Initial commit - Spring Batch Importer Pipeline

.gitignore

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+.gitignore
+/importer/nbproject/private/
+/importer/dist/
+/importer/build/
+/importer/target/
+/importer/src/main/resources/application.properties
+/importer/nbproject/
+/importer/nb-configuration.xml

importer/pom.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<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">
+    <modelVersion>4.0.0</modelVersion>
+    <name>cBioPortal Importer Pipeline</name>
+    <description>Spring Batch importer pipeline</description>
+    <artifactId>importer</artifactId>
+    <version>0.1.0</version>
+
+    <parent>
+        <groupId>org.cbio.portal.pipelines</groupId>
+        <artifactId>master</artifactId>
+        <version>0.1.0</version>
+    </parent>
+
+
+    <dependencies>
+        <dependency>
+            <groupId>org.mskcc.cbio</groupId>
+            <artifactId>model</artifactId>
+            <version>0.1.0</version>
+            <type>jar</type>
+        </dependency>
+        <dependency>
+            <groupId>org.mskcc.cbio</groupId>
+            <artifactId>persistence-jdbc</artifactId>
+            <version>0.1.0</version>
+            <type>jar</type>
+        </dependency>
+
+        <dependency>
+          <groupId>org.springframework</groupId>
+          <artifactId>spring-web</artifactId>
+        </dependency>   
+        <dependency>
+          <groupId>commons-lang</groupId>
+          <artifactId>commons-lang</artifactId>
+          <version>2.4</version>
+        </dependency>
+        <dependency>
+          <groupId>commons-cli</groupId>
+          <artifactId>commons-cli</artifactId>
+          <version>1.3</version>
+        </dependency>
+        <dependency>
+          <groupId>commons-collections</groupId>
+          <artifactId>commons-collections</artifactId>
+          <type>jar</type>
+        </dependency>
+
+        <!-- for Spring JDBC, BasicDataSource usage -->   
+        <dependency>
+          <groupId>org.springframework</groupId>
+          <artifactId>spring-jdbc</artifactId>
+          <type>jar</type>
+        </dependency>
+        <dependency>
+          <groupId>commons-dbcp</groupId>
+          <artifactId>commons-dbcp</artifactId>
+          <type>jar</type>
+        </dependency>
+        <dependency>
+         <groupId>mysql</groupId>
+         <artifactId>mysql-connector-java</artifactId>
+       </dependency>
+
+        <dependency>
+          <groupId>com.google.guava</groupId>
+          <artifactId>guava</artifactId>
+          <version>19.0</version>
+          <type>jar</type>
+        </dependency>
+    </dependencies>
+
+
+  <build>
+    <!-- this plugin will allow us to share resources with children -->
+<!--    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-resources-plugin</artifactId>
+        <version>2.6</version>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-site-plugin</artifactId>
+        <version>3.4</version>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-release-plugin</artifactId>
+        <version>2.5.3</version>
+      </plugin>
+    </plugins>-->
+
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <version>3.5.1</version>
+          <configuration>
+            <source>1.8</source>
+            <target>1.8</target>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>            
+    <repositories>
+        <repository>
+            <id>model-mvn-repo</id>
+            <url>https://raw.github.com/angelicaochoa/persistence/model-0.1.0-mvn-repo/</url>
+            <snapshots>
+                <enabled>true</enabled>
+                <updatePolicy>always</updatePolicy>
+            </snapshots>
+        </repository>
+        <repository>
+            <id>persistence-mybatis-mvn-repo</id>
+            <url>https://raw.github.com/angelicaochoa/persistence/persistence-mybatis-0.1.0-mvn-repo/</url>
+            <snapshots>
+                <enabled>true</enabled>
+                <updatePolicy>always</updatePolicy>
+            </snapshots>
+        </repository>
+        <repository>
+            <id>persistence-jdbc-mvn-repo</id>
+            <url>https://raw.github.com/angelicaochoa/persistence/persistence-jdbc-0.1.0-mvn-repo/</url>
+            <snapshots>
+                <enabled>true</enabled>
+                <updatePolicy>always</updatePolicy>
+            </snapshots>
+        </repository>
+    </repositories>
+</project>

