[Obo-svn-commit] SF.net SVN: obo:[1945] phenote/trunk

[<azu...@us...>]

Revision: 1945
          http://obo.svn.sourceforge.net/obo/?rev=1945&view=rev
Author:   azurebrd
Date:     2008-07-31 22:05:27 +0000 (Thu, 31 Jul 2008)

Log Message:
-----------
Changed Strain to Host Strain, added new type called Strain

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

Modified: phenote/trunk/conf/worm.cfg
===================================================================
--- phenote/trunk/conf/worm.cfg	2008-07-31 21:44:47 UTC (rev 1944)
+++ phenote/trunk/conf/worm.cfg	2008-07-31 22:05:27 UTC (rev 1945)
@@ -132,7 +132,7 @@
          <ontology name="Haplo" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/>
   </field>
   <field name="Genotype" enable="true"/>
-  <field name="Strain" enable="true"/>
+  <field name="Host Strain" enable="true"/>
 
   <field name="Genetic Intx Desc" datatag="IntxDesc" enable="true" groups="default"/> -->
   <field name="NBP" datatag="PhenotypeTextRemark" enable="true" type="READ_ONLY" groups="default"/>

Modified: phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2008-07-31 21:44:47 UTC (rev 1944)
+++ phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2008-07-31 22:05:27 UTC (rev 1945)
@@ -303,7 +303,7 @@
         updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
         postgres_table = "app_genotype"; tag_name = "Genotype"; tag_value = chr.getValueString(tag_name);
         updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
-        postgres_table = "app_strain"; tag_name = "Strain"; tag_value = chr.getValueString(tag_name);
+        postgres_table = "app_strain"; tag_name = "Host Strain"; tag_value = chr.getValueString(tag_name);
         updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
         postgres_table = "app_obj_remark"; tag_name = "Object Remark"; tag_value = chr.getValueString(tag_name);
         updateNormalField(c, s, joinkey, postgres_table, tag_name, tag_value);
@@ -605,7 +605,7 @@
       if (postgres_value == "") { } else { c1.setValue("Genotype",postgres_value); }				// assign the queried value
       postgres_table = "app_strain"; postgres_value = ""; // postgres_value = "No postgres value assigned";
       postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
-      if (postgres_value == "") { } else { c1.setValue("Strain",postgres_value); }				// assign the queried value
+      if (postgres_value == "") { } else { c1.setValue("Host Strain",postgres_value); }				// assign the queried value
       postgres_table = "app_obj_remark"; postgres_value = ""; // postgres_value = "No postgres value assigned";
       postgres_value = queryPostgresCharacter(s, postgres_table, postgres_value, joinkey);
       if (postgres_value == "") { } else { c1.setValue("Object Remark",postgres_value); }				// assign the queried value

Modified: phenote/trunk/src/java/phenote/dataadapter/worm/WormConstraint.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/worm/WormConstraint.java	2008-07-31 21:44:47 UTC (rev 1944)
+++ phenote/trunk/src/java/phenote/dataadapter/worm/WormConstraint.java	2008-07-31 22:05:27 UTC (rev 1945)
@@ -70,7 +70,14 @@
           if (chr.hasValue("Object Remark")) { } else {
             warning = true; message += "Character "+pgdbid+" Mapped Wrong and has no Object Remark.  "; } } }
 
+      tag_name = "Object Type";
+      if ( chr.hasValue(tag_name) ) { 
+        String object_type = chr.getValueString(tag_name);
+        if (object_type.equals("Strain")) { 
+          if (chr.hasValue("Host Strain")) {
+            warning = true; message += "Character "+pgdbid+" is of type Strain and has data for Host Strain.  "; } } }
 
+
       if (chr.hasValue("NBP")) { 
           return ConstraintStatus.makeOK(); }
         else { 


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