enable to override DBMSConfigurator props using JRE -D arguments; pre…

…fix props with KL_
pgdurand · Oct 30, 2020 · 2f1337e · 2f1337e
1 parent 9e92600
commit 2f1337e
Show file tree

Hide file tree

Showing 4 changed files with 42 additions and 53 deletions.
diff --git a/src/bzh/plealog/dbmirror/ui/LocalDBPanel.java b/src/bzh/plealog/dbmirror/ui/LocalDBPanel.java
@@ -80,6 +80,11 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.jgoodies.forms.builder.DefaultFormBuilder;
+import com.jgoodies.forms.layout.FormLayout;
+import com.plealog.genericapp.api.EZEnvironment;
+import com.plealog.genericapp.api.file.EZFileManager;
+
 import bzh.plealog.dbmirror.fetcher.DBServerConfig;
 import bzh.plealog.dbmirror.fetcher.PFTPLoaderDescriptor;
 import bzh.plealog.dbmirror.fetcher.PLocalLoader;
@@ -90,7 +95,6 @@
 import bzh.plealog.dbmirror.ui.resources.DBMSMessages;
 import bzh.plealog.dbmirror.util.Utils;
 import bzh.plealog.dbmirror.util.conf.DBMSAbstractConfig;
-import bzh.plealog.dbmirror.util.conf.DBMSConfigurator;
 import bzh.plealog.dbmirror.util.conf.DBMirrorConfig;
 import bzh.plealog.dbmirror.util.descriptor.DBDescriptor;
 import bzh.plealog.dbmirror.util.descriptor.DBDescriptorUtils;
@@ -103,11 +107,6 @@
 import bzh.plealog.dbmirror.util.sequence.SequenceValidatorTaxon;
 import bzh.plealog.dbmirror.util.sequence.TaxonMatcherHelper;
 
-import com.jgoodies.forms.builder.DefaultFormBuilder;
-import com.jgoodies.forms.layout.FormLayout;
-import com.plealog.genericapp.api.EZEnvironment;
-import com.plealog.genericapp.api.file.EZFileManager;
-
 /**
  * This class implements a panel enabling a user to use the KDMS Lucene Indexer
  * system given a set of data files.
@@ -1351,15 +1350,15 @@ public void actionPerformed(ActionEvent e) {
           // In case of a previous filter, takes the filtered files
 
           final File current = new File(file);
-          foundFiles = new File(DBMSConfigurator.TMP_FILTER_DIRECTORY)
+          foundFiles = new File(DBMSAbstractConfig.getWorkingFilterPath())
               .list(new FilenameFilter() {
                 @Override
                 public boolean accept(File dir, String name) {
                   return current.getName().equalsIgnoreCase(name);
                 }
               });
           if ((foundFiles != null) && (foundFiles.length == 1)) {
-            databankFiles.add(new File(DBMSConfigurator.TMP_FILTER_DIRECTORY,
+            databankFiles.add(new File(DBMSAbstractConfig.getWorkingFilterPath(),
                 foundFiles[0]));
 
