obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 172)

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Revision: 364
          http://svn.sourceforge.net/obo/?rev=364&view=rev
Author:   mgibson
Date:     2007-02-07 14:46:44 -0800 (Wed, 07 Feb 2007)

Log Message:
-----------
changed -i to -u --initialConfig to --updateConfig
initial config is pase - as update config covers it
finally moved config cmmd line options to CommandLine class where they belong
so now it wont show that annoying message dont know -c option - took me long
enough 

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/main/CommandLine.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================

--- phenote/trunk/src/java/phenote/config/Config.java	2007-02-07 21:57:41 UTC (rev 363)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-02-07 22:46:44 UTC (rev 364)
@@ -41,10 +41,13 @@
   private boolean uvicGraphEnabled = false; // default false for now
   private String reposUrlDir;
   private String version;
+  private boolean configInitialized = false;
 
   /** singleton */
   private Config() {}
 
+  public boolean isInitialized() { return configInitialized; }
+
   /** This is setting config file with nothing to do with personal config
    this is for the servlet where config file location is set in web.xml */
   public void setConfigFile(String configFile) throws ConfigException {
@@ -56,12 +59,12 @@
       files is used - the -i option if you will. The initial config file will
       get copied to .phenote/my-phenote.cfg if it doesnt already exist. if it
       exists then this file is ignored */
-  public void setInitialConfigFile(String configFile) throws ConfigException {
-    //if (configFile==null) configFile = getDefaultFile();
-    //setConfigFile(configFile,true,false,true); // last true should be false!
-    updateConfigFileWithNewVersion(configFile);
-    //setConfigFile(configFile,true,false);
-  }
+//   public void setInitialConfigFile(String configFile) throws ConfigException {
+//     //if (configFile==null) configFile = getDefaultFile();
+//     //setConfigFile(configFile,true,false,true); // last true should be false!
+//     updateConfigFileWithNewVersion(configFile);
+//     //setConfigFile(configFile,true,false);
+//   }
 
   // --update - set up cmd line!
   public void updateConfigFileWithNewVersion(String configFile) throws ConfigException {
@@ -109,6 +112,9 @@
     //System.out.println("config file: "+configUrl);
     parseXmlFile(configFile); // throws ex
 
+    // if we got here we succeeded in setting config
+    configInitialized = true;
+
     //System.out.println("testing config writeback");
     //new ConfigWriter().writeConfig(this,new File(FileUtil.getDotPhenoteDir(),"my-phenote.cfg"));
   }

Modified: phenote/trunk/src/java/phenote/main/CommandLine.java
===================================================================
--- phenote/trunk/src/java/phenote/main/CommandLine.java	2007-02-07 21:57:41 UTC (rev 363)
+++ phenote/trunk/src/java/phenote/main/CommandLine.java	2007-02-07 22:46:44 UTC (rev 364)
@@ -4,6 +4,8 @@
 import com.townleyenterprises.command.CommandParser;
 import com.townleyenterprises.command.DefaultCommandListener;
 
+import phenote.config.Config;
+import phenote.config.ConfigException;
 import phenote.dataadapter.DataAdapterI;
 import phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter;
 import phenote.dataadapter.phenoxml.PhenoXmlAdapter;
@@ -22,9 +24,11 @@
   private CommandOption inputFile = new InputFileCommandOption();
   //private CommandOption inputFmtOption = new InputFormatCommandOption();
   private CommandOption writeFile = new WriteFileCommandOption();
-  //private CommandOption updateConfig 
+  private CommandOption updateConfig = new UpdateConfigCommandOption();
+  private CommandOption setConfig = new SetConfigCommandOption();
 
-  CommandOption[] options = new CommandOption[] { inputFile, writeFile };
+  CommandOption[] options = new CommandOption[] { inputFile, writeFile, updateConfig,
+                                                  setConfig };
 
   // this guarantees that we get the right classes (compile time check)
   private final static String PHENOXML = PhenoXmlAdapter.class.getName();
@@ -117,7 +121,44 @@
     return adapter;
   }
 
+  private class UpdateConfigCommandOption extends CommandOption {
+    private final static String help =
+    "Specify config file to update from app conf, adds in new config fields."
+    +" if nothing to update just loads config file as is";
+    private UpdateConfigCommandOption() {
+      // true -> has argument
+      super("updateConfig",'u',true,"config file",help);
+    }
+    public void execute() throws Exception {
+      //System.out.println("executing update config command option "+getArg());
+      try { Config.inst().updateConfigFileWithNewVersion(getArg()); }
+      catch (ConfigException e) { loadDefaultConfig("overwrite",e); }
+    }
+  }
 
