obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 163)

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Revision: 595
          http://svn.sourceforge.net/obo/?rev=595&view=rev
Author:   mgibson
Date:     2007-05-15 12:00:03 -0700 (Tue, 15 May 2007)

Log Message:
-----------
can now config how you want master/template config to interact with local and
how often (always,on update) and you can no put in an overriding url to use
for master/template config - this allows one to more easily add the config in
as now you can just use the subversion http and subversion it in and also
allows for changing config without having to muck with the webstart jar where
they are jammed in 

  <master-to-local-config mode="WIPEOUT" when="ALWAYS" 
     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn.cfg" />

Modified Paths:
--------------
    phenote/trunk/conf/birn.cfg
    phenote/trunk/conf/ncbo.cfg
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/phenote-config.xsd
    phenote/trunk/conf/zfin-standalone.cfg
    phenote/trunk/jars/phenoteconfigbeans.jar
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/ConfigWriter.java
    phenote/trunk/src/java/phenote/main/CommandLine.java
    phenote/trunk/src/java/phenote/main/Phenote.java
    phenote/trunk/src/java/phenote/util/FileUtil.java

Modified: phenote/trunk/conf/birn.cfg
===================================================================

--- phenote/trunk/conf/birn.cfg	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/conf/birn.cfg	2007-05-15 19:00:03 UTC (rev 595)
@@ -1,8 +1,9 @@
-<phenote-configuration version="1.3-beta1" xmlns="phenote/config/xml">
+<phenote-configuration xmlns="phenote/config/xml">
                                        
   <!-- wipeout always means that the master will always wipeout the local copy
     in this mode modifying the local is useless -->
-  <master-to-local-config mode="WIPEOUT_ALWAYS"/>
+  <master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn.cfg" />
 
   <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
   <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
@@ -34,7 +35,7 @@
         file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
   </field>
 
-  <field name="Type?(forEntity 1?)" enable="true"/>
+  <field name="Type? (eg Tissue)" enable="true"/>
 
   <field name="Quality" syntax-abbrev="Q" enable="true">
     <ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/conf/ncbo.cfg	2007-05-15 19:00:03 UTC (rev 595)
@@ -1,5 +1,10 @@
 <?xml version="1.3.1" encoding="UTF-8"?>
-<ns:phenote-configuration version="1.1.2" xmlns:ns="phenote/config/xml">
+
+<ns:phenote-configuration xmlns:ns="phenote/config/xml">
+
+  <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/ncbo.cfg" />
+
   <ns:log config-file="conf/log4j-standalone.xml"/>
 
   <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/conf/phenote-config.rnc	2007-05-15 19:00:03 UTC (rev 595)
@@ -18,10 +18,13 @@
   }
 
 ## specify how the master config interacts with local/cached config
-## WIPEOUT_ALWAYS master will always wipe out local every run
-## UPDATE_WITH_VERSION_CHANGE (default) update/merge master with local on version change
+## WIPEOUT master will always wipe out local every run
+## UPDATE (default) update/merge master with local
+## when is ALWAYS,ON_VERSION_CHANGE,INIT
 master-to-local-config = element master-to-local-config {
-  attribute mode { xsd:string }
+  attribute mode { xsd:string },
+  attribute when { xsd:string },
+  attribute overriding-master-url { xsd:string }
 }
 
 queryable-dataadapter = element queryable-dataadapter {

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/conf/phenote-config.xsd	2007-05-15 19:00:03 UTC (rev 595)
@@ -20,6 +20,8 @@
   <xs:element name="master-to-local-config">
     <xs:complexType>
       <xs:attribute name="mode" use="required" type="xs:string"/>
+      <xs:attribute name="when" use="required" type="xs:string"/>
+      <xs:attribute name="overriding-master-url" use="required" type="xs:string"/>
     </xs:complexType>
   </xs:element>
   <xs:element name="queryable-dataadapter">

Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/conf/zfin-standalone.cfg	2007-05-15 19:00:03 UTC (rev 595)
@@ -1,5 +1,10 @@
 <?xml version="1.3.1" encoding="UTF-8"?>
-<ns:phenote-configuration version="1.1.2" xmlns:ns="phenote/config/xml">
+
+<ns:phenote-configuration xmlns:ns="phenote/config/xml">
+
+  <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/zfin-standalone.cfg" />
+
   <ns:log config-file="conf/log4j-standalone.xml"/>
 
 
@@ -7,15 +12,16 @@
                   enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter"
                   enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
+  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
 
   <ns:uvic-graph enable="false"/>
   <ns:term-history enable="false"/>
   <ns:auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
-  <ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
+  <ns:update-timer timer="4"/><!--set to 0 if you want to bypass the check; time in seconds-->
   
   <ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
+
   <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
   <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
   <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
@@ -28,7 +34,8 @@
     <ns:ontology name="ZF" file="zebrafish_anatomy.obo"
                   repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish"
                   namespace="zebrafish_anatomy"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
+    <ns:ontology name="GO"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
   </ns:field>
 
   <ns:field name="Stage" syntax-abbrev="T" enable="true">
@@ -36,7 +43,8 @@
   </ns:field>
 
   <ns:field name="Quality" syntax-abbrev="Q" enable="true">
-    <ns:ontology name="PATO" file="quality.obo" repos-subdir="phenotype"/>
+    <ns:ontology name="PATO"
+      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
   </ns:field>
 
   <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
@@ -45,7 +53,7 @@
     <ns:ontology name="ZF" file="zebrafish_anatomy.obo"
                  repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish" 
                  namespace="zebrafish_anatomy"/>
-    <ns:ontology name="GO" file="gene_ontology.obo" repos-subdir="genomic-proteomic"/>
+    <ns:ontology name="GO" file="gene_ontology.obo"/>
   </ns:field>
 
   <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">

Modified: phenote/trunk/jars/phenoteconfigbeans.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-05-15 19:00:03 UTC (rev 595)
@@ -49,13 +49,17 @@
   /** enabled & disabled */
   private List<FieldConfig> allFields = new ArrayList<FieldConfig>();
   private String logConfigFile = "conf/log4j.xml"; // default log config file
+  // maybe should be using xmlbean where possible?
   private boolean uvicGraphEnabled = false; // default false for now
   private boolean termHistoryEnabled = false;   //default to false for now
   private boolean autoUpdateEnabled = true; //default to true if not in config
   private int updateTimer = 0; //default is to not wait
   private String reposUrlDir;
   private String version;
-  private String masterToLocalConfigMode;
+  //private String masterToLocalConfigMode;
+  //private MasterToLocalConfig masterToLocalBean;
+  private PhenoteConfiguration phenoConfigBean; // cache the xml parse bean??
+
   private boolean configInitialized = false;
   private final static String myphenoteFile = "my-phenote";
 
@@ -221,15 +225,16 @@
   }
 
 
-  /** ConfigMode INNER CLASS */
+  /** ConfigMode INNER CLASS - outer class? */
   private class ConfigMode {
 
-    private String mode = "";
+    //private String mode = "";
     //private boolean updateWithNewVersion=false;
     private boolean masterExists = true;
     private URL masterUrl;
     private File localFile; //dotConfFile;
     private boolean cmdLineWipeout=false;
+    private MasterToLocalConfig masterToLocalBean;
 
     private ConfigMode(String masterConfig,boolean merge,boolean cmdLineWipeout) 
       throws ConfigException {
@@ -247,29 +252,85 @@
       if (!masterExists && !localFile.exists())
         throw new ConfigException("Cfg file doesnt exist in app nor .phenote/conf");
 
