Changeset 2677

Timestamp:

03/08/10 13:30:16 (2 years ago)

Author:

mswertz

Message:

Prepared for multi-column xref_labels.
Cleaned out models to accomodate this.
Note: this is not complete yet!

Location:

molgenis/3.3/src/org/molgenis

Files:

• generators/DataTypeGen.java.ftl (modified) (14 diffs)
• generators/R/REntityGen.R.ftl (modified) (4 diffs)
• generators/csv/CsvReaderGen.java.ftl (modified) (8 diffs)
• generators/db/JDBCDatabaseGen.java.ftl (modified) (2 diffs)
• generators/db/JDBCMetaDatabaseGen.java.ftl (modified) (4 diffs)
• generators/db/MapperCommons.subclass_per_table.java.ftl (modified) (8 diffs)
• generators/db/MapperMrefs.java.ftl (modified) (4 diffs)
• generators/db/MultiqueryMapperGen.java.ftl (modified) (1 diff)
• generators/doc/DotDocGen.java.ftl (modified) (4 diffs)
• generators/doc/DotDocMinimalGen.java.ftl (modified) (2 diffs)
• generators/doc/EntityModelDocGen.java.ftl (modified) (1 diff)
• generators/doc/FileFormatDocGen.java.ftl (modified) (2 diffs)
• generators/doc/ObjectModelDocGen.java.ftl (modified) (4 diffs)
• generators/doc/TableDocGen.java.ftl (modified) (1 diff)
• generators/doc/TextUmlGen.java.ftl (modified) (2 diffs)
• generators/fieldtypes/MrefField.java (modified) (5 diffs)
• generators/fieldtypes/XrefField.java (modified) (4 diffs)
• generators/server/SoapApiGen.java.ftl (modified) (2 diffs)
• generators/sql/MySqlAlterSubclassPerTableGen.mysql.ftl (modified) (1 diff)
• generators/sql/MySqlCreateSubclassPerTableGen.mysql.ftl (modified) (1 diff)
• model/MolgenisModel.java (modified) (4 diffs)
• model/MolgenisModelParser.java (modified) (7 diffs)
• model/MolgenisModelValidator.java (modified) (19 diffs)
• model/elements/DBSchema.java (modified) (2 diffs)
• model/elements/Entity.java (modified) (17 diffs)
• model/elements/Field.java (modified) (20 diffs)
• model/elements/Form.java (modified) (3 diffs)
• model/elements/Matrix.java (modified) (4 diffs)
• model/elements/Model.java (modified) (2 diffs)
• model/elements/View.java (modified) (3 diffs)

molgenis/3.3/src/org/molgenis/generators/DataTypeGen.java.ftl

@@ -74 +74 @@
         <#assign type_label = field.getType().toString()>
         <#if type_label == "user" || type_label="xref" || type_label="mref">
-                        <#assign xref_entity = model.getEntity(JavaName(field.XRefEntity))>
+                        <#assign xref_entity = field.xrefEntity>
 import ${xref_entity.namespace}.${JavaName(xref_entity)};                       
         </#if>  
@@ -97 +97 @@
         public ${type(field)} get${JavaName(field)}();
         public void set${JavaName(field)}(${type(field)} _${name(field)});
-                        <#if type_label == "user" || type_label == "xref" || type_label == "mref" || type_label == "enum" >
-                                <#if type_label == "enum">
+                <#if type_label == "enum">
         public java.util.List<ValueLabel> get${JavaName(field)}Options();
-                                </#if>
-                                <#if type_label == "user" || type_label="xref">
-        //public void set${JavaName(field)}(${JavaName(field.XRefEntity)} _${name(field)});                             
-        public String get${JavaName(field)}Label();
-        public void set${JavaName(field)}Label(String label);           
-                                <#elseif type_label == "mref">
-        //public void set${JavaName(field)}(List<${JavaName(field.XRefEntity)}> _${name(field)}List);   
-        public java.util.List<String> get${JavaName(field)}Labels();
-        public void set${JavaName(field)}Labels(java.util.List<String> labels);                                                 
-                                </#if>
-                        </#if>  
-
-                        <#if type_label == "file" || type_label=="image" >
+                <#elseif type_label="xref">                     
+                        <#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+        public String get${JavaName(field)}_${label}();
+        public void set${JavaName(field)}_${label}(String ${name(field)}_${label});
+                        </#list></#if>          
+                <#elseif type_label == "mref">  
+                        <#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+        public java.util.List<String> get${JavaName(field)}_${label}();
+        public void set${JavaName(field)}_${label}(java.util.List<String> ${name(field)}_${label}List); 
+                        </#list></#if>                                          
+                <#elseif type_label == "file" || type_label=="image" >
         public File get${JavaName(field)}File();
-        
         public void set${JavaName(field)}File(File file);
                         </#if>
@@ -126 +122 @@
                 <#assign type_label = field.getType().toString()>
         private ${type(field)} _${name(field)} = ${default(field)};
-                <#if type_label == "user" || type_label == "xref" || type_label == "mref" || type_label == "enum">
-                        <#if type_label == "enum">
+                <#if type_label == "enum">
+        private String _${name(field)}_label = null;
         private java.util.List<ValueLabel> _${name(field)}_options = new ArrayList<ValueLabel>();
-                        </#if>
-                        <#if type_label == "mref">
-        private java.util.List<String> _${name(field)}_labels = new ArrayList<String>();
-        private java.util.List<${JavaName(field.getXRefEntity())}> _${name(field)}_objects= new ArrayList<${JavaName(field.getXRefEntity())}>();                                        
-                        <#else>
-        private String _${name(field)}_label = null;
-                                <#if type_label == "xref">
-        private  ${JavaName(field.getXRefEntity())} _${name(field)}_object = null;                              
-                                </#if>
-                        </#if>
-                </#if>
-                <#if type_label == "file" || type_label=="image" >
+                <#elseif type_label == "xref">
+                        <#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+        private String _${name(field)}_${label} = null;                                         
+                        </#list></#if>
+        private  ${JavaName(field.xrefEntity)} _${name(field)}_object = null;                           
+                <#elseif type_label == "mref">
+                        <#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+        private java.util.List<String> _${name(field)}_${label} = new ArrayList<String>();
+                        </#list></#if>  
+        private java.util.List<${JavaName(field.xrefEntity)}> _${name(field)}_objects= new ArrayList<${JavaName(field.xrefEntity)}>();                                          
+                <#elseif type_label == "file" || type_label=="image" >
         private File _${name(field)}_file = null;
                 </#if>
@@ -154 +149 @@
         
         <#list entity.getFields() as f>
-                <#assign type_label = f.getType().toString()>
-                <#if type_label == "enum">
+                <#if f.type == "enum">
                 //options for enum ${JavaName(f)}
                         <#list f.getEnumOptions() as option>
@@ -210 +204 @@
                 <#if type_label == "xref">
                 if(this._${name(field)}_object != null)
-                        return this._${name(field)}_object.get${JavaName(field.getXRefField())}();
+                        return this._${name(field)}_object.get${JavaName(field.xrefField)}();
                 <#elseif type_label == "mref">
                 if(this._${name(field)}_objects != null && this._${name(field)}_objects.size() > 0)
                 {
                         ${type(field)} result = ${default(field)};
-                        for(${JavaName(field.getXRefEntity())} o: _${name(field)}_objects) result.add(o.get${JavaName(field.getXRefField())}());
+                        for(${JavaName(field.xrefEntity)} o: _${name(field)}_objects) result.add(o.get${JavaName(field.xrefField)}());
                         //this should be smarter, like a List that automatically syncs...
                         //and this also doesn't give an informative error why it is not modifiable
@@ -232 +226 @@
                 <#if type_label == "mref">
                 //check what type the elements in the list are made off because List<E> has same erasure
-                //if ${JavaName(field.getXRefEntity())} then tye should go in the object list
-                if( _${name(field)} != null && _${name(field)}.size()>0 && _${name(field)} instanceof ${JavaName(field.getXRefEntity())})
+                //if ${JavaName(field.xrefEntity)} then tye should go in the object list
+                if( _${name(field)} != null && _${name(field)}.size()>0 && _${name(field)} instanceof ${JavaName(field.xrefEntity)})
                 {
                         this._${name(field)}_objects = _${name(field)};
                         //need to copy ids to this._${name(field)} because get${JavaName(field)} does this.
                         //this._${name(field)} = ${default(field)};
-                        //for(${JavaName(field.getXRefEntity())} o: _${name(field)}_objects) result.add(o.get${JavaName(field.getXRefField())}());      
+                        //for(${JavaName(field.xrefEntity)} o: _${name(field)}_objects) result.add(o.get${JavaName(field.xrefField)}());        
                 }
                 //else make list empty
                 else
                 {
-                        this._${name(field)}_objects = new java.util.ArrayList<${JavaName(field.getXRefEntity())}>();
+                        this._${name(field)}_objects = new java.util.ArrayList<${JavaName(field.xrefEntity)}>();
                 
                         if(this._${name(field)} != null)
@@ -259 +253 @@
         }
         
+        <#-- data type specific methods -->
         <#if type_label =="date">
         /**
@@ -268 +263 @@
                 this.set${JavaName(field)}(string2date(datestring));
         }       
-        </#if>  
-        
-        <#if type_label == "user" || type_label == "xref" || type_label == "mref">/**
-         * Get a pretty label for cross reference ${JavaName(field)} to <a href="${JavaName(field.getXRefEntity())}.html#${JavaName(field.getXRefField())}">${JavaName(field.getXRefEntity())}.${JavaName(field.getXRefField())}</a>.
-         */<#elseif type_label == "enum">/**
+        <#elseif type_label == "enum" >  
+        /**
          * Get tha label for enum ${JavaName(field)}.
-         */</#if>
-        <#if type_label == "user" || type_label == "xref" || type_label == "enum" >      
+         */
         public String get${JavaName(field)}Label()
         {
-                <#if type_label != "enum">if(this._${name(field)}_object != null)
-                        return this._${name(field)}_object.get${JavaName(field.getXRefLabelString())}().toString();</#if>
                 return this._${name(field)}_label;
         }
         
-        <#if type_label == "xref">
-        /**
-         * Set the ${field.description}. Automatically calls this.set${JavaName(field)}(${name(field)}.get${JavaName(field.getXRefField())});
+        /**
+         * ${JavaName(field)} is enum. This method returns all available enum options.
+         */
+        public java.util.List<ValueLabel> get${JavaName(field)}Options()
+        {
+                return _${name(field)}_options;
+        }       
+        
+        <#elseif type_label == "xref">
+        /**
+         * Set the ${field.description}. Automatically calls this.set${JavaName(field)}(${name(field)}.get${JavaName(field.xrefField)});
          * @param _${name(field)}
          */
-        public void set${JavaName(field)}(${JavaName(field.getXRefEntity())} ${name(field)})
-        {
-                this.set${JavaName(field)}(${name(field)}.get${JavaName(field.getXRefField())}());
-        }       
-        </#if>
+        public void set${JavaName(field)}(${JavaName(field.xrefEntity)} ${name(field)})
+        {
+                this.set${JavaName(field)}(${name(field)}.get${JavaName(field.xrefField)}());
+        }       
+         
+<#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+        /**
+         * Get a pretty label ${label} for cross reference ${JavaName(field)} to ${JavaName(field.xrefEntity)}.${JavaName(field.xrefField)}.
+         */
+        public String get${JavaName(field)}_${label}()
+        {                       
+                return _${name(field)}_${label};
+        }               
+        
+        /**
+         * Set a pretty label for cross reference ${JavaName(field)} to <a href="${JavaName(field.xrefEntity)}.html#${JavaName(field.xrefField)}">${JavaName(field.xrefEntity)}.${JavaName(field.xrefField)}</a>.
+         */
+        public void set${JavaName(field)}_${label}(String ${name(field)}_${label})
+        {
+                _${name(field)}_${label} = ${name(field)}_${label};
+                //clear the object cache
+                _${name(field)}_object = null;
+        }               
+</#list></#if>
+         
         
