protein-page.xml</exclude>
</excludes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<targetPath>${project.build.directory}/</targetPath>
<includes>
<include>interpro-protein-page.xml</include>
</includes>
</resource>
<resource>
<directory>src/main/webapp/</directory>
<filtering>true</filtering>
<excludes>
<exclude>WEB-INF/tags/**</exclude>
<exclude>WEB-INF/jsp/**</exclude>
<exclude>WEB-INF/web.xml</exclude>
</excludes>
</resource>
<resource>
<directory>src/main/webapp/</directory>
<filtering>true</filtering>
<targetPath>${project.build.directory}/classes/</targetPath>
<excludes>
<exclude>WEB-INF/tags/**</exclude>
<exclude>WEB-INF/jsp/**</exclude>
<exclude>WEB-INF/web.xml</exclude>
</excludes>
</resource>
<!--Copies SVG templates and dependencies into the target directory-->
<!--These files are then part of the I5 assembly process (see jms-implementation module: assembly.xml)-->
<resource>
<directory>src/test/resources/uk/ac/ebi/interpro/scan/web/freeMarker/svg</directory>
<filtering>false</filtering>
<targetPath>${project.build.directory}/classes/resources/freeMarker/svg</targetPath>
<excludes>
<exclude>SVGFreeMarkerTest-context.xml</exclude>
<exclude>data/**</exclude>
</excludes>
</resource>
</resources>
<!--Plugin allows to create the WAR file at the same time as the JAR file by running simply mvn clean install goal-->
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>${mvn.war.version}</version>
<executions>
<execution>
<id>make-a-war</id>
<phase>compile</phase>
<goals>
<goal>war</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<configuration>
<argLine>-Xmx256m</argLine>
</configuration>
</plugin>
</plugins>
</build>
<!--
NOTE:
All of the following profiles expect a file webapp/WEB-INF/spring/users.properties.
Copy the file example-users.properties and uncomment the final line to get this working (in test).
-->
<profiles>
<profile>
<id>jetty</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<!-- Use Maven goal "jetty:run-war" for filtering to take place -->
<properties>
<default.log.level>debug</default.log.level>
<third.party.log.level>info</third.party.log.level>
<!-- In the Jetty profile just use a relative path to the copies of the entry colours properties file
and entry hierarchy CSV file in version control. NOTE: This data may not have been generated recently,
or from the protein database you are currently using (IPPRO etc) therefore will introduce
inconsistencies! But that's OK, Jetty profile is used for development, not production! -->
<match.data.webservice.url>http://wwwint.ebi.ac.uk/interpro-rest/match/
</match.data.webservice.url>
<structural.match.data.webservice.url>http://wwwint.ebi.ac.uk/interpro-rest/structure/
</structural.match.data.webservice.url>
<!--Model creation files-->
<!--Entry hierarchy data-->
<entryHierarchyDataResourceId>entryHierarchyDataClassPathResourceId</entryHierarchyDataResourceId>
<entry.hierarchy.file.loc>${basedir}/src/main/resources/entry_hierarchy.csv</entry.hierarchy.file.loc>
<!--Entry GO data-->
<entryToGoDataResourceId>entryToGoDataClassPathResourceId</entryToGoDataResourceId>
<entry.go.file.loc>${basedir}/src/main/resources/entry_to_go.psv</entry.go.file.loc>
<!--Entry colours-->
<entry.colours.file.loc>classpath:entry_colours.properties</entry.colours.file.loc>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>${mvn.war.version}</version>
<configuration>
<warName>interpro-protein-page</warName>
<webResources>
<resource>
<directory>${basedir}/src/main/webapp/WEB-INF/spring</directory>
<filtering>true</filtering>
<targetPath>WEB-INF/spring</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
<!-- http://wiki.eclipse.org/Jetty/Feature/Jetty_Maven_Plugin -->
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<!--Set version explicitly if get errors on Windows:-->
<version>${jetty.version}</version>
<configuration>
<war>${project.build.directory}/interpro-protein-page.war</war>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>production</id>
<!-- Profile for deploying on production tomcats:
1) Update the full InterProScan 5 project to pick up all commits and build:
cd /nfs/seqdb/production/interpro/web/interproscan-read-only/core; svn up; mvn clean install
2) Now package the web application:
cd /nfs/seqdb/production/interpro/web/interproscan-read-only/core/web; mvn -Pproduction clean package
3) Deploy with Tomcat manager application
-->
<properties>
<default.log.level>warn</default.log.level>
<third.party.log.level>warn</third.party.log.level>
<deployment.folder>${project.basedir}</deployment.folder>
<!-- In this production profile use a full path to the copies of the entry colours properties file
and entry hierarchy CSV file on the file system. The files are derived data, not under version control.
