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A service that implements the FHIR standard
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Profile Snapshot not being generated #4018

Open EniacMlezi opened 2 months ago

EniacMlezi commented 2 months ago

Describe the bug During validation of a Resource on Create (ProfileValidationOnCreate = true), I get the following error: Internal logic failure: StructureDefinition 'http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode' has no snapshot component. (Parameter 'sd')

Which is true, but shouldn't profile snapshots be generated?

These are the profiles I'm trying to use: SoapLine:

{
  "resourceType": "StructureDefinition",
  "id": "nl-core-SOAPReport.SOAPLine",
  "text": {
    "status": "empty",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">No narrative is provided for definitional resources. A human-readable rendering can be found in the implementation guide(s) where this resource is used.</div>"
  },
  "url": "http://nictiz.nl/fhir/StructureDefinition/nl-core-SOAPReport.SOAPLine",
  "name": "NlcoreSOAPReportSOAPLine",
  "title": "nl core SOAPReport.SOAPLine",
  "status": "draft",
  "publisher": "Nictiz",
  "contact": [
    {
      "name": "Nictiz",
      "telecom": [
        {
          "system": "url",
          "value": "https://www.nictiz.nl",
          "use": "work"
        }
      ]
    }
  ],
  "description": "A SOAP report is a textual report of a (partial) consult with relation to a single problem according to the SOAP structure. SOAP (acronym for subjective, objective, assessment, plan) is a method used by health professionals to structurally record information that comes up during contact between the patient and a health professionals in the patient's record. The following standardized format is used for reporting:\r\n\r\n* Subjective: the patient's complaint and request for help and the amnesic data\r\n* Objective: the findings from the physical and supplementary examination.\r\n* Assessment: the working hypothesis and the thinking process, for example a differential diagnosis of the healthcare professional.\r\n* Plan: the diagnostic plan or treatment plan and what has been discussed or agreed with the patient.\r\n\r\nThe SOAP report is mainly used in general practice care.\r\n\r\nNote: the zib doesn't state explicitly if zib SOAPReport pertains a consult or a partial consult, but it has become clear that the zib, and thus this profile, should be interpreted as a partial consult with relation to a single problem (see <https://bits.nictiz.nl/browse/ZIB-1474>). The text above has been adjusted according to this insight.",
  "purpose": "A derived profile from [zib-SOAPReport.SOAPLine](http://nictiz.nl/fhir/StructureDefinition/zib-SOAPReport.SOAPLine) to provide a version better suited for implementation purposes. This profile augments the base profile with elements found in the various use cases that have adopted the zib.",
  "copyright": "Copyright and related rights waived via CC0, https://creativecommons.org/publicdomain/zero/1.0/. This does not apply to information from third parties, for example a medical terminology system. The implementer alone is responsible for identifying and obtaining any necessary licenses or authorizations to utilize third party IP in connection with the specification or otherwise.",
  "fhirVersion": "4.0.1",
  "mapping": [
    {
      "identity": "zib-soapreport-v1.0-2020EN",
      "uri": "https://zibs.nl/wiki/SOAPReport-v1.0(2020EN)",
      "name": "zib SOAPReport-v1.0(2020EN)"
    }
  ],
  "kind": "resource",
  "abstract": false,
  "type": "Observation",
  "baseDefinition": "http://nictiz.nl/fhir/StructureDefinition/zib-SOAPReport.SOAPLine",
  "derivation": "constraint",
  "differential": {
    "element": [
      {
        "id": "Observation",
        "path": "Observation",
        "comment": "Zib SOAPReport is implemented using two profiles: this profile implements the SOAPLine concept of the zib, while <http://nictiz.nl/fhir/StructureDefinition/nl-core-SOAPReport> represents the SOAPReport concept of the zib.",
        "alias": [
          "nl-core-SOAPReport.SOAPLine"
        ]
      },
      {
        "id": "Observation.subject",
        "path": "Observation.subject",
        "type": [
          {
            "code": "Reference",
            "targetProfile": [
              "http://hl7.org/fhir/StructureDefinition/Patient",
              "http://hl7.org/fhir/StructureDefinition/Group",
              "http://hl7.org/fhir/StructureDefinition/Device",
              "http://hl7.org/fhir/StructureDefinition/Location",
              "http://nictiz.nl/fhir/StructureDefinition/nl-core-Patient"
            ]
          }
        ]
      }
    ]
  }
}

