Merge pull request #106 from icanbwell/fix_generating_xhtml_properties

add xhtml type
icanbwell · Dec 10, 2021 · 7cf1888 · 7cf1888
2 parents dd23b21 + 781269a
commit 7cf1888
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Showing 11 changed files with 63 additions and 50 deletions.
diff --git a/spark.Dockerfile b/spark.Dockerfile
@@ -1,4 +1,4 @@
-FROM imranq2/spark_python:0.1.25
+FROM imranq2/spark_python:0.1.34
 # https://github.com/imranq2/docker.spark_python
 USER root
 

diff --git a/spark_auto_mapper_fhir/complex_types/narrative.py b/spark_auto_mapper_fhir/complex_types/narrative.py
@@ -18,6 +18,9 @@
     # status (NarrativeStatus)
     from spark_auto_mapper_fhir.value_sets.narrative_status import NarrativeStatusCode
 
+    # div (xhtml)
+    from spark_auto_mapper_fhir.fhir_types.xhtml import FhirXHtml
+
 
 # This file is auto-generated by generate_classes so do not edit manually
 # noinspection PyPep8Naming
@@ -36,6 +39,7 @@ def __init__(
         id_: Optional[FhirString] = None,
         extension: Optional[FhirList[ExtensionBase]] = None,
         status: NarrativeStatusCode,
+        div: FhirXHtml,
     ) -> None:
         """
             A human-readable summary of