Different behaviour of (un)marshaller vs JAXB reference implementation #84

manstis · 2021-06-01T20:41:57Z

I was trialling the XML (un)marshallers generated by the @XMLMapper annotation.

The issues below do not exist when using the JAXB reference implementation in a normal JRE.

You can clone/fetch https://github.com/manstis/marshaller to see the behaviours:

marshaller-api contains the annotated POJO model classes (generated from XSD)
marshaller-client and marshaller-server are the GWT webapp; run it (see README) and press the buttons.
marshaller-jre deserialises and serialises the XML using the same POJOs but JAXB reference implementation.

The issues are:

Deserialisation

The deserialisation does not work correctly for @JAXBElementRefs. It can be made to work with the inclusion of the @XmlUnwrappedCollection annotation on collections however cases that are not collections fail to de-serialise. Furthermore use of the of XmlUnwrappedCollection should not be necessary (as it is not needed by the JAXB reference implementation).

Model class

public class Attribute {
  ...
    @XmlElementRefs({
        @XmlElementRef(name = "SimplePredicate", namespace = "http://www.dmg.org/PMML-4_4", type = SimplePredicate.class, required = false),
        @XmlElementRef(name = "CompoundPredicate", namespace = "http://www.dmg.org/PMML-4_4", type = CompoundPredicate.class, required = false),
        @XmlElementRef(name = "SimpleSetPredicate", namespace = "http://www.dmg.org/PMML-4_4", type = SimpleSetPredicate.class, required = false),
        @XmlElementRef(name = "True", namespace = "http://www.dmg.org/PMML-4_4", type = True.class, required = false),
        @XmlElementRef(name = "False", namespace = "http://www.dmg.org/PMML-4_4", type = False.class, required = false)
    })
    protected ICompoundPredicate predicate;
  ...
}

Generated code
(Compare this to how it works for collections with the @XmlUnwrappedCollection annotation. Deserialisation fails as the generated code fails to find a deserialiser for SimplePredicate as only a deserialiser for predicate has been registered).

public class AttributeBeanXMLDeserializerImpl extends AbstractBeanXMLDeserializer<Attribute> {
  ...
map.put("predicate", new BeanPropertyDeserializer<Attribute, com.anstis.pmml.model.ICompoundPredicate>() {

            @Override()
            protected XMLDeserializer<?> newDeserializer(org.treblereel.gwt.xml.mapper.api.stream.XMLReader reader) {
                return new Function<String, XMLDeserializer<com.anstis.pmml.model.ICompoundPredicate>>() {

                    @Override()
                    public XMLDeserializer apply(String value) {
                        if ("True".equals(value))
                            return new com.anstis.pmml.model.TrueBeanXMLDeserializerImpl();
                        if ("CompoundPredicate".equals(value))
                            return new com.anstis.pmml.model.CompoundPredicateBeanXMLDeserializerImpl();
                        if ("False".equals(value))
                            return new com.anstis.pmml.model.FalseBeanXMLDeserializerImpl();
                        if ("SimplePredicate".equals(value))
                            return new com.anstis.pmml.model.SimplePredicateBeanXMLDeserializerImpl();
                        if ("SimpleSetPredicate".equals(value))
                            return new com.anstis.pmml.model.SimpleSetPredicateBeanXMLDeserializerImpl();
                        throw new Error(value);
                    }
                }.apply(xsiTagChooser.apply(reader));
            }
   ...
        });
  ...
}

XML

<Attribute partialScore="-9">
  <SimplePredicate field="department" operator="isMissing"/>
</Attribute>

Serialisation

Generation of the serialisers does not seem to consider use of @JAXBElementRefs at all and the resulting XML does not have element names matching the sub-class names listed in the separate @JAXBElementRef annotations. For example an Attribute POJO (from above) with ICompoundPredicate predicate property equal to an instance of SimplePredicate should have the XML from serialisation as <SimplePredicate ..../> (also as above).

The text was updated successfully, but these errors were encountered:

treblereel · 2021-06-09T13:14:23Z

sorry, missed this ...
@manstis thank you for your report, i ll try to fix it asap

manstis · 2021-06-17T10:18:10Z

I believe the interpretation of XMLElementRefs is incorrect.

