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[Obo-svn-commit] SF.net SVN: obo: [980] phenote/trunk/conf/phenomap.cfg

From: <ba...@us...> - 2007-10-08 21:10:33

Revision: 980
          http://obo.svn.sourceforge.net/obo/?rev=980&view=rev
Author:   balhoff
Date:     2007-10-08 14:10:36 -0700 (Mon, 08 Oct 2007)

Log Message:
-----------
Fixed phenomap config to check for and download ontology updates.  Fixes tracker issue 1809784.

Modified Paths:
--------------
    phenote/trunk/conf/phenomap.cfg

Modified: phenote/trunk/conf/phenomap.cfg
===================================================================
--- phenote/trunk/conf/phenomap.cfg	2007-10-08 20:26:12 UTC (rev 979)
+++ phenote/trunk/conf/phenomap.cfg	2007-10-08 21:10:36 UTC (rev 980)
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<ns:phenote-configuration version="1.0" xmlns:ns="phenote/config/xml" name="PhenoMaP Configuration" author="Jim Balhoff" description="This configuration is used by curators with the PhenoMaP project at NESCent.">
+<ns:phenote-configuration version="1.1" xmlns:ns="phenote/config/xml" name="PhenoMaP Configuration" author="Jim Balhoff" description="This configuration is used by curators with the PhenoMaP project at NESCent.">
    
   <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS"/>
   <ns:log config-file="conf/log4j-phenomap.xml"/>
@@ -8,7 +8,6 @@
   <ns:auto-update-ontologies enable="true"/>
   <ns:update-timer timer="0"/>
   <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
-  <ns:obo-repository url-dir="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/"/>
 
   <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
@@ -28,15 +27,15 @@
   <ns:field name="Specimen Count" syntax-abbrev="SpecimenCount" enable="true" groups="default specimen-list"/>
   <ns:field name="Preparation" syntax-abbrev="SpecimenPreparation" enable="true" groups="default specimen-list"/>
   <ns:field name="Entity" syntax-abbrev="E" enable="true" groups="default">
-    <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
-    <ns:ontology name="Entity" file="teleost_anatomy.obo" repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish" namespace="teleost_anatomy"/>
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
+    <ns:ontology name="Entity" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fishteleost_anatomy.obo" namespace="teleost_anatomy"/>
   </ns:field>
   <ns:field name="Quality" syntax-abbrev="Q" enable="true" groups="default">
-    <ns:ontology name="Quality" file="quality.obo" repos-subdir="phenotype"/>
+    <ns:ontology name="Quality" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
   </ns:field>
   <ns:field name="Additional Entity" syntax-abbrev="E2" enable="true" groups="default">
-    <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
-    <ns:ontology name="Additional Entity" file="teleost_anatomy.obo" repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish"/>
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
+    <ns:ontology name="Additional Entity" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fishteleost_anatomy.obo"/>
   </ns:field>
   <ns:field name="Measurement" syntax-abbrev="M" enable="true" groups="default"/>
   <ns:field name="Unit" syntax-abbrev="U" enable="true" groups="default">


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[Obo-svn-commit] SF.net SVN: obo: [979] phenote/trunk/conf

From: <ba...@us...> - 2007-10-08 20:26:08

Revision: 979
          http://obo.svn.sourceforge.net/obo/?rev=979&view=rev
Author:   balhoff
Date:     2007-10-08 13:26:12 -0700 (Mon, 08 Oct 2007)

Log Message:
-----------
Removed colwidth attributes from config - not used anymore.

Modified Paths:
--------------
    phenote/trunk/conf/antibody.cfg
    phenote/trunk/conf/birn.cfg

Modified: phenote/trunk/conf/antibody.cfg
===================================================================
--- phenote/trunk/conf/antibody.cfg	2007-10-08 19:10:44 UTC (rev 978)
+++ phenote/trunk/conf/antibody.cfg	2007-10-08 20:26:12 UTC (rev 979)
@@ -41,7 +41,7 @@
     <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
     <ns:ontology name="SP" file="spatial.obo"/>
   </ns:field>
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150">
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
     <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" name="Quality"/>
   </ns:field>
   <ns:field name="Stage" syntax-abbrev="stage">

Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg	2007-10-08 19:10:44 UTC (rev 978)
+++ phenote/trunk/conf/birn.cfg	2007-10-08 20:26:12 UTC (rev 979)
@@ -12,16 +12,16 @@
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
   <!--******************** FIELD DEFINITIONS ***********************-->
   <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
-  <ns:field name="Pub" datatag="PUB" enable="true" desc="The provenance for this data" colwidth="150"/>
+  <ns:field name="Pub" datatag="PUB" enable="true" desc="The provenance for this data"/>
 
 
   <!-- for smart atlas -->
   <ns:field name="Image Name" datatag="imagename" enable="true" desc="Name of image"/>
 
-  <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a     mouse strain or some other identifying factor" colwidth="67"/>
-  <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely" colwidth="96"/>
+  <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a     mouse strain or some other identifying factor"/>
+  <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
 
-  <ns:field name="Entity" datatag="E" min-completion-chars="2" enable="true" colwidth="150">
+  <ns:field name="Entity" datatag="E" min-completion-chars="2" enable="true">
     <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
     <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
@@ -35,11 +35,11 @@
        file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/-->
   </ns:field>
 
-  <ns:field name="Quality" datatag="Q" enable="true" colwidth="150">
+  <ns:field name="Quality" datatag="Q" enable="true">
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo" name="Quality"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="2" enable="true" colwidth="114">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="2" enable="true">
     <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
     <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
@@ -53,9 +53,9 @@
        file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/-->
   </ns:field>
 
-  <ns:field name="Compare To" datatag="Compar" enable="true" colwidth="112"/>
-  <ns:field name="Description" datatag="Desc" enable="true" colwidth="189"/>
-  <ns:field name="Comment" datatag="Comm" enable="true" colwidth="886"/>
+  <ns:field name="Compare To" datatag="Compar" enable="true"/>
+  <ns:field name="Description" datatag="Desc" enable="true"/>
+  <ns:field name="Comment" datatag="Comm" enable="true"/>
   <ns:field name="Image Source" datatag="imagesource" enable="true" desc="Source of image"/>
   <ns:field name="Annot type" datatag="annotationtype" enable="true" desc="Point,line,area,entireimage"/>
   <ns:field name="Regions" datatag="regions" enable="true" desc="comma delim list of regions, break into sep chars?"/>


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[Obo-svn-commit] SF.net SVN: obo: [978] phenote/trunk/doc/phenote-website

From: <nl...@us...> - 2007-10-08 19:11:43

Revision: 978
          http://obo.svn.sourceforge.net/obo/?rev=978&view=rev
Author:   nlw
Date:     2007-10-08 12:10:44 -0700 (Mon, 08 Oct 2007)

Log Message:
-----------
revise
website: revised dates/notes, etc.

Modified Paths:
--------------
    phenote/trunk/doc/phenote-website/events.shtml
    phenote/trunk/doc/phenote-website/index.shtml

Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml	2007-10-08 16:04:33 UTC (rev 977)
+++ phenote/trunk/doc/phenote-website/events.shtml	2007-10-08 19:10:44 UTC (rev 978)
@@ -17,23 +17,16 @@
 	</div>
 
 	<h1>Upcoming Events, 2007</h1>
-	<h2>September</h2>
-	<ul>
-	  <li>
-	  </li>
-	</ul>
 
 	<h2>October</h2>
 	<ul>
-	  <li>Oct 2, Phenote Users Group, Online
-	  </li>
 	<li>Oct 23-25, Ontology Best Practices Workshop, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA
 	</li>
 	</ul>
 
 	<h2>November</h2>
 	<ul>
-	  <li>Nov 6, Phenote Users Group, Online
+	  <li>Nov 1, Phenote Users Group, Online via WebEx
 	  </li>
 	<li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
 	</ul>
@@ -45,6 +38,10 @@
 	</ul>
 
 	<h1>Past News and Events, 2007</h1>
+	<h2>October</h2>
+	  <li>Oct 2, Phenote Users Group, Online via WebEx
+	  </li>
+
 	<h2>September</h2>
 	<ul>
 	  <li>Sept 17, New website released

Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml	2007-10-08 16:04:33 UTC (rev 977)
+++ phenote/trunk/doc/phenote-website/index.shtml	2007-10-08 19:10:44 UTC (rev 978)
@@ -102,7 +102,7 @@
 	    <li class="events">
 	  <p class="quick_link">
 	    <img src="images/star.gif" alt=""  class="icon_green"/>	      
-	    <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, October 4, 8:30am, Online 
+	    <a href="http://www.phenote.org/irc_chat">User's Group Monthly Meeting</a>, November 1, 9:00am, Online 
 	    </p>
 	    </li> 
 	  </ul>
@@ -129,7 +129,8 @@
 	  <!--No news is good news!-->
 	  
 	  <!-- Do not destry the following event template -->
-	    <p>09.17.2007 - New website rolled out!  The website has the same
+	  <p>10.02.2007 - Phenote user's group to be moved to first Thursday of each month, 9am.  Join us for our next meeting on November 1st over WebEx!</p>
+	  <p>09.17.2007 - New website rolled out!  The website has the same
 	    content as the old one, just with a new look-and-feel.</p>
 	    <p> 08.28.2007 - 
 	    <a href="http://www.phenote.org/download.shtml">New Phenote Beta available: 1.4-beta3!</a> </p>


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[Obo-svn-commit] SF.net SVN: obo: [977] phenote/trunk

From: <mg...@us...> - 2007-10-08 16:04:36

Revision: 977
          http://obo.svn.sourceforge.net/obo/?rev=977&view=rev
Author:   mgibson
Date:     2007-10-08 09:04:33 -0700 (Mon, 08 Oct 2007)

Log Message:
-----------
made addititviy false - as jim noticed - which makes for non redundant message
to log file - thanks jim for noticing that

Modified Paths:
--------------
    phenote/trunk/conf/log4j.xml
    phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Modified: phenote/trunk/conf/log4j.xml
===================================================================
--- phenote/trunk/conf/log4j.xml	2007-10-08 14:57:22 UTC (rev 976)
+++ phenote/trunk/conf/log4j.xml	2007-10-08 16:04:33 UTC (rev 977)
@@ -19,7 +19,7 @@
         </layout>
     </appender>
 
-    <category name="phenote" additivity="true">
+    <category name="phenote" additivity="false">
         <priority value="debug"/>
         <appender-ref ref="MAIN" />
         <appender-ref ref="console"/>

Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-10-08 14:57:22 UTC (rev 976)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-10-08 16:04:33 UTC (rev 977)
@@ -502,7 +502,7 @@
   }
 
   /** Load obo session with obo edit adapter, unless previously loaded - reuse 
-   this is old - phase out! */
+   this is old - phase out! - multi obos */
   private void loadOboSession(Ontology o,OntologyConfig oc) throws OntologyException {
     // check cache of ontologies to see if ontology file already loaded
     if (fileIsInCache(oc.getFile())) {
@@ -525,7 +525,8 @@
     o.setTimestamp(previousOntol.getTimestamp());
     o.setSource(previousOntol.getSource());
   }
-  /** If repository is configured loads obo from repos if local out of date */
+  /** If repository is configured loads obo from repos if local out of date
+   old - phase out - multi obo sessions*/
   private void loadOboSessionCheckRepos(Ontology o,OntologyConfig oc)
     throws OntologyException {
 		int progress = phenote.loadingScreen.getStartupProgress();

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-08 14:57:22 UTC (rev 976)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-08 16:04:33 UTC (rev 977)
@@ -74,20 +74,21 @@
   public static void main(String[] args) {
     standalone = true; // i think this is ok
  
-      // Check whether the root logger has an appender; there does not appear
-      // to be a more direct way to check whether Log4J has already been 
-      // initialized.  Note that the root logger's appender can always be
-      // set to a NullAppender, so this does not restrict the utility of
-      // the logging in any way.
-      Logger rl = LogManager.getRootLogger();
-      Enumeration<?> appenders = rl.getAllAppenders();
-      if (!appenders.hasMoreElements()) {
-        System.out.println("Log4J configuration failed, using default configuration settings");
-        BasicConfigurator.configure(); 
-        rl.setLevel(Level.INFO);
-        LOG = LogManager.getLogger(Phenote.class);
-      }
+    // Check whether the root logger has an appender; there does not appear
+    // to be a more direct way to check whether Log4J has already been 
+    // initialized.  Note that the root logger's appender can always be
+    // set to a NullAppender, so this does not restrict the utility of
+    // the logging in any way.
+    Logger rl = LogManager.getRootLogger();
+    Enumeration<?> appenders = rl.getAllAppenders();
+    if (!appenders.hasMoreElements()) {
+      System.out.println("Log4J configuration failed, using default configuration settings");
+      BasicConfigurator.configure(); 
+      rl.setLevel(Level.INFO);
+      LOG = LogManager.getLogger(Phenote.class);
+    }
     
+
     // writes error events to log
     ErrorManager.inst().addErrorListener(new LogErrorListener());
     String v = "This is Phenote version "+PhenoteVersion.versionString();


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[Obo-svn-commit] SF.net SVN: obo: [976] phenote/trunk/phenote

From: <mg...@us...> - 2007-10-08 14:57:19

Revision: 976
          http://obo.svn.sourceforge.net/obo/?rev=976&view=rev
Author:   mgibson
Date:     2007-10-08 07:57:22 -0700 (Mon, 08 Oct 2007)

Log Message:
-----------
added conf to phenote script classpath to pick up log4j config file

Modified Paths:
--------------
    phenote/trunk/phenote

Modified: phenote/trunk/phenote
===================================================================
--- phenote/trunk/phenote	2007-10-08 02:04:37 UTC (rev 975)
+++ phenote/trunk/phenote	2007-10-08 14:57:22 UTC (rev 976)
@@ -1,6 +1,7 @@
 #!/bin/sh
 
-PHENOTE_CLASSPATH=classfiles
+## have to add conf directory to pick up log4j config file
+PHENOTE_CLASSPATH=classfiles:conf
 for file in jars/*.jar; do 
   if [ $file != jars/phenote.jar ]; then 
     #echo "Adding ${file} to CLASSPATH"


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[Obo-svn-commit] SF.net SVN: obo: [975] phenote/trunk

From: <ba...@us...> - 2007-10-08 02:04:34

Revision: 975
          http://obo.svn.sourceforge.net/obo/?rev=975&view=rev
Author:   balhoff
Date:     2007-10-07 19:04:37 -0700 (Sun, 07 Oct 2007)

Log Message:
-----------
Simplified log4j configuration.  "log4j.xml" should be in classpath and is automatically used by log4j.  If a different logging configuration is desired, a custom file can be specified via Java properties, such as on command-line as -Dlog4j.configuration="pathtofile".

Modified Paths:
--------------
    phenote/trunk/build.xml
    phenote/trunk/src/java/phenote/main/CommandLine.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Added Paths:
-----------
    phenote/trunk/conf/log4j.xml

Removed Paths:
-------------
    phenote/trunk/conf/log4j-standalone.xml

Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2007-10-07 00:29:05 UTC (rev 974)
+++ phenote/trunk/build.xml	2007-10-08 02:04:37 UTC (rev 975)
@@ -95,6 +95,8 @@
             <!-- arg value="-c configfilehereventually"/ -->
             <classpath>
                 <pathelement path="${classfiles}"/>
+            	<!-- for log4j -->
+            	<pathelement path="${conf}"/>
                 <fileset dir="${lib}">
                     <include name="*.jar"/>
                     <exclude name="phenote.jar"/>
@@ -240,6 +242,7 @@
             <fileset dir="${classfiles}"/>
             <fileset dir="." includes="obo-files/" excludes="obo-files/old"/>
             <fileset file="${conf}/*.cfg"/>
+        	<fileset file="${conf}/log4j.xml"/>
 	    <fileset dir="." includes="${conf}/*.xml"/>
 	    <fileset dir="." includes="images/"/>
             <fileset dir="doc/phenote-website" includes="help/**"/>

Deleted: phenote/trunk/conf/log4j-standalone.xml
===================================================================
--- phenote/trunk/conf/log4j-standalone.xml	2007-10-07 00:29:05 UTC (rev 974)
+++ phenote/trunk/conf/log4j-standalone.xml	2007-10-08 02:04:37 UTC (rev 975)
@@ -1,33 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-
-<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
-<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
-
-    <appender name="MAIN" class="org.apache.log4j.RollingFileAppender">
-        <param name="File" value="phenote_log4j.log" />
-        <param name="Append" value="true" />
-        <param name="MaxFileSize" value="1MB" />
-        <param name="MaxBackupIndex" value="10" />
-        <layout class="org.apache.log4j.PatternLayout">
-            <param name="ConversionPattern" value="%d [%t] %-5p %c{2} - %m%n"/>
-        </layout>
-    </appender>
-
-    <appender name="console" class="org.apache.log4j.ConsoleAppender">
-        <layout class="org.apache.log4j.PatternLayout">
-            <param name="ConversionPattern" value="%d [%t] %-5p %c{2} - %m%n"/>
-        </layout>
-    </appender>
-
-    <category name="phenote" additivity="true">
-        <priority value="debug"/>
-        <appender-ref ref="MAIN" />
-        <appender-ref ref="console"/>
-    </category>
-
-    <root>
-        <priority value="info" />
-        <appender-ref ref="MAIN" />
-    </root>
-</log4j:configuration>
-

Copied: phenote/trunk/conf/log4j.xml (from rev 964, phenote/trunk/conf/log4j-standalone.xml)
===================================================================
--- phenote/trunk/conf/log4j.xml	                        (rev 0)
+++ phenote/trunk/conf/log4j.xml	2007-10-08 02:04:37 UTC (rev 975)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+    <appender name="MAIN" class="org.apache.log4j.RollingFileAppender">
+        <param name="File" value="phenote_log4j.log" />
+        <param name="Append" value="true" />
+        <param name="MaxFileSize" value="1MB" />
+        <param name="MaxBackupIndex" value="10" />
+        <layout class="org.apache.log4j.PatternLayout">
+            <param name="ConversionPattern" value="%d [%t] %-5p %c{2} - %m%n"/>
+        </layout>
+    </appender>
+
+    <appender name="console" class="org.apache.log4j.ConsoleAppender">
+        <layout class="org.apache.log4j.PatternLayout">
+            <param name="ConversionPattern" value="%d [%t] %-5p %c{2} - %m%n"/>
+        </layout>
+    </appender>
+
+    <category name="phenote" additivity="true">
+        <priority value="debug"/>
+        <appender-ref ref="MAIN" />
+        <appender-ref ref="console"/>
+    </category>
+
+    <root>
+        <priority value="info" />
+        <appender-ref ref="MAIN" />
+    </root>
+</log4j:configuration>
+

Modified: phenote/trunk/src/java/phenote/main/CommandLine.java
===================================================================
--- phenote/trunk/src/java/phenote/main/CommandLine.java	2007-10-07 00:29:05 UTC (rev 974)
+++ phenote/trunk/src/java/phenote/main/CommandLine.java	2007-10-08 02:04:37 UTC (rev 975)
@@ -1,7 +1,5 @@
 package phenote.main;
 
-import org.apache.log4j.xml.DOMConfigurator;
-
 import phenote.config.Config;
 import phenote.config.ConfigException;
 import phenote.dataadapter.DataAdapterI;
@@ -174,8 +172,9 @@
     }
     public void execute() throws Exception {
       logSpecified = true;
+      // this has been superseded by just using default log4j initialization procedure
 //      try {
-        DOMConfigurator.configure(getArg());
+//        DOMConfigurator.configure(getArg());
 //       }
 //       catch (FileNotFoundException e) { 
 //         //phenote.splashScreen.setProgress("bad file:"+e.getMessage(),10);

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-07 00:29:05 UTC (rev 974)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-08 02:04:37 UTC (rev 975)
@@ -10,7 +10,6 @@
 import java.io.FileNotFoundException;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
@@ -30,7 +29,6 @@
 import org.apache.log4j.Level;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
-import org.apache.log4j.xml.DOMConfigurator;
 
 import phenote.charactertemplate.CharacterTemplateController;
 import phenote.config.Config;
@@ -75,37 +73,20 @@
 
   public static void main(String[] args) {
     standalone = true; // i think this is ok
-    // set up logging with default logger until we read in log file from
-    // config file
-    try { 
-      URL u = FileUtil.findUrl(Config.defaultLogConfigFile);
-      DOMConfigurator.configure(u);
-    }
-    catch (FileNotFoundException e) {
-      System.out.println("Default log cfg file not found "+e);
-      // should then configure up default log with sys out and .phenote file...
-      // stolen from apollo
-      // Attempt to detect whether the standard Log4J configuration has failed
-      // (e.g., because the conf file in the log4j.configuration variable was not
-      // found.)  If it has failed then fall back to the default configuration 
-      // implemented in BasicConfigurator.
-      //static {
+ 
       // Check whether the root logger has an appender; there does not appear
       // to be a more direct way to check whether Log4J has already been 
       // initialized.  Note that the root logger's appender can always be
       // set to a NullAppender, so this does not restrict the utility of
       // the logging in any way.
       Logger rl = LogManager.getRootLogger();
-      Enumeration appenders = rl.getAllAppenders();
-      
+      Enumeration<?> appenders = rl.getAllAppenders();
       if (!appenders.hasMoreElements()) {
         System.out.println("Log4J configuration failed, using default configuration settings");
         BasicConfigurator.configure(); 
         rl.setLevel(Level.INFO);
+        LOG = LogManager.getLogger(Phenote.class);
       }
-      LOG = LogManager.getLogger(Phenote.class);
-      //}
-    }
     
     // writes error events to log
     ErrorManager.inst().addErrorListener(new LogErrorListener());
@@ -148,22 +129,9 @@
     4.	loading into datamodel - display name - this is the bulk of the time
   */    
 
-    // put this is in a phenote.util.Log class? - get file from config - default?
     phenote.splashScreen.setProgress("Configuring...", 10);
     phenote.loadingScreen.setMessageText("Loading configuration: "+Config.inst().getConfigName());
     phenote.loadingScreen.setProgress(5);
-    // LOG4J
-    if (!phenote.commandLine.isLogSpecified()) {
-      try { DOMConfigurator.configure(Config.inst().getLogConfigUrl()); }
-      catch (FileNotFoundException e) { 
-        phenote.splashScreen.setProgress("bad file:"+e.getMessage(),10);
-        phenote.loadingScreen.setMessageText("Bad config: "+e.getMessage());
-        LOG.error(e.getMessage());
-      }
-    }
-
-    LOG.debug("debug test2 of log4j");
-
     phenote.splashScreen.setProgress("Initializing Ontologies...", 20);
     phenote.loadingScreen.setMessageText("Initializing Ontologies");
     phenote.loadingScreen.setProgress(10);


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[Obo-svn-commit] SF.net SVN: obo: [974] obo-database/trunk/rdf/d2rq/obd-d2rq.n3

From: <cmu...@us...> - 2007-10-07 00:29:01

Revision: 974
          http://obo.svn.sourceforge.net/obo/?rev=974&view=rev
Author:   cmungall
Date:     2007-10-06 17:29:05 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/rdf/d2rq/obd-d2rq.n3

Modified: obo-database/trunk/rdf/d2rq/obd-d2rq.n3
===================================================================
--- obo-database/trunk/rdf/d2rq/obd-d2rq.n3	2007-10-07 00:19:23 UTC (rev 973)
+++ obo-database/trunk/rdf/d2rq/obd-d2rq.n3	2007-10-07 00:29:05 UTC (rev 974)
@@ -61,6 +61,7 @@
       d2rq:join "node.node_id = is_a_link.node_id" ;
       d2rq:belongsToClassMap map:Node .
 
+# reify all links
 map:nodeLink a d2rq:PropertyBridge ;
       d2rq:property oban:link ;
       d2rq:uriPattern "node/@@link.object_id@@" ;


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[Obo-svn-commit] SF.net SVN: obo: [972] obo-database/trunk

From: <cmu...@us...> - 2007-10-07 00:02:09

Revision: 972
          http://obo.svn.sourceforge.net/obo/?rev=972&view=rev
Author:   cmungall
Date:     2007-10-06 17:02:13 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/bin/obd-create-db.pl
    obo-database/trunk/bin/obd-load-db-from-obo.pl

Added Paths:
-----------
    obo-database/trunk/build/build-omim/

Modified: obo-database/trunk/bin/obd-create-db.pl
===================================================================
--- obo-database/trunk/bin/obd-create-db.pl	2007-10-07 00:01:00 UTC (rev 971)
+++ obo-database/trunk/bin/obd-create-db.pl	2007-10-07 00:02:13 UTC (rev 972)
@@ -46,10 +46,15 @@
 run("psql $args < $sqldir/obd-core-functions.plpgsql ");
 
 if ($conf_file) {
+    my $dir = `dirname $conf_file`;
+    chomp $dir;
     open(F,$conf_file);
     while(<F>) {
         chomp;
         if (/^http:/ || /^file:/) {
+            if (/^file:\.\/(.*)/) {
+                $_ = "file://$dir/$1";
+            }
             push(@files, $_);
         }
         else {

Modified: obo-database/trunk/bin/obd-load-db-from-obo.pl
===================================================================
--- obo-database/trunk/bin/obd-load-db-from-obo.pl	2007-10-07 00:01:00 UTC (rev 971)
+++ obo-database/trunk/bin/obd-load-db-from-obo.pl	2007-10-07 00:02:13 UTC (rev 972)
@@ -58,6 +58,9 @@
         $file=$nu;
         $is_tmp=1;
     }
+    elsif ($file =~ /^file:(.*)$/) {
+        $file = $1;
+    }
     my $ifile = "$file.implied.obo";
     if ($use_reasoner) {
         run("obo2obo -o -saveallimpliedlinks $ifile $file");


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[Obo-svn-commit] SF.net SVN: obo: [971] obo-database/trunk

From: <cmu...@us...> - 2007-10-07 00:01:01

Revision: 971
          http://obo.svn.sourceforge.net/obo/?rev=971&view=rev
Author:   cmungall
Date:     2007-10-06 17:01:00 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Added Paths:
-----------
    obo-database/trunk/conf/
    obo-database/trunk/conf/fma-part-slim.obo
    obo-database/trunk/conf/obd-go.conf
    obo-database/trunk/conf/obd-phenotype.conf

Added: obo-database/trunk/conf/fma-part-slim.obo
===================================================================
--- obo-database/trunk/conf/fma-part-slim.obo	                        (rev 0)
+++ obo-database/trunk/conf/fma-part-slim.obo	2007-10-07 00:01:00 UTC (rev 971)
@@ -0,0 +1 @@
+link /Users/cjm/cvs/fma-conversion/fma-part-slim.obo
\ No newline at end of file


Property changes on: obo-database/trunk/conf/fma-part-slim.obo
___________________________________________________________________
Name: svn:special
   + *

Added: obo-database/trunk/conf/obd-go.conf
===================================================================
--- obo-database/trunk/conf/obd-go.conf	                        (rev 0)
+++ obo-database/trunk/conf/obd-go.conf	2007-10-07 00:01:00 UTC (rev 971)
@@ -0,0 +1,10 @@
+relationship
+ro_proposed
+quality
+biological_process
+molecular_function
+cellular_component
+cell
+chebi
+go_xp_cell
+go_xp_chebi

Added: obo-database/trunk/conf/obd-phenotype.conf
===================================================================
--- obo-database/trunk/conf/obd-phenotype.conf	                        (rev 0)
+++ obo-database/trunk/conf/obd-phenotype.conf	2007-10-07 00:01:00 UTC (rev 971)
@@ -0,0 +1,16 @@
+relationship
+ro_proposed
+quality
+zebrafish_anatomy
+fly_anatomy
+adult_mouse_anatomy
+biological_process
+molecular_function
+cellular_component
+cell
+mammalian_phenotype
+mammalian_phenotype_xp
+plant_trait
+plant_trait_xp
+chebi
+file:./fma-part-slim.obo


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[Obo-svn-commit] SF.net SVN: obo: [970] obo-database/trunk

From: <cmu...@us...> - 2007-10-06 23:54:01

Revision: 970
          http://obo.svn.sourceforge.net/obo/?rev=970&view=rev
Author:   cmungall
Date:     2007-10-06 16:54:01 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/bin/obd-create-db.pl

Added Paths:
-----------
    obo-database/trunk/build/
    obo-database/trunk/build/Makefile
    obo-database/trunk/build/Makefile-Build-Generic
    obo-database/trunk/build/build-hgnc/
    obo-database/trunk/build/build-hgnc/Makefile
    obo-database/trunk/build/build-hgnc/hgnc-map.xsl
    obo-database/trunk/build/build-hgnc/hgnc.tab
    obo-database/trunk/build/build-homologene/
    obo-database/trunk/build/build-ncbi-gene/

Modified: obo-database/trunk/bin/obd-create-db.pl
===================================================================
--- obo-database/trunk/bin/obd-create-db.pl	2007-10-06 23:04:21 UTC (rev 969)
+++ obo-database/trunk/bin/obd-create-db.pl	2007-10-06 23:54:01 UTC (rev 970)
@@ -49,13 +49,12 @@
     open(F,$conf_file);
     while(<F>) {
         chomp;
-        if (/^http:/ || /$file:/) {
+        if (/^http:/ || /^file:/) {
             push(@files, $_);
         }
         else {
             push(@files,"http://purl.org/obo/obo-all/$_/$_.obo");
         }
-#        push(@files,"obo-all/$_/$_.obo");
     }
     close(F);
 }

Added: obo-database/trunk/build/Makefile
===================================================================
--- obo-database/trunk/build/Makefile	                        (rev 0)
+++ obo-database/trunk/build/Makefile	2007-10-06 23:54:01 UTC (rev 970)
@@ -0,0 +1,22 @@
+.PRECIOUS: %.obo
+
+%.obd-createdb:
+	obd-create-db.pl -d $* && touch $@
+.PRECIOUS: %.obd-createdb
+
+%.obd-load: %.obo %.obd-createdb
+	obd-load-db-from-obo.pl -d $* $(OBD_LOAD_ARGS) $< >& $@.log && touch $@
+.PRECIOUS: %.obd-load
+
+%.obd-pgdump: %.obd-load
+	pg_dump -d $* > $@.tmp && mv $@.tmp $@
+
+%.obd-node.obdsql:
+	selectall_xml.pl -d $* /obd-node-export > $@.tmp && mv $@.tmp $@
+
+%.obd-node-tagval.obdsql:
+	selectall_xml.pl -d $* /obd-node-tagval-export > $@.tmp && mv $@.tmp $@
+
+%.gz: %
+	gzip $<
+

Added: obo-database/trunk/build/Makefile-Build-Generic
===================================================================
--- obo-database/trunk/build/Makefile-Build-Generic	                        (rev 0)
+++ obo-database/trunk/build/Makefile-Build-Generic	2007-10-06 23:54:01 UTC (rev 970)
@@ -0,0 +1 @@
+link Makefile
\ No newline at end of file


Property changes on: obo-database/trunk/build/Makefile-Build-Generic
___________________________________________________________________
Name: svn:special
   + *

Added: obo-database/trunk/build/build-hgnc/Makefile
===================================================================
--- obo-database/trunk/build/build-hgnc/Makefile	                        (rev 0)
+++ obo-database/trunk/build/build-hgnc/Makefile	2007-10-06 23:54:01 UTC (rev 970)
@@ -0,0 +1,2 @@
+hgnc.tab:
+	wget -O $@ 'http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl?title=Genew+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_locus_type&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_name_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_eg_id&col=gd_other_ids_list&col=gd_pub_refseq_ids&col=gd_gene_fam_name&col=md_eg_id&col=md_mim_id&col=md_refseq_id&col=md_prot_id&col=md_ensembl_id&status=Approved&status=Entry+Withdrawn&status_opt=2&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag'

Added: obo-database/trunk/build/build-hgnc/hgnc-map.xsl
===================================================================
--- obo-database/trunk/build/build-hgnc/hgnc-map.xsl	                        (rev 0)
+++ obo-database/trunk/build/build-hgnc/hgnc-map.xsl	2007-10-06 23:54:01 UTC (rev 970)
@@ -0,0 +1,12 @@
+<map>
+  <colgroup id="genotype" unique="Genotype">
+    <instance>
+      <id select="HGNC_ID"/>
+      <instance_of>SO:0000704</instance_of> <!-- gene -->
+      <name select="ApprovedSymbol"/>
+      <synonym>
+        <synonym_text scope="EXACT" select="ApprovedSymbol"/>
+      </synonym>
+    </instance>
+  </colgroup>
+</map>

