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‎README.md

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@@ -6,7 +6,7 @@ Enumerated sequence feature service.
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[![Build Status](https://travis-ci.org/nmdp-bioinformatics/service-feature.svg?branch=master)](https://travis-ci.org/nmdp-bioinformatics/service-feature)
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###Hacking service-feature
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### Hacking service-feature
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Install
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To build
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$ mvn install
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Documentation
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[Wiki](https://github.com/nmdp-bioinformatics/service-feature/wiki) has extensive documentation on usage and deployment.

‎docker/docker-compose-dev.yml

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environment:
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MYSQL_DATABASE: feature
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MYSQL_ROOT_PASSWORD: supersecretpwd
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# If using Docker Toolbox, ssh into your vm and make a /data directory
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# before using this docker-compose file.
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volumes:
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- data:/var/lib/mysql
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phpmyadmin:
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image: phpmyadmin/phpmyadmin
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image: phpmyadmin/phpmyadmin:5.1
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container_name: myadmin
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environment:
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- PMA_ARBITRARY=1

‎pom.xml

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> http://www.gnu.org/licenses/lgpl.html
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-->
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<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/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.nmdp.service</groupId>
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<artifactId>service-parent</artifactId>
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<version>2</version>
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</parent>
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<groupId>org.nmdp.service</groupId>
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<artifactId>feature-multimodule</artifactId>
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<version>1.0.9-SNAPSHOT</version>
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<packaging>pom</packaging>
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<name>feature-multimodule</name>
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<url>https://github.com/nmdp-bioinformatics/service-feature</url>
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<description>Enumerated sequence feature service.</description>
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<inceptionYear>2014</inceptionYear>
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<scm>
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<connection>scm:git:[email protected]:nmdp-bioinformatics/service-feature.git</connection>
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<developerConnection>scm:git:[email protected]:nmdp-bioinformatics/service-feature.git</developerConnection>
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<url>[email protected]:nmdp-bioinformatics/service-feature.git</url>
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</scm>
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<licenses>
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<license>
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<name>GNU Lesser General Public License (LGPL)</name>
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<url>http://www.gnu.org/licenses/lgpl.html</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<developers>
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<developer>
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<id>mheuer-nmdp</id>
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<name>Michael Heuer (NMDP)</name>
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</developer>
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</developers>
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<modules>
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<module>domain</module>
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<module>service</module>
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<module>service-impl</module>
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<module>service-jdbi</module>
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<module>resource</module>
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<module>dropwizard</module>
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<module>dropwizard-jdbi</module>
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<module>client</module>
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<module>tools</module>
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</modules>
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<dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>mysql</groupId>
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<artifactId>mysql-connector-java</artifactId>
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<version>5.1.35</version>
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</dependency>
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<dependency>
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<groupId>org.dishevelled</groupId>
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<artifactId>dsh-compress</artifactId>
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<version>1.1</version>
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</dependency>
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<dependency>
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<groupId>org.dishevelled</groupId>
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<artifactId>dsh-commandline</artifactId>
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<version>1.1</version>
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</dependency>
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<dependency>
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<groupId>org.dishevelled</groupId>
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<artifactId>dsh-multi-map</artifactId>
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<version>1.0</version>
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</dependency>
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<dependency>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.nmdp.service</groupId>
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<artifactId>common-dropwizard</artifactId>
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<version>1.0</version>
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</dependency>
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</dependencies>
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</dependencyManagement>
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<artifactId>service-parent</artifactId>
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<version>2</version>
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</parent>
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<artifactId>feature-multimodule</artifactId>
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<version>1.0.9-SNAPSHOT</version>
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<packaging>pom</packaging>
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<name>feature-multimodule</name>
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<url>https://github.com/nmdp-bioinformatics/service-feature</url>
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<description>Enumerated sequence feature service.</description>
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<inceptionYear>2014</inceptionYear>
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<scm>
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<connection>
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scm:git:[email protected]:nmdp-bioinformatics/service-feature.git
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</connection>
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<developerConnection>
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scm:git:[email protected]:nmdp-bioinformatics/service-feature.git
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</developerConnection>
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<url>[email protected]:nmdp-bioinformatics/service-feature.git</url>
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</scm>
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<licenses>
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<license>
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<name>GNU Lesser General Public License (LGPL)</name>
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<url>http://www.gnu.org/licenses/lgpl.html</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<developers>
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<developer>
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<id>mheuer-nmdp</id>
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<name>Michael Heuer (NMDP)</name>
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</developer>
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</developers>
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<modules>
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<module>domain</module>
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<module>service</module>
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<module>service-impl</module>
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<module>service-jdbi</module>
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<module>resource</module>
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<module>dropwizard</module>
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<module>dropwizard-jdbi</module>
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<module>client</module>
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<module>tools</module>
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</modules>
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<dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>mysql</groupId>
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<artifactId>mysql-connector-java</artifactId>
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<version>5.1.49</version>
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</dependency>
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<dependency>
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<groupId>org.dishevelled</groupId>
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<artifactId>dsh-compress</artifactId>
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<version>1.1</version>
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</dependency>
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<dependency>
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<groupId>org.dishevelled</groupId>
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<artifactId>dsh-commandline</artifactId>
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<version>1.1</version>
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</dependency>
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<dependency>
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<groupId>org.dishevelled</groupId>
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<artifactId>dsh-multi-map</artifactId>
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<version>1.0</version>
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</dependency>
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<dependency>
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<groupId>org.nmdp.service</groupId>
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<artifactId>common-dropwizard</artifactId>
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<version>1.0</version>
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</dependency>
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</dependencies>
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</dependencyManagement>
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</project>
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‎service-jdbi/src/main/java/org/nmdp/service/feature/service/jdbi/JdbiFeatureService.java

