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creating branch for tree-dedup

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webapps/dnet-container-openaireplus/branches/tree-dedup/pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
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         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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    <parent>
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        <groupId>eu.dnetlib</groupId>
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        <artifactId>dnet45-container-parent</artifactId>
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        <version>1.0.0-SNAPSHOT</version>
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        <relativePath></relativePath>
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    </parent>
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    <modelVersion>4.0.0</modelVersion>
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    <groupId>eu.dnetlib</groupId>
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    <artifactId>dnet-container-openaireplus</artifactId>
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    <packaging>war</packaging>
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    <version>3.0.0-SNAPSHOT</version>
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    <dependencies>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-objectStore-ui</artifactId>
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            <version>[2.0.0-SNAPSHOT,3)</version>
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        </dependency>
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        <!-- Common components in every container -->
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-log4j-inspector</artifactId>
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            <version>[1.0.0,2.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-schemas</artifactId>
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            <version>[1.0.0,2.0.0)</version>
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        </dependency>
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        <!-- Common services in every container -->
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-enabling-hnm-service</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-enabling-hcm-service</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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        </dependency>
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        <!-- Enabling services service -->
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-enabling-services</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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            <exclusions>
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                <exclusion>
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                    <groupId>apache</groupId>
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                    <artifactId>commons-pool</artifactId>
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                </exclusion>
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            </exclusions>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-enabling-inspector</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-resultset-inspector</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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        </dependency>
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        <!-- Manager Service Resource Orchestration (required for workflows) -->
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-msro-service</artifactId>
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            <version>[3.0.0,4.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-mongo-logging</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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        </dependency>
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		<!-- Modular User Interfaces -->
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-ui</artifactId>
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			<version>[3.0.0,4.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-workflows-ui</artifactId>
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			<version>[4.0.0,5.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-is-ui</artifactId>
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			<version>[2.0.1,3.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-repositories-ui</artifactId>
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			<version>[4.0.0,5.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-oai-explorer-ui</artifactId>
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			<version>[2.0.0,3.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-oai-modular-ui</artifactId>
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			<version>[3.0.0,4.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-vocabularies-ui</artifactId>
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			<version>[2.0.1,3.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-cleaning-rules-ui</artifactId>
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			<version>[2.0.0,3.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-database-ui</artifactId>
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			<version>[2.0.0,3.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-modular-index-ui</artifactId>
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			<version>[2.0.8,3.0.0)</version>
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		</dependency>
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        <!-- Aggregation services -->
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-mongo-mdstore</artifactId>
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            <version>[6.0.0,7.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-modular-collector-service</artifactId>
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            <version>[3.0.0,4.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-s3-objectStore</artifactId>
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            <version>[2.0.0,3.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-data-transformation-service</artifactId>
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            <version>[3.0.0,4.0.0)</version>
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        </dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>cnr-enabling-database-service</artifactId>
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			<version>[3.0.0,4.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-openaireplus-profiles</artifactId>
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			<version>[1.0.0,2.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>cnr-data-utility-cleaner-service</artifactId>
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			<version>[3.0.0,4.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-openaireplus-workflows</artifactId>
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			<version>[7.0.0-SNAPSHOT,8.0.0)</version>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-deduplication</artifactId>
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			<version>[1.6.7,2.0.0)</version>
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			<exclusions>
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				<exclusion>
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					<groupId>eu.dnetlib</groupId>
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					<artifactId>dnet-openaireplus-mapping-utils</artifactId>
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				</exclusion>
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			</exclusions>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-hadoop-service</artifactId>
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			<version>[2.0.0,3.0.0)</version>
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			<exclusions>
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				<exclusion>
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					<groupId>org.jruby</groupId>
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					<artifactId>jruby-complete</artifactId>
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				</exclusion>
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				<exclusion>
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					<groupId>org.apache.httpcomponents</groupId>
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					<artifactId>httpclient</artifactId>
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				</exclusion>
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			</exclusions>
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		</dependency>
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		<dependency>
207
			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-actionmanager-service</artifactId>
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			<version>[5.0.0,6.0.0)</version>
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			<exclusions>
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				<exclusion>
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					<groupId>eu.dnetlib</groupId>
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					<artifactId>dnet-openaireplus-mapping-utils</artifactId>
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				</exclusion>
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			</exclusions>
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		</dependency>
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		<dependency>
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			<groupId>eu.dnetlib</groupId>
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			<artifactId>dnet-download-service</artifactId>
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			<version>[2.0.0,3.0.0)</version>
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		</dependency>
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		<dependency>
223
			<groupId>eu.dnetlib</groupId>
224
			<artifactId>dnet-download-plugins</artifactId>
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			<version>[2.0.0,3.0.0)</version>
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		</dependency>
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        <dependency>
229
            <groupId>eu.dnetlib</groupId>
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            <artifactId>cnr-inspector-security</artifactId>
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            <version>[1.0.0,2.0.0)</version>
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        </dependency>
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        <dependency>
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            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-webapp-monitoring</artifactId>
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            <version>[1.0.0,2.0.0)</version>
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        </dependency>
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        <dependency>
240
            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-openaire-blacklist</artifactId>
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            <version>[1.0.0,2.0.0)</version>
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	        <exclusions>
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		        <exclusion>
245
			        <groupId>eu.dnetlib</groupId>
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			        <artifactId>dnet-openaireplus-mapping-utils</artifactId>
247
		        </exclusion>
248
	        </exclusions>
249