Added: obo-database/trunk/build/build-hgnc/hgnc.tab
===================================================================
--- obo-database/trunk/build/build-hgnc/hgnc.tab	                        (rev 0)
+++ obo-database/trunk/build/build-hgnc/hgnc.tab	2007-10-06 23:54:01 UTC (rev 970)
@@ -0,0 +1,27380 @@
+HGNC ID	Approved Symbol	Approved Name	Status	Locus Type	Previous Symbols	Previous Names	Aliases	Name Aliases	Chromosome	Accession Numbers	Entrez Gene ID	Specialist Database IDs	RefSeq IDs	Gene Family Name	Entrez Gene ID (mapped data)	OMIM ID (mapped data)	RefSeq (mapped data)	UniProt ID (mapped data)	Ensembl ID (mapped data)
+HGNC:5	A1BG	alpha-1-B glycoprotein	Approved	undef					19q		1	, , , , , , , , , I43.950	NM_130786		1	138670	NM_130786	P04217	ENSG00000121410
+HGNC:6	A1S9T~withdrawn	symbol withdrawn, see UBE1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:7	A2M	alpha-2-macroglobulin	Approved	gene with protein product, function known or inferred			FWP007, S863-7, CPAMD5		12p13.31	BX647329, X68728, M11313	2	, , , , , , , , , I39.001	NM_000014		2	103950	NM_000014	P01023	ENSG00000175899
+HGNC:23336	A2ML1	alpha-2-macroglobulin-like 1	Approved	gene with protein product, function known or inferred	CPAMD9	"C3 and PZP-like, alpha-2-macroglobulin domain containing 9"	FLJ25179		12p13	AK057908	144568	, , , , , , , , , 	NM_144670		144568	610627	NM_144670	Q6ZW52	ENSG00000166535
+HGNC:8	A2MP	alpha-2-macroglobulin pseudogene	Approved	pseudogene					12p13.3-p12.3	M24415		, , , , , , , , , 			3				
+HGNC:10	A2MRAP~withdrawn	symbol withdrawn, see LRPAP1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:9	A2MR~withdrawn	symbol withdrawn, see LRP1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:30005	A3GALT2	alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)	Approved	gene with protein product, function known or inferred				"iGb3 synthase"	1p35.1		127550	, , , , , , , , , 	NM_001080438		127550		XM_940724	Q5T0B8	ENSG00000184389
+HGNC:18149	A4GALT	alpha 1,4-galactosyltransferase (globotriaosylceramide synthase)	Approved	gene with protein product, function known or inferred		"alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"	A14GALT	"Gb3 synthase", " CD77 synthase"	22q13.2		53947	, , , , , , , , , 	NM_017436		53947	607922	NM_017436	Q9NPC4	ENSG00000128274
+HGNC:17968	A4GNT	alpha-1,4-N-acetylglucosaminyltransferase	Approved	gene with protein product, function unknown			alpha4GnT		3p14.3	AF141315	51146	, , , , , , , , , 	NM_016161		51146		NM_016161	Q9UNA3	ENSG00000118017
+HGNC:1	A12M1~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:2	A12M2~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:3	A12M3~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:4	A12M4~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:13666	AAAS	achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)	Approved	undef					12q13	AJ289841		, , , , , , , , , 			8086	605378	NM_015665	Q9NRG9	ENSG00000094914
+HGNC:12	AABT~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:13	AAC1~withdrawn	symbol withdrawn, see NAT1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:14	AAC2~withdrawn	symbol withdrawn, see NAT2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:15	AACP	arylamide acetylase pseudogene	Approved	pseudogene			NATP		8p22	X17060		, , , , , , , , , 			11				
+HGNC:21298	AACS	acetoacetyl-CoA synthetase	Approved	gene with protein product, function known or inferred			FLJ12389, SUR-5		12q24.31	AK022451	65985	, , , , , , , , , 	NM_023928		65985		NM_023928	Q86V21	ENSG00000081760
+HGNC:18226	AACSL	acetoacetyl-CoA synthetase-like	Approved	gene with protein product, function unknown					5q35		401224	, , , , , , , , , 	XM_373104		401224		XM_936764		
+HGNC:13792	AACT~withdrawn	symbol withdrawn, see SERPINA3	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:17	AADAC	arylacetamide deacetylase (esterase)	Approved	gene with protein product, function known or inferred			DAC, CES5A1		3q21.3-q25.2	L32179	13	, , , , , , , , , S09.991	NM_001086		13	600338	NM_001086	P22760	ENSG00000114771
+HGNC:29260	AADACL1	arylacetamide deacetylase-like 1	Approved	gene with protein product, function unknown			KIAA1363		3q26.31	AB037784	57552	, , , , , , , , , S09.992	NM_020792		57552		NM_020792	Q6PIU2	ENSG00000144959
+HGNC:24427	AADACL2	arylacetamide deacetylase-like 2	Approved	gene with protein product, function unknown			MGC72001		3q25.1	BC065724	344752	, , , , , , , , , 	NM_207365		344752		NM_207365	Q6P093	ENSG00000197953
+HGNC:32037	AADACL3	arylacetamide deacetylase-like 3	Approved	gene with protein product, inferred			OTTHUMG00000001887		1p36.21		126767	, , , , , , , , , 	XM_928294		126767		XM_928294		ENSG00000188984
+HGNC:32038	AADACL4	arylacetamide deacetylase-like 4	Approved	gene with protein product, function unknown			OTTHUMG00000001889		1p36.21		343066	, , , , , , , , , 	NM_001013630		343066		NM_001013630	Q5VUY2	ENSG00000204518
+HGNC:17929	AADAT	aminoadipate aminotransferase	Approved	gene with protein product, function known or inferred			KATII, KAT2	"kynurenine aminotransferase II", "L kynurenine/alpha aminoadipate aminotransferase"	4q33	AF097994	51166	, , , , , , , , , 	NM_016228		51166		NM_016228	Q8N5Z0	ENSG00000109576
+HGNC:19679	AAK1	AP2 associated kinase 1	Approved	gene with protein product, function known or inferred			KIAA1048		2p24.3-p14	AB028971	22848	, , , , , , , , , 	NM_014911		22848		XM_941900	Q2M2I8	ENSG00000115977
+HGNC:18	AAMP	angio-associated, migratory cell protein	Approved	gene with protein product, function unknown					2q	AB209790	14	, , , , , , , , , 	NM_001087		14	603488	NM_001087	Q13685	ENSG00000127837
+HGNC:19	AANAT	arylalkylamine N-acetyltransferase	Approved	gene with protein product, function known or inferred			SNAT		17q25	U40347	15	, , , , , , , , , 	NM_001088		15	600950	NM_001088	Q16613	ENSG00000129673
+HGNC:20	AARS	alanyl-tRNA synthetase	Approved	gene with protein product, function known or inferred				"alanine tRNA ligase 1, cytoplasmic"	16q22	D32050	16	, , , , , , , , , 	NM_001605	aaRS2	16	601065	NM_001605	P49588	ENSG00000090861
+HGNC:21022	AARS2	alanyl-tRNA synthetase 2, mitochondrial (putative)	Approved	gene with protein product, function unknown	AARSL	"alanyl-tRNA synthetase like"	KIAA1270, bA444E17.1	"alanine tRNA ligase 2, mitochondrial (putative)"	6p21.1	AB033096	57505	, , , , , , , , , 	NM_020745	aaRS2	57505		NM_020745	Q5JTZ9	ENSG00000124608
+HGNC:28417	AARSD1	alanyl-tRNA synthetase domain containing 1	Approved	gene with protein product, function unknown			MGC2744		17q21.31	BC004172	80755	, , , , , , , , , 	NM_025267		80755		NM_025267	Q9BTE6	ENSG00000108825
+HGNC:14235	AASDHPPT	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	Approved	gene with protein product, function known or inferred			LYS5, CGI-80, AASD-PPT		11q22	AF302110	60496	, , , , , , , , , 	NM_015423		60496	607756	NM_015423	Q9NRN7	ENSG00000149313
+HGNC:17366	AASS	aminoadipate-semialdehyde synthase	Approved	undef			LORSDH, LKRSDH		7q31.3	AF229180	10157	, , , , , , , , , 			10157	605113	NM_005763	Q9UDR5	ENSG00000008311
+HGNC:19235	AATF	apoptosis antagonizing transcription factor	Approved	gene with protein product, function known or inferred			DED, CHE-1, CHE1		17q12	AF083208	26574	, , , , , , , , , 	NM_012138		26574	608463	NM_012138	Q9NY61	ENSG00000108270
+HGNC:21	AATK	apoptosis-associated tyrosine kinase	Approved	gene with protein product, function known or inferred			AATYK, KIAA0641, LMTK1, LMR1	"lemur tyrosine kinase 1"	17q25.3	AB014541	9625	, , , , , , , , , 	NM_004920		9625	605276	XM_001128317	Q6ZMQ8	ENSG00000181409
+HGNC:22	AAVS1	adeno-associated virus integration site 1	Approved	region			AAV		19q13	S51329	17	, , , , , , , , , 			17	102699			
+HGNC:11	AA~withdrawn	symbol withdrawn, see TEAD1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:23	ABAT	4-aminobutyrate aminotransferase	Approved	gene with protein product, function known or inferred			GABAT		16p13.2	L32961	18	, , , , , , , , , 	NM_020686		18	137150	NM_000663	P80404	ENSG00000183044
+HGNC:24	ABC1~withdrawn	symbol withdrawn, see ABCA1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:25	ABC2~withdrawn	symbol withdrawn, see ABCA2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:26	ABC3~withdrawn	symbol withdrawn, see ABCA3	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:28	ABC7~withdrawn	symbol withdrawn, see ABCB7	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:27	ABC50~withdrawn	symbol withdrawn, see ABCF1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:29	ABCA1	ATP-binding cassette, sub-family A (ABC1), member 1	Approved	gene with protein product, function known or inferred	ABC1, HDLDT1		TGD	"Tangier disease"	9q31	AJ012376	19	, , , , , , , , , 	NM_005502	ABC	19	600046	NM_005502	O95477	ENSG00000165029
+HGNC:32	ABCA2	ATP-binding cassette, sub-family A (ABC1), member 2	Approved	gene with protein product, function known or inferred	ABC2				9q34	U18235	20	, , , , , , , , , 	NM_001606	ABC	20	600047	NM_001606	Q9BZC7	ENSG00000107331
+HGNC:33	ABCA3	ATP-binding cassette, sub-family A (ABC1), member 3	Approved	gene with protein product, function known or inferred	ABC3		ABC-C, EST111653, LBM180		16p13.3	U78735	21	, , , , , , , , , 	NM_001089	ABC	21	601615	NM_001089	Q99758	ENSG00000167972
+HGNC:34	ABCA4	ATP-binding cassette, sub-family A (ABC1), member 4	Approved	gene with protein product, function known or inferred	STGD1, ABCR, RP19, STGD		FFM, ARMD2	"Stargardt disease"	1p22	U88667	24	, , , , , , , , , 	NM_000350	ABC	24	601691	NM_000350	P78363	ENSG00000198691
+HGNC:35	ABCA5	ATP-binding cassette, sub-family A (ABC1), member 5	Approved	undef			EST90625		17q21-q25	U66672		, , , , , , , , , 		ABC	23461		NM_018672	Q8WWZ7	ENSG00000154265
+HGNC:36	ABCA6	ATP-binding cassette, sub-family A (ABC1), member 6	Approved	undef			EST155051		17q21	U66680		, , , , , , , , , 		ABC	23460		NM_080284	Q8N139	ENSG00000154262
+HGNC:37	ABCA7	ATP-binding cassette, sub-family A (ABC1), member 7	Approved	gene with protein product, function known or inferred			ABCX		19p13.3	AF328787	10347	, , , , , , , , , 	NM_019112	ABC	10347	605414	NM_033308	Q8IZY2	ENSG00000064687
+HGNC:38	ABCA8	ATP-binding cassette, sub-family A (ABC1), member 8	Approved	undef			KIAA0822		17q24	AB020629		, , , , , , , , , 		ABC	10351		NM_007168	O94911	ENSG00000141338
+HGNC:39	ABCA9	ATP-binding cassette, sub-family A (ABC1), member 9	Approved	gene with protein product, function known or inferred			EST640918		17q24	AF423307	10350	, , , , , , , , , 	NM_172386	ABC	10350		NM_080283	Q8IUA7	ENSG00000154258
+HGNC:30	ABCA10	ATP-binding cassette, sub-family A (ABC1), member 10	Approved	undef			EST698739		17q24	AY247065		, , , , , , , , , 		ABC	10349		NM_080282	Q8WWZ4	ENSG00000154263
+HGNC:31	ABCA11	ATP-binding cassette, sub-family A (ABC1), member 11 (pseudogene)	Approved	pseudogene			EST1133530, FLJ14297		4p16.3	AK024359		, , , , , , , , , 	NM_024903	ABC	79963		NR_002451	Q4W5N1	
+HGNC:14637	ABCA12	ATP-binding cassette, sub-family A (ABC1), member 12	Approved	undef			DKFZP434G232		2q35	AF418105		, , , , , , , , , 		ABC	26154	607800	NM_015657	Q86UK0	ENSG00000144452
+HGNC:14638	ABCA13	ATP-binding cassette, sub-family A (ABC1), member 13	Approved	gene with protein product, function known or inferred			FLJ33876, FLJ33951		7p12.3	AY204751	154664	, , , , , , , , , 	NM_152701	ABC	154664	607807	NM_152701	Q86UQ4	ENSG00000179869
+HGNC:32972	ABCA17P	ATP-binding cassette, sub-family A (ABC1), member 17 (pseudogene)	Approved	pseudogene, transcribed					16p13.3			, , , , , , , , , 			767559				
+HGNC:40	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	Approved	gene with protein product, function known or inferred	PGY1, MDR1, CLCS	"colchicin sensitivity"	P-gp, CD243, GP170, ABC20		7q21.12	M14758	5243	, , CD243, , , , , , , 	NM_000927	ABC, CD	5243	171050	NM_000927	P08183	ENSG00000085563
+HGNC:11563	ABCB2~withdrawn	symbol withdrawn, see TAP1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:11564	ABCB3~withdrawn	symbol withdrawn, see TAP2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:45	ABCB4	ATP-binding cassette, sub-family B (MDR/TAP), member 4	Approved	gene with protein product, function known or inferred	PGY3, MDR3		MDR2, PFIC-3, GBD1		7q21	M23234	5244	, , , , , , , , , 	NM_000443	ABC	5244	171060	NM_018849	P21439	ENSG00000005471
+HGNC:46	ABCB5	ATP-binding cassette, sub-family B (MDR/TAP), member 5	Approved	undef			EST422562		7p14	U66692		, , , , , , , , , 		ABC	340273		NM_178559	Q2M3G0	ENSG00000004846
+HGNC:47	ABCB6	ATP-binding cassette, sub-family B (MDR/TAP), member 6	Approved	undef			EST45597, umat		2q33-q36	AF070598		, , , , , , , , , 		ABC	10058	605452	NM_005689	Q9NP58	ENSG00000115657
+HGNC:48	ABCB7	ATP-binding cassette, sub-family B (MDR/TAP), member 7	Approved	gene with protein product, function known or inferred	ABC7		EST140535, Atm1p, ASAT		Xq13.3	AF038950	22	, , , , , , , , , 	NM_004299	ABC	22	300135	NM_004299	O75027	ENSG00000131269
+HGNC:49	ABCB8	ATP-binding cassette, sub-family B (MDR/TAP), member 8	Approved	undef			EST328128, M-ABC1		7q35-q36	AF047690		, , , , , , , , , 		ABC	11194	605464	NM_007188	Q9NUT2	ENSG00000197150
+HGNC:50	ABCB9	ATP-binding cassette, sub-family B (MDR/TAP), member 9	Approved	undef			EST122234		12q24	U66676		, , , , , , , , , 		ABC	23457	605453	NM_019624	Q9NP78	ENSG00000150967
+HGNC:41	ABCB10	ATP-binding cassette, sub-family B (MDR/TAP), member 10	Approved	undef			EST20237		1q32	U18237		, , , , , , , , , 		ABC	23456	605454	NM_012089	Q9NRK6	ENSG00000135776
+HGNC:14114	ABCB10P	ATP-binding cassette, sub-family B (MDR/TAP), member 10 pseudogene	Approved	pseudogene			M-ABC2, MABC2		15q13-q14	AF218417		, , , , , , , , , 		ABC	56476				
+HGNC:42	ABCB11	ATP-binding cassette, sub-family B (MDR/TAP), member 11	Approved	undef	BSEP, PFIC2		ABC16, SPGP, PFIC-2, PGY4		2q24	AF091582		, , , , , , , , , 		ABC	8647	603201	NM_003742	O95342	ENSG00000073734
+HGNC:51	ABCC1	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	Approved	undef	MRP, MRP1		GS-X		16p13.1	L05628		, , , , , , , , , 		ABC	4363	158343	NM_019898	P33527	ENSG00000103222
+HGNC:53	ABCC2	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	Approved	undef	CMOAT		DJS, MRP2, cMRP		10q24	U63970		, , , , , , , , , 		ABC	1244	601107	NM_000392	Q92887	ENSG00000023839
+HGNC:54	ABCC3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	Approved	undef			MRP3, cMOAT2, EST90757, MLP2, MOAT-D		17q21	Y17151		, , , , , , , , , 	NM_020038	ABC	8714	604323	NM_003786	O15438	ENSG00000108846
+HGNC:55	ABCC4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	Approved	undef			MRP4, EST170205, MOAT-B		13q31	U66682		, , , , , , , , , 		ABC	10257	605250	NM_005845	O15439	ENSG00000125257
+HGNC:56	ABCC5	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	Approved	gene with protein product, function known or inferred			MRP5, SMRP, EST277145, MOAT-C		3q27	AF104942	10057	, , , , , , , , , 	NM_005688	ABC	10057	605251	NM_005688	O15440	ENSG00000114770
+HGNC:57	ABCC6	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	Approved	gene with protein product, function known or inferred	ARA, PXE	"pseudoxanthoma elasticum"	MRP6, EST349056, MLP1		16p13.1	AF076622		, , , , , , , , , 		ABC	368	603234	NM_001171	O95255	ENSG00000091262
+HGNC:33352	ABCC6P1	ATP-binding cassette, sub-family C, member 6 pseudogene 1	Approved	pseudogene					16p12.3	BC075833		, , , , , , , , , 			653190		NR_003569		
+HGNC:33353	ABCC6P2	ATP-binding cassette, sub-family C, member 6 pseudogene 2	Approved	pseudogene					16p13.11			, , , , , , , , , 			100034250				
+HGNC:58	ABCC7~withdrawn	symbol withdrawn, see CFTR	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:59	ABCC8	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	Approved	undef	SUR, HRINS		HI, PHHI, SUR1, MRP8		11p15.1	L78207		, , , , , , , , , 		ABC	6833	600509	NM_000352	Q09428	ENSG00000006071
+HGNC:60	ABCC9	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	Approved	gene with protein product, function known or inferred			SUR2, CMD1O		12p12.1	AF061323	10060	, , , , , , , , , 	NM_005691	ABC	10060	601439	NM_020298	O60706	ENSG00000069431
+HGNC:52	ABCC10	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	Approved	undef			EST182763, MRP7, SIMRP7		6p12.3	U66684		, , , , , , , , , 	NM_033450	ABC	89845		NM_033450	Q5T3U5	ENSG00000124574
+HGNC:14639	ABCC11	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	Approved	undef			MRP8		16q12	AF367202		, , , , , , , , , 		ABC	85320	607040	NM_145186	Q96J66	ENSG00000121270
+HGNC:14640	ABCC12	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	Approved	undef			MRP9		16-16q12	AY040220		, , , , , , , , , 		ABC	94160	607041	NM_033226	Q96J65	ENSG00000140798
+HGNC:16022	ABCC13	ATP-binding cassette, sub-family C (CFTR/MRP), member 13	Approved	gene with protein product, function known or inferred			PRED6, C21orf73		21q11.2	AF418600		, , , , , , , , , 		ABC	150000	608835	XR_017890	Q9NSE7	
+HGNC:61	ABCD1	ATP-binding cassette, sub-family D (ALD), member 1	Approved	gene with protein product, function known or inferred	ALD		AMN, ALDP, adrenoleukodystrophy		Xq28	Z21876	215	, , , , , , , , , 	NM_000033	ABC	215	300371	NM_000033	P33897	ENSG00000101986
+HGNC:62	ABCD1P1	ATP-binding cassette, sub-family D (ALD), member 1, pseudogene 1	Approved	pseudogene					2p11	U90290		, , , , , , , , , 		ABC	23785				
+HGNC:63	ABCD1P2	ATP-binding cassette, sub-family D (ALD), member 1, pseudogene 2	Approved	pseudogene			bA453N3.6		10p11	U90288		, , , , , , , , , 		ABC	26983				
+HGNC:64	ABCD1P3	ATP-binding cassette, sub-family D (ALD), member 1, pseudogene 3	Approved	pseudogene					16p11	U90289		, , , , , , , , , 		ABC	26982				
+HGNC:65	ABCD1P4	ATP-binding cassette, sub-family D (ALD), member 1, pseudogene 4	Approved	pseudogene					22q11	U90291		, , , , , , , , , 		ABC	26957				
+HGNC:66	ABCD2	ATP-binding cassette, sub-family D (ALD), member 2	Approved	undef	ALDL1		ALDR, ALDRP		12q11-q12	U28150		, , , , , , , , , 		ABC	225	601081	NM_005164	Q9UBJ2	ENSG00000173208
+HGNC:67	ABCD3	ATP-binding cassette, sub-family D (ALD), member 3	Approved	gene with protein product, function known or inferred	PXMP1		PMP70		1p22-p21	M81182	5825	, , , , , , , , , 	NM_002858	ABC	5825	170995	NM_002858	P28288	ENSG00000117528
+HGNC:68	ABCD4	ATP-binding cassette, sub-family D (ALD), member 4	Approved	undef	PXMP1L		PMP69, P70R, EST352188		14q24	AF009746		, , , , , , , , , 		ABC	5826	603214	NM_020324	O14678	ENSG00000119688
+HGNC:69	ABCE1	ATP-binding cassette, sub-family E (OABP), member 1	Approved	gene with protein product, function known or inferred	RNASEL1, RNASELI, RNS4I		RLI, OABP		4q31	X74987	6059	, , , , , , , , , 	NM_002940	ABC	6059	601213	NM_002940	P61221	ENSG00000164163
+HGNC:70	ABCF1	ATP-binding cassette, sub-family F (GCN20), member 1	Approved	undef	ABC50		EST123147		6p21.33	AF027302		, , , , , , , , , 		ABC	23	603429	NM_001090	Q8NE71	ENSG00000204574
+HGNC:71	ABCF2	ATP-binding cassette, sub-family F (GCN20), member 2	Approved	undef			EST133090		7q35-q36	AJ005016		, , , , , , , , , 		ABC	10061		NM_007189	Q9UG63	ENSG00000033050
+HGNC:72	ABCF3	ATP-binding cassette, sub-family F (GCN20), member 3	Approved	undef			EST201864		3q25.1-q25.2	U66685		, , , , , , , , , 		ABC	55324		NM_018358	Q9NUQ8	ENSG00000161204
+HGNC:73	ABCG1	ATP-binding cassette, sub-family G (WHITE), member 1	Approved	undef			ABC8		21q22.3	U34919		, , , , , , , , , 		ABC	9619	603076	NM_207628	P45844	ENSG00000160179
+HGNC:74	ABCG2	ATP-binding cassette, sub-family G (WHITE), member 2	Approved	gene with protein product, function known or inferred			EST157481, MXR, BCRP, ABCP, CDw338		4q22-q23	AF103796	9429	, , CDw338, , , , , , , 	NM_004827	ABC, CD	9429	603756	NM_004827	Q9UNQ0	ENSG00000118777
+HGNC:13884	ABCG4	ATP-binding cassette, sub-family G (WHITE), member 4	Approved	undef			WHITE2		11q23	AJ300465		, , , , , , , , , 		ABC	64137	607784	NM_022169	Q9H172	ENSG00000172350
+HGNC:13886	ABCG5	ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin 1)	Approved	undef					2p21	T93792		, , , , , , , , , 		ABC	64240	605459	NM_022436	Q9H222	ENSG00000138075
+HGNC:13887	ABCG8	ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)	Approved	gene with protein product, function unknown					2p21	AF320294	64241	, , , , , , , , , 	NM_022437	ABC	64241	605460	NM_022437	Q9H221	ENSG00000143921
+HGNC:75	ABCR~withdrawn	symbol withdrawn, see ABCA4	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:17553	ABHD1	abhydrolase domain containing 1	Approved	undef			LABH1, FLJ36128		2p23.3	AK093447	84696	, , , , , , , , , 		ABHD	84696		NM_032604	Q96SE0	ENSG00000143994
+HGNC:18717	ABHD2	abhydrolase domain containing 2	Approved	gene with protein product, function known or inferred			LABH2		15q26.1	X12433	11057	, , , , , , , , , 		ABHD	11057		NM_152924	P08910	ENSG00000140526
+HGNC:18718	ABHD3	abhydrolase domain containing 3	Approved	undef			LABH3		18q11.1	AK024880	171586	, , , , , , , , , 		ABHD	171586		NM_138340	Q8WU67	ENSG00000158201
+HGNC:20154	ABHD4	abhydrolase domain containing 4	Approved	gene with protein product, function unknown			FLJ12816		14q11.1	AK022878	63874	, , , , , , , , , S33.013		ABHD	63874		NM_022060	Q8TB40	ENSG00000100439
+HGNC:21396	ABHD5	abhydrolase domain containing 5	Approved	gene with protein product, function unknown			CGI-58, NCIE2		3p25.3-p24.3	AF007132	51099	, , , , , , , , , S33.975	NM_016006	ABHD	51099	604780	NM_016006	Q8WTS1	ENSG00000011198
+HGNC:21398	ABHD6	abhydrolase domain containing 6	Approved	gene with protein product, function unknown					3p21.2	AF225418	57406	, , , , , , , , , S33.977	NM_020676	ABHD	57406		NM_020676	Q9BV23	ENSG00000163686
+HGNC:23758	ABHD7	abhydrolase domain containing 7	Approved	gene with protein product, function known or inferred			EPHXRP, FLJ90341		1p22.1	AK074822	253152	, , , , , , , , , S33.974	NM_173567	ABHD	253152		NM_173567	Q8IUS5	ENSG00000172031
+HGNC:23759	ABHD8	abhydrolase domain containing 8	Approved	gene with protein product, function known or inferred			FLJ11743, MGC14280, MGC2512		19p13.12	AK021805	79575	, , , , , , , , , S33.011	NM_024527	ABHD	79575		NM_024527	Q96I13	ENSG00000127220
+HGNC:23760	ABHD9	abhydrolase domain containing 9	Approved	gene with protein product, function known or inferred			FLJ22408		19p13.13	AK026061	79852	, , , , , , , , , S33.978	NM_024794	ABHD	79852		NM_024794	Q9H6B9	ENSG00000105131
+HGNC:25656	ABHD10	abhydrolase domain containing 10	Approved	gene with protein product, function known or inferred			FLJ11342		3q13.2	AL713726	55347	, , , , , , , , , S09.062	NM_018394	ABHD	55347		NM_018394	Q9NUJ1	ENSG00000144827
+HGNC:16407	ABHD11	abhydrolase domain containing 11	Approved	gene with protein product, function known or inferred	WBSCR21	"Williams Beuren syndrome chromosome region 21"	PP1226		7q11.23	AF217971		, , , , , , , , , S33.976		ABHD	83451		NM_148915	Q8NFV4	ENSG00000106077
+HGNC:15868	ABHD12	abhydrolase domain containing 12	Approved	gene with protein product, function unknown	C20orf22	"chromosome 20 open reading frame 22"	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A		20p11.21	AL117442		, , , , , , , , , S09.054	NM_015600	ABHD	26090		NM_015600	Q8N2K0	ENSG00000100997
+HGNC:19837	ABHD12B	abhydrolase domain containing 12B	Approved	gene with protein product, function unknown	C14orf29	"chromosome 14 open reading frame 29"	BEM46L3		14q21.3	BG698443	145447	, , , , , , , , , S09.061		ABHD	145447		NM_181814	Q7Z5M8	ENSG00000131969
+HGNC:20293	ABHD13	abhydrolase domain containing 13	Approved	gene with protein product, function unknown	C13orf6	"chromosome 13 open reading frame 6"	bA153I24.2, FLJ14906, BEM46L1		13q33.2	AK027812	84945	, , , , , , , , , 	NM_032859	ABHD	84945		NM_032859	Q7L211	ENSG00000139826
+HGNC:24538	ABHD14A	abhydrolase domain containing 14A	Approved	gene with protein product, function unknown			DKFZP564O243, DORZ1		3p21.1	AY358201	25864	, , , , , , , , , S33.981	NM_015407	ABHD	25864		NM_015407	Q9BUJ0	ENSG00000042022
+HGNC:28235	ABHD14B	abhydrolase domain containing 14B	Approved	gene with protein product, function unknown			MGC15429, CIB		3p21.2	AK075112	84836	, , , , , , , , , 	NM_032750	ABHD	84836		NM_032750	Q96IU4	ENSG00000114779
+HGNC:11320	ABI1	abl-interactor 1	Approved	undef	SSH3BP1	"spectrin SH3 domain binding protein 1"	E3B1, ABI-1		10p11.2-p12	U87166	10006	, , , , , , , , , 	NM_005470		10006	603050	NM_001012751	Q8IZP0	ENSG00000136754
+HGNC:20035	ABI1P	abl-interactor 1 pseudogene	Approved	pseudogene	SSH3BP1P	"spectrin SH3 domain binding protein 1 pseudogene"			14q22			, , , , , , , , , 			326268				
+HGNC:24011	ABI2	abl interactor 2	Approved	gene with protein product, function known or inferred			ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2		2	AF260261	10152	, , , , , , , , , 	NM_005759		10152	606442	NM_005759	Q9NYB9	ENSG00000138443
+HGNC:29859	ABI3	ABI gene family, member 3	Approved	gene with protein product, function known or inferred			NESH, SSH3BP3		17q21.3	AB037886	51225	, , , , , , , , , 	NM_016428		51225	606363	NM_016428	Q9P2A4	ENSG00000108798
+HGNC:17265	ABI3BP	ABI gene family, member 3 (NESH) binding protein	Approved	gene with protein product, function unknown			NESHBP, DKFZP586L2024, TARSH		3q12	AB056106		, , , , , , , , , 			25890	606279	NM_015429	Q7Z7G0	ENSG00000154175
+HGNC:76	ABL1	v-abl Abelson murine leukemia viral oncogene homolog 1	Approved	gene with protein product, function known or inferred	ABL		JTK7, c-ABL, p150, v-abl		9q34.1	M14752	25	, , , , , , , , , 	NM_007313		25	189980	NM_007313	P00519	ENSG00000097007
+HGNC:77	ABL2	v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)	Approved	gene with protein product, function known or inferred	ABLL		ARG		1q25.2	M14904	27	, , , , , , , , , 	NM_005158		27	164690	NM_007314	P42684	ENSG00000143322
+HGNC:78	ABLIM1	actin binding LIM protein 1	Approved	undef	LIMAB1, ABLIM		abLIM, limatin		10q25	AF005654		, , , , , , , , , 			3983	602330	NM_002313	O14639	ENSG00000099204
+HGNC:19195	ABLIM2	actin binding LIM protein family, member 2	Approved	gene with protein product, function known or inferred		"actin binding LIM protein 2"	KIAA1808		4p16-p15	AB058711		, , , , , , , , , 			84448		NM_032432	Q6H8Q1	ENSG00000163995
+HGNC:29132	ABLIM3	actin binding LIM protein family, member 3	Approved	gene with protein product, function unknown			KIAA0843		5q33.1	AB020650	22885	, , , , , , , , , 	NM_014945		22885		NM_014945	O94929	ENSG00000173210
+HGNC:79	ABO	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)	Approved	gene with protein product, function known or inferred			A3GALNT, A3GALT1		9q34.2	AF134415	28	, , , , , , , , , 	NM_020469	bloodgroup	28	110300	NM_020469	P16442	ENSG00000175164
+HGNC:80	ABP1	amiloride binding protein 1 (amine oxidase (copper-containing))	Approved	gene with protein product, function known or inferred			AOC1, DAO		7q34-qter	AK092514	26	, , , , , , , , , 	NM_001091		26	104610	NM_001091	P19801	ENSG00000002726
+HGNC:81	ABR	active BCR-related gene	Approved	undef			MDB		17p13	L19704		, , , , , , , , , 			29	600365	NM_001092	Q12979	ENSG00000159842
+HGNC:30655	ABRA	actin-binding Rho activating protein	Approved	gene with protein product, function known or inferred			STARS		8q23.1	AF503617	137735	, , , , , , , , , 	NM_139166		137735	609747	NM_139166	Q8N0Z2	ENSG00000174429
+HGNC:17369	ABT1	activator of basal transcription 1	Approved	undef					6p21.31	AB027258		, , , , , , , , , 			29777		NM_013375	Q9ULW3	ENSG00000146109
+HGNC:18275	ABTB1	ankyrin repeat and BTB (POZ) domain containing 1	Approved	undef			BPOZ, EF1ABP		3q21	AB053324		, , , , , , , , , 			80325	608308	NM_172028	Q969K4	ENSG00000114626
+HGNC:23842	ABTB2	ankyrin repeat and BTB (POZ) domain containing 2	Approved	gene with protein product, function known or inferred			DKFZP586C1619		11p13	AK056863	25841	, , , , , , , , , 	NM_145804		25841		NM_145804	Q8N961	ENSG00000166016
+HGNC:82	ACAA1	acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl-Coenzyme A thiolase)	Approved	undef					3p23-p22	X14813	30	, , , , , , , , , 	NM_001607		30	604054	NM_001607	P09110	ENSG00000060971