         <#elseif type_label="mref">
-        public java.util.List<String> get${JavaName(field)}Labels()
+<#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>       
+        /**
+         * Get a pretty label for cross reference ${JavaName(field)} to <a href="${JavaName(field.xrefEntity)}.html#${JavaName(field.xrefField)}">${JavaName(field.xrefEntity)}.${JavaName(field.xrefField)}</a>.
+         */
+        public java.util.List<String> get${JavaName(field)}_${label}()
         {
                 if(this._${name(field)}_objects != null && this._${name(field)}_objects.size() > 0)
                 {
                         java.util.List<String> result = new java.util.ArrayList<String>();
-                        for(${JavaName(field.getXRefEntity())} o: _${name(field)}_objects) result.add(o.get${JavaName(field.getXRefLabelString())}().toString());
+                        for(${JavaName(field.xrefEntity)} o: _${name(field)}_objects) result.add(o.get${JavaName(label)}().toString());
                         //this should be smarter, like a List that automatically syncs...
                         //and this also doesn't give an informative error why it is not modifiable
                         return java.util.Collections.unmodifiableList(result);
                 }               
-                return  _${name(field)}_labels;
-        }       
-        </#if>
-        
-        <#if type_label == "enum">
-        /**
-         * ${JavaName(field)} is enum. This method returns all available enum options.
-         */
-        </#if>  
-        <#if type_label == "enum" >
-        public java.util.List<ValueLabel> get${JavaName(field)}Options()
-        {
-                return _${name(field)}_options;
-        }
-        </#if>
-        
-        <#if type_label == "user" || type_label == "xref" >
-        /**
-         * Set a pretty label for cross reference ${JavaName(field)} to <a href="${JavaName(field.getXRefEntity())}.html#${JavaName(field.getXRefField())}">${JavaName(field.getXRefEntity())}.${JavaName(field.getXRefField())}</a>.
-         */
-        public void set${JavaName(field)}Label(String label)
-        {
-                _${name(field)}_label = label;
-                //deprecates the object cache
-                _${name(field)}_object = null;
-        }
-        <#elseif type_label="mref">
-        public void set${JavaName(field)}Labels(java.util.List<String> labels)
-        {
-                _${name(field)}_labels = labels;
-                //deprecates the object cache
+                return  _${name(field)}_${label};
+        }
+        
+        public void set${JavaName(field)}_${label}(java.util.List<String> ${name(field)}_${label})
+        {
+                _${name(field)}_${label} = ${name(field)}_${label};
+                //clear the object cache
                 _${name(field)}_objects = null;
-        }       
-        </#if>  
-
-        <#if type_label == "file"  || type_label=="image" >
+        }               
+</#list></#if>          
+        
+        <#elseif type_label == "file"  || type_label=="image" >
         /**
          * get${JavaName(field)}() is a textual pointer to a file. get${JavaName(field)}AttachedFile() can be used to retrieve the full paht to this file.
@@ -357 +354 @@
                 _${name(field)}_file = file;
         }
-                </#if>
-<#--</#if>      -->
-        </#foreach>     
+        </#if>
+
+</#foreach>     
 
         /**
@@ -370 +367 @@
                 if (name.toLowerCase().equals("${name(field)?lower_case}"))
                         return get${JavaName(field)}();
-                <#if field.type == "xref" || field.type == "enum" >     
-                if(name.toLowerCase().equals("${name(field)?lower_case}_${name(field.getXRefLabelString())?lower_case}"))
+                <#if field.type == "enum" >     
+                if(name.toLowerCase().equals("${name(field)?lower_case}_label"))
                         return get${JavaName(field)}Label();
-                </#if>
-                <#if field.type == "mref">
-                if(name.toLowerCase().equals("${name(field)?lower_case}_${name(field.getXRefLabelString())?lower_case}"))
-                        return get${JavaName(field)}Labels();           
+                <#elseif field.type == "xref" || field.type == "mref">
+<#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>       
+                if(name.toLowerCase().equals("${name(field)?lower_case}_${label?lower_case}"))
+                        return get${JavaName(field)}_${label}();
+</#list></#if>                  
                 </#if>
         </#foreach>             
@@ -413 +411 @@
                 </#if>                  
                 <#if f.type == "xref">                  
-                        //set label for field ${JavaName(f)}
-                        this.set${JavaName(f)}Label(tuple.getString("${name(f)}_${name(f.getXRefLabelString())}"));                             
+                        <#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>           
+                        //set label ${label} for xref field ${JavaName(f)}
+                        this.set${JavaName(f)}_${label}(tuple.getString("${name(f)}_${name(label)}"));  
+                        </#list></#if>                  
                 </#if>                          
                 </#if>
@@ -438 +438 @@
                                 this.set${JavaName(f)}( values );                       
                         }
-                        //set label for field ${JavaName(f)}    
-                        if( tuple.getObject("${name(f)}_${name(f.getXRefLabelString())}")!= null ) 
+                        <#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>
+                        //set labels ${label} for mref field ${JavaName(f)}     
+                        if( tuple.getObject("${name(f)}_${name(label)}")!= null ) 
                         {
                                 java.util.List<String> values = new ArrayList<String>();
-                                java.util.List<Object> mrefs = tuple.getList("${name(f)}_${name(f.getXRefLabelString())}");
+                                java.util.List<Object> mrefs = tuple.getList("${name(f)}_${name(label)}");
                                 if(mrefs != null) for(Object ref: mrefs)
                                 {
                                         values.add(ref.toString());
                                 }                                                       
-                                this.set${JavaName(f)}Labels( values );                 
-                        }                                               
-                        <#elseif f.name?lower_case != "type" || !entity.hasAncestor()>
+                                this.set${JavaName(f)}_${label}( values );                      
+                        }       
+                        </#list></#if>                                  
+                <#elseif f.name?lower_case != "type" || !entity.hasAncestor()>
                         //set ${JavaName(f)}
                         <#if f.type == "xref">  
-                        if( strict || tuple.get${settertype(f)}("${name(f)}_${name(f.getXRefField())}") != null) this.set${JavaName(f)}(tuple.get${settertype(f)}("${name(f)}_${name(f.getXRefField())}"));             
-                        if( tuple.get${settertype(f)}("${name(entity)}.${name(f)}_${name(f.getXRefField())}") != null) this.set${JavaName(f)}(tuple.get${settertype(f)}("${name(entity)}.${name(f)}_${name(f.getXRefField())}"));
+                        if( strict || tuple.get${settertype(f)}("${name(f)}_${name(f.xrefField)}") != null) this.set${JavaName(f)}(tuple.get${settertype(f)}("${name(f)}_${name(f.xrefField)}"));               
+                        if( tuple.get${settertype(f)}("${name(entity)}.${name(f)}_${name(f.xrefField)}") != null) this.set${JavaName(f)}(tuple.get${settertype(f)}("${name(entity)}.${name(f)}_${name(f.xrefField)}"));
                         //alias of xref
                         if( tuple.getObject("${name(f)}") != null) this.set${JavaName(f)}(tuple.get${settertype(f)}("${name(f)}"));
                         if( tuple.getObject("${name(entity)}.${name(f)}") != null) this.set${JavaName(f)}(tuple.get${settertype(f)}("${name(entity)}.${name(f)}"));
                         //set label for field ${JavaName(f)}
-                        if( strict || tuple.getObject("${name(f)}_${name(f.getXRefLabelString())}") != null) this.set${JavaName(f)}Label(tuple.getString("${name(f)}_${name(f.getXRefLabelString())}"));                        
-                        if( tuple.getObject("${name(entity)}.${name(f)}_${name(f.getXRefLabelString())}") != null ) this.set${JavaName(f)}Label(tuple.getString("${name(entity)}.${name(f)}_${name(f.getXRefLabelString())}"));                         
+                                <#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>
+                        if( strict || tuple.getObject("${name(f)}_${name(label)}") != null) this.set${JavaName(f)}_${label}(tuple.getString("${name(f)}_${name(label)}"));                      
+                        if( tuple.getObject("${name(entity)}.${name(f)}_${name(label)}") != null ) this.set${JavaName(f)}_${label}(tuple.getString("${name(entity)}.${name(f)}_${name(label)}"));                               
+                                </#list></#if>
                         <#elseif f.type == "nsequence">
                         if( strict || tuple.getNSequence("${name(f)}") != null)this.set${JavaName(f)}(tuple.getNSequence("${name(f)}"));
@@ -496 +500 @@
                 <#else>
                 result+= "${name(field)}='" + get${JavaName(field)}()+"'<#if field_has_next> </#if>";
-                <#if field.type == "xref">
-                result+= " ${name(field)}_${name(field.getXRefLabelString())}='" + get${JavaName(field)}Label()+"' ";
-                </#if>
-                <#if field.type == "mref">
-                result+= " ${name(field)}_${name(field.getXRefLabelString())}='" + get${JavaName(field)}Labels()+"' ";
-                </#if>
-                <#--if field.type == "xref" || field.type == "enum">
-                if(verbose) result+= " ${name(field)}_options='" + get${JavaName(field)}Options()+"'<#if field_has_next> </#if>";
-                </#if-->
+                        <#if field.type == "xref" || field.type == "mref">
+                                <#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+                result+= " ${name(field)}_${name(label)}='" + get${JavaName(field)}_${label}()+"' ";
+                                </#list></#if>
+                        </#if>
                 </#if>
 </#list>
@@ -535 +535 @@
                 fields.add("${name(field)}");
                 <#if field.type="xref" || field.type="mref">
-                fields.add("${name(field)}_${name(field.getXRefLabelString())}");
+                        <#if field.xrefLabelNames[0] != field.xrefFieldName><#list field.xrefLabelNames as label>
+                fields.add("${name(field)}_${name(label)}");
+                        </#list></#if>
                 </#if>
         </#list>                

molgenis/3.3/src/org/molgenis/generators/R/REntityGen.R.ftl

@@ -42 +42 @@
                         
     <#list skey_fields as f><#if f.type == "xref">
-    <#assign session_var = ".MOLGENIS$session." + RName(f.getXRefEntity()) + "."+ RName(f.getXRefField())>
-    <#assign xref_entity = model.getEntity(f.getXRefEntity())>
+    <#assign session_var = ".MOLGENIS$session." + RName(f.xrefEntity) + "."+ RName(f.xrefField)>
+    <#assign xref_entity = f.xrefEntity>
     #add missing xref values from session parameters (optional)
-    if(.usesession && is.null(data_frame$${RName(f)}__${RName(f.getXRefField())}) && !is.null(${session_var}))    
+    if(.usesession && is.null(data_frame$${RName(f)}__${RName(f.xrefField)}) && !is.null(${session_var}))    
     {
         data_frame$${RName(f)} = ${session_var}
@@ -64 +64 @@
 
 #freely find ${JavaName(entity)} 
-find.${RName(entity)} <- function( <#list allFields(entity) as f><#if f.type="xref">${RName(f)}_${RName(f.getXRefField())}=NULL<#if f.getXRefLabelString()?exists && f.getXRefField() != f.getXRefLabelString()>, ${RName(f)}_${RName(f.getXRefLabelString())}=NULL</#if><#else>${RName(f)}=NULL</#if> <#if f_has_next>, </#if></#list>, .usesession = T, .verbose=T )
+find.${RName(entity)} <- function( <#list allFields(entity) as f><#if f.type="xref">${RName(f)}_${RName(f.xrefField)}=NULL<#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>, ${RName(f)}_${RName(label)}=NULL</#list></#if><#else>${RName(f)}=NULL</#if> <#if f_has_next>, </#if></#list>, .usesession = T, .verbose=T )
 {
         #add session parameters
     <#list skey_fields as f><#if f.type == "xref">
-    <#assign session_var = ".MOLGENIS$session." + RName(f.getXRefEntity()) + "."+ RName(f.getXRefField())>
-    <#assign xref_entity = model.getEntity(f.getXRefEntity())>
-    if(.usesession && is.null(${RName(f)}_${RName(f.getXRefField())}) && !is.null(${session_var}))    
+    <#assign session_var = ".MOLGENIS$session." + RName(f.xrefEntity) + "."+ RName(f.xrefField)>
+    <#assign xref_entity = f.xrefEntity>
+    if(.usesession && is.null(${RName(f)}_${RName(f.xrefField)}) && !is.null(${session_var}))    
     {
-        ${RName(f)}_${RName(f.getXRefField())} = ${session_var}
-        cat("Using ${RName(f)}_${RName(f.getXRefField())} (${RName(pkey(xref_entity))}='",${session_var},"'", sep="")
+        ${RName(f)}_${RName(f.xrefField)} = ${session_var}
+        cat("Using ${RName(f)}_${RName(f.xrefField)} (${RName(pkey(xref_entity))}='",${session_var},"'", sep="")
 <#list skeys(xref_entity) as skey><#list key_fields(skey) as f>        
                 cat(", ${RName(f)}='",.MOLGENIS$session.${RName(xref_entity)}.${RName(f)},"'", sep="")
@@ -91 +91 @@
 #add data.frame of ${JavaName(entity)} or each column individually
 #note: each column must have the same length
-add.${RName(entity)} <- function(.data_frame=NULL<#list allFields(entity) as f><#if f.type="xref">, ${RName(f)}_${RName(f.getXRefField())}=NULL<#if f.getXRefLabelString()?exists && f.getXRefField() != f.getXRefLabelString()>, ${RName(f)}_${RName(f.getXRefLabelString())}=NULL</#if><#elseif !f.auto>, ${RName(f)}=NULL</#if></#list>, .usesession = T, .verbose=T )
+add.${RName(entity)} <- function(.data_frame=NULL<#list allFields(entity) as f><#if f.type="xref">, ${RName(f)}_${RName(f.xrefField)}=NULL<#if f.type="xref">${RName(f)}_${RName(f.xrefField)}=NULL<#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>, ${RName(f)}_${RName(label)}=NULL</#list></#if></#if><#elseif !f.auto>, ${RName(f)}=NULL</#if></#list>, .usesession = T, .verbose=T )
 {
         .data_frame = .create.${RName(entity)}(.data_frame, mget(ls(),environment()), .usesession = .usesession, .verbose = .verbose)
@@ -111 +111 @@
         #add session parameters
     <#list skey_fields as f><#if f.type == "xref">
-    <#assign session_var = ".MOLGENIS$session." + RName(f.getXRefEntity()) + "."+ RName(f.getXRefField())>
-    <#assign xref_entity = model.getEntity(f.getXRefEntity())>
+    <#assign session_var = ".MOLGENIS$session." + RName(f.xrefEntity) + "."+ RName(f.xrefField)>
+    <#assign xref_entity = f.xrefEntity>
     if(is.null(${RName(f)}) && !is.null(${session_var}))    
     {