The "Ant Task Example" in the JAXB documentation shows that the property name itself (in this example tasks) does not become a container for the list of child XML elements (iAddressListRef in MapperXML's documentation).

<target>
  <jar>
   ....
  </jar>
  <javac>
   ....
  </javac>
</target>

vs

<iAddressListRef>
  <_Address1>
    <address>AAAAA</address>
  </_Address1>
</iAddressListRef>

I am investigating how best to fix.

treblereel · 2021-06-25T17:10:40Z

@manstis correct me if i am wrong, looks like the fix is just processing the collection, annotated with @XMLElementRefs as XmlUnwrappedCollection ?

so pitty, can't use XmlElementRef because we need to know all subtypes of annotated field to generate (de)marshallers, so only XmlElementRefs left

class Target {
        @XmlElementRef
         List<Task> tasks;
     }

manstis · 2021-06-25T18:08:03Z

Well, it all depends whether mapper-xml is meant to be a client-side implementation of the JAXB marshallers.

To be honest I was thinking to propose the removal of @XmlUnwrappedCollection as it's not needed by the JAXB reference implementation that runs in the JRE... unless there are insurmountable problems represented client-side; e.g. in order to drop @XmlUnwrappedCollection we'd need reflection to be available. IDK.

I can easily add @XmlUnwrappedCollection when generating the POJOs if we must but I was hoping the serialiser/deserialiser generated with mapper-xml would be able to work only with the JAXB annotations.

Can you explain why @XmlUnwrappedCollection came into being?

manstis · 2021-06-25T18:27:13Z

I do have another problem where an attempt to deserialise a property is being made by the wrong deserializer.

If run my webapp and click the "Load XML" button the following error is thrown:

Unknown property 'SimplePredicate' in (de)serializer com.anstis.pmml.model.CharacteristicBeanXMLDeserializer

The chain of deserialisers is:

ScorecardBeanXMLDeserializerImpl; handles Characteristics:
Deserialiser

map.put("Characteristics", new BeanPropertyDeserializer<Scorecard, com.anstis.pmml.model.Characteristics>() {

            @Override()
            protected XMLDeserializer<?> newDeserializer(org.treblereel.gwt.xml.mapper.api.stream.XMLReader reader) {
                return new com.anstis.pmml.model.CharacteristicsBeanXMLDeserializerImpl();
            }

POJO

    @XmlElement(name = "Characteristics", required = true)
    protected Characteristics characteristics;

XML

  <Scorecard modelName="SampleScorecard" functionName="regression" useReasonCodes="true" reasonCodeAlgorithm="pointsBelow" initialScore="0" baselineMethod="other">
...
    <Characteristics>
      <Characteristic name="departmentScore" reasonCode="RC1" baselineScore="19">
        <Attribute partialScore="-9">
          <SimplePredicate field="department" operator="isMissing"/>
        </Attribute>
        <Attribute partialScore="19">
...

CharacteristicsBeanXMLDeserializerImpl handles the Characteristic list:
Deserialiser

        map.put("Characteristic", new BeanPropertyDeserializer<Characteristics, java.util.List<com.anstis.pmml.model.Characteristic>>() {

            @Override()
            protected XMLDeserializer<?> newDeserializer(org.treblereel.gwt.xml.mapper.api.stream.XMLReader reader) {
                return ListXMLDeserializer.newInstance(new Function<String, XMLDeserializer<com.anstis.pmml.model.Characteristic>>() {

                    @Override()
                    public XMLDeserializer apply(String value) {
                        return new com.anstis.pmml.model.CharacteristicBeanXMLDeserializerImpl();
                    }
                });
            }

POJO

    @XmlElement(name = "Characteristic", required = true)
    protected List<Characteristic> characteristic;

XML

    <Characteristics>
      <Characteristic name="departmentScore" reasonCode="RC1" baselineScore="19">
        <Attribute partialScore="-9">
          <SimplePredicate field="department" operator="isMissing"/>
        </Attribute>
        <Attribute partialScore="19">
          <SimplePredicate field="department" operator="equal" value="marketing"/>
        </Attribute>
        <Attribute partialScore="3">
          <SimplePredicate field="department" operator="equal" value="engineering"/>
        </Attribute>
        <Attribute partialScore="6">
          <SimplePredicate field="department" operator="equal" value="business"/>
        </Attribute>
      </Characteristic>
      <Characteristic name="ageScore" reasonCode="RC2" baselineScore="18">
        <Attribute partialScore="-1">
          <SimplePredicate field="age" operator="isMissing"/>
        </Attribute>