+HGNC:83	ACAA2	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase)	Approved	undef			DSAEC		18	D16294		, , , , , , , , , 			10449	604770	NM_006111	P42765	ENSG00000167315
+HGNC:84	ACACA	acetyl-Coenzyme A carboxylase alpha	Approved	undef	ACAC, ACC		ACC1		17q21	U19822		, , , , , , , , , 			31	200350	NM_198834	Q13085	ENSG00000132142
+HGNC:85	ACACB	acetyl-Coenzyme A carboxylase beta	Approved	gene with protein product, function known or inferred			HACC275, ACC2, ACCB		12q24.1	U89344	32	, , , , , , , , , 	NM_001093		32	601557	NM_001093	O00763	ENSG00000076555
+HGNC:87	ACAD8	acyl-Coenzyme A dehydrogenase family, member 8	Approved	undef					11q25	AF126245	27034	, , , , , , , , , 	NM_014384		27034	604773	NM_014384	Q9UKU7	ENSG00000151498
+HGNC:21497	ACAD9	acyl-Coenzyme A dehydrogenase family, member 9	Approved	gene with protein product, function known or inferred			NPD002, MGC14452		3q21.3	AF078854	28976	, , , , , , , , , 	NM_014049		28976	611103	NM_014049	Q9H845	ENSG00000177646
+HGNC:21597	ACAD10	acyl-Coenzyme A dehydrogenase family, member 10	Approved	gene with protein product, function unknown			MGC5601		12q24.12	AY323912	80724	, , , , , , , , , 	NM_025247		80724	611181	NM_025247	Q6JQN1	ENSG00000111271
+HGNC:30211	ACAD11	acyl-Coenzyme A dehydrogenase family, member 11	Approved	gene with protein product, function unknown			FLJ12592		3q22.1	BC019607	84129	, , , , , , , , , 	NM_032169.3		84129		NM_032169	Q709F0	ENSG00000113971
+HGNC:88	ACADL	acyl-Coenzyme A dehydrogenase, long chain	Approved	gene with protein product, function known or inferred			LCAD, ACAD4		2q34-q35	M74096	33	, , , , , , , , , 	NM_001608		33	609576	NM_001608	P28330	ENSG00000115361
+HGNC:89	ACADM	acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain	Approved	gene with protein product, function known or inferred			MCAD, MCADH, ACAD1		1p31	M16827	34	, , , , , , , , , 			34	607008	NM_000016	P11310	ENSG00000117054
+HGNC:90	ACADS	acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain	Approved	gene with protein product, function known or inferred			SCAD, ACAD3		12q24.31	M26393	35	, , , , , , , , , 	NM_000017		35	606885	NM_000017	P16219	ENSG00000122971
+HGNC:91	ACADSB	acyl-Coenzyme A dehydrogenase, short/branched chain	Approved	gene with protein product, function known or inferred			SBCAD, ACAD7		10q25-q26	U12778	36	, , , , , , , , , 	NM_001609		36	600301	NM_001609	P45954	ENSG00000196177
+HGNC:92	ACADVL	acyl-Coenzyme A dehydrogenase, very long chain	Approved	gene with protein product, function known or inferred			VLCAD, LCACD, ACAD6		17p13-17p11	BC012912	37	, , , , , , , , , 	NM_000018		37	609575	NM_001033859	P49748	ENSG00000072778
+HGNC:86	ACAD~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:319	ACAN	aggrecan	Approved	gene with protein product, function known or inferred	MSK16, CSPG1, AGC1	"chondroitin sulfate proteoglycan 1", "aggrecan 1"	CSPGCP	"aggrecan proteoglycan"	15q26.1	M55172	176	, , , , , , , , , 	NM_001135	AGC, proteoglycan	176	155760	NM_013227	P16112	ENSG00000157766
+HGNC:93	ACAT1	acetyl-Coenzyme A acetyltransferase 1 (acetoacetyl Coenzyme A thiolase)	Approved	gene with protein product, function known or inferred	ACAT		THIL		11q22.3	D90228	38	, , , , , , , , , 	NM_000019		38	607809	NM_000019	P24752	ENSG00000075239
+HGNC:94	ACAT2	acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)	Approved	undef					6q25.3-q26	AF356877		, , , , , , , , , 			39	100678	NM_005891	Q9BWD1	ENSG00000120437
+HGNC:15453	ACBD3	acyl-Coenzyme A binding domain containing 3	Approved	gene with protein product, function known or inferred	GOLPH1, GOCAP1	"golgi complex associated protein 1, 60kDa"	GCP60		1q41	AB043587	64746	, , , , , , , , , 	NM_022735		64746	606809	NM_022735	Q9H3P7	ENSG00000182827
+HGNC:23337	ACBD4	acyl-Coenzyme A binding domain containing 4	Approved	gene with protein product, function known or inferred			FLJ13322		17q21.31	BC029164	79777	, , , , , , , , , 	NM_024722		79777		NM_024722	Q8NC06	ENSG00000181513
+HGNC:23338	ACBD5	acyl-Coenzyme A binding domain containing 5	Approved	gene with protein product, function known or inferred			DKFZp434A2417, KIAA1996		10p12.1	AF505653	91452	, , , , , , , , , 	NM_145698		91452		NM_001042473	Q5T8D3	ENSG00000107897
+HGNC:23339	ACBD6	acyl-Coenzyme A binding domain containing 6	Approved	gene with protein product, function known or inferred			MGC2404		1q25.1	BC006505	84320	, , , , , , , , , 	NM_032360		84320		NM_032360	Q9BR61	ENSG00000135847
+HGNC:17715	ACBD7	acyl-Coenzyme A binding domain containing 7	Approved	gene with protein product, function unknown			FLJ38219, bA455B2.2		10	AK095538		, , , , , , , , , 			414149		NM_001039844	Q8N6N7	ENSG00000176244
+HGNC:96	ACBP~withdrawn	symbol withdrawn, see CPN2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:99	ACCN1	amiloride-sensitive cation channel 1, neuronal (degenerin)	Approved	gene with protein product, function known or inferred	ACCN		ASIC2a, ASIC2, BNC1, BNaC1, hBNaC1, MDEG		17q11.2-q12	AL834182	40	, , , , , , , , , 	NM_183377, NM_001094		40	601784	XM_001125040	Q16515	ENSG00000108684
+HGNC:100	ACCN2	amiloride-sensitive cation channel 2, neuronal	Approved	gene with protein product, function known or inferred			BNaC2, hBNaC2		12q12	U78181	41	, , , , , , , , , 	NM_020039		41	602866	NM_020039	P78348	ENSG00000110881
+HGNC:101	ACCN3	amiloride-sensitive cation channel 3	Approved	undef		"amiloride-sensitive cation channel 3, testis"	ASIC3, TNaC1		7q35	AB010575		, , , , , , , , , 			9311		NM_020321	Q9UHC3	ENSG00000197150
+HGNC:21263	ACCN4	amiloride-sensitive cation channel 4, pituitary	Approved	gene with protein product, function known or inferred			ASIC4, BNAC4		2q36.1	AJ271643	55515	, , , , , , , , , 	NM_018674		55515	606715	NM_018674	Q96FT7	ENSG00000072182
+HGNC:17537	ACCN5	amiloride-sensitive cation channel 5, intestinal	Approved	gene with protein product, function known or inferred			INAC, HINAC		4q31.3-q32	AJ252011	51802	, , , , , , , , , 			51802		NM_017419	Q9NY37	ENSG00000023843
+HGNC:98	ACCN~withdrawn	symbol withdrawn, see ACCN1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:14594	ACCPN~withdrawn	symbol withdrawn, see SLC12A6	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:97	ACC~withdrawn	symbol withdrawn, see ACACA	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:25070	ACD	adrenocortical dysplasia homolog (mouse)	Approved	gene with protein product, function unknown			24432, Ptop, Pip1		16q22	AF070535	65057	, , , , , , , , , 	NM_022914		65057	609377	NM_022914	Q96AP0	ENSG00000102977
+HGNC:2707	ACE	angiotensin I converting enzyme (peptidyl-dipeptidase A) 1	Approved	gene with protein product, function known or inferred	DCP1		ACE1, CD143		17q23	J04144		, , CD143, , , , , , , 		CD	1636	106180	NM_152830	P12821	ENSG00000159640
+HGNC:13557	ACE2	angiotensin I converting enzyme (peptidyl-dipeptidase A) 2	Approved	undef					Xp22	AF291820		, , , , , , , , , M02.006			59272	300335	NM_021804	Q9BYF1	ENSG00000130234
+HGNC:107	ACHAP~withdrawn	symbol withdrawn, see CUTA	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:108	ACHE	acetylcholinesterase (Yt blood group)	Approved	gene with protein product, function known or inferred	YT	"acetylcholinesterase (YT blood group)"			7q22		43	, , , , , , , , , S09.979	NM_015831	bloodgroup	43	100740	NM_000665	P22303	ENSG00000087085
+HGNC:109	ACHM1	achromatopsia (rod monochromacy) 1	Approved	phenotype only	RMCH				14			, , , , , , , , , 			6021	603096			
+HGNC:110	ACHM2~withdrawn	symbol withdrawn, see CNGA3	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:111	ACHM3~withdrawn	symbol withdrawn, see CNGB3	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:112	ACHRD~withdrawn	symbol withdrawn, see CHRND	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:113	ACHRG~withdrawn	symbol withdrawn, see CHRNG	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:106	ACH~withdrawn	symbol withdrawn, see FGFR3	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:17066	ACIN1	apoptotic chromatin condensation inducer 1	Approved	gene with protein product, function known or inferred	ACINUS	"apoptotic chromatin condensation inducer in the nucleus"	KIAA0670		14q11.2	AB014570	22985	, , , , , , , , , 	NM_014977		22985	604562	NM_014977	Q9UKV3	ENSG00000100813
+HGNC:114	ACLS	acrocallosal syndrome	Approved	phenotype only					12p13.3-p11.2			, , , , , , , , , 			46	200990			
+HGNC:115	ACLY	ATP citrate lyase	Approved	gene with protein product, function known or inferred			ATPCL, CLATP, ACL		17q21.2	X64330	47	, , , , , , , , , 	NM_001096		47	108728	NM_001096	P53396	ENSG00000131473
+HGNC:116	ACMG~withdrawn	entry withdrawn	Entry Withdrawn	undef								, , , , , , , , , 							
+HGNC:19288	ACMSD	aminocarboxymuconate semialdehyde decarboxylase	Approved	undef					2q14.3	AB071418	130013	, , , , , , , , , 			130013	608889	NM_138326	Q8TDX5	ENSG00000153086
+HGNC:21752	ACN9	ACN9 homolog (S. cerevisiae)	Approved	gene with protein product, function unknown			DC11		7q22.1	BC028409	57001	, , , , , , , , , 	NM_020186		57001		NM_020186	Q9NRP4	ENSG00000196636
+HGNC:117	ACO1	aconitase 1, soluble	Approved	gene with protein product, function known or inferred	IREB1		IRP1, IREBP		9p21.1	M58510	48	, , , , , , , , , 	NM_002197		48	100880	NM_002197	P21399	ENSG00000122729
+HGNC:118	ACO2	aconitase 2, mitochondrial	Approved	gene with protein product, function known or inferred			ACONM		22q13.2	AH006514	50	, , , , , , , , , 	NM_001098		50	100850	NM_001098	Q99798	ENSG00000100412
+HGNC:33128	ACOT1	acyl-CoA thioesterase 1	Approved	gene with protein product, function known or inferred			ACH2, CTE-1, LACH2		14q24.3	DQ082754	641371	, , , , , , , , , 	NM_001037161	ACOT	641371		NM_001037161	Q86TX2	ENSG00000184227
+HGNC:18431	ACOT2	acyl-CoA thioesterase 2	Approved	gene with protein product, function known or inferred			Mte1, ZAP128	"mitochondrial acyl-CoA thioesterase 1"	14q24.3	AY005822, AK001939	10965	, , , , , , , , , 	NM_006821	ACOT	10965	609972	NM_006821	P49753	ENSG00000119673
+HGNC:19748	ACOT4	acyl-CoA thioesterase 4	Approved	gene with protein product, function known or inferred			FLJ31235, PTE-Ib, PTE2B		14q24.1	BC031799	122970	, , , , , , , , , 	NM_152331	ACOT	122970		NM_152331	Q8N9L9	ENSG00000177465
+HGNC:33159	ACOT6	acyl-CoA thioesterase 6	Approved	gene with protein product, function known or inferred	C14orf42	"chromosome 14 open reading frame 42"			14q24.3	DQ082756, BF109853	641372	, , , , , , , , , 	NM_001037162	ACOT	641372		NM_001037162	Q3I5F7	ENSG00000205669
+HGNC:24157	ACOT7	acyl-CoA thioesterase 7	Approved	gene with protein product, function known or inferred			BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	"brain acyl CoA hydrolase"	1p36	AB074417	11332	, , , , , , , , , 	NM_007274	ACOT	11332	602587	NM_181865	O00154	ENSG00000097021
+HGNC:15919	ACOT8	acyl-CoA thioesterase 8	Approved	gene with protein product, function known or inferred	PTE1	"peroxisomal acyl-CoA thioesterase", "peroxisomal acyl-CoA thioesterase 1"	hACTE-III, hTE, PTE-2		20pter-p12.3	AF014404	10005	, , , , , , , , , 	NM_183386	ACOT	10005	608123	NM_183385	O14734	ENSG00000101473
+HGNC:17152	ACOT9	acyl-CoA thioesterase 9	Approved	gene with protein product, function known or inferred			CGI-16, MT-ACT48, ACATE2		Xp22.11	AF132950	23597	, , , , , , , , , 	NM_012332	ACOT	23597		NM_001037171	Q9Y305	ENSG00000123130
+HGNC:18156	ACOT11	acyl-CoA thioesterase 11	Approved	gene with protein product, function known or inferred	THEA	"thioesterase, adipose associated"	STARD14, BFIT, KIAA0707, BFIT1, THEM1		1p32.3	AB014607	26027	, , , , , , , , , 	NM_015547	ACOT	26027	606803	NM_147161	Q8WXI4	ENSG00000162390
+HGNC:24436	ACOT12	acyl-CoA thioesterase 12	Approved	gene with protein product, function known or inferred			Cach, THEAL, STARD15		5q14.1	AB078619	134526	, , , , , , , , , 	NM_130767	ACOT	134526		NM_130767	Q8WYK0	ENSG00000172497
+HGNC:119	ACOX1	acyl-Coenzyme A oxidase 1, palmitoyl	Approved	undef			PALMCOX		17q24-17q25	U03254		, , , , , , , , , 			51	609751	NM_007292	Q15067	ENSG00000161533
+HGNC:120	ACOX2	acyl-Coenzyme A oxidase 2, branched chain	Approved	undef			BRCACOX, BRCOX		3p14.3	X95190		, , , , , , , , , 			8309	601641	NM_003500	Q99424	ENSG00000168306
+HGNC:121	ACOX3	acyl-Coenzyme A oxidase 3, pristanoyl	Approved	undef					4p15.3	Y11411		, , , , , , , , , 			8310	603402	NM_003501	O15254	ENSG00000087008
+HGNC:25621	ACOXL	acyl-Coenzyme A oxidase-like	Approved	gene with protein product, function unknown			FLJ11042		2		55289	, , , , , , , , , 	NM_018308		55289		NM_018308	Q9NUZ1	ENSG00000153093
+HGNC:122	ACP1	acid phosphatase 1, soluble	Approved	undef					2p25	M87546		, , , , , , , , , 		PTP2	52	171500	NM_007099	P24666	ENSG00000143727
+HGNC:123	ACP2	acid phosphatase 2, lysosomal	Approved	gene with protein product, function known or inferred					11p11.2	X15525	53	, , , , , , , , , 	NM_001610		53	171650	NM_001610	P11117	ENSG00000134575
+HGNC:124	ACP5	acid phosphatase 5, tartrate resistant	Approved	undef					19p13.3-p13.2	X14618		, , , , , , , , , 			54	171640	NM_001611	P13686	ENSG00000102575
+HGNC:29609	ACP6	acid phosphatase 6, lysophosphatidic	Approved	gene with protein product, function known or inferred			LPAP, ACPL1		1q21	BC009965	51205	, , , , , , , , , 	NM_016361		51205		NM_016361	Q9NPH0	ENSG00000162836
+HGNC:26303	ACPL2	acid phosphatase-like 2	Approved	gene with protein product, function unknown			FLJ23751		3q23		92370	, , , , , , , , , 	NM_152282		92370		NM_001037172	Q8TE99	ENSG00000155893
+HGNC:125	ACPP	acid phosphatase, prostate	Approved	undef			ACP3, ACP-3		3q21-qter			, , , , , , , , , 	NM_001099		55	171790	NM_001099	P15309	ENSG00000014257
+HGNC:14376	ACPT	acid phosphatase, testicular	Approved	gene with protein product, function known or inferred					19q13.4	AF321918		, , , , , , , , , 	NM_033068		93650	606362	NM_080789	Q9BZG2	ENSG00000142513
+HGNC:126	ACR	acrosin	Approved	gene with protein product, function known or inferred				"preproacrosin"	22q13-qter	CR456366	49	, , , , , , , , , S01.223	NM_001097		49	102480	NM_001097	P10323	ENSG00000100312
+HGNC:17195	ACRBP	acrosin binding protein	Approved	undef			SP32		12pter-p13.31	AB051833		, , , , , , , , , 			84519	608352	NM_032489	Q8NEB7	ENSG00000111644
+HGNC:15805	ACRC	acidic repeat containing	Approved	gene with protein product, function unknown					Xq13.1	AJ311392		, , , , , , , , , 			93953	300369	NM_052957	Q96QF7	ENSG00000147174
+HGNC:127	ACRV1	acrosomal vesicle protein 1	Approved	undef			SPACA2, SP-10	"sperm protein 10"	11p12-q13	AK223335		, , , , , , , , , 	NM_001612		56	102525	NM_020113	P26436	ENSG00000134940
+HGNC:128	ACS3~withdrawn	symbol withdrawn, see TWIST1	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:29567	ACSBG1	acyl-CoA synthetase bubblegum family member 1	Approved	gene with protein product, function known or inferred			BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	"bubblegum", "very long-chain acyl-CoA synthetase", "lipidosin"	15q23-q24	AB014531	23205	, , , , , , , , , 	NM_015162	ACS	23205		NM_015162	Q96GR2	ENSG00000103740
+HGNC:24174	ACSBG2	acyl-CoA synthetase bubblegum family member 2	Approved	gene with protein product, function unknown			BGR, PRTD-NY3, DKFZp434K1635	"bubblegum related protein"	19p13.3		81616	, , , , , , , , , 	NM_030924	ACS	81616		NM_030924	Q5FVE4	ENSG00000130377
+HGNC:3569	ACSL1	acyl-CoA synthetase long-chain family member 1	Approved	gene with protein product, function known or inferred	FACL2	"fatty-acid-Coenzyme A ligase, long-chain 2"	LACS2, LACS, ACS1, LACS1, FACL1	"lignoceroyl-CoA synthase", "long-chain fatty-acid-coenzyme A ligase 1"	4q35	BC026290	2180	, , , , , , , , , 	NM_001995	ACS	2180	152425	NM_001995	P33121	ENSG00000151726
+HGNC:3570	ACSL3	acyl-CoA synthetase long-chain family member 3	Approved	gene with protein product, function known or inferred	FACL3	"fatty-acid-Coenzyme A ligase, long-chain 3"	ACS3, PRO2194		2q34-q35	D89053	2181	, , , , , , , , , 	NM_004457	ACS	2181	602371	NM_203372	O95573	ENSG00000123983
+HGNC:3571	ACSL4	acyl-CoA synthetase long-chain family member 4	Approved	gene with protein product, function known or inferred	FACL4, MRX63, MRX68	"fatty-acid-Coenzyme A ligase, long-chain 4", "mental retardation, X-linked 63", "mental retardation, X-linked 68"	ACS4, LACS4	"lignoceroyl-CoA synthase", " long-chain fatty-acid-Coenzyme A ligase 4"	Xq22.3-q23	BC034959	2182	, , , , , , , , , 	NM_004458	ACS	2182	300157	NM_004458	O60488	ENSG00000068366
+HGNC:16526	ACSL5	acyl-CoA synthetase long-chain family member 5	Approved	gene with protein product, function known or inferred	FACL5	"fatty-acid-Coenzyme A ligase, long-chain 5"	ACS5, ACS2	"FACL5 for fatty acid coenzyme A ligase 5", "long-chain acyl-CoA synthetase 5", "long-chain fatty acid coenzyme A ligase 5", "fatty-acid-Coenzyme A ligase, long-chain 5"	10q25.1-q25.2	AB033899	51703	, , , , , , , , , 	NM_016234	ACS	51703	605677	NM_016234	Q9ULC5	ENSG00000197142
+HGNC:16496	ACSL6	acyl-CoA synthetase long-chain family member 6	Approved	gene with protein product, function known or inferred	FACL6	"fatty-acid-Coenzyme A ligase, long-chain 6"	KIAA0837, ACS2, LACS5, LACS2		5q31	AB020644	23305	, , , , , , , , , 	NM_015256	ACS	23305	604443	NM_001009185	Q9UKU0	ENSG00000164398
+HGNC:18049	ACSM1	acyl-CoA synthetase medium-chain family member 1	Approved	gene with protein product, function known or inferred	BUCS1	"butyryl Coenzyme A synthetase 1"	MACS1		16p12.3	AB059429	116285	, , , , , , , , , 	NM_052956	ACS	116285		NM_052956	Q08AH1	ENSG00000166743
+HGNC:32017	ACSM2A	acyl-CoA synthetase medium-chain family member 2A	Approved	gene with protein product, function known or inferred	ACSM2	"acyl-CoA synthetase medium-chain family member 2"	A-923A4.1, MGC150530		16p12.3	AK091878, AK096039	123876	, , , , , , , , , 	NM_001010845	ACS	123876		XM_936869		
+HGNC:30931	ACSM2B	acyl-CoA synthetase medium-chain family member 2B	Approved	gene with protein product, function known or inferred	ACSM2	"acyl-CoA synthetase medium-chain family member 2"	HXMA, HYST1046	"xenobiotic/medium chain fatty acid:CoA ligase"	16p12.3	AY160217	348158	, , , , , , , , , 	NM_182617	ACS	348158		XM_001126353	Q68CK6	ENSG00000183747
+HGNC:10522	ACSM3	acyl-CoA synthetase medium-chain family member 3	Approved	gene with protein product, function known or inferred	SAH	"SA (rat hypertension-associated) homolog", "SA hypertension-associated homolog (rat)"	SA		16p13.11	D16350	6296	, , , , , , , , , 	NM_005622	ACS	6296	145505	NM_202000	Q53FZ2	ENSG00000005187
+HGNC:16091	ACSS1	acyl-CoA synthetase short-chain family member 1	Approved	gene with protein product, function known or inferred	ACAS2L	"acetyl-Coenzyme A synthetase 2 (AMP forming)-like"	dJ568C11.3, AceCS2L, MGC33843		20p11.23-p11.21		84532	, , , , , , , , , 	NM_032501	ACS	84532		NM_032501	Q9NUB1	ENSG00000154930
+HGNC:15814	ACSS2	acyl-CoA synthetase short-chain family member 2	Approved	gene with protein product, function known or inferred	ACAS2	"acetyl-Coenzyme A synthetase 2 (ADP forming)"	ACS, ACSA, AceCS, dJ1161H23.1		20q11.22	AF263614	55902	, , , , , , , , , 	NM_018677	ACS	55902	605832	NM_018677	Q9NR19	ENSG00000131069
+HGNC:129	ACTA1	actin, alpha 1, skeletal muscle	Approved	gene with protein product, function known or inferred	ACTA				1q42.13	J00068	58	, , , , , , , , , 	NM_001100		58	102610	NM_001100	P68133	ENSG00000143632
+HGNC:130	ACTA2	actin, alpha 2, smooth muscle, aorta	Approved	gene with protein product, function known or inferred			ACTSA		10q22-q24	X13839	59	, , , , , , , , , 	NM_001613		59	102620	NM_001613	P62736	ENSG00000107796
+HGNC:131	ACTA3~withdrawn	symbol withdrawn, see ACTG2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:132	ACTB	actin, beta	Approved	gene with protein product, function known or inferred					7p15-p12	M28424	60	, , , , , , , , , 	NM_001101		60	102630	NM_001101	P60709	ENSG00000075624
+HGNC:133	ACTBL1	actin, beta-like 1	Approved	gene with protein product, function known or inferred			POTE22		22q11.1	AY466021	23784	, , , , , , , , , 	NM_001004053		23784	608913	NM_001004053	Q6S545	
+HGNC:17780	ACTBL2	actin, beta-like 2	Approved	gene with protein product, function unknown					reserved			, , , , , , , , , 			548634				
+HGNC:30182	ACTBL3	actin, beta-like 3	Approved	gene with protein product, function unknown					reserved			, , , , , , , , , 			548635				
+HGNC:134	ACTBP1	actin, beta pseudogene 1	Approved	retrogene			CR619662		Xq12		61	, , , , , , , , , 			61				
+HGNC:135	ACTBP2	actin, beta pseudogene 2	Approved	pseudogene					5q14.1		62	, , , , , , , , , 	NG_003019		62				
+HGNC:136	ACTBP3	actin, beta pseudogene 3	Approved	retrogene					18q21.33		63	, , , , , , , , , 			63				
+HGNC:137	ACTBP4	actin, beta pseudogene 4	Approved	retrogene					5q23.3		64	, , , , , , , , , 			64				
+HGNC:138	ACTBP5	actin, beta pseudogene 5	Approved	retrogene					7q36.1		65	, , , , , , , , , 			65				
+HGNC:139	ACTBP6	actin, beta pseudogene 6	Approved	pseudogene					8			, , , , , , , , , 			66				
+HGNC:140	ACTBP7	actin, beta pseudogene 7	Approved	pseudogene					15q15.3	V00479		, , , , , , , , , 			67				
+HGNC:141	ACTBP8	actin, beta pseudogene 8	Approved	pseudogene			ACTBP2		6q13	V00481		, , , , , , , , , 	NG_000840		68				
+HGNC:142	ACTBP9	actin, beta pseudogene 9	Approved	pseudogene					18q21.33	D50604		, , , , , , , , , 			69				
+HGNC:31819	ACTBP10	actin, beta pseudogene 10	Approved	pseudogene					14			, , , , , , , , , 			446207				
+HGNC:143	ACTC1	actin, alpha, cardiac muscle 1	Approved	gene with protein product, function known or inferred	ACTC	"actin, alpha, cardiac muscle"	CMD1R		15q11-q14	BC009978	70	, , , , , , , , , 	NM_005159		70	102540	NM_005159	P68032	ENSG00000159251
+HGNC:144	ACTG1	actin, gamma 1	Approved	gene with protein product, function known or inferred	ACTG, DFNA20, DFNA26	"deafness, autosomal dominant 20; deafness, autosomal dominant 26"			17q25		71	, , , , , , , , , 	NM_001614		71	102560	NM_001614	P63261	ENSG00000184009
+HGNC:145	ACTG2	actin, gamma 2, smooth muscle, enteric	Approved	undef	ACTL3, ACTA3				2p13.1			, , , , , , , , , 	NM_001615		72	102545	NM_001615	P63267	ENSG00000163017
+HGNC:146	ACTGP1	actin, gamma pseudogene 1	Approved	pseudogene					3	D50658		, , , , , , , , , 			73				
+HGNC:147	ACTGP2	actin, gamma pseudogene 2	Approved	pseudogene	ACTL2				Yq11			, , , , , , , , , 			74				
+HGNC:148	ACTGP3	actin, gamma pseudogene 3	Approved	pseudogene					20p13-20p13	AF196978		, , , , , , , , , 			75				
+HGNC:149	ACTGP4	actin, gamma pseudogene 4	Approved	pseudogene					1p21			, , , , , , , , , 			76				
+HGNC:150	ACTGP5	actin, gamma pseudogene 5	Approved	pseudogene					1p21			, , , , , , , , , 			77				
+HGNC:151	ACTGP6	actin, gamma pseudogene 6	Approved	pseudogene					1p21			, , , , , , , , , 			78				
+HGNC:152	ACTGP7	actin, gamma pseudogene 7	Approved	pseudogene					1p21			, , , , , , , , , 			79				
+HGNC:153	ACTGP8	actin, gamma pseudogene 8	Approved	pseudogene					1p21			, , , , , , , , , 			80				
+HGNC:154	ACTGP9	actin, gamma pseudogene 9	Approved	pseudogene					6p	D50659		, , , , , , , , , 			82				
+HGNC:155	ACTGP10	actin, gamma pseudogene 10	Approved	pseudogene	ACTL1	"actin-like 1"			Xp11.22	AL139396	83	, , , , , , , , , 			83				
+HGNC:156	ACTL2~withdrawn	symbol withdrawn, see ACTGP2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:157	ACTL3~withdrawn	symbol withdrawn, see ACTG2	Symbol Withdrawn	undef								, , , , , , , , , 							
+HGNC:158	ACTL4	actin-like 4	Approved	undef					3pter-q21		84	, , , , , , , , , 			84				
+HGNC:159	ACTL5	actin-like 5	Approved	unknown			ACTFIB		21q22.3		85	, , , , , , , , , 			85				
+HGNC:24124	ACTL6A	actin-like 6A	Approved	gene with protein product, function known or inferred			Actl6, BAF53A		3	AK098691	86	, , , , , , , , , 	NM_004301		86	604958	NM_177989	O96019	ENSG00000136518
+HGNC:160	ACTL6B	actin-like 6B	Approved	undef	ACTL6	"actin-like 6"	BAF53B		7q22	AB015906	51412	, , , , , , , , , 	NM_016188		51412		NM_016188	O94805	ENSG00000077080
+HGNC:161	ACTL7A	actin-like 7A	Approved	gene with protein product, function unknown					9q31	BC014610	10881	, , , , , , , , , 	NM_006687		10881	604303	NM_006687	Q9Y615	ENSG00000187003
+HGNC:162	ACTL7B	actin-like 7B	Approved	gene with protein product, function unknown					9q31	BC033789	10880	, , , , , , , , , 	NM_006686		10880	604304	NM_006686	Q9Y614	ENSG00000148156
+HGNC:24018	ACTL8	actin-like 8	Approved	gene with protein product, function unknown					1p36.2-p35	AK057339	81569	, , , , , , , , , 	NM_030812		81569		XM_001134367	Q9H568	ENSG00000117148
+HGNC:163	ACTN1	actinin, alpha 1	Approved	gene with protein product, function known or inferred					14q24.1	M95178	87	, , , , , , , , , 	NM_001102		87	102575	NM_001102	P12814	ENSG00000072110
+HGNC:164	ACTN2	actinin, alpha 2	Approved	gene with protein product, function known or inferred					1q42-q43	BC047901	88	, , , , , , , , , 	NM_001103		88	102573	NM_001103	P35609	ENSG00000077522
+HGNC:165	ACTN3	actinin, alpha 3	Approved	undef					11q13-q14	M86407	89	, , , , , , , , , 	NM_001104		89	102574	NM_001104	Q08043	ENSG00000204633
+HGNC:166	ACTN4	actinin, alpha 4	Approved	undef					19q13	D89980		, , , , , , , , , 			81	604638	NM_004924	O43707	ENSG00000130402
+HGNC:167	ACTR1A	ARP1 actin-related protein 1 homolog A, centractin alpha (yeast)	Approved	undef		"ARP1 (actin-related protein 1, yeast) homolog A (centractin alpha)"	ARP1		10q24	X82206		, , , , , , , , , 			10121	605143	NM_005736	P61163	ENSG00000138107
+HGNC:168	ACTR1B	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	Approved	undef	CTRN2	"ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"			2q11.1-q11.2	X82207		, , , , , , , , , 			10120	605144	NM_005735	P42025	ENSG00000115073
+HGNC:169	ACTR2	ARP2 actin-related protein 2 homolog (yeast)	Approved	undef		"ARP2 (actin-related protein 2, yeast) homolog"	ARP2		2p	AF006082		, , , , , , , , , 			10097	604221	NM_005722	P61160	ENSG00000138071
+HGNC:170	ACTR3	ARP3 actin-related protein 3 homolog (yeast)	Approved	undef		"ARP3 (actin-related protein 3, yeast) homolog"	ARP3		2q13	AF006083		, , , , , , , , , 			10096	604222	NM_005721	P61158	ENSG00000115091
+HGNC:17256	ACTR3B	ARP3 actin-related protein 3 homolog B (yeast)	Approved	gene with protein product, function unknown			ARP11, ARP3beta		7q34		57180	, , , , , , , , , 	NM_020445		57180		NM_020445	Q9P1U1	ENSG00000133627
+HGNC:31820	ACTR3P1	ARP3 actin-related protein 3 homolog (yeast) pseudogene 1	Approved	pseudogene					14			, , , , , , , , , 			446208				
+HGNC:14671	ACTR5	ARP5 actin-related protein 5 homolog (yeast)	Approved	undef		"ARP5 (actin-related protein 5, yeast) homolog"	FLJ12785		20q12	AK022847	79913	, , , , , , , , , 	NM_024855		79913		NM_024855	Q9H9F9	ENSG00000101442
+HGNC:24025	ACTR6	ARP6 actin-related protein 6 homolog (yeast)	Approved	gene with protein product, function known or inferred			ARP6, FLJ13433		12	AF212251	64431	, , , , , , , , , 	NM_022496		64431		NM_022496	Q9GZN1	ENSG00000075089
+HGNC:14672	ACTR8	ARP8 actin-related protein 8 homolog (yeast)	Approved	gene with protein product, function known or inferred		"ARP8 (actin-related protein 8, yeast) homolog"			3p21.31		93973	, , , , , , , , , 	NM_022899		93973		NM_022899	Q9H981	ENSG00000113812
+HGNC:17372	ACTR10	actin-related protein 10 homolog (S. cerevisiae)	Approved	gene with protein product, function unknown			HARP11, ACTR11		14q22.3	AF220190		, , , , , , , , , 			55860		NM_018477	Q9NZ32	ENSG00000131966
+HGNC:24027	ACTRT1	actin-related protein T1	Approved	gene with protein product, function unknown			AIP1, KIAA0705, ARIP1, Arp-T1		Xq25	AF440739	139741	, , , , , , , , , 	NM_138289		139741	300487	NM_138289	Q8TDG2	ENSG00000123165
+HGNC:24026	ACTRT2	actin-related protein T2	Approved	gene with protein product, function unknown			Arp-T2, ARPM2, FLJ25424		1p36.3	AF440740, AB057364	140625	, , , , , , , , , 	NM_080431		140625	608535	NM_080431	Q8TDY3	ENSG00000169717
+HGNC:171	ACVR1	activin A receptor, type I	Approved	gene with protein product, function known or inferred	ACVRLK2		SKR1, ALK2		2q23-q24		90	, , , , , , , , , 	NM_001105		90	102576	NM_001105	Q04771	ENSG00000115170
+HGNC:172	ACVR1B	activin A receptor, type IB	Approved	gene with protein product, function known or ...
 