        </dependency>
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251
        <dependency>
252
            <groupId>eu.dnetlib</groupId>
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            <artifactId>dnet-modular-mdstore-ui</artifactId>
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            <version>[1.0.0-SNAPSHOT, 2.0.0)</version>
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        </dependency>
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257
        <dependency>
258
            <groupId>xerces</groupId>
259
            <artifactId>xercesImpl</artifactId>
260
            <version>2.11.0</version>
261
            <scope>compile</scope>
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        </dependency>
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264
        <dependency>
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            <groupId>eu.dnetlib</groupId>
266
            <artifactId>dnet-mapreduce-jobs</artifactId>
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            <version>[1.1.11-solr75-SNAPSHOT]</version>
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            <exclusions>
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                <exclusion>
270
                    <groupId>eu.dnetlib</groupId>
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                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
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                </exclusion>
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            </exclusions>
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        </dependency>
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        <dependency>
277
            <groupId>javax.servlet</groupId>
278
            <artifactId>javax.servlet-api</artifactId>
279
            <version>${javax.servlet.version}</version>
280
            <scope>provided</scope>
281
        </dependency>
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        <!-- SWAGGER -->
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        <dependency>
285
            <groupId>com.fasterxml.jackson.datatype</groupId>
286
            <artifactId>jackson-datatype-joda</artifactId>
287
            <version>2.6.6</version>
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            <exclusions>
289
                <exclusion>
290
                    <groupId>com.fasterxml.jackson.core</groupId>
291
                    <artifactId>jackson-annotations</artifactId>
292
                </exclusion>
293
            </exclusions>
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        </dependency>
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        <dependency>
296
            <groupId>joda-time</groupId>
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            <artifactId>joda-time</artifactId>
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            <version>2.8.2</version>
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        </dependency>
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        <dependency>
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            <groupId>io.springfox</groupId>
303
            <artifactId>springfox-swagger2</artifactId>
304
            <version>${springfox-version}</version>
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        </dependency>
306
        <dependency>
307
            <groupId>io.springfox</groupId>
308
            <artifactId>springfox-swagger-ui</artifactId>
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            <version>${springfox-version}</version>
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        </dependency>
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        <dependency>
313
            <groupId>org.hibernate</groupId>
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            <artifactId>hibernate-validator</artifactId>
315
            <version>5.2.4.Final</version>
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        </dependency>
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    </dependencies>
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    <properties>
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        <springfox-version>2.5.0</springfox-version>
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    </properties>
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</project>
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/eu/dnetlib/cnr-site.properties
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container.hostname								= 	localhost
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services.is.store.database.bean          		=   persistentExistDatabase
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#services.is.store.database.bean                = 	temporaryExistDatabase
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dnet.data.path 									=	/var/lib/dnet45
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services.registration.default.hnmlocator   		=   dynamicHNMLocator
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services.schemas								=	classpath*:/eu/dnetlib/test/schemas/**/*.xsd
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services.msro.reindex.limit      				=   100
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#services.msro.disabled.beans   				=   reindexOAIPostCleaningEFGHandler,reindexOAIPostEditEFGHandler,reindexPostEditEFGHandler
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services.aggregator.host						=	localhost
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services.aggregator.name        				=   DRIVER
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services.aggregator.country						=	EE
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services.msro.data.source.resolver				=	extendedDataSourceResolver
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services.registry.pending.resource.manager		=	compatPendingManager
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transport.soap.force.local.address				=	true
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msro.wf.nodes.mdstoreSearch.format 				=	OAF
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msro.wf.nodes.mdstoreSearch.interpretation 		=	cleaned
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msro.wf.nodes.download.xpathMetadataId 			=	//*[local-name()='objIdentifier']/text()
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dnet.modular.ui.authorization.manager 			=	simpleAuthenticationManager
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dnet.modular.ui.authorization.default.superAdmin=	admin
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# MSRO SPECIFIC
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services.msro.graph.updateindex.incremental		=	classpath:/eu/dnetlib/enabling/manager/msro/wf/update-index-incremental.wf.xml
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dnet.datasource.updater 						=   openaireplusDatasourceUpdater
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hbase.mapred.datatable 							=	db_openaireplus
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hbase.actions.table 							=	db_actions
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# Mail configuration
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msro.wf.mail.smtp.host = smtp.isti.cnr.it
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msro.wf.mail.smtp.user = smtp-dnet
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msro.wf.mail.smtp.password = hhr*7932
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msro.wf.mail.cc = michele.artini@isti.cnr.it
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service.index.solr.rank.enable=true
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services.publisher.oai.host=localhost
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services.publisher.oai.port=27017
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#services.objectstore.dao=fSObjectstoreDao
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services.transformation.blacklist_api = http://localhost:8280/validator-service/worfklows?request=GetBlacklistedRecords&datasourceId=
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# REST API CONFIGURATION
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api.rest.title          =   Override property 'api.rest.title' to set an informative title
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api.rest.description    =   Override property 'api.rest.description' to set an informative description
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api.rest.license        =   LICENSED UNDER A CREATIVE COMMONS ATTRIBUTION 4.0 INTERNATIONAL LICENSE.
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api.rest.license.url    =   https://creativecommons.org/licenses/by/4.0
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api.rest.contact.name   =   D-Net team
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api.rest.contact.url    =   http://www.d-net.research-infrastructures.eu
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api.rest.contact.email  =   dnet-team@isti.cnr.it
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# SWAGGER
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springfox.documentation.swagger.v2.path     =   /api-docs
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spring.jackson.date-format                  =   io.swagger.RFC3339DateFormat
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spring.jackson.serialization.WRITE_DATES_AS_TIMESTAMPS=false
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dnet.openaire.db.name = dnet_openaire
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dnet.openaire.db.password = dnetPwd
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openaire.api.directindex.autocommit.active=false
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services.objectstore.dao=S3ObjectstoreDao
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dnet.objectStore.s3.accessKey =AK0MM6C2BYA0K1PNJYYX
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dnet.objectStore.s3.secretKey =fpeiqUUpKAUOtO6JWMWLTxxlSxJ+yGYwHozm3jHK
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dnet.objectStore.s3.endPoint =s3.icm.edu.pl
75
dnet.objectStore.s3.objectStoreBucket =openaire-mdstore-dev
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oozie.service.loc =  http://hadoop-edge3.garr-pa1.d4science.org:11000/oozie/
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dnet.openaire.messageManager.host = broker1-dev-dnet.d4science.org
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dnet.openaire.messageManager.username = r_admin
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dnet.openaire.messageManager.password = 9g8fed7gpohef9y84th98h
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/eu/dnetlib/applicationContext-ehcache.xml
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<beans xmlns="http://www.springframework.org/schema/beans"
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	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:p="http://www.springframework.org/schema/p"
3
	xmlns:util="http://www.springframework.org/schema/util" xmlns:cache="http://www.springframework.org/schema/cache"
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	xmlns:jaxws="http://cxf.apache.org/jaxws" xmlns:template="http://dnetlib.eu/springbeans/template"
5
	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
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                        http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd
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						http://www.springframework.org/schema/cache http://www.springframework.org/schema/cache/spring-cache.xsd
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						http://cxf.apache.org/jaxws http://cxf.apache.org/schemas/jaxws.xsd">
9

