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Merge branch 'v1.3'
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‎.gitignore‎

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.settings/
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.classpath
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.settings/
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.classpath
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nb-configuration.xml
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nbproject/
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/target/
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/bin/
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.vagrant/
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/target/
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/bin/
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.vagrant/
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/nbactions.xml

‎README.md‎

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@@ -5,30 +5,62 @@ accessed by the front-end or presentation layer. This application is targeted
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at a non-EE Java container such as Tomcat, using JPA and JAX/RS (Jersey implementation)
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for persistence layer and web API implementation.
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## Running the back-end
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## Notes on building the application
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The DOE CODE services API project is built using the maven build system, configured
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via the pom.xml in the project base folder. In order to facilitate shared configuration
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elements amongst this and other supporting applications, certain environment-specific
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options and settings have been migrated into a shared resources folder separate from
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each application.
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This folder is assumed to be in the developer's "home" folder, under the path "shared-resources/doecode/".
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This folder should contain a standard Java properties file containing the desired
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configuration elements, customized to your specific environment(s) as needed. One
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might have a file for development, testing, and production, or as many other disparate
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configurations as dictated by your own systems.
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The configuration elements are detailed below, and should be in these properties
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files with your personal values. In the maven build process, these properties
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are included according to the "environment" defined variable, which defaults to "development".
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Therefore, unless overridden, the $HOME/shared-resources/doecode/development.properties file
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should contain your default environmental settings.
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The "environment" value may be altered by your own private profiles, or through
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the use of the command line switch -Denvironment=desired-value of maven at build time.
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In order to activate and load "test.properties" from your shared-resources for example:
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```bash
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mvn -Denvironment=test package
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```
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## Configuration Elements used
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The application will run on most back-end Java EE platforms, tested
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specifically on Jetty and Tomcat. This assumes one already has a persistence
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store up-and-running; define your access information via a local maven
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profile, ensure you define:
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store up-and-running.
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These properties are loaded from the "environment.properties" configuration file
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and should correspond to environmental settings per your setup.
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Parameter | Definition
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--- | ---
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${database.driver} | the JDBC database driver to use
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${database.url} | the JDBC URL to access
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${database.username} | the database user (with create/alter schema permission)
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${database.password} | the user's password
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${serviceapi.host} | base URL for validation services
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${publishing.host} | base URL for submitting final metadata to OSTI (via /submit API)
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${datacite.username} | (optional) DataCite user account name for registering DOIs
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${datacite.password} | (optional) DataCite account password for DOI registration
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${datacite.baseurl} | (optional) DataCite base URL prefix to use for DOI registration
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${datacite.prefix} | (optional) DataCite registration DOI prefix value
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${index.url} | (optional) URL to indexing service (e.g., SOLR, see below)
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${search.url} | (optional) base URL to searching service (SOLR, see below)
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${site.url} | base URL of the client front-end services
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${email.host} | SMTP host name for sending confirmation emails
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${email.from} | The user name to use for sending above emails
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database.driver | the JDBC database driver to use
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database.url | the JDBC URL to access
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database.username | the database user (with create/alter schema permission)
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database.password | the user's password
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serviceapi.host | base URL for validation services
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publishing.host | base URL for submitting final metadata to OSTI (via /submit API)
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datacite.username | (optional) DataCite user account name for registering DOIs
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datacite.password | (optional) DataCite account password for DOI registration
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datacite.baseurl | (optional) DataCite base URL prefix to use for DOI registration
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datacite.prefix | (optional) DataCite registration DOI prefix value
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index.url | (optional) URL to indexing service (e.g., SOLR, see below)
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search.url | (optional) base URL to searching service (SOLR, see below)
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site.url | base URL of the client front-end services
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email.host | SMTP host name for sending confirmation emails
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email.from | The user name to use for sending above emails
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If optional parameters, such as the DataCite settings, are left blank, those features
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will not apply.
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```bash
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mvn jetty:run
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```
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or
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# or
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```bash
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mvn tomcat:run
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```
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command line switch to override:
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```bash
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mvn -P *your-profile* -Dcatalina.base=$HOME jetty:run
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mvn -P *your-profile* -Dcatalina.base=$HOME -Denvironment=*your-environment* jetty:run
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```
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to have logs in $HOME/logs/doecode.log via log4j default configuration.
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The value of ${database.driver} is org.apache.derby.jdbc.EmbeddedDriver for Derby.
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The value of ${database.driver} is org.apache.derby.jdbc.EmbeddedDriver for Derby. You
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may wish to have a specific configuration file in your shared-resources to
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facilitate this build and run process.
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## API services
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‎pom.xml‎

