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fix xml serialization for CAOM-2.4 #183

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merged 2 commits into from
Nov 7, 2024
Merged

fix xml serialization for CAOM-2.4 #183

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64183ce
fix xml serialization for CAOM-2.4
pdowler Nov 6, 2024
f525f20
caom2-viz: remove bintray plugin
pdowler Nov 6, 2024
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1 change: 0 additions & 1 deletion caom2-viz/build.gradle
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
plugins {
id 'maven'
id 'maven-publish'
id 'com.jfrog.bintray' version '1.7.1'
id 'application'
id 'checkstyle'
}
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2 changes: 1 addition & 1 deletion caom2/build.gradle
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Expand Up @@ -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'
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1 change: 1 addition & 0 deletions caom2/src/main/java/ca/nrc/cadc/caom2/xml/ObservationReader.java
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Expand Up @@ -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);
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33 changes: 33 additions & 0 deletions caom2/src/main/java/ca/nrc/cadc/caom2/xml/ObservationWriter.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);

Expand Down Expand Up @@ -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);
}
Expand Down Expand Up @@ -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);
}
Expand Down Expand Up @@ -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);
}
Expand Down Expand Up @@ -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) {
Expand Down
10 changes: 6 additions & 4 deletions caom2/src/main/resources/CAOM-2.4.xsd
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Expand Up @@ -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">
Expand Down Expand Up @@ -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>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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">
Expand Down
11 changes: 8 additions & 3 deletions caom2/src/test/java/ca/nrc/cadc/caom2/xml/Caom2TestInstances.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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

Expand All @@ -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);
Expand All @@ -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");
Expand Down
24 changes: 8 additions & 16 deletions caom2/src/test/java/ca/nrc/cadc/caom2/xml/ObservationReaderWriterTest.java
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Expand Up @@ -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);
Expand All @@ -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);
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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);
}
Expand All @@ -1394,7 +1387,6 @@ protected void compareDataQuality(DataQuality expected, DataQuality actual)
{
if (expected == null && actual == null)
return;

assertNotNull(expected);
assertNotNull(actual);

Expand Down
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