  
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	<!-- THIS FILE MUST CONTAIN THE CACHEMANAGER DECALRED IN DEPENDENCY MODULES
11
		THAT MUST BE USED BY THE CONTAINER BECAUSE WE CANNOT HAVE MULTIPLE <cache:annotation-driven> 
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		IN DIFFERENT MODULES. -->
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		<cache:annotation-driven cache-manager="isCacheManager" />
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		<!-- ADD TO THE ARRAY OF CACHE MANAGERS THE CACHE MANAGER DEFINED IN MODULES" APPLICATION CONTEXTS -->
16
		<bean id="isCacheManager" class="org.springframework.cache.support.CompositeCacheManager">
17
    		<property name="cacheManagers">
18
        		<array>
19
			        <!-- <ref bean="resultSetCacheManager" /> -->
20
           	 		<ref bean="issnCacheManager" />
21
        		</array>
22
    		</property>
23
    		<property name="fallbackToNoOpCache" value="true" />
24
		</bean>
25

  
26
</beans>
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/eu/dnetlib/applicationContext-locators.xml
1
<?xml version="1.0" encoding="UTF-8"?>
2
<beans xmlns="http://www.springframework.org/schema/beans"
3
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:jaxws="http://cxf.apache.org/jaxws"
4
	xmlns:sec="http://cxf.apache.org/configuration/security" xmlns:wsa="http://cxf.apache.org/ws/addressing"
5
	xmlns:p="http://www.springframework.org/schema/p" xmlns:http="http://cxf.apache.org/transports/http/configuration"
6
	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
7
    http://cxf.apache.org/ws/addressing http://cxf.apache.org/schemas/ws-addr-conf.xsd
8
    http://cxf.apache.org/configuration/security http://cxf.apache.org/schemas/configuration/security.xsd
9
    http://cxf.apache.org/transports/http/configuration http://cxf.apache.org/schemas/configuration/http-conf.xsd
10
    http://cxf.apache.org/jaxws http://cxf.apache.org/schemas/jaxws.xsd">
11

  
12
	<!-- service locators: TODO: parameterize via properties -->
13
	<bean id="transformationServiceLocator" class="eu.dnetlib.enabling.tools.DynamicServiceLocator"
14
		p:clazz="eu.dnetlib.data.transformation.service.rmi.TransformationService"
15
		p:lookUpLocator-ref="lookupLocator" p:serviceResolver-ref="serviceResolver" />
16