[truncated message content]

[Obo-svn-commit] SF.net SVN: obo: [969] obo-database/trunk

From: <cmu...@us...> - 2007-10-06 23:04:20

Revision: 969
          http://obo.svn.sourceforge.net/obo/?rev=969&view=rev
Author:   cmungall
Date:     2007-10-06 16:04:21 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Added Paths:
-----------
    obo-database/trunk/data-build/
    obo-database/trunk/data-build/Makefile
    obo-database/trunk/data-build/Makefile-Build-Generic
    obo-database/trunk/data-build/build-hgnc/
    obo-database/trunk/data-build/build-hgnc/Makefile
    obo-database/trunk/data-build/build-homologene/
    obo-database/trunk/data-build/build-homologene/Makefile
    obo-database/trunk/data-build/build-ncbi-gene/
    obo-database/trunk/data-build/build-ncbi-gene/Makefile
    obo-database/trunk/data-build/build-omim/
    obo-database/trunk/data-build/build-omim/Makefile

Added: obo-database/trunk/data-build/Makefile
===================================================================
--- obo-database/trunk/data-build/Makefile	                        (rev 0)
+++ obo-database/trunk/data-build/Makefile	2007-10-06 23:04:21 UTC (rev 969)
@@ -0,0 +1 @@
+link Makefile-Build-Generic
\ No newline at end of file


Property changes on: obo-database/trunk/data-build/Makefile
___________________________________________________________________
Name: svn:special
   + *

Added: obo-database/trunk/data-build/Makefile-Build-Generic
===================================================================
--- obo-database/trunk/data-build/Makefile-Build-Generic	                        (rev 0)
+++ obo-database/trunk/data-build/Makefile-Build-Generic	2007-10-06 23:04:21 UTC (rev 969)
@@ -0,0 +1,22 @@
+.PRECIOUS: %.obo
+
+%.obd-createdb:
+	obd-create-db.pl -d $* && touch $@
+.PRECIOUS: %.obd-createdb
+
+%.obd-load: %.obo %.obd-createdb
+	obd-load-db-from-obo.pl -d $* $(OBD_LOAD_ARGS) $< >& $@.log && touch $@
+.PRECIOUS: %.obd-load
+
+%.obd-pgdump: %.obd-load
+	pg_dump -d $* > $@.tmp && mv $@.tmp $@
+
+%.obd-node.obdsql:
+	selectall_xml.pl -d $* /obd-node-export > $@.tmp && mv $@.tmp $@
+
+%.obd-node-tagval.obdsql:
+	selectall_xml.pl -d $* /obd-node-tagval-export > $@.tmp && mv $@.tmp $@
+
+%.gz: %
+	gzip $<
+

Added: obo-database/trunk/data-build/build-hgnc/Makefile
===================================================================
--- obo-database/trunk/data-build/build-hgnc/Makefile	                        (rev 0)
+++ obo-database/trunk/data-build/build-hgnc/Makefile	2007-10-06 23:04:21 UTC (rev 969)
@@ -0,0 +1,2 @@
+hgnc.tab:
+	wget -O $@ 'http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl?title=Genew+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_locus_type&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_name_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_eg_id&col=gd_other_ids_list&col=gd_pub_refseq_ids&col=gd_gene_fam_name&col=md_eg_id&col=md_mim_id&col=md_refseq_id&col=md_prot_id&col=md_ensembl_id&status=Approved&status=Entry+Withdrawn&status_opt=2&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag'

Added: obo-database/trunk/data-build/build-homologene/Makefile
===================================================================
--- obo-database/trunk/data-build/build-homologene/Makefile	                        (rev 0)
+++ obo-database/trunk/data-build/build-homologene/Makefile	2007-10-06 23:04:21 UTC (rev 969)
@@ -0,0 +1,34 @@
+OBD_LOAD_ARGS=--split 10000
+DB = obd_ncbi_gene
+
+TAXA = 7227 7955 9606 10090
+
+GINFOS = $(patsubst %,genes-%.gene_info,$(TAXA))
+OBO = $(patsubst %,genes-%.gene_info_ontol.obo,$(TAXA))
+PRO = $(patsubst %,genes-%.gene_info_ontol.pro,$(TAXA))
+
+all: $(GINFOS) $(PRO) $(OBO)
+
+homologene.data:
+	wget -O $@ ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data
+.PRECIOUS: homologene.data
+
+%-homol_db.pro: %.data
+	blip -i $< -f homoltbl io-convert -u homoltbl_bridge_to_homol -to homol_db:pro -o $@.tmp && mv $@.tmp $@
+.PRECIOUS: %-homol_db.pro
+
+%-curation_db.pro: %-homol_db.pro
+	blip -i $< -f homol_db:pro io-convert -u homol_bridge_to_ontol -to curation_db:pro -o $@.tmp && mv $@.tmp $@
+.PRECIOUS: %-curation_db.pro
+
+%_ontol.annotation-obo: %-curation_db.pro
+	blip -i $< -f curation_db:pro io-convert -to curation_obo -o $@.tmp && mv $@.tmp $@
+.PRECIOUS: %_ontol.annotation-obo
+
+%_ontol.obo: %-curation_db.pro
+	blip -i $< -f curation_db:pro io-convert -u curation_bridge_to_ontol -to obo -o $@.tmp && mv $@.tmp $@
+.PRECIOUS: %_ontol.obo
+
+
+include ../Makefile-Build-Generic
+

Added: obo-database/trunk/data-build/build-ncbi-gene/Makefile
===================================================================
--- obo-database/trunk/data-build/build-ncbi-gene/Makefile	                        (rev 0)
+++ obo-database/trunk/data-build/build-ncbi-gene/Makefile	2007-10-06 23:04:21 UTC (rev 969)
@@ -0,0 +1,30 @@
+DB = obd_ncbi_gene
+
+TAXA = 7227 7955 9606 10090
+
+GINFOS = $(patsubst %,genes-%.gene_info,$(TAXA))
+OBO = $(patsubst %,genes-%.gene_info_ontol.obo,$(TAXA))
+PRO = $(patsubst %,genes-%.gene_info_ontol.pro,$(TAXA))
+
+all: $(GINFOS) $(PRO) $(OBO)
+load: $(patsubst %,genes-%.gene_info_ontol.obd-load,$(TAXA))
+
+gene_info.gz:
+	wget -O $@ ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
+.PRECIOUS: gene_info.gz
+
+genes-%.gene_info: gene_info.gz
+	zcat $< | ./taxfilter.pl $* > $@
+
+genes-%.gene_info_ontol.obo: genes-%.gene_info_ontol.pro
+	blip -i $< -f ontol_db:pro io-convert -to obo -o $@
+
+genes-%.gene_info_ontol.pro: genes-%.gene_info
+	blip -i $< -u gene_bridge_to_ontol io-convert -to ontol_db:pro -o $@
+
+gene_info_ontol.pro: gene_info.gz
+	blip -u gene_bridge_to_class io-convert -i $< -f gzip/gene_info -to ontol_db:pro -o $@
+.PRECIOUS: gene_info_ontol.pro
+
+include ../Makefile-Build-Generic
+

Added: obo-database/trunk/data-build/build-omim/Makefile
===================================================================
--- obo-database/trunk/data-build/build-omim/Makefile	                        (rev 0)
+++ obo-database/trunk/data-build/build-omim/Makefile	2007-10-06 23:04:21 UTC (rev 969)
@@ -0,0 +1,30 @@
+DB = obd_omim
+
+# todo: MIM vs OMIM
+
+GINFOS = $(patsubst %,genes-%.gene_info,$(TAXA))
+OBO = $(patsubst %,genes-%.gene_info_ontol.obo,$(TAXA))
+PRO = $(patsubst %,genes-%.gene_info_ontol.pro,$(TAXA))
+
+all: $(GINFOS) $(PRO) $(OBO)
+load: $(patsubst %,genes-%.gene_info_ontol.obd-load,$(TAXA))
+
+gene_info.gz:
+	wget -O $@ ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
+.PRECIOUS: gene_info.gz
+
+genes-%.gene_info: gene_info.gz
+	zcat $< | ./taxfilter.pl $* > $@
+
+genes-%.gene_info_ontol.obo: genes-%.gene_info_ontol.pro
+	blip -i $< -f ontol_db:pro io-convert -to obo -o $@
+
+genes-%.gene_info_ontol.pro: genes-%.gene_info
+	blip -i $< -u gene_bridge_to_ontol io-convert -to ontol_db:pro -o $@
+
+gene_info_ontol.pro: gene_info.gz
+	blip -u gene_bridge_to_class io-convert -i $< -f gzip/gene_info -to ontol_db:pro -o $@
+.PRECIOUS: gene_info_ontol.pro
+
+include ../Makefile-Build-Generic
+


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[Obo-svn-commit] SF.net SVN: obo: [968] obo-database/trunk/sql

From: <cmu...@us...> - 2007-10-06 22:08:04

Revision: 968
          http://obo.svn.sourceforge.net/obo/?rev=968&view=rev
Author:   cmungall
Date:     2007-10-06 15:03:11 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/sql/obd-core-schema.sql
    obo-database/trunk/sql/obd-core-views.sql
    obo-database/trunk/sql/users.sql

Modified: obo-database/trunk/sql/obd-core-schema.sql
===================================================================
--- obo-database/trunk/sql/obd-core-schema.sql	2007-10-06 21:52:37 UTC (rev 967)
+++ obo-database/trunk/sql/obd-core-schema.sql	2007-10-06 22:03:11 UTC (rev 968)
@@ -15,17 +15,18 @@
 	UNIQUE(uid)
 );
 ALTER TABLE node add source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE;
+ALTER TABLE node add loaded_from_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE;
 
-COMMENT ON TABLE node IS 'An element of a graph. A graph consists of a collection of nodes n1, n2, ... and a collection of edges between nodes. Nodes can represent Instances, Relations, and Types. RDF: typically corresponds to a resource';
-COMMENT ON COLUMN node.uid IS 'A unique identifier for this node. Must be EITHER a valid URI OR a valid OBO ID.';
-COMMENT ON COLUMN node.uri IS 'See W3 specs for definition of URI';
-COMMENT ON COLUMN node.label IS 'A piece of text intended for display for humans. Should follow preferred term conventions';
-COMMENT ON COLUMN node.metatype IS 'Enumeration that determines what kind of entity this node represents. Choices are: I=instance (aka token, individual, particular). R=relation (aka linktype, relationship type. roughly equivalent to slots, owl properties, DL role names). C=class (universal, type, pattern, term)';
-COMMENT ON COLUMN node.is_anonymous IS 'true if the node represents an entity that does not have a unique handle. RDF: corresponds to bNodes';
-COMMENT ON COLUMN node.is_transitive IS 'If metatype=R, and this node represents a relation, then normal transitivity rules hold';
-COMMENT ON COLUMN node.is_obsolete IS 'True if node identifies a historical record of what was once considered a valid instance, type or relation';
-COMMENT ON COLUMN node.source_id IS 'A node representing an information resource in which the node was originally inserted. Equivalent to OBO-Namespace. TODO: formalize relationship to RDF named graphs';
-COMMENT ON COLUMN node.is_reiflink IS 'true if node identifies an instance of a statement or link. If this is true, there should be a row R in the link table with R.reiflink_node_id equal to the primary key of this row. RDF Equivalent: reification - the subject, predicate and object triples are implicit';
+COMMENT ON TABLE node IS 'An element of a graph. A graph consists of a collection of nodes n1, n2, ... and a collection of edges between nodes. Nodes can represent Instances (eg a particular organ), Relations (eg part_of), and Types (classes) (eg the type "Lung"). RDFMap: typically corresponds to a resource';
+COMMENT ON COLUMN node.uid IS 'A unique identifier for this node. Must be EITHER a valid URI OR a valid OBO ID. The latter is of bipartite form IDSPACE:LOCALID';
+COMMENT ON COLUMN node.uri IS 'See W3 specs for definition of URI. URIs are optional. Can be generated automaticallt from uid';
+COMMENT ON COLUMN node.label IS 'A piece of text intended for display for humans. Also known as "preferred term" in skos, "name" in obo. Also used for the canonical symbol for an entity';
+COMMENT ON COLUMN node.metatype IS 'Enumeration that determines the semantics of the node. Choices are: I=instance (aka token, individual, particular). R=relation (aka linktype, relationship type. roughly equivalent to slots, owl properties, DL role names). C=class (universal, type, pattern, term). Annotations (propositions) are of type I';
+COMMENT ON COLUMN node.is_anonymous IS 'true if the node represents an entity that does not have a stable persistent identifier. The node only makes sense in the context of the surrounding graph. An example would be a post-composed expression combining classes that themselves have stable IDs. RDFMap: corresponds to bNodes';
+COMMENT ON COLUMN node.is_transitive IS 'X R Y and Y R Z => X R Z. Should only be used when metatype=R';
+COMMENT ON COLUMN node.is_obsolete IS 'True if node represents a historical record of what was once considered a valid instance, type or relation. Note that this changes the semantics of the node';
+COMMENT ON COLUMN node.source_id IS 'A node representing an information resource in which the node was originally inserted. Equivalent to OBO-Namespace';
+COMMENT ON COLUMN node.is_reiflink IS 'true if this node identifies an instance of a statement or link. If this is true, there should be a row R in the link table with R.reiflink_node_id equal to the primary key of this row. RDF Closest Equivalent: reification - the subject, predicate and object triples are implicit AND/OR named graphs. At this stage the mapping is unclear. May be better to treat as a proposition in IKL';
 
 CREATE INDEX node_source_indx ON node(source_id);
 CREATE INDEX node_label ON node(label);
@@ -52,17 +53,18 @@
         object_quantifier_only BOOLEAN NOT NULL DEFAULT 'f',
 	combinator CHAR(1) NOT NULL DEFAULT '',
         source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
+        loaded_from_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
 	is_obsolete BOOLEAN NOT NULL DEFAULT 'f',
 
-        --- should reiflink_node_id also be part of key? multiple statements. YES
-	CONSTRAINT link_unique_c UNIQUE(reiflink_node_id, predicate_id, object_id)
+        --- should reiflink_node_id also be part of key? multiple statements. YES; but this means we can have multi values for NULL
+	CONSTRAINT link_unique_c UNIQUE(reiflink_node_id, is_negated, node_id, predicate_id, object_id, when_id, combinator, source_id)
 );
-COMMENT ON TABLE link IS 'An element of a graph. Edges link nodes. Edges have labels (predicates)';
-COMMENT ON COLUMN link.when_id IS 'some relations are time-index; this points to a time point or interval instance for when the link statement holds. Note this is real time, not database time. RDF: does not correpond. If this column is non-null, special transforms must be applied to turn the OBD graph into an RDF graph';
+COMMENT ON TABLE link IS 'An element of a graph. Edges link nodes. Edges have labels (predicates). The semantics of the link are dependent on the values of particular columns. ';
 COMMENT ON COLUMN link.reiflink_node_id IS 'A reference to a node that represents a statement or other narrative entity asserting this link. If this reference is NULL then the reification context is considered to be the whole database. All Annotations (sensu biomedical curation) are narrative entities positing links. RDF: if this is non-NULL, there is an implicit SPO reification quad';
 COMMENT ON COLUMN link.node_id IS 'The entity for which the link directly applies. Can refer to a C, R or I. RDF: subject';
 COMMENT ON COLUMN link.node_id IS 'The relation that holds between the node and the object. Must refer to a R node. RDF: predicate';
 COMMENT ON COLUMN link.object_id IS 'The entity for which the node stands in some relation R to (where R is the predicate_id). Any node metatype. RDF: object';
+COMMENT ON COLUMN link.when_id IS 'some relations are time-indexed; this points to a time point or interval instance for when the link statement holds. Note this is real time, not database time. RDF: does not correpond. If this column is non-null, special transforms must be applied to turn the OBD graph into an RDF graph';
 COMMENT ON COLUMN link.is_metadata IS 'True if the link is for node metadata. Metadata applies to the node itself and not the entity represented by the node. Equivalent to annotation properties in OWL';
 COMMENT ON COLUMN link.is_inferred IS 'True if this link is implied/entailed via some other link. TODO: reasoning provenance chain';
 COMMENT ON COLUMN link.is_instantiation IS 'True if this link is a relation of type OBO_REL:instance_of (or rdf:type). Note this is redundant, but it can speed queries';
@@ -78,7 +80,7 @@
    blank - disjunctive
 each set of links is grouped by combinator and treated as a distinct set,
 so it is possible to have all of:
- a collection of necessary conditions ('')
+ a collection of necessary conditions ("")
  a collection of necessary+sufficient conditions by set-intersection (I)
  a collection of necessary+sufficient conditions by set-union (U)
 specified directly for a node
@@ -113,6 +115,18 @@
 in the link_cardinality table';
 
 
+CREATE TABLE link_argument (
+        link_argument_id        SERIAL PRIMARY KEY,
+	link_id INTEGER NOT NULL,
+	FOREIGN KEY (link_id) REFERENCES link(link_id) ON DELETE CASCADE,
+	predicate_id INTEGER NOT NULL,
+	FOREIGN KEY (predicate_id) REFERENCES node(node_id) ON DELETE CASCADE,
+	object_id INTEGER NOT NULL,
+	FOREIGN KEY (object_id) REFERENCES node(node_id) ON DELETE CASCADE
+);
+
+COMMENT ON TABLE link_argument IS 'n-ary relations (not involving time)';
+
 CREATE TABLE link_inference (
         link_inference_id        SERIAL PRIMARY KEY,
 	link_id INTEGER NOT NULL,
@@ -148,12 +162,14 @@
 	FOREIGN KEY (object_id) REFERENCES node(node_id) ON DELETE CASCADE,
 	is_inferred BOOLEAN NOT NULL DEFAULT 'f',
         source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
+        loaded_from_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
 
 	CONSTRAINT sameas_unique_c UNIQUE(node_id, object_id, source_id)
 );
 COMMENT ON TABLE sameas IS 'STATUS: under discussion. Should we use the generic link table? Currently, no; rationale: sameas is a metamodel relation and not a relation between distinct entities in reality';
 
 CREATE TABLE tagval (
+        tagval_id        SERIAL PRIMARY KEY,
 	node_id INTEGER NOT NULL,
 	FOREIGN KEY (node_id) REFERENCES node(node_id) ON DELETE CASCADE,
 	tag_id INTEGER NOT NULL,
@@ -161,7 +177,8 @@
 	datatype_id INTEGER,
 	FOREIGN KEY (datatype_id) REFERENCES node (node_id) ON DELETE CASCADE,
 	val TEXT NOT NULL,
-        source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE
+        source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
+        loaded_from_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE
 
 );
 
@@ -173,7 +190,7 @@
 COMMENT ON COLUMN tagval.source_id IS 'A node representing an information resource in which the tagval was originally asserted. Equivalent to OBO-Namespace. TODO: formalize relationship to RDF named graphs';
 
 CREATE INDEX tagval_nt_index ON tagval(node_id, tag_id);
-CREATE INDEX tagval_label_indx ON tagval(val);
+--CREATE INDEX tagval_label_indx ON tagval(val);
 
 CREATE TABLE alias (
 	alias_id SERIAL PRIMARY KEY,
@@ -183,7 +200,8 @@
 	type_id INTEGER,
 	FOREIGN KEY (type_id) REFERENCES node(node_id) ON DELETE CASCADE,
 	label VARCHAR NOT NULL,
-        source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE
+        source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
+        loaded_from_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE
 );
 COMMENT ON TABLE alias IS 'Alternate label for node. Intended for humans';
 COMMENT ON COLUMN alias.node_id IS 'Node to which this alias applies';
@@ -202,8 +220,9 @@
 	scope VARCHAR, --?
 	type_id INTEGER,
 	FOREIGN KEY (type_id) REFERENCES node(node_id) ON DELETE CASCADE,
-	label VARCHAR NOT NULL,
-        source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE
+	label TEXT NOT NULL,
+        source_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE,
+        loaded_from_id INTEGER REFERENCES node(node_id) ON DELETE CASCADE
 );
 COMMENT ON TABLE description IS 'Narrative text intended for humans describing what entity the node represents';
 COMMENT ON COLUMN description.node_id IS 'Node to which this description applies';
@@ -213,7 +232,7 @@
 COMMENT ON COLUMN description.source_id IS 'A node representing an information resource in which the description was originally asserted. Equivalent to OBO-Namespace. TODO: formalize relationship to RDF named graphs';
 
 CREATE INDEX description_nt_indx ON description(node_id,type_id);
-CREATE INDEX description_label_indx ON description(label);
+-- CREATE INDEX description_label_indx ON description(label);  too big for index?
 
 CREATE TABLE node_xref (
 	node_id INTEGER NOT NULL,

Modified: obo-database/trunk/sql/obd-core-views.sql
===================================================================
--- obo-database/trunk/sql/obd-core-views.sql	2007-10-06 21:52:37 UTC (rev 967)
+++ obo-database/trunk/sql/obd-core-views.sql	2007-10-06 22:03:11 UTC (rev 968)
@@ -70,7 +70,7 @@
   combinator,
   source_id
  FROM link;
-COMMENT ON VIEW 'A link in the reverse direction. Example_of_use:
+COMMENT ON VIEW revlink IS 'A link in the reverse direction. Example_of_use:
 SELECT * FROM node INNER JOIN revlink USING (node_id). May be useful
 for inverse DAG traversal. Has no real-world semantics';
 
@@ -143,8 +143,16 @@
  SELECT link.*
  FROM link INNER JOIN is_a_relation ON (predicate_id=is_a_relation.node_id)
  WHERE combinator='';
+
 COMMENT ON VIEW is_a_link IS 'A link of type "is_a" that is not a combinator/union';
 
+CREATE OR REPLACE VIEW non_is_a_basic_link AS
+ SELECT link.*
+ FROM link
+ WHERE combinator=''
+  AND predicate_id NOT IN (SELECT node_id FROM is_a_relation);
+COMMENT ON VIEW non_is_a_basic_link IS 'A link of type that is not "is_a", and not a combinator/union';
+
 CREATE OR REPLACE VIEW asserted_is_a_link AS SELECT * FROM is_a_link WHERE is_inferred='f';
 COMMENT ON VIEW asserted_is_a_link IS 'An is_a_link that is not inferred (ie it is asserted)';
 
@@ -233,6 +241,41 @@
  WHERE
   link1.link_id != link2.link_id;
 
+COMMENT ON VIEW consecutive_link_pair IS 'A pair of links in which the
+object of one matches the node of another. For example, X is_a Y + Y
+part_of Z';
+
+CREATE OR REPLACE VIEW sibling_link_pair AS
+ SELECT
+  link1.*,
+  link1.node_id AS sibling_node_id,
+  link2.predicate_id AS sibling_predicate_id,
+  link2.is_inferred AS sibling_is_inferred
+ FROM
+  link AS link1
+  INNER JOIN link AS link2 ON (link1.object_id=link2.object_id)
+ WHERE
+  link1.link_id != link2.link_id;
+
+COMMENT ON VIEW sibling_link_pair IS 'A pair of links that share
+the same object_id';
+
+CREATE OR REPLACE VIEW parent_link_pair AS
+ SELECT
+  link1.*,
+  link2.predicate_id AS parent_predicate_id,
+  link1.object_id AS parent_object_id,
+  link2.is_inferred AS parent_is_inferred
+ FROM
+  link AS link1
+  INNER JOIN link AS link2 ON (link1.node_id=link2.node_id)
+ WHERE
+  link1.link_id != link2.link_id;
+
+COMMENT ON VIEW parent_link_pair IS 'A pair of links that share
+the same node_id';
+
+
 CREATE OR REPLACE VIEW cyclic_link_pair AS
  SELECT
   *
@@ -240,6 +283,10 @@
   consecutive_link_pair
  WHERE
   node_id = next_object_id;
+
+COMMENT ON VIEW cyclic_link_pair IS 'A consecutive_link_pair in which
+the main link node equals the succeeding link object';
+
  
 CREATE OR REPLACE VIEW cyclic_link_pair_with_nodes AS
  SELECT
@@ -260,8 +307,10 @@
   INNER JOIN node AS object_node ON  (consecutive_link_pair.next_object_id=object_node.node_id)
  WHERE
   node.node_id = next_object_id;
- 
 
+COMMENT ON VIEW cyclic_link_pair IS 'A cyclic_link_pair with node
+information; a convenience view';
+
 -- ************************************************************
 -- GRAPH TOPOLOGY VIEWS
 -- ************************************************************
@@ -275,13 +324,26 @@
   node
  WHERE NOT EXISTS (SELECT * FROM link WHERE link.node_id=node.node_id);
 
+COMMENT ON VIEW graph_root_node IS 'A node that has no links from it';
+
 CREATE OR REPLACE VIEW graph_root_class_node AS 
  SELECT * FROM graph_root_node WHERE metatype='C';
+
+COMMENT ON VIEW graph_root_class_node IS 'A class_node that has no
+links from it';
+
 CREATE OR REPLACE VIEW graph_root_relation_node AS 
  SELECT * FROM graph_root_node WHERE metatype='R';
+
+COMMENT ON VIEW graph_root_relation_node IS 'A relation_node that has no
+links from it';
+
 CREATE OR REPLACE VIEW graph_root_instance_node AS 
  SELECT * FROM graph_root_node WHERE metatype='I';
 
+COMMENT ON VIEW graph_root_instance_node IS 'A instance_node that has no
+links from it';
+
 CREATE OR REPLACE VIEW graph_leaf_node AS
  SELECT
   *
@@ -289,14 +351,26 @@
   node
  WHERE NOT EXISTS (SELECT * FROM link WHERE link.object_id=node.node_id);
 
+COMMENT ON VIEW graph_leaf_node IS 'A node that has no links to it';
+
 CREATE OR REPLACE VIEW graph_leaf_class_node AS 
  SELECT * FROM graph_leaf_node WHERE metatype='C';
+
+COMMENT ON VIEW graph_lead_class_node IS 'A class_node that has no
+links to it';
+
 CREATE OR REPLACE VIEW graph_leaf_relation_node AS 
  SELECT * FROM graph_leaf_node WHERE metatype='R';
+
+COMMENT ON VIEW graph_lead_class_node IS 'A relation_node that has no
+links to it';
+
 CREATE OR REPLACE VIEW graph_leaf_instance_node AS 
  SELECT * FROM graph_leaf_node WHERE metatype='I';
 
--- too slow..
+COMMENT ON VIEW graph_lead_instance_node IS 'An instance_node that has no
+links to it';
+
 CREATE OR REPLACE VIEW graph_root_id_by_relation AS
  SELECT DISTINCT
   nodepred.node_id,
@@ -307,6 +381,10 @@
   LEFT OUTER JOIN link ON (nodepred.node_id=link.object_id)
  WHERE link.node_id IS NULL;
 
+COMMENT ON VIEW graph_root_id_by_relation IS 'A node that has no links
+from it of a certain edge relation type. NOTE: **this view is
+currently too slow** materialize??';
+
 -- ************************************************************
 -- JOINS
 -- ************************************************************
@@ -358,13 +436,31 @@
         obj.metatype AS object_metatype
  FROM node_link INNER JOIN node AS obj ON (node_link.object_id=obj.node_id);
 
+COMMENT ON VIEW link_to_node IS 'Link joined to node via
+link.object_id. Join: link * object.node. Example: querying this via the node_id for "Tenth
+thoracic vertebra", then the query will return link_to_node rows for
+"is_a Thoracic vertebrae" and "has_part Bony part of eleventh thoracic
+vertebra"';
+
 CREATE OR REPLACE VIEW link_to_instance AS
  SELECT * FROM link_to_node WHERE object_metatype='I';
+
+COMMENT ON VIEW link_to_instance IS 'a link_to_node whete the node is
+an instance';
+
 CREATE OR REPLACE VIEW link_to_class AS
  SELECT * FROM link_to_node WHERE object_metatype='C';
+
+COMMENT ON VIEW link_to_class IS 'a link_to_node whete the node is
+a class';
+
 CREATE OR REPLACE VIEW link_to_relation AS
  SELECT * FROM link_to_node WHERE object_metatype='R';
 
+COMMENT ON VIEW link_to_relation IS 'a link_to_node whete the node is
+a relation';
+
+
 -- %% node * link * node (triple) %%
 
 CREATE OR REPLACE VIEW node_link_node AS
@@ -376,15 +472,23 @@
         obj.metatype AS object_metatype
  FROM node_link INNER JOIN node AS obj ON (node_link.object_id=obj.node_id);
 