ZIB SoapLine:

{
  "resourceType": "StructureDefinition",
  "id": "zib-SOAPReport.SOAPLine",
  "text": {
    "status": "empty",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">No narrative is provided for definitional resources. A human-readable rendering can be found in the implementation guide(s) where this resource is used.</div>"
  },
  "url": "http://nictiz.nl/fhir/StructureDefinition/zib-SOAPReport.SOAPLine",
  "name": "ZibSOAPReportSOAPLine",
  "title": "zib SOAPReport.SOAPLine",
  "status": "draft",
  "publisher": "Nictiz",
  "contact": [
    {
      "name": "Nictiz",
      "telecom": [
        {
          "system": "url",
          "value": "https://www.nictiz.nl",
          "use": "work"
        }
      ]
    }
  ],
  "description": "A SOAP report is a textual report of a (partial) consult with relation to a single problem according to the SOAP structure. SOAP (acronym for subjective, objective, assessment, plan) is a method used by health professionals to structurally record information that comes up during contact between the patient and a health professionals in the patient's record. The following standardized format is used for reporting:\r\n\r\n* Subjective: the patient's complaint and request for help and the amnesic data\r\n* Objective: the findings from the physical and supplementary examination.\r\n* Assessment: the working hypothesis and the thinking process, for example a differential diagnosis of the healthcare professional.\r\n* Plan: the diagnostic plan or treatment plan and what has been discussed or agreed with the patient.\r\n\r\nThe SOAP report is mainly used in general practice care.\r\n\r\nNote: the zib doesn't state explicitly if zib SOAPReport pertains a consult or a partial consult, but it has become clear that the zib, and thus this profile, should be interpreted as a partial consult with relation to a single problem (see <https://bits.nictiz.nl/browse/ZIB-1474>). The text above has been adjusted according to this insight.",
  "purpose": "This Observation resource represents the SOAPLine concept of the Dutch [zib ('Zorginformatiebouwsteen', i.e. Health and Care Information Model) SOAPReport v1.0 (2020)](https://zibs.nl/wiki/SOAPReport-v1.0(2020EN)).",
  "copyright": "Copyright and related rights waived via CC0, https://creativecommons.org/publicdomain/zero/1.0/. This does not apply to information from third parties, for example a medical terminology system. The implementer alone is responsible for identifying and obtaining any necessary licenses or authorizations to utilize third party IP in connection with the specification or otherwise.",
  "fhirVersion": "4.0.1",
  "mapping": [
    {
      "identity": "zib-soapreport-v1.0-2020EN",
      "uri": "https://zibs.nl/wiki/SOAPReport-v1.0(2020EN)",
      "name": "zib SOAPReport-v1.0(2020EN)"
    }
  ],
  "kind": "resource",
  "abstract": true,
  "type": "Observation",
  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation",
  "derivation": "constraint",
  "differential": {
    "element": [
      {
        "id": "Observation",
        "path": "Observation",
        "short": "SOAPLine",
        "comment": "Zib SOAPReport is implemented using two profiles: this profile implements the SOAPLine concept of the zib, while <http://nictiz.nl/fhir/StructureDefinition/zib-SOAPReport> represents the SOAPReport concept of the zib.",
        "alias": [
          "SOEPRegel"
        ],
        "constraint": [
          {
            "key": "zib-SOAPReport-1",
            "severity": "error",
            "human": "In a SOAP report an ICPC code may be assigned, but only to the S and A line.",
            "expression": "extension('http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode').exists() implies (code.coding.where(code = '255362007' and system = 'http://snomed.info/sct').exists() or code.coding.where(code = '129265001' and system = 'http://snomed.info/sct').exists())"
          }
        ],
        "mapping": [
          {
            "identity": "zib-soapreport-v1.0-2020EN",
            "map": "NL-CM:13.6.4",
            "comment": "SOAPLine"
          }
        ]
      },
      {
        "id": "Observation.extension:soapLineCode",
        "path": "Observation.extension",
        "sliceName": "soapLineCode",
        "type": [
          {
            "code": "Extension",
            "profile": [
              "http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode"
            ]
          }
        ],
        "condition": [
          "zib-SOAPReport-1"
        ]
      },
      {
        "id": "Observation.extension:soapLineCode.value[x]",
        "path": "Observation.extension.value[x]",
        "condition": [
          "zib-SOAPReport-1"
        ]
      },
      {
        "id": "Observation.status",
        "path": "Observation.status",
        "comment": "Unless explicitly recorded, a value of _final_ would be expected."
      },
      {
        "id": "Observation.code",
        "path": "Observation.code",
        "short": "SOAPLineHeader",
        "definition": "The name of the SOAP line as a coded description. In a SOAP report this can be one of the following: subjective, objective, assessment or plan.",
        "alias": [
          "SOEPRegelNaam"
        ],
        "condition": [
          "zib-SOAPReport-1"
        ],
        "binding": {
          "strength": "required",
          "valueSet": "http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.13.6.2--20200901000000"
        },
        "mapping": [
          {
            "identity": "zib-soapreport-v1.0-2020EN",
            "map": "NL-CM:13.6.6",
            "comment": "SOAPLineHeader"
          }
        ]
      },
      {
        "id": "Observation.code.coding",
        "path": "Observation.code.coding",
        "condition": [
          "zib-SOAPReport-1"
        ]
      },
      {
        "id": "Observation.value[x]",
        "path": "Observation.value[x]",
        "slicing": {
          "discriminator": [
            {
              "type": "type",
              "path": "$this"
            }
          ],
          "rules": "open"
        }
      },
      {
        "id": "Observation.value[x]:valueString",
        "path": "Observation.value[x]",
        "sliceName": "valueString",
        "short": "SOAPLineText",
        "definition": "The actual content of the section as free formatted text.",
        "alias": [
          "SOEPRegelTekst"
        ],
        "type": [
          {
            "code": "string"
          }
        ],
        "mapping": [
          {
            "identity": "zib-soapreport-v1.0-2020EN",
            "map": "NL-CM:13.6.7",
            "comment": "SOAPLineText"
          }
        ]
      }
    ]
  }
}