CharacteristicBeanXMLDeserializerImpl handles individual Characteristic:
Deserialiser

        map.put("Attribute", new BeanPropertyDeserializer<Characteristic, java.util.List<com.anstis.pmml.model.Attribute>>() {

            @Override()
            protected XMLDeserializer<?> newDeserializer(org.treblereel.gwt.xml.mapper.api.stream.XMLReader reader) {
                return ListXMLDeserializer.newInstance(new Function<String, XMLDeserializer<com.anstis.pmml.model.Attribute>>() {

                    @Override()
                    public XMLDeserializer apply(String value) {
                        return new com.anstis.pmml.model.AttributeBeanXMLDeserializerImpl();
                    }
                });
            }

POJO

    @XmlElement(name = "Attribute", required = true)
    protected List<Attribute> attribute;

XML

      <Characteristic name="departmentScore" reasonCode="RC1" baselineScore="19">
        <Attribute partialScore="-9">
          <SimplePredicate field="department" operator="isMissing"/>
        </Attribute>
        <Attribute partialScore="19">
          <SimplePredicate field="department" operator="equal" value="marketing"/>
        </Attribute>
        <Attribute partialScore="3">
          <SimplePredicate field="department" operator="equal" value="engineering"/>
        </Attribute>
        <Attribute partialScore="6">
          <SimplePredicate field="department" operator="equal" value="business"/>
        </Attribute>
      </Characteristic>

The SimplePredicate should be handled by the Attribute deserialiser:
Deserialiser

        map.put("predicate", new BeanPropertyDeserializer<Attribute, com.anstis.pmml.model.ICompoundPredicate>() {

            @Override()
            protected XMLDeserializer<?> newDeserializer(org.treblereel.gwt.xml.mapper.api.stream.XMLReader reader) {
                return new Function<String, XMLDeserializer<com.anstis.pmml.model.ICompoundPredicate>>() {

                    @Override()
                    public XMLDeserializer apply(String value) {
                        if ("True".equals(value))
                            return new com.anstis.pmml.model.TrueBeanXMLDeserializerImpl();
                        if ("CompoundPredicate".equals(value))
                            return new com.anstis.pmml.model.CompoundPredicateBeanXMLDeserializerImpl();
                        if ("False".equals(value))
                            return new com.anstis.pmml.model.FalseBeanXMLDeserializerImpl();
                        if ("SimplePredicate".equals(value))
                            return new com.anstis.pmml.model.SimplePredicateBeanXMLDeserializerImpl();
                        if ("SimpleSetPredicate".equals(value))
                            return new com.anstis.pmml.model.SimpleSetPredicateBeanXMLDeserializerImpl();
                        throw new Error(value);
                    }
                }.apply(xsiTagChooser.apply(reader));
            }

POJO

    protected List<Extension> extension;
    @XmlElementRefs({
        @XmlElementRef(name = "SimplePredicate", namespace = "http://www.dmg.org/PMML-4_4", type = SimplePredicate.class, required = false),
        @XmlElementRef(name = "CompoundPredicate", namespace = "http://www.dmg.org/PMML-4_4", type = CompoundPredicate.class, required = false),
        @XmlElementRef(name = "SimpleSetPredicate", namespace = "http://www.dmg.org/PMML-4_4", type = SimpleSetPredicate.class, required = false),
        @XmlElementRef(name = "True", namespace = "http://www.dmg.org/PMML-4_4", type = True.class, required = false),
        @XmlElementRef(name = "False", namespace = "http://www.dmg.org/PMML-4_4", type = False.class, required = false)
    })
    protected ICompoundPredicate predicate;

XML

        <Attribute partialScore="-3">
          <SimplePredicate field="age" operator="lessOrEqual" value="18"/>
        </Attribute>
        <Attribute partialScore="0">
          <CompoundPredicate booleanOperator="and">
            <SimplePredicate field="age" operator="greaterThan" value="18"/>
            <SimplePredicate field="age" operator="lessOrEqual" value="29"/>
          </CompoundPredicate>
        </Attribute>

