revert deployment changes (#217)

Author: William Welling

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/ApplicationSetup.java

@@ -24,7 +24,6 @@
  */
 public class ApplicationSetup implements ServletContextListener {
 	private static final String APPLICATION_SETUP_PATH = "config/applicationSetup.n3";
-	private static final String APPLICATION_SETUP_DEFAULT_PATH = "config/default.applicationSetup.n3";
 
 	private ServletContext ctx;
 	private StartupStatus ss;
@@ -46,8 +45,6 @@ public void contextInitialized(ServletContextEvent sce) {
 			this.vitroHomeDir = VitroHomeDirectory.find(ctx);
 			ss.info(this, vitroHomeDir.getDiscoveryMessage());
 
-			this.vitroHomeDir.populate();
-
 			locateApplicationConfigFile();
 			loadApplicationConfigFile();
 			createConfigurationBeanLoader();
@@ -66,19 +63,11 @@ public void contextInitialized(ServletContextEvent sce) {
 	private void locateApplicationConfigFile() {
 		Path path = this.vitroHomeDir.getPath().resolve(APPLICATION_SETUP_PATH);
 
-		if (!Files.exists(path) || !Files.isReadable(path)) {
-			path = this.vitroHomeDir.getPath().resolve(APPLICATION_SETUP_DEFAULT_PATH);
-		}
-
 		if (!Files.exists(path)) {
-			throw new IllegalStateException("Neither '" + APPLICATION_SETUP_PATH + "' nor '" +
-					APPLICATION_SETUP_DEFAULT_PATH + "' were found in " +
-					this.vitroHomeDir.getPath());
+			throw new IllegalStateException("'" + path + "' does not exist.");
 		}
 		if (!Files.isReadable(path)) {
-			throw new IllegalStateException("No readable '" + APPLICATION_SETUP_PATH + "' nor '" +
-					APPLICATION_SETUP_DEFAULT_PATH + "' files were found in " +
-					this.vitroHomeDir.getPath());
+			throw new IllegalStateException("Can't read '" + path + "'");
 		}
 		this.configFile = path;
 	}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/application/VitroHomeDirectory.java

@@ -4,46 +4,25 @@
 
 import static edu.cornell.mannlib.vitro.webapp.application.BuildProperties.WEBAPP_PATH_BUILD_PROPERTIES;
 
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStreamWriter;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
+import javax.naming.InitialContext;
 import javax.servlet.ServletContext;
 
-import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
-import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import edu.cornell.mannlib.vitro.webapp.config.ContextProperties;
-
 /**
- * Encapsulates some of the info relating to and initializes the Vitro home directory.
+ * Encapsulates some of the info relating to the Vitro home directory.
  */
 public class VitroHomeDirectory {
 	private static final Log log = LogFactory.getLog(VitroHomeDirectory.class);
 
-	private static final String DIGEST_FILE_NAME = "digest.md5";
-
-	private static final Pattern CHECKSUM_PATTERN = Pattern.compile("^[a-f0-9]{32} \\*.+$");
-
 	public static VitroHomeDirectory find(ServletContext ctx) {
 		HomeDirectoryFinder finder = new HomeDirectoryFinder(ctx);
 		return new VitroHomeDirectory(ctx, finder.getPath(),
@@ -73,219 +52,6 @@ public String getDiscoveryMessage() {
 		return discoveryMessage;
 	}
 
