Feature/refactor

pom.xml

@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.reactome.release</groupId>
 			<artifactId>release-common-lib</artifactId>
-			<version>2.0.0-SNAPSHOT</version>
+			<version>2.0.0</version>
 		</dependency>
 		<dependency>
 			<groupId>com.beust</groupId>

src/main/java/org/reactome/release/cosmicupdate/COSMICFileManager.java

@@ -0,0 +1,110 @@
+package org.reactome.release.cosmicupdate;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.reactome.release.common.dataretrieval.cosmic.COSMICFileRetriever;
+import org.reactome.util.general.GUnzipCallable;
+
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.time.Duration;
+import java.util.List;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.stream.Collectors;
+
+public class COSMICFileManager {
+    private static final Logger logger = LogManager.getLogger();
+
+    private final Config config;
+
+    public COSMICFileManager(Config config) {
+        this.config = config;
+    }
+
+    public void unzipFiles() throws InterruptedException {
+        ExecutorService execService = Executors.newCachedThreadPool();
+        // The files are large, and it could be slow to unzip them sequentially, so we will unzip them in parallel.
+        execService.invokeAll(getGUnzipCallables());
+        execService.shutdown();
+    }
+
+    /**
+     * Clean up the uncompressed data files. Don't remove the zipped files, because if you need to run this code again,
+     * you'll be stuck waiting for the files to download again. Try to avoid removing the zipped files until
+     * you're *sure* this step has run successfully.
+     */
+    public void cleanupFiles() {
+        List<String> filesToDelete = getConfig().getAllCOSMICLocalFilePaths();
+        for (String file : filesToDelete) {
+            deleteFile(file);
+        }
+    }
+
+    /**
+     * Download the data files from COSMIC if older than the specified duration
+     */
+    public void downloadFiles(Duration fileAge) {
+        for (Config.FileConfig fileConfig : getConfig().getFileConfigs() ) {
+            downloadFile(fileConfig, fileAge);
+        }
+    }
+
+    private void downloadFile(Config.FileConfig config, Duration fileAge) {
+        try {
+            COSMICFileRetriever retriever = new COSMICFileRetriever();
+            retriever.setDataURL(new URI(config.getUrl()));
+            retriever.setFetchDestination(config.getDestination());
+            retriever.setMaxAge(fileAge);
+            retriever.setUserName(getConfig().getCosmicUsername());
+            retriever.setPassword(getConfig().getCosmicPassword());
+
+            logger.info("Downloading {} to {}", retriever.getDataURL(), config.getDestination());
+            retriever.fetchData();
+        } catch (URISyntaxException e) {
+            throw new RuntimeException("Invalid URL for " + config.getDescription(), e);
+        } catch (Exception e) {
+            throw new RuntimeException("Error downloading " + config.getDescription(), e);
+        }
+    }
+
+    /**
+     * Deletes a file and logs a message about the deletion.
+     * @param filePath Path of the file to delete
+     */
+    private void deleteFile(String filePath) {
+        try {
+            Files.deleteIfExists(Paths.get(filePath));
+            logger.info("{} was deleted.", filePath);
+        } catch (IOException e) {
+            logger.warn("IOException caught while cleaning up the data file: \"" + filePath + "\". " +
+                "You may need to manually remove any remaining files.", e);
+        }
+    }
+
+    private List<GUnzipCallable> getGUnzipCallables() {
+        return getConfig().getAllCOSMICLocalFilePaths().stream()
+            .map(this::getGUnzipCallable)
+            .collect(Collectors.toList());
+    }
+
+    private GUnzipCallable getGUnzipCallable(String filePathAsString) {
+        return new GUnzipCallable(getGZippedFilePath(filePathAsString), getGUnzippedFilePath(filePathAsString));
+    }
+
+    private Path getGZippedFilePath(String filePathAsString) {
+        return Paths.get(getGUnzippedFilePath(filePathAsString) + ".gz");
+    }
+
+    private Path getGUnzippedFilePath(String filePathAsString) {
+        return Paths.get(filePathAsString);
+    }
+
+    private Config getConfig() {
+        return this.config;
+    }
+}