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Merge pull request #1114 from MPDL-Innovations/develop
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Release 3.0
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bastiensaquet committed Jul 16, 2015
2 parents 8793316 + 751e884 commit 8ac989a
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3 changes: 3 additions & 0 deletions README.md
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<p>For a full description of the imeji software and detailed information of the functionalities please visit the <a href="http://imeji.org/" target="_blank" title="imeji software description">imeji software</a> page.</p>
<p>imeji is developed by the <a href="http://imeji.org/community/" target="_blank" title="imeji community">imeji community</a> under the <a href="http://hub.opensolaris.org/bin/download/Main/licensing/cddllicense.txt" target="_blank">CDDL-License</a>.</p>

<h2>REST API v1</h2>
<p>See <a href="https://github.com/imeji-community/imeji/wiki/A_Home-imeji-API-V1">REST API v1 (imeji Community wiki)</a><p>

<h2>The imeji demo version</h2>
<p>Try the <a href="http://demo.imeji.org/" title="Go to the demo page" target="_blank">demo version</a></p>

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120 changes: 59 additions & 61 deletions pom.xml
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@@ -1,11 +1,10 @@
<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">
<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">
<modelVersion>4.0.0</modelVersion>
<artifactId>imeji</artifactId>
<groupId>org.imeji</groupId>
<name>imeji</name>
<packaging>war</packaging>
<version>2.0.0.1-SNAPSHOT</version>
<version>3.0.0.1-SNAPSHOT</version>
<url>http://imeji.org</url>
<description>The imeji open source software offers a dedicated metadata management by supporting a non- restrictive metadata schema definition, as simple as liked or as complex as needed.</description>
<licenses>
Expand All @@ -21,8 +20,8 @@
</organization>
<scm>
<url>https://github.com/imeji-community/imeji</url>
<connection>scm:git:git://github.com/imeji-community/imeji.git</connection>
<developerConnection>scm:git:git@github.com:imeji-community/imeji.git</developerConnection>
<connection>scm:git:git@github.com:MPDL-Innovations/imeji.git</connection>
<developerConnection>scm:git:git@github.com:MPDL-Innovations/imeji.git</developerConnection>
<tag>develop</tag>
</scm>
<issueManagement>
Expand Down Expand Up @@ -96,17 +95,17 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<!-- Setting this property so that generated project uses correct version
<!-- Setting this property so that generated project uses correct version
of richfaces. -->
<org.richfaces.bom.version>4.3.7.Final</org.richfaces.bom.version>
<!-- Used by Tomcat to trip version Nr when deploy WAR package, e.g., imeji_1.0_screenshot->imeji -->
<project.warName>imeji</project.warName>
<!-- <sonar.host.url>http://localhost:9000</sonar.host.url>-->
<!-- <sonar.exclusions></sonar.exclusions>-->
<!-- <sonar.host.url>http://localhost:9000</sonar.host.url> -->
<!-- <sonar.exclusions></sonar.exclusions> -->
</properties>
<repositories>
<!-- <repository> <id>central</id> <url>http://central</url> <releases>
<enabled>true</enabled> </releases> <snapshots> <enabled>true</enabled> </snapshots>
<!-- <repository> <id>central</id> <url>http://central</url> <releases>
<enabled>true</enabled> </releases> <snapshots> <enabled>true</enabled> </snapshots>
</repository> -->
<repository>
<id>prime-repo</id>
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<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
<configuration>
<!-- Exclude imeji.properties from war file, because it should be copied
<!-- Exclude imeji.properties from war file, because it should be copied
to application server conf directory -->