-	/**
-	 * Populates VIVO home directory with files required to run.
-	 * 
-	 * NOTE: Will not overwrite any modified files on redeploy.
-	 */
-	public void populate() {
-		File vhdDir = getPath().toFile();
-
-		if (!vhdDir.isDirectory() || vhdDir.list() == null) {
-			throw new RuntimeException("Application home dir is not a directory! " + vhdDir);
-		}
-
-		Map<String, String> digest = untar(vhdDir);
-
-		writeDigest(digest);
-	}
-
-	/**
-	 * A non-destructive untar process that returns checksum digest of tarred files.
-	 * 
-	 * Checksum digest can be manually created with the following command.
-	 * 
-	 * `find /vivo/home -type f | cut -c3- | grep -E '^bin/|^config/|^rdf/' | xargs md5sum > /vivo/home/digest.md5`
-	 * 
-	 * @param destination VIVO home directory
-	 * @return digest of each files checksum
-	 */
-	private Map<String, String> untar(File destination) {
-		log.info("Syncing VIVO home at: " + destination.getPath());
-
-		Map<String, String> digest = new HashMap<>();
-		Map<String, String> storedDigest = loadDigest();
-
-		TarArchiveEntry tarEntry;
-		try (
-			InputStream homeDirTar = getHomeDirTar();
-			TarArchiveInputStream tarInput = new TarArchiveInputStream(homeDirTar);
-		) {
-			while ((tarEntry = tarInput.getNextTarEntry()) != null) {
-
-				// Use the example configurations
-				String outFilename = tarEntry.getName().replace("example.", "");
-				File outFile = new File(destination, outFilename);
-
-				// Is the entry a directory?
-				if (tarEntry.isDirectory()) {
-					if (!outFile.exists()) {
-						outFile.mkdirs();
-					}
-				} else {
-					// Entry is a File
-					boolean write = true;
-
-					// reading bytes into memory to avoid having to unreliably reset stream
-					byte[] bytes = IOUtils.toByteArray(tarInput);
-					String newFileChecksum = checksum(bytes);
-					digest.put(outFilename, newFileChecksum);
-
-					// if file already exists and stored digest contains the file,
-					// check to determine if it has changed
-					if (outFile.exists() && storedDigest.containsKey(outFilename)) {
-						String existingFileChecksum = checksum(outFile);
-						// if file has not changed in home and is not the same as new file, overwrite
-						write = storedDigest.get(outFilename).equals(existingFileChecksum)
-							&& !existingFileChecksum.equals(newFileChecksum);
-					}
-
-					if (write) {
-						outFile.getParentFile().mkdirs();
-						try (
-							InputStream is = new ByteArrayInputStream(bytes);
-							FileOutputStream fos = new FileOutputStream(outFile);
-						) {
-							IOUtils.copy(is, fos);
-							log.info(outFile.getAbsolutePath() + " source has changed and has not been "
-							         + "edited in home, updated file has been copied to home directory.");
-						}
-					} else {
-						log.debug(outFile.getAbsolutePath() + " has been preserved.");
-					}
-				}
-			}
-		} catch (IOException | NoSuchAlgorithmException e) {
-			throw new RuntimeException("Error creating home directory!", e);
-		}
-
-		return digest;
-	}
-
-	/**
-	 * Load checksum digest of VIVO home directory.
-	 * 
-	 * @return checksum digest
-	 */
-	private Map<String, String> loadDigest() {
-		File storedDigest = new File(getPath().toFile(), DIGEST_FILE_NAME);
-		if (storedDigest.exists() && storedDigest.isFile()) {
-			log.info("Reading VIVO home digest: " + storedDigest.getPath());
-			try {
-				return FileUtils
-					.readLines(storedDigest, StandardCharsets.UTF_8)
-					.stream()
-					.filter(CHECKSUM_PATTERN.asPredicate())
-					.map(this::split)
-					.collect(Collectors.toMap(this::checksumFile, this::checksumValue));
-			} catch (IOException e) {
-				throw new RuntimeException("Error reading VIVO home checksum digest!", e);
-			}
-		}
-		log.info("VIVO home digest not found: " + storedDigest.getPath());
-
-		return new HashMap<>();
-	}
-
-	/**
-	 * Write VIVO home checksum digest following md5 format; `<checksum> *<file>`.
-	 * 
-	 * @param digest checksum digest to write
-	 */
-	private void writeDigest(Map<String, String> digest) {
-		File storedDigest = new File(getPath().toFile(), DIGEST_FILE_NAME);
-		try (
-			FileOutputStream fos = new FileOutputStream(storedDigest); 
-			OutputStreamWriter osw = new OutputStreamWriter(fos);
-		) {
-			for (Map.Entry<String, String> entry : digest.entrySet()) {
-				String filename = entry.getKey();
-				String checksum = entry.getValue();
-				osw.write(String.format("%s *%s\n", checksum, filename));
-			}
-		} catch (IOException e) {
-			throw new RuntimeException("Error writing home directory checksum digest!", e);
-		}
-		log.info("VIVO home digest created: " + storedDigest.getPath());
-	}
-
-	/**
-	 * Split checksum.
-	 * 
-	 * @param checksum checksum delimited by space and asterisks `<checksum> *<file>`
-	 * @return split checksum
-	 */
-	private String[] split(String checksum) {
-		return checksum.split("\\s+");
-	}
-
-	/**
-	 * Get value from split checksum.
-	 * 
-	 * @param checksum split checksum
-	 * @return checksum value
-	 */
-	private String checksumValue(String[] checksum) {
-		return checksum[0];
-	}
-
-	/**
-	 * Return file from split checksum.
-	 * 
-	 * @param checksum split checksum
-	 * @return filename
-	 */
-	private String checksumFile(String[] checksum) {
-		return checksum[1].substring(1);
-	}
-
-	/**
-	 * Get md5 checksum from file.
-	 * 
-	 * @param file file
-	 * @return md5 checksum as string
-	 * @throws IOException
-	 * @throws NoSuchAlgorithmException
-	 */
-	private String checksum(File file) throws IOException, NoSuchAlgorithmException {
-		return checksum(FileUtils.readFileToByteArray(file));
-	}
-
-	/**
-	 * Get md5 checksum from bytes.
-	 * 
-	 * @param bytes bytes from file
-	 * @return md5 checksum as string
-	 * @throws NoSuchAlgorithmException
-	 */
-	private String checksum(byte[] bytes) throws NoSuchAlgorithmException {
-		MessageDigest md = MessageDigest.getInstance("MD5");
-		md.update(bytes);
-		// bytes to hex
-		StringBuilder result = new StringBuilder();
-		for (byte b : md.digest()) {
-			result.append(String.format("%02x", b));
-		}
-
-		return result.toString();
-	}
-
-	/**
-	 * Get prepacked VIVO home tar file as input stream.
-	 * 
-	 * @return input stream of VIVO home tar file
-	 */
-	private InputStream getHomeDirTar() {
-		String tarLocation = "/WEB-INF/resources/home-files/vivo-home.tar";
-		InputStream tar = ctx.getResourceAsStream(tarLocation);
-		if (tar == null) {
-			log.error("Application home tar not found in: " + tarLocation);
-			throw new RuntimeException("Application home tar not found in: " + tarLocation);
-		}
-
-		return tar;
-	}
-
 	/**
 	 * Find something that specifies the location of the Vitro home directory.
 	 * Look in the JDNI environment, the system properties, and the
@@ -326,12 +92,23 @@ public Path getPath() {
 		}
 