           } else {

diff --git a/src/bzh/plealog/dbmirror/util/conf/DBMSAbstractConfig.java b/src/bzh/plealog/dbmirror/util/conf/DBMSAbstractConfig.java
@@ -60,6 +60,7 @@ public class DBMSAbstractConfig {
   private static String                  _logAppFileName;
   private static String                  _logAppFile;
   private static String                  _workingTmpPath;
+  private static String                  _filterWorkingTmpPath;
   private static String                  _externalBinPath;
   private static String                  _confPath;
   private static String                  _startDate;
@@ -87,15 +88,15 @@ public class DBMSAbstractConfig {
   public static final String             CONF_PATH_NAME               = "conf";
   public static final String             EXT_PATH_NAME                = "external";
   public static final String             BIN_PATH_NAME                = "bin";
-  private static final String            APP_HOME_PROP_KEY            = "KL_HOME";
-  private static final String            APP_WORKING_DIR_PROP_KEY     = "KL_WORKING_DIR";
-  private static final String            APP_CONF_DIR_PROP_KEY        = "KL_CONF_DIR";
-  public  static final String            APP_DEBUG_MODE_PROP_KEY      = "KL_DEBUG";
-  private static final String            APP_LOG_FILE_PROP_KEY        = "KL_LOG_FILE";
-  private static final String            LCL_MIRROR_PROP_KEY          = "MIRROR_HOME";
+  public static final String             APP_KEY_PREFIX               = "KL_";
+  private static final String            APP_HOME_PROP_KEY            = APP_KEY_PREFIX+"HOME";
+  private static final String            APP_WORKING_DIR_PROP_KEY     = APP_KEY_PREFIX+"WORKING_DIR";
+  private static final String            APP_CONF_DIR_PROP_KEY        = APP_KEY_PREFIX+"CONF_DIR";
+  public  static final String            APP_DEBUG_MODE_PROP_KEY      = APP_KEY_PREFIX+"DEBUG";
+  private static final String            APP_LOG_FILE_PROP_KEY        = APP_KEY_PREFIX+"LOG_FILE";
   private static final String            USER_DIR_PROP_KEY            = "user.dir";
 
-  private static final String            DEF_DB_PATH                  = "biobanks";
+  private static final String            DEF_DB_PATH                  = "beedeem_banks_repository";
 
   // file containing the DB_XREFs definition
   public static final String             DB_XREF_CONF_FILE            = "dbxrefsForFasta.config";
@@ -167,7 +168,7 @@ public static String getLocalMirrorPath() {
 
     if (_localMirrorPath != null)
       return _localMirrorPath;
-    String path = pruneQuotes(System.getProperty(LCL_MIRROR_PROP_KEY));
+    String path = pruneQuotes(System.getProperty(APP_KEY_PREFIX+DBMSConfigurator.MIRROR_PATH));
     if (path != null) {
       _localMirrorPath = path;
     } else {
@@ -278,11 +279,27 @@ public static String getWorkingPath() {
     return _workingTmpPath;
   }
 
-  public static void setWorkingPath(String path) {
-    _workingTmpPath = Utils.terminatePath(path);
-    LOGGER.debug("working path: " + _workingTmpPath);
+  public static String getWorkingFilterPath() {
+    if (_filterWorkingTmpPath != null)
+      return _filterWorkingTmpPath;
+    _filterWorkingTmpPath = Utils.terminatePath(getWorkingPath()+"filter");
+    File f = new File(_filterWorkingTmpPath);
+    if (!f.exists()) {
+      f.mkdirs();
+    } else {
+      try {
+        FileUtils.cleanDirectory(f);
+      } catch (IOException e) {
+        // do not throw exception for this
+        LoggerCentral.warn(
+            LOGGER,
+            "Unable to manage the tmp filter directory in '"
+                + _filterWorkingTmpPath + "' : "
+                + e.getMessage());
+      }
+    }
+    return _filterWorkingTmpPath;
   }
-
   /**
    * Returns the path pointing to external binaries. The path specifically
    * points to the OS localized dir (linux, windows or macos).
@@ -501,31 +518,7 @@ public static void initializeConfigurator(String kdmsConfFile) {
       LoggerCentral.info(LOGGER, "*** START APPLICATION *** " + new Date());
       LoggerCentral.info(LOGGER, "Configuration:");
       _configurator.dumpContent(LOGGER);
-
-      // manage the tmp filter directory
-      try {
-        DBMSConfigurator.TMP_FILTER_DIRECTORY = DBMSExecNativeCommand
-            .formatNativePath(
-                (Utils.terminatePath(DBMSAbstractConfig.getLocalMirrorPath()) + "tmp")
-                    .replace(File.separatorChar, '|'), false, false).replace(
-                '|', File.separatorChar);
-        File tmpFilterDirectory = new File(
-            DBMSConfigurator.TMP_FILTER_DIRECTORY);
-        if (!tmpFilterDirectory.exists()) {
-          tmpFilterDirectory.mkdirs();
-        } else {
-          FileUtils.cleanDirectory(tmpFilterDirectory);
-        }
-      } catch (IOException e) {
-        // do not throw exception for this
-        LoggerCentral.warn(
-            LOGGER,
-            "Unable to manage the tmp filter directory in '"
-                + DBMSConfigurator.TMP_FILTER_DIRECTORY + "' : "
-                + e.getMessage());
-      }
     }
-
   }
 