<packagingExcludes>**/imeji.properties</packagingExcludes>
<warName>${project.warName}</warName>
Expand Down Expand Up @@ -248,19 +247,14 @@
<phase>process-resources</phase>
<configuration>
<tasks>
<!-- copying the jaxb files into the build directories, because of
<!-- copying the jaxb files into the build directories, because of
the xml schema handling issue (marshalling and unmarshalling) -->
<!-- those files will not be copied into the build directories, Maven
<!-- those files will not be copied into the build directories, Maven
does not copy them automatically!!! -->
<copy file="src/main/java/de/mpg/j2j/misc/jaxb.index"
tofile="${project.build.directory}/classes/de/mpg/j2j/misc/jaxb.index" />
<copy file="src/main/java/de/mpg/imeji/logic/vo/jaxb.index"
tofile="${project.build.directory}/classes/de/mpg/imeji/logic/vo/jaxb.index" />
<copy file="src/main/java/de/mpg/imeji/logic/ingest/vo/jaxb.index"
tofile="${project.build.directory}/classes/de/mpg/imeji/logic/ingest/vo/jaxb.index" />
<copy
file="src/main/java/de/mpg/imeji/logic/vo/predefinedMetadata/jaxb.index"
tofile="${project.build.directory}/classes/de/mpg/imeji/logic/vo/predefinedMetadata/jaxb.index" />
<copy file="src/main/java/de/mpg/j2j/misc/jaxb.index" tofile="${project.build.directory}/classes/de/mpg/j2j/misc/jaxb.index" />
<copy file="src/main/java/de/mpg/imeji/logic/vo/jaxb.index" tofile="${project.build.directory}/classes/de/mpg/imeji/logic/vo/jaxb.index" />
<copy file="src/main/java/de/mpg/imeji/logic/ingest/vo/jaxb.index" tofile="${project.build.directory}/classes/de/mpg/imeji/logic/ingest/vo/jaxb.index" />
<copy file="src/main/java/de/mpg/imeji/logic/vo/predefinedMetadata/jaxb.index" tofile="${project.build.directory}/classes/de/mpg/imeji/logic/vo/predefinedMetadata/jaxb.index" />
</tasks>
</configuration>
<goals>
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</plugins>
<pluginManagement>
<plugins>
<!--This plugin's configuration is used to store Eclipse m2e settings
<!--This plugin's configuration is used to store Eclipse m2e settings
only. It has no influence on the Maven build itself. -->
<plugin>
<groupId>org.eclipse.m2e</groupId>
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</plugins>
</pluginManagement>
</build>
<!-- <dependencyManagement> <dependencies> <dependency> <groupId>org.richfaces</groupId>
<artifactId>richfaces-bom</artifactId> <version>${org.richfaces.bom.version}</version>
<!-- <dependencyManagement> <dependencies> <dependency> <groupId>org.richfaces</groupId>
<artifactId>richfaces-bom</artifactId> <version>${org.richfaces.bom.version}</version>
<scope>import</scope> <type>pom</type> </dependency> </dependencies> </dependencyManagement> -->
<dependencies>
<dependency>
Expand All @@ -339,11 +333,11 @@
<artifactId>commons-lang3</artifactId>
<version>3.3.2</version>
</dependency>
<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-tdb</artifactId>
<version>0.9.4-SNAPSHOT</version> </dependency> <dependency> <groupId>org.apache.jena</groupId>
<artifactId>apache-jena</artifactId> <version>2.10.1</version> <type>pom</type>
<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-tdb</artifactId>
<version>0.9.4-SNAPSHOT</version> </dependency> <dependency> <groupId>org.apache.jena</groupId>
<artifactId>apache-jena</artifactId> <version>2.10.1</version> <type>pom</type>
</dependency> -->
<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-tdb</artifactId>
<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-tdb</artifactId>
<version>0.10.1</version> </dependency> -->
<dependency>
<groupId>org.apache.jena</groupId>
Expand Down Expand Up @@ -386,6 +380,11 @@
<version>3.1</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
Expand All @@ -397,14 +396,14 @@
<version>1.3</version>
</dependency>
<!-- START JSF 2 -->
<!-- <dependency> <groupId>javax.faces</groupId> <artifactId>javax.faces-api</artifactId>
