SDC library, it does not set the answer to the definition field if the field type is choice type. #674

santosh-pingle · 2021-07-26T02:21:29Z

Describe the bug
Definition url is "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.value.value",
Observation.value is abstract Type, it is declared as value property in Observation resource class.
To update the answer to the definition field(Observation.value.value), it is required to create instances of fields present in the definition url.

"item": [
    {
      "text": "Temperature",
      "type": "group",
      "linkId": "5.0.0",
      "code": [
        {
          "code": "8310-5",
          "display": "Temperature",
          "system": "http://loinc.org"
        }
      ],
      "definition": "http://hl7.org/fhir/StructureDefinition/Observation",
      "extension": [
        {
          "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
          "valueExpression": {
            "language": "application/x-fhir-query",
            "expression": "Observation",
            "name": "temperature"
          }
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
          "valueCodeableConcept": {
            "coding": [
              {
                "system": "http://hl7.org/fhir/questionnaire-item-control",
                "code": "page",
                "display": "Page"
              }
            ],
            "text": "Page"
          }
        }
      ],
      "item": [
        {
          "text": "Add instructions for capturing temperature",
          "type": "display",
          "linkId": "5.0.1"
        },
        {
          "type": "group",
          "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.value",
          "extension": [
            {
              "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemExtractionContext",
              "valueExpression": {
                "language": "application/x-fhir-query",
                "expression": "Quantity",
                "name": "quantity"
              }
            }
          ],
          "item": [
            {
              "definition": "http://hl7.org/fhir/StructureDefinition/Observation#Observation.value.value",
              "text": "Record temperature",
              "type": "decimal",
              "linkId": "5.1.0",
              "extension": [
                {
                  "url": "http://hl7.org/fhir/StructureDefinition/minValue",
                  "valueDecimal": 35.0
                },
                {
                  "url": "http://hl7.org/fhir/StructureDefinition/maxValue",
                  "valueDecimal": 45.0
                }
              ]
            },
            {
              "text": "Unit",

Component
SDC library

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

ekigamba · 2021-07-26T08:08:34Z

@santosh-pingle Can you print the error you are getting here?

santosh-pingle · 2021-07-26T09:15:51Z

@ekigamba
Issue 1 :
It was throwing an Instantiation exception
java.lang.InstantiationException: java.lang.Class<org.hl7.fhir.r4.model.Type> cannot be instantiated
at java.lang.Class.newInstance(Native Method)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extractField(ResourceMapper.kt:253)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extractFields(ResourceMapper.kt:207)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extractField(ResourceMapper.kt:233)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extractFields(ResourceMapper.kt:207)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extractByDefinitions(ResourceMapper.kt:116)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extract(ResourceMapper.kt:92)
at com.google.android.fhir.datacapture.mapping.ResourceMapper.extract$default(ResourceMapper.kt:89)

Below fix is added by considering expression value of extension which is declared in questionnaire json.
https://github.com/google/android-fhir/pull/675/files#diff-4d2985aba5e8203b97cc5dc2eac7dbbd0c7832be34a27036d1ecfb8e4a3a3e50R261

Issue 2
Now, definition field returns null for nested field on abstract type and does not update the answer.

https://github.com/google/android-fhir/pull/675/files#diff-4d2985aba5e8203b97cc5dc2eac7dbbd0c7832be34a27036d1ecfb8e4a3a3e50R451
https://github.com/google/android-fhir/pull/675/files#diff-4d2985aba5e8203b97cc5dc2eac7dbbd0c7832be34a27036d1ecfb8e4a3a3e50R451

santosh-pingle · 2021-07-26T09:59:50Z

@epicadk

Could you please give me more insights on " I think maybe you could update the title to
.... is choice type"

ekigamba · 2021-07-26T10:16:41Z

@santosh-pingle This seems to be an edge-case that we were not aware of. Is this the standard for properties of value for all Resources? If so, you can create a generic solution that will fix this. The only issue is that the specification clearly states that you should have valueDecimal and not just value as the property. However, I can see the ~~HL7~~ HAPI models only have value and uses the abstract Type to hold all other types

santosh-pingle · 2021-07-26T10:48:34Z

@ekigamba
I am not sure about the standard for properties of value for all Resources, but its declared as value field/property name for QuantityValue data type and many more (CodeableConcept, StringType ..) in Observation resource.
Therefore, definition url is declared as Observation.value in questionnaire and not as Observation.quantityValue.

