[Obo-svn-commit] SF.net SVN: obo: [850] phenote/trunk/conf

[<mg...@us...>]

Revision: 850
          http://obo.svn.sourceforge.net/obo/?rev=850&view=rev
Author:   mgibson
Date:     2007-08-29 14:17:47 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
put min-completion-chars="4" into entity fields with lots of ontologies
or 3 or 2
changed some syntax-abbrev to new datatag

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/phenote-config.xsd
    phenote/trunk/conf/smart-atlas.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/birn2.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -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" datatag="E" enable="true">
+  <ns:field name="Entity" min-completion-chars="4" 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" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" 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	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/demo.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -33,12 +33,12 @@
   "http://www.your-repository.com/your_obo_file.obo"), then this site 
   will be checked for updates -->
   
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
-  <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
-  <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
+  <ns:field name="Pub" datatag="PUB" enable="true"/>
+  <ns:field name="Genotype" datatag="GT" enable="true"/>
+  <ns:field name="Genetic Context" datatag="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
-  <ns:field name="Entity" syntax-abbrev="E" enable="true">
+  <ns:field name="Entity" datatag="E" min-completion-chars="3" 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="fma_obo.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
@@ -46,11 +46,11 @@
     <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
     <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.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: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" syntax-abbrev="E2" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="3" 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="fma_obo.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
@@ -58,16 +58,16 @@
     <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
     <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
   </ns:field>
-  <ns:field name="Time" syntax-abbrev="T" enable="true"/>
-  <ns:field name="Count" syntax-abbrev="C" enable="true"/>
-  <ns:field name="Unit" syntax-abbrev="U" enable="true">
+  <ns:field name="Time" datatag="T" enable="true"/>
+  <ns:field name="Count" datatag="C" enable="true"/>
+  <ns:field name="Unit" datatag="U" enable="true">
     <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.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="Evidence" syntax-abbrev="EC" enable="false">
+  <ns:field name="Description" datatag="Desc" enable="true"/>
+  <ns:field name="Evidence" datatag="EC" enable="false">
     <ns:ontology name="Evidence" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo"/>
   </ns:field>
   <!-- ******************** REVISION HISTORY *********************** --> 

Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/flybase.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -29,15 +29,15 @@
   
   <!-- ******************** FIELD DEFINITIONS *********************** --> 
 
-  <ns:field name="Pub" syntax-abbrev="PUB"/>                      
+  <ns:field name="Pub" datatag="PUB"/>                      
 
-  <ns:field name="Genotype" syntax-abbrev="GT" type="FREE_TEXT"/>
+  <ns:field name="Genotype" datatag="GT" type="FREE_TEXT"/>
 
-  <ns:field name="Genetic Context" syntax-abbrev="GC">
+  <ns:field name="Genetic Context" datatag="GC">
     <ns:ontology  file="context.obo"/>
   </ns:field>
 
-  <ns:field name="Entity" syntax-abbrev="E">
+  <ns:field name="Entity" datatag="E" min-completion-chars="3">
      <!-- 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"/>
@@ -47,19 +47,19 @@
      <ns:ontology name="SP" file="spatial.obo"/>
   </ns:field>
 
-  <ns:field name="Quality"  syntax-abbrev="Q">
+  <ns:field name="Quality"  datatag="Q">
     <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" />
   </ns:field>
 
-  <ns:field name="Absent" syntax-abbrev="Tag">
+  <ns:field name="Absent" datatag="AbsentTag">
     <ns:ontology file="quality.obo" slim="absent_slim" />
   </ns:field>
 
-  <ns:field name="Abnormal" syntax-abbrev="Tag">
+  <ns:field name="Abnormal" datatag="Tag">
     <ns:ontology file="quality.obo" slim="abnormal_slim" />
   </ns:field>
 
-  <ns:field name="Description" syntax-abbrev="Desc"/>
+  <ns:field name="Description" datatag="Desc"/>
 
   <!-- ******************** REVISION HISTORY *********************** --> 
   <!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo;  

Modified: phenote/trunk/conf/parameciumDB.cfg
===================================================================
--- phenote/trunk/conf/parameciumDB.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/parameciumDB.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -31,7 +31,7 @@
  
   <ns:field name="Description" syntax-abbrev="Desc"/>
   
-  <ns:field name="Entity" syntax-abbrev="E">
+  <ns:field name="Entity" syntax-abbrev="E" min-completion-chars="2">
     <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	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/phenote-config.rnc	2007-08-29 21:17:47 UTC (rev 850)
@@ -19,7 +19,8 @@
     autocomplete-settings,
     field*,
     group*,
-    data-input-servlet
+    data-input-servlet,
+    character-mode
   }
 
 ## specify how the master config interacts with local/cached config
@@ -71,6 +72,16 @@
   attribute obsolete { xsd:boolean }
 }
 
+## what implementation of CharacterI to use, CHARACTER or OBO_ANNOTATION
+character-mode = element character-mode {
+  ## type of character to use
+  attribute mode { "CHARACTER" | "OBO_ANNOTATION" },
+  ## if using OBO_ANNOTATION, then specify the java mapping class to use
+  ## full java class name, eg phenote.datamodel.BasicAnnotationMappingDriver
+  attribute mapping { xsd:string }
+}
+
+## this is pase and should be phased out
 obo-repository = element obo-repository { attribute url-dir {xsd:string} }
 
 field = 

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/phenote-config.xsd	2007-08-29 21:17:47 UTC (rev 850)
@@ -15,6 +15,7 @@
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:group"/>
         <xs:element ref="x:data-input-servlet"/>
+        <xs:element ref="x:character-mode"/>
       </xs:sequence>
       <xs:attribute name="version" use="required" type="xs:string"/>
       <xs:attribute name="description" use="required" type="xs:string"/>
@@ -74,6 +75,11 @@
       <xs:attribute name="obsolete" use="required" type="xs:boolean"/>
     </xs:complexType>
   </xs:element>
+  <xs:element name="character-mode">
+    <xs:complexType>
+      <xs:attribute name="mode" use="required" type="xs:string"/>
+    </xs:complexType>
+  </xs:element>
   <xs:element name="obo-repository">
     <xs:complexType>
       <xs:attribute name="url-dir" use="required" type="xs:string"/>

Modified: phenote/trunk/conf/smart-atlas.cfg
===================================================================
--- phenote/trunk/conf/smart-atlas.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/smart-atlas.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -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" enable="true">
+  <ns:field name="Entity" datatag="E" min-completion-chars="4"  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" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" 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"/>


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