molgenis/3.3/src/org/molgenis/generators/csv/CsvReaderGen.java.ftl

@@ -46 +46 @@
 <#list allFields(entity) as f>
         <#if f.type=="xref" || f.type=="mref">
-        <#assign xref_entity = model.getEntity(f.getXRefEntity())>
+        <#assign xref_entity = f.xrefEntity>
 ${imports(model, xref_entity, "")}
         </#if>
@@ -57 +57 @@
 {
         <#assign has_xrefs=false />
-        <#list allFields(entity) as f><#if (f.type == 'xref' || f.type == 'mref') && f.getXRefLabelString() != f.getXRefField()><#assign has_xrefs=true>
-        //foreign key map for field '${name(f)}' (${name(f.getXRefEntity())}.${name(f.getXRefLabelString())} -> ${name(f.getXRefEntity())}.${name(f.getXRefField())})                   
+        <#list allFields(entity) as f><#if (f.type == 'xref' || f.type == 'mref') && f.getXrefLabelNames()[0] != f.xrefFieldName><#assign has_xrefs=true>
+        //foreign key map for field '${name(f)}' (${name(f.xrefEntity)}.${csv(f.xrefLabelNames)} -> ${name(f.xrefEntity)}.${name(f.xrefField)})                 
         final Map<String,Integer> ${name(f)}Keymap = new TreeMap<String,Integer>();
         </#if></#list>  
@@ -69 +69 @@
                 //cache for imported objects
                 final List<${JavaName(entity)}> ${name(entity)}List = new ArrayList<${JavaName(entity)}>(BATCH_SIZE);
-                                final IntegerWrapper total = new IntegerWrapper(0);
+                final IntegerWrapper total = new IntegerWrapper(0);
                 reader.setMissingValues(missingValues);
                 reader.parse(new CsvReaderListener()
@@ -81 +81 @@
                                 object.set(tuple, false);                               
                                 //only override values that have been set.
-                                ${name(entity)}List.add(object);
-                                <#--need proper secundary key usage!-->
-                                <#list allFields(entity) as f><#if (f.type == 'xref') && f.getXRefLabelString() != f.getXRefField()>
-                                //foreign key '${name(f)}' (${name(f.getXRefEntity())}.${name(f.getXRefLabelString())} -> ?)
-                                if(object.get${JavaName(f)}Label() != null) ${name(f)}Keymap.put(object.get${JavaName(f)}Label(), null);        
-                                </#if><#if (f.type == 'mref') && f.getXRefLabelString() != f.getXRefField()>
-                                if(object.get${JavaName(f)}Labels() != null) for(String mref_label: object.get${JavaName(f)}Labels()) ${name(f)}Keymap.put(mref_label, null);   
-                                </#if></#list>                                  
+                                ${name(entity)}List.add(object);                
                                 
                                 //add in batches
@@ -94 +87 @@
                                 {
                                         //resolve foreign keys
-                                        resolveForeignKeys(db, ${name(entity)}List);
+                                        //is this not done elsewhere already? resolveForeignKeys(db, ${name(entity)}List);
                                         
                                         <#if entity.xref_label?exists>
-                                        //update objects in the database using secundary key '${entity.xrefLabel}' defined in xref_label
-                                        db.update(${name(entity)}List,dbAction,"${entity.xref_label}");
+                                        //update objects in the database using secundary key(s) '${csv(entity.xrefLabelNames)}' defined in xref_label
+                                        db.update(${name(entity)}List,dbAction, "${entity.xref_label}");
                                         <#elseif entity.getAllKeys()?size &gt; 1>
                                         //update objects in the database using secundary key(<#list entity.getAllKeys()[1].fields as field><#if field_index != 0>,</#if>${field.name}</#list>) '${entity.getAllKeys()[1].fields[0].name}'
@@ -117 +110 @@
                 if(!${name(entity)}List.isEmpty()){
                         //resolve remaing foreign keys
-                        resolveForeignKeys(db, ${name(entity)}List);
+                        //is this not done in mapper? resolveForeignKeys(db, ${name(entity)}List);
                         <#if entity.xref_label?exists>
                         //update objects in the database using secundary key '${entity.xrefLabel}' defined in xref_label
@@ -137 +130 @@
         }       
         
-        private void resolveForeignKeys(Database db, List<${JavaName(entity)}> ${name(entity)}List) throws Exception
+<#--    private void resolveForeignKeys(Database db, List<${JavaName(entity)}> ${name(entity)}List) throws Exception
         {
-                <#list allFields(entity) as f><#if (f.type == 'xref' || f.type == 'mref') && f.getXRefLabelString() != f.getXRefField()>
-                //resolve foreign key '${name(f)}' xref_labels to id (${name(f.getXRefEntity())}.${name(f.getXRefLabelString())} -> ${name(f.getXRefEntity())}.${name(f.getXRefField())})
+                <#list allFields(entity) as f><#if (f.type == 'xref' || f.type == 'mref') && f.xrefLabels[0] != f.getXRefField()>
+                //resolve foreign key '${name(f)}' xref_labels to id (${name(f.getXRefEntity())}.${csv(f.getXRefLabelString())} -> ${name(f.getXRefEntity())}.${name(f.getXRefField())})
+                
+                /
+                
                 List<${JavaName(f.XRefEntity)}> ${name(f)}List = db.query(${JavaName(f.getXRefEntity())}.class).in("${f.getXRefLabelString()}",new ArrayList<Object>(${name(f)}Keymap.keySet())).find();
                 for(${JavaName(f.XRefEntity)} xref :  ${name(f)}List)
@@ -175 +171 @@
                 ${name(f)}Keymap.clear();
                 </#if></#list>  
-        }
+        }-->
 }
 

molgenis/3.3/src/org/molgenis/generators/db/JDBCDatabaseGen.java.ftl

@@ -23 +23 @@
 import javax.sql.DataSource;
 
+import org.molgenis.MolgenisOptions;
 import org.molgenis.framework.db.DatabaseException;
 import org.molgenis.framework.db.jdbc.DataSourceWrapper;
@@ -45 +46 @@
                 this.setup();
         }
+        
+        public JDBCDatabase(MolgenisOptions options)
+        {
+                super(options);
+                this.setup();
+        }
+        
+        public JDBCDatabase()
+        {
+                super(new MolgenisOptions());
+                this.setup();
+        }
 
         public JDBCDatabase(String propertiesFilePath) throws FileNotFoundException, IOException, DatabaseException

molgenis/3.3/src/org/molgenis/generators/db/JDBCMetaDatabaseGen.java.ftl

@@ -29 +29 @@
 package ${package};
 
+import java.util.Arrays;
+
 import org.molgenis.framework.db.DatabaseException;
 import org.molgenis.model.elements.Entity;
@@ -56 +58 @@
                         <#list entity.getFields() as field><#if field.name?lower_case != "type">
                         Field ${name(entity)}_${name(field)}_field = new Field(${name(entity)}_entity, "${field.name}", Field.Type.getType("${field.type}"));
-                        <#if field.type == "xref" || field.type == "mref">${name(entity)}_${name(field)}_field.setXRefVariables("${field.XRefEntity}", "${field.XRefField}","${field.XRefLabelString}");</#if>
+                        <#if field.auto>
+                        ${name(entity)}_${name(field)}_field.setAuto(true);
+                        </#if>
+                        <#if field.type == "xref" || field.type == "mref">${name(entity)}_${name(field)}_field.setXRefVariables("${field.xrefEntityName}", "${field.xrefFieldName}",Arrays.asList(new String[]{${csv(field.xrefLabelNames)}}));</#if>
                         ${name(entity)}_entity.addField(${name(entity)}_${name(field)}_field);
                         </#if></#list>
@@ -63 +68 @@
                         </#list></#if></#list>
                         
-                        <#list entities as entity><#if !entity.abstract>
+                        <#list entities as entity><#if !entity.abstract && !entity.association>
                         Entity ${name(entity)}_entity = new Entity("${entity.name}",this.getDatabase());<#if entity.hasImplements()>
                         ${name(entity)}_entity.setImplements(new String[]{${csv(entity.implements)}});</#if><#if entity.hasAncestor()>
@@ -69 +74 @@
                         <#list entity.getFields() as field><#if field.name?lower_case != "type">
                         Field ${name(entity)}_${name(field)}_field = new Field(${name(entity)}_entity, "${field.name}", Field.Type.getType("${field.type}"));
-                        <#if field.type == "xref" || field.type == "mref">${name(entity)}_${name(field)}_field.setXRefVariables("${field.XRefEntity}", "${field.XRefField}","${field.XRefLabelString}");</#if>
+                        <#if field.auto>
+                        ${name(entity)}_${name(field)}_field.setAuto(true);
+                        </#if>
+                        <#if field.type == "xref" || field.type == "mref">${name(entity)}_${name(field)}_field.setXRefVariables("${field.xrefEntityName}", "${field.xrefFieldName}",Arrays.asList(new String[]{${csv(field.xrefLabelNames)}}));</#if>
                         ${name(entity)}_entity.addField(${name(entity)}_${name(field)}_field);
                         </#if></#list>

molgenis/3.3/src/org/molgenis/generators/db/MapperCommons.subclass_per_table.java.ftl

@@ -40 +40 @@
                 return "SELECT <#list viewFields(entity) as f>${SqlName(f.entity)}.${SqlName(f)}<#if f_has_next>"
                           +", </#if></#list>"<#list viewFields(entity,"xref") as f>
-                          +", xref${f_index}.${SqlName(f.getXRefLabelString())} AS ${SqlName(f)}_${SqlName(f.getXRefLabelString())}"</#list>
+                          <#list f.xrefLabelNames as label>+", xref${f_index}.${SqlName(label)} AS ${SqlName(f)}_${SqlName(label)}"
+                          </#list></#list>
                           +" FROM ${SqlName(entity)} "<#list superclasses(entity)?reverse as superclass><#if name(superclass) != name(entity)>
                           +" INNER JOIN ${SqlName(superclass)} ON (${SqlName(entity)}.${SqlName(pkey(entity))} = ${SqlName(superclass)}.${SqlName(pkey(entity))})"</#if></#list>
                           <#list viewFields(entity,"xref") as f>
-                          <#assign xref_entity = model.getEntity(f.getXRefEntity())/> 
-                          <#assign xref_field = xref_entity.getField(f.getXRefField())/>
-                          <#assign xref_label = xref_entity.getAllField(f.getXRefLabelString()) /><#--can be from supertype!!-->
-                          <#if name(xref_field.entity) != name(xref_label.entity)>+" LEFT JOIN ${SqlName(xref_label.entity)} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"
-                          <#else>+" LEFT JOIN ${SqlName(f.getXRefEntity())} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"</#if></#list>;
+                          <#assign xref_entity = f.xrefEntity /> 
+                          <#assign xref_field = f.xrefField />
+                          <#list f.xrefLabels as labelField><#--can be from supertype!!-->
+                          <#if name(xref_field.entity) != name(labelField.entity)>+" LEFT JOIN ${SqlName(labelField.entity)} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"
+                          <#else>+" LEFT JOIN ${SqlName(f.xrefEntity)} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"</#if></#list></#list>;
         }       
 
@@ -56 +57 @@
                           +" FROM ${SqlName(entity)} "<#list superclasses(entity)?reverse as superclass><#if name(superclass) != name(entity)>
                           +" INNER JOIN ${SqlName(superclass)} ON (${SqlName(entity)}.${SqlName(pkey(entity))} = ${SqlName(superclass)}.${SqlName(pkey(entity))})"</#if></#list><#list viewFields(entity,"xref") as f>
-                          <#assign xref_entity = model.getEntity(f.getXRefEntity())/> 
-                          <#assign xref_field = xref_entity.getField(f.getXRefField())/>
-                          <#assign xref_label = xref_entity.getAllField(f.getXRefLabelString()) /><#--can be from supertype!!-->
-                          <#if name(xref_field.entity) != name(xref_label.entity)>+" LEFT JOIN ${SqlName(xref_label.entity)} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"
-                          <#else>+" LEFT JOIN ${SqlName(f.getXRefEntity())} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"</#if></#list>;
+                          <#assign xref_entity = f.xrefEntity/> 
+                          <#assign xref_field = f.xrefField/>
+                          <#list f.xrefLabels as labelField><#--can be from supertype!!-->
+                          <#if name(xref_field.entity) != name(labelField.entity)>+" LEFT JOIN ${SqlName(labelField.entity)} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"
+                          <#else>+" LEFT JOIN ${SqlName(f.xrefEntity)} AS xref${f_index} ON ${SqlName(f.getEntity())}.${SqlName(f)}=xref${f_index}.${SqlName(xref_field)}"</#if></#list></#list>;
         }
         