User input value for temperature is required to be updated as Quantity.value, which is Observation.quantityValue.value as per specification and Observation.value.value as per hl7.fhir.r4.model model
https://hl7.org/fhir/R4/bodytemp.html

ekigamba · 2021-07-26T14:23:33Z

@santosh-pingle
The above is mostly correct. However, as per the spec if the property is described as value[X], the actual property is either of the listed sub-items such as valueString, valueDateTime, valueQuantity as seen in this QuestionnaireResponse example https://www.hl7.org/fhir/questionnaireresponse-example-f201-lifelines.json.html. The HAPI models don't follow this. I guess what I mean is that Authoring a questionnaire for definition-based extraction requires following the FHIR models/data-types and not the HAPI models. The current implementation infers the Type from the HAPI Model assuming that the models strictly follow the FHIR specification, in cases whereby this isn't the case, we need to handle that separately. I think that this is such a case and you can come up with a generic fix in cases where the inferred data-type is Type and the field starts with value

For the other errors above, I see that this assumes multiple resource generation for definition-based extraction was implemented. I am not sure of the current state but we had an issue tracking this here #504

epicadk · 2021-07-26T14:43:22Z

@epicadk

Could you please give me more insights on " I think maybe you could update the title to .... is choice type"

Sorry, I wasn't really sure so I wanted to research a bit before commenting.
Anyways what I wanted to say was that Quantity.value is a choice type so maybe an appropriate title for the issue would be

SDC library, it does not set the answer to the definition field if the field type is choice type

because you'll face the same issue for other choice type fields (like Extension.Value)

refer http://www.hl7.org/fhir/formats.html#choice
list of all choice types http://www.hl7.org/fhir/choice-elements.json

In hapi the Type type is only used for choice types,
as the org.hl7.fhir.r4.model.Type javdoc says

An element that is a type. Used when the element type in FHIR is a choice of more than one data type

refer https://github.com/hapifhir/org.hl7.fhir.core/blob/99fcac64ac35ca7dc3a4aa9922684ac7fdb0ee7b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Type.java#L39

santosh-pingle · 2021-07-26T16:26:17Z

@epicadk
Could you please give me more insights on " I think maybe you could update the title to .... is choice type"

Sorry, I wasn't really sure so I wanted to research a bit before commenting.
Anyways what I wanted to say was that Quantity.value is a choice type so maybe an appropriate title for the issue would be

SDC library, it does not set the answer to the definition field if the field type is choice type

because you'll face the same issue for other choice type fields (like Extension.Value)

refer http://www.hl7.org/fhir/formats.html#choice
list of all choice types http://www.hl7.org/fhir/choice-elements.json

In hapi the Type type is only used for choice types,
as the org.hl7.fhir.r4.model.Type javdoc says

An element that is a type. Used when the element type in FHIR is a choice of more than one data type

refer https://github.com/hapifhir/org.hl7.fhir.core/blob/99fcac64ac35ca7dc3a4aa9922684ac7fdb0ee7b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Type.java#L39

Sure, I have updated title with choice type.

santosh-pingle · 2021-07-26T16:42:53Z

@ekigamba

@santosh-pingle
The above is mostly correct. However, as per the spec if the property is described as value[X], the actual property is either of the listed sub-items such as valueString, valueDateTime, valueQuantity as seen in this QuestionnaireResponse example https://www.hl7.org/fhir/questionnaireresponse-example-f201-lifelines.json.html. The HAPI models don't follow this. I guess what I mean is that Authoring a questionnaire for definition-based extraction requires following the FHIR models/data-types and not the HAPI models. The current implementation infers the Type from the HAPI Model assuming that the models strictly follow the FHIR specification, in cases whereby this isn't the case, we need to handle that separately. I think that this is such a case and you can come up with a generic fix in cases where the inferred data-type is Type and the field starts with value

For the other errors above, I see that this assumes multiple resource generation for definition-based extraction was implemented. I am not sure of the current state but we had an issue tracking this here #504

Yes, FHIR model data types need to be considered in definition based extraction while fixing this issue with generic approach.

santosh-pingle · 2021-07-26T16:48:38Z

Working on it.

santosh-pingle · 2021-07-28T07:34:41Z

I will try to create PR by eod today to unblock #625

santosh-pingle added type:bug Something isn't working data-capture labels Jul 26, 2021

santosh-pingle mentioned this issue Jul 26, 2021

Initiate new screener encounter #625

Closed

santosh-pingle changed the title ~~SDC library, it does not set the answer to the definition field if the field type is abstract type.~~ SDC library, it does not set the answer to the definition field if the field type is choice type. Jul 26, 2021

santosh-pingle mentioned this issue Jul 28, 2021

Update answers to the choice of data type field. #676

Merged

8 tasks

Tarun-Bhardwaj added the Q3 2021 label Aug 3, 2021

santosh-pingle closed this as completed in #676 Aug 4, 2021

Tarun-Bhardwaj removed the Q3 2021 label Aug 20, 2021

Tarun-Bhardwaj assigned santosh-pingle Aug 20, 2021

Tarun-Bhardwaj added the Released label Sep 27, 2021

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SDC library, it does not set the answer to the definition field if the field type is choice type. #674

SDC library, it does not set the answer to the definition field if the field type is choice type. #674

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SDC library, it does not set the answer to the definition field if the field type is choice type. #674

SDC library, it does not set the answer to the definition field if the field type is choice type. #674

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