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Common code shared among all PharmGKB projects.
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package org.pharmgkb.common.util;

import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.nio.file.FileSystemNotFoundException;
import java.nio.file.FileSystems;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collections;
import com.google.common.base.Preconditions;
import org.apache.commons.lang3.StringUtils;
import org.checkerframework.checker.nullness.qual.Nullable;


/**
 * Utility methods for working with {@link Path}s.
 *
 * @author Mark Woon
 */
public final class PathUtils {

  /**
   * Private constructor to prevent instantiation of utility class.
   */
  private PathUtils() {
  }


  /**
   * Gets the name of the file.
   * Does not validate if {@code file} is a regular file.
   */
  public static String getFilename(Path file) {
    Preconditions.checkNotNull(file);

    return file.getName(file.getNameCount() - 1).toString();
  }


  /**
   * Gets the file extension, if one exists.  Does not include ".".
   * Does not validate if {@code file} is a regular file.
   */
  public static @Nullable String getFileExtension(Path file) {
    String filename = getFilename(file);
    int idx = filename.lastIndexOf(".");
    if (idx == -1) {
      return null;
    }
    return StringUtils.stripToNull(filename.substring(idx + 1));
  }

  /**
   * Gets the base name of the file (i.e. file name without the extension).
   * Does not validate if {@code file} is a regular file.
   */
  public static String getBaseFilename(Path file) {
    Preconditions.checkNotNull(file);

    String fileName = getFilename(file);
    int idx = fileName.lastIndexOf(".");
    if (idx == -1) {
      return fileName;
    }
    return fileName.substring(0, idx);
  }


  /**
   * Converts a resource file name into a {@link Path}.
   *
   * @param filename a relative filename from root (e.g. {@code org/pharmgkb/common/file.txt})
   */
  public static Path getPathToResource(String filename) {
    Preconditions.checkNotNull(filename);

    if (filename.startsWith("/")) {
      filename = filename.substring(1);
    }

    URL url = PathUtils.class.getClassLoader().getResource(filename);
    return getPath(url, filename);
  }

  /**
   * Converts a resource file name into a {@link Path}.
   *
   * @param clz the class the filename is relative to
   * @param filename a relative filename from root (e.g. {@code org/pharmgkb/common/file.txt})
   */
  public static Path getPathToResource(Class clz, String filename) {
    Preconditions.checkNotNull(filename);

    URL url = clz.getResource(filename);
    return getPath(url, filename);
  }


  private static Path getPath(@Nullable URL url, String filename) {
    if (url == null) {
      throw new IllegalArgumentException("No such resource: " + filename);
    }
    try {
      URI uri = url.toURI();
      if (url.getProtocol().equalsIgnoreCase("jar")) {
        try {
          FileSystems.getFileSystem(uri);
        } catch (FileSystemNotFoundException ex) {
          try {
            FileSystems.newFileSystem(uri, Collections.emptyMap());
          } catch (IOException ex2) {
            throw new IllegalStateException("Unable to create zip/jar filesystem", ex2);
          }
        }
      }

      return Paths.get(uri);

    } catch (URISyntaxException ex) {
      // should never happen
      throw new IllegalStateException("Filename '" + filename + "' translated to invalid URI (" + url + ")", ex);
    }
  }
}