@@ -71 +72 @@
                 </#list>        
                 <#list viewFields(entity,"xref") as f>          
-                <#assign xref_entity = model.getEntity(f.getXRefEntity())/> 
-                <#assign xref_field = xref_entity.getField(f.getXRefField())/>
-                <#assign xref_label = xref_entity.getAllField(f.getXRefLabelString()) /><#--can be from supertype!!-->
+                <#assign xref_entity = f.xrefEntity/> 
+                <#assign xref_field = f.xrefField/>
                 //alias for query on id field of xref entity
                 if("${name(f)}_${name(xref_field)}".equalsIgnoreCase(fieldName)) return "${SqlName(f.entity)}.${SqlName(f)}";
-                //alias for query on label of the xref entity
-                if("${name(f)}_${name(xref_label)}".equalsIgnoreCase(fieldName)) return "xref${f_index}.${SqlName(xref_label)}";
+                //alias(es) for query on label of the xref entity
+                        <#list f.xrefLabelNames as label>
+                if("${name(f)}_${name(label)}".equalsIgnoreCase(fieldName)) return "xref${f_index}.${SqlName(label)}";
+                        </#list>
                 </#list>                                
                 return fieldName;
@@ -88 +90 @@
                 <#assign type= f.type>
                 <#if type == "user" || type == "xref" || type == "mref">                
-                <#assign type = model.getEntity(f.getXRefEntity()).getField(f.getXRefField()).getType()/>
+                <#assign type = f.xrefField.type/>
                 if("${name(f)}".equalsIgnoreCase(fieldName) || "${name(f.entity)}.${name(f)}".equalsIgnoreCase(fieldName)) return Type.${type?upper_case};
                 if("${name(f)}_${name(xref_label)}".equalsIgnoreCase(fieldName) || "${name(f.entity)}.${name(f)}_${name(xref_label)}".equalsIgnoreCase(fieldName)) return Type.STRING;
@@ -102 +104 @@
         {
 <#assign has_xrefs=false>               
-<#list allFields(entity) as f><#if f.type == 'xref' && f.getXRefLabelString() != f.getXRefField()><#assign has_xrefs=true>      
-                //create foreign key map for field '${name(f)}' (${name(f.getXRefEntity())}.${name(f.getXRefLabelString())} -> ${name(f.getXRefEntity())}.${name(f.getXRefField())})                    
-                final java.util.Map<String,Integer> ${name(f)}Keymap = new java.util.TreeMap<String,Integer>();
+<#list allFields(entity) as f><#if f.type == 'xref' &&   f.xrefLabelNames[0] != f.xrefFieldName><#assign has_xrefs=true>        
+                //create foreign key map for field '${name(f)}' to ${name(f.xrefEntity)}.${name(f.xrefField)} using ${csv(f.xrefLabelNames)})   
+                //we will use a hash of the values to ensure that entities are only queried once        
+                final java.util.Map<String,QueryRule> ${name(f)}Rules = new java.util.TreeMap<String,QueryRule>();
 </#if></#list>  
 <#if has_xrefs>         
-                //find all keys to be mapped    
+                //create all query rules        
                 for(${JavaName(entity)} object: entities)
                 {
-<#list allFields(entity) as f><#if f.type == 'xref' && f.getXRefLabelString() != f.getXRefField()>
-                        //foreign key '${name(f)}' (${name(f.getXRefEntity())}.${name(f.getXRefLabelString())} -> ?)
-                        if(object.get${JavaName(f)}Label() != null) ${name(f)}Keymap.put(object.get${JavaName(f)}Label(), null);        
+<#list allFields(entity) as f><#if f.type == 'xref' && f.xrefLabelNames[0] != f.xrefFieldName>
+                <#if f.xrefLabelNames?size &gt; 1>
+                        //create xref rule filtering on the combination of labels ${csv(f.xrefLabelNames)}
+                        {
+                                List<QueryRule> rules = new ArrayList<QueryRule>();
+                                String key = "";
+                                <#list f.xrefLabelNames as label>
+                                rules.add(new QueryRule("${f.name}_${label}", Operator.EQUALS, object.get${JavaName(f)}_${label}()));   
+                                key +=  object.get${JavaName(f)}_${label}();
+                                </#list>                        
+                                QueryRule complexRule = new QueryRule(rules);
+                                nestedRule.or(true);
+                                ${name(f)}Rules.put(key, nestedRule);
+                        }
+                <#else>
+                        //create xref rule filtering on the label ${csv(f.xrefLabelNames)}
+                        {
+                                QueryRule xrefFilter = new QueryRule("${f.name}_${f.xrefLabelNames[0]}", Operator.EQUALS, object.get${JavaName(f)}_${f.xrefLabelNames[0]}());
+                                xrefFilter.setOr(true);
+                                ${name(f)}Rules.put(object.get${JavaName(f)}_${f.xrefLabelNames[0]}(), xrefFilter);
+                        }
+                </#if>  
 </#if></#list>
                 }
 
-<#list allFields(entity) as f><#if f.type == 'xref' && f.getXRefLabelString() != f.getXRefField()>
-                //resolve foreign key '${name(f)}' (${name(f.getXRefEntity())}.${name(f.getXRefLabelString())} -> ${name(f.getXRefEntity())}.${name(f.getXRefField())})
-                List<${JavaName(f.XRefEntity)}> ${name(f)}List = getDatabase().query(${JavaName(f.getXRefEntity())}.class).in("${f.getXRefLabelString()}",new ArrayList<Object>(${name(f)}Keymap.keySet())).find();
-                for(${JavaName(f.XRefEntity)} xref :  ${name(f)}List)
-                {
-                        ${name(f)}Keymap.put(xref.get${JavaName(f.getXRefLabelString())}().toString(), xref.get${JavaName(f.getXRefField())}());
-                }               
+<#list allFields(entity) as f><#if f.type == 'xref' && f.xrefLabelNames[0] != f.xrefFieldName>
+                //resolve foreign key field '${name(f)}' to ${name(f.xrefEntity)}.${name(f.xrefField)} using ${csv(f.xrefLabelNames)})
+                final java.util.Map<String,Integer> ${name(f)}_Labels_to_IdMap = new java.util.TreeMap<String,Integer>();
+                <#list f.xrefLabelNames as label>
+                
+                List<${JavaName(f.xrefEntity)}> ${name(f)}List = getDatabase().find(${JavaName(f.xrefEntity)}.class, (QueryRule[])${name(f)}Rules.values().toArray());
+                for(${JavaName(f.xrefEntity)} xref :  ${name(f)}List)
+                {
+                        String key = "";
+                        <#list f.xrefLabelNames as label>
+                        key +=  xref.get${JavaName(label)}();
+                        </#list>                
+                        ${name(f)}_Labels_to_IdMap.put(key, xref.get${JavaName(f.xrefField)}());
+                }
+                </#list>                
 </#if></#list>
 
@@ -129 +159 @@
                 {
                         ${JavaName(entity)} object = entities.get(i);           
-                        <#list allFields(entity) as f><#if f.type == 'xref'  && f.getXRefLabelString() != f.getXRefField()>
-                        if(object.get${JavaName(f)}Label() != null) 
-                        {
-                                if(${name(f)}Keymap.get(object.get${JavaName(f)}Label()) == null) throw new DatabaseException("Cannot find ${f.getXRefEntity()} for ${name(f)}_${name(f.getXRefLabelString())} '"+object.get${JavaName(f)}Label()+"'");
-                                object.set${JavaName(f)}(${name(f)}Keymap.get(object.get${JavaName(f)}Label()));
+                        <#list allFields(entity) as f><#if f.type == 'xref'  && f.xrefLabelNames[0] != f.xrefFieldName>
+                        //update object using label fields ${csv(f.xrefLabelNames)}
+                        {
+                                String key = "";
+                                <#list f.xrefLabelNames as label>
+                                key +=  object.get${JavaName(f)}_${label}();
+                                object.set${JavaName(f)}(${name(f)}_Labels_to_IdMap.get(key));
+                                </#list>
                         }
                         </#if></#list>  
-                        entities.set(i, object);                                                        
+                                                
                 }
 </#if>          
@@ -172 +205 @@
                         }                       
                 }
-                else if("${field.name}_${field.getXRefLabelString()}".equalsIgnoreCase(rule.getField()))
+                <#list field.xrefLabelNames as label>
+                else if("${field.name}_${label}".equalsIgnoreCase(rule.getField()))
                 {
                         // replace with id filter based on the many-to-many links in
                         // ${field.getMrefName()}
                         List<${JavaName(field.getMrefName())}> mref_mapping_entities = db.find(${JavaName(field.getMrefName())}.class, new QueryRule(
-                                        "${SqlName(field.getXRefEntity())}_${SqlName(field.getXRefLabelString())}", rule.getOperator(), rule.getValue()));
+                                        "${SqlName(field.xrefEntity)}_${SqlName(label)}", rule.getOperator(), rule.getValue()));
                         if (mref_mapping_entities.size() > 0)
                         {
@@ -190 +224 @@
                         }
                 }
+                </#list>
                 <#assign else = true>                           
                 </#if>

molgenis/3.3/src/org/molgenis/generators/db/MapperMrefs.java.ftl

@@ -24 +24 @@
                                 //assign ids
                                 List<Integer> ids = new ArrayList<Integer>();
-                                List<String> labels = new ArrayList<String>();
+                                <#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>
+                                List<String> ${label}List = new ArrayList<String>();
+                                </#list></#if>
                                 for(${JavaName(mref_entity)} ref: existing_mrefs)
                                 {
                                         ids.add(ref.get${JavaName(mref_remote_field)}());
-                                        labels.add(ref.get${JavaName(mref_remote_field)}Label());
+                                        <#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>
+                                        ${label}List.add(ref.get${JavaName(mref_remote_field)}_${label}());
+                                        </#list></#if>
                                 }       
                                 entity.set${JavaName(f)}(ids);
-                                entity.set${JavaName(f)}Labels(labels);
-                                //put it back (grrr)
-                                entities.set(i,entity);                         
+                                <#if f.xrefLabelNames[0] != f.xrefFieldName><#list f.xrefLabelNames as label>
+                                entity.set${JavaName(f)}_${label}(${label}List);
+                                </#list></#if>                  
                         }
                 }
@@ -54 +58 @@
                         {
                                 //retrieve currently known mrefs
-                                QueryRule rule = new QueryRule( "${name(mref_local_field)}", QueryRule.Operator.EQUALS, entity.get${JavaName(f)}() );
-                                List<${mref_entity}> existing_mrefs = getDatabase().find( ${mref_entity}.class, rule );
+                                QueryRule rule = new QueryRule( "${mref_local_field}", QueryRule.Operator.EQUALS, entity.get${JavaName(pkey(entity))}() );
+                                List<${JavaName(mref_entity)}> existing_mrefs = getDatabase().find( ${JavaName(mref_entity)}.class, rule );
 
                                 // check for removals
@@ -71 +75 @@
                                 for (Integer ref : entity.get${JavaName(f)}())
                                 {
-
-                                        ${mref_entity} new_mref = new ${mref_entity}();
-                                        new_mref.set${JavaName(mref_local_field)}( entity.get${JavaName(pkey(entity))}() );
-                                        new_mref.set${JavaName(mref_remote_field)}( ref );
-                                        if (!existing_mrefs.contains( new_mref ))
+                                        if(!existing_ids.contains(ref))
                                         {
-                                                ${JavaName(mref_entity)} new_mref1 = new ${JavaName(mref_entity)}();
-                                                new_mref1.set${JavaName(mref_local_field)}( entity.get${JavaName(pkey(entity))}() );
-                                                new_mref1.set${JavaName(mref_remote_field)}( ref );
-                                                toAdd.add( new_mref1 );
+                                                ${JavaName(mref_entity)} new_mref = new ${JavaName(mref_entity)}();
+                                                new_mref.set${JavaName(mref_local_field)}( entity.get${JavaName(pkey(entity))}() );
+                                                new_mref.set${JavaName(mref_remote_field)}( ref );
+                                                toAdd.add( new_mref );
                                         }
                                 }
@@ -105 +105 @@
                         {
                                 //retrieve currently known mrefs
-                                QueryRule rule = new QueryRule( "${name(mref_local_field)}", QueryRule.Operator.EQUALS, entity.get${JavaName(f)}() );
-                                List<${mref_entity}> existing_mrefs = getDatabase().find( ${mref_entity}.class, rule );
+                                QueryRule rule = new QueryRule( "${name(mref_local_field)}", QueryRule.Operator.EQUALS, entity.get${JavaName(pkey(entity))}() );
+                                List<${JavaName(mref_entity)}> existing_mrefs = getDatabase().find( ${JavaName(mref_entity)}.class, rule );
 