-      if (masterExists) {
-        Config cfg = new Config();
-        try {
-          cfg.parseXmlFile(masterConfig);
-          if (cfg.masterToLocalConfigMode != null)
-            mode = cfg.masterToLocalConfigMode;
-        } catch (ConfigException x) {} // do nothing? err msg?
-      }
+      parseModeXml(masterConfig);
     }
+
+    private void parseModeXml(String masterConfig) throws ConfigException {
+      if (!masterExists) return;
+      Config cfg = new Config();
+      try {
+        cfg.parseXmlFile(masterConfig);
+        //if (cfg.masterToLocalConfigMode != null)  mode = cfg.masterToLocalConfigMode;
+        if (cfg.phenoConfigBean == null) return;
+        masterToLocalBean = cfg.phenoConfigBean.getMasterToLocalConfig();
+        //mode = masterToLocalBean.getMode()
+        loadMasterOverrideUrl();
+      } catch (ConfigException x) {} // do nothing? err msg?
+    }
+
+    /** if have master override - load it! */
+    private void loadMasterOverrideUrl() {
+      if (!haveXmlBean()) return;
+      String urlString = getXmlBean().getOverridingMasterUrl();
+      if (urlString==null) return;
+      try {
+        URL u = new URL(urlString); // throws MalformedURLEx
+        u.openStream(); // throws IOEx
+        masterUrl = u; // no exception thrown - we're ok
+        masterExists = true; // actually this has to be true silly
+      } catch (Exception e) {} // masterUrl not set
+    }
+
+    private boolean haveXmlBean() { return masterToLocalBean != null; }
+    private MasterToLocalConfig getXmlBean() { return masterToLocalBean; }
+
     private boolean isWipeout() {
       if (!masterExists) return false;
       if (!localFileExists()) return true; // init
       if (cmdLineWipeout) return true;
-      return mode.equals("WIPEOUT_ALWAYS");
+      return configIsWipeout(); //mode.equals("WIPEOUT");
       //return (!dotConfFile.exists() || overwritePersonalCfg)
     }
     
+    private boolean configIsWipeout() {
+      if (!haveXmlBean() || masterToLocalBean.getMode() == null)
+        return false;
+      return masterToLocalBean.getMode().equals("WIPEOUT");
+    }
+
     /** not sure if this belongs in this class?? */
     private void doWipeout() throws ConfigException {
+      
+      if (!isAlways() && versionSame()) {
+        sameVersionMessage("writing over");
+        return;
+      }
+
       doWipeoutMessage();
+      // this shouldnt be copy!!! read in write out to get version!
       copyUrlToFile(masterUrl,localFile); // Ex  put method in inner class?
     }
 
+    private void sameVersionMessage(String type) {
+      System.out.println("Template & local config have same version "+phenoteVersion()+
+                         ", not "+type+" local cfg");
+    }
+
+    private boolean versionSame() throws ConfigException {
+      if (!localFileExists()) return false;
+      Config localCfg = new Config();
+      localCfg.parseXmlFile(localFileString());
+      return versionSame(localCfg.version);
+    }
+
+    private String phenoteVersion() { return PhenoteVersion.versionString(); }
+
+    private boolean versionSame(String version) {
+      if (version == null) return false;
+      if (PhenoteVersion.versionString() == null) return false;
+      return (version.equals(phenoteVersion()));
+    }
+
     private void doWipeoutMessage() {
       String s = !localFileExists() ? " does not exist" : " getting overwritten";
       System.out.println(localFile+s+" Copying "+masterUrl);
@@ -281,18 +342,27 @@
       else return true; // for now...
     }
     private boolean isUpdateWithNewVersion() {
-      return isUpdate(); // for now
+      return isUpdate() && !isUpdateAlways(); // for now
     }
     private boolean isUpdateAlways() {
-      return isUpdate() && !isUpdateWithNewVersion(); // always false at moment
+      if (!isUpdate()) return false;  //!isUpdateWithNewVersion();
+      return isAlways();
     }
     