SoapLineCode Extension:

{
  "resourceType": "StructureDefinition",
  "id": "ext-SOAPReport.SOAPLineCode",
  "text": {
    "status": "empty",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">No narrative is provided for definitional resources. A human-readable rendering can be found in the implementation guide(s) where this resource is used.</div>"
  },
  "url": "http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode",
  "name": "ExtSOAPReportSOAPLineCode",
  "title": "ext SOAPReport.SOAPLineCode",
  "status": "draft",
  "publisher": "Nictiz",
  "contact": [
    {
      "name": "Nictiz",
      "telecom": [
        {
          "system": "url",
          "value": "https://www.nictiz.nl",
          "use": "work"
        }
      ]
    }
  ],
  "description": "An extension to provide the SOAPLine code. The extension can be seen as an addition to the SOAPLineHeader and SOAPLineText concept mapped to the code and text element.",
  "purpose": "This extension represents the SOAPLineCode concept of the Dutch [zib ('Zorginformatiebouwsteen', i.e. Health and Care Information Model) SOAPReport v1.0 (2020)](https://zibs.nl/wiki/SOAPReport-v1.0(2020EN)).",
  "copyright": "Copyright and related rights waived via CC0, https://creativecommons.org/publicdomain/zero/1.0/. This does not apply to information from third parties, for example a medical terminology system. The implementer alone is responsible for identifying and obtaining any necessary licenses or authorizations to utilize third party IP in connection with the specification or otherwise.",
  "fhirVersion": "4.0.1",
  "mapping": [
    {
      "identity": "zib-soapreport-v1.0-2020EN",
      "uri": "https://zibs.nl/wiki/SOAPReport-v1.0(2020EN)",
      "name": "zib SOAPReport-v1.0(2020EN)"
    }
  ],
  "kind": "complex-type",
  "abstract": false,
  "context": [
    {
      "type": "element",
      "expression": "Observation"
    }
  ],
  "type": "Extension",
  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",
  "derivation": "constraint",
  "differential": {
    "element": [
      {
        "id": "Extension",
        "path": "Extension",
        "max": "1"
      },
      {
        "id": "Extension.url",
        "path": "Extension.url",
        "fixedUri": "http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode"
      },
      {
        "id": "Extension.value[x]",
        "path": "Extension.value[x]",
        "short": "SOAPLineCode",
        "definition": "Coded values can be added to a line that describe essential aspects of the line.\r\nIn a SOAP report an ICPC code may be assigned, but only to the S and A line.",
        "alias": [
          "SOEPRegelCode"
        ],
        "type": [
          {
            "code": "CodeableConcept"
          }
        ],
        "binding": {
          "strength": "required",
          "valueSet": "http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.13.6.1--20200901000000"
        },
        "mapping": [
          {
            "identity": "zib-soapreport-v1.0-2020EN",
            "map": "NL-CM:13.6.5",
            "comment": "SOAPLineCode"
          }
        ]
      },
      {
        "id": "Extension.value[x].coding",
        "path": "Extension.value[x].coding",
        "binding": {
          "strength": "required",
          "valueSet": "http://decor.nictiz.nl/fhir/ValueSet/2.16.840.1.113883.2.4.3.11.60.40.2.13.6.1--20200901000000"
        }
      }
    ]
  }
}