                                 // check for removals

molgenis/3.3/src/org/molgenis/generators/db/MultiqueryMapperGen.java.ftl

@@ -60 +60 @@
 <#list entity.getAllFields() as f>
         <#if f.type=="xref" || f.type=="mref">
-                <#assign xref_entity = model.getEntity(f.getXRefEntity())> 
+                <#assign xref_entity = f.xrefEntity> 
 import ${xref_entity.getNamespace()}.${JavaName(xref_entity)};
                 <#if f.type=="mref"><#assign mref_entity = model.getEntity(f.mrefName)>

molgenis/3.3/src/org/molgenis/generators/doc/DotDocGen.java.ftl

@@ -62 +62 @@
                                         </#if>
                 
-                        label = "{<#if entity.abstract>Interface:</#if>${JavaName(entity)}<#if entity.hasImplements()>\n implements ${csv(entity.getImplements())}</#if><#if entity.hasAncestor()>\n extends ${name(entity.getAncestor())}</#if>|<#list entity.implementedFields as f><#if !f.system>${name(f)} : ${f.type}<#if f.type=="xref" || f.type="mref">-&gt;${name(f.getXRefEntity())}</#if><#if !f.nillable>*</#if>\l</#if></#list>}"
+                        label = "{<#if entity.abstract>Interface:</#if>${JavaName(entity)}<#if entity.hasImplements()>\n implements ${csv(entity.getImplements())}</#if><#if entity.hasAncestor()>\n extends ${name(entity.getAncestor())}</#if>|<#list entity.implementedFields as f><#if !f.system>${name(f)} : ${f.type}<#if f.type=="xref" || f.type="mref">-&gt;${name(f.xrefEntity)}</#if><#if !f.nillable>*</#if>\l</#if></#list>}"
                 ]
 
@@ -93 +93 @@
                                         </#if>
                 
-                        label = "{<#if entity.abstract>Interface:</#if>${JavaName(entity)}<#if entity.hasImplements()>\n implements ${csv(entity.getImplements())}</#if><#if entity.hasAncestor()>\n extends ${name(entity.getAncestor())}</#if>|<#list entity.implementedFields as f><#if !f.system>${name(f)} : ${f.type}<#if f.type=="xref" || f.type="mref">-&gt;${name(f.getXRefEntity())}</#if><#if !f.nillable>*</#if>\l</#if></#list>}"
+                        label = "{<#if entity.abstract>Interface:</#if>${JavaName(entity)}<#if entity.hasImplements()>\n implements ${csv(entity.getImplements())}</#if><#if entity.hasAncestor()>\n extends ${name(entity.getAncestor())}</#if>|<#list entity.implementedFields as f><#if !f.system>${name(f)} : ${f.type}<#if f.type=="xref" || f.type="mref">-&gt;${name(f.xrefEntity)}</#if><#if !f.nillable>*</#if>\l</#if></#list>}"
                 ]
 </#if></#list>
@@ -131 +131 @@
                 <#list entity.fields as f>
                         <#if f.type=="xref">
-                "${JavaName(entity)}" -> "${JavaName(f.XRefEntity)}" [
+                "${JavaName(entity)}" -> "${JavaName(f.xrefEntity)}" [
                         headlabel = "<#if f.nillable>0..</#if>1"
                         taillabel = "*"
@@ -156 +156 @@
                 <#list entity.fields as f >
                         <#if f.type=="mref">    
-                "${JavaName(f.XRefEntity)}" -> "${JavaName(entity)}"[
+                "${JavaName(f.xrefEntity)}" -> "${JavaName(entity)}"[
                         ]
                                         <#assign mref_names = mref_names + [f.getMrefName()]>

molgenis/3.3/src/org/molgenis/generators/doc/DotDocMinimalGen.java.ftl

@@ -113 +113 @@
         <#if !entity.system>
                 <#list entity.fields as f>
-                        <#if f.type=="xref" && entities?seq_contains(model.getEntity(f.getXRefEntity())) && !model.getEntity(f.getXRefEntity()).system>
-                "${name(entity)}" -> "${f.getXRefEntity()}"
+                        <#if f.type=="xref" && entities?seq_contains(f.xrefEntity) && !f.xrefEntity.system>
+                "${name(entity)}" -> "${f.xrefEntity}"
                         </#if>
                 </#list>
@@ -134 +134 @@
         <#if !entity.system>
                 <#list entity.fields as f >
-                        <#if f.type=="mref" && entities?seq_contains(model.getEntity(f.getXRefEntity())) && !model.getEntity(f.getXRefEntity()).system> 
+                        <#if f.type=="mref" && entities?seq_contains(f.xrefEntity) && !f.xrefEntity.system>     
                                 <#if !mref_names?seq_contains(f.getMrefName())>
-                "${f.getXRefEntity()}" -> "${name(entity)}"
+                "${f.xrefEntity}" -> "${name(entity)}"
                                         <#assign mref_names = mref_names + [f.getMrefName()]>
                                 </#if>  

molgenis/3.3/src/org/molgenis/generators/doc/EntityModelDocGen.java.ftl

@@ -40 +40 @@
                 <td ${color}>
 <#if field.type=="xref">
-references(${field.getXRefEntity()}.${field.getXRefField()}),
+references(${field.xrefEntityName}.${field.xrefFieldName}),
 <#elseif field.type=="mref">
-references-many(${field.getXRefEntity()}.${field.getXRefField()}),</#if>
+references-many(${field.xrefEntityName}.${field.xrefFieldName}),</#if>
 <#if field.isNillable()><#else>not null, </#if>
 <#if field.isAuto()>auto, <#else></#if>

molgenis/3.3/src/org/molgenis/generators/doc/FileFormatDocGen.java.ftl

@@ +1 @@
+<#include "GeneratorHelper.ftl">
 <#function csv items>
         <#local result = "">
@@ -16 +17 @@
 <#macro render_field field>
         <tr>
-                <td width="150">${field.name?lower_case}<#if field.type == "xref" || field.type =="mref">_${field.getXRefLabelString()?lower_case}</#if></td>
+                <td width="150">${field.name?lower_case}<#if field.type == "xref" || field.type =="mref">_${csv(field.xrefLabelNames)}</#if></td>
                 <td width="50">${field.type}</td>
                 <td width="20"><#if !field.isNillable() && !field.isAuto()>Y<#else>&nbsp;</#if></td>
-                <td><#if field.description != "">${field.description}.<br/></#if><#if field.type == "xref" || field.type =="mref"> Requires a matching value in column '${field.getXRefLabelString()?lower_case}' in <a href="#${field.getXRefEntity()}_entity">${field.getXRefEntity()?lower_case}.txt</a> for each reference 
+                <td><#if field.description != "">${field.description}.<br/></#if><#if field.type == "xref" || field.type =="mref"> Requires a matching value in column(s) '${csv(field.xrefLabelNames)?lower_case}' in <a href="#${name(field.xrefEntity)}_entity">${name(field.xrefEntity)}.txt</a> for each reference 
                 <#if field.type="mref">. <br/>More than one reference can be added separated by '|', for example: ref1|ref2|ref3.</#if></#if>.</td>
         </tr>   

molgenis/3.3/src/org/molgenis/generators/doc/ObjectModelDocGen.java.ftl

@@ -26 +26 @@
 <#assign attributes = false>
 <#assign inherited_attributes = false>
+<#assign unique_constraints = false>
 <#list entity.fields as field>
 <#if field.type == "xref" || field.type=="mref">
@@ -35 +36 @@
 <#list entity.inheritedFields as field>
 <#if !field.system><#assign inherited_attributes = true></#if>
+</#list>
+<#list entity.keys as key>
+<#assign unique_constraints= true>
 </#list>
 <#if inherited_attributes>
@@ -75 +79 @@
 <td ${color}>
 <b>${field.name}</b>: <#if field.type=="xref">
-${field.getXRefEntity()} (<#if field.nillable>0<#else>1</#if>..1)
+${field.xrefEntity.name} (<#if field.nillable>0<#else>1</#if>..1)
 <#elseif field.type=="mref">
-${field.getXRefEntity()} (<#if field.nillable>0<#else>1</#if>..n)</#if>
+${field.xrefEntity.name} (<#if field.nillable>0<#else>1</#if>..n)</#if>
 </td>
 </tr>
@@ -83 +87 @@
 </#if>
 </#list>
+</table>
+</#if>
+<#if unique_constraints>
+<p>
+<u>Constraints:</u>
+<table> 
+<#list entity.keys as key>
+<tr>
+<td ${color}>
+<b>unique(${csv(key.fields)})</b>: 
+</td>
+</tr>
+<tr><td style="padding-left: 50px;">
+<#if key.description?exists>${key.description}<#elseif key.fields?size &gt; 1>The combination of fields ${csv(key.fields)} is unique within an ${entity.name}<#else>Field ${csv(key.fields)} is unique within an ${entity.name}</#if>.
+</td></tr>
+</#list>
+</p>
 </table>
 </#if>

molgenis/3.3/src/org/molgenis/generators/doc/TableDocGen.java.ftl

@@ -102 +102 @@
                 ENUM options: ${csv( field.getEnumOptions() )}
 <#elseif field.type=="xref">
-                References(${field.getXRefEntity()})
+                References(${field.xrefEntityName})
 <#elseif field.type=="mref">
-                References(${field.getXRefEntity()}) via linktable.     
+                References(${field.xrefEntityName}) via linktable.      
 <#else>
                 &nbsp;

molgenis/3.3/src/org/molgenis/generators/doc/TextUmlGen.java.ftl

@@ -54 +54 @@
 
 association
-  navigable role ${field.name}: ${field.XRefField}[*];
+  navigable role ${field.name}: ${field.xrefField}[*];
   role : ${entity.name}[1]; 
 end;
@@ -60 +60 @@
 
 association
-  navigable role ${field.name}: ${field.XRefField}[*];
+  navigable role ${field.name}: ${field.xrefField}[*];
   role : ${entity.name}[*]; 
 end;

molgenis/3.3/src/org/molgenis/generators/fieldtypes/MrefField.java

@@ -10 +10 @@
         public String getJavaPropertyType() throws MolgenisModelException
         {
-                Entity e_ref = this.getEntityByName(f.getXRefEntity());
-                Field f_ref = e_ref.getField(f.getXRefField());
+                Entity e_ref = f.getXrefEntity();
+                Field f_ref = f.getXrefField();
                 return "java.util.List<"+getFieldType(f_ref).getJavaPropertyType()+">";
         }
@@ -18 +18 @@
         public String getJavaPropertyDefault() throws MolgenisModelException
         {
-                Entity e_ref = this.getEntityByName(f.getXRefEntity());
-                Field f_ref = e_ref.getField(f.getXRefField());
+                Entity e_ref = f.getXrefEntity();
+                Field f_ref = f.getXrefField();
                 //if(f.getDefaultValue() == null || f.getDefaultValue() == "") "new java.util.ArrayList<"+getFieldType(f_ref).getJavaPropertyType(f_ref)+">()";
                 //FIXME can there be defaults here?
@@ -28 +28 @@
         public String getJavaSetterType() throws MolgenisModelException
         {
-                Entity e_ref = this.getEntityByName(f.getXRefEntity());
-                Field f_ref = e_ref.getField(f.getXRefField());
+                Entity e_ref = f.getXrefEntity();
+                Field f_ref = f.getXrefField();
                 return "new java.util.ArrayList<"+getFieldType(f_ref).getJavaSetterType()+">()";
         }
@@ -37 +37 @@
         {
                 //FIXME this function should be never called???
-                return getFieldType(getEntityByName(f.getXRefEntity()).getField(f.getXRefField())).getMysqlType();
+                return getFieldType(f.getXrefField()).getMysqlType();
         }
 
@@ -43 +43 @@
         public String getHsqlType() throws MolgenisModelException
         {
-                return getFieldType(getEntityByName(f.getXRefEntity()).getField(f.getXRefField())).getHsqlType();
+                return getFieldType(f.getXrefField()).getHsqlType();
         }
 

molgenis/3.3/src/org/molgenis/generators/fieldtypes/XrefField.java

@@ -11 +11 @@
         public String getJavaPropertyType() throws MolgenisModelException
         {
-                Entity e_ref = this.getEntityByName(f.getXRefEntity());
-                Field f_ref = e_ref.getField(f.getXRefField());
+                Entity e_ref = f.getXrefEntity();
+                Field f_ref = f.getXrefField();
                 return getFieldType(f_ref).getJavaPropertyType();
         }
@@ -27 +27 @@
         {
                 