+COMMENT ON VIEW node_link_node IS 'A join between two nodes via a
+link. Join: link * node * object.node. This is a convenience view to avoid having to explicitly make
+the join. Example: SELECT * FROM node_link_node WHERE
+node_label="apoptosis"';
+
 CREATE OR REPLACE VIEW instance_link_instance AS
  SELECT * FROM node_link_node
  WHERE node_metatype='I' AND object_metatype='I';
+
 CREATE OR REPLACE VIEW instance_link_class AS
  SELECT * FROM node_link_node
  WHERE node_metatype='I' AND object_metatype='C';
+
 CREATE OR REPLACE VIEW class_link_instance AS
  SELECT * FROM node_link_node
  WHERE node_metatype='C' AND object_metatype='I';
+
 CREATE OR REPLACE VIEW class_link_class AS
  SELECT * FROM node_link_node
  WHERE node_metatype='C' AND object_metatype='C';
@@ -397,6 +501,10 @@
         pred.metatype AS pred_metatype
  FROM link INNER JOIN node AS pred ON (predicate_id=pred.node_id);
 
+COMMENT ON VIEW link_with_pred IS 'A join between a link and a
+predicate node. link * predicate.node. Convenience view to avoid
+having to explicitly make the join';
+
 CREATE OR REPLACE VIEW link_with_pred_uid AS
  SELECT link.*,
         pred.uid AS pred_uid
@@ -410,6 +518,18 @@
         pred.metatype AS pred_metatype
  FROM node_link_node INNER JOIN node AS pred ON (predicate_id=pred.node_id);
 
+COMMENT ON VIEW node_link_node_with_pred IS 'A join between a subject
+node, an object node and a predicate node via a link. Join: link *
+node * object.node * predicate.node. Convenience view';
+
+CREATE OR REPLACE VIEW node_with_source AS
+ SELECT node.*,
+        source.uid AS source_uid,
+        source.label AS source_label
+ FROM node LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id);
+
+
+
 -- ************************************************************
 -- OBO METAMODEL
 -- ************************************************************
@@ -417,13 +537,18 @@
 SET search_path TO obd_obo_metamodel_view,obd_prejoins_view,obd_core_view,public;
 
 CREATE OR REPLACE VIEW in_subset_link AS
- SELECT *
+ SELECT
+  link.link_id,
+  link.node_id          AS node_id,
+  link.object_id        AS subset_node_id
  FROM
-  link_with_pred
+  link_with_pred AS link
  WHERE
   pred_uid='oboMetaModel:inSubset';
 
+COMMENT ON VIEW in_subset_link IS 'holds if node_id belongs to the subset_node_id';
 
+
 -- ************************************************************
 -- ANNOTATION MODEL
 -- ************************************************************
@@ -436,6 +561,8 @@
  FROM link_with_pred_uid AS pl
  WHERE pred_uid='oban:posits';
 
+COMMENT ON VIEW posits_link IS 'holds if node_id is a annotation node asserting link_reifnode_id';
+
 CREATE OR REPLACE VIEW link_to_link AS
  SELECT 
         link_in.node_id         AS in_node_id,
@@ -455,10 +582,31 @@
  SELECT * FROM node
  WHERE node_id IN (SELECT node_id FROM link WHERE reiflink_node_id IS NOT NULL);
 
+CREATE OR REPLACE VIEW annotation_count_by_annotated_entity_and_source AS
+ SELECT
+  source.uid   AS source_uid,
+  source.label AS source_label,
+  ae.uid,
+  ae.label,
+  count(link.*)
+ FROM 
+        link
+        INNER JOIN node AS source ON (link.source_id=source.node_id)
+        INNER JOIN node AS ae ON (link.node_id=ae.node_id)
+ WHERE
+  reiflink_node_id IS NOT NULL
+ GROUP BY
+  source.uid,
+  source.label,
+  ae.uid,
+  ae.label;
+
+
+
 -- instance of an annotation and the statement posited in the annotation
 CREATE OR REPLACE VIEW annotation_node_J_link AS
  SELECT
-  node.*,
+  n.*,
   link.node_id AS subject_id
  FROM annotation_node AS n
   INNER JOIN link ON (n.node_id=link.reiflink_node_id);
@@ -500,11 +648,11 @@
 
 CREATE OR REPLACE VIEW annotation_evidence AS 
  SELECT 
-        annotation.*,
+        annotation_node.*,
         has_evidence.object_id  AS evidence_id,
         has_evidence.is_inferred
- FROM           annotation
-  INNER JOIN    link_J_predicate AS has_evidence ON (node_id)
+ FROM           annotation_node
+  INNER JOIN    link_J_predicate AS has_evidence USING (node_id)
  WHERE
   has_evidence.predicate_uid='oban:has_evidence';
 
@@ -554,47 +702,60 @@
 CREATE SCHEMA obd_aggregate_view;
 SET search_path TO obd_aggregate_view,obd_annotation_view,obd_prejoins_view, obd_obo_metamodel_view,obd_core_view,public;
 
-CREATE OR REPLACE VIEW statementcount_by_source AS 
- SELECT source.uid,source.label, count(sn.node_id)
+CREATE OR REPLACE VIEW statement_count_by_source AS 
+ SELECT source.uid,source.label, count(sn.node_id) AS statement_count
  FROM statement_node AS sn
   INNER JOIN node AS source ON (sn.source_id=source.node_id)
  GROUP BY source.uid,source.label;
 
-CREATE OR REPLACE VIEW nodecount_by_source AS 
- SELECT source.uid,source.label, count(node.node_id)
+CREATE OR REPLACE VIEW node_count_by_source AS 
+ SELECT source.uid,source.label, count(node.node_id) AS node_count
  FROM node LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
  GROUP BY source.uid,source.label;
 
-CREATE OR REPLACE VIEW linkcount_by_source AS 
- SELECT source.uid,source.label, count(link.link_id)
+CREATE OR REPLACE VIEW node_count_by_source_id AS 
+ SELECT node.source_id, count(node.node_id) AS node_count
+ FROM node
+ GROUP BY node.source_id;
+
+CREATE OR REPLACE VIEW link_count_by_source AS 
+ SELECT source.uid,source.label, count(link.link_id) AS link_count
  FROM link LEFT OUTER JOIN node AS source ON (link.source_id=source.node_id)
  GROUP BY source.uid,source.label;
 
-CREATE OR REPLACE VIEW reified_linkcount_by_source AS 
- SELECT source.uid,source.label, count(link.link_id)
+CREATE OR REPLACE VIEW link_count_by_source_id AS 
+ SELECT link.source_id, count(link.link_id) AS link_count
+ FROM link
+ GROUP BY source_id;
+
+CREATE OR REPLACE VIEW annotation_count_by_source AS 
+ SELECT source.uid,source.label, count(link.link_id) AS link_count
  FROM link LEFT OUTER JOIN node AS source ON (link.source_id=source.node_id)
  WHERE reiflink_node_id IS NOT NULL
  GROUP BY source.uid,source.label;
 
-CREATE OR REPLACE VIEW linkcount_by_predicate_and_source AS 
- SELECT source.uid,source.label, pred.uid AS pred_uid, pred.label AS pred_label,count(link.link_id)
+COMMENT ON VIEW annotation_count_by_source IS 'Number of reified
+links (annotations) grouped by source';
+
+CREATE OR REPLACE VIEW link_count_by_predicate_and_source AS 
+ SELECT source.uid,source.label, pred.uid AS pred_uid, pred.label AS pred_label,count(link.link_id) AS link_count
  FROM link LEFT OUTER JOIN node AS source ON (link.source_id=source.node_id)
            INNER JOIN node AS pred ON (pred.node_id=link.predicate_id)
  GROUP BY source.uid,source.label,pred.uid,pred.label;
 
-CREATE OR REPLACE VIEW linkcount_by_node_source AS 
- SELECT source.uid,source.label, count(link.link_id)
+CREATE OR REPLACE VIEW link_count_by_node_source AS 
+ SELECT source.uid,source.label, count(link.link_id) AS link_count
  FROM link 
         INNER JOIN node USING (node_id) 
         LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
  GROUP BY source.uid,source.label;
 
-CREATE OR REPLACE VIEW linkcount_by_node_and_object_source AS 
+CREATE OR REPLACE VIEW link_count_by_node_and_object_source AS 
  SELECT node_source.uid AS node_source_uid,
         node_source.label AS node_source_label,
         obj_source.uid AS obj_source_uid,
         obj_source.label AS obj_source_label,
-        count(link.link_id)
+        count(link.link_id) AS link_count
  FROM   link 
         INNER JOIN node USING (node_id) 
         LEFT OUTER JOIN node AS node_source ON (node.source_id=node_source.node_id)
@@ -606,40 +767,167 @@
           obj_source_label;
 
 CREATE OR REPLACE VIEW inter_ontology_linkcount AS 
- SELECT * FROM linkcount_by_node_and_object_source WHERE node_source_uid!=obj_source_uid;
+ SELECT * 
+ FROM link_count_by_node_and_object_source 
+ WHERE node_source_uid != obj_source_uid;
 
-CREATE OR REPLACE VIEW linkcount_by_relation_and_node_source AS 
- SELECT pred.uid AS relation_uid,pred.label AS relation_label,source.uid,source.label, count(link.link_id)
+CREATE OR REPLACE VIEW link_count_by_relation_and_node_source AS 
+ SELECT pred.uid AS relation_uid,pred.label AS relation_label,source.uid,source.label, count(link.link_id) AS link_count
  FROM link LEFT OUTER JOIN node AS source ON (link.source_id=source.node_id)
         INNER JOIN node AS pred ON (link.predicate_id=pred.node_id)
  GROUP BY pred.uid,pred.label,source.uid,source.label;
 
-CREATE OR REPLACE VIEW linkcount_by_metatype_and_source AS 
- SELECT source.uid,source.label, is_inferred, combinator, count(link.link_id)
+CREATE OR REPLACE VIEW link_count_by_metatype_and_source AS 
+ SELECT source.uid,source.label, is_inferred, combinator, count(link.link_id) AS link_count
  FROM link 
         LEFT OUTER JOIN node AS source ON (link.source_id=source.node_id)
  GROUP BY source.uid,source.label, is_inferred, combinator;
 
-CREATE OR REPLACE VIEW linkcount_by_metatype_and_node_source AS 
- SELECT source.uid,source.label, is_inferred, combinator, count(link.link_id)
+CREATE OR REPLACE VIEW link_count_by_metatype_and_node_source AS 
+ SELECT source.uid,source.label, is_inferred, combinator, count(link.link_id) AS link_count
  FROM link 
         INNER JOIN node USING (node_id) 
         LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
  GROUP BY source.uid,source.label, is_inferred, combinator;
 
-CREATE OR REPLACE VIEW implied_linkcount_by_node_source AS 
- SELECT source.uid,source.label, count(link.link_id)
+CREATE OR REPLACE VIEW implied_link_count_by_node_source AS 
+ SELECT source.uid,source.label, count(link.link_id) AS link_count
  FROM link 
         INNER JOIN node USING (node_id) 
         LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
  WHERE link.is_inferred='t'
  GROUP BY source.uid,source.label;
 
-CREATE OR REPLACE VIEW nodecount_by_metatype_and_node_source AS 
- SELECT node.metatype,source.uid,source.label, count(node.node_id)
+CREATE OR REPLACE VIEW node_count_by_metatype_and_node_source AS 
+ SELECT node.metatype,source.uid,source.label, count(node.node_id) AS node_count
  FROM node LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
  GROUP BY node.metatype,source.uid,source.label;
 
+CREATE OR REPLACE VIEW annotated_entity_count_by_source AS 
+ SELECT source.uid,source.label, count(DISTINCT node.node_id) AS annotated_entity_count
+ FROM link 
+        INNER JOIN node USING (node_id) 
+        LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
+ WHERE
+  reiflink_node_id IS NOT NULL
+ GROUP BY source.uid,source.label;
+
+CREATE OR REPLACE VIEW annotated_entity_count_by_source_id AS 
+ SELECT node.source_id, count(DISTINCT node.node_id) AS annotated_entity_count
+ FROM link 
+      INNER JOIN node USING (node_id) 
+ WHERE
+  reiflink_node_id IS NOT NULL
+ GROUP BY node.source_id;
+
+CREATE OR REPLACE VIEW source_summary AS 
+ SELECT 
+        source.uid,source.label, 
+        nc.node_count,
+        lc.link_count,
+        aec.annotated_entity_count
+ FROM
+  node AS source
+  INNER JOIN node_count_by_source_id AS nc ON (nc.source_id=source.node_id)
+  LEFT OUTER JOIN link_count_by_source_id AS lc ON (lc.source_id=source.node_id)
+  LEFT OUTER JOIN annotated_entity_count_by_source_id AS aec ON (aec.source_id=source.node_id);
+ 
+CREATE OR REPLACE VIEW node_count_by_document_source AS 
+ SELECT source.uid,source.label, count(node.node_id) AS node_count
+ FROM node 
+  INNER JOIN node_audit USING (node_id)
+  INNER JOIN node AS source ON (node_audit.source_id=source.node_id)
+ GROUP BY source.uid,source.label;
+
+
+
+-- todo
+-- so far only shows meaningful results for class AE nodes
+CREATE OR REPLACE VIEW annotated_entity_count_by_type AS 
+ SELECT type_node.uid, type_node.label, count(DISTINCT link.node_id) AS annotated_entity_count
+ FROM link
+        INNER JOIN is_a_link USING (node_id)
+        INNER JOIN node AS type_node ON (is_a_link.object_id=type_node.node_id)
+ WHERE
+  link.reiflink_node_id IS NOT NULL
+ GROUP BY type_node.uid, type_node.label;
+
+
+--- per node-level aggregates:
+
+CREATE OR REPLACE VIEW link_count_by_node AS
+ SELECT
+  node.uid                      AS node_uid,
+  node.label                    AS node_label,
+  node.source_id                AS node_source_id,
+  count(DISTINCT link_id)       AS link_count
+ FROM node INNER JOIN link USING (node_id)
+ GROUP BY
+  node.uid,
+  node.label,
+  node.source_id;
+
+CREATE OR REPLACE VIEW asserted_link_count_by_node AS
+ SELECT
+  node.uid                      AS node_uid,
+  node.label                    AS node_label,
+  node.source_id                AS node_source_id,
+  count(DISTINCT link_id)       AS link_count
+ FROM node INNER JOIN asserted_link USING (node_id)
+ GROUP BY
+  node.uid,
+  node.label,
+  node.source_id;
+
+CREATE OR REPLACE VIEW linked_object_count_by_node AS
+ SELECT
+  node.uid                      AS node_uid,
+  node.label                    AS node_label,
+  node.source_id                AS node_source_id,
+  count(DISTINCT link.object_id) AS link_count
+ FROM node INNER JOIN link USING (node_id)
+ GROUP BY
+  node.uid,
+  node.label,
+  node.source_id;
+
+CREATE OR REPLACE VIEW asserted_linked_object_count_by_node AS
+ SELECT
+  node.uid                      AS node_uid,
+  node.label                    AS node_label,
+  node.source_id                AS node_source_id,
+  count(DISTINCT asserted_link.object_id) AS link_count
+ FROM node INNER JOIN asserted_link USING (node_id)
+ GROUP BY
+  node.uid,
+  node.label,
+  node.source_id;
+
+CREATE OR REPLACE VIEW link_count_by_object_node AS
+ SELECT
+  obj.uid AS object_uid,
+  obj.label AS object_label,
+  obj.source_id AS object_source_id,
+  count(DISTINCT link_id)       AS link_count
+ FROM node AS obj INNER JOIN link ON (obj.node_id=link.object_id)
+ GROUP BY
+  obj.uid,
+  obj.label,
+  obj.source_id;
+
+CREATE OR REPLACE VIEW asserted_link_count_by_object_node AS
+ SELECT
+  obj.uid AS object_uid,
+  obj.label AS object_label,
+  obj.source_id AS object_source_id,
+  count(DISTINCT link_id)       AS link_count
+ FROM node AS obj INNER JOIN asserted_link ON (obj.node_id=asserted_link.object_id)
+ GROUP BY
+  obj.uid,
+  obj.label,
+  obj.source_id;
+
+
 -- ************************************************************
 -- INFORMATION CONTENT
 -- ************************************************************
@@ -661,7 +949,7 @@
 
 CREATE OR REPLACE VIEW count_of_annotated_entity AS
  SELECT 
-  count(DISTINCT object_id) AS total
+  count(DISTINCT node_id) AS total
  FROM
   asserted_link
  WHERE
@@ -680,6 +968,7 @@
  SELECT 
   node_id,
 --  evidence_id,
+  tbc.total                                          AS annotated_entity_count,
   - log(cast(tbc.total AS float) / t.total) / log(2) AS shannon_information
  FROM
   count_of_annotated_entity_by_class_node_and_evidence  AS tbc,
@@ -702,4 +991,103 @@
   class_node_entropy_by_evidence
   INNER JOIN node USING (node_id);
 
+COMMENT ON VIEW
+class_node_entropy_by_evidence_with_node_and_auto_label IS 'each class
+that has an annotation (asserted and implied) together with the
+information content of the class, based on the overall background set
+of annotations. TODO: choice of background set. TODO: different
+relations for deductive closure. USE NOTES: order by
+shannon_information for most informative results';
 
+CREATE OR REPLACE VIEW annotation_with_information_content AS
+ SELECT
+  asserted_link.*,
+  annotated_entity_count,
+  shannon_information
+ FROM
+  asserted_link
+  INNER JOIN class_node_entropy_by_evidence AS cne ON (asserted_link.object_id = cne.node_id)
+ WHERE
+  reiflink_node_id IS NOT NULL;
+
+CREATE OR REPLACE VIEW avg_annotation_information_content_by_source AS
+ SELECT
+  source.uid, source.label, avg(ai.shannon_information)
+ FROM 
+  annotation_with_information_content AS ai
+  INNER JOIN node ON (ai.node_id=node.node_id)
+  INNER JOIN node AS source ON (node.source_id=source.node_id)
+ GROUP BY source.uid,source.label;
+  
+-- ************************************************************
+-- AUDIT INFO
+-- ************************************************************
+CREATE SCHEMA owl;
+SET search_path TO owl,obd_prejoins_view, obd_obo_metamodel_view,obd_core_view,public;
+
+CREATE OR REPLACE VIEW n_subClassOf_n AS
+ SELECT
+  link_id,
+  node_id,
+  OBJECT_id AS subClassOf_id,
+  source_id
+ FROM
+  is_a_link;
+
+CREATE OR REPLACE VIEW n_subClassOf_r AS
+ SELECT
+  link_id,
+  node_id,
+  link_id AS Restriction_id,
+  source_id
+ FROM
+  non_is_a_basic_link;
+
+CREATE OR REPLACE VIEW n_subClassOf_nr AS
+ SELECT
+  *
+ FROM link
+ UNION
+ SELECT
+  link_id,
+  node_id,
+  source_id,
+  Restriction_id
+ FROM n_subClassOf_r;
+
+CREATE OR REPLACE VIEW subClassOf_nr AS
+ SELECT
+  node.uri,
+  n_subClassOf_nr.*
+ FROM
+  n_subClassOf_nr
+  INNER JOIN node USING (node_id);
+
+CREATE OR REPLACE VIEW subClassOf AS
+ SELECT
+  subClassOf_nr.*,
+  x  
+ FROM
+  subClassOf_nr
+  INNER JOIN node USING (node_id);
+
+
+-- ************************************************************
+-- AUDIT INFO
+-- ************************************************************
+CREATE SCHEMA obd_audit_view;
+SET search_path TO obd_audit_view,public;
+
+CREATE OR REPLACE VIEW node_audit_summary AS
+ SELECT
+  max(loadtime)  AS max_loadtime,  
+  min(loadtime)  AS min_loadtime
+ FROM
+  node_audit;
+
+CREATE OR REPLACE VIEW node_max_loadtime_by_source AS 
+ SELECT source.uid,source.label, max(loadtime) AS max_loadtime
+ FROM node LEFT OUTER JOIN node AS source ON (node.source_id=source.node_id)
+  INNER JOIN node_audit ON (node.node_id=node_audit.node_id)
+ GROUP BY source.uid,source.label;
+

Modified: obo-database/trunk/sql/users.sql
===================================================================
--- obo-database/trunk/sql/users.sql	2007-10-06 21:52:37 UTC (rev 967)
+++ obo-database/trunk/sql/users.sql	2007-10-06 22:03:11 UTC (rev 968)
@@ -1 +1 @@
-ALTER USER cjm SET search_path TO obd_statistical_view,obd_aggregate_view,obd_annotation_view,obd_prejoins_view, obd_obo_metamodel_view,obd_core_view,public;
+ALTER USER cjm SET search_path TO obd_statistical_view,obd_aggregate_view,obd_annotation_view,obd_prejoins_view, obd_obo_metamodel_view,obd_core_view,obd_denormalized,public;


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[Obo-svn-commit] SF.net SVN: obo: [967] obo-database/trunk/bin

From: <cmu...@us...> - 2007-10-06 21:52:34

Revision: 967
          http://obo.svn.sourceforge.net/obo/?rev=967&view=rev
Author:   cmungall
Date:     2007-10-06 14:52:37 -0700 (Sat, 06 Oct 2007)

Log Message:
-----------


Modified Paths:
--------------
    obo-database/trunk/bin/obd-create-db.pl
    obo-database/trunk/bin/obd-load-db-from-obo.pl

Modified: obo-database/trunk/bin/obd-create-db.pl
===================================================================
--- obo-database/trunk/bin/obd-create-db.pl	2007-10-06 01:51:14 UTC (rev 966)
+++ obo-database/trunk/bin/obd-create-db.pl	2007-10-06 21:52:37 UTC (rev 967)
@@ -5,6 +5,7 @@
 my $dbhost = '';
 my @files = ();
 my $dump_as;
+my $conf_file;
 while (my $opt = shift @ARGV) {
     if ($opt =~ /^\-/) {
         if ($opt eq '-d' || $opt eq '--database') {
@@ -13,6 +14,9 @@
         elsif ($opt eq '-h' || $opt eq '--host') {
             $dbhost = shift @ARGV;
         }
+        elsif ($opt eq '-c' || $opt eq '--conf') {
+            $conf_file = shift @ARGV;
+        }
         elsif ($opt eq '--dump') {
             $dump_as = shift @ARGV;
         }
@@ -41,6 +45,21 @@
 run("psql $args < $sqldir/obd-core-views.sql ");
 run("psql $args < $sqldir/obd-core-functions.plpgsql ");
 
+if ($conf_file) {
+    open(F,$conf_file);
+    while(<F>) {
+        chomp;
+        if (/^http:/ || /$file:/) {
+            push(@files, $_);
+        }
+        else {
+            push(@files,"http://purl.org/obo/obo-all/$_/$_.obo");
+        }
+#        push(@files,"obo-all/$_/$_.obo");
+    }
+    close(F);
+}
+
 foreach my $file (@files) {
     my $dbiargs = $dbhost ? "-h $dbhost -d $db" : "-d $db";
     run("obd-load-db-from-obo.pl $dbiargs $file");

Modified: obo-database/trunk/bin/obd-load-db-from-obo.pl
===================================================================
--- obo-database/trunk/bin/obd-load-db-from-obo.pl	2007-10-06 01:51:14 UTC (rev 966)
+++ obo-database/trunk/bin/obd-load-db-from-obo.pl	2007-10-06 21:52:37 UTC (rev 967)
@@ -7,7 +7,7 @@
 my $use_reasoner = $ENV{OBD_USE_OBOEDIT_REASONER} || 0;
 my $dump;
 my $split;
-my $nodelete;
+my $nodelete = 1;
 my @parse_args = ();
 while ($ARGV[0] =~ /^\-/) {
     my $opt = shift @ARGV;
@@ -26,6 +26,9 @@
     elsif ($opt eq '--nodelete') {
         $nodelete = 1;
     }
+    elsif ($opt eq '--delete') {
+        $nodelete = 0;
+    }
     elsif ($opt eq '--split') {
         $split = shift @ARGV;
     }
@@ -43,10 +46,18 @@
 print STDERR "Loading\n";
 
 foreach my $file (@files) {
+    # only deletes if asked..
     unless ($nodelete) {
         clear_previous($file);
     }
     print STDERR "Converting File: $file\n";
+    my $is_tmp = 0;
+    if ($file =~ /^http:.*\/(.*)$/) {
+        my $nu = $1;
+        run("wget -O $nu $file");
+        $file=$nu;
+        $is_tmp=1;
+    }
     my $ifile = "$file.implied.obo";
     if ($use_reasoner) {
         run("obo2obo -o -saveallimpliedlinks $ifile $file");
@@ -61,6 +72,9 @@
     else {
         run("go2fmt.pl @parse_args -x oboxml_to_obd_prestore $ifile | stag-storenode.pl -p xml -cache node=1 -d $d -");
     }
+    if ($is_tmp) {
+        unlink($file);
+    }
     print STDERR "Loaded File: $ifile\n";
 }
 if ($dump) {
@@ -92,6 +106,7 @@
     }
     close(F);
     foreach my $source (keys %ns) {
+        print STDERR "source: $source\n";
         my ($source_id) = $dbh->selectrow_array("SELECT node_id FROM node WHERE uid='$source'");
         return unless $source_id;
         foreach my $table (qw(link sameas tagval alias description)) {


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[Obo-svn-commit] SF.net SVN: obo: [966] phenote/trunk/src/java/phenote/dataadapter/worm/ WormAdapter.java

From: <azu...@us...> - 2007-10-06 01:51:10

Revision: 966
          http://obo.svn.sourceforge.net/obo/?rev=966&view=rev
Author:   azurebrd
Date:     2007-10-05 18:51:14 -0700 (Fri, 05 Oct 2007)

Log Message:
-----------
Not sure I changed anything, but getting the latest in just in case

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java

Modified: phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2007-10-05 21:49:31 UTC (rev 965)
+++ phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2007-10-06 01:51:14 UTC (rev 966)
@@ -51,18 +51,75 @@
     return "Commit To Worm DB";
   }
 
-  public void delete() {
+  public void delete(Connection c, Statement s) {
     List<CharacterI> l = EditManager.inst().getDeletedAnnotations();
     try {
       for (CharacterI chr : l) {
         String pgdbid = chr.getValueString("PGDBID");
         if (pgdbid == null) continue;
-        System.out.println("Delete "+pgdbid+" end"); }
+        System.out.println("Delete "+pgdbid+" end"); 
+        int colI = 0; int boxI = 0;					// initialize column to zero
+        String match = find(".* - ([0-9]+) - [0-9]+", pgdbid);  	// Find a tempname followed by space - space number
+        if (match != null) { boxI = Integer.parseInt(match); }	// get the column number if there is one
+        match = find(".* - [0-9]+ - ([0-9]+)", pgdbid);  	// Find a tempname followed by space - space number
+        if (match != null) { colI = Integer.parseInt(match); }	// get the column number if there is one
+        match = find("(.*) - [0-9]+ - [0-9]+", pgdbid);  	// Find a tempname followed by space - space number
+        if (match != null) { pgdbid = match; }		// query for this, otherwise keep the default value
+        String joinkey = pgdbid;			// assign the tempname / allele to the joinkey 
+        System.out.println("Delete "+pgdbid+" Join "+joinkey+" Box "+boxI+" Col "+colI+" end"); 
+
+//      These have only box and not column
+//        String postgres_table = "app_paper"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+//        postgres_table = "app_person"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+//        postgres_table = "app_phenotype"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+//        postgres_table = "app_paper_remark"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+//        postgres_table = "app_intx_desc"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        String postgres_table = "app_curator"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_term"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_phen_remark"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_anat_term"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_lifestage"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_nature"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_func"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_temperature"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_preparation"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_penetrance"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_percent"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_range"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_quantity"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_quantity_remark"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_heat_sens"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_heat_degree"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_cold_sens"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_cold_degree"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_mat_effect"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_pat_effect"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_genotype"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_strain"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+        postgres_table = "app_obj_remark"; nullPostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI);
+      }
     } catch (Exception e) {
       System.out.println("Could not delete character: " + e);
     }
   }
 
+  public void nullPostgresBoxCol(Connection c, Statement s, String postgres_table, String joinkey, int boxI, int colI) {
+    String postgres_value = "No postgres value assigned";
+    postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey, boxI, colI);
+    if ( (postgres_value.equals("No postgres value assigned")) || (postgres_value.equals("postgres value is null")) ) { } else { 
+      updatePostgresBoxCol(c, s, postgres_table, joinkey, boxI, colI, null); }
+  }
+
+  private void updatePostgresBoxCol(Connection c, Statement s, String postgres_table, String joinkey, int boxI, int colI, String value) {
+    PreparedStatement ps = null;	// intialize postgres insert 
+    try { ps = c.prepareStatement("INSERT INTO "+postgres_table+" VALUES (?, ?, ?, ?)"); ps.setString(1, joinkey); ps.setInt(2, boxI); ps.setInt(3, colI); ps.setString(4, value); }
+    catch (SQLException se) {
+      System.out.println("We got an exception while preparing our insert: that probably means our SQL is invalid"); se.printStackTrace(); System.exit(1); }
+    try { ps.executeUpdate(); } 	
+    catch (SQLException se) { System.out.println("We got an exception while executing an update: possibly bad SQL, or check the connection."); se.printStackTrace(); System.exit(1); }
+  } // private void updatePostgresCol(String postgres_table, String joinkey, int colI, String value)
+
+
   public CharacterI getCharacterReference(String refID) throws DataAdapterEx {
     CharacterListManager clm = CharacterListManager.getCharListMan("referenceMaker");
     for (CharacterI chr : clm.getCharList()) {
@@ -305,7 +362,7 @@
 
     } // for (CharacterI chr : charList.getList())
 
-    delete();
+    delete(c, s);
     // if alleleQueried... wipe out allele and insert
     // else if Pub queried... wipe out pub and insert
     // else  - new insert & deletes(from transactions)
@@ -470,7 +527,7 @@
   private CharacterListI queryPostgresCharacterReferenceList(String group, CharacterListI charList, Statement s, String joinkey, int boxI, int colI) {
       // populate a phenote character based on postgres value by joinkey, then append to character list
     try {
-      CharacterI c1 = CharacterIFactory.makeChar();						// create a new character for a phenote row
+      CharacterI c1 = CharacterIFactory.makeChar();				// create a new character for a phenote row
 
       String pubID = null; String title = null; String personID = null; String name = null; String nbp = null;
 
@@ -519,7 +576,7 @@
   private CharacterListI queryPostgresCharacterMainList(String group, CharacterListI charList, Statement s, String joinkey, int boxI, int colI) {
       // populate a phenote character based on postgres value by joinkey, then append to character list
     try {
-      CharacterI c1 = CharacterIFactory.makeChar();						// create a new character for a phenote row
+      CharacterI c1 = CharacterIFactory.makeChar();				// create a new character for a phenote row
 
       c1.setValue("Object Name",joinkey);					// assign the allele and the column
       String alleleColumn = joinkey+" - "+boxI+" - "+colI;


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[Obo-svn-commit] SF.net SVN: obo: [965] phenote/trunk

From: <mg...@us...> - 2007-10-05 21:49:30

Revision: 965
          http://obo.svn.sourceforge.net/obo/?rev=965&view=rev
Author:   mgibson
Date:     2007-10-05 14:49:31 -0700 (Fri, 05 Oct 2007)

Log Message:
-----------
can now sort by id for completion
impetus was zfins stages which id order is same as
development order conveniently - and doesnt make sense to
do alphabetically
configged for field with sort-by="ID"

Modified Paths:
--------------
    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/OntologyConfig.java
    phenote/trunk/src/java/phenote/datamodel/Ontology.java
    phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-10-05 19:52:28 UTC (rev 964)
+++ phenote/trunk/conf/phenote-config.rnc	2007-10-05 21:49:31 UTC (rev 965)
@@ -122,6 +122,8 @@
     ## this is to optimize slow completion w many ontologies 
     ## with new threading optimization this is being phased out
     attribute min-completion-chars { xsd:int },
+    # for ontol completion what to sort terms by, default is NAME
+    attribute sort-by { "NAME" | "ID" },
     postcomp?,
     ontology*
   } 

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-10-05 19:52:28 UTC (rev 964)
+++ phenote/trunk/conf/phenote-config.xsd	2007-10-05 21:49:31 UTC (rev 965)
@@ -143,6 +143,14 @@
       <xs:attribute name="groups" type="xs:IDREFS"/>
       <xs:attribute name="copy-field" use="required" type="xs:boolean"/>
       <xs:attribute name="min-completion-chars" use="required" type="xs:int"/>
+      <xs:attribute name="sort-by" use="required">
+        <xs:simpleType>
+          <xs:restriction base="xs:token">
+            <xs:enumeration value="NAME"/>
+            <xs:enumeration value="ID"/>
+          </xs:restriction>
+        </xs:simpleType>
+      </xs:attribute>
     </xs:complexType>
   </xs:element>
   <xs:element name="ontology">

Modified: phenote/trunk/conf/zfin-standalone.cfg
===================================================================
--- phenote/trunk/conf/zfin-standalone.cfg	2007-10-05 19:52:28 UTC (rev 964)
+++ phenote/trunk/conf/zfin-standalone.cfg	2007-10-05 21:49:31 UTC (rev 965)
@@ -25,14 +25,14 @@
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
   
   <!-- ******************** FIELD DEFINITIONS *********************** --> 
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
+  <ns:field name="Pub" datatag="PUB" enable="true"/>
 
-  <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
+  <ns:field name="Genotype" datatag="GT" enable="true"/>
 
   <ns:field name="Image File" enable="true" desc="The image filename to attribute this phenotype character."/>
 
 
-  <ns:field name="Entity" syntax-abbrev="E" enable="true">
+  <ns:field name="Entity" datatag="E" enable="true">
     <ns:ontology name="Relationship"  is-postcomp-rel="true"
        file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" />
     <ns:ontology name="ZF"  namespace="zebrafish_anatomy"
@@ -41,17 +41,17 @@
       file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
   </ns:field>
 
-  <ns:field name="Stage" syntax-abbrev="T" enable="true">
+  <ns:field name="Stage" datatag="T" sort-by="ID" enable="true">
     <ns:ontology name="Stage"  namespace="zebrafish_stages" 
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"/>
   </ns:field>
 
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
+  <ns:field name="Quality" datatag="Q" enable="true">
     <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">
+  <ns:field name="Add'l Entity" datatag="E2" enable="true">
     <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="ZF" namespace="zebrafish_anatomy"
@@ -59,11 +59,11 @@
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
   </ns:field>
 
-  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
+  <ns:field name="Abnormal" datatag="Tag" enable="true">
     <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
   </ns:field>
 
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
+  <ns:field name="Description" datatag="Desc" enable="true"/>
 
   <!-- ******************** REVISION HISTORY *********************** --> 
   <!-- 05.20.2007 - Added master-to-local config option to UPDATE on VERSION_CHANGE

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

Modified: phenote/trunk/src/java/phenote/config/OntologyConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/OntologyConfig.java	2007-10-05 19:52:28 UTC (rev 964)
+++ phenote/trunk/src/java/phenote/config/OntologyConfig.java	2007-10-05 21:49:31 UTC (rev 965)
@@ -10,12 +10,6 @@
 /** May not even have ontology file (free text eg genotype) rename FieldConfig? */
 public class OntologyConfig {
 
-  //public String name;
-  //public String namespace; // this should replace filterOut
-  //public String filterOut; // public?
-  //private String slim;
-  //private String reposSubdir; // pase!
-  //private boolean isPostCompRel = false;
   /** just the filename - no path/url */
   public String ontologyFile;
   /** if url given for file then this string gets set (or old backward compatible repos
@@ -34,14 +28,7 @@
   OntologyConfig(phenote.config.xml.OntologyDocument.Ontology o,FieldConfig fc) {
     ontologyBean = o;
     fieldConfig = fc;
-    //name = o.getName()!=null ? o.getName() : fieldName;
     setFile(o.getFile());
-    //if (o.getNamespace() != null) namespace = o.getNamespace();
-//    if (o.getFilterOut() != null) filterOut = o.getFilterOut();
-    //slim = o.getSlim()!=null ? o.getSlim() : null;
-    //if (o.getReposSubdir()!=null) reposSubdir = o.getReposSubdir();
-    // if xgetIsPostCompRel != null
-    //isPostCompRel = o.getIsPostcompRel(); // hmm what will return when not set??
     