importer/src/main/java/org/cbio/portal/pipelines/importer/ImporterPipeline.java

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+/*
+ * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center.
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
+ * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder
+ * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no
+ * obligations to provide maintenance, support, updates, enhancements or
+ * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be
+ * liable to any party for direct, indirect, special, incidental or
+ * consequential damages, including lost profits, arising out of the use of this
+ * software and its documentation, even if Memorial Sloan-Kettering Cancer
+ * Center has been advised of the possibility of such damage.
+ */
+
+/*
+ * This file is part of cBioPortal.
+ *
+ * cBioPortal is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+package org.cbio.portal.pipelines.importer;
+
+import org.cbio.portal.pipelines.importer.config.BatchConfiguration;
+
+import java.io.*;
+import java.util.*;
+import org.apache.commons.cli.*;
+import org.apache.commons.logging.*;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.ConfigurableApplicationContext;
+import org.springframework.batch.core.*;
+import org.springframework.batch.core.launch.JobLauncher;
+
+/**
+ *
+ * @author ochoaa
+ */
+@SpringBootApplication
+public class ImporterPipeline {
+
+    private static final Log LOG = LogFactory.getLog(ImporterPipeline.class);   
+
+    private static Options getOptions(String[] args) {
+        Options gnuOptions = new Options();
+        gnuOptions.addOption("h", "help", false, "shows this help document and quits.")
+            .addOption("i", "import_study", true, "Cancer study directory to import")
+                .addOption("d", "delete_study", true, "Cancer study identifier for deleting study");
+        return gnuOptions;
+    }
+
+    private static void help(Options gnuOptions, int exitStatus) {
+        HelpFormatter helpFormatter = new HelpFormatter();
+        helpFormatter.printHelp("ImporterPipeline", gnuOptions);
+        System.exit(exitStatus);
+    }
+
+    private static void launchImporterJob(String[] args, String stagingDirectory) throws Exception {
+
+        SpringApplication app = new SpringApplication(ImporterPipeline.class);
+        ConfigurableApplicationContext ctx = app.run(args);
+        JobLauncher jobLauncher = ctx.getBean(JobLauncher.class);
+
+        Job batchImporterJob = ctx.getBean(BatchConfiguration.BATCH_STUDY_IMPORTER_JOB, Job.class);        
+
+        JobParameters jobParameters = new JobParametersBuilder()
+                .addString("stagingDirectory", stagingDirectory)
+                .addDate("date", new Date())
+                .toJobParameters();
+
+        JobExecution jobExecution = jobLauncher.run(batchImporterJob, jobParameters);
+        if (jobExecution.getExitStatus().getExitCode().equals("STOPPED")) {
+            LOG.error("Error importing cancer study.");
+        }
+        ctx.close();
+    }
+
+    private static void launchDeleteStudyJob(String[] args, String cancerStudyIdentifier) throws Exception {
+        SpringApplication app = new SpringApplication(ImporterPipeline.class);
+        ConfigurableApplicationContext ctx = app.run(args);
+        JobLauncher jobLauncher = ctx.getBean(JobLauncher.class);
+
+        Job deleteStudyJob = ctx.getBean(BatchConfiguration.DELETE_CANCER_STUDY_JOB, Job.class);
+
+        JobParameters jobParameters = new JobParametersBuilder()
+                .addString("cancerStudyIdentifier", cancerStudyIdentifier)
+                .toJobParameters();
+
+        JobExecution jobExecution = jobLauncher.run(deleteStudyJob, jobParameters);
+        ctx.close();
+    }
+
+    public static void main(String[] args) throws Exception {
+        Options gnuOptions = ImporterPipeline.getOptions(args);
+        CommandLineParser parser = new GnuParser();
+        CommandLine commandLine = parser.parse(gnuOptions, args);
+        if (commandLine.hasOption("h") ||
+            (!commandLine.hasOption("i") && !commandLine.hasOption("d"))) {
+            help(gnuOptions, 0);
+        }
+
+        if (commandLine.hasOption("d")) {
+            String cancerStudyIdentifier = commandLine.getOptionValue("d");
+            launchDeleteStudyJob(args, cancerStudyIdentifier);
+        }
+
+        if (commandLine.hasOption("i")) {
+            String stagingDirectory = commandLine.getOptionValue("i");
+            if (!(new File(stagingDirectory).exists())) {
+                LOG.error("Staging directory does not exist - please check argument: " + stagingDirectory);
+                System.exit(2);
+            }
+            launchImporterJob(args, stagingDirectory);
+        }
+    }
+
+}