+  private class SetConfigCommandOption extends CommandOption {
+    private final static String help =
+      "Specify config file to set from app conf, careful this wipes out previous config";
+    private SetConfigCommandOption() {
+      super("configSet",'c',true,"config file",help); // true -> has arg
+    }
+    public void execute() throws Exception {
+      try { Config.inst().setOverwriteConfigFile(getArg()); }
+      catch (ConfigException e) { loadDefaultConfig("overwrite",e); }
+    }
+  }
+
+  private void loadDefaultConfig(String m, ConfigException e) {
+    System.out.println("Yikes! Failed to "+m+" config file "+e+" gonna try "
+                       +"loading default config");
+    try { Config.inst().loadDefaultConfigFile(); }
+    catch (ConfigException ce) { 
+      System.out.println("bummer - even default config fails. we're hosed! "+ce);
+    }
+  }
+    
+
+
   /** INPUT FILE COMMAND OPTION */
   private class InputFileCommandOption extends CommandOption {
     private final static String help =

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-02-07 21:57:41 UTC (rev 363)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-02-07 22:46:44 UTC (rev 364)
@@ -109,67 +109,74 @@
   }
 
   private void doCommandLine(String[] args) {
-    doCommandLineOld(args); // -c -i  --> move to CommandLine!
+    //doCommandLineOld(args); // -c -i  --> move to CommandLine!
     try { commandLine.setArgs(args); } // no log yet - sys.out
     catch (Exception e) { System.out.println("Command line read failed"+e); }
-  }
-
-  /** for now just looking for '-c configFile.cfg', use command line package
-      if we need to get more sophisticated 
-      so if user has personal config file should override this - however maybe 
-      there should be a distinction between initial config file and user made configs
-      well really the initials are db/species specific - so could be 
-      --initialConfig zf|fb|obd - actually da heck with that with entity chooser just
-      put all 3 ontologies in one which is then the default (unspecified on cmd line)
-      and -c file.cfg will load/overwrite that cfg into .phenote/my-phenote.cfg 
-      (if it exists) - we can always add --init later if we need it 
-      -c overwrites, -i doesnt -i is for initial startup of phenote */
-  private void doCommandLineOld(String[] args) {
-    String configFile = getConfigFileFromCommandLine(args);
-    // if no config file specified then set default initial config file. this will be
-    // overridden by a personal config file if it exists
-    //if (configFile == null) configFile = Config.DEFAULT_CONFIG_FILE; stored in file
-    try {
-      if (isOverwriteConfigFile(args)) //causes wipeout move of app file to .phenote
-        Config.inst().setOverwriteConfigFile(configFile); 
-      else if (isInitialConfigFile(args))
-        Config.inst().setInitialConfigFile(configFile);
-      //else if update...
-      else // no command line config file specified - use last one specified (cache)
-        Config.inst().loadDefaultConfigFile();
-    } catch (ConfigException e) {
-      //LOG.fatal("EXITING! Fatal error in config file: "+e.getMessage());
-      LOG.error("Error in config file! "+e.getMessage());
-      e.printStackTrace(); // log?
-      //System.exit(1); // isnt this a bit extreme?
-      System.out.println("Yikes! config exception "+e+" gonna try loading default"
-                         +" config");
+    // no config set from command line use default
+    if (!Config.inst().isInitialized()) { 
       try { Config.inst().loadDefaultConfigFile(); }
       catch (ConfigException ce) { 
-        System.out.println("bummer - even default config fails. we're hosed! "+ce);
+        System.out.println("default config has failed. we're hosed! "+ce);
       }
     }
   }
 
-  // change to -m for merge?? - move to CommandLine!
-  private boolean isInitialConfigFile(String args[]) {
-    if (args == null || args.length < 2) return false;
-    return args[0].equals("-i");
-  }
-  private boolean isOverwriteConfigFile(String args[]) {
-    if (args == null || args.length < 2) return false;
-    return args[0].equals("-c");
-  }
+//   /** for now just looking for '-c configFile.cfg', use command line package
+//       if we need to get more sophisticated 
+//       so if user has personal config file should override this - however maybe 
+//       there should be a distinction between initial config file and user made configs
+//       well really the initials are db/species specific - so could be 
+//       --initialConfig zf|fb|obd - actually da heck with that with entity chooser just
+//       put all 3 ontologies in one which is then the default (unspecified on cmd line)
+//       and -c file.cfg will load/overwrite that cfg into .phenote/my-phenote.cfg 
+//       (if it exists) - we can always add --init later if we need it 
+//       -c overwrites, -i doesnt -i is for initial startup of phenote */
+//   private void doCommandLineOld(String[] args) {
+//     String configFile = getConfigFileFromCommandLine(args);
+//     // if no config file specified then set default initial config file. this will be
+//     // overridden by a personal config file if it exists
+//     //if (configFile == null) configFile = Config.DEFAULT_CONFIG_FILE; stored in file
+//     try {
+//       if (isOverwriteConfigFile(args)) //causes wipeout move of app file to .phenote
+//         Config.inst().setOverwriteConfigFile(configFile); 
+//       else if (isInitialConfigFile(args))
+//         Config.inst().setInitialConfigFile(configFile);
+//       //else if update...
+//       else // no command line config file specified - use last one specified (cache)
+//         Config.inst().loadDefaultConfigFile();
+//     } catch (ConfigException e) {
+//       //LOG.fatal("EXITING! Fatal error in config file: "+e.getMessage());
+//       LOG.error("Error in config file! "+e.getMessage());
+//       e.printStackTrace(); // log?
+//       //System.exit(1); // isnt this a bit extreme?
+//       System.out.println("Yikes! config exception "+e+" gonna try loading default"
+//                          +" config");
+//       try { Config.inst().loadDefaultConfigFile(); }
+//       catch (ConfigException ce) { 
+//         System.out.println("bummer - even default config fails. we're hosed! "+ce);
+//       }
+//     }
+//   }
 