NOTE: These should have been generated at the time of the last release, therefore will be consistent
with the current public database -->
<match.data.webservice.url>http://wwwint.ebi.ac.uk/interpro-rest/match/
</match.data.webservice.url>
<structural.match.data.webservice.url>http://wwwint.ebi.ac.uk/interpro-rest/structure/
</structural.match.data.webservice.url>
<resourceWebPath>/interpro-protein-page/resources</resourceWebPath>
<!--Model creation files-->
<!--Entry hierarchy data-->
<entryHierarchyDataResourceId>entryHierarchyDataURLResourceId</entryHierarchyDataResourceId>
<entry.hierarchy.file.loc>/ebi/production/interpro/production/i5webdata/live/entry_hierarchy.csv
</entry.hierarchy.file.loc>
<!--Entry GO data-->
<entryToGoDataResourceId>entryToGoDataURLResourceId</entryToGoDataResourceId>
<entry.go.file.loc>/ebi/production/interpro/production/i5webdata/live/entry_to_go.psv
</entry.go.file.loc>
<!--Entry colours-->
<entry.colours.file.loc>
file:/ebi/production/interpro/production/i5webdata/live/entry_colours.properties
</entry.colours.file.loc>
<pathToImages>http://www.ebi.ac.uk/interpro</pathToImages>
</properties>
<build>
<finalName>interpro-protein-page</finalName>
<plugins>
<plugin>
<groupId>com.keyboardsamurais.maven</groupId>
<artifactId>maven-timestamp-plugin</artifactId>
<version>1.0</version>
<configuration>
<propertyName>timestamp</propertyName>
<!-- timestampPattern using SimpleDateFormat format. -->
<timestampPattern>yyyyMMdd-HHmm</timestampPattern>
</configuration>
<executions>
<execution>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>${mvn.war.version}</version>
<configuration>
<warName>interpro-protein-page-${timestamp}</warName>
<webResources>
<resource>
<directory>${basedir}/src/main/webapp/WEB-INF/spring</directory>
<filtering>true</filtering>
<targetPath>WEB-INF/spring</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>localhost-tomcat</id>
<!--
1. Profile to deploy to Tomcat running on the current local desktop machine!
(Once-only)
Add the following XML to your ~/.m2/settings.xml file, to provide the server credentials:
<settings>
<servers>
<server>
<id>localhost</id>
<username>tomcat</username>
<password>THE REAL PASSWORD</password>
</server>
</servers>
</settings>
2) Commit your (tested) changes to subversion, wherever you may be building them.
2) OPTIONALLY, If you have changed any code that the web module is dependent upon (e.g. in model):
cd ~/Projects/i5/interproscan/core; mvn clean install
3) Build and deploy the web application:
cd ~/Projects/i5/interproscan/core/web; mvn -Plocalhost-tomcat clean tomcat:redeploy
-->
<properties>
<default.log.level>warn</default.log.level>
<third.party.log.level>warn</third.party.log.level>
<deployment.folder>${basedir}/target</deployment.folder>
<!-- In the localhost profile just use a relative path to the copies of the entry colours properties file
and entry hierarchy CSV file in version control. NOTE: This data may not have been generated recently,
or from the protein database you are currently using (IPPRO etc) therefore will introduce
inconsistencies! But that's OK, this profile is used for development/testing, not production! -->
<match.data.webservice.url>http://wwwint.ebi.ac.uk/interpro-rest/match/
</match.data.webservice.url>
<structural.match.data.webservice.url>http://wwwint.ebi.ac.uk/interpro-rest/structure/
</structural.match.data.webservice.url>
<resourceWebPath>/interpro-protein-page/resources</resourceWebPath>
<!--Model creation files-->
<!--Entry hierarchy data-->
<entryHierarchyDataResourceId>entryHierarchyDataURLResourceId</entryHierarchyDataResourceId>
<entry.hierarchy.file.loc>${basedir}/src/main/resources/entry_hierarchy.csv</entry.hierarchy.file.loc>
<!--Entry GO data-->
<entryToGoDataResourceId>entryToGoDataURLResourceId</entryToGoDataResourceId>
<entry.go.file.loc>${basedir}/src/main/resources/entry_to_go.psv</entry.go.file.loc>
<!--Entry colours-->
<entry.colours.file.loc>file:${basedir}/src/main/resources/entry_colours.properties
</entry.colours.file.loc>
<pathToImages>/interpro-protein-page/resources</pathToImages>
</properties>
<build>
<finalName>interpro-protein-page</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>${mvn.war.version}</version>
<configuration>
<warName>interpro-protein-page</warName>
<webResources>
<resource>
<directory>${basedir}/src/main/webapp/WEB-INF/spring</directory>
<filtering>true</filtering>
<targetPath>WEB-INF/spring</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
<!-- Plugin to automatically deploy the war file to Tomcat running on localhost. -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>tomcat-maven-plugin</artifactId>
<configuration>
<url>http://localhost:8080/manager</url>
<server>localhost</server>
<!-- See note above for server credentials -->
<mode>both</mode>
<contextFile>${project.build.directory}/interpro-protein-page.xml
</contextFile>
<warFile>${project.build.directory}/interpro-protein-page.war
</warFile>
<path>/interpro-protein-page</path>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>i5-web</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<resourceWebPath>/resources</resourceWebPath>
<pathToImages>/interpro</pathToImages>
</properties>
</profile>
</profiles>
</project>
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