 		public void getVhdFromJndi() {
-			String vhdPath = ContextProperties.findJndiProperty(VHD_JNDI_PATH);
-			log.debug("'" + VHD_JNDI_PATH + "' as specified by JNDI: " + vhdPath);
-			String message = String.format(
-					"JNDI environment '%s' was set to '%s'",
-					VHD_JNDI_PATH, vhdPath);
-			foundLocations.add(new Found(Paths.get(vhdPath), message));
+			try {
+				String vhdPath = (String) new InitialContext()
+						.lookup(VHD_JNDI_PATH);
+				if (vhdPath == null) {
+					log.debug("Didn't find a JNDI value at '" + VHD_JNDI_PATH
+							+ "'.");
+				} else {
+					log.debug("'" + VHD_JNDI_PATH + "' as specified by JNDI: "
+							+ vhdPath);
+					String message = String.format(
+							"JNDI environment '%s' was set to '%s'",
+							VHD_JNDI_PATH, vhdPath);
+					foundLocations.add(new Found(Paths.get(vhdPath), message));
+				}
+			} catch (Exception e) {
+				log.debug("JNDI lookup failed. " + e);
+			}
 		}
 
 		private void getVhdFromSystemProperties() {

api/src/main/java/edu/cornell/mannlib/vitro/webapp/config/ConfigurationPropertiesImpl.java

@@ -32,10 +32,8 @@ public class ConfigurationPropertiesImpl extends ConfigurationProperties {
 
 	public ConfigurationPropertiesImpl(InputStream stream,
 			Map<String, String> preemptiveProperties,
-			Map<String, String> buildProperties,
-			Map<String, String> contextProperties) throws IOException {
+			Map<String, String> buildProperties) throws IOException {
 		Map<String, String> map = new HashMap<>(buildProperties);
-		map.putAll(contextProperties);
 
 		Properties props = loadFromPropertiesFile(stream);
 		for (String key: props.stringPropertyNames()) {