Modify Time.unit type to UnitsTime enum

Also adds the TimeI implementation for the Python and C++ language bindings, including object factories and IceMapper code. The Java implementation is also an implementor of `ModelBased` so that IceMapper can convert back and forth to ome.model.units instances. For the next unit implementation (i.e. `Length`), it will likely be better to introduce code generation of the `ome.model.units` implementations rather than hand-writing them. Note: a workaround was needed for the generation of unique constant names in Ice since constants must vary in more than just capitalization which fails for SI prefixes like M and m.
ome · Oct 14, 2014 · d586e43 · d586e43
1 parent 98e7353
commit d586e43
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Showing 22 changed files with 652 additions and 42 deletions.
diff --git a/components/blitz/resources/omero/model/Time.ice b/components/blitz/resources/omero/model/Time.ice
@@ -20,6 +20,8 @@
 #ifndef CLASS_TIME
 #define CLASS_TIME
 
+#include <omero/model/UnitsTime.ice>
+
 module omero {
 
     module model {
@@ -33,7 +35,7 @@ module omero {
        **/
       double value;
 
-      string unit;
+      UnitsTime unit;
 
       /**
        **/
@@ -45,11 +47,11 @@ module omero {
 
       /**
        **/
-      string getUnit();
+      UnitsTime getUnit();
 
       /**
        **/
-      void setUnit(string unit);
+      void setUnit(UnitsTime unit);
 
       Time copy();
 

diff --git a/components/blitz/resources/templates/combined.vm b/components/blitz/resources/templates/combined.vm
@@ -122,7 +122,31 @@ DECLARATION BLOCK:
 [$ice]     module enums {
 #foreach($prop in $type.properties)
 #if($prop.class.name == "ome.dsl.EntryField")
-[$ice]         const string ${Pojo}${prop.name.replaceAll("[^a-zA-Z0-9]","")} = "${prop.name}";
+### HACK: the enum
+### bf/components/xsd-fu/xsd-fu: def enum_value_name()
+#set($enumSymbol = ${prop.name.replaceAll("[^a-zA-Z0-9]","")})
+#if($Pojo.startsWith("Units"))
+#set($enumSymbol1 = ${enumSymbol.substring(1)})
+#if($prop.name.startsWith("M"))
+#set($enumSymbol = "mega${enumSymbol1}")
+#elseif($prop.name.startsWith("G"))
+#set($enumSymbol = "giga${enumSymbol1}")
+#elseif($prop.name.startsWith("P"))
+#set($enumSymbol = "peta${enumSymbol1}")
+#elseif($prop.name.startsWith("E"))
+#set($enumSymbol = "exa${enumSymbol1}")
+#elseif($prop.name.startsWith("Z"))
+#set($enumSymbol = "zetta${enumSymbol1}")
+#elseif($prop.name.startsWith("Y"))
+#set($enumSymbol = "yotta${enumSymbol1}")
+#elseif($prop.name.startsWith("T") && !$prop.name.startsWith("o"))
+#set($enumSymbol = "tera${enumSymbol1}")
+#elseif($prop.name.startsWith("µ"))
+#set($enumSymbol = "micro${enumSymbol1}")
+#end
+#end
+#set($enumName = "${Pojo}${enumSymbol}")
+[$ice]         const string ${enumName} = "${prop.name}";
 #end
 #end
 [$ice]     };

diff --git a/components/blitz/resources/templates/cpp_obj_reg.vm b/components/blitz/resources/templates/cpp_obj_reg.vm
@@ -18,6 +18,7 @@
 //
 
 \#include <omero/ObjectFactoryRegistrar.h>
+\#include <omero/model/TimeI.h>
 #foreach($type in $types)
 #if(!$type.abstract)
 \#include <omero/model/${type.shortname}I.h>
@@ -31,31 +32,49 @@ namespace omero {
 #if(!$type.abstract)
 #set( $ObjFac = "${type.shortname}ObjectFactory" )
     class ${ObjFac} : virtual public Ice::ObjectFactory {
-    public:
-    ${ObjFac}() : Ice::ObjectFactory() { }
 
