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Merge pull request #439 from maheshpalanroche/issue_438 

Added the copying of "extension" fields
This commit is contained in:
Grahame Grieve 2021-03-29 10:31:18 +10:00 committed by GitHub
parent 58055aeaa6 30be8a0dc1
commit 9fe7ea729d
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5 changed files with 226 additions and 102 deletions
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8
RELEASE_NOTES.md
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@ -1,2 +1,6 @@
* minor fixes in code generators for R4B
* add default value to Medication Request during conversion from dstu2 to r4
* add test for Observation conversion from 10 to 40
* add procedures conversion form dstu2 to r4
* add medication conversion from dstu2 to r4
* add copy of extension field for Enumeration fieldtype by Resource.copy
* minor fixes in code generators for R4B
* add default value to Medication Request during conversion from dstu2 to r4

108
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Enumeration.java
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@ -1,39 +1,40 @@
package org.hl7.fhir.r4.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;
import java.util.ArrayList;
import org.hl7.fhir.instance.model.api.IBaseEnumeration;
@ -43,34 +44,34 @@ import ca.uhn.fhir.model.api.annotation.DatatypeDef;
Copyright (c) 2011+, HL7, Inc
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/**
* Primitive type "code" in FHIR, where the code is tied to an enumerated list of possible values
*
*
*/
@DatatypeDef(name = "code", isSpecialization = true)
public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T>, ICoding {
@ -80,7 +81,7 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
/**
* Constructor
*
*
* @deprecated This no-arg constructor is provided for serialization only - Do not use
*/
@Deprecated
@ -117,10 +118,17 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
setValue(theValue);
}
@Override
public Enumeration<T> copy() {
return new Enumeration<T>(myEnumFactory, getValue());
}
@Override
public Enumeration<T> copy() {
Enumeration dst= new Enumeration(this.myEnumFactory, (Enum)this.getValue());
//Copy the Extension
if (extension != null) {
dst.extension = new ArrayList();
for (Extension i : extension)
dst.extension.add(i.copy());
};
return dst;
}
@Override
protected String encode(T theValue) {
@ -145,7 +153,7 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
}
return null;
}
@SuppressWarnings("unchecked")
@Override
public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {

56
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/ResourceCopyTests.java Normal file
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@ -0,0 +1,56 @@
package org.hl7.fhir.r4.test;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.formats.IParser;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.formats.XmlParser;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.EOperationOutcome;
import org.hl7.fhir.r4.utils.NarrativeGenerator;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import java.io.*;
public class ResourceCopyTests {
@Test
public void testCopyExtensionForEnumerationField() throws FHIRException {
// Create new Observation and set the Extension with field value without status field set.
Observation obs = new Observation();
obs.getStatusElement().getExtension().add(new Extension().setUrl("Sampleurl"));
obs.getStatusElement().getExtension().add(new Extension().setUrl("Sampleurl2"));
Observation copyObs = obs.copy();
Assertions.assertEquals(obs.hasStatusElement(),copyObs.hasStatusElement(),"Status Element not copied ");
Assertions.assertEquals(obs.getStatusElement().hasExtension(),copyObs.getStatusElement().hasExtension(),"Status Element Extension not copied ");
Assertions.assertEquals(obs.getStatusElement().getExtension().get(0).getUrl(),copyObs.getStatusElement().getExtension().get(0).getUrl(),"Status Element Extension url not copied ");
Assertions.assertEquals(obs.getStatusElement().getExtension().get(1).getUrl(),copyObs.getStatusElement().getExtension().get(1).getUrl(),"Status Element Extension url not copied ");
//Verify the object at toplevel using equals Deep
Assertions.assertEquals(obs.equalsDeep(copyObs),true,"DeepEquals fails");
}
@Test
public void testCopyEnumerationField() throws FHIRException, IOException {
// Create new Observation and set the Extension with field value as well as status field set .
Observation obs = new Observation();
obs.setStatus(Observation.ObservationStatus.AMENDED);
obs.getStatusElement().getExtension().add(new Extension().setUrl("Sampleurl"));
Observation copyObs = obs.copy();
Assertions.assertEquals(obs.getStatus(),copyObs.getStatus(),"Status not copied ");
Assertions.assertEquals(obs.hasStatusElement(),copyObs.hasStatusElement(),"Status Element not copied ");
Assertions.assertEquals(obs.getStatusElement().hasExtension(),copyObs.getStatusElement().hasExtension(),"Status Element Extension not copied ");
Assertions.assertEquals(obs.getStatusElement().getExtension().get(0).getUrl(),copyObs.getStatusElement().getExtension().get(0).getUrl(),"Status Element Extension url not copied ");
//Verify the object at toplevel using equals Deep
Assertions.assertEquals(obs.equalsDeep(copyObs),true,"DeepEquals fails");
}
}