As you can see; I have a @XmlElementRefs on a NON-collection field. IDK if this is the bug (support for this scenario).

treblereel · 2021-06-25T18:57:09Z

@manstis thanks you for your detailed report, i am working on it right now.

treblereel · 2021-06-30T02:50:15Z

@manstis i hope now it's fixed #85

the only thing isn't really clear for me, is namespace processing, but looks like you don't need it

treblereel · 2021-06-30T02:55:51Z

@XmlElements is also must be fixed ...

manstis · 2021-07-01T11:50:54Z

@treblereel I checked out your branch and built locally.

Unfortunately my "PMML" model still presents the Unknown property 'SimplePredicate' in (de)serializer com.anstis.pmml.model.CharacteristicBeanXMLDeserializerImpl error I reported. Did you try my use case?

tiagobento · 2021-07-01T13:53:31Z

Mirrored this on https://issues.redhat.com/browse/KOGITO-5457. Please continue the discussions here.

treblereel · 2021-07-01T13:56:19Z

@manstis ok, one moment plz ...

treblereel · 2021-07-02T17:05:06Z

@manstis hmm, no exception

  @Test
  public void test1() throws XMLStreamException {

    Attribute attribute = new Attribute();
    SimplePredicate simplePredicate = new SimplePredicate();

    attribute.setPredicate(simplePredicate);
    String xml = mapper.write(attribute);

    System.out.println("RESULT \n" + xml);

    assertEquals(xml, mapper.write(mapper.read(mapper.write(attribute))));
  }

with branch @XmlElementRefs_fix

manstis · 2021-07-02T19:25:24Z

If I run the equivalent in the JRE using the JAXB reference implementation, it works fine:

Attribute attribute = new Attribute();
SimplePredicate simplePredicate = new SimplePredicate();
attribute.setPredicate(simplePredicate);

JAXBContext context = JAXBContext.newInstance(Attribute.class);
context.createMarshaller().marshal(attribute, System.out);

This therefore remains an issue with the mapper-xml generated (JAXB) unmarshaller :-(

manstis · 2021-07-02T19:41:42Z

@manstis hmm, no exception

  @Test
  public void test1() throws XMLStreamException {

    Attribute attribute = new Attribute();
    SimplePredicate simplePredicate = new SimplePredicate();

    attribute.setPredicate(simplePredicate);
    String xml = mapper.write(attribute);

    System.out.println("RESULT \n" + xml);

    assertEquals(xml, mapper.write(mapper.read(mapper.write(attribute))));
  }

with branch @XmlElementRefs_fix

BTW, it's the unmarshalling that is failing; not the marshalling. See the JAXB RI equivalent here.

treblereel · 2021-07-02T19:56:14Z

@manstis here is marshalling -> unmarshalling->marshalling -> unmarshalling

it doesn't throw an exception

  Attribute_XMLMapperImpl mapper = Attribute_XMLMapperImpl.INSTANCE;


  assertNotNull(
        mapper.read(
            "<?xml version='1.0' encoding='UTF-8'?><Attribute><Extension/><SimplePredicate><Extension/></SimplePredicate></Attribute>"));

ps: it's not a master, it's branch @XmlElementRefs_fix

manstis · 2021-07-02T20:04:57Z

Yes, I know it's on the branch @treblereel.

Can you try the whole PMML file I am using and not just the Attribute snippet? The issue seems to be when unmarshalling a collection of Attributes within a Characteristic.

treblereel · 2021-07-02T20:46:41Z

yeap, sure

manstis · 2021-07-02T20:57:31Z

@treblereel FYI, I've re-checked I'm using the correct mapper-xml branch locally and that the unmarshalling error remains.

treblereel · 2021-07-05T18:17:08Z

@manstis i have added PMMLTest.java based on your pmml beans, no exception :(

May i ask you to attach your xml ?

manstis · 2021-07-05T19:27:47Z

@treblereel Sure, I appreciate your time investigating. It is available here.

manstis · 2021-07-05T19:29:15Z

It unmarshals fine using JAXB's Reference Implementation.

