DB 5.1__DEV11: unit support for time

components/blitz/resources/omero/model/Time.ice

@@ -0,0 +1,59 @@
+/*
+ * Copyright (C) 2014 University of Dundee & Open Microscopy Environment.
+ * All rights reserved.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+#ifndef CLASS_TIME
+#define CLASS_TIME
+
+module omero {
+
+    module model {
+
+      /**
+       **/
+    ["protected"] class Time
+    {
+
+      /**
+       **/
+      double value;
+
+      string unit;
+
+      /**
+       **/
+      double getValue();
+
+      /**
+       **/
+      void setValue(double time);
+
+      /**
+       **/
+      string getUnit();
+
+      /**
+       **/
+      void setUnit(string unit);
+
+      Time copy();
+
+    };
+  };
+};
+#endif 

components/blitz/resources/templates/combined.vm

@@ -601,6 +601,8 @@ and protect later FOREACH blocks with "if (name == 'id' || name == 'details') sk
 [$jav]     		       copy.${property.name}Seq.add( item == null ? null : (${property.shortType}) item.proxy() );
 [$jav]                 }
 [$jav]             }
+#elseif($property.type.startsWith("ome.model.units"))
+[$jav]             copy.${property.name} = ${property.name} == null ? null : (${property.shortType}) ${property.name}.copy();
 #elseif($property.type.startsWith("ome") || $property.type.startsWith("IObject"))
 [$jav]             copy.${property.name} = ${property.name} == null ? null : (${property.shortType}) ${property.name}.proxy();
 #else

components/blitz/src/ome/formats/OMEROMetadataStoreClient.java

@@ -865,6 +865,15 @@ public InstanceProvider getInstanceProvider()
     // RTYPES
     //
 
+    public omero.model.Time toTime(Double value)
+    {
+        if (value == null) return null;
+        omero.model.Time t = new omero.model.TimeI();
+        t.setValue(value);
+        t.setUnit("ms"); // FIXME
+        return t;
+    }
+
   /**
      * Transforms a Java type into the corresponding OMERO RType.
      *
@@ -5783,7 +5792,7 @@ public void setPlaneExposureTime(Double exposureTime, int imageIndex,
             int planeIndex)
     {
         PlaneInfo o = getPlane(imageIndex, planeIndex);
-        o.setExposureTime(toRType(exposureTime));
+        o.setExposureTime(toTime(exposureTime));
     }
 
     /* (non-Javadoc)

components/blitz/src/ome/services/blitz/impl/OmeroMetadata.java

@@ -364,6 +364,11 @@ private Double fromRType(RDouble v)
         return v == null? null : v.getValue();
     }
 
+    private Double fromRType(omero.model.Time v)
+    {
+        return v == null? null : v.getValue();
+    }
+
     private Integer fromRType(RInt v)
     {
         return v == null? null : v.getValue();

components/blitz/src/omero/model/TimeI.java

@@ -0,0 +1,66 @@
+/*
+ * Copyright (C) 2014 University of Dundee & Open Microscopy Environment.
+ * All rights reserved.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package omero.model;
+
+/**
+ * Blitz wrapper around the {@link ome.model.util.Time} class.
+ *
+ * @author Josh Moore, josh at glencoesoftware.com
+ */
+public class TimeI extends Time {
+
+    private static final long serialVersionUID = 1L;
+
+    public final static Ice.ObjectFactory Factory = new Ice.ObjectFactory() {
+
+        public Ice.Object create(String arg0) {
+            return new TimeI();
+        }
+
+        public void destroy() {
+            // no-op
+        }
+
+    };
+
+    public double getValue(Ice.Current current) {
+        return this.value;
+    }
+
+    public void setValue(double time, Ice.Current current) {
+        this.value = time;
+    }
+
+    public String getUnit(Ice.Current current) {
+        return this.unit;
+    }
+
+    public void setUnit(String unit, Ice.Current current) {
+        this.unit = unit;
+    }
+
+    public Time copy(Ice.Current ignore) {
+        TimeI copy = new TimeI();
+        copy.setValue(getValue());
+        copy.setUnit(getUnit());
+        return copy;
+    }
+
+}

components/dsl/resources/ome/dsl/object.vm

@@ -965,6 +965,28 @@ implements java.io.Serializable, IObject
 #end
 
 #end## End isLink
+#elseif($prop.foreignKey && $prop.type.startsWith("ome.model.units")) ## UNITS
+
+   /**
+    * Many-to-one unit-based field ${type.id}.${prop.name} (${prop.type})
+    */
+    @javax.persistence.Embedded
+#if($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") )
+    } )
+#end
+    public ${prop.fieldType} get${prop.nameCapped}() {
+        $errorIfUnloaded
+        return this.${prop.name};
+    }
+
+    public void set${prop.nameCapped}(${prop.fieldType} ${prop.name}) {
+        $errorIfUnloaded
+        this.${prop.name} = ${prop.name};
+    }
+
 #elseif($prop.foreignKey)## REGULAR M-1 ##################################TYPE
 #set( $fetchType = "LAZY")
 #if($prop.actualType.abstract)