+    private boolean isAlways() {
+      if (!haveXmlBean()) return false;
+      String when = masterToLocalBean.getWhen();
+      if (when == null) return false;
+      return when.equals("ALWAYS");
+    }
+
+
     private boolean isUpdateable(String version) {
+      if (!isUpdate()) return false;
       if (isUpdateAlways()) return true;
       if (!isUpdateWithNewVersion()) return false;
       // version
-      if (version == null) return false;
-      return (!version.equals(PhenoteVersion.versionString()));
+      return !versionSame(version);
     }
 
 
@@ -363,7 +433,8 @@
     //String version = PhenoteVersion.versionString();//newCfg.version
     //if (mode.isUpdateWithNewVersion() && version != null && version.equals(oldCfg.version)) {
     if (!mode.isUpdateable(oldCfg.version)) {
-      System.out.println("System & user config same version, not updating cfg");
+      //System.out.println("System & user config same version, not updating cfg");
+      mode.sameVersionMessage("updating");
       return;
     }
     else
@@ -575,23 +646,24 @@
       PhenoteConfigurationDocument pcd = 
         PhenoteConfigurationDocument.Factory.parse(configUrl);//configFile);
       pcd.validate(); //???
-      PhenoteConfiguration pc = pcd.getPhenoteConfiguration();
+      phenoConfigBean = pcd.getPhenoteConfiguration();
 
-      version = pc.getVersion();
+      version = phenoConfigBean.getVersion();
 
-      MasterToLocalConfig m = pc.getMasterToLocalConfig();
-      if (m != null && m.getMode() != null)
-        masterToLocalConfigMode = m.getMode();
+      //MasterToLocalConfig m 
+//         = phenoConfigBean.getMasterToLocalConfig();
+//       if (m != null && m.getMode() != null)
+//         masterToLocalConfigMode = m.getMode();
 
       // LOG CONFIG FILE
-      Log log = pc.getLog();
+      Log log = phenoConfigBean.getLog();
       if (log != null && log.getConfigFile() != null) {
         logConfigFile = log.getConfigFile();
       }
       
       // DATA ADAPTERS  <dataadapter name="phenoxml" enable="true"/>
 
-      Dataadapter[] adapters = pc.getDataadapterArray();
+      Dataadapter[] adapters = phenoConfigBean.getDataadapterArray();
       for (Dataadapter da : adapters) {
         DataAdapterConfig dac = new DataAdapterConfig(da);
         addAdapConfig(dac);
@@ -599,7 +671,7 @@
         //addDataAdapterFromString(name);
       }
 
-      QueryableDataadapter[] queryAdaps = pc.getQueryableDataadapterArray();
+      QueryableDataadapter[] queryAdaps = phenoConfigBean.getQueryableDataadapterArray();
       for (QueryableDataadapter da : queryAdaps) {
         QueryableAdapConfig qac = new QueryableAdapConfig(da);
         addQueryAdapCfg(qac);
@@ -607,32 +679,32 @@
 
 
       // GRAPH
-      UvicGraph gr = pc.getUvicGraph();
+      UvicGraph gr = phenoConfigBean.getUvicGraph();
       if (gr != null)
         uvicGraphEnabled = gr.getEnable();
 
       // TERM HISTORY
-      TermHistory history = pc.getTermHistory();
+      TermHistory history = phenoConfigBean.getTermHistory();
       if (history != null)
         termHistoryEnabled = history.getEnable();
 
       // AUTO UPDATE OF ONTOLOGIES
-      AutoUpdateOntologies autoUpdate = pc.getAutoUpdateOntologies();
+      AutoUpdateOntologies autoUpdate = phenoConfigBean.getAutoUpdateOntologies();
       if (autoUpdate != null)
         autoUpdateEnabled = autoUpdate.getEnable();
 
       // TIMER for UPDATE OF ONTOLOGIES
-      UpdateTimer time = pc.getUpdateTimer();
+      UpdateTimer time = phenoConfigBean.getUpdateTimer();
       if (time != null)
 	  updateTimer = time.getTimer().intValue();
 