  
17
	<bean id="downloadServiceLocator" class="eu.dnetlib.enabling.tools.DynamicServiceLocator"
18
		p:clazz="eu.dnetlib.data.download.rmi.DownloadService"
19
		p:lookUpLocator-ref="lookupLocator" p:serviceResolver-ref="serviceResolver" />
20

  
21
	<bean id="dynamicHadoopServiceLocator" class="eu.dnetlib.enabling.tools.DynamicServiceLocator" 
22
		p:clazz="eu.dnetlib.data.hadoop.rmi.HadoopService"
23
		p:lookUpLocator-ref="lookupLocator" p:serviceResolver-ref="serviceResolver" />
24

  
25
</beans>
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/log4j.properties
1
### Root Level ###
2
log4j.rootLogger=WARN, LOGFILE, CONSOLE
3

  
4
### Configuration for the LOGFILE appender ###
5
log4j.appender.LOGFILE=org.apache.log4j.RollingFileAppender
6
log4j.appender.LOGFILE.MaxFileSize=25MB
7
log4j.appender.LOGFILE.MaxBackupIndex=10
8
log4j.appender.LOGFILE.File=logs/is/dnet.log
9
log4j.appender.LOGFILE.Append=true
10
log4j.appender.LOGFILE.layout=org.apache.log4j.PatternLayout
11
log4j.appender.LOGFILE.layout.ConversionPattern=[%-5p] %d %c - %m%n
12

  
13
### Configuration for the CONSOLE appender ###
14
log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
15
log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
16
log4j.appender.CONSOLE.layout.ConversionPattern=[%-5p] %d %c - %m%n
17

  
18
### Configuration for the QUERIES appender ###
19
log4j.appender.QUERIES=org.apache.log4j.RollingFileAppender
20
log4j.appender.QUERIES.MaxFileSize=25MB
21
log4j.appender.QUERIES.MaxBackupIndex=10
22
log4j.appender.QUERIES.File=logs/xqueries.log
23
log4j.appender.QUERIES.Append=true
24
log4j.appender.QUERIES.layout=org.apache.log4j.PatternLayout
25
log4j.appender.QUERIES.layout.ConversionPattern=[%-5p] %d %c - %m%n
26

  
27
org.apache.cxf.Logger=org.apache.cxf.common.logging.Log4jLogger
28

  
29
### Application Level ###
30
log4j.logger.eu.dnetlib=INFO
31
log4j.logger.eu.dnetlib.enabling.is.sn=INFO
32
log4j.logger.org.apache.cxf.interceptor=FATAL
33
log4j.logger.org.apache.cxf.ws.addressing.ContextUtils=FATAL
34
log4j.logger.eu.dnetlib.enabling.tools.AbstractBaseService=INFO
35
log4j.logger.eu.dnetlib.xml.database.LoggingTrigger=WARN
36
log4j.logger.eu.dnetlib.enabling.tools.registration.ServiceRegistrator=INFO
37
log4j.logger.eu.dnetlib.enabling.inspector=FATAL
38
log4j.logger.eu.dnetlib.enabling.inspector.SubscriptionController=DEBUG
39
log4j.logger.eu.dnetlib.springutils.stringtemplate.StringTemplateViewResolver=FATAL
40
log4j.logger.eu.dnetlib.enabling.is.sn.SynchronousNotificationSenderImpl=WARN
41
log4j.logger.eu.dnetlib.enabling.tools.LocalServiceResolverImpl=WARN
42
log4j.logger.eu.dnetlib.enabling.is.sn.NotificationInvokerImpl=WARN
43
log4j.logger.eu.dnetlib.data.collective=INFO
44
log4j.logger.eu.dnetlib.data.objectstore.s3=INFO
45
log4j.logger.eu.dnetlib.data.hadoop.utils.ScanFactory=DEBUG
46
log4j.logger.org.apache.xerces.parsers.SAXParser=OFF
47
log4j.logger.eu.dnetlib.conf.PropertyFetcher=WARN
48
#log4j.logger.eu.dnetlib.data.transform.XsltRowTransformerFactory=DEBUG
49

  
50
log4j.logger.eu.dnetlib.enabling.is.sn.ISSNServiceImpl=OFF
51
log4j.logger.eu.dnetlib.enabling.datasources.DatasourceManagerClients=FATAL
52
log4j.logger.eu.dnetlib.data.mdstore.modular.mongodb.utils.MetadataCheckJob=DEBUG
53
log4j.logger.eu.dnetlib.enabling.is.sn.ISSNServiceCore=WARN
54
log4j.logger.eu.dnetlib.xml.database.exist.ExistDatabase=WARN
55
log4j.logger.eu.dnetlib.enabling.is.store.AbstractContentInitializer=FATAL
56