   /**

diff --git a/src/bzh/plealog/dbmirror/util/conf/DBMSConfigurator.java b/src/bzh/plealog/dbmirror/util/conf/DBMSConfigurator.java
@@ -77,11 +77,6 @@ public static enum LUCENE_LK_VALUES {LK_DEFAULT, LK_NATIVE, LK_SIMPLE};
 		  LONG_FILE_NAME, FDB_PRG_NAME, FDB_PATH_NAME, UI_SHOW_PATH, COPY_WORKERS,
 		  FASTA_VOLSIZE, LUCENE_FS, LUCENE_LOCK, ASPERA_KEY, ASPERA_BIN};
 
-  public static String              TMP_FILTER_DIRECTORY = Utils
-                                                             .terminatePath(DBMSAbstractConfig
-                                                                 .getLocalMirrorPath())
-                                                             + "tmp";
-
   public DBMSConfigurator() {
     try {
       _pConfig = new PropertiesConfiguration();
@@ -153,7 +148,9 @@ public void load(String path, boolean listenReload) throws IOException {
    * @see java.util.Properties#getProperty(java.lang.String)
    */
   public String getProperty(String key) {
-    return _pConfig.getString(key);
+    //this was added to enable overriding config file properties using java -D arguments.
+    String value = DBMSAbstractConfig.pruneQuotes(System.getProperty(DBMSAbstractConfig.APP_KEY_PREFIX+key));
+    return value !=null ? value : _pConfig.getString(key);
   }
 
   /**

diff --git a/src/bzh/plealog/dbmirror/util/sequence/SequenceFileManager.java b/src/bzh/plealog/dbmirror/util/sequence/SequenceFileManager.java
@@ -35,7 +35,7 @@
 import org.apache.commons.logging.Log;
 
 import bzh.plealog.dbmirror.util.Utils;
-import bzh.plealog.dbmirror.util.conf.DBMSConfigurator;
+import bzh.plealog.dbmirror.util.conf.DBMSAbstractConfig;
 import bzh.plealog.dbmirror.util.descriptor.DatabankFormat;
 import bzh.plealog.dbmirror.util.log.LoggerCentral;
 
@@ -108,7 +108,7 @@ public void abortProcess() {
   public SequenceFileManager(String sequenceFilepath,
       DatabankFormat databankFormat, Log logger, JProgressBar progressBar)
       throws IOException {
-    setTmpFileDirectory(DBMSConfigurator.TMP_FILTER_DIRECTORY);
+    setTmpFileDirectory(DBMSAbstractConfig.getWorkingFilterPath());
     this.sequenceFile = new File(sequenceFilepath);
     this.databankFormat = databankFormat;
     this.progressBar = progressBar;
@@ -142,7 +142,7 @@ public SequenceFileManager(String sequenceFilepath,
    */
   public SequenceFileManager(BufferedReader reader, BufferedWriter writer,
       DatabankFormat databankFormat, Log logger) {
-    setTmpFileDirectory(DBMSConfigurator.TMP_FILTER_DIRECTORY);
+    setTmpFileDirectory(DBMSAbstractConfig.getWorkingFilterPath());
     this.databankFormat = databankFormat;
     this.logger = logger;
     this.validators = new ArrayList<ISequenceValidator>();