108
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Enumeration.java
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@ -1,39 +1,40 @@
package org.hl7.fhir.r5.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;
import java.util.ArrayList;
import org.hl7.fhir.instance.model.api.IBaseEnumeration;
@ -43,34 +44,34 @@ import ca.uhn.fhir.model.api.annotation.DatatypeDef;
Copyright (c) 2011+, HL7, Inc
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/**
* Primitive type "code" in FHIR, where the code is tied to an enumerated list of possible values
*
*
*/
@DatatypeDef(name = "code", isSpecialization = true)
public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T>, ICoding {
@ -80,7 +81,7 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
/**
* Constructor
*
*
* @deprecated This no-arg constructor is provided for serialization only - Do not use
*/
@Deprecated
@ -117,10 +118,17 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
setValue(theValue);
}
@Override
public Enumeration<T> copy() {
return new Enumeration<T>(myEnumFactory, getValue());
}
@Override
public Enumeration<T> copy() {
Enumeration dst= new Enumeration(this.myEnumFactory, (Enum)this.getValue());
//Copy the Extension
if (extension != null) {
dst.extension = new ArrayList();
for (Extension i : extension)
dst.extension.add(i.copy());
};
return dst;
}
@Override
protected String encode(T theValue) {
@ -145,7 +153,7 @@ public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements
}
return null;
}
@SuppressWarnings("unchecked")
@Override
public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {

48
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceCopyTests.java Normal file
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@ -0,0 +1,48 @@
package org.hl7.fhir.r5.test;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.Observation;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.io.IOException;
public class ResourceCopyTests {
@Test
public void testCopyExtensionForEnumerationField() throws FHIRException {
// Create new Observation and set the Extension with field value without status field set.
Observation obs = new Observation();
obs.getStatusElement().getExtension().add(new Extension().setUrl("Sampleurl"));
obs.getStatusElement().getExtension().add(new Extension().setUrl("Sampleurl2"));
Observation copyObs = obs.copy();
Assertions.assertEquals(obs.hasStatusElement(),copyObs.hasStatusElement(),"Status Element not copied ");
Assertions.assertEquals(obs.getStatusElement().hasExtension(),copyObs.getStatusElement().hasExtension(),"Status Element Extension not copied ");
Assertions.assertEquals(obs.getStatusElement().getExtension().get(0).getUrl(),copyObs.getStatusElement().getExtension().get(0).getUrl(),"Status Element Extension url not copied ");
Assertions.assertEquals(obs.getStatusElement().getExtension().get(1).getUrl(),copyObs.getStatusElement().getExtension().get(1).getUrl(),"Status Element Extension url not copied ");
//Verify the object at toplevel using equals Deep
Assertions.assertEquals(obs.equalsDeep(copyObs),true,"DeepEquals fails");
}
@Test
public void testCopyEnumerationField() throws FHIRException, IOException {
// Create new Observation and set the Extension with field value as well as status field set .
Observation obs = new Observation();
obs.setStatus(Enumerations.ObservationStatus.AMENDED);
obs.getStatusElement().getExtension().add(new Extension().setUrl("Sampleurl"));
Observation copyObs = obs.copy();
Assertions.assertEquals(obs.getStatus(),copyObs.getStatus(),"Status not copied ");
Assertions.assertEquals(obs.hasStatusElement(),copyObs.hasStatusElement(),"Status Element not copied ");
Assertions.assertEquals(obs.getStatusElement().hasExtension(),copyObs.getStatusElement().hasExtension(),"Status Element Extension not copied ");
Assertions.assertEquals(obs.getStatusElement().getExtension().get(0).getUrl(),copyObs.getStatusElement().getExtension().get(0).getUrl(),"Status Element Extension url not copied ");
//Verify the object at toplevel using equals Deep
Assertions.assertEquals(obs.equalsDeep(copyObs),true,"DeepEquals fails");
}
}