  
57
log4j.logger.org.apache.hadoop.hbase.mapreduce.TableInputFormatBase=FATAL
58

  
59
log4j.logger.eu.dnetlib.msro.openaireplus.workflows.nodes.claims=DEBUG
60

  
61
### Spring ###
62
log4j.logger.org.springframework=ERROR
63

  
64
### XQUERIES ###
65
#log4j.logger.eu.dnetlib.enabling.is.store=DEBUG
66
###interceptors for xml database ###
67
## Additivity = false means: do not inherit the appenders from the rootLogger. ##
68
#  This allows the log of interceptor to be output of one only appender: QUERIES #
69
#  See: http://examples.javacodegeeks.com/enterprise-java/log4j/log4j-additivity-property-example/ #
70
##
71
log4j.additivity.eu.dnetlib.enabling.tools.LogInterceptor = false
72
log4j.logger.eu.dnetlib.enabling.tools.LogInterceptor=DEBUG, QUERIES
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/log4j.properties.normal
1
### Root Level ###
2
log4j.rootLogger=WARN, LOGFILE, CONSOLE
3

  
4
### Configuration for the LOGFILE appender ###
5
log4j.appender.LOGFILE=org.apache.log4j.RollingFileAppender
6
log4j.appender.LOGFILE.MaxFileSize=25MB
7
log4j.appender.LOGFILE.MaxBackupIndex=10
8
log4j.appender.LOGFILE.File=logs/dnet.log
9
log4j.appender.LOGFILE.Append=true
10
log4j.appender.LOGFILE.layout=org.apache.log4j.PatternLayout
11
log4j.appender.LOGFILE.layout.ConversionPattern=[%-5p] %d %c - %m%n
12

  
13
### Configuration for the CONSOLE appender ###
14
log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
15
log4j.appender.CONSOLE.layout=org.apache.log4j.PatternLayout
16
log4j.appender.CONSOLE.layout.ConversionPattern=[%-5p] %d %c - %m%n
17

  
18
org.apache.cxf.Logger=org.apache.cxf.common.logging.Log4jLogger
19

  
20
### Application Level ###
21
log4j.logger.eu.dnetlib=INFO
22
log4j.logger.eu.dnetlib.enabling.is.sn=INFO
23
log4j.logger.org.apache.cxf.interceptor=FATAL
24
log4j.logger.org.apache.cxf.ws.addressing.ContextUtils=FATAL
25
log4j.logger.eu.dnetlib.enabling.tools.AbstractBaseService=INFO
26
log4j.logger.eu.dnetlib.xml.database.LoggingTrigger=WARN
27
log4j.logger.eu.dnetlib.enabling.tools.registration.ServiceRegistrator=INFO
28
log4j.logger.eu.dnetlib.enabling.inspector=FATAL
29
log4j.logger.eu.dnetlib.enabling.inspector.SubscriptionController=DEBUG
30
log4j.logger.eu.dnetlib.springutils.stringtemplate.StringTemplateViewResolver=FATAL             
31
log4j.logger.eu.dnetlib.enabling.is.sn.SynchronousNotificationSenderImpl=WARN
32
log4j.logger.eu.dnetlib.enabling.tools.LocalServiceResolverImpl=WARN
33
log4j.logger.eu.dnetlib.enabling.is.sn.NotificationInvokerImpl=WARN
34
log4j.logger.eu.dnetlib.data.collective=INFO
35
log4j.logger.eu.dnetlib.data.hadoop.utils.ScanFactory=DEBUG
36
log4j.logger.org.apache.xerces.parsers.SAXParser=OFF
37
log4j.logger.eu.dnetlib.conf.PropertyFetcher=WARN
38
#log4j.logger.eu.dnetlib.data.transform.XsltRowTransformerFactory=DEBUG
39

  
40
log4j.logger.eu.dnetlib.enabling.is.sn.ISSNServiceImpl=OFF
41
log4j.logger.eu.dnetlib.enabling.datasources.DatasourceManagerClients=FATAL
42
log4j.logger.eu.dnetlib.data.mdstore.modular.mongodb.utils.MetadataCheckJob=DEBUG
43
log4j.logger.eu.dnetlib.enabling.is.sn.ISSNServiceCore=WARN
44
log4j.logger.eu.dnetlib.xml.database.exist.ExistDatabase=WARN
45
log4j.logger.eu.dnetlib.enabling.is.store.AbstractContentInitializer=FATAL
46

  
47
log4j.logger.org.apache.hadoop.hbase.mapreduce.TableInputFormatBase=FATAL
48

  
49
### Spring ###
50
log4j.logger.org.springframework=ERROR
51

  
52
log4j.logger.eu.dnetlib.openaire=DEBUG
53

  
54

  
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/META-INF/services/javax.xml.transform.TransformerFactory
1
net.sf.saxon.TransformerFactoryImpl
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/resources/META-INF/cxf/org.apache.cxf.Logger
1
org.apache.cxf.common.logging.Log4jLogger
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/java/eu/dnetlib/swagger/configuration/SwaggerDocumentationConfig.java
1
package eu.dnetlib.swagger.configuration;
2

  
3
import eu.dnetlib.common.rmi.DNetRestDocumentation;
4
import org.springframework.beans.factory.annotation.Value;
5
import org.springframework.context.annotation.Bean;
6
import org.springframework.context.annotation.Configuration;
7
import springfox.documentation.builders.ApiInfoBuilder;
8
import springfox.documentation.builders.RequestHandlerSelectors;
9
import springfox.documentation.service.ApiInfo;
10
import springfox.documentation.service.Contact;
11
import springfox.documentation.spi.DocumentationType;
12
import springfox.documentation.spring.web.plugins.Docket;
13
import springfox.documentation.swagger2.annotations.EnableSwagger2;
14