FHIR Version? R4

Data provider? SQL Server

To Reproduce Steps to reproduce the behavior:

  1. Set ProfileValidationOnCreate = true
  2. POST the above profiles
  3. POST A SoapLine, like: 
    {
"id": "00db645f-557c-490a-9a48-46377b6a2cde",
"resourceType": "Observation",
"meta": {
    "profile": [
    "http://nictiz.nl/fhir/StructureDefinition/nl-core-SOAPReport.SOAPLine"
    ]
},
"extension": [
    {
        "url": "http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode",
        "valueCodeableConcept": {
            "coding": { "system":"http://hl7.org/fhir/sid/icpc-1-nl", "code": "T90", "display": "Diabetes mellitus" }
        }
    }
],
"status": "final",
"encounter": {
    "type": "Encounter",
    "reference": "Encounter/34833a30-44f9-42f6-9eb3-2786ddf0cee5"
},
"valueString": "test",
"code": {
    "coding": [
    {
        "system": "http://snomed.info/sct",
        "code": "260224007",
        "display": "Objective"
    }
    ]
}
}

Expected behavior 201 Created result.

Actual behavior 400 Bad Request:

"issue": [
        {
            "severity": "fatal",
            "code": "exception",
            "details": {
                "coding": [
                    {
                        "system": "http://hl7.org/fhir/dotnet-api-operation-outcome",
                        "code": "5003"
                    }
                ],
                "text": "Internal logic failure: StructureDefinition 'http://nictiz.nl/fhir/StructureDefinition/ext-SOAPReport.SOAPLineCode' has no snapshot component. (Parameter 'sd')"
            },
            "location": [
                "Observation // OperationOutcome.Location is deprecated, please use OperationOutcome.Expression"
            ],
            "expression": [
                "Observation"
            ]
        }
    ]
EniacMlezi commented 2 months ago

Looks like this could be a possible fix: https://github.com/FirelyTeam/firely-net-sdk/issues/1786

EniacMlezi commented 2 months ago

Just tested it out, seems to be working with this patch:

diff --git a/src/Microsoft.Health.Fhir.Shared.Core/Features/Validation/ProfileValidator.cs b/src/Microsoft.Health.Fhir.Shared.Core/Features/Validation/ProfileValidator.cs
index 9ed39c7be..ccf7e573b 100644
--- a/src/Microsoft.Health.Fhir.Shared.Core/Features/Validation/ProfileValidator.cs
+++ b/src/Microsoft.Health.Fhir.Shared.Core/Features/Validation/ProfileValidator.cs
@@ -27,7 +27,7 @@ namespace Microsoft.Health.Fhir.Core.Features.Validation

             try
             {
-                _resolver = new MultiResolver(new CachedResolver(ZipSource.CreateValidationSource(), options.Value.CacheDurationInSeconds), profilesResolver);
+                _resolver = new SnapshotSource(new MultiResolver(new CachedResolver(ZipSource.CreateValidationSource(), options.Value.CacheDurationInSeconds), profilesResolver));
             }
             catch (Exception)
             {
@@ -41,7 +41,7 @@ namespace Microsoft.Health.Fhir.Core.Features.Validation
             var ctx = new ValidationSettings()
             {
                 ResourceResolver = _resolver,
-                GenerateSnapshot = true,
+                GenerateSnapshot = false,
                 Trace = false,
                 ResolveExternalReferences = false,
             };
EXPEkesheth commented 1 month ago

Thanks for suggesting the change, we will review the PR and revert back #AB125854