Merge pull request #183 from pdowler/main

fix xml serialization for CAOM-2.4

caom2-viz/build.gradle

@@ -1,7 +1,6 @@
 plugins {
     id 'maven'
     id 'maven-publish'
-    id 'com.jfrog.bintray' version '1.7.1'
     id 'application'
     id 'checkstyle'
 }

caom2/build.gradle

@@ -15,7 +15,7 @@ sourceCompatibility = 1.8
 
 group = 'org.opencadc'
 
-version = '2.4.8'
+version = '2.4.9'
 
 description = 'OpenCADC CAOM library'
 def git_url = 'https://github.com/opencadc/caom2'

caom2/src/main/java/ca/nrc/cadc/caom2/xml/ObservationReader.java

@@ -907,6 +907,7 @@ protected void addPlanes(Set<Plane> planes, Element parent,
             plane.metrics = getMetrics(planeElement, namespace, rc);
             plane.quality = getQuality(planeElement, namespace, rc);
 
+            plane.observable = getObservable(planeElement, namespace, rc);
             plane.position = getPosition(planeElement, namespace, rc);
             plane.energy = getEnergy(planeElement, namespace, rc);
             plane.time = getTime(planeElement, namespace, rc);

caom2/src/main/java/ca/nrc/cadc/caom2/xml/ObservationWriter.java

@@ -83,6 +83,7 @@
 import ca.nrc.cadc.caom2.Environment;
 import ca.nrc.cadc.caom2.Instrument;
 import ca.nrc.cadc.caom2.Metrics;
+import ca.nrc.cadc.caom2.Observable;
 import ca.nrc.cadc.caom2.Observation;
 import ca.nrc.cadc.caom2.ObservationURI;
 import ca.nrc.cadc.caom2.Part;
@@ -765,6 +766,7 @@ protected void addPlanesElement(Set<Plane> planes, Element parent,
                 addElement("calibrationLevel", String.valueOf(plane.calibrationLevel.getValue()), planeElement);
             }
             addProvenanceElement(plane.provenance, planeElement, dateFormat);
+            addObservableElement(plane.observable, planeElement);
             addMetricsElement(plane.metrics, planeElement, dateFormat);
             addQuaility(plane.quality, planeElement, dateFormat);
 
@@ -850,6 +852,12 @@ protected void addPositionElement(Position comp, Element parent) {
         if (comp.resolution != null) {
             addNumberElement("resolution", comp.resolution, e);
         }
+        if (comp.resolutionBounds != null) {
+            Element rb = getCaom2Element("resolutionBounds");
+            addNumberElement("lower", comp.resolutionBounds.getLower(), rb);
+            addNumberElement("upper", comp.resolutionBounds.getUpper(), rb);
+            e.addContent(rb);
+        }
         if (comp.sampleSize != null) {
             addNumberElement("sampleSize", comp.sampleSize, e);
         }
@@ -897,6 +905,12 @@ protected void addEnergyElement(Energy comp, Element parent) {
         if (comp.resolvingPower != null) {
             addNumberElement("resolvingPower", comp.resolvingPower, e);
         }
+        if (comp.resolvingPowerBounds != null) {
+            Element rb = getCaom2Element("resolvingPowerBounds");
+            addNumberElement("lower", comp.resolvingPowerBounds.getLower(), rb);
+            addNumberElement("upper", comp.resolvingPowerBounds.getUpper(), rb);
+            e.addContent(rb);
+        }
         if (comp.sampleSize != null) {
             addNumberElement("sampleSize", comp.sampleSize, e);
         }
@@ -956,6 +970,12 @@ protected void addTimeElement(Time comp, Element parent) {
         if (comp.resolution != null) {
             addNumberElement("resolution", comp.resolution, e);
         }
+        if (comp.resolutionBounds != null) {
+            Element rb = getCaom2Element("resolutionBounds");
+            addNumberElement("lower", comp.resolutionBounds.getLower(), rb);
+            addNumberElement("upper", comp.resolutionBounds.getUpper(), rb);
+            e.addContent(rb);
+        }
         if (comp.sampleSize != null) {
             addNumberElement("sampleSize", comp.sampleSize, e);
         }
@@ -1064,6 +1084,19 @@ protected void addProvenanceElement(Provenance provenance, Element parent,
         parent.addContent(element);
     }
 