       // Repos url dir
-      OboRepository or = pc.getOboRepository();
+      OboRepository or = phenoConfigBean.getOboRepository();
       if (or != null && or.getUrlDir() != null)
         reposUrlDir = or.getUrlDir();
 
       // FIELDS
-      Field[] fields = pc.getFieldArray();
+      Field[] fields = phenoConfigBean.getFieldArray();
       for (Field f : fields) {
         makeFieldConfig(f);
       }

Modified: phenote/trunk/src/java/phenote/config/ConfigWriter.java
===================================================================
--- phenote/trunk/src/java/phenote/config/ConfigWriter.java	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/src/java/phenote/config/ConfigWriter.java	2007-05-15 19:00:03 UTC (rev 595)
@@ -16,6 +16,10 @@
 import phenote.dataadapter.DataAdapterI;
 import phenote.main.PhenoteVersion;
 
+/** Im realizing now ive done this all wrong - as theres really 2 redundant datamodels
+    for the config - the xml beans, and phenotes own and there really should be just
+    the xml beans - then you dont have to do all this back & forth between them
+    hindsight is 20 20 */
 class ConfigWriter {
 
   private Config config;

Modified: phenote/trunk/src/java/phenote/main/CommandLine.java
===================================================================
--- phenote/trunk/src/java/phenote/main/CommandLine.java	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/src/java/phenote/main/CommandLine.java	2007-05-15 19:00:03 UTC (rev 595)
@@ -174,7 +174,7 @@
       super("inputFile",'f',true,"filename",help);
     }
     public void execute() throws Exception {
-      //System.out.println("executing input fileConf command option "+getArg());
+      //System.out.println("executing input file command option "+getArg());
       getReadOptions().setFilename(getArg());
       setAdapterForFile(getReadOptions(), false);
     }

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-05-15 19:00:03 UTC (rev 595)
@@ -150,7 +150,7 @@
   private void doCommandLine(String[] args) {
     try { commandLine.setArgs(args); } // sets config if specified
     catch (Exception e) { // no log yet - sys.out
-      System.out.println("Command line read failed: "+e); e.printStackTrace();}
+      System.out.println("Command line read failed: "+e); }//e.printStackTrace();
     // no config set from command line use default
     if (!Config.inst().isInitialized()) { 
       try { Config.inst().loadDefaultConfigFile(); }

Modified: phenote/trunk/src/java/phenote/util/FileUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtil.java	2007-05-14 23:10:35 UTC (rev 594)
+++ phenote/trunk/src/java/phenote/util/FileUtil.java	2007-05-15 19:00:03 UTC (rev 595)
@@ -72,6 +72,8 @@
   
   private static String sep(String a, String b) { return a + FILE_SEPARATOR + b; }
 
+
+  /** split into findMaster?ConfigUrl & findOboUrl!!! */
   public static URL findUrl(String filename) throws FileNotFoundException {
     List<URL> possibleUrls = getPossibleUrls(filename);
     for (URL u : possibleUrls) {
@@ -87,7 +89,9 @@
   // suffix - or who cares?
   // ok this is even sillier as it will look in .phenote for obo files and not for 
   // conf files - which is what the app wants but really there needs to be 2 different
-  // methods - this is sheer laziness!
+  // methods - this is sheer laziness! also with separate methods can print out
+  // better error message
+  // split into getPossibleMaster?ConfigUrls & getPossibleOboUrls
   private static List<URL> getPossibleUrls(String filename) {
     List<URL> urls = new ArrayList(5);
     // hmmm - should full path go last? can be problem with running from
@@ -106,6 +110,7 @@
     return urls;
   }
 
+  // make an inner class for this?
   private static void addFile(String filename,List<URL> urls) {
     try {
       URL u = new File(filename).toURL();


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obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 163)

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