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<groupId>gov.osti</groupId>
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<artifactId>doecode</artifactId>
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<packaging>war</packaging>
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<version>1.1</version>
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<name>DOE Code Web Application</name>
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<version>1.3</version>
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<name>DOE Code Web Application (Server)</name>
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<url>http://maven.apache.org</url>
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<properties>
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<jackson.version>2.9.0</jackson.version>
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<projectName>doecodeapi</projectName>
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<datacite.url>https://mds.test.datacite.org/</datacite.url>
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<environment>development</environment>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<dependencies>
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<dependency>
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<groupId>junit</groupId>
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<version>1.3.2</version>
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</dependency>
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<dependency>
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<groupId>org.apache.shiro</groupId>
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<artifactId>shiro-web</artifactId>
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<version>1.3.2</version>
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</dependency>
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<dependency>
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<groupId>org.secnod.shiro</groupId>
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<artifactId>shiro-jersey</artifactId>
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<version>0.2.0</version>
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</dependency>
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<dependency>
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<groupId>io.jsonwebtoken</groupId>
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<artifactId>jjwt</artifactId>
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<version>0.7.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.shiro</groupId>
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<artifactId>shiro-web</artifactId>
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<version>1.3.2</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-email</artifactId>
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<version>1.4</version>
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</dependency>
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<dependency>
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<groupId>org.eclipse.jgit</groupId>
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<artifactId>org.eclipse.jgit</artifactId>
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<version>4.8.0.201706111038-r</version>
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<type>jar</type>
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</dependency>
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</dependencies>
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<dependency>
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<groupId>org.secnod.shiro</groupId>
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<artifactId>shiro-jersey</artifactId>
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<version>0.2.0</version>
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</dependency>
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<dependency>
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<groupId>io.jsonwebtoken</groupId>
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<artifactId>jjwt</artifactId>
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<version>0.7.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-email</artifactId>
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<version>1.4</version>
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</dependency>
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<!-- git support -->
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<dependency>
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<groupId>org.eclipse.jgit</groupId>
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<artifactId>org.eclipse.jgit</artifactId>
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<version>4.8.0.201706111038-r</version>
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<type>jar</type>
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</dependency>
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<!-- SVN support -->
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<dependency>
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<groupId>org.tmatesoft.svnkit</groupId>
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<artifactId>svnkit</artifactId>
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<version>1.9.0</version>
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<type>jar</type>
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</dependency>
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</dependencies>
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<build>
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<finalName>${projectName}</finalName>
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</resources>
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<plugins>
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<!-- support shared resources properties files -->
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>properties-maven-plugin</artifactId>
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<version>1.0.0</version>
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<executions>
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<execution>
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<phase>initialize</phase>
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<goals>
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<goal>read-project-properties</goal>
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</goals>
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<configuration>
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<files>
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<file>${user.home}/shared-resources/doecode/${environment}.properties</file>
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</files>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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</webApp>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.tomcat.maven</groupId>
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<artifactId>tomcat7-maven-plugin</artifactId>
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<version>2.2</version>
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<configuration>
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<url>http://${host}:${port}/manager/text</url>
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<server>${server}</server>
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<path>/${projectName}</path>
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<warFile>${project.build.directory}/${projectName}.war</warFile>
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<path>/${projectName}</path>
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</configuration>
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</plugin>
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<!-- tomcat deployment -->
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<plugin>
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<groupId>org.apache.tomcat.maven</groupId>
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<artifactId>tomcat7-maven-plugin</artifactId>
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<version>2.2</version>
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<configuration>
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<server>${server}</server>
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<url>http://${host}:${port}/manager/text</url>
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<path>/${projectName}</path>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<configuration>
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<source>${jdk.version}</source>
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<target>${jdk.version}</target>
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<encoding>${project.build.sourceEncoding}</encoding>
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</configuration>
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<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-resources-plugin</artifactId>
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<version>2.4.3</version>
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<configuration>
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<encoding>${project.build.sourceEncoding}</encoding>
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</configuration>
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</plugin>
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‎src/main/java/gov/osti/connectors/SourceForge.java‎

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// the logger implementation
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private static final Logger log = LoggerFactory.getLogger(SourceForge.class);
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// pattern to match for PROJECT NAME
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private static final Pattern PROJECT_NAME_PATTERN = Pattern.compile("/projects/(.*)$");
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private static final Pattern PROJECT_NAME_PATTERN = Pattern.compile("/(?:p|projects)/([a-zA-Z0-9_-]+).*$");
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/**
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* initialize this Connector
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*
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* Assumes it contains "sourceforge.net" and the PATH contains the
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* "project/project-name" value.
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* SF might also be of the form: sourceforge.net/p/project-name or sf.net/p/project-name
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* for example.
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*
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* @param url the URL to process
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* @return the PROJECT NAME if possible, or null if not
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// protection against bad URL input
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if (null!=uri.getHost()) {
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if (uri.getHost().contains("sourceforge.net") ||
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uri.getHost().contains("sf.net")) {
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return null;

‎src/main/java/gov/osti/entity/Agent.java‎

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import com.fasterxml.jackson.annotation.JsonIgnore;
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import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
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import gov.osti.services.Validation;
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import java.io.Serializable;
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import javax.persistence.Column;
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import javax.persistence.GeneratedValue;
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public String getOrcid() {
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return orcid;
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}
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8989
public void setOrcid(String orcid) {
90-
this.orcid = orcid;
90+
this.orcid = Validation.formatORCID(orcid, "dashed");
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}
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/**

‎src/main/java/gov/osti/entity/DOECodeMetadata.java‎

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}
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@Size (max = 255, message = "Recipient name is limited to 255 characters.")
498-
@Column (name = "RECIPIENT_NAME")
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@Column (name = "RECIPIENT_NAME", length = 255)
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public String getRecipientName() {
500500
return recipientName;
501501
}
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613613
}
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public void setOwner(String owner) {
616+
owner = owner != null ? owner.toLowerCase() : owner;
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this.owner = owner;
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}
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‎src/main/java/gov/osti/entity/Site.java‎

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@Entity
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@Table(name="sites")
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@NamedQueries ({
18-
@NamedQuery (name = "Site.findByDomain", query = "SELECT s FROM Site s JOIN s.emailDomains d WHERE d = :domain")
18+
@NamedQuery (name = "Site.findByDomain", query = "SELECT s FROM Site s JOIN s.emailDomains d WHERE d = lower(:domain)")
1919
})
2020
public class Site implements Serializable {
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