From: Sasha Sherstnev Date: Fri, 8 Nov 2013 10:21:41 +0000 (+0000) Subject: Add properties configuration to the system X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6a7e9f2b0e54c8dfd1adc223a51c28725368eb6b;p=proteocache.git Add properties configuration to the system --- diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component index 108b089..701a517 100644 --- a/.settings/org.eclipse.wst.common.component +++ b/.settings/org.eclipse.wst.common.component @@ -6,6 +6,8 @@ + + diff --git a/conf/Proteocache.properties b/conf/Proteocache.properties new file mode 100644 index 0000000..1f1c5cf --- /dev/null +++ b/conf/Proteocache.properties @@ -0,0 +1,9 @@ +################################################################################# +# Cassandra host or IP +# test server is 10.0.115.190 +cassandra.host=localhost + +################################################################################# +# Jpred sources +cassandra.jpred.web=true +cassandra.jpred.local=false \ No newline at end of file diff --git a/engine/compbio/engine/ProteoCachePropertyHelperManager.java b/engine/compbio/engine/ProteoCachePropertyHelperManager.java new file mode 100644 index 0000000..4615297 --- /dev/null +++ b/engine/compbio/engine/ProteoCachePropertyHelperManager.java @@ -0,0 +1,150 @@ +/* Copyright (c) 2009 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * 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. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ + +package compbio.engine; + +import java.io.File; +import java.io.IOException; +import java.net.URISyntaxException; +import java.net.URL; + +import org.apache.log4j.Logger; + +import compbio.util.PropertyHelper; +import compbio.util.Util; + +public final class ProteoCachePropertyHelperManager { + + private static Logger log = Logger.getLogger(ProteoCachePropertyHelperManager.class); + private static PropertyHelper ph = null; + + /** + * Ways to fix path problem: + * 1) find a path to WEB-INF directory based on the path to a known class. + * Then prepend this absolute path to the rest of paths + * pros: no input from user + * cons: relocation of the source may cause problems + * + * 2) Require users to add configuration directories to the class + * path and then load entries from it. + * pros: + * cons: Many paths needs to be added. Put significant burden on the user. + * Hard to tell web appl server to add these entries to its class path. + * + * 3) Ask for project source directory explicitly in the configuration. + * pros: + * cons: similar to 1, but this initial configuration file must reside in + * well known location! Why ask users what can be found automatically? + * + * 4) Have everything in the location already in class path for tomcat. + * pros: + * cons: only classes and lib/*.jar are added, Eclipse will remove non + * classses from classes dir. + * + * Try 1 - succeed. + * + * @return an instance + */ + public static PropertyHelper getPropertyHelper() { + if (ph == null) { + try { + File MainPropertyFile = getResourceFromClasspath("conf/Proteocache.properties"); + ph = new PropertyHelper(MainPropertyFile); + } catch (IOException e) { + log.warn("Cannot read property files! Reason: " + e.getLocalizedMessage(), e.getCause()); + } + } + return ph; + } + + static File getResourceFromClasspath(String resourceName) { + assert !Util.isEmpty(resourceName); + String locPath = getLocalPath(); + File prop = new File(locPath + resourceName); + if (!prop.exists()) { + log.warn("Could not find a resource " + resourceName + " in the classpath!"); + } + return prop; + } + + /** + * Method return the absolute path to the project root directory. It assumes + * the following structure of the project: + * project-root: + * conf/settings + * binaries + * WEB-INF/classes/compbio/engine/conf/PropertyHelperManager.class + * If the structure changes it must be reflected in this method + * + * @return the local path + * @throws RuntimeException + * if cannot determine the local path + */ + public static String getLocalPath() { + String clname = ProteoCachePropertyHelperManager.class.getSimpleName(); + URL url = ProteoCachePropertyHelperManager.class.getResource(clname + ".class"); + File f = null; + try { + f = new File(url.toURI()); + // Iterate up the hierarchy to find a root project directory + for (int i = 0; i < 5; i++) { + f = f.getParentFile(); + } + } catch (URISyntaxException e) { + String mes = "Could not find resources path! Problems locating PropertyHelperManager class! "; + log.error(mes + e.getLocalizedMessage(), e.getCause()); + throw new RuntimeException(mes + e.getLocalizedMessage(), e.getCause()); + } catch (IllegalArgumentException e) { + // Classes are in the jar file, using different method to determine + // the path new File(INCORRECT URL) throws it + String mes = "It looks like classes are in the jar file. " + + "Attempting a different method to determinine the path to the resources"; + log.debug(mes + e.getLocalizedMessage(), e.getCause()); + try { + f = new File(ProteoCachePropertyHelperManager.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()); + + // Iterate up the hierarchy to find a root project directory + // This time there is not need to walk up all class packages + // WEB_APPL_NAME\WEB-INF\lib\JAR-FILE-NAME + // jws2-1.0\WEB-INF\lib\full-jws2-1.0.jar + for (int i = 0; i < 3; i++) { + f = f.getParentFile(); + } + } catch (URISyntaxException e1) { + log.error("Could not find resources path! " + e1.getLocalizedMessage(), e1.getCause()); + throw new RuntimeException("Could not find resources path! ", e1.getCause()); + } + } + log.debug("Project directory is: " + f.getAbsolutePath()); + return f.getAbsolutePath() + File.separator; + } + + public static int getIntProperty(String propValue) { + if (!Util.isEmpty(propValue)) { + return Integer.parseInt(propValue.trim()); + } + return -1; + } + + public static boolean getBooleanProperty(String propValue) { + if (!Util.isEmpty(propValue)) { + propValue = propValue.trim(); + return Boolean.parseBoolean(propValue); + } + return false; + }}