+    protected void addObservableElement(Observable observable, Element parent) {
+        if (observable == null) {
+            return;
+        }
+
+        Element obsE = getCaom2Element("observable");
+        parent.addContent(obsE);
+
+        Element ucdE = getCaom2Element("ucd");
+        ucdE.setText(observable.getUCD());
+        obsE.addContent(ucdE);
+    }
+
     protected void addMetricsElement(Metrics metrics, Element parent,
             DateFormat dateFormat) {
         if (metrics == null) {

caom2/src/main/resources/CAOM-2.4.xsd

@@ -446,7 +446,7 @@
             <xs:extension base="caom2:CaomEntity">
                 <xs:sequence>
                     <xs:element name="uri" type="xs:anyURI"/>
-                    <xs:element name="productType" type="caom2:ProductType"/>
+                    <xs:element name="productType" type="xs:string"/>
                     <xs:element name="releaseType" type="caom2:ReleaseType"/>
 
                     <xs:element name="contentRelease" type="xs:string" minOccurs="0">
@@ -481,7 +481,7 @@
             <xs:extension base="caom2:CaomEntity">
                 <xs:sequence>
                     <xs:element name="name" type="xs:string" minOccurs="1"/>
-                    <xs:element name="productType" type="caom2:ProductType" minOccurs="0"/>
+                    <xs:element name="productType" type="xs:string" minOccurs="0"/>
                     <xs:element name="chunks" type="caom2:Chunks" minOccurs="0"/>
                 </xs:sequence>
             </xs:extension>
@@ -500,7 +500,7 @@
         <xs:complexContent>
             <xs:extension base="caom2:CaomEntity">
                 <xs:sequence>
-                    <xs:element name="productType" type="caom2:ProductType" minOccurs="0"/>
+                    <xs:element name="productType" type="xs:string" minOccurs="0"/>
                     <xs:element name="naxis" type="xs:integer" minOccurs="0"/>
                     <xs:element name="observableAxis" type="xs:integer" minOccurs="0"/>
                     <xs:element name="positionAxis1" type="xs:integer" minOccurs="0"/>
@@ -764,6 +764,7 @@
         </xs:restriction>
     </xs:simpleType>
 
+    <!-- open vocabulary in 2.4
     <xs:simpleType name="ProductType">
         <xs:restriction base="xs:string">
             <xs:enumeration value="science"/>
@@ -777,7 +778,8 @@
             <xs:enumeration value="thumbnail"/>
         </xs:restriction>
     </xs:simpleType>
-
+    -->
+
     <!-- open vocabulary in 2.3
     <xs:simpleType name="DataProductType">
         <xs:restriction base="xs:string">

caom2/src/test/java/ca/nrc/cadc/caom2/xml/Caom2TestInstances.java

@@ -83,6 +83,7 @@
 import ca.nrc.cadc.caom2.Environment;
 import ca.nrc.cadc.caom2.Instrument;
 import ca.nrc.cadc.caom2.Metrics;
+import ca.nrc.cadc.caom2.Observable;
 import ca.nrc.cadc.caom2.ObservationIntentType;
 import ca.nrc.cadc.caom2.ObservationURI;
 import ca.nrc.cadc.caom2.Part;
@@ -389,6 +390,7 @@ protected Set<Plane> getPlanes()
                 p.provenance = getProvenance();
                 p.metrics = getMetrics();
                 p.quality = new DataQuality(Quality.JUNK);
+                p.observable = new Observable("phot.count");
 
                 // alphabetical so easier to trace and debug metaChecksum computation
 
@@ -397,17 +399,18 @@ protected Set<Plane> getPlanes()
                 p.energy.bounds = new SampledInterval(400e-6, 900e-6);
                 p.energy.bounds.getSamples().add(new Interval(400e-6, 500e-6));
                 p.energy.bounds.getSamples().add(new Interval(800e-6, 900e-6));
-                p.energy.dimension = 2l;
+                p.energy.dimension = 2L;
                 for (EnergyBand eb : EnergyBand.values()) {
                     p.energy.getEnergyBands().add(eb);
                 }
                 p.energy.resolvingPower = 2.0;
+                p.energy.resolvingPowerBounds = new Interval(2.0, 5.0);
                 p.energy.restwav = 600e-9;
                 p.energy.sampleSize = 100e-6;
                 p.energy.transition = new EnergyTransition("H", "alpha");
 