-  private String getConfigFileFromCommandLine(String args[]) {
-    // need 2 args
-    if (args == null || args.length < 2) return null;
-    //String firstArg = args[0];
-    if (!isInitialConfigFile(args) && !isOverwriteConfigFile(args)) return null;
-    String configFile = args[1];
-    return configFile;
-  }
+//   // change to -m for merge?? - move to CommandLine!
+//   private boolean isInitialConfigFile(String args[]) {
+//     if (args == null || args.length < 2) return false;
+//     return args[0].equals("-i");
+//   }
+//   private boolean isOverwriteConfigFile(String args[]) {
+//     if (args == null || args.length < 2) return false;
+//     return args[0].equals("-c");
+//   }
 
+//   private String getConfigFileFromCommandLine(String args[]) {
+//     // need 2 args
+//     if (args == null || args.length < 2) return null;
+//     //String firstArg = args[0];
+//     if (!isInitialConfigFile(args) && !isOverwriteConfigFile(args)) return null;
+//     String configFile = args[1];
+//     return configFile;
+//   }
+
   public Frame getFrame() { return frame; }
 
   private void makeWindow() {


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.




2006	Jan	Feb	Mar	Apr	May	Jun	Jul (18)	Aug (33)	Sep (30)	Oct (27)	Nov (59)	Dec (30)
2007	Jan (67)	Feb (44)	Mar (70)	Apr (73)	May (119)	Jun (31)	Jul (92)	Aug (86)	Sep (76)	Oct (152)	Nov (156)	Dec (85)
2008	Jan (111)	Feb (121)	Mar (107)	Apr (102)	May (45)	Jun (65)	Jul (62)	Aug (133)	Sep (56)	Oct (56)	Nov (17)	Dec (15)
2009	Jan (10)	Feb (5)	Mar (10)	Apr (14)	May (49)	Jun (94)	Jul (67)	Aug (23)	Sep (9)	Oct (92)	Nov (26)	Dec (51)
2010	Jan (105)	Feb (83)	Mar (52)	Apr (59)	May (68)	Jun (71)	Jul (127)	Aug (49)	Sep (91)	Oct (27)	Nov (33)	Dec (26)
2011	Jan (26)	Feb (45)	Mar (26)	Apr (28)	May (17)	Jun (15)	Jul (45)	Aug (33)	Sep (50)	Oct (22)	Nov (10)	Dec (21)
2012	Jan (33)	Feb (24)	Mar (36)	Apr (60)	May (60)	Jun (43)	Jul (114)	Aug (19)	Sep (35)	Oct (24)	Nov (64)	Dec (12)
2013	Jan (54)	Feb (58)	Mar (51)	Apr (46)	May (21)	Jun (29)	Jul (25)	Aug (25)	Sep (13)	Oct (7)	Nov (14)	Dec (27)
2014	Jan (10)	Feb (7)	Mar (16)	Apr (14)	May (19)	Jun (8)	Jul (15)	Aug (11)	Sep (5)	Oct (11)	Nov (11)	Dec (4)
2015	Jan (52)	Feb (27)	Mar (22)	Apr (17)	May (2)	Jun (2)	Jul (2)	Aug (2)	Sep (2)	Oct	Nov (2)	Dec
2016	Jan (2)	Feb	Mar	Apr (2)	May (1)	Jun (1)	Jul (3)	Aug (2)	Sep (2)	Oct (2)	Nov (2)	Dec
2017	Jan	Feb	Mar (1)	Apr (1)	May (4)	Jun	Jul	Aug (1)	Sep (1)	Oct (2)	Nov	Dec (1)
2018	Jan	Feb	Mar (4)	Apr	May (2)	Jun (2)	Jul (2)	Aug (2)	Sep (1)	Oct (2)	Nov (1)	Dec
2019	Jan	Feb	Mar	Apr	May	Jun	Jul (2)	Aug	Sep	Oct	Nov	Dec (3)
2020	Jan	Feb	Mar	Apr	May (2)	Jun (3)	Jul	Aug	Sep (2)	Oct	Nov	Dec

obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 172)

obo-svn-commit — sends mail for all commits to svn repository