     // for now ignoring if name set as there was a bug where name was getting set
     // to "Entity" in the -u .phenote/conf file - woops
@@ -264,24 +251,23 @@
     if (isPostCompRel()) // only set if true, if not there default false
       oldOC.setIsPostCompRel(isPostCompRel());
   }
+
+  public boolean sortById() {
+    if (fieldConfig.getFieldBean().getSortBy() == null) return false;
+    return fieldConfig.getFieldBean().getSortBy() == Field.SortBy.ID;
+  }
 }
 
-    //if (isPostCompRel)  fc.setPostCompRelOntCfg(this);
-  //static OntologyConfig defaultPato = new OntologyConfig("Pato","attribute_and_value.obo");
-
-  //OntologyConfig() {} // not sure this is actually needed/used
-//   private OntologyConfig(String name,FieldConfig fc) {
-//     fieldConfig = fc;
-//     setName(name);//this.name = name;
-//   }
-//   OntologyConfig(String name, String file, String filterOut) {
-//     this(name,file);
-//     this.filterOut = filterOut;
-//   }
-//   OntologyConfig(String name, String file, String filterOut,String slim) {
-//     this(name,file,filterOut);
-//     this.slim = slim;
-//   }
-//   void writePostComp(Field f) {// annoying as shares a lot with ontology
-//     Postcomp pc = f.addNewPostcomp();
-//     pc.setRelationshipOntology(getFile());  }
+  //public String name;
+  //public String namespace; // this should replace filterOut
+  //public String filterOut; // public?
+  //private String slim;
+  //private String reposSubdir; // pase!
+  //private boolean isPostCompRel = false;
+    //name = o.getName()!=null ? o.getName() : fieldName;
+    //if (o.getNamespace() != null) namespace = o.getNamespace();
+//    if (o.getFilterOut() != null) filterOut = o.getFilterOut();
+    //slim = o.getSlim()!=null ? o.getSlim() : null;
+    //if (o.getReposSubdir()!=null) reposSubdir = o.getReposSubdir();
+    // if xgetIsPostCompRel != null
+    //isPostCompRel = o.getIsPostcompRel(); // hmm what will return when not set??

Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-10-05 19:52:28 UTC (rev 964)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-10-05 21:49:31 UTC (rev 965)
@@ -43,11 +43,16 @@
   //private String filename; // may neec to revive for version/metadata?
   private String version;
   private OBOSession oboSession;
+  // presorting things is faster but problematic, as syns dont get sorted
+  // if we could limit output(??) then sorting on fly might be fast enough
+  // with limiting output may wanna do scoring but then lose alphabetical?
+  // maybe have different modes/preferences
   private Collection<OBOClass> sortedTerms; // was List
   private Collection<OBOClass> sortedObsoleteTerms;
   private List<OBOProperty> sortedRelations;
   private String slim; 
-  private String filterOutString;
+  private boolean sortById = false;
+  private String filterOutString; // phase out
   /** well this stuff is specific to ontologies from files (eg obo), perhaps there
       needs to be some sort of wrapper or subclass? need to think about this...
       for now just shoving in here */
@@ -69,6 +74,7 @@
     // get id filter, slim, & possible namespace from oc...
     name = oc.getName();
     slim = oc.getSlim();
+    sortById = oc.sortById();
     // if namespace specified and is valid load that
     if (oc.hasNamespace()) {
       String namespace = oc.getNamespace();
@@ -293,6 +299,7 @@
     //Query<OBOClass, OBOClass> nsQuery =
     Namespace[] spacesArray = spaces.toArray(new Namespace[0]);
     NamespaceQuery nsQuery = new NamespaceQuery(spacesArray);
+    if (sortById) nsQuery.setComparator(new IdComparator());
     // create a new query engine on the session we just loaded
     QueryEngine engine = new QueryEngine(oboSession);
     
@@ -302,6 +309,7 @@
     // true -> cache result ??? do we need to cache - i dont think so
     // BUG - this includes obsoletes!
     nsQuery.setAllowObsoletes(false);
+    // NameSpaceQuery sorts be term name
     sortedTerms = engine.query(nsQuery, false);
     //sortedTerms = QueryUtil.getResults(engine.query(nsQuery, false));
     //log().debug(spacesArray[0]+" Non-obsolete: got " + sortedTerms.size()+" namespace hits in " + (System.currentTimeMillis() - time)+ "ms # of namespaces: "+spaces.size());
@@ -352,5 +360,20 @@
     }
     return filteredList;
   }
+
+
+  private class IdComparator implements Comparator<OBOClass> {
+    public int compare(OBOClass o1, OBOClass o2) {
+      return o1.getID().compareToIgnoreCase(o2.getID());
+    }
+  }
+
 }
 
+//   private class IdSortedNamespaceQuery extends NamespaceQuery {
+//     protected Comparator<OBOClass> comparator = new Comparator<OBOClass>() {
+//       public int compare(OBOClass o1, OBOClass o2) {
+//         return o1.getID().compareToIgnoreCase(o2.getID());
+//       }
+//     };
+//   }

Modified: phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-10-05 19:52:28 UTC (rev 964)
+++ phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-10-05 21:49:31 UTC (rev 965)
@@ -201,6 +201,8 @@
       return searchTermList.getList();
 
     int i =0;
+    // ontologyTermList (from Ontology) is presorted already by term name
+    // if sorted by term id (eg zf stage) SearchTermList i think needs to know that?
     for (OBOClass oboClass : ontologyTermList) {
     //for (int i=0; i<ontologyTermList.size(); i++) {
 


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[Obo-svn-commit] SF.net SVN: obo: [964] phenote/trunk

From: <ba...@us...> - 2007-10-05 19:52:25

Revision: 964
          http://obo.svn.sourceforge.net/obo/?rev=964&view=rev
Author:   balhoff
Date:     2007-10-05 12:52:28 -0700 (Fri, 05 Oct 2007)

Log Message:
-----------
Implemented tracker request 1804172 - added menu item to copy selected specimen list items as an unresolved phylogeny for editing in external program.

Modified Paths:
--------------
    phenote/trunk/conf/phenomap.cfg
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
    phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/charactertemplate/SpecimenListController.java
    phenote/trunk/src/java/phenote/util/Collections.java

Removed Paths:
-------------
    phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java

Modified: phenote/trunk/conf/phenomap.cfg
===================================================================
--- phenote/trunk/conf/phenomap.cfg	2007-10-05 16:49:46 UTC (rev 963)
+++ phenote/trunk/conf/phenomap.cfg	2007-10-05 19:52:28 UTC (rev 964)
@@ -15,7 +15,7 @@
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
   <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="true"/>
   
-  <ns:group name="specimen-list" title="Specimen List" container="window" interface="character-template">
+  <ns:group name="specimen-list" title="Specimen List" container="window" interface="character-template" group_adapter="phenote.charactertemplate.SpecimenListController">
   	<ns:templatechooser title="Phylogeny Chooser" adapter="phenote.charactertemplate.TreeChooser" field="Taxon"/>
   </ns:group>
   <ns:group name="default" title="Default Group" container="window" interface="default"/>

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-10-05 16:49:46 UTC (rev 963)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -117,19 +117,19 @@
   }
   
   public void deleteSelectedCharacters() {
-    this.editManager.deleteChars(this.selectionModel.getSelected());
+    this.editManager.deleteChars(this.getSelectionModel().getSelected());
   }
   
   public void duplicateSelectedCharacters() {
-    this.editManager.copyChars(this.selectionModel.getSelected());
+    this.editManager.copyChars(this.getSelectionModel().getSelected());
   }
   
   public void markSelectedCharacters() {
-    this.setCharactersAreMarked(this.selectionModel.getSelected(), true);
+    this.setCharactersAreMarked(this.getSelectionModel().getSelected(), true);
   }
   
   public void unmarkSelectedCharacters() {
-    this.setCharactersAreMarked(this.selectionModel.getSelected(), false);
+    this.setCharactersAreMarked(this.getSelectionModel().getSelected(), false);
   }
   
   public void undo() {
@@ -183,6 +183,20 @@
     Phenote.getPhenote().getFrame().toFront();
   }
   
+  public EventSelectionModel<CharacterI> getSelectionModel() {
+    return this.selectionModel;
+  }
+  
+  public JFrame getWindow() {
+    if (this.window == null) {
+      this.window = new JFrame(this.getGroupTitle());
+      final JComponent panel = this.createPanel();
+      this.window.getContentPane().add(panel);
+      this.window.setSize(panel.getSize());
+    }
+    return this.window;
+  }
+  
   public void templateChoiceChanged(TemplateChooser source) {
     this.setMarkedCharacters(source.getChosenTemplates(Collections.unmodifiableList(this.sortedCharacters)));
     this.showCharacterTemplate();
@@ -221,11 +235,11 @@
   
   private void setSelectionWithCharacters(List<CharacterI> characters) {
     this.filterField.setText("");
-    this.selectionModel.clearSelection();
+    this.getSelectionModel().clearSelection();
     for (CharacterI character : characters) {
       final int index = this.filteredCharacters.indexOf(character);
       if (index > -1) {
-        this.selectionModel.addSelectionInterval(index, index);
+        this.getSelectionModel().addSelectionInterval(index, index);
         Rectangle rect = this.characterTemplateTable.getCellRect(index, 0, false);
         this.characterTemplateTable.scrollRectToVisible(rect);
       }
@@ -290,16 +304,8 @@
     }
   }
   
-  private JFrame getWindow() {
-    if (this.window == null) {
-      this.window = new JFrame(this.getGroupTitle());
-      final JComponent panel = this.createPanel();
-      this.window.getContentPane().add(panel);
-      this.window.setSize(panel.getSize());
-    }
-    return this.window;
-  }
   
+  
   private JComponent createPanel() {
     SwingEngine swix = new SwingEngine(this);
     try {

Deleted: phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java	2007-10-05 16:49:46 UTC (rev 963)
+++ phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -1,34 +0,0 @@
-package phenote.charactertemplate;
-
-import jebl.evolution.graphs.Node;
-import jebl.evolution.trees.RootedTree;
-import jebl.gui.trees.treeviewer.painters.BasicLabelPainter;
-
-import org.geneontology.oboedit.datamodel.OBOClass;
-
-import phenote.datamodel.CharFieldManager;
-import phenote.datamodel.TermNotFoundException;
-
-public class OntologyTermPainter extends BasicLabelPainter {
-
-  public OntologyTermPainter(String title, RootedTree tree, PainterIntent intent) {
-    super(title, tree, intent);
-  }
-
-  public OntologyTermPainter(String title, RootedTree tree, PainterIntent intent, int defaultSize) {
-    super(title, tree, intent, defaultSize);
-  }
-
-  @Override
-  protected String getLabel(Node node) {
-    final String defaultLabel =  super.getLabel(node);
-    if (defaultLabel == null) return defaultLabel;
-    try {
-      OBOClass term = CharFieldManager.inst().getOboClass(defaultLabel.trim());
-      return " " + term.getName() + " [" + defaultLabel.trim() + "] ";
-    } catch (TermNotFoundException e) {
-      return defaultLabel;
-    }
-  }
- 
-}

Added: phenote/trunk/src/java/phenote/charactertemplate/SpecimenListController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/SpecimenListController.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/charactertemplate/SpecimenListController.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -0,0 +1,70 @@
+package phenote.charactertemplate;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import org.apache.log4j.Logger;
+
+import phenote.datamodel.CharFieldException;
+import phenote.datamodel.CharacterI;
+import phenote.util.Collections;
+
+public class SpecimenListController extends CharacterTemplateController {
+  
+  private static final String COPY_NEWICK_ACTION = "copyAsNewick";
+
+  public SpecimenListController(String groupName) {
+    super(groupName);
+    this.addMenuItems();
+  }
+  
+  public void copyAsNewick() {
+    final String separator = ",";
+    final String taxonList = Collections.join(this.getSelectedTaxonNames(), separator);
+    final String newick = String.format("(%s)", taxonList);
+    Toolkit.getDefaultToolkit().getSystemClipboard().setContents(new StringSelection(newick), null);
+  }
+  
+  private Set<String> getSelectedTaxonNames() {
+    final Set<String> taxa = new HashSet<String>();
+    for (CharacterI character : this.getSelectionModel().getSelected()) {
+      try {
+        taxa.add(String.format("'%s'", character.getValueString("Taxon")));
+      } catch (CharFieldException e) {
+        log().error("Couldn't get taxon name", e);
+        e.printStackTrace();
+      }
+    }
+    return taxa;
+  }
+
+  private void addMenuItems() {
+    // this is kind of temporary until menus are refactored
+    final JMenu editMenu = new JMenu("Edit");
+    this.getWindow().getJMenuBar().add(editMenu);
+    final JMenuItem menuItem = new JMenuItem("Copy as Newick tree");
+    editMenu.add(menuItem);
+    menuItem.setActionCommand(COPY_NEWICK_ACTION);
+    menuItem.addActionListener(new SpecimenListActionListener());
+  }
+  
+  private Logger log() {
+    return Logger.getLogger(SpecimenListController.class);
+  }
+  
+  private class SpecimenListActionListener implements ActionListener {
+    public void actionPerformed(ActionEvent event) {
+      if (event.getActionCommand().equals(COPY_NEWICK_ACTION)) {
+        SpecimenListController.this.copyAsNewick();
+      }
+    }
+  }
+  
+}

Modified: phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java	2007-10-05 16:49:46 UTC (rev 963)
+++ phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -26,16 +26,13 @@
 import jebl.evolution.trees.Tree;
 import jebl.evolution.trees.Utils;
 import jebl.gui.trees.treeviewer.TreeViewer;
-import jebl.gui.trees.treeviewer.painters.BasicLabelPainter;
 
 import org.apache.log4j.Logger;
-import org.geneontology.oboedit.datamodel.OBOClass;
 import org.swixml.SwingEngine;
 
 import phenote.dataadapter.CharListChangeEvent;
 import phenote.dataadapter.CharListChangeListener;
 import phenote.dataadapter.CharacterListManager;
-import phenote.datamodel.CharFieldValue;
 import phenote.datamodel.CharacterI;
 import phenote.util.FileUtil;
 
@@ -69,16 +66,11 @@
       this.log().error("CharField not set for TreeChooser - no matching templates.");
       return Collections.emptyList();
     }
-    final Collection<String> chosenTermIDs = this.getChosenTermIDs();
+    final Collection<String> selectedTaxa = this.getSelectedTaxonNames();
     final Collection<CharacterI> chosenTemplates = new ArrayList<CharacterI>();
     for (CharacterI character : candidates) {
-      final CharFieldValue fieldValue = character.getValue(this.getCharField()); 
-      if (fieldValue.isTerm()) {
-        OBOClass term = fieldValue.getTerm();
-        if ((term != null) && (chosenTermIDs.contains(term.getID()))) {
-          chosenTemplates.add(character);
-        }
-      } else if (chosenTermIDs.contains(fieldValue.getName())){
+      final String valueString = character.getValueString(this.getCharField());
+      if (selectedTaxa.contains(valueString)) {
         chosenTemplates.add(character);
       }
     }
@@ -89,15 +81,11 @@
     try {
       Tree tree = this.importTree(treeText);
       this.getTreeViewer().setTree(tree);
-      // must reset label painters every time tree is changed, because TreeViewer creates new ones
-      final OntologyTermPainter ontologyTermTipPainter = new OntologyTermPainter("Tip Labels", this.getTreeViewer().getTreePane().getTree(), BasicLabelPainter.PainterIntent.TIP);
-      final OntologyTermPainter ontologyTermNodePainter = new OntologyTermPainter("Node Labels", this.getTreeViewer().getTreePane().getTree(), BasicLabelPainter.PainterIntent.NODE);
-      this.getTreeViewer().getTreePane().setTaxonLabelPainter(ontologyTermTipPainter);
-      this.getTreeViewer().getTreePane().setNodeLabelPainter(ontologyTermNodePainter);
       if (this.newickFieldLabel != null) this.newickFieldLabel.setForeground(Color.BLACK);
     }
     catch (ImportException e) {
       if (this.newickFieldLabel != null) this.newickFieldLabel.setForeground(Color.RED);
+      log().error("Invalid Newick tree", e);
     } 
   }
   
@@ -106,16 +94,16 @@
     this.tryLoadDefaultDataFile();
   }
   
-  private Set<String> getChosenTermIDs() {
-    final Set<String> termIDs = new HashSet<String>();
+  private Set<String> getSelectedTaxonNames() {
+    final Set<String> taxa = new HashSet<String>();
     final Set<Node> nodes = this.getTreeViewer().getTreePane().getSelectedNodes();
     final Tree tree = this.getTreeViewer().getTreePane().getTree();
     for (Node node : nodes) {
       if (tree.isExternal(node)) {
-        termIDs.add(tree.getTaxon(node).getName());
+        taxa.add(tree.getTaxon(node).getName());
       }
     }
-    return termIDs;
+    return taxa;
   }
   
   private TreeViewer getTreeViewer() {
@@ -181,9 +169,9 @@
         String newick = (new BufferedReader(new FileReader(treeFile))).readLine();
         this.setNewickTree(newick);
       } catch (FileNotFoundException e) {
-        log().error("Could open tree file", e);
+        log().error("Could not open tree file", e);
       } catch (IOException e) {
-        log().error("Could open tree file", e);
+        log().error("Could not open tree file", e);
       }
     }
   }

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-10-05 16:49:46 UTC (rev 963)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -1206,6 +1206,7 @@
     Group grp = getGroup(groupStr);
     String classString = grp.getGroupAdapter();
     if (classString == null) return null;
+    if (grp.getInterface().equals(Group.Interface.CHARACTER_TEMPLATE)) return null;
     try {
       // should we cache in hash and insure 1 instance???
       Class<?> c = Class.forName(classString);

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-05 16:49:46 UTC (rev 963)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -8,6 +8,8 @@
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.FileNotFoundException;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Enumeration;
@@ -30,8 +32,6 @@
 import org.apache.log4j.Logger;
 import org.apache.log4j.xml.DOMConfigurator;
 
-import com.sun.java.help.impl.SwingWorker;
-
 import phenote.charactertemplate.CharacterTemplateController;
 import phenote.config.Config;
 import phenote.config.ConfigException;
@@ -238,10 +238,31 @@
   private void createGroupWindows() {
     for (Group group : getGroupsByContainer(Group.Container.WINDOW)) {
       if (group.getInterface().equals(Group.Interface.CHARACTER_TEMPLATE)) {
-        new CharacterTemplateController(group.getName());
+        createTemplateController(group.getGroupAdapter(), group.getName());
       }
     }
   }
+  
+  private CharacterTemplateController createTemplateController(String className, String groupName) {
+    final String errorMessage = "Failed creating CharacterTemplate";
+    try {
+      Class<?> adapterClass = Class.forName(className);
+      Constructor<?> constructor = adapterClass.getConstructor(String.class);
+      Object templateController = constructor.newInstance(groupName);
+      return (CharacterTemplateController)templateController;
+    } catch (ClassNotFoundException e) {
+      LOG.error(errorMessage, e);
+    } catch (InstantiationException e) {
+      LOG.error(errorMessage, e);
+    } catch (IllegalAccessException e) {
+      LOG.error(errorMessage, e);
+    } catch (NoSuchMethodException e) {
+      LOG.error(errorMessage, e);
+    } catch (InvocationTargetException e) {
+      LOG.error(errorMessage, e);
+    }
+    return null;
+  }
 
   /** do group guis specified for a tab(not window) - for tab in main window */
   private void createGroupTabs() {

Added: phenote/trunk/src/java/phenote/util/Collections.java
===================================================================
--- phenote/trunk/src/java/phenote/util/Collections.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/util/Collections.java	2007-10-05 19:52:28 UTC (rev 964)
@@ -0,0 +1,20 @@
+package phenote.util;
+
+import java.util.Collection;
+import java.util.Iterator;
+
+public class Collections {
+
+  private Collections(){}
+
+  public static String join(Collection<?> collection, String separator) {
+    final Iterator<?> iterator = collection.iterator();
+    final StringBuffer buffer = new StringBuffer();
+    while (iterator.hasNext()) {
+      buffer.append(iterator.next());
+      if (iterator.hasNext()) buffer.append(separator);
+    }
+    return buffer.toString();
+  }
+
+}


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[Obo-svn-commit] SF.net SVN: obo: [963] phenote/trunk/src/java/phenote

From: <mg...@us...> - 2007-10-05 16:49:43

Revision: 963
          http://obo.svn.sourceforge.net/obo/?rev=963&view=rev
Author:   mgibson
Date:     2007-10-05 09:49:46 -0700 (Fri, 05 Oct 2007)

Log Message:
-----------
OntologyManager -> CharFieldManager
much better name - doesnt just do ontologies manages all the char fields

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java
    phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java
    phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
    phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java
    phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
    phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java
    phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
    phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java
    phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java
    phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java
    phenote/trunk/src/java/phenote/datamodel/CharField.java
    phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java
    phenote/trunk/src/java/phenote/datamodel/Character.java
    phenote/trunk/src/java/phenote/edit/AddTransaction.java
    phenote/trunk/src/java/phenote/edit/EditManager.java
    phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java
    phenote/trunk/src/java/phenote/gui/SelectionHistory.java
    phenote/trunk/src/java/phenote/gui/ShrimpDag.java
    phenote/trunk/src/java/phenote/gui/TermInfo.java
    phenote/trunk/src/java/phenote/gui/TermRequestGUI.java
    phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java
    phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
    phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java
    phenote/trunk/src/java/phenote/servlet/AdminController.java
    phenote/trunk/src/java/phenote/servlet/PhenoteController.java

Modified: phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/charactertemplate/OntologyTermPainter.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -6,7 +6,7 @@
 
 import org.geneontology.oboedit.datamodel.OBOClass;
 
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.TermNotFoundException;
 
 public class OntologyTermPainter extends BasicLabelPainter {
@@ -24,7 +24,7 @@
     final String defaultLabel =  super.getLabel(node);
     if (defaultLabel == null) return defaultLabel;
     try {
-      OBOClass term = OntologyManager.inst().getOboClass(defaultLabel.trim());
+      OBOClass term = CharFieldManager.inst().getOboClass(defaultLabel.trim());
       return " " + term.getName() + " [" + defaultLabel.trim() + "] ";
     } catch (TermNotFoundException e) {
       return defaultLabel;

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -37,7 +37,7 @@
 import phenote.datamodel.AnnotationMappingDriver;
 import phenote.datamodel.BasicAnnotationMappingDriver;
 import phenote.datamodel.CharField;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.gui.SearchFilterType;
 import phenote.gui.SearchParams;
 import phenote.main.PhenoteVersion;
@@ -1180,19 +1180,19 @@
         return aGroup;
       }
     }
-    if (groupName.equals(OntologyManager.DEFAULT_GROUP)) // OntMan?
+    if (groupName.equals(CharFieldManager.DEFAULT_GROUP)) // OntMan?
       return createDefaultGroup(); // ??
     //return null; // ex? return default?
     return getDefaultGroup(); // if all fails just return default?? or null??
   }
 
   public Group getDefaultGroup() {
-    return getGroup(OntologyManager.DEFAULT_GROUP);
+    return getGroup(CharFieldManager.DEFAULT_GROUP);
   }
 
   private Group createDefaultGroup() {
     Group g = phenoConfigBean.addNewGroup();
-    g.setName(OntologyManager.DEFAULT_GROUP);
+    g.setName(CharFieldManager.DEFAULT_GROUP);
     return g;
   }
 

Modified: phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/AbstractGroupAdapter.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -15,7 +15,7 @@
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterListI;
 import phenote.datamodel.Ontology;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.edit.CharChangeListener;
 import phenote.edit.CharChangeEvent;
 
@@ -108,7 +108,7 @@
 
   public void setDestinationField(String fieldName) {
     try {
-      destinationCharField = OntologyManager.inst().getCharFieldForName(fieldName);
+      destinationCharField = CharFieldManager.inst().getCharFieldForName(fieldName);
     }
     catch (CharFieldException e) { // popup? throw ex?
       log().error("Cant find destination field "+fieldName+" for group "+group

Modified: phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -13,7 +13,7 @@
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterList;
 import phenote.datamodel.CharacterListI;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 
 /** Contains current CharacterList. sends out CharacterListChanged events
     when character list has changed */
@@ -31,7 +31,7 @@
 
   // default()?
   public static CharacterListManager main() {
-    return getCharListMan(OntologyManager.DEFAULT_GROUP);
+    return getCharListMan(CharFieldManager.DEFAULT_GROUP);
   }
 
   /** Returns "default" CharacterListManager */ 
@@ -43,7 +43,7 @@
   }
 
   public static CharacterListManager getCharListMan(String group) {
-    if (group == null) group = OntologyManager.DEFAULT_GROUP; // ??
+    if (group == null) group = CharFieldManager.DEFAULT_GROUP; // ??
     if (groupToListMan.get(group) == null) {
       CharacterListManager e = new CharacterListManager(); // (group) ?
       groupToListMan.put(group,e);

Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -40,7 +40,7 @@
 import phenote.datamodel.CharField;
 import phenote.datamodel.Ontology;
 import phenote.datamodel.OntologyException;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.error.ErrorEvent;
 import phenote.error.ErrorManager;
 import phenote.gui.SynchOntologyDialog;
@@ -55,7 +55,7 @@
 
   private static OntologyDataAdapter singleton;
   //private Config config; cant cache may change
-  private OntologyManager ontologyManager = OntologyManager.inst();
+  private CharFieldManager ontologyManager = CharFieldManager.inst();
   private boolean initializingOntologies = false;
   private Map<String,Ontology> fileToOntologyCache = new HashMap<String,Ontology>();
   private OBOMetaData adapterMetaData;

Modified: phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/delimited/DelimFieldParser.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -6,7 +6,7 @@
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharFieldValue;
 import phenote.datamodel.CharFieldException;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.TermNotFoundException;
 
 /** A class that parses a single field out of a tab delimited line.
@@ -32,13 +32,13 @@
       try {
         // should i strip "ID" now, or see if there is afield with ID at end?
         // which of course would be awkward but not inconceivable
-        cf = OntologyManager.inst().getCharFieldForName(head);
+        cf = CharFieldManager.inst().getCharFieldForName(head);
       }
       catch (CharFieldException e) { // column not a char field
         // so term id headers have ID at end so try stripping off
         if (head.endsWith("ID")) {
           head = head.substring(0,head.length()-3);
-          try { cf = OntologyManager.inst().getCharFieldForName(head); }
+          try { cf = CharFieldManager.inst().getCharFieldForName(head); }
           catch (CharFieldException x) { cf = null; } // already is really
         }
       }

Modified: phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -13,7 +13,7 @@
 import phenote.datamodel.CharFieldValue;
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterIFactory;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.CharFieldException;
 
 /** I stole this from phenosyntaxchar, but modifying for tab delimited.  will
@@ -70,7 +70,7 @@
     //try {
     // ontology manager should have char fields in order of config which should be
     // syntax order - hope this isnt too presumptious
-    for (CharField cf : OntologyManager.inst().getCharFieldList()) {
+    for (CharField cf : CharFieldManager.inst().getCharFieldList()) {
       //if its a free text field - only one col necessary.
       //if its an ontology field - need two cols (one for ID, the other for text)
       // the label from config & char field should be the same, so dont need to get
@@ -104,7 +104,7 @@
     //try {
     // ontology manager should have char fields in order of config which should be
     // syntax order - hope this isnt too presumptious
-    for (CharField cf : OntologyManager.inst().getCharFieldList()) {
+    for (CharField cf : CharFieldManager.inst().getCharFieldList()) {
       if (character.hasValue(cf)) {
         sb.append(makeValue(character.getValue(cf)));
       }
@@ -208,7 +208,7 @@
 //      log().error("No value given for column"+fieldNum);
       return;  //don't need to populate a CharField if no value
     }    
-    OntologyManager om = OntologyManager.inst();
+    CharFieldManager om = CharFieldManager.inst();
     //try { // there can be more than one field for a fieldNum??? - MG
     //List<CharField> fields = Config.inst().getCharFieldsForDelimited(fieldNum);//Ex
     if (!Config.inst().hasEnbldCharField(fieldNum)) {

Modified: phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -5,7 +5,7 @@
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.Character;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.TermNotFoundException;
 
 public class FlyCharacter implements FlyCharacterI {
@@ -78,7 +78,7 @@
     if (id == null || id.equals(""))
       throw new TermException("Failed to get term id "+id);
     try {
-      OBOClass oc = OntologyManager.inst().getOboClass(id); // ex
+      OBOClass oc = CharFieldManager.inst().getOboClass(id); // ex
       if (!oc.getName().equals(name))
         throw new TermException("Data name "+name+" and ontology name "+oc.getName()+
                                 "are inconsistent for id "+id);