components/insight/SRC/org/openmicroscopy/shoola/agents/util/EditorUtil.java

@@ -2127,10 +2127,10 @@ public static Map<String, Object> transformPlaneInfo(PlaneInfo plane)
                 notSet.remove(DELTA_T);
                 details.put(DELTA_T, roundValue(o.getValue()));
             }
-            o = plane.getExposureTime();
-            if (o != null) {
+            omero.model.Time t = plane.getExposureTime();
+            if (t != null) {
                 notSet.remove(EXPOSURE_TIME);
-                details.put(EXPOSURE_TIME, roundValue(o.getValue()));
+                details.put(EXPOSURE_TIME, roundValue(t.getValue()));
             }
             o = plane.getPositionX();
             if (o != null) {

components/model/resources/mappings/acquisition.ome.xml

@@ -128,7 +128,7 @@
 			<!-- Note: positionY is stored in StagePosition in model-->
 			<optional name="positionZ" type="double"/>
 			<!-- Note: positionZ is stored in StagePosition in model-->
-			<optional name="exposureTime" type="double"/>
+			<optional name="exposureTime" type="ome.model.units.Time"/>
 			<!-- Note: exposureTime is stored in PlaneTiming in model-->
 			<!-- TODO: see mac notes -->
 		</properties>

components/model/src/ome/model/units/Time.java

@@ -0,0 +1,69 @@
+/*
+ * Copyright (C) 2014 University of Dundee & Open Microscopy Environment.
+ * All rights reserved.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along
+ * with this program; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package ome.model.units;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Embeddable;
+
+/**
+ * class storing both a time duration (double) and a unit for that duration
+ * (e.g. ns, ms, s, etc.)
+ */
+@Embeddable
+public class Time implements Serializable {
+
+    private static final long serialVersionUID = 1L;
+
+    // ~ Constructors
+    // =========================================================================
+
+    public Time() {
+    }
+
+    // ~ Fields
+    // =========================================================================
+
+    /**
+     * float representation of the time, i.e. duration, represented by this
+     * field.
+     */
+    private double value;
+
+    /**
+     * string representation of the units which should be considering when
+     * producing a representation of the {@link #time} field.
+     */
+    private String unit;
+
+    // ~ Property accessors : used primarily by Hibernate
+    // =========================================================================
+
+    @Column(name = "value", nullable = false)
+    public double getValue() {
+        return this.value;
+    }
+
+    @Column(name = "unit", nullable = false)
+    public String getUnit() {
+        return this.unit;
+    }
+
+}

etc/omero.properties

@@ -16,7 +16,7 @@ omero.managed.dir=${omero.data.dir}/ManagedRepository
 
 omero.db.authority=export.openmicroscopy.org
 omero.db.version=OMERO5.1DEV
-omero.db.patch=10
+omero.db.patch=11
 omero.db.host=localhost
 omero.db.name=omero
 omero.db.user=omero

sql/psql/OMERO5.1DEV__10/psql-footer.sql → sql/psql/OMERO5.1DEV__11/psql-footer.sql

@@ -543,6 +543,7 @@
   CREATE INDEX i_planeinfo_owner ON planeinfo(owner_id);
   CREATE INDEX i_planeinfo_group ON planeinfo(group_id);
   CREATE INDEX i_PlaneInfo_pixels ON planeinfo(pixels);
+  CREATE INDEX i_PlaneInfo_exposureTime ON planeinfo(exposureTime);
   CREATE INDEX i_planeinfoannotationlink_owner ON planeinfoannotationlink(owner_id);
   CREATE INDEX i_planeinfoannotationlink_group ON planeinfoannotationlink(group_id);
   CREATE INDEX i_PlaneInfoAnnotationLink_parent ON planeinfoannotationlink(parent);
@@ -1556,7 +1557,7 @@ alter table dbpatch alter message set default 'Updating';
 -- running so that if anything goes wrong, we'll have some record.
 --
 insert into dbpatch (currentVersion, currentPatch, previousVersion, previousPatch, message)
-             values ('OMERO5.1DEV',  10,    'OMERO5.1DEV',   0,             'Initializing');
+             values ('OMERO5.1DEV',  11,    'OMERO5.1DEV',   0,             'Initializing');
 
 --
 -- Temporarily make event columns nullable; restored below.
@@ -2552,7 +2553,7 @@ after delete on originalfile
 -- Here we have finished initializing this database.
 update dbpatch set message = 'Database ready.', finished = clock_timestamp()
   where currentVersion = 'OMERO5.1DEV' and
-        currentPatch = 10 and
+        currentPatch = 11 and
         previousVersion = 'OMERO5.1DEV' and
         previousPatch = 0;
 

sql/psql/OMERO5.1DEV__10/schema.sql → sql/psql/OMERO5.1DEV__11/schema.sql

@@ -1669,6 +1669,7 @@
         id int8 not null,
         deltaT float8,
         permissions int8 not null,
+        exposureTimeUnit varchar(255),
         exposureTime float8,
         positionX float8,
         positionY float8,