<scope>provided</scope> </dependency> <dependency> <groupId>org.glassfish</groupId>
<artifactId>javax.faces</artifactId> <scope>compile</scope> </dependency>
<dependency> <groupId>javax.servlet</groupId> <artifactId>javax.servlet-api</artifactId>
<scope>provided</scope> </dependency> <dependency> <groupId>javax.servlet.jsp</groupId>
<artifactId>jsp-api</artifactId> <scope>provided</scope> </dependency> <dependency>
<groupId>javax.el</groupId> <artifactId>el-api</artifactId> <scope>provided</scope>
</dependency> <dependency> <groupId>javax.servlet.jsp.jstl</groupId> <artifactId>jstl-api</artifactId>
<!-- <dependency> <groupId>javax.faces</groupId> <artifactId>javax.faces-api</artifactId>
<scope>provided</scope> </dependency> <dependency> <groupId>org.glassfish</groupId>
<artifactId>javax.faces</artifactId> <scope>compile</scope> </dependency>
<dependency> <groupId>javax.servlet</groupId> <artifactId>javax.servlet-api</artifactId>
<scope>provided</scope> </dependency> <dependency> <groupId>javax.servlet.jsp</groupId>
<artifactId>jsp-api</artifactId> <scope>provided</scope> </dependency> <dependency>
<groupId>javax.el</groupId> <artifactId>el-api</artifactId> <scope>provided</scope>
</dependency> <dependency> <groupId>javax.servlet.jsp.jstl</groupId> <artifactId>jstl-api</artifactId>
</dependency> -->
<!-- test -->
<dependency>
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<artifactId>jai-codec</artifactId>
<version>1.1.3</version>
</dependency>
<!-- User standalone jxb, instead of jdk embedded version, because of problem
<!-- User standalone jxb, instead of jdk embedded version, because of problem
with prefix mapping -->
<dependency>
<groupId>com.sun.xml.bind</groupId>
Expand All @@ -455,13 +454,13 @@
<version>1.2.0</version>
</dependency>
<!-- Start: bio formats dependencies -->
<!-- <dependency> <groupId>openmicroscopy</groupId> <artifactId>bio-formats</artifactId>
<version>4.4.8</version> </dependency> <dependency> <groupId>openmicroscopy</groupId>
<artifactId>loci-common</artifactId> <version>4.4.8</version> </dependency>
<dependency> <groupId>openmicroscopy</groupId> <artifactId>ome-xml</artifactId>
<version>4.4.8</version> </dependency> <dependency> <groupId>openmicroscopy</groupId>
<!-- <dependency> <groupId>openmicroscopy</groupId> <artifactId>bio-formats</artifactId>
<version>4.4.8</version> </dependency> <dependency> <groupId>openmicroscopy</groupId>
<artifactId>loci-common</artifactId> <version>4.4.8</version> </dependency>
<dependency> <groupId>openmicroscopy</groupId> <artifactId>ome-xml</artifactId>
<version>4.4.8</version> </dependency> <dependency> <groupId>openmicroscopy</groupId>
<artifactId>scifio</artifactId> <version>4.4.8</version> </dependency> -->
<!-- <dependency> <groupId>openmicroscopy</groupId> <artifactId>loci-tools</artifactId>
<!-- <dependency> <groupId>openmicroscopy</groupId> <artifactId>loci-tools</artifactId>
<version>4.4.8</version> <type>pom</type> </dependency> -->
<!-- End: bio formats dependencies -->
<!-- pdf handling -->
Expand Down Expand Up @@ -525,22 +524,24 @@
<version>1.9</version>
</dependency>
<!-- END: Digilib integration -->
<!-- <dependency> <groupId>org.apache.tika</groupId> <artifactId>tika-server</artifactId>
<!-- <dependency> <groupId>org.apache.tika</groupId> <artifactId>tika-server</artifactId>
<version>1.5</version> </dependency> -->
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-parsers</artifactId>
<version>1.5</version>
<version>1.8</version>
</dependency>
<dependency>
<groupId>com.drewnoakes</groupId>
<artifactId>metadata-extractor</artifactId>
<version>2.6.2</version>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
<version>1.4.01</version>
</dependency>
<!-- <dependency> <groupId>com.drewnoakes</groupId> <artifactId>metadata-extractor</artifactId>
<version>2.8.0</version> </dependency> -->