Modified: phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -12,7 +12,7 @@
 import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharFieldValue;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.CharFieldException;
 import phenote.config.Config;
 import phenote.config.ConfigException;
@@ -57,7 +57,7 @@
 
       // ontology manager should have char fields in order of config which should be
       // syntax order - hope this isnt too presumptious
-      for (CharField cf : OntologyManager.inst().getCharFieldList()) {
+      for (CharField cf : CharFieldManager.inst().getCharFieldList()) {
         if (character.hasValue(cf)) {
           sb.append(Config.inst().getSyntaxAbbrevForCharField(cf)).append("=");//ex
           if (isFreeText(cf)) sb.append('"'); // free text gets quoted
@@ -159,7 +159,7 @@
       return;
     }
     
-    OntologyManager om = OntologyManager.inst();
+    CharFieldManager om = CharFieldManager.inst();
     
     try {
       // so this is funny but there can be more than one char field for an abbrev - for

Modified: phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -34,7 +34,7 @@
 import phenote.datamodel.CharacterList;
 import phenote.datamodel.CharFieldEnum; // ?
 import phenote.datamodel.CharFieldException;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.TermNotFoundException;
 import phenote.dataadapter.AbstractFileAdapter;
 import phenote.dataadapter.CharacterListManager;
@@ -103,7 +103,7 @@
   }
   
   private CharacterI newCharacterFromPhenotypeManifestation(PhenotypeManifestation pm) {
-    OntologyManager ontologyManager = OntologyManager.inst();
+    CharFieldManager ontologyManager = CharFieldManager.inst();
     CharacterI character = CharacterIFactory.makeChar();
     ManifestIn mi = pm.getManifestIn();
     if (mi != null) {

Modified: phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -28,12 +28,12 @@
 
 
   public List<CharField> getAllCharFields() {
-    return OntologyManager.inst().getCharFieldList();
+    return CharFieldManager.inst().getCharFieldList();
   }
   
   public CharField getCharFieldForName(String fieldName)
     throws CharFieldException {
-    return OntologyManager.inst().getCharFieldForName(fieldName);
+    return CharFieldManager.inst().getCharFieldForName(fieldName);
   }
 
   protected OBOClass getTerm(CharField cf) {

Modified: phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -54,7 +54,7 @@
 
   /** retrieves prop from obo session by id, if not there then creates one */
   protected OBOProperty getRelation(String id, String name) {
-    OBOProperty p = OntologyManager.inst().getRelation(id);
+    OBOProperty p = CharFieldManager.inst().getRelation(id);
     if (p != null) return p;
     return new OBOPropertyImpl(id,name);
   }

Modified: phenote/trunk/src/java/phenote/datamodel/CharField.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharField.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/datamodel/CharField.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -212,11 +212,11 @@
       OBOClass oboClass=null;
 
       // POST COMP - move this to char field value?
-      if (OntologyManager.inst().isPostComp(valueString)) {
+      if (CharFieldManager.inst().isPostComp(valueString)) {
         try {
           // just gets first ontology for now - fix this!
           OBOSession os = getOntology().getOboSession();
-          oboClass = OntologyManager.inst().getPostComp(os,valueString);
+          oboClass = CharFieldManager.inst().getPostComp(os,valueString);
         }
         catch (TermNotFoundException e) {}
       }

Modified: phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -24,10 +24,10 @@
     actually manages CharFields(which may have ontologies) - rename CharFieldManager? yes!
     gets initialized by OntologyDataAdapter which loops through FieldConfigs and passes
     CharFields to OntMan */
-public class OntologyManager {
+public class CharFieldManager {
 
 
-  private static OntologyManager singleton;
+  private static CharFieldManager singleton;
   /** CharFields generically hold zero or more ontologies - are charFields that dont
    have ontologies in this list?? yes */
   private List<CharField> charFieldList = new ArrayList<CharField>();
@@ -38,7 +38,7 @@
 
 
   /** Singleton */
-  private OntologyManager() {
+  private CharFieldManager() {
     // always have user & date field by default
     // should be at end in case displayed??
 //     CharField dateCreated =
@@ -46,9 +46,9 @@
 //     addField(dateCreated);
   }
 
-  public static OntologyManager inst() {
+  public static CharFieldManager inst() {
     if (singleton == null)
-      singleton = new OntologyManager();
+      singleton = new CharFieldManager();
     return singleton;
   }
 

Modified: phenote/trunk/src/java/phenote/datamodel/Character.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Character.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/datamodel/Character.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -81,12 +81,12 @@
   }
 
   public CharField getCharFieldForName(String fieldName) throws CharFieldException {
-    return OntologyManager.inst().getCharFieldForName(fieldName);
+    return CharFieldManager.inst().getCharFieldForName(fieldName);
   }
 
   /** return all char fields configured, both currently used or null in char */
   public List<CharField> getAllCharFields() {
-    return OntologyManager.inst().getCharFieldList();
+    return CharFieldManager.inst().getCharFieldList();
   }
 
 

Modified: phenote/trunk/src/java/phenote/edit/AddTransaction.java
===================================================================
--- phenote/trunk/src/java/phenote/edit/AddTransaction.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/edit/AddTransaction.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -12,7 +12,7 @@
 import phenote.datamodel.CharFieldValue;
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterListI;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 
 /** For adding a character (not a char field/subpart - thats an update) */
 
@@ -38,7 +38,7 @@
   public void editModel() {
     getCharList().add(addChar);
     // automatically put in date_created???  //try {
-    CharField dateField = OntologyManager.inst().getDateCreatedField();
+    CharField dateField = CharFieldManager.inst().getDateCreatedField();
     CharFieldValue v = new CharFieldValue(getDate(),addChar,dateField);
     addChar.setValue(dateField,v);
     //} catch (CharFieldException e) { System.out.println("no date_created field"); } //?

Modified: phenote/trunk/src/java/phenote/edit/EditManager.java
===================================================================
--- phenote/trunk/src/java/phenote/edit/EditManager.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/edit/EditManager.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -11,7 +11,7 @@
 import phenote.datamodel.Character;
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharacterIFactory;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 
 /** The way editing works is gui makes update transaction (see CharFieldGui and
     AutoComboBox) and calls
@@ -48,7 +48,7 @@
 
   // gets the "default" (group) edit manager
   public static EditManager inst() {
-    return getEditManager(OntologyManager.DEFAULT_GROUP);
+    return getEditManager(CharFieldManager.DEFAULT_GROUP);
 //     if (singleton == null)
 //       singleton = new EditManager();
 //     return singleton;
@@ -56,7 +56,7 @@
 
   // ??
   public static EditManager getEditManager(String group) {
-    if (group == null) group = OntologyManager.DEFAULT_GROUP;
+    if (group == null) group = CharFieldManager.DEFAULT_GROUP;
     if (groupToEditMan.get(group) == null) {
       CharacterListManager c = CharacterListManager.getCharListMan(group);
       EditManager e = new EditManager(c); // group?

Modified: phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableFormat.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -8,7 +8,7 @@
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.OntologyException;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import ca.odell.glazedlists.GlazedLists;
 import ca.odell.glazedlists.gui.AdvancedTableFormat;
 
@@ -30,7 +30,7 @@
 
   public Object getColumnValue(CharacterI character, int column) {
     try {
-      CharField cf = OntologyManager.inst().getCharField(column, this.representedGroup);
+      CharField cf = CharFieldManager.inst().getCharField(column, this.representedGroup);
       return character.getValueString(cf);
     } 
     catch (OntologyException e) {

Modified: phenote/trunk/src/java/phenote/gui/SelectionHistory.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SelectionHistory.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/SelectionHistory.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -32,7 +32,7 @@
 
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.CharFieldEnum;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.TermNotFoundException;
 import phenote.edit.EditManager;
 import phenote.edit.CharChangeEvent;
@@ -220,7 +220,7 @@
 //	    	System.out.println("link to *"+id+"* selected");
 	        if (id == null) return;
 	        try {
-	          OBOClass term = OntologyManager.inst().getOboClass(id); // ex
+	          OBOClass term = CharFieldManager.inst().getOboClass(id); // ex
 	          currentOboClass = term;
 	          // send out term selection (non mouse over) for DAG view
 	          Object src = SelectionHistory.this;

Modified: phenote/trunk/src/java/phenote/gui/ShrimpDag.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/ShrimpDag.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/ShrimpDag.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -5,7 +5,7 @@
 import ca.uvic.csr.shrimp.gui.QueryView.QueryView;
 import org.geneontology.oboedit.datamodel.OBOSession;
 import phenote.datamodel.Ontology;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.gui.selection.SelectionManager;
 import phenote.gui.selection.TermSelectionEvent;
 import phenote.gui.selection.TermSelectionListener;
@@ -37,7 +37,7 @@
    */
   public void initOntologies() {
     // do this in a separate thread! no need to hold up phenote with this
-    for (Ontology o : OntologyManager.inst().getAllOntologies()) {
+    for (Ontology o : CharFieldManager.inst().getAllOntologies()) {
       // oboViewer.loadOboSession(o.getOboSession());
     }
   }
@@ -70,7 +70,7 @@
     // just hard wire to go for now
     //Ontology o = OntologyManager.inst().getOntologyForName("ZF");
     // fly causes an endless loop - oh my
-    Ontology o = OntologyManager.inst().getOntologyForName("Fly");
+    Ontology o = CharFieldManager.inst().getOntologyForName("Fly");
     //Ontology o = OntologyManager.inst().getOntologyForName("Human Anatomy");
     if (o == null) {
       System.out.println("no ontol for dag");

Modified: phenote/trunk/src/java/phenote/gui/TermInfo.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/TermInfo.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -24,7 +24,7 @@
 
 import org.geneontology.oboedit.datamodel.OBOClass;
 
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.TermNotFoundException;
 import phenote.error.ErrorEvent;
 import phenote.error.ErrorListener;
@@ -190,7 +190,7 @@
     		naviIndex--;
     		id = getTermFromNaviHistory(naviIndex);
     		try {
-    			OBOClass term = OntologyManager.inst().getOboClass(id); // ex
+    			OBOClass term = CharFieldManager.inst().getOboClass(id); // ex
     			setTextFromOboClass(term);
     			// send out term selection (non mouse over) for DAG view
           TermInfo.this.selectionManager.selectTerm(TermInfo.this, term, true);
@@ -206,7 +206,7 @@
     		naviIndex++;
     		String id = getTermFromNaviHistory(naviIndex);
     		try {
-    			OBOClass term = OntologyManager.inst().getOboClass(id); // ex
+    			OBOClass term = CharFieldManager.inst().getOboClass(id); // ex
     			setTextFromOboClass(term);
     			// send out term selection (non mouse over) for DAG view
           TermInfo.this.selectionManager.selectTerm(TermInfo.this, term, true);
@@ -327,7 +327,7 @@
       String id = HtmlUtil.getIdFromHyperlink(e);
       if (id == null) return;
       try {
-        OBOClass term = OntologyManager.inst().getOboClass(id); // ex
+        OBOClass term = CharFieldManager.inst().getOboClass(id); // ex
         setTextFromOboClass(term);
         addTermToNaviHistory(id);
         // send out term selection (non mouse over) for DAG view

Modified: phenote/trunk/src/java/phenote/gui/TermRequestGUI.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TermRequestGUI.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/TermRequestGUI.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -24,7 +24,7 @@
 import org.jdesktop.layout.GroupLayout;
 import org.jdesktop.layout.LayoutStyle;
 
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.datamodel.Ontology;
 
 
@@ -87,7 +87,7 @@
 		ontologyLabel.setText("Ontology");
 
 		ontologyComboBox = new JComboBox();
-  	for (Ontology o : OntologyManager.inst().getAllOntologies()) {
+  	for (Ontology o : CharFieldManager.inst().getAllOntologies()) {
       ontologyComboBox.addItem(o.getName());
     }
 //    ontologyComboBox.addActionListener(new OntologyChooserListener());

Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -18,7 +18,7 @@
 import phenote.dataadapter.GroupAdapterI;
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharacterI;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.edit.EditManager;
 import phenote.gui.selection.SelectionManager;
 import ca.odell.glazedlists.swing.EventSelectionModel;
@@ -33,7 +33,7 @@
   
   private List<CharFieldGui> charFieldGuiList = new ArrayList<CharFieldGui>(8);
   private SearchParamPanel searchParamPanel; // searchParamManager?
-  private OntologyManager ontologyManager = OntologyManager.inst();
+  private CharFieldManager ontologyManager = CharFieldManager.inst();
   private JPanel fieldPanel;
   private JTabbedPane jTabbedPane;
   private String group;
@@ -96,7 +96,7 @@
   } 
 
   private void setGroup(String g) {
-    if (g == null) this.group = OntologyManager.DEFAULT_GROUP;
+    if (g == null) this.group = CharFieldManager.DEFAULT_GROUP;
     else this.group = g;
   }
 

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -21,7 +21,7 @@
 import phenote.datamodel.CharacterI;
 import phenote.datamodel.Ontology;
 import phenote.datamodel.OntologyException;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.edit.CompoundTransaction;
 import phenote.gui.selection.UseTermEvent;
 import phenote.gui.selection.UseTermListener;
@@ -86,7 +86,7 @@
     if (term == null) return;
     if (ontologyChooserCombo == null) return;
     try {
-      Ontology o = OntologyManager.inst().getOntologyForTerm(term);
+      Ontology o = CharFieldManager.inst().getOntologyForTerm(term);
       ontologyChooserCombo.setSelectedItem(o.getName());
     }
     catch (OntologyException e) {

Modified: phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -8,7 +8,7 @@
 
 import org.geneontology.oboedit.datamodel.OBOClass;
 
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 
 /** Controller for term & character selection */
 public class SelectionManager {
@@ -21,13 +21,13 @@
 
   /** return main/default instance */
   public static SelectionManager inst() {
-    return getSelMan(OntologyManager.DEFAULT_GROUP);
+    return getSelMan(CharFieldManager.DEFAULT_GROUP);
 //     if (singleton == null) singleton = new SelectionManager();
 //     return singleton;
   }
 
   public static SelectionManager getSelMan(String group) {
-    if (group == null) group = OntologyManager.DEFAULT_GROUP; // ??
+    if (group == null) group = CharFieldManager.DEFAULT_GROUP; // ??
    if (groupToSelMan.get(group) == null) {
       SelectionManager s = new SelectionManager();
       groupToSelMan.put(group,s);

Modified: phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java
===================================================================
--- phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/jobs/OntologyUpdateJob.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -6,7 +6,7 @@
 import org.springframework.scheduling.quartz.QuartzJobBean;
 import phenote.dataadapter.OntologyDataAdapter;
 import phenote.datamodel.Ontology;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 
 import java.io.File;
 import java.util.Date;
@@ -30,13 +30,13 @@
     LOG.info("Started Ontology Update Job: " + ontologyName);
 
 
-    Ontology ontology = OntologyManager.inst().getOntologyForName(ontologyName);
+    Ontology ontology = CharFieldManager.inst().getOntologyForName(ontologyName);
     if (ontology == null) {
       // In case no ontology has ever been loaded.
       // we assume we run in lazy initialization mode
       // and need to initialize first.
       OntologyDataAdapter.initialize();
-      ontology = OntologyManager.inst().getOntologyForName(ontologyName);
+      ontology = CharFieldManager.inst().getOntologyForName(ontologyName);
       // Check if ontology by this name is found
       if (ontology == null)
         LOG.warn("No Ontology with name :" + ontologyName + " found!");

Modified: phenote/trunk/src/java/phenote/servlet/AdminController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/AdminController.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/servlet/AdminController.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -7,7 +7,7 @@
 import javax.servlet.http.HttpServletResponse;
 
 import phenote.datamodel.Ontology;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 
 import java.util.List;
 
@@ -20,7 +20,7 @@
   public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response) throws Exception {
 
     AdminBean form = new AdminBean();
-    List<Ontology> ontologies = OntologyManager.inst().getAllOntologies();
+    List<Ontology> ontologies = CharFieldManager.inst().getAllOntologies();
     form.setOntologies(ontologies);
 
     return new ModelAndView("admin", "formBean", form);

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2007-10-05 16:43:19 UTC (rev 962)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2007-10-05 16:49:46 UTC (rev 963)
@@ -8,7 +8,7 @@
 import phenote.dataadapter.OntologyDataAdapter;
 import phenote.datamodel.Ontology;
 import phenote.datamodel.OntologyException;
-import phenote.datamodel.OntologyManager;
+import phenote.datamodel.CharFieldManager;
 import phenote.gui.SearchFilterType;
 import phenote.gui.SearchParams;
 import phenote.gui.field.CompListSearcher;
@@ -166,7 +166,7 @@
    * throws ex if ontolName not found
    */
   private Ontology getOntology(String ontolName) throws OntologyException {
-    return OntologyManager.inst().getOntologyForName(ontolName);
+    return CharFieldManager.inst().getOntologyForName(ontolName);
   }
 
   private static String q(String s) {


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[Obo-svn-commit] SF.net SVN: obo: [962] phenote/trunk/src/java/phenote/datamodel

From: <mg...@us...> - 2007-10-05 16:43:15

Revision: 962
          http://obo.svn.sourceforge.net/obo/?rev=962&view=rev
Author:   mgibson
Date:     2007-10-05 09:43:19 -0700 (Fri, 05 Oct 2007)

Log Message:
-----------
renaming ontology manager to char field manager
will change code with next checkin
i found with svn renames things get screwy if you edit after rename
ok maybe im paranoid but i did hit problems

Added Paths:
-----------
    phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java

Removed Paths:
-------------
    phenote/trunk/src/java/phenote/datamodel/OntologyManager.java

Copied: phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java (from rev 957, phenote/trunk/src/java/phenote/datamodel/OntologyManager.java)
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java	2007-10-05 16:43:19 UTC (rev 962)
@@ -0,0 +1,288 @@
+package phenote.datamodel;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.geneontology.oboedit.datamodel.OBOClass;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+import org.geneontology.oboedit.datamodel.OBOSession;
+import org.geneontology.oboedit.postcomp.ParseException;
+import org.geneontology.oboedit.postcomp.PostcompUtil;
+import org.geneontology.oboedit.postcomp.TokenMgrError;
+import org.geneontology.oboedit.util.TermUtil;
+
+import phenote.config.Config;
+import phenote.config.xml.FieldDocument.Field.Type;
+
+//import phenote.datamodel.CharFieldEnum;
+//import phenote.datamodel.OboUtil;
+
+/** Manages all of the ontologies. Should there be an ontology package - whats funny
+    is that ontologies have obo filenames that they parse so they are sort of
+    data adapterish 
+    actually manages CharFields(which may have ontologies) - rename CharFieldManager? yes!
+    gets initialized by OntologyDataAdapter which loops through FieldConfigs and passes
+    CharFields to OntMan */
+public class OntologyManager {
+
+
+  private static OntologyManager singleton;
+  /** CharFields generically hold zero or more ontologies - are charFields that dont
+   have ontologies in this list?? yes */
+  private List<CharField> charFieldList = new ArrayList<CharField>();
+  /** OBOSession holds all ontologies */
+  private OBOSession oboSession;
+
+  public final static String DEFAULT_GROUP = "default";
+
+
+  /** Singleton */
+  private OntologyManager() {
+    // always have user & date field by default
+    // should be at end in case displayed??
+//     CharField dateCreated =
+//       new CharField("Date Created","date_created",Type.DATE);
+//     addField(dateCreated);
+  }
+
+  public static OntologyManager inst() {
+    if (singleton == null)
+      singleton = new OntologyManager();
+    return singleton;
+  }
+
+  /** OntologyDataAdapter adds fields */
+  public void addField(CharField cf) {
+    charFieldList.add(cf);
+  }
+
+  public void setOboSession(OBOSession s) { oboSession = s; }
+  public OBOSession getOboSession() { return oboSession; }
+
+  /** returns relation of id from obo session, null if dont have */
+  public OBOProperty getRelation(String id) {
+    for (OBOProperty p : TermUtil.getRelationshipTypes(oboSession)) {
+      if (p.getID().equals(id))
+        return p;
+    }
+    return null;
+  }
+
+  /** get char field for int. 0 based. based on order in config file
+   CharacterTableModel relies on this order */
+  public CharField getCharField(int i) throws OntologyException {
+    if (i<0) throw new OntologyException("error, asking for negative char field"); 
+    if (i >= charFieldList.size())
+      throw new OntologyException("number "+i+" char field does not exist"); // ex
+    return charFieldList.get(i);
+  }
+
+  public CharField getCharField(int i, String group) throws OntologyException {
+    if (i<0) throw new OntologyException("error, asking for negative char field"); 
+    if (i >= getNumberOfFields(group))
+      throw new OntologyException("number "+i+" char field does not exist");
+    return getCharFieldListForGroup(group).get(i);
+  }
+
+  public CharField getCharFieldForName(String fieldName) throws CharFieldException {
+    if (fieldName == null) throw new CharFieldException("Char field string is null");
+    for (CharField cf : getCharFieldList()) {
+      //if (cf.getName().equalsIgnoreCase(fieldName))
+      if (cf.isField(fieldName)) // checks name and datatag
+        return cf;
+    }
+    throw new CharFieldException("No field for "+fieldName);
+  }
+
+  // ?
+  private CharField getCharFieldForEnum(CharFieldEnum en) throws CharFieldException {
+    try { return getCharFieldForName(en.getName()); }
+    catch (CharFieldException e) { return getCharFieldForName(en.getTag()); }
+  }
+
+  /** If date_created doesnt exist then create it - its a fundamental */
+  public CharField getDateCreatedField() {
+    try { return getCharFieldForEnum(CharFieldEnum.DATE_CREATED); }
+    catch (CharFieldException e) {
+      // if !config.doCreateDate throw CFex??
+      CharField dateCreated = new CharField(CharFieldEnum.DATE_CREATED);
+      addField(dateCreated);
+      return dateCreated;
+    }
+  }
+
+
+  /** This is where the ontologies are in a generic fashion. A char field
+      has one or more ontologies (entity char field often has more than ontology)*/
+  public List<CharField> getCharFieldList() { return charFieldList; }
+  public int getNumberOfFields() { return charFieldList.size(); }
+  private int getNumberOfFields(String group) {
+    return getCharFieldListForGroup(group).size();
+  }
+  
+  /** should this be stored as a data structure? */
+  public List<CharField> getCharFieldListForGroup(String groupName) {
+    List<CharField> charFields = new ArrayList<CharField>();
+    final List<String> fieldNames = Config.inst().getFieldsInGroup(groupName); 
+    for (CharField field : this.getCharFieldList()) {
+      if (fieldNames.contains(field.getName())) {
+        charFields.add(field);
+      }
+    }
+    return charFields;
+  }
+
+  public List<Ontology> getAllOntologies() {
+    List<Ontology> ontologies = new ArrayList<Ontology>();
+    for (CharField cf : charFieldList)
+      ontologies.addAll(cf.getOntologyList());
+    return ontologies;
+  }
+
+  /** Returns ontology with name, null if not found */
+  public Ontology getOntologyForName(String ontologyName) { // static?
+    for (CharField cf : inst().getCharFieldList()) {
+      if (cf.hasOntology(ontologyName))
+        return cf.getOntologyForName(ontologyName);
+    }
+    return null;
+  }
+
+  /** Searches all ontologies for id - this could be even more savvy and utilize
+      the id prefix AO,GO,PATO... 
+      Should this deal with post comp? if ^ then create a post comp term on fly? 
+      im not sure if this is the right place for it, maybe method should be renamed
+      but ill put it here for now 
+      merge this with getOboClassWithEx? */
+  public OBOClass getOboClass(String id) throws TermNotFoundException {
+    OBOClass oboClass;
+// this seems to be the sole reason for ontology list - silly! use char fields!
+    //Iterator<Ontology> iter = getAllOntologies().iterator(); // allOntologyList
+    //while (iter.hasNext()) {
+    for (Ontology o : getAllOntologies()) {
+      //Ontology o = iter.next();
+      try { oboClass = o.getTerm(id); }
+      catch (TermNotFoundException e) { continue; }
+      if (oboClass != null)
+        return oboClass;
+    }
+    // not sure if we need both onotlogy exception & termnotfoundEx ?? redundant?
+    throw new TermNotFoundException("ID "+id+" not found in loaded ontologies");
+  }
+
+  // used to be used by phenoSynChar - no longer
+//   public OBOClass getTermOrPostComp(String id) throws TermNotFoundException {
+//     if (isPostComp(id))
+//       return getPostComp(id);
+//     else
+//       return getOboClassWithExcep(id);
+//   }
+
+  // phase out - put ex in getOboClass!
+  public OBOClass getOboClassWithExcep(String id) throws TermNotFoundException {
+    OBOClass term = getOboClass(id);
+    if (term == null)
+      throw new TermNotFoundException("ID "+id+" not found in loaded ontologies");
+    return term;
+  }
+
+
+  /** returns true if contains ^ - is this rather presumptious or is ^ reserved */
+  boolean isPostComp(String id) {
+    if (id == null) return false;
+    return id.contains("^");
+  }
+
+  /** parse string GO:123^part_of(AO:345) into post comp obo class 
+      This will be replaced with obo edits post comp parse utility */
+  OBOClass getPostComp(OBOSession os, String id) throws TermNotFoundException {
+//     Pattern pat = Pattern.compile("([^\\^]+)\\^([^\\(]*)\\(([^\\)]*)\\)");
+//     Matcher m = pat.matcher(id);
+//     boolean found = m.find();
+//     if (!found) throw new TermNotFoundException("Invalid post comp expression "+id);
+//     String genus,rel,diff;
+//     try {
+//       //log().debug("pattern found for "+id+"? "+found+" g0 "+m.group(0)+" g1 "+m.group(1)+" g2 "+m.group(2)+" g3 "+m.group(3));
+//       genus = m.group(1);
+//       rel = m.group(2);
+//       diff = m.group(3);
+//     } catch (RuntimeException e) { // IllegalState, IndexOutOfBounds
+//       throw new TermNotFoundException("Invalid post comp expression "+id);
+//     }
+
+//     OBOClass gTerm = getOboClassWithExcep(genus); // throws ex
+//     // OBOProperty = getOboRelationshipProperty(rel) - from rel obo - todo
+//     OBOProperty p = new OBOPropertyImpl("OBO_REL:"+rel,rel);
+//     OBOClass dTerm = getOboClassWithExcep(diff);
+    
+//     return OboUtil.makePostCompTerm(gTerm,p,dTerm);
+    
+    // from obo edit!
+    try {
+      // System.out.println("OntMan getting postcomp for "+id+" OS "+os);
+      // obo session now has all ontologies!
+      return PostcompUtil.createPostcompObject(os,id);
+    }
+    catch (ParseException e) {
+
+      // ok this is hacky but pre1.2 phenote used relationship names instead of ids
+      // eg located_in instead of OBO_REL:located_in, so before we throw our hands up
+      // we should try slipping in an OBO_REL: and see if that works
+      if (!id.contains("^OBO_REL:")) {
+        log().error("Post comp failed for "+id+" gonna try inserting ^OBO_REL:");
+        String oboRelId = id.replace("^","^OBO_REL:");
+        try {
+          OBOClass o = PostcompUtil.createPostcompObject(os,oboRelId);
+          // no exception - it worked!
+          log().error("inserting OBO_REL: worked - please update your datafile");
+          return o;
+        }
+        catch (ParseException x) { log().error("Inserting ^OBO_REL: didnt work"); }
+      }
+
+      String m = "\nInvalid post comp expression "+id+" "+e.getMessage();
+      log().error(m);
+      throw new TermNotFoundException(m);
+    }
+    // post comp parser can throw a plain old exception on parse failure
+    // this should be an exception not an error!!!
+    catch (TokenMgrError x) {
+      log().error("parse of post comp term failed "+x);
+      throw new TermNotFoundException(x);
+    }
+  }
+  
+  /** Currently iterates through every ontology looking for term, if this proves too
+      inefficient we could do something with ID prefixes */
+  public Ontology getOntologyForTerm(OBOClass term) throws OntologyException {
+    for (CharField cf : charFieldList) {
+      for (Ontology o : cf.getOntologyList())
+        if (o.hasTerm(term))
+          return o;
+    }
+    throw new OntologyException(term+" not found in ontologies");
+  }
+
+
+  private Logger log;
+  private Logger log() {
+    if (log == null) log = Logger.getLogger(getClass());
+    return log;
+  }
+
+}
+
+  // previously used by term info
+//   /** for obo class find its char field enum via ontology & char field */
+//   public CharFieldEnum getCharFieldEnumForOboClass(OBOClass oboClass) {
+//     for (CharField cf : charFieldList) {
+//       //if (!cf.hasOntologies()) continue; // is this needed? not sure
+//       for (Ontology ont : cf.getOntologyList()) {
+//         if (ont.hasOboClass(oboClass))
+//           return cf.getCharFieldEnum();
+//       }
+//     }
+//     return null; // this shouldnt happen - err msg?
+//   } 
+