-    ~${ObjFac}() {}
+        public:
+        ${ObjFac}() : Ice::ObjectFactory() { }
 
-    Ice::ObjectPtr create(const std::string& type) {
-        return new omero::model::${type.shortname}I();
+        ~${ObjFac}() {}
+
+        Ice::ObjectPtr create(const std::string& /*type*/) {
+            return new omero::model::${type.shortname}I();
         }
 
-    void destroy() {}
+        void destroy() {}
+
     };
 #end
 #end
 
     class PermissionsObjectFactory : virtual public Ice::ObjectFactory {
-    public:
-    PermissionsObjectFactory() : Ice::ObjectFactory() { }
 
-    ~PermissionsObjectFactory() {}
+        public:
+        PermissionsObjectFactory() : Ice::ObjectFactory() { }
 
-    Ice::ObjectPtr create(const std::string& type) {
-        return new omero::model::PermissionsI();
-    }
+        ~PermissionsObjectFactory() {}
+
+        Ice::ObjectPtr create(const std::string& /*type*/) {
+            return new omero::model::PermissionsI();
+        }
+
+        void destroy() {}
+
+    };
+
+    class TimeObjectFactory : virtual public Ice::ObjectFactory {
+
+        public:
+        TimeObjectFactory() : Ice::ObjectFactory() { }
+
+        ~TimeObjectFactory() {}
+
+        Ice::ObjectPtr create(const std::string& type) {
+            return new omero::model::TimeI();
+        }
 
-    void destroy() {}
+        void destroy() {}
 
     };
 
@@ -69,6 +88,7 @@ namespace omero {
 
   void registerObjectFactory(const Ice::CommunicatorPtr ic) {
     conditionalAdd("::omero::model::Permissions", ic, new PermissionsObjectFactory());
+    conditionalAdd("::omero::model::Time", ic, new TimeObjectFactory());
 #foreach($type in $types)
 #if(!$type.abstract)
     conditionalAdd("::omero::model::${type.shortname}", ic,  new ${type.shortname}ObjectFactory());

diff --git a/components/blitz/resources/templates/java_ice_map.vm b/components/blitz/resources/templates/java_ice_map.vm
@@ -78,6 +78,11 @@ public class IceMap {
         _ome2omero.put(ome.model.roi.Rect.class, omero.model.SmartRectI.class);
         _ome2omero.put(ome.model.roi.Label.class, omero.model.SmartTextI.class);
 
+        // Units
+        _ome2omero.put(ome.model.units. Time.class, omero.model.TimeI.class);
+        _omero2ome.put(omero.model.Time.class, ome.model.units.Time.class);
+        _omero2ome.put(omero.model.TimeI.class, ome.model.units.Time.class);
+
         // Sealing
         OMEtoOMERO = Collections.unmodifiableMap(_ome2omero);
         OMEROtoOME = Collections.unmodifiableMap(_omero2ome);

diff --git a/components/blitz/resources/templates/java_obj_reg.vm b/components/blitz/resources/templates/java_obj_reg.vm
@@ -23,6 +23,7 @@ import omero.util.ObjectFactoryRegistry;
 
 import omero.model.DetailsI;
 import omero.model.PermissionsI;
+import omero.model.TimeI;
 
 import Ice.Communicator;
 import Ice.Object;
@@ -37,6 +38,7 @@ public class ModelObjectFactoryRegistry extends ObjectFactoryRegistry {
         // Non-conditional
         ic.addObjectFactory(DetailsI.makeFactory(client), DetailsI.ice_staticId());
         ic.addObjectFactory(PermissionsI.Factory, PermissionsI.ice_staticId());
+        ic.addObjectFactory(TimeI.makeFactory(client), TimeI.ice_staticId());
 
         // Conditional
         super.setIceCommunicator(ic);
@@ -48,6 +50,7 @@ public class ModelObjectFactoryRegistry extends ObjectFactoryRegistry {
         // Non-conditional
         ic.addObjectFactory(DetailsI.Factory, DetailsI.ice_staticId());
         ic.addObjectFactory(PermissionsI.Factory, PermissionsI.ice_staticId());
+        ic.addObjectFactory(TimeI.Factory, TimeI.ice_staticId());
 