                 p.polarization = new Polarization();
-                p.polarization.dimension = 3l;
+                p.polarization.dimension = 3L;
                 p.polarization.states = new TreeSet<PolarizationState>();
                 p.polarization.states.add(PolarizationState.I);
                 p.polarization.states.add(PolarizationState.Q);
@@ -432,16 +435,18 @@ protected Set<Plane> getPlanes()
                 }
                 p.position.dimension = new Dimension2D(1024, 2048);
                 p.position.resolution = 0.05;
+                p.position.resolutionBounds = new Interval(0.04, 0.06);
                 p.position.sampleSize = 0.025;
                 p.position.timeDependent = false;
 
                 p.time = new Time();
                 p.time.bounds = new SampledInterval(50000.25, 50000.75);
                 p.time.bounds.getSamples().add(new Interval(50000.25, 50000.40));
                 p.time.bounds.getSamples().add(new Interval(50000.50, 50000.75));
-                p.time.dimension = 2l;
+                p.time.dimension = 2L;
                 p.time.exposure = 666.0;
                 p.time.resolution = 0.5;
+                p.time.resolutionBounds = new Interval(0.5, 0.5);
                 p.time.sampleSize = 0.15;
 
                 p.custom = new CustomAxis("FARADAY");

caom2/src/test/java/ca/nrc/cadc/caom2/xml/ObservationReaderWriterTest.java

@@ -1105,8 +1105,6 @@ protected void comparePlanes(Set<Plane> expected, Set<Plane> actual) throws NoSu
             assertNotNull(expectedPlane);
             assertNotNull(actualPlane);
 
-            compareEntity(expectedPlane, actualPlane);
-
             assertEquals(expectedPlane.getProductID(), actualPlane.getProductID());
             assertEquals(expectedPlane.creatorID, actualPlane.creatorID);
             assertEquals(expectedPlane.metaRelease, actualPlane.metaRelease);
@@ -1118,7 +1116,11 @@ protected void comparePlanes(Set<Plane> expected, Set<Plane> actual) throws NoSu
             compare(expectedPlane.metrics, actualPlane.metrics);
             compare(expectedPlane.observable, actualPlane.observable);
 
-            compareComputed(expectedPlane, actualPlane);
+            compare(expectedPlane.position, actualPlane.position);
+            compare(expectedPlane.energy, actualPlane.energy);
+            compare(expectedPlane.time, actualPlane.time);
+            compare(expectedPlane.polarization, actualPlane.polarization);
+            compare(expectedPlane.custom, actualPlane.custom);
 
             compareDataQuality(expectedPlane.quality, actualPlane.quality);
             compareProvenance(expectedPlane.provenance, actualPlane.provenance);
@@ -1176,15 +1178,6 @@ protected void compare(Observable expected, Observable actual)
         assertEquals(expected.getUCD(), actual.getUCD());
     }
 
-    protected void compareComputed(Plane expected, Plane actual)
-    {
-        compare(expected.position, actual.position);
-        compare(expected.energy, actual.energy);
-        compare(expected.time, actual.time);
-        compare(expected.polarization, actual.polarization);
-        compare(expected.custom, actual.custom);
-    }
-
     protected void compare(Position expected, Position actual)
     {
         if (expected == null)
@@ -1381,11 +1374,11 @@ protected void compare(Shape expected, Shape actual) {
     }
 
     protected void compare(Interval expected, Interval actual) {
-        if (expected == null)
-        {
-            Assert.assertNull(actual);
+        if (expected == null && actual == null) {
             return;
         }
+        assertNotNull(expected);
+        assertNotNull(actual);
         Assert.assertEquals(expected.getLower(), actual.getLower(), 0.0);
         Assert.assertEquals(expected.getUpper(), actual.getUpper(), 0.0);
     }
@@ -1394,7 +1387,6 @@ protected void compareDataQuality(DataQuality expected, DataQuality actual)
     {
         if (expected == null && actual == null)
             return;
-
         assertNotNull(expected);
         assertNotNull(actual);