Deleted: phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/OntologyManager.java	2007-10-05 14:09:53 UTC (rev 961)
+++ phenote/trunk/src/java/phenote/datamodel/OntologyManager.java	2007-10-05 16:43:19 UTC (rev 962)
@@ -1,288 +0,0 @@
-package phenote.datamodel;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.geneontology.oboedit.datamodel.OBOClass;
-import org.geneontology.oboedit.datamodel.OBOProperty;
-import org.geneontology.oboedit.datamodel.OBOSession;
-import org.geneontology.oboedit.postcomp.ParseException;
-import org.geneontology.oboedit.postcomp.PostcompUtil;
-import org.geneontology.oboedit.postcomp.TokenMgrError;
-import org.geneontology.oboedit.util.TermUtil;
-
-import phenote.config.Config;
-import phenote.config.xml.FieldDocument.Field.Type;
-
-//import phenote.datamodel.CharFieldEnum;
-//import phenote.datamodel.OboUtil;
-
-/** Manages all of the ontologies. Should there be an ontology package - whats funny
-    is that ontologies have obo filenames that they parse so they are sort of
-    data adapterish 
-    actually manages CharFields(which may have ontologies) - rename CharFieldManager? yes!
-    gets initialized by OntologyDataAdapter which loops through FieldConfigs and passes
-    CharFields to OntMan */
-public class OntologyManager {
-
-
-  private static OntologyManager singleton;
-  /** CharFields generically hold zero or more ontologies - are charFields that dont
-   have ontologies in this list?? yes */
-  private List<CharField> charFieldList = new ArrayList<CharField>();
-  /** OBOSession holds all ontologies */
-  private OBOSession oboSession;
-
-  public final static String DEFAULT_GROUP = "default";
-
-
-  /** Singleton */
-  private OntologyManager() {
-    // always have user & date field by default
-    // should be at end in case displayed??
-//     CharField dateCreated =
-//       new CharField("Date Created","date_created",Type.DATE);
-//     addField(dateCreated);
-  }
-
-  public static OntologyManager inst() {
-    if (singleton == null)
-      singleton = new OntologyManager();
-    return singleton;
-  }
-
-  /** OntologyDataAdapter adds fields */
-  public void addField(CharField cf) {
-    charFieldList.add(cf);
-  }
-
-  public void setOboSession(OBOSession s) { oboSession = s; }
-  public OBOSession getOboSession() { return oboSession; }
-
-  /** returns relation of id from obo session, null if dont have */
-  public OBOProperty getRelation(String id) {
-    for (OBOProperty p : TermUtil.getRelationshipTypes(oboSession)) {
-      if (p.getID().equals(id))
-        return p;
-    }
-    return null;
-  }
-
-  /** get char field for int. 0 based. based on order in config file
-   CharacterTableModel relies on this order */
-  public CharField getCharField(int i) throws OntologyException {
-    if (i<0) throw new OntologyException("error, asking for negative char field"); 
-    if (i >= charFieldList.size())
-      throw new OntologyException("number "+i+" char field does not exist"); // ex
-    return charFieldList.get(i);
-  }
-
-  public CharField getCharField(int i, String group) throws OntologyException {
-    if (i<0) throw new OntologyException("error, asking for negative char field"); 
-    if (i >= getNumberOfFields(group))
-      throw new OntologyException("number "+i+" char field does not exist");
-    return getCharFieldListForGroup(group).get(i);
-  }
-
-  public CharField getCharFieldForName(String fieldName) throws CharFieldException {
-    if (fieldName == null) throw new CharFieldException("Char field string is null");
-    for (CharField cf : getCharFieldList()) {
-      //if (cf.getName().equalsIgnoreCase(fieldName))
-      if (cf.isField(fieldName)) // checks name and datatag
-        return cf;
-    }
-    throw new CharFieldException("No field for "+fieldName);
-  }
-
-  // ?
-  private CharField getCharFieldForEnum(CharFieldEnum en) throws CharFieldException {
-    try { return getCharFieldForName(en.getName()); }
-    catch (CharFieldException e) { return getCharFieldForName(en.getTag()); }
-  }
-
-  /** If date_created doesnt exist then create it - its a fundamental */
-  public CharField getDateCreatedField() {
-    try { return getCharFieldForEnum(CharFieldEnum.DATE_CREATED); }
-    catch (CharFieldException e) {
-      // if !config.doCreateDate throw CFex??
-      CharField dateCreated = new CharField(CharFieldEnum.DATE_CREATED);
-      addField(dateCreated);
-      return dateCreated;
-    }
-  }
-
-
-  /** This is where the ontologies are in a generic fashion. A char field
-      has one or more ontologies (entity char field often has more than ontology)*/
-  public List<CharField> getCharFieldList() { return charFieldList; }
-  public int getNumberOfFields() { return charFieldList.size(); }
-  private int getNumberOfFields(String group) {
-    return getCharFieldListForGroup(group).size();
-  }
-  
-  /** should this be stored as a data structure? */
-  public List<CharField> getCharFieldListForGroup(String groupName) {
-    List<CharField> charFields = new ArrayList<CharField>();
-    final List<String> fieldNames = Config.inst().getFieldsInGroup(groupName); 
-    for (CharField field : this.getCharFieldList()) {
-      if (fieldNames.contains(field.getName())) {
-        charFields.add(field);
-      }
-    }
-    return charFields;
-  }
-
-  public List<Ontology> getAllOntologies() {
-    List<Ontology> ontologies = new ArrayList<Ontology>();
-    for (CharField cf : charFieldList)
-      ontologies.addAll(cf.getOntologyList());
-    return ontologies;
-  }
-
-  /** Returns ontology with name, null if not found */
-  public Ontology getOntologyForName(String ontologyName) { // static?
-    for (CharField cf : inst().getCharFieldList()) {
-      if (cf.hasOntology(ontologyName))
-        return cf.getOntologyForName(ontologyName);
-    }
-    return null;
-  }
-
-  /** Searches all ontologies for id - this could be even more savvy and utilize
-      the id prefix AO,GO,PATO... 
-      Should this deal with post comp? if ^ then create a post comp term on fly? 
-      im not sure if this is the right place for it, maybe method should be renamed
-      but ill put it here for now 
-      merge this with getOboClassWithEx? */
-  public OBOClass getOboClass(String id) throws TermNotFoundException {
-    OBOClass oboClass;
-// this seems to be the sole reason for ontology list - silly! use char fields!
-    //Iterator<Ontology> iter = getAllOntologies().iterator(); // allOntologyList
-    //while (iter.hasNext()) {
-    for (Ontology o : getAllOntologies()) {
-      //Ontology o = iter.next();
-      try { oboClass = o.getTerm(id); }
-      catch (TermNotFoundException e) { continue; }
-      if (oboClass != null)
-        return oboClass;
-    }
-    // not sure if we need both onotlogy exception & termnotfoundEx ?? redundant?
-    throw new TermNotFoundException("ID "+id+" not found in loaded ontologies");
-  }
-
-  // used to be used by phenoSynChar - no longer
-//   public OBOClass getTermOrPostComp(String id) throws TermNotFoundException {
-//     if (isPostComp(id))
-//       return getPostComp(id);
-//     else
-//       return getOboClassWithExcep(id);
-//   }
-
-  // phase out - put ex in getOboClass!
-  public OBOClass getOboClassWithExcep(String id) throws TermNotFoundException {
-    OBOClass term = getOboClass(id);
-    if (term == null)
-      throw new TermNotFoundException("ID "+id+" not found in loaded ontologies");
-    return term;
-  }
-
-
-  /** returns true if contains ^ - is this rather presumptious or is ^ reserved */
-  boolean isPostComp(String id) {
-    if (id == null) return false;
-    return id.contains("^");
-  }
-
-  /** parse string GO:123^part_of(AO:345) into post comp obo class 
-      This will be replaced with obo edits post comp parse utility */
-  OBOClass getPostComp(OBOSession os, String id) throws TermNotFoundException {
-//     Pattern pat = Pattern.compile("([^\\^]+)\\^([^\\(]*)\\(([^\\)]*)\\)");
-//     Matcher m = pat.matcher(id);
-//     boolean found = m.find();
-//     if (!found) throw new TermNotFoundException("Invalid post comp expression "+id);
-//     String genus,rel,diff;
-//     try {
-//       //log().debug("pattern found for "+id+"? "+found+" g0 "+m.group(0)+" g1 "+m.group(1)+" g2 "+m.group(2)+" g3 "+m.group(3));
-//       genus = m.group(1);
-//       rel = m.group(2);
-//       diff = m.group(3);
-//     } catch (RuntimeException e) { // IllegalState, IndexOutOfBounds
-//       throw new TermNotFoundException("Invalid post comp expression "+id);
-//     }
-
-//     OBOClass gTerm = getOboClassWithExcep(genus); // throws ex
-//     // OBOProperty = getOboRelationshipProperty(rel) - from rel obo - todo
-//     OBOProperty p = new OBOPropertyImpl("OBO_REL:"+rel,rel);
-//     OBOClass dTerm = getOboClassWithExcep(diff);
-    
-//     return OboUtil.makePostCompTerm(gTerm,p,dTerm);
-    
-    // from obo edit!
-    try {
-      // System.out.println("OntMan getting postcomp for "+id+" OS "+os);
-      // obo session now has all ontologies!
-      return PostcompUtil.createPostcompObject(os,id);
-    }
-    catch (ParseException e) {
-
-      // ok this is hacky but pre1.2 phenote used relationship names instead of ids
-      // eg located_in instead of OBO_REL:located_in, so before we throw our hands up
-      // we should try slipping in an OBO_REL: and see if that works
-      if (!id.contains("^OBO_REL:")) {
-        log().error("Post comp failed for "+id+" gonna try inserting ^OBO_REL:");
-        String oboRelId = id.replace("^","^OBO_REL:");
-        try {
-          OBOClass o = PostcompUtil.createPostcompObject(os,oboRelId);
-          // no exception - it worked!
-          log().error("inserting OBO_REL: worked - please update your datafile");
-          return o;
-        }
-        catch (ParseException x) { log().error("Inserting ^OBO_REL: didnt work"); }
-      }
-
-      String m = "\nInvalid post comp expression "+id+" "+e.getMessage();
-      log().error(m);
-      throw new TermNotFoundException(m);
-    }
-    // post comp parser can throw a plain old exception on parse failure
-    // this should be an exception not an error!!!
-    catch (TokenMgrError x) {
-      log().error("parse of post comp term failed "+x);
-      throw new TermNotFoundException(x);
-    }
-  }
-  
-  /** Currently iterates through every ontology looking for term, if this proves too
-      inefficient we could do something with ID prefixes */
-  public Ontology getOntologyForTerm(OBOClass term) throws OntologyException {
-    for (CharField cf : charFieldList) {
-      for (Ontology o : cf.getOntologyList())
-        if (o.hasTerm(term))
-          return o;
-    }
-    throw new OntologyException(term+" not found in ontologies");
-  }
-
-
-  private Logger log;
-  private Logger log() {
-    if (log == null) log = Logger.getLogger(getClass());
-    return log;
-  }
-
-}
-
-  // previously used by term info
-//   /** for obo class find its char field enum via ontology & char field */
-//   public CharFieldEnum getCharFieldEnumForOboClass(OBOClass oboClass) {
-//     for (CharField cf : charFieldList) {
-//       //if (!cf.hasOntologies()) continue; // is this needed? not sure
-//       for (Ontology ont : cf.getOntologyList()) {
-//         if (ont.hasOboClass(oboClass))
-//           return cf.getCharFieldEnum();
-//       }
-//     }
-//     return null; // this shouldnt happen - err msg?
-//   } 
-


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[Obo-svn-commit] SF.net SVN: obo: [961] phenote/trunk/src/java/phenote/datamodel/ AnnotationCharacter.java

From: <mg...@us...> - 2007-10-05 14:09:51

Revision: 961
          http://obo.svn.sourceforge.net/obo/?rev=961&view=rev
Author:   mgibson
Date:     2007-10-05 07:09:53 -0700 (Fri, 05 Oct 2007)

Log Message:
-----------
fixed duplication/cloning bug where object wast cloning - the "cache" of the
object has to be cloned

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java

Modified: phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java	2007-10-04 21:03:47 UTC (rev 960)
+++ phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java	2007-10-05 14:09:53 UTC (rev 961)
@@ -177,6 +177,7 @@
     }
     else if (isObjectGenusField(cf)) {
       cfv = objectGenus;
+      // cold also see if diff or not and get from annot, below is if no diff
 //       LinkedObject link = annotation.getObject();
 //       if (link != null && TermUtil.isClass(link)) {
 //         OBOClass postComp = TermUtil.getClass(link);
@@ -228,8 +229,11 @@
 		return driver.getCharFieldValue(s, character, field);
 	}
 
-	public CharacterI cloneCharacter() {
-		Annotation clone = (Annotation) annotation.clone();
-		return new AnnotationCharacter(clone, driver);
-	}
+  public CharacterI cloneCharacter() {
+    Annotation clone = (Annotation) annotation.clone();
+    AnnotationCharacter a =  new AnnotationCharacter(clone, driver);
+    a.objectGenus = objectGenus.cloneCharFieldValue();
+    a.objectDifferentia = objectDifferentia.cloneCharFieldValue();
+    return a;
+  }
 }


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[Obo-svn-commit] SF.net SVN: obo: [960] phenote/trunk/conf/phenomap.cfg

From: <ba...@us...> - 2007-10-04 21:03:42

Revision: 960
          http://obo.svn.sourceforge.net/obo/?rev=960&view=rev
Author:   balhoff
Date:     2007-10-04 14:03:47 -0700 (Thu, 04 Oct 2007)

Log Message:
-----------
Missing a space.

Modified Paths:
--------------
    phenote/trunk/conf/phenomap.cfg

Modified: phenote/trunk/conf/phenomap.cfg
===================================================================
--- phenote/trunk/conf/phenomap.cfg	2007-10-04 21:00:13 UTC (rev 959)
+++ phenote/trunk/conf/phenomap.cfg	2007-10-04 21:03:47 UTC (rev 960)
@@ -20,7 +20,7 @@
   </ns:group>
   <ns:group name="default" title="Default Group" container="window" interface="default"/>
   
-  <ns:field name="Publication" syntax-abbrev="PUB" enable="true"groups="default specimen-list"/>
+  <ns:field name="Publication" syntax-abbrev="PUB" enable="true" groups="default specimen-list"/>
   <ns:field name="Taxon" syntax-abbrev="GT" enable="true" groups="default specimen-list">
   	<ns:ontology name="Taxon" file="finkandfink_Taxa.obo" namespace="teleost-taxonomy"/>
   </ns:field>


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[Obo-svn-commit] SF.net SVN: obo: [959] phenote/trunk

From: <ba...@us...> - 2007-10-04 21:00:10

Revision: 959
          http://obo.svn.sourceforge.net/obo/?rev=959&view=rev
Author:   balhoff
Date:     2007-10-04 14:00:13 -0700 (Thu, 04 Oct 2007)

Log Message:
-----------
Adding preliminary fish taxonomy ontology for PhenoMap.

Modified Paths:
--------------
    phenote/trunk/conf/phenomap.cfg

Added Paths:
-----------
    phenote/trunk/obo-files/finkandfink_Taxa.obo

Modified: phenote/trunk/conf/phenomap.cfg
===================================================================
--- phenote/trunk/conf/phenomap.cfg	2007-10-04 18:57:16 UTC (rev 958)
+++ phenote/trunk/conf/phenomap.cfg	2007-10-04 21:00:13 UTC (rev 959)
@@ -20,29 +20,33 @@
   </ns:group>
   <ns:group name="default" title="Default Group" container="window" interface="default"/>
   
-  <ns:field name="Publication" syntax-abbrev="PUB" enable="true" colwidth="150" groups="default specimen-list"/>
-  <ns:field name="Taxon" syntax-abbrev="GT" enable="true" colwidth="150" groups="default specimen-list"/>
-  <ns:field name="Catalog Number" syntax-abbrev="Specimen" enable="true" colwidth="150" groups="default specimen-list"/>
-  <ns:field name="Specimen Count" syntax-abbrev="SpecimenCount" enable="true" colwidth="150" groups="default specimen-list"/>
-  <ns:field name="Preparation" syntax-abbrev="SpecimenPreparation" enable="true" colwidth="150" groups="default specimen-list"/>
-  <ns:field name="Entity" syntax-abbrev="E" enable="true" colwidth="150" groups="default">
+  <ns:field name="Publication" syntax-abbrev="PUB" enable="true"groups="default specimen-list"/>
+  <ns:field name="Taxon" syntax-abbrev="GT" enable="true" groups="default specimen-list">
+  	<ns:ontology name="Taxon" file="finkandfink_Taxa.obo" namespace="teleost-taxonomy"/>
+  </ns:field>
+  <ns:field name="Catalog Number" syntax-abbrev="Specimen" enable="true" groups="default specimen-list"/>
+  <ns:field name="Specimen Count" syntax-abbrev="SpecimenCount" enable="true" groups="default specimen-list"/>
+  <ns:field name="Preparation" syntax-abbrev="SpecimenPreparation" enable="true" groups="default specimen-list"/>
+  <ns:field name="Entity" syntax-abbrev="E" enable="true" groups="default">
     <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
     <ns:ontology name="Entity" file="teleost_anatomy.obo" repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish" namespace="teleost_anatomy"/>
   </ns:field>
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150" groups="default">
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true" groups="default">
     <ns:ontology name="Quality" file="quality.obo" repos-subdir="phenotype"/>
   </ns:field>
-  <ns:field name="Additional Entity" syntax-abbrev="E2" enable="true" colwidth="150" groups="default">
+  <ns:field name="Additional Entity" syntax-abbrev="E2" enable="true" groups="default">
     <ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
     <ns:ontology name="Additional Entity" file="teleost_anatomy.obo" repos-subdir="anatomy/gross_anatomy/animal_gross_anatomy/fish"/>
   </ns:field>
-  <ns:field name="Measurement" syntax-abbrev="M" enable="true" colwidth="150" groups="default"/>
-  <ns:field name="Unit" syntax-abbrev="U" enable="true" colwidth="150" groups="default">
+  <ns:field name="Measurement" syntax-abbrev="M" enable="true" groups="default"/>
+  <ns:field name="Unit" syntax-abbrev="U" enable="true" groups="default">
     <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
   </ns:field>
-  <ns:field name="Compare To" datatag="Compar" enable="true" groups="default"/>
-  <ns:field name="Textual Description" syntax-abbrev="Desc" enable="true" colwidth="150" groups="default"/>
-  <ns:field name="Image URI" syntax-abbrev="URI" enable="true" colwidth="150" groups="default"/>
-  <ns:field name="Notes" syntax-abbrev="Notes" enable="true" colwidth="150" groups="default"/>
+  <ns:field name="Compare To" syntax-abbrev="Compar" enable="true" groups="default">
+  	<ns:ontology name="Compare To" file="finkandfink_Taxa.obo" namespace="teleost-taxonomy"/>
+  </ns:field>
+  <ns:field name="Textual Description" syntax-abbrev="Desc" enable="true" groups="default"/>
+  <ns:field name="Image URI" syntax-abbrev="URI" enable="true" groups="default"/>
+  <ns:field name="Notes" syntax-abbrev="Notes" enable="true" groups="default"/>
   
 </ns:phenote-configuration>
\ No newline at end of file

Added: phenote/trunk/obo-files/finkandfink_Taxa.obo
===================================================================
--- phenote/trunk/obo-files/finkandfink_Taxa.obo	                        (rev 0)
+++ phenote/trunk/obo-files/finkandfink_Taxa.obo	2007-10-04 21:00:13 UTC (rev 959)
@@ -0,0 +1,375 @@
+format-version: 1.2
+date: 02:10:2007 15:27
+saved-by: peter
+auto-generated-by: OBO-Edit 1.101
+default-namespace: teleost-taxonomy
+
+[Term]
+id: TTO: 1029899
+name: Prochilodus vimboides
+is_a: TTO:101208 ! Prochilodus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1
+name: Craniata
+
+[Term]
+id: TTO:10000001
+name: Eigenmannia sp.
+is_a: TTO:104678 ! Eigenmannia
+property_value: has_rank TTO:Unknown_species
+
+[Term]
+id: TTO:10000002
+name: Sternopygus sp.
+is_a: TTO:102060 ! Sternopygus
+property_value: has_rank TTO:Unknown_species
+
+[Term]
+id: TTO:1003114
+name: Notemigonus crysoleucus
+is_a: TTO:100967 ! Notemigonus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1003239
+name: Opsariichthys uncirostris
+is_a: TTO:103159 ! Opsariichthys
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1004143
+name: Chalceus macrolepidotus
+is_a: TTO:100825 ! Chalceus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1004205
+name: Hepsetus odoe
+is_a: TTO:109162 ! Hepsetus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1004213
+name: Xenocharax spilurus
+is_a: TTO:103438 ! Xenocharax
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1004343
+name: Rhoadsia altipinna
+is_a: TTO:105589 ! Rhoadsia
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:100558
+name: Chanos
+is_a: TTO:10720 ! Chanidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:1006103
+name: Rhabdolichops troscheli
+is_a: TTO:107098 ! Rhabdolichops
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:100825
+name: Chalceus
+is_a: TTO:10910 ! Characidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:100967
+name: Notemigonus
+is_a: TTO:10760 ! Cyprinidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:101208
+name: Prochilodus
+is_a: TTO:10855 ! Prochilodontidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:101842
+name: Brycon
+is_a: TTO:10910 ! Characidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:102060
+name: Sternopygus
+is_a: TTO:11231 ! Sternopygidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:1027661
+name: Chanos chanos
+is_a: TTO:100558 ! Chanos
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1028504
+name: Bryconamericus brevirostris
+is_a: TTO:105385 ! Bryconamericus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:102915
+name: Diplomystes
+is_a: TTO:10920 ! Diplomystidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:1029536
+name: Brycon dentex
+is_a: TTO:101842 ! Brycon
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1030110
+name: Platyurosternarchus macrostomus
+synonym: "Sternarchus macrostoma" EXACT []
+is_a: TTO:110391 ! Platyurosternarchus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:103159
+name: Opsariichthys
+is_a: TTO:10760 ! Cyprinidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:103339
+name: Auchenoglanis
+is_a: TTO:10940 ! Bagridae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:103438
+name: Xenocharax
+is_a: TTO:10820 ! Citharinidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:1046341
+name: Diplomystes chilensis
+synonym: "Diplomystes papillosus" EXACT []
+is_a: TTO:102915 ! Diplomystes
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:104678
+name: Eigenmannia
+is_a: TTO:11231 ! Sternopygidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:105055
+name: Zacco
+is_a: TTO:10760 ! Cyprinidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:1051779
+name: Zacco temminckii
+is_a: TTO:105055 ! Zacco
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:105268
+name: Sternarchorhamphus
+is_a: TTO:11232 ! Apteronotidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:105385
+name: Bryconamericus
+is_a: TTO:10910 ! Characidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:105589
+name: Rhoadsia
+is_a: TTO:10910 ! Characidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:1056213
+name: Auchenoglanis monkei
+synonym: "Parauchenoglanis guttatus" EXACT []
+is_a: TTO:103339 ! Auchenoglanis
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:1062171
+name: Sternopygus macrurus
+is_a: TTO:102060 ! Sternopygus
+property_value: has_rank TTO:species
+
+[Term]
+id: TTO:107098
+name: Rhabdolichops
+is_a: TTO:11231 ! Sternopygidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:10720
+name: Chanidae
+is_a: TTO:1350 ! Gonorynchiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:10760
+name: Cyprinidae
+is_a: TTO:1360 ! Cypriniformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:10820
+name: Citharinidae
+is_a: TTO:1370 ! Characiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:10827
+name: Hepsetidae
+is_a: TTO:1370 ! Characiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:10855
+name: Prochilodontidae
+is_a: TTO:1370 ! Characiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:10910
+name: Characidae
+is_a: TTO:1370 ! Characiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:109162
+name: Hepsetus
+is_a: TTO:10827 ! Hepsetidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:10920
+name: Diplomystidae
+is_a: TTO:1380 ! Siluriformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:10940
+name: Bagridae
+is_a: TTO:1380 ! Siluriformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:110391
+name: Platyurosternarchus
+is_a: TTO:11232 ! Apteronotidae
+property_value: has_rank TTO:genus
+
+[Term]
+id: TTO:11231
+name: Sternopygidae
+is_a: TTO:1390 ! Gymnotiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:11232
+name: Apteronotidae
+is_a: TTO:1390 ! Gymnotiformes
+property_value: has_rank TTO:family
+
+[Term]
+id: TTO:1350
+name: Gonorynchiformes
+is_a: TTO:18 ! Actinopterygii
+property_value: has_rank TTO:order
+
+[Term]
+id: TTO:1360
+name: Cypriniformes
+is_a: TTO:18 ! Actinopterygii
+property_value: has_rank TTO:order
+
+[Term]
+id: TTO:1370
+name: Characiformes
+is_a: TTO:18 ! Actinopterygii
+property_value: has_rank TTO:order
+
+[Term]
+id: TTO:1380
+name: Siluriformes
+is_a: TTO:18 ! Actinopterygii
+property_value: has_rank TTO:order
+
+[Term]
+id: TTO:1390
+name: Gymnotiformes
+is_a: TTO:18 ! Actinopterygii
+property_value: has_rank TTO:order
+
+[Term]
+id: TTO:18
+name: Actinopterygii
+is_a: TTO:1 ! Craniata
+property_value: has_rank TTO:class
+
+[Term]
+id: TTO:class
+name: class
+xref: NCBITaxon:class
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:family
+name: family
+xref: NCBITaxon:family
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:genus
+name: genus
+xref: NCBITaxon:genus
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:order
+name: order
+xref: NCBITaxon:order
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:species
+name: species
+xref: NCBITaxon:species
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:taxonomic_rank
+name: taxonomic_rank
+xref: NCBITaxon:taxonomic_rank
+
+[Term]
+id: TTO:Unknown_species
+name: Unknown species
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:Unknown_species_group
+name: Unknown species group
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+
+[Term]
+id: TTO:Unnamed_species
+name: Unnamed species
+is_a: TTO:taxonomic_rank ! taxonomic_rank
+


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[Obo-svn-commit] SF.net SVN: obo: [958] phenote/trunk/src/java/phenote/gui/field/ TermCompList.java

From: <ba...@us...> - 2007-10-04 18:57:12

Revision: 958
          http://obo.svn.sourceforge.net/obo/?rev=958&view=rev
Author:   balhoff
Date:     2007-10-04 11:57:16 -0700 (Thu, 04 Oct 2007)

Log Message:
-----------
Removing some unused code to avoid confusion.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-10-04 18:05:47 UTC (rev 957)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-10-04 18:57:16 UTC (rev 958)
@@ -76,25 +76,6 @@
       //fieldPanel.addPostCompButton(postCompButton);
     }
   }
-
-  /**
-   * char in table changed - setCurrentOboClass & text
-   */
-  protected void setValueFromChar(CharacterI chr) {
-    if (chr == null) {
-      log().error("ERROR: attempt to set fields from null character"); // ex?
-      return;
-    }
-    if (!chr.hasValue(getCharField())) {
-      currentOboClass = null; // makes getCurTermRelName ""
-      setText(""); // actually calls getCurTermRelNm which is ""
-      return;
-    }
-
-    OBOClass selCharTerm = chr.getValue(getCharField()).getOboClass();
-    setOboClass(selCharTerm); // doesnt allow null
-    setOntologyChooserFromTerm(selCharTerm);
-  }
   
   protected void setCharFieldValue(CharFieldValue value) {
     this.setOboClass(value.getOboClass());


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[Obo-svn-commit] SF.net SVN: obo: [957] phenote/trunk/src/java/phenote

From: <ba...@us...> - 2007-10-04 18:05:48

Revision: 957
          http://obo.svn.sourceforge.net/obo/?rev=957&view=rev
Author:   balhoff
Date:     2007-10-04 11:05:47 -0700 (Thu, 04 Oct 2007)

Log Message:
-----------
This should fix various interface glitches due to multithreading during app initialization.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/CharacterTableController.java
    phenote/trunk/src/java/phenote/main/Phenote.java

Modified: phenote/trunk/src/java/phenote/gui/CharacterTableController.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableController.java	2007-10-04 18:00:11 UTC (rev 956)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableController.java	2007-10-04 18:05:47 UTC (rev 957)
@@ -12,7 +12,6 @@
 import javax.swing.JPopupMenu;
 import javax.swing.JTable;
 import javax.swing.JTextField;
-import javax.swing.SwingUtilities;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
@@ -137,11 +136,7 @@
   }
   
   private void addInitialBlankCharacter() {
-    SwingUtilities.invokeLater(new Runnable() {
-      public void run() {
-        CharacterTableController.this.getEditManager().addInitialCharacter();
-      }
-    });
+    this.getEditManager().addInitialCharacter();
   }
   
   private void setSelectionWithCharacters(List<CharacterI> characters) {

Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-04 18:00:11 UTC (rev 956)
+++ phenote/trunk/src/java/phenote/main/Phenote.java	2007-10-04 18:05:47 UTC (rev 957)
@@ -19,6 +19,7 @@
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 import javax.swing.UnsupportedLookAndFeelException;
 import javax.swing.border.EmptyBorder;
@@ -226,8 +227,12 @@
   }
   
   public void initGui() {
-    makeMainWindow(); // ok this is silly
-    this.createGroupWindows();
+    SwingUtilities.invokeLater(new Runnable() {
+      public void run() {
+        makeMainWindow();
+        createGroupWindows();
+      }
+    });
   }
 
   private void createGroupWindows() {


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[Obo-svn-commit] SF.net SVN: obo: [956] phenote/trunk/src/java/phenote/datamodel

From: <mg...@us...> - 2007-10-04 18:00:08

Revision: 956
          http://obo.svn.sourceforge.net/obo/?rev=956&view=rev
Author:   mgibson
Date:     2007-10-04 11:00:11 -0700 (Thu, 04 Oct 2007)

Log Message:
-----------
fixed bug where genotype free text field was showing up in gui
for obo mapping
problem was it gets saved in obo model as dangling class 
and it was retrieving then as a class
but char fields value/char field still thinks of itself as string
and string value was null
so now getValue returns the String name of the dangling genotype/subject
if char field is not a term

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java
    phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java

Modified: phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java	2007-10-04 15:42:26 UTC (rev 955)
+++ phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java	2007-10-04 18:00:11 UTC (rev 956)
@@ -167,6 +167,10 @@
     CharFieldValue cfv = null;
     if (isSubjectField(cf)) {
       LinkedObject subject = annotation.getSubject();
+      // For char fields that are free text, in obo as dangling class - just rip out
+      // name
+      if (subject!= null && !cf.isTerm())
+        return new CharFieldValue(subject.getName(),this,cf);
       if (subject instanceof OBOClass) {
         cfv = new CharFieldValue((OBOClass) subject, this, cf);
       }

Modified: phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java	2007-10-04 15:42:26 UTC (rev 955)
+++ phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java	2007-10-04 18:00:11 UTC (rev 956)
@@ -31,8 +31,8 @@
    * AnnotationOntology to contain these properties. This is here just to keep
    * the example simple
    */
-  protected static final OBOProperty GENOTYPE_REL = new OBOPropertyImpl(
-    "oban:has_genotype", "has_genotype");
+  protected static final OBOProperty GENOTYPE_REL =
+  new OBOPropertyImpl("oban:has_genotype", "has_genotype");
   protected static final OBOProperty HAS_QUALITY_REL = new OBOPropertyImpl(
     "pato:has_quality", "has_quality");
   


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[Obo-svn-commit] SF.net SVN: obo: [955] phenote/trunk

From: <mg...@us...> - 2007-10-04 15:42:24

Revision: 955
          http://obo.svn.sourceforge.net/obo/?rev=955&view=rev
Author:   mgibson
Date:     2007-10-04 08:42:26 -0700 (Thu, 04 Oct 2007)

Log Message:
-----------
disable min comp chars
took it out of a few configs
cant take it out of birn configs until release - as it gets 
wiped out from svn
but should take out for birn release
min comp chars optimization has been made irrelevant by threading
and it had quirky behaviour on delete for sure
and now that theres completion on demand with arrow button
dont need min comp chars = 1 to kill pre loading of comp terms
maybe do release soon?

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg
    phenote/trunk/conf/demo.cfg
    phenote/trunk/conf/flybase.cfg
    phenote/trunk/conf/parameciumDB.cfg
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/smart-atlas.cfg
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/conf/birn2.cfg	2007-10-04 15:42:26 UTC (rev 955)
@@ -23,7 +23,7 @@
   <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a
     mouse strain or some other identifying factor"/>
   <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
-  <ns:field name="Entity" min-completion-chars="1" datatag="E" enable="true">
+  <ns:field name="Entity" min-completion-chars="2" datatag="E" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
@@ -43,7 +43,7 @@
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="1" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="2" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>

Modified: phenote/trunk/conf/demo.cfg
===================================================================
--- phenote/trunk/conf/demo.cfg	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/conf/demo.cfg	2007-10-04 15:42:26 UTC (rev 955)
@@ -38,7 +38,7 @@
   <ns:field name="Genetic Context" datatag="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
-  <ns:field name="Entity" datatag="E" min-completion-chars="1" enable="true">
+  <ns:field name="Entity" datatag="E" enable="true">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
@@ -50,7 +50,7 @@
     <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
     <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
   </ns:field>
-  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="1" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" enable="true">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />

Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/conf/flybase.cfg	2007-10-04 15:42:26 UTC (rev 955)
@@ -37,7 +37,7 @@
     <ns:ontology  file="context.obo"/>
   </ns:field>
 
-  <ns:field name="Entity" datatag="E" min-completion-chars="1">
+  <ns:field name="Entity" datatag="E">
      <!-- postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/ -->
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>

Modified: phenote/trunk/conf/parameciumDB.cfg
===================================================================
--- phenote/trunk/conf/parameciumDB.cfg	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/conf/parameciumDB.cfg	2007-10-04 15:42:26 UTC (rev 955)
@@ -31,7 +31,7 @@
  
   <ns:field name="Description" syntax-abbrev="Desc"/>
   
-  <ns:field name="Entity" syntax-abbrev="E" min-completion-chars="2">
+  <ns:field name="Entity" syntax-abbrev="E">
     <ns:ontology name="Paramecium Anatomy" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/para.obo"/>
     <ns:ontology name="Paramecium Ontology" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/paro.obo"/>
     <ns:ontology name="Gene Onotology" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/go.obo"/>

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/conf/phenote-config.rnc	2007-10-04 15:42:26 UTC (rev 955)
@@ -120,6 +120,7 @@
     attribute copy-field { xsd:boolean },
     ## the amount of letters/chars a user has to type before completion happens
     ## this is to optimize slow completion w many ontologies 
+    ## with new threading optimization this is being phased out
     attribute min-completion-chars { xsd:int },
     postcomp?,
     ontology*

Modified: phenote/trunk/conf/smart-atlas.cfg
===================================================================
--- phenote/trunk/conf/smart-atlas.cfg	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/conf/smart-atlas.cfg	2007-10-04 15:42:26 UTC (rev 955)
@@ -30,7 +30,7 @@
   <ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
   <ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
 
-  <ns:field name="Entity" datatag="E" min-completion-chars="1"  enable="true">
+  <ns:field name="Entity" datatag="E" min-completion-chars="2"  enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
@@ -52,7 +52,7 @@
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="1" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="2" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-10-03 21:52:29 UTC (rev 954)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-10-04 15:42:26 UTC (rev 955)
@@ -269,7 +269,8 @@
     // too soon - text field doesnt have text yet.... hmmmm....
     String input = getText();
     // If length of input is shorter than minimum required for completion do nothing
-    if (input.length() < minCompChars) return;
+    // disabling this - with threading dont need - and its buggy
+    //if (input.length() < minCompChars) return;
     // returns a list of CompletionTerms (checks if relations)
     // if input is empty will return whole list (if configged)
     //log().debug("got new completion request for input "+input+" time "+time());


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