  
15
@Configuration
16
@EnableSwagger2
17
public class SwaggerDocumentationConfig {
18

  
19
    @Value("${api.rest.contact.name}")
20
    private String contactName;
21

  
22
    @Value("${api.rest.contact.url}")
23
    private String contactUrl;
24

  
25
    @Value("${api.rest.contact.email}")
26
    private String contactEmail;
27

  
28
	@Value("${api.rest.title}")
29
	private String title;
30

  
31
	@Value("${api.rest.description}")
32
	private String description;
33

  
34
	@Value("${api.rest.license}")
35
	private String license;
36
	@Value("${api.rest.license.url}")
37
	private String licenseUrl;
38

  
39
    @Bean
40
    public Docket customImplementation(){
41
        return new Docket(DocumentationType.SWAGGER_2)
42
                .select()
43
			        //.apis(RequestHandlerSelectors.any())
44
                    //.apis(RequestHandlerSelectors.basePackage("eu.dnetlib.**.controller.*"))
45
		            //.apis(RequestHandlerSelectors.withClassAnnotation(RestController.class))
46
		            .apis(RequestHandlerSelectors.withClassAnnotation(DNetRestDocumentation.class))
47
                    //.paths(PathSelectors.ant("/ds/**"))
48
                    .build()
49
                .directModelSubstitute(org.joda.time.LocalDate.class, java.sql.Date.class)
50
                .directModelSubstitute(org.joda.time.DateTime.class, java.util.Date.class)
51
                .apiInfo(apiInfo());
52
    }
53

  
54
	private ApiInfo apiInfo() {
55
		return new ApiInfoBuilder()
56
				.title(title)
57
				.description(description)
58
				.license(license)
59
				.licenseUrl(licenseUrl)
60
				.termsOfServiceUrl("")
61
				.version("1.0.0")
62
				.contact(new Contact(contactName, contactUrl, contactEmail))
63
				.build();
64
	}
65

  
66
}
0 67

  
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/java/eu/dnetlib/swagger/configuration/RFC3339DateFormat.java
1
package eu.dnetlib.swagger.configuration;
2

  
3
import java.text.FieldPosition;
4
import java.util.Date;
5

  
6
import com.fasterxml.jackson.databind.util.ISO8601DateFormat;
7
import com.fasterxml.jackson.databind.util.ISO8601Utils;
8

  
9
public class RFC3339DateFormat extends ISO8601DateFormat {
10

  
11
  // Same as ISO8601DateFormat but serializing milliseconds.
12
  @Override
13
  public StringBuffer format(Date date, StringBuffer toAppendTo, FieldPosition fieldPosition) {
14
    String value = ISO8601Utils.format(date, true);
15
    toAppendTo.append(value);
16
    return toAppendTo;
17
  }
18

  
19
}
0 20

  
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/java/eu/dnetlib/swagger/configuration/ApiOriginFilter.java
1
package eu.dnetlib.swagger.configuration;
2

  
3
import java.io.IOException;
4
import javax.servlet.*;
5
import javax.servlet.http.HttpServletResponse;
6

  
7
public class ApiOriginFilter implements Filter {
8
	@Override
9
	public void doFilter(ServletRequest request, ServletResponse response,
10
			FilterChain chain) throws IOException, ServletException {
11
		HttpServletResponse res = (HttpServletResponse) response;
12
		res.addHeader("Access-Control-Allow-Origin", "*");
13
		res.addHeader("Access-Control-Allow-Methods", "GET, POST, DELETE, PUT");
14
		res.addHeader("Access-Control-Allow-Headers", "Content-Type");
15
		chain.doFilter(request, response);
16
	}
17

  
18
	@Override
19
	public void destroy() {
20
	}
21

  
22
	@Override
23
	public void init(FilterConfig filterConfig) throws ServletException {
24
	}
25
}
0 26

  
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/java/eu/dnetlib/swagger/configuration/HomeController.java
1
package eu.dnetlib.swagger.configuration;
2

  
3
import org.springframework.stereotype.Controller;
4
import org.springframework.web.bind.annotation.RequestMapping;
5

  
6
/**
7
 * Home redirection to swagger api documentation 
8
 */
9
@Controller
10
public class HomeController {
11

  
12
	@RequestMapping(value = "/docs")
13
	public String index() {
14
		return "redirect:swagger-ui.html";
15
	}
16
}
0 17

  
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/java/eu/dnetlib/swagger/configuration/ApiResponseMessage.java
1
package eu.dnetlib.swagger.configuration;
2

  
3
import javax.xml.bind.annotation.XmlTransient;
4

  
5
@javax.xml.bind.annotation.XmlRootElement
6
public class ApiResponseMessage {
7
	public static final int ERROR = 1;
8
	public static final int WARNING = 2;
9
	public static final int INFO = 3;
10
	public static final int OK = 4;
11
	public static final int TOO_BUSY = 5;
12