         // Conditional
         super.setIceCommunicator(ic);

diff --git a/components/blitz/resources/templates/py_obj_reg.vm b/components/blitz/resources/templates/py_obj_reg.vm
@@ -53,13 +53,27 @@ class DetailsObjectFactory(Ice.ObjectFactory):
     def destroy(self):
         pass
 
+class TimeObjectFactory(Ice.ObjectFactory):
+
+    from omero_model_TimeI import TimeI
+
+    def __init__(self, client = None):
+        self.client = client
+
+    def create(self, type):
+        return self.TimeI(self.client)
+
+    def destroy(self):
+        pass
+
 def conditionalAdd(name, ic, of):
     if not ic.findObjectFactory(name):
         ic.addObjectFactory(of, name)
 
 def registerObjectFactory(ic, client = None):
     conditionalAdd("::omero::model::Permissions", ic, PermissionsObjectFactory())
     conditionalAdd("::omero::model::Details", ic, DetailsObjectFactory(client))
+    conditionalAdd("::omero::model::Time", ic, TimeObjectFactory(client))
 #foreach($type in $types)
 #if(!$type.abstract)
     conditionalAdd("::omero::model::${type.shortname}", ic,  ${type.shortname}ObjectFactory())

diff --git a/components/blitz/src/ome/formats/OMEROMetadataStoreClient.java b/components/blitz/src/ome/formats/OMEROMetadataStoreClient.java
@@ -868,9 +868,11 @@ public InstanceProvider getInstanceProvider()
     public omero.model.Time toTime(Double value)
     {
         if (value == null) return null;
+        omero.model.UnitsTime ut = new omero.model.UnitsTimeI();
+        ut.setValue(rstring("ms")); // FIXME
         omero.model.Time t = new omero.model.TimeI();
         t.setValue(value);
-        t.setUnit("ms"); // FIXME
+        t.setUnit(ut);
         return t;
     }
 

diff --git a/components/blitz/src/omero/model/TimeI.java b/components/blitz/src/omero/model/TimeI.java
@@ -19,27 +19,37 @@
 
 package omero.model;
 
+import ome.model.ModelBased;
+import ome.util.Filterable;
+import ome.util.ModelMapper;
+import ome.util.ReverseModelMapper;
+
 /**
  * Blitz wrapper around the {@link ome.model.util.Time} class.
  *
  * @author Josh Moore, josh at glencoesoftware.com
  */
-public class TimeI extends Time {
+public class TimeI extends Time implements ModelBased {
 
     private static final long serialVersionUID = 1L;
 
-    public final static Ice.ObjectFactory Factory = new Ice.ObjectFactory() {
+    public static final Ice.ObjectFactory makeFactory(final omero.client client) {
 
-        public Ice.Object create(String arg0) {
-            return new TimeI();
-        }
+        return new Ice.ObjectFactory() {
 
-        public void destroy() {
-            // no-op
-        }
+            public Ice.Object create(String arg0) {
+                return new TimeI();
+            }
 
+            public void destroy() {
+                // no-op
+            }
+
+        };
     };
 
+    public final static Ice.ObjectFactory Factory = makeFactory(null);
+
     public double getValue(Ice.Current current) {
         return this.value;
     }
@@ -48,11 +58,11 @@ public void setValue(double time, Ice.Current current) {
         this.value = time;
     }
 
-    public String getUnit(Ice.Current current) {
+    public UnitsTime getUnit(Ice.Current current) {
         return this.unit;
     }
 
-    public void setUnit(String unit, Ice.Current current) {
+    public void setUnit(UnitsTime unit, Ice.Current current) {
         this.unit = unit;
     }
 
@@ -63,4 +73,25 @@ public Time copy(Ice.Current ignore) {
         return copy;
     }
 