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*/
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package org.nmdp.service.feature.service.jdbi;
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import static com.google.common.base.Preconditions.checkArgument;
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import static com.google.common.base.Preconditions.checkNotNull;
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import java.util.List;
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import javax.annotation.concurrent.Immutable;
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import com.google.inject.Inject;
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import org.nmdp.service.feature.Feature;
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import org.nmdp.service.feature.service.DnaAlphabet;
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import org.nmdp.service.feature.service.FeatureService;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import javax.annotation.concurrent.Immutable;
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import java.sql.SQLIntegrityConstraintViolationException;
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import java.util.List;
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import static com.google.common.base.Preconditions.checkArgument;
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import static com.google.common.base.Preconditions.checkNotNull;
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/**
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* JDBI feature service.
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*/
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private final FeatureDao featureDao;
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private static final Logger logger = LoggerFactory.getLogger(JdbiFeatureService.class);
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private static final int MAX_INSERT_FEATURE_TRIES = 10;
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@Inject
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JdbiFeatureService(final FeatureDao featureDao) {
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checkNotNull(featureDao);
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if (logger.isTraceEnabled()) {
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logger.trace("next accession locusId " + locusId + " termId " + termId + " rank " + rank);
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}
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long featureId = insertFeature(locusId, termId, rank, accession, sequenceId);
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int insertTries = 0;
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long featureId = 0;
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do {
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insertTries++;
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try {
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featureId = insertFeature(locusId, termId, rank, accession, sequenceId);
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} catch (RuntimeException se) {
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if (se.getCause() instanceof SQLIntegrityConstraintViolationException) {
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logger.warn(se.getCause().getMessage());
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// Try next accession number
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accession = featureDao.nextAccession(locusId, termId, rank);
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logger.info("Retrying with a new accession number");
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// Give up after trying for MAX_INSERT_FEATURE_TRIES
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if (insertTries == MAX_INSERT_FEATURE_TRIES) {
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logger.warn("Giving up after " + MAX_INSERT_FEATURE_TRIES +
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" tries to get a new accession number");
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throw se;
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}
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} else {
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throw se;
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}
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}
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} while (featureId < 1);
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if (logger.isTraceEnabled()) {
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logger.trace("finding feature by featureId " + featureId);

‎service-jdbi/src/main/sql/README.md

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# Database Setup
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See [Data Import](https://github.com/nmdp-bioinformatics/service-feature/wiki/Data-import) page on wiki for full details.
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Run the SQL files in the following order to initialize the database.
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```
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mysql-drop.sql
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mysql-create.sql
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mysql-load-imgt-hla.sql
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mysql-load-hgnc.sql
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mysql-load-sequence-ontology.sql
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```

‎service-jdbi/src/main/sql/mysql-create.sql

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`sequence_id` bigint not null,
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`accession` bigint not null,
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primary key (`feature_id`),
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index (`locus_id`,`term_id`,`rank`,`accession`),
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index (`locus_id`,`term_id`,`rank`,`sequence_id`),
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unique key `unique_feature` (`locus_id`,`term_id`,`rank`,`accession`),
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index feature_sequence (`locus_id`,`term_id`,`rank`,`sequence_id`),
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constraint foreign key (`locus_id`) references locus (`locus_id`),
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constraint foreign key (`term_id`) references term (`term_id`),
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constraint foreign key (`sequence_id`) references sequence (`sequence_id`)

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