  
13
	int code;
14
	String type;
15
	String message;
16
	
17
	public ApiResponseMessage(){}
18
	
19
	public ApiResponseMessage(int code, String message){
20
		this.code = code;
21
		switch(code){
22
		case ERROR:
23
			setType("error");
24
			break;
25
		case WARNING:
26
			setType("warning");
27
			break;
28
		case INFO:
29
			setType("info");
30
			break;
31
		case OK:
32
			setType("ok");
33
			break;
34
		case TOO_BUSY:
35
			setType("too busy");
36
			break;
37
		default:
38
			setType("unknown");
39
			break;
40
		}
41
		this.message = message;
42
	}
43

  
44
	@XmlTransient
45
	public int getCode() {
46
		return code;
47
	}
48

  
49
	public void setCode(int code) {
50
		this.code = code;
51
	}
52

  
53
	public String getType() {
54
		return type;
55
	}
56

  
57
	public void setType(String type) {
58
		this.type = type;
59
	}
60

  
61
	public String getMessage() {
62
		return message;
63
	}
64

  
65
	public void setMessage(String message) {
66
		this.message = message;
67
	}
68
}
0 69

  
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/java/eu/dnetlib/EndpointDocController.java
1
package eu.dnetlib;
2

  
3
import java.util.List;
4
import java.util.Set;
5
import java.util.stream.Collectors;
6
import java.util.stream.Stream;
7

  
8
import org.springframework.beans.factory.annotation.Autowired;
9
import org.springframework.web.bind.annotation.RequestMapping;
10
import org.springframework.web.bind.annotation.RequestMethod;
11
import org.springframework.web.bind.annotation.RestController;
12
import org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerMapping;
13

  
14
/**
15
 * Created by claudio on 30/11/2016.
16
 */
17
@RestController
18
public class EndpointDocController {
19

  
20
	@Autowired
21
	private List<RequestMappingHandlerMapping> handlerMappings;
22

  
23
	@RequestMapping(value = "/endpointdoc", method = RequestMethod.GET)
24
	public Set<String> show() {
25
		return handlerMappings.stream()
26
				.map(r -> r.getHandlerMethods().entrySet().stream()
27
					.map(k -> k.getKey())
28
					.map(i -> i.toString()))
29
				.reduce(Stream::concat)
30
				.orElseGet(Stream::empty)
31
				.collect(Collectors.toSet());
32
	}
33

  
34
}
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/webapp/WEB-INF/dispatcher-servlet.xml
1
<?xml version="1.0" encoding="UTF-8"?>
2
<beans xmlns="http://www.springframework.org/schema/beans"
3
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:p="http://www.springframework.org/schema/p"
4
	xmlns:context="http://www.springframework.org/schema/context"
5
	xmlns:mvc="http://www.springframework.org/schema/mvc"
6
	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
7
		http://www.springframework.org/schema/context
8
        http://www.springframework.org/schema/context/spring-context.xsd
9
        http://www.springframework.org/schema/mvc
10
        http://www.springframework.org/schema/mvc/spring-mvc.xsd">
11

  
12
	<mvc:annotation-driven />
13

  
14
	<context:component-scan base-package="eu.dnetlib"/>
15

  
16
	<import resource="classpath*:/eu/dnetlib/**/webContext*.xml" />
17

  
18
	<bean id="beanHandlerMapping" p:order="1"
19
		class="org.springframework.web.servlet.handler.BeanNameUrlHandlerMapping" />
20
	
21
	<bean class="org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter" />
22
	
23
	<mvc:resources mapping="/resources/**" location="classpath:/eu/dnetlib/web/resources/" />
24

  
25
	<mvc:resources mapping="swagger-ui.html" location="classpath:/META-INF/resources/" />
26
	<mvc:resources mapping="/webjars/**" location="classpath:/META-INF/resources/webjars/" />
27

  
28
</beans>
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/webapp/WEB-INF/web.xml
1
<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
2
	xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd"
3
	version="3.0">
4
	<display-name>DNet-2.0 container web app</display-name>
5
	<context-param>
6
		<param-name>contextConfigLocation</param-name>
7
		<param-value>/WEB-INF/applicationContext.xml</param-value>
8
	</context-param>
9
	<filter>
10
		<filter-name>springSecurityFilterChain</filter-name>
11
		<filter-class>org.springframework.web.filter.DelegatingFilterProxy</filter-class>
12
	</filter>
13
	<filter>
14
		<filter-name>encodingFilter</filter-name>
15
		<filter-class>org.springframework.web.filter.CharacterEncodingFilter</filter-class>
16
		<init-param>
17
			<param-name>encoding</param-name>
18
			<param-value>UTF-8</param-value>
19
		</init-param>
20
		<init-param>
21
			<param-name>forceEncoding</param-name>
22
			<param-value>true</param-value>
23
		</init-param>
24
	</filter>
25
	<filter-mapping>
26
		<filter-name>encodingFilter</filter-name>
27
		<url-pattern>/*</url-pattern>
28
	</filter-mapping>
29