-                return getFieldType(getEntityByName(f.getXRefEntity()).getField(f.getXRefField())).getJavaSetterType();
+                return getFieldType(f.getXrefField()).getJavaSetterType();
         }
         
@@ -34 +34 @@
         {
                 
-                return getFieldType(getEntityByName(f.getXRefEntity()).getField(f.getXRefField())).getMysqlType();
+                return getFieldType(f.getXrefField()).getMysqlType();
         }
 
@@ -40 +40 @@
         public String getHsqlType() throws MolgenisModelException
         {
-                return getFieldType(getEntityByName(f.getXRefEntity()).getField(f.getXRefField())).getHsqlType();
+                return getFieldType(f.getXrefField()).getHsqlType();
         }
 }

molgenis/3.3/src/org/molgenis/generators/server/SoapApiGen.java.ftl

@@ -63 +63 @@
         @WebResult(name = "${name(entity)}List")
         public List<${JavaName(entity)}> find${JavaName(entity)}(<#list allFields(entity) as f><#assign type_label = f.getType().toString()>     
-                @WebParam(name = "${name(f)}") ${type(f)} ${name(f)}<#if (type_label == "user" || type_label == "xref" || type_label == "mref" || type_label == "enum") && f.getXRefLabelString() != "" >,
-                @WebParam(name = "${name(f)}_${f.getXRefLabelString()}") ${type(f)} ${name(f)}_${f.getXRefLabelString()}</#if><#if f_has_next>,</#if></#list>)
+                @WebParam(name = "${name(f)}") ${type(f)} ${name(f)}<#if (type_label == "xref" || type_label == "mref") && f.xrefLabelNames[0] != f.xrefFieldName >,
+                <#list f.xrefLabelNames as label>@WebParam(name = "${name(f)}_${label}") ${type(f)} ${name(f)}_${label}</#list></#if><#if f_has_next>,</#if></#list>)
         {
                 try
@@ -84 +84 @@
         @WebResult(name = "${name(entity)}Csv")
         public String find${JavaName(entity)}Csv(<#list allFields(entity) as f><#assign type_label = f.getType().toString()>     
-                @WebParam(name = "${name(f)}") ${type(f)} ${name(f)}<#if (type_label == "user" || type_label == "xref" || type_label == "mref" || type_label == "enum") && f.getXRefLabelString() != "" >,
-                @WebParam(name = "${name(f)}_${f.getXRefLabelString()}") ${type(f)} ${name(f)}_${f.getXRefLabelString()}</#if><#if f_has_next>,</#if></#list>)
+                @WebParam(name = "${name(f)}") ${type(f)} ${name(f)}<#if (type_label == "user" || type_label == "xref" || type_label == "mref" ) && f.xrefLabelNames[0] != f.xrefFieldName >,
+                <#list f.xrefLabelNames as label>@WebParam(name = "${name(f)}_${label}") ${type(f)} ${name(f)}_${label}</#list></#if><#if f_has_next>,</#if></#list>)
         {
                 try

molgenis/3.3/src/org/molgenis/generators/sql/MySqlAlterSubclassPerTableGen.mysql.ftl

@@ -111 +111 @@
 <#list entities as entity><#if !entity.isAbstract()>
 <#list dbFields(entity) as f><#if f.type == "xref">
-ALTER TABLE ${SqlName(entity)} ADD FOREIGN KEY (${SqlName(f)}) REFERENCES ${SqlName(model.getEntity(f.XRefEntity))} (${SqlName(f.XRefField)}) ON DELETE RESTRICT;
+ALTER TABLE ${SqlName(entity)} ADD FOREIGN KEY (${SqlName(f)}) REFERENCES ${SqlName(f.xrefEntity)} (${SqlName(f.xrefField)}) ON DELETE RESTRICT;
 </#if></#list>
 </#if></#list>

molgenis/3.3/src/org/molgenis/generators/sql/MySqlCreateSubclassPerTableGen.mysql.ftl

@@ -73 +73 @@
 <#list entities as entity><#if !entity.isAbstract()>
 <#list dbFields(entity) as f><#if f.type == "xref">
-ALTER TABLE ${SqlName(entity)} ADD FOREIGN KEY (${SqlName(f)}) REFERENCES ${SqlName(model.getEntity(f.XRefEntity))} (${SqlName(f.XRefField)}) ON DELETE RESTRICT;
+ALTER TABLE ${SqlName(entity)} ADD FOREIGN KEY (${SqlName(f)}) REFERENCES ${SqlName(f.xrefEntity)} (${SqlName(f.xrefField)}) ON DELETE RESTRICT;
 </#if></#list>
 </#if></#list>

molgenis/3.3/src/org/molgenis/model/MolgenisModel.java

@@ -32 +32 @@
 
                         model = MolgenisModelParser.parseDbSchema(options.model_database);
+                        
+                        logger.debug("read: " + model);
 
                         //if (!options.exclude_system) Model.createSystemTables(model);
@@ -39 +41 @@
                         model = MolgenisModelParser.parseUiSchema(options.path + options.model_userinterface, model);
                         //if (options.force_molgenis_package == true) model.setName("molgenis");
+                        
+                        logger.debug("validated: " + model);
                 }
                 catch (MolgenisModelException e)
@@ -133 +137 @@
                         if (field.getType().toString() == "xref")
                         {
-                                dependencies.add(field.getXRefEntity()); // xref fields
+                                dependencies.add(field.getXrefEntityName()); // xref fields
                                 // including all children, it can relate to that
                                 // dependencies.addAll(model.getEntity(field.getXRefEntity())
@@ -140 +144 @@
                                 // model.getEntity(field.getXRefEntity()).getParents());
 
-                                Entity xrefEntity = model.getEntity(field.getXRefEntity());
+                                Entity xrefEntity = field.getXrefEntity();
 
                                 // also all subclasses have this xref!!!!

molgenis/3.3/src/org/molgenis/model/MolgenisModelParser.java

@@ -122 +122 @@
                 if (xref_label != null && !xref_label.equals(""))
                 {
-                        entity.setXrefLabel(element.getAttribute("xref_label"));
+                        List<String> xref_labels = new ArrayList<String>();
+                        xref_labels.addAll(Arrays.asList(xref_label.split(",")));
+                        entity.setXrefLabels(xref_labels);
                 }
 
@@ -196 +198 @@
                                 keys.add(f);
                         }
+                        
+                        //description
+                        String key_description = null;
+                        if (elem.hasAttribute("description")) key_description = elem.getAttribute("description");
 
                         // check if keys
@@ -203 +209 @@
                         try
                         {
-                                entity.addKey(keys, elem.getAttribute("subclass").equals("true"), null);
+                                entity.addKey(keys, elem.getAttribute("subclass").equals("true"), key_description);
                                 // might be duplicate key
                         }
@@ -464 +470 @@
                                                         + entity.getName() + "'");
 
-                        field.setXRefVariables(xref_entity, xref_field, xref_label);
+                        List<String> xref_labels = Arrays.asList(xref_label.split(","));
+                        
+                        field.setXRefVariables(xref_entity, xref_field, xref_labels);
 
                         // optional custom naming instead of default
@@ -744 +752 @@
                         }
                 }
-                logger.debug("read: " + model);
 
                 return model;
@@ -860 +867 @@
 
                         // ACTIONS
-                        form.setActions(new ArrayList<String>());
-                        String actions = element.getAttribute("actions");
-                        if (actions != null && actions != "")
-                        {
-                                String[] actionArr = actions.split(",");
-                                for (String action : actionArr)
-                                {
-                                        form.getActions().add(action.trim());
+                        form.setCommands(new ArrayList<String>());
+                        String commands = element.getAttribute("commands");
+                        if (commands != null && commands != "")
+                        {
+                                String[] commandArray = commands.split(",");
+                                for (String command : commandArray)
+                                {
+                                        form.getCommands().add(command.trim());
                                 }
                         }
@@ -1086 +1093 @@
                                         try
                                         {
-                                                field.setXRefVariables(field.getXRefEntity(), "id", "id");
+                                                field.setXrefLabelNames(Arrays.asList(new String[]{"id"}));
                                         }
                                         catch (Exception e)

molgenis/3.3/src/org/molgenis/model/MolgenisModelValidator.java

@@ -8 +8 @@
 import org.apache.log4j.Logger;
 import org.molgenis.MolgenisOptions;
+import org.molgenis.framework.db.DatabaseException;
 import org.molgenis.model.elements.Entity;
 import org.molgenis.model.elements.Field;
@@ -58 +59 @@
                                 if (f.getType().equals(Field.Type.XREF_SINGLE) || f.getType().equals(Field.Type.XREF_MULTIPLE))
                                 {
-                                        if (f.getXRefLabelString() == null || f.getXRefLabelString().equals(f.getXRefField()))
-                                        {
-                                                Entity xref_entity = model.getEntity(f.getXRefEntity());
-                                                f.setXrefLabel(xref_entity.getXrefLabel());
+                                        if (!f.getXrefLabelsTemp().get(0).equals(f.getXrefFieldName()))
+                                        {
+                                                // Entity xref_entity =
+                                                // model.getEntity(f.getXRefEntity());
+                                                // f.setXrefLabels(xref_entity.getXrefLabels());
                                         }
                                 }
@@ -133 +135 @@
 
                                         // retrieve the references to the entity+field
-                                        Entity xref_entity_to = model.getEntity(xref_field_from.getXRefEntity());
-                                        Field xref_field_to = xref_entity_to.getField(xref_field_from.getXRefField());
+                                        Entity xref_entity_to = xref_field_from.getXrefEntity();
+                                        Field xref_field_to = xref_field_from.getXrefField();
 
                                         // TODO: check whether this link is already present
@@ -164 +166 @@
                                                                 false, false, false, null);
                                                 field.setXRefVariables(xref_entity_to.getName(), xref_field_to.getName(), xref_field_from
-                                                                .getXRefLabelString());
+                                                                .getXrefLabelsTemp());
                                                 linktable.addField(field);
                                                 unique.add(field);
@@ -174 +176 @@
                                                                         false, false, false, null);
 
-                                                        field.setXRefVariables(xref_entity_from.getName(), key.getName(), "");
+                                                        // null xreflabel
+                                                        field.setXRefVariables(xref_entity_from.getName(), key.getName(), null);
 
                                                         linktable.addField(field);
@@ -233 +236 @@
                                         try
                                         {
-                                                referenced = model.getEntity(field.getXRefEntity());
+                                                referenced = field.getXrefEntity();
                                         }
                                         catch (Exception e)
@@ -295 +298 @@
                                 if (field.getType() == Field.Type.XREF_SINGLE || field.getType() == Field.Type.XREF_MULTIPLE)
                                 {
-                                        String xref_entity_name = field.getXRefEntity();
-                                        String xref_field_name = field.getXRefField();
-                                        String xref_label_name = field.getXRefLabelString();
+                                        String xref_entity_name = field.getXrefEntityName();
+                                        String xref_field_name = field.getXrefFieldName();
+                                        List<String> xref_label_names = field.getXrefLabelsTemp();
 
                                         Entity xref_entity = model.getEntity(xref_entity_name);
@@ -304 +307 @@
                                                         + "' does not exist for field " + entityname + "." + fieldname);
 
-                                        if (!xref_entity.getName().equals(field.getXRefEntity())) throw new MolgenisModelException(
+                                        if (!xref_entity.getName().equals(field.getXrefEntityName())) throw new MolgenisModelException(
                                                         "xref entity '" + xref_entity_name + "' does not exist for field " + entityname + "."
                                                                         + fieldname + " (note: entity names are case-sensitive)");
@@ -316 +319 @@
                                                         + "' does not exist for field " + entityname + "." + fieldname);
 
-                                        Field xref_label = xref_entity.getAllField(xref_label_name);
-                                        if (xref_label == null) throw new MolgenisModelException("xref label '" + xref_label_name
-                                                        + "' does not exist for field " + entityname + "." + fieldname);
-
-                                        if (xref_label.isNillable()) throw new MolgenisModelException("'" + xref_label_name
-                                                        + "' cannot be used as xref label for field '" + entityname + "." + fieldname
-                                                        + "' because it can be null (nullable='true')");
+                                        for (String xref_label_name : xref_label_names)
+                                        {
+                                                Field xref_label = null;
+                                                // test if label is defined as {entity}.{field}
+                                                if (xref_label_name.contains("."))
+                                                {
+                                                        try
+                                                        {
+                                                                xref_label = model.findField(xref_label_name);
+                                                        }
+                                                        catch (DatabaseException e)
+                                                        {
+                                                        }
+                                                        ;
+                                                }
+                                                // else assume {entity} == xref_entity
+                                                else
+                                                {
+                                                        xref_label = xref_entity.getAllField(xref_label_name);
+                                                }
+                                                if (xref_label == null) throw new MolgenisModelException("xref label '" + xref_label_name
+                                                                + "' does not exist for field " + entityname + "." + fieldname);
+
+                                                if (xref_label.isNillable()) throw new MolgenisModelException("'" + xref_label_names
+                                                                + "' cannot be used as xref label for field '" + entityname + "." + fieldname
+                                                                + "' because it can be null (nullable='true')");
+
+                                                // TODO check if the labels are unique
+                                        }
 