+    @Override
+    public void copyObject(Filterable model, ModelMapper mapper) {
+        if (model instanceof ome.model.units.Time) { 
+            ome.model.units.Time t = (ome.model.units.Time) model;
+            this.value = t.getValue();
+            this.unit = (omero.model.UnitsTime) mapper.findTarget(t.getUnit());
+        } else {
+            throw new IllegalArgumentException(
+              "Time cannot copy from " +
+              (model==null ? "null" : model.getClass().getName()));
+        }
+    }
+
+    @Override
+    public Filterable fillObject(ReverseModelMapper mapper) {
+        ome.model.units.Time t = new ome.model.units.Time();
+        t.setValue(getValue());
+        t.setUnit((ome.model.enums.UnitsTime) mapper.reverse( (ome.model.ModelBased) getUnit()));
+        return t;
+    }
+
 }
diff --git a/components/blitz/src/omero/util/IceMapper.java b/components/blitz/src/omero/util/IceMapper.java
@@ -723,6 +723,31 @@ public static ome.parameters.Filter convert(Filter f) {
         return filter;
     }
 
+    public omero.model.Time convert(ome.model.units.Time t) {
+        if (t == null) {
+            return null;
+        }
+        omero.model.TimeI copy = new omero.model.TimeI();
+        copy.setValue(t.getValue());
+        copy.setUnit((omero.model.UnitsTime) map(t.getUnit()));
+        return copy;
+    }
+
+     public ome.model.units.Time convert(omero.model.Time t) {
+        if (t == null) {
+            return null;
+        }
+        ome.model.units.Time copy = new ome.model.units.Time();
+        copy.setValue(t.getValue());
+        try {
+            copy.setUnit((ome.model.enums.UnitsTime) reverse(t.getUnit()));
+        } catch (ApiUsageException e) {
+            throw new IllegalArgumentException(
+                    "convert(omero.model.Time) failed", e);
+        }
+        return copy;
+     }
+
     /**
      * Convert a String&rarr;String map's values to {@link RString}s.
      * <code>null</code> values are dropped completely.

diff --git a/components/dsl/resources/ome/dsl/object.vm b/components/dsl/resources/ome/dsl/object.vm
@@ -974,7 +974,9 @@ implements java.io.Serializable, IObject
 #if($prop.type.equals("ome.model.units.Time"))
      @javax.persistence.AttributeOverrides( {
             @javax.persistence.AttributeOverride(name="value", column = @javax.persistence.Column(name="${prop.name}") ),
-            @javax.persistence.AttributeOverride(name="unit", column = @javax.persistence.Column(name="${prop.name}Unit") )
+    } )
+     @javax.persistence.AssociationOverrides( {
+            @javax.persistence.AssociationOverride(name="unit", joinColumns = @javax.persistence.JoinColumn(name="exposureTimeUnit") )
     } )
 #end
     public ${prop.fieldType} get${prop.nameCapped}() {

diff --git a/components/dsl/resources/ome/dsl/psql-footer.vm b/components/dsl/resources/ome/dsl/psql-footer.vm
@@ -468,6 +468,12 @@ alter table event alter column experimentergroup set not null;
 ##  as name, next from (select ome_nextval('seq_event') as next) as nv;
 
 ## ENUMS
+
+-- temporarily disable the not null constraints
+alter table pixelstype alter column bitsize drop not null;
+alter table unitstime alter column measurementsystem drop not null;
+
+
 #foreach($enum in $types)
 #foreach($prop in $enum.properties)
 #set($table = ${enum.typeToColumn($enum.id)} )
@@ -490,7 +496,12 @@ update pixelstype set bitsize = 32 where value = 'float';
 update pixelstype set bitsize = 64 where value = 'double';
 update pixelstype set bitsize = 64 where value = 'complex';
 update pixelstype set bitsize = 128 where value = 'double-complex';
+
+update unitstime set measurementsystem = 'SI.SECOND';
+
+-- reactivate not null constraints
 alter table pixelstype alter column bitsize set not null;
+alter table unitstime alter column measurementsystem set not null;
 
 --
 -- Cryptographic functions for specifying UUID