  
30
	<filter-mapping>
31
		<filter-name>springSecurityFilterChain</filter-name>
32
		<url-pattern>/*</url-pattern>
33
	</filter-mapping>
34

  
35

  
36

  
37

  
38
	<listener>
39
		<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
40
	</listener>
41
	<servlet>
42
		<servlet-name>CXFServlet</servlet-name>
43
		<servlet-class>org.apache.cxf.transport.servlet.CXFServlet</servlet-class>
44
		<load-on-startup>1</load-on-startup>
45
	</servlet>
46
	<servlet>
47
		<servlet-name>dispatcher</servlet-name>
48
		<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
49
		<load-on-startup>1</load-on-startup>
50
	</servlet>
51
	<servlet-mapping>
52
		<servlet-name>dispatcher</servlet-name>
53
		<url-pattern>/mvc/*</url-pattern>
54
	</servlet-mapping>
55
	<servlet-mapping>
56
		<servlet-name>CXFServlet</servlet-name>
57
		<url-pattern>/services/*</url-pattern>
58
	</servlet-mapping>
59
</web-app>
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/webapp/WEB-INF/applicationContext.xml
1
<?xml version="1.0" encoding="UTF-8"?>
2

  
3
<beans xmlns="http://www.springframework.org/schema/beans"
4
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:p="http://www.springframework.org/schema/p"
5
	xmlns:context="http://www.springframework.org/schema/context"
6
	xmlns:cxf="http://cxf.apache.org/core"
7
	xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
8
	http://www.springframework.org/schema/context
9
           http://www.springframework.org/schema/context/spring-context.xsd
10
           http://cxf.apache.org/core http://cxf.apache.org/schemas/core.xsd">
11

  
12
	<import resource="classpath:META-INF/cxf/cxf.xml" />
13
	<import resource="classpath:META-INF/cxf/cxf-extension-jaxws.xml" />
14
	<import resource="classpath:META-INF/cxf/cxf-servlet.xml" />
15

  
16
	<import resource="classpath*:/eu/dnetlib/**/applicationContext*.xml" />
17

  
18
	<context:annotation-config />
19
	<!-- if the following import is not the last one, something overrides bus 
20
		configuration disabling logging and any other customized feature. -->
21
	<import resource="./cxf.xml" />
22

  
23
</beans>
webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/webapp/WEB-INF/cxf.xml
1
<?xml version="1.0" encoding="UTF-8"?>
2
<beans xmlns="http://www.springframework.org/schema/beans"
3
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:cxf="http://cxf.apache.org/core"
4
	xmlns:http="http://cxf.apache.org/transports/http/configuration"
5
	xmlns:wsa="http://cxf.apache.org/ws/addressing" xmlns:p="http://www.springframework.org/schema/p"
6
	xmlns:pol="http://cxf.apache.org/policy" xmlns:condbean="http://dnetlib.eu/springbeans/condbean"
7
	xsi:schemaLocation="
8
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
9
http://cxf.apache.org/ws/addressing http://cxf.apache.org/schemas/ws-addr-conf.xsd
10
http://cxf.apache.org/transports/http/configuration http://cxf.apache.org/schemas/configuration/http-conf.xsd
11
http://cxf.apache.org/policy http://cxf.apache.org/schemas/policy.xsd
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	<!-- <cxf:bus> -->
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		<!--
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webapps/dnet-container-openaireplus/branches/tree-dedup/src/main/webapp/index.html
1
<table style="width :100%">
2
	<tr><td style="text-align:center; width:100%"><a href="http://www.d-net.research-infrastructures.eu/"><img src='images/d-netLogo.png'/></a></td></tr>
3
</table>
4
<table style="width :100%">
5
	<tr>
6
		<td style="text-align:center"><a href="mvc/inspector"><img src='images/admin.svg' style="width:200px" /> </a></td>
7
		<td style="text-align:center"><a href="mvc/ui/index.do"><img src='images/User.png' style="width:200px"/> </a></td>
8
		<td style="text-align:center"><a href="monitoring"><img src='images/monitor.png' style="width:200px"/> </a></td>	
9
	</tr>
10
	<tr>
11
		<td style="text-align:center">if this container runs the IS, you can access the web interface <a href="mvc/inspector">here</a><br/></img></td>
12
		<td style="text-align:center">if this container runs the user interfaces, you can access them <a href="mvc/ui/index.do">here</a><br/></img></td>
13
		<td style="text-align:center">if this container is monitored, you can access the monitoring web interface <a href="monitoring">here</a></td>	
14
	</tr>
15
</table>
webapps/dnet-container-openaireplus/branches/tree-dedup/deploy.info
1
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	"deploy_repository": "dnet4-snapshots", 
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	"version": "4", 
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	"mail": "sandro.labruzzo@isti.cnr.it,michele.artini@isti.cnr.it,claudio.atzori@isti.cnr.it,alessia.bardi@isti.cnr.it", 
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	"deploy_repository_url": "http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots", 
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	"name": "dnet-container-openaireplus",
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	"nightly" : "true",
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	"cron" : "0 0 0 1/1 * ? *"
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