                                         if (xref_field.getType().equals(Field.Type.TEXT)) throw new MolgenisModelException("xref field '"
@@ -385 +410 @@
 
                         if (autocount > 1) throw new MolgenisModelException(
-                                        "there can be only one auto column and it must be the primary key for entity '" + entityname + "'");
+                                        "there should be only one auto column and it must be the primary key for entity '" + entityname
+                                                        + "'");
+
+                        if (!entity.isAbstract() && autocount < 1)
+                        {
+                                throw new MolgenisModelException(
+                                                "there should be one auto column for each root entity and it must be the primary key for entity '"
+                                                                + entityname + "'");
+                        }
                 }
 
@@ -430 +463 @@
 
                                                         field.setSystem(true);
-                                                        field.setXRefVariables(iface.getName(), key.getName(), key.getName());
+                                                        field.setXRefVariables(iface.getName(), key.getName(), null);
                                                         field.setHidden(true);
 
@@ -436 +469 @@
                                                                         + " to " + entity.getName());
                                                         entity.addField(field);
-                                                        entity.addKey(field, iface.getKeys().get(0).getDescription());
+                                                        // entity.addKey(field,
+                                                        // iface.getKeys().get(0).getDescription());
                                                 }
                                         }
@@ -482 +516 @@
 
                                                         field.setSystem(true);
-                                                        field.setXRefVariables(parent.getName(), key.getName(), "");
+                                                        field.setXRefVariables(parent.getName(), key.getName(), null);
                                                         field.setHidden(true);
 
@@ -591 +625 @@
                 if (options.db_driver.contains("hsql")) keywords.addAll(Arrays.asList(HSQL_KEYWORDS));
 
-                if (model.getName().contains(" ")) 
+                if (model.getName().contains(" "))
                 {
                         throw new MolgenisModelException("model name '" + model.getName()
                                         + "' illegal: it cannot contain spaces. Use 'label' if you want to show a name with spaces.");
                 }
-                
-//              if(!containsOnlyLetters(model.getName()))
-//              {
-//                      throw new MolgenisModelException("model name '" + model.getName()
-//                                      + "' illegal: it can only contain letters, no numbers or dots");
-//              }
+
+                // if(!containsOnlyLetters(model.getName()))
+                // {
+                // throw new MolgenisModelException("model name '" + model.getName()
+                // + "' illegal: it can only contain letters, no numbers or dots");
+                // }
 
                 for (Module m : model.getModules())
@@ -610 +644 @@
                                                 + "' illegal: it cannot contain spaces. Use 'label' if you want to show a name with spaces.");
                         }
-//                      if(!containsOnlyLetters(m.getName()))
-//                      {
-//                              throw new MolgenisModelException("module name '" + m.getName()
-//                                              + "' illegal: it can only contain letters, no numbers or dots");
-//                      }
-                        
+                        // if(!containsOnlyLetters(m.getName()))
+                        // {
+                        // throw new MolgenisModelException("module name '" + m.getName()
+                        // + "' illegal: it can only contain letters, no numbers or dots");
+                        // }
+
                 }
 
@@ -653 +687 @@
                                 if (f.getType().equals(Field.Type.XREF_SINGLE) || f.getType().equals(Field.Type.XREF_MULTIPLE))
                                 {
-                                        String xref_entity = f.getXRefEntity();
+                                        String xref_entity = f.getXrefEntityName();
                                         if (xref_entity != null
                                                         && (keywords.contains(xref_entity.toUpperCase()) || keywords.contains(xref_entity
@@ -708 +742 @@
                         }
                 }
-                
-                for(UISchema screen: model.getUserinterface().getAllChildren())
-                {
-                        if(screen.getName().contains(" "))
-                        {
-                                throw new MolgenisModelException("ui element '"+screen.getName()+"illegal: it cannot contain spaces. If you want to have a name with spaces use the 'label' attribute");
+
+                for (UISchema screen : model.getUserinterface().getAllChildren())
+                {
+                        if (screen.getName().contains(" "))
+                        {
+                                throw new MolgenisModelException(
+                                                "ui element '"
+                                                                + screen.getName()
+                                                                + "illegal: it cannot contain spaces. If you want to have a name with spaces use the 'label' attribute");
                         }
                 }
@@ -733 +770 @@
                                         {
                                                 // correct for uppercase/lowercase typo's
-                                                Entity xrefEntity = model.getEntity(f.getXRefEntity());
+                                                Entity xrefEntity = f.getXrefEntity();
                                                 f.setXRefEntity(xrefEntity.getName());
 
-                                                String xrefField = xrefEntity.getAllField(f.getXRefField()).getName();
-                                                String xrefLabel = xrefEntity.getAllField(f.getXRefLabelString()).getName();
-                                                if (xrefLabel == null) xrefLabel = xrefField;
-                                                f.setXRefVariables(xrefEntity.getName(), xrefField, xrefLabel);
+                                                String xrefField = f.getXrefField().getName();
+
+                                                List<String> xrefLabels = f.getXrefLabelsTemp();
+                                                List<String> correctedXrefLabels = new ArrayList<String>();
+                                                for (String xrefLabel : xrefLabels)
+                                                {
+                                                        correctedXrefLabels.add(xrefEntity.getAllField(xrefLabel).getName());
+                                                }
+                                                f.setXRefVariables(xrefEntity.getName(), xrefField, correctedXrefLabels);
                                         }
                                         catch (Exception exception)
@@ -869 +911 @@
                         return " ERROR[STRING EMPTY] ";
         }
-        
+
         private static boolean containsOnlyLetters(String name)
         {

molgenis/3.3/src/org/molgenis/model/elements/DBSchema.java

@@ -38 +38 @@
         private List<Module> modules = new ArrayList<Module>();
         
+        private Model model;
+        
+        public Model getModel()
+        {
+                return model;
+        }
+
+        public void setModel(Model model)
+        {
+                this.model = model;
+        }
+
         // constructor(s)
         /**
@@ -47 +59 @@
          *            tree.
          */
-        public DBSchema(String name, DBSchema parent)
+        public DBSchema(String name, DBSchema parent, Model model)
         {
                 super(name, parent);
+                this.model = model;
         }
 

molgenis/3.3/src/org/molgenis/model/elements/Entity.java

@@ -65 +65 @@
         /** Trigger type */
         private String decorator;
-        
-        /** Default label to be used for Xrefs */
-        private String xrefLabel;
+
+        /** Default label(s) to be used for Xrefs */
+        private List<String> xrefLabels;
 
         // constructor(s)
@@ -99 +99 @@
         public Entity(String name, String label, DBSchema parent)
         {
-                super(name, parent);
+                super(name, parent, parent.getModel());
 
                 this.label = label;
@@ -129 +129 @@
         public Entity(String name, String label, DBSchema parent, boolean system)
         {
-                super(name, parent);
+                super(name, parent, parent.getModel());
 
                 // this.name = name;
@@ -497 +497 @@
         public Vector<Field> getImplementedFields() throws MolgenisModelException
         {
-                Vector<Field> all_fields = new Vector<Field>();
+                Map<String, Field> all_fields = new LinkedHashMap<String, Field>();
 
                 // first fields of the interfaces
@@ -506 +506 @@
                         {
                                 ifaceField.setEntity(this);
-                                all_fields.add(ifaceField);
+                                all_fields.put(ifaceField.getName().toLowerCase(), ifaceField);
                         }
                 }
@@ -513 +513 @@
                 for (Field f : getFields())
                 {
-                        if (!all_fields.contains(f))
-                        {
-                                all_fields.add(f);
-                        }
-                        else
-                        // replace with local variant
-                        {
-                                all_fields.set(all_fields.indexOf(f), f);
-                        }
-                }
-
-                return all_fields;
-        }
-        
+                        all_fields.put(f.getName().toLowerCase(), f);
+                }
+
+                return new Vector(all_fields.values());
+        }
+
         public boolean hasSuperclassField(String fieldname) throws MolgenisModelException
         {
                 Vector<Field> fields = getAncestor().getAllFields();
-                for(Field f : fields) {
-                        if(f.getName().equals(fieldname)) {
+                for (Field f : fields)
+                {
+                        if (f.getName().equals(fieldname))
+                        {
                                 return true;
                         }
@@ -540 +534 @@
         public Vector<Field> getInheritedFields() throws MolgenisModelException
         {
-                Map <String,Field> all_fields = new LinkedHashMap<String,Field>();
+                Map<String, Field> all_fields = new LinkedHashMap<String, Field>();
 
                 // second fields of the interfaces
@@ -548 +542 @@
                         for (Field ifaceField : ifaceFields)
                         {
-                                //ifaceField.setEntity(this);
-                                        all_fields.put(ifaceField.getName(), ifaceField);
+                                // ifaceField.setEntity(this);
+                                all_fields.put(ifaceField.getName().toLowerCase(), ifaceField);
                         }
                 }
@@ -558 +552 @@
                         for (Field f : getAncestor().getAllFields())
                         {
-                                all_fields.put(f.getName(), f);
+                                all_fields.put(f.getName().toLowerCase(), f);
                         }
                 }
@@ -564 +558 @@
                 // skip self...
                 return new Vector(all_fields.values());
-                
-        }
-        
+
+        }
+
         /**
          * @throws MolgenisModelException
@@ -572 +566 @@
         public Vector<Field> getAllFields() throws MolgenisModelException
         {
-                Map <String,Field> all_fields = new LinkedHashMap<String,Field>();
+                Map<String, Field> all_fields = new LinkedHashMap<String, Field>();
 
                 // second fields of the interfaces
@@ -581 +575 @@
                         {
                                 ifaceField.setEntity(this);
-                                        all_fields.put(ifaceField.getName(), ifaceField);
+                                all_fields.put(ifaceField.getName().toLowerCase(), ifaceField);
                         }
                 }
@@ -590 +584 @@
                         for (Field f : getAncestor().getAllFields())
                         {
-                                all_fields.put(f.getName(), f);
+                                all_fields.put(f.getName().toLowerCase(), f);
                         }
                 }
@@ -597 +591 @@
                 for (Field f : getFields())
                 {
-                        all_fields.put(f.getName(), f);
+                        all_fields.put(f.getName().toLowerCase(), f);
                 }
                 return new Vector(all_fields.values());
@@ -862 +856 @@
                 for (Field field : getAllFields())
                 {
-                        //logger.debug("testing: " + this.getName()+ "."+field.getName());
+                        // logger.debug("testing: " + this.getName()+ "."+field.getName());
 
                         if (name.equalsIgnoreCase(field.getName()))
@@ -1040 +1034 @@
                 {
                         Entity parent_entity = (Entity) getParent().get(this.parents.lastElement());
-                        if(parent_entity == null) throw new MolgenisModelException("Superclass "+ this.parents.lastElement()+" unknown for entity "+this.getName());
+                        if (parent_entity == null) throw new MolgenisModelException("Superclass " + this.parents.lastElement()
+                                        + " unknown for entity " + this.getName());
                         result.add(parent_entity.getKeys().firstElement());
                 }
 
-                // get key from implements
+                // get other keys from implements
                 if (hasImplements())
                 {
@@ -1204 +1199 @@
                 this.addKey(fields, subclass, description);
         }
-        
+
         public int getNumberOfReferencesTo(Entity e) throws MolgenisModelException
         {
                 int count = 0;
-                for (Field field : this.getXRefFields()) {
-                        String xrefEntity = field.getXRefEntity();
-                        if(xrefEntity != null && xrefEntity.equals(e.getName()))
-                                count++;
+                for (Field field : this.getXRefFields())
+                {
+                        String xrefEntity = field.getXrefEntityName();
+                        if (xrefEntity != null && xrefEntity.equals(e.getName())) count++;
                 }
                 return count;
         }
 
-        public String getXrefLabel()
-        {
-                return xrefLabel;
-        }
-
-        public void setXrefLabel(String xrefLabel)
-        {
-                this.xrefLabel = xrefLabel;
+        public List<String> getXrefLabels()
+        {
+                return xrefLabels;
+        }
+
+        public void setXrefLabels(List<String> xrefLabels)
+        {
+                this.xrefLabels = xrefLabels;
+        }
+
+        public Model getModel()
+        {
+                return this.getRoot().getModel();
         }
 }

molgenis/3.3/src/org/molgenis/model/elements/Field.java

@@ -14 +14 @@
 import java.io.Serializable;
 import java.sql.Types;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 import java.util.Vector;
 
-import org.apache.log4j.Logger;
+import org.molgenis.framework.db.DatabaseException;
+import org.molgenis.generators.GeneratorHelper;
 import org.molgenis.model.MolgenisModelException;
 