https://github.com/manstis/marshaller/blob/main/marshaller-jre/src/main/java/com/anstis/pmml/jaxb/Main.java#L24

manstis · 2021-07-05T19:45:30Z

@treblereel The XML produced from the generated marshallers is wrong:

<?xml version='1.0' encoding='UTF-8'?>
<PMML>
<AnomalyDetectionModel>
  <Extension/>
</AnomalyDetectionModel>
<Scorecard baselineMethod="other" reasonCodeAlgorithm="pointsBelow">
  <Extension/>
  <Characteristics>
    <Extension/>
  <Characteristic>
    <Characteristic>
      <Extension/>
      <Attribute>
        <Attribute reasonCode="code -539804736" partialScore="0.7535918206821989">
          <Extension/>
          <SimplePredicate>
            <Extension/>
          </SimplePredicate>
        </Attribute>
        <Attribute reasonCode="code -2034742762" partialScore="0.6081749931167616">
          <Extension/>
          <SimplePredicate>
            <Extension/>
          </SimplePredicate>
        </Attribute>
        <Attribute reasonCode="code -310489214" partialScore="0.37911382999971766">
          <Extension/>
          <SimplePredicate>
            <Extension/>
          </SimplePredicate>
        </Attribute>
        <Attribute reasonCode="code 1002600342" partialScore="0.4530774516551558">
          <Extension/>
          <SimplePredicate>
            <Extension/>
          </SimplePredicate>
        </Attribute>
        <Attribute reasonCode="code 2000510915" partialScore="0.8483799343127182">
          <Extension/>
          <SimplePredicate>
            <Extension/>
          </SimplePredicate>
        </Attribute>
        <Attribute reasonCode="code 1357614927" partialScore="0.6452062432246841">
          <Extension/>
          <SimplePredicate>
            <Extension/>
          </SimplePredicate>
        </Attribute>
      </Attribute>
    </Characteristic>
  </Characteristic>
</Characteristics>
</Scorecard>
<Extension/>
</PMML>

Please note the double Characteristic and Attribute elements:

  <Characteristic>
    <Characteristic>
      <Extension/>
      <Attribute>
        <Attribute reasonCode="code -539804736" partialScore="0.7535918206821989">
    ...

treblereel · 2021-07-09T04:46:51Z

@manstis you were right, my collection (de)ser is wrong, so i reimplemented it to be more jaxb compatible.

so remarshalled https://raw.githubusercontent.com/manstis/marshaller/main/marshaller-jre/src/main/resources/jaxb/pmml.xml

is:

<?xml version='1.0' encoding='UTF-8'?>
<PMML version="4.4">
	<Header copyright="www.dmg.org" description="Sample scorecard">
		<Timestamp/>
	</Header>
	<DataDictionary>
		<DataField optype="categorical" dataType="string" isCyclic="0" name="department"/>
		<DataField optype="continuous" dataType="integer" isCyclic="0" name="age"/>
		<DataField optype="continuous" dataType="double" isCyclic="0" name="income"/>
		<DataField optype="continuous" dataType="double" isCyclic="0" name="overallScore"/>
	</DataDictionary>
	<Scorecard functionName="regression" baselineMethod="other" initialScore="0.0" modelName="SampleScorecard" useReasonCodes="true" reasonCodeAlgorithm="pointsBelow">
		<MiningSchema>
			<MiningField invalidValueTreatment="asMissing" name="department" outliers="asIs" usageType="active"/>
			<MiningField invalidValueTreatment="asMissing" name="age" outliers="asIs" usageType="active"/>
			<MiningField invalidValueTreatment="asMissing" name="income" outliers="asIs" usageType="active"/>
			<MiningField invalidValueTreatment="returnInvalid" name="overallScore" outliers="asIs" usageType="predicted"/>
		</MiningSchema>
		<Output>
			<OutputField ruleFeature="consequent" dataType="double" isMultiValued="0" rankBasis="confidence" optype="continuous" feature="predictedValue" name="Final Score" rank="1" rankOrder="descending" algorithm="exclusiveRecommendation"/>
			<OutputField ruleFeature="consequent" dataType="string" isMultiValued="0" rankBasis="confidence" optype="categorical" feature="reasonCode" name="Reason Code 1" rank="1" rankOrder="descending" algorithm="exclusiveRecommendation"/>
			<OutputField ruleFeature="consequent" dataType="string" isMultiValued="0" rankBasis="confidence" optype="categorical" feature="reasonCode" name="Reason Code 2" rank="2" rankOrder="descending" algorithm="exclusiveRecommendation"/>
			<OutputField ruleFeature="consequent" dataType="string" isMultiValued="0" rankBasis="confidence" optype="categorical" feature="reasonCode" name="Reason Code 3" rank="3" rankOrder="descending" algorithm="exclusiveRecommendation"/>
		</Output>
		<Characteristics>
			<Characteristic baselineScore="19.0" name="departmentScore" reasonCode="RC1">
				<Attribute partialScore="-9.0">
					<SimplePredicate field="department" operator="isMissing"/>
				</Attribute>
				<Attribute partialScore="19.0">
					<SimplePredicate field="department" value="marketing" operator="equal"/>
				</Attribute>
				<Attribute partialScore="3.0">
					<SimplePredicate field="department" value="engineering" operator="equal"/>
				</Attribute>
				<Attribute partialScore="6.0">
					<SimplePredicate field="department" value="business" operator="equal"/>
				</Attribute>
			</Characteristic>
			<Characteristic baselineScore="18.0" name="ageScore" reasonCode="RC2">
				<Attribute partialScore="-1.0">
					<SimplePredicate field="age" operator="isMissing"/>
				</Attribute>
				<Attribute partialScore="-3.0">
					<SimplePredicate field="age" value="18" operator="lessOrEqual"/>
				</Attribute>
				<Attribute partialScore="0.0">
					<CompoundPredicate booleanOperator="and">
						<SimplePredicate field="age" value="18" operator="greaterThan"/>
						<SimplePredicate field="age" value="29" operator="lessOrEqual"/>
					</CompoundPredicate>
				</Attribute>
				<Attribute partialScore="12.0">
					<CompoundPredicate booleanOperator="and">
						<SimplePredicate field="age" value="29" operator="greaterThan"/>
						<SimplePredicate field="age" value="39" operator="lessOrEqual"/>
					</CompoundPredicate>
				</Attribute>
				<Attribute partialScore="18.0">
					<SimplePredicate field="age" value="39" operator="greaterThan"/>
				</Attribute>
			</Characteristic>
			<Characteristic baselineScore="10.0" name="incomeScore" reasonCode="RC3">
				<Attribute partialScore="5.0">
					<SimplePredicate field="income" operator="isMissing"/>
				</Attribute>
				<Attribute partialScore="26.0">
					<SimplePredicate field="income" value="1000" operator="lessOrEqual"/>
				</Attribute>
				<Attribute partialScore="5.0">
					<CompoundPredicate booleanOperator="and">
						<SimplePredicate field="income" value="1000" operator="greaterThan"/>
						<SimplePredicate field="income" value="2500" operator="lessOrEqual"/>
					</CompoundPredicate>
				</Attribute>
				<Attribute partialScore="-3.0">
					<SimplePredicate field="income" value="2500" operator="greaterThan"/>
				</Attribute>
			</Characteristic>
		</Characteristics>
	</Scorecard>
</PMML>

treblereel · 2021-07-09T04:49:34Z

and yeah, @XmlUnwrappedCollection is totally useless and must me eliminated

manstis · 2021-07-12T13:01:32Z

Hi @treblereel I can confirm your changes in #85 resolve the issues I've reported. Many thanks.

I have some other issues now but I will investigate what may be causing them (if I marshal the classes to XML I am getting quite a few attributes set that were not in the original XML). IDK whether it's an unmarshalling or marshalling issue at the moment; or even something else. I'll investigate and let your know.

For now, please feel free to merge #85, resolve this issue and close https://issues.redhat.com/browse/KOGITO-5457.

treblereel mentioned this issue Jun 30, 2021

@xml element refs fix #85

Merged

treblereel closed this as completed Jul 12, 2021

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Different behaviour of (un)marshaller vs JAXB reference implementation #84

Different behaviour of (un)marshaller vs JAXB reference implementation #84

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Different behaviour of (un)marshaller vs JAXB reference implementation #84

Different behaviour of (un)marshaller vs JAXB reference implementation #84

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manstis commented Jun 1, 2021

Deserialisation

Serialisation

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