<!-- REST -->
<dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
Expand Down Expand Up @@ -605,12 +606,12 @@
<version>2.13</version>
</dependency>

<!-- <dependency> <groupId>com.sun.jersey</groupId> <artifactId>jersey-json</artifactId>
<!-- <dependency> <groupId>com.sun.jersey</groupId> <artifactId>jersey-json</artifactId>
<version>1.8</version> </dependency> -->

<!-- <dependency> <groupId>net.java.dev.jai-imageio</groupId> <artifactId>jai-imageio-core-standalone</artifactId>
<version>1.2-pre-dr-b04-2011-07-04</version> </dependency> <dependency> <groupId>org.devlib.schmidt</groupId>
<artifactId>imageinfo</artifactId> <version>1.9</version> <type>jar</type>
<!-- <dependency> <groupId>net.java.dev.jai-imageio</groupId> <artifactId>jai-imageio-core-standalone</artifactId>
<version>1.2-pre-dr-b04-2011-07-04</version> </dependency> <dependency> <groupId>org.devlib.schmidt</groupId>
<artifactId>imageinfo</artifactId> <version>1.9</version> <type>jar</type>
<scope>compile</scope> </dependency> -->
<dependency>
<groupId>de.mpg.mpdl.service.connector</groupId>
Expand All @@ -632,7 +633,7 @@
<profile>
<id>env-development</id>
<properties>
<!-- TO avoid warning File encoding has not been set, using platform
<!-- TO avoid warning File encoding has not been set, using platform
encoding Cp1252, i.e. build is platform dependent! -->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<!-- the jdk version to use -->
Expand Down Expand Up @@ -684,12 +685,9 @@
<phase>install</phase>
<configuration>
<tasks>
<delete quiet="true"
file="${tomcat.webapps}/${project.warName}.war" />
<delete quiet="true" file="${tomcat.webapps}/${project.warName}.war" />
<delete quiet="true" dir="${tomcat.webapps}/${project.warName}" />
<copy overwrite="true"
file="${project.build.directory}/${project.warName}.war"
tofile="${tomcat.webapps}/${project.warName}.war" />
<copy overwrite="true" file="${project.build.directory}/${project.warName}.war" tofile="${tomcat.webapps}/${project.warName}.war" />
</tasks>
</configuration>
<goals>
Expand Down Expand Up @@ -750,7 +748,7 @@
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<!-- TO avoid warning File encoding has not been set, using platform
<!-- TO avoid warning File encoding has not been set, using platform
encoding Cp1252, i.e. build is platform dependent! -->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<!-- the jdk version to use -->
Expand Down
25 changes: 11 additions & 14 deletions src/main/java/de/mpg/imeji/exceptions/AlreadyExistsException.java
Original file line number Diff line number Diff line change
@@ -1,19 +1,16 @@
package de.mpg.imeji.exceptions;

import com.hp.hpl.jena.Jena;

public class AlreadyExistsException extends ImejiException
{
private static final long serialVersionUID = 4123172628332785494L;
public class AlreadyExistsException extends ImejiException {
private static final long serialVersionUID = 4123172628332785494L;

/**
* Constructor for a new {@link AlreadyExistsException}
*
* @param message
*/
public AlreadyExistsException(String message) {
super(message);
}

/**
* Constructor for a new {@link AlreadyExistsException}
*
* @param message
*/
public AlreadyExistsException(String message)
{
super(message);
}

}
62 changes: 29 additions & 33 deletions src/main/java/de/mpg/imeji/exceptions/AuthenticationError.java
Original file line number Diff line number Diff line change
@@ -1,43 +1,39 @@
/*
*
*
* CDDL HEADER START
*
* The contents of this file are subject to the terms of the
* Common Development and Distribution License, Version 1.0 only
* (the "License"). You may not use this file except in compliance
* with the License.
*
* You can obtain a copy of the license at license/ESCIDOC.LICENSE
* or http://www.escidoc.de/license.
* See the License for the specific language governing permissions
* and limitations under the License.
*
* When distributing Covered Code, include this CDDL HEADER in each
* file and include the License file at license/ESCIDOC.LICENSE.
* If applicable, add the following below this CDDL HEADER, with the
* fields enclosed by brackets "[]" replaced with your own identifying
* information: Portions Copyright [yyyy] [name of copyright owner]
*
*
* The contents of this file are subject to the terms of the Common Development and Distribution
* License, Version 1.0 only (the "License"). You may not use this file except in compliance with
* the License.
*
* You can obtain a copy of the license at license/ESCIDOC.LICENSE or http://www.escidoc.de/license.
* See the License for the specific language governing permissions and limitations under the
* License.
*
* When distributing Covered Code, include this CDDL HEADER in each file and include the License
* file at license/ESCIDOC.LICENSE. If applicable, add the following below this CDDL HEADER, with
* the fields enclosed by brackets "[]" replaced with your own identifying information: Portions
* Copyright [yyyy] [name of copyright owner]
*
* CDDL HEADER END
*/
/*
* Copyright 2006-2007 Fachinformationszentrum Karlsruhe Gesellschaft
* für wissenschaftlich-technische Information mbH and Max-Planck-
* Gesellschaft zur Förderung der Wissenschaft e.V.
* All rights reserved. Use is subject to license terms.
* Copyright 2006-2007 Fachinformationszentrum Karlsruhe Gesellschaft für
* wissenschaftlich-technische Information mbH and Max-Planck- Gesellschaft zur Förderung der
* Wissenschaft e.V. All rights reserved. Use is subject to license terms.
*/
package de.mpg.imeji.exceptions;

public class AuthenticationError extends ImejiException
{
private static final long serialVersionUID = 6128275500671470459L;

/**
* Constructor for HTTP 401 Unauthorized
*/
public AuthenticationError(String message)
{
super(message);
}

public class AuthenticationError extends ImejiException {
private static final long serialVersionUID = 6128275500671470459L;

/**
* Constructor for HTTP 401 Unauthorized
*/
public AuthenticationError(String message) {
super(message);
minimizeStacktrace();
}

}

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