@@ -25 +29 @@
  * 
  * @author RA Scheltema
+ * @author MA Swertz
  * @version 1.0.0
  */
@@ -34 +39 @@
         public static enum Type
         {
-                /**Ontology type*/
-                ONTOLOGY("ontology","%s"),
+                /** Ontology type */
+                ONTOLOGY("ontology", "%s"),
                 /** The type is unknown, this case should raise an exception. */
                 UNKNOWN("unknown", ""),
@@ -66 +71 @@
                 /** The type of the field is file. */
                 FILE("file", "%s"),
-                /** special type of file, namely images*/
-                IMAGE("image","%s"),
+                /** special type of file, namely images */
+                IMAGE("image", "%s"),
                 /** */
                 ENUM("enum", "%s"),
@@ -239 +244 @@
         public Field(Entity parent, String name, Type type)
         {
-                this(parent, type, name, name, false,false,false,null);
+                this(parent, type, name, name, false, false, false, null);
         }
 
@@ -263 +268 @@
          *            Indicates whether this field is readonly.
          */
-        public Field(Entity parent, Type type, String name, String label, boolean auto, boolean nillable, boolean readonly, String default_value)
+        public Field(Entity parent, Type type, String name, String label, boolean auto, boolean nillable, boolean readonly,
+                        String default_value)
         {
                 this.entity = parent;
@@ -285 +291 @@
                 this.xref_table = "";
                 this.xref_field = "";
-                this.xref_label = "";
+                this.xref_labels = new ArrayList<String>();
 
                 //
@@ -320 +326 @@
                 this.xref_table = field.xref_table;
                 this.xref_field = field.xref_field;
-                this.xref_label = field.xref_label;
+                this.xref_labels = field.xref_labels;
                 this.mref_name = field.mref_name;
 
@@ -369 +375 @@
                                 DBSchema root = entity.getRoot();
 
-                                Entity xref_entity = (Entity) root.get(getXRefEntity());
-                                Field xref_field = xref_entity.getField(getXRefField());
-
-                                return xref_field.getFormatString();
+                                return this.getXrefField().getFormatString();
                         }
                         catch (Exception e)
@@ -443 +446 @@
                 return this.nillable;
         }
-        
+
         public void setReadonly(boolean readonly)
         {
@@ -662 +665 @@
          *             Type.XREF_MULTIPLE
          */
-        public void setXRefVariables(String entity, String field, String label) // throws
+        public void setXRefVariables(String entity, String field, List<String> labels) // throws
         // Exception
         {
@@ -673 +676 @@
                 this.xref_table = entity;
                 this.xref_field = field;
-                this.xref_label = label;
+                this.xref_labels = labels;
         }
 
@@ -686 +689 @@
          *             Type.XREF_MULTIPLE
          */
-        public String getXRefEntity() throws MolgenisModelException
+        public Entity getXrefEntity() throws MolgenisModelException
+        {
+                return this.getEntity().getModel().getEntity(this.getXrefEntityName());
+        }
+
+        public String getXrefEntityName() throws MolgenisModelException
         {
                 if (this.type != Type.XREF_SINGLE && this.type != Type.XREF_MULTIPLE)
-                 {
-                 throw new MolgenisModelException("Field '"+this.getEntity().getName()+"."+this.getName()+"' is not a XREF, so xref-table cannot be retrieved.");
+                {
+                        throw new MolgenisModelException("Field '" + this.getEntity().getName() + "." + this.getName()
+                                        + "' is not a XREF, so xref-table cannot be retrieved.");
                 }
 
                 return this.xref_table;
+
         }
 
@@ -702 +712 @@
          * 
          * @return The name of the field of the entity this field is referencing.
+         * @throws Exception 
          * @throws Exception
          *             When this field is not of type Type.XREF_SINGLE or
          *             Type.XREF_MULTIPLE
          */
-        public String getXRefField() // throws Exception
-        {
-                // if (this.type != Type.XREF_SINGLE && this.type != Type.XREF_MULTIPLE)
-                // {
-                // throw new Exception("Field is not a XREF, so xref-field cannot be
-                // retrieved.");
-                // }
-
+        public Field getXrefField() throws MolgenisModelException // throws Exception
+        {
+                if (this.type != Type.XREF_SINGLE && this.type != Type.XREF_MULTIPLE)
+                {
+                        throw new MolgenisModelException("Field is not a XREF, so xref-field cannot be retrieved.");
+                }
+
+                return this.getXrefEntity().getField(this.getXrefFieldName());
+        }
+
+        public String getXrefFieldName()
+        {
                 return this.xref_field;
         }
@@ -722 +737 @@
          * 
          * @return The label of this reference.
+         * @throws MolgenisModelException
          * @throws Exception
          *             When this field is not of type Type.XREF_SINGLE or
          *             Type.XREF_MULTIPLE
          */
-        public XRefLabel getXRefLabel() throws Exception
-        {
-                if (this.type != Type.XREF_SINGLE && this.type != Type.XREF_MULTIPLE) throw new Exception("Field is not a XREF, so xref-label cannot be retrieved.");
-
-                XRefLabel label = new XRefLabel();
-                if (xref_label.contains("{"))
-                {
-                        int pos = 0;
-                        int old = 0;
-
-                        while (pos != -1)
-                        {
-                                // find the next occurence of a field-name
-                                pos = xref_label.indexOf('{', old);
-                                if (pos != -1)
-                                {
-                                        // expand the format-string
-                                        label.format += xref_label.substring(old, pos) + "%s";
-
-                                        // find the end-position of the field-name
-                                        old = xref_label.indexOf('}', pos);
-                                        if (old == -1) throw new Exception("Unterminated field-name in xref-label:\n" + xref_label);
-
-                                        // add the field-name to the vector
-                                        label.fields.add(xref_label.substring(pos + 1, old));
-                                }
-                                else
-                                {
-                                }
-
-                                old++;
-                        }
-                }
-                else
-                {
-                        if (xref_label == null || xref_label.equals("")) xref_label = this.xref_field;
-                        label.format = "%s";
-                        label.fields.add(xref_label);
-                }
-
-                return label;
-        }
-
-        /**
-         * Gets the xref_label as string. For the parsed version:
-         * 
-         * @see #getXRefLabel()
-         */
-        public String getXRefLabelString()
-        {
-                if(this.xref_label == "" || this.xref_label == null)
-                        return this.xref_field;
-                return this.xref_label;
+        public List<String> getXrefLabelNames() throws MolgenisModelException
+        {
+                // label name = replace '.' and replace entity name if label entity ==
+                // xref_entity
+                List<String> label_names = new ArrayList<String>();
+                for (String label : this.getXrefLabelsTemp())
+                        label_names.add(label.replace(".", "_").replace(this.getXrefEntity() + "_", ""));
+                return label_names;
+        }
+
+        public List<Field> getXrefLabels() throws DatabaseException, MolgenisModelException
+        {
+                List<Field> result = new ArrayList<Field>();
+
+                for (String label : getXrefLabelsTemp())
+                {
+                        if (label.contains(".")) result.add(this.getEntity().getModel().findField(label));
+                        else
+                                result.add(this.getEntity().getModel().findField(this.getXrefEntity().getName() + "." + label));
+                }
+
+                return result;
+        }
+
+        public List<String> getXrefLabelsTemp()
+        {
+                if (xref_labels == null || xref_labels.size() == 0) return Arrays.asList(new String[]
+                { this.xref_field });
+                return xref_labels;
         }
 
@@ -819 +811 @@
                 this.mref_name = linktable;
         }
-        
+
         public String getMrefLocalid()
         {
@@ -886 +878 @@
                 str += ", type=" + type.tag;
                 if (type == Field.Type.STRING || type == Field.Type.CHAR) str += "[" + varchar_length + "]";
-                else if (type == Field.Type.XREF_SINGLE || type == Field.Type.XREF_MULTIPLE) str += "[" + xref_table + "->" + xref_field + "]";
-                if(type == Field.Type.XREF_MULTIPLE) str += ", mref_name="+this.mref_name +", mref_localid="+this.mref_localid+", mref_remoteid="+this.mref_remoteid;
-                if (type == Field.Type.XREF_SINGLE || type == Field.Type.XREF_MULTIPLE) str +=", xref_label="+getXRefLabelString();
-                
+                else if (type == Field.Type.XREF_SINGLE || type == Field.Type.XREF_MULTIPLE) str += "[" + xref_table + "->"
+                                + xref_field + "]";
+                if (type == Field.Type.XREF_MULTIPLE) str += ", mref_name=" + this.mref_name + ", mref_localid="
+                                + this.mref_localid + ", mref_remoteid=" + this.mref_remoteid;
+                if (type == Field.Type.XREF_SINGLE || type == Field.Type.XREF_MULTIPLE) str += ", xref_label="
+                                + new GeneratorHelper(null).toCsv(this.xref_labels);
+
                 // settings
                 str += ", auto=" + auto;
@@ -989 +984 @@
          * is the label of the reference.
          */
-        private String xref_label;
+        private List<String> xref_labels;
         /**
          * When this field is of type Type.XREF_MULTIPLE, this is the name of the
@@ -995 +990 @@
          */
         private String mref_name;
-        
+
         private String mref_localid;
-        
+
         private String mref_remoteid;
 
@@ -1066 +1061 @@
         {
                 this.xref_field = xrefField;
+
+        }
+
+        public void setXrefLabelNames(List<String> labelNames)
+        {
+                this.xref_labels = labelNames;
                 
         }
-
-        public void setXrefLabel(String xrefLabel) throws MolgenisModelException
-        {
-                this.setXRefVariables(this.getXRefEntity(), this.getXRefField(), xrefLabel);
-        }
 }

molgenis/3.3/src/org/molgenis/model/elements/Form.java

@@ -165 +165 @@
 
         /** */
-        private List<String> actionPlugins;
+        private List<String> commandPlugins;
 
         /** */
@@ -320 +320 @@
         }
 
-        public List<String> getActions()
-        {
-                return actionPlugins;
-        }
-
-        public void setActions(List<String> actionPlugins)
-        {
-                this.actionPlugins = actionPlugins;
+        public List<String> getCommands()
+        {
+                return commandPlugins;
+        }
+
+        public void setCommands(List<String> actionPlugins)
+        {
+                this.commandPlugins = actionPlugins;
         }
 
@@ -340 +340 @@
         }
         
+        public String toString()
+        {
+                String commands = "";
+                for(String command: getCommands()) commands += command +",";
+                return String.format("Form(name=%s, entity=%s, commands=%s)", getName(), getRecord().getName(), commands);
+        }
 }

molgenis/3.3/src/org/molgenis/model/elements/Matrix.java

@@ -35 +35 @@
         public Matrix(String name, DBSchema parent)
         {
-                super(name, parent);
+                super(name, parent, parent.getModel());
         }
 
@@ -97 +97 @@
                         Entity e = (Entity) get(this.content_entity);
                         Field row_field = e.getField(this.row);
-                        return (Entity) get(row_field.getXRefEntity());
+                        return row_field.getXrefEntity();
                         // return model.getEntity(row_field.getXRefEntity());
                 }
@@ -120 +120 @@
                         Field col_field = ce.getField(col);
                         // get from the field the entity that is 'xref-ed' by the row
-                        return (Entity) get(col_field.getXRefEntity());
+                        return col_field.getXrefEntity();
                 }
         }
@@ -142 +142 @@
                 // "+container_field.getXRefEntity());
                 // get from the field the entity that is 'xref-ed' by the row
-                return (Entity) get(container_field.getXRefEntity());
+                return container_field.getXrefEntity();
         }
 

molgenis/3.3/src/org/molgenis/model/elements/Model.java

@@ -32 +32 @@
                 this.name = name;
 
-                database = new DBSchema(name, null);
+                database = new DBSchema(name, null, this);
                 userinterface = new UISchema(name, null);
                 methods = new MethodSchema(name, null);
@@ -435 +435 @@
                 for (UISchema u : getUserinterface().getAllChildren())
                 {
-                        result.append(u.getType() + ": " + u.getName() + "\n");
+                        result.append(u.toString()+"\n");
                 }
 

molgenis/3.3/src/org/molgenis/model/elements/View.java

@@ -37 +37 @@
         public View(String name, String label, DBSchema parent)
         {
-                super(name, parent);
+                super(name, parent, parent.getModel());
                 
                 //
@@ -160 +160 @@
                                 
                                 try {
-                                        if (field.getXRefEntity().equals(entity.getName()))
+                                        if (field.getXrefEntity().equals(entity.getName()))
                                                 xrefs.add(field);
                                 } catch (Exception ex) {;}
@@ -172 +172 @@
                                 
                                 try {
-                                        if (field.getXRefEntity().equals(e.getName()))
+                                        if (field.getXrefEntity().equals(e.getName()))
                                                 xrefs.add(field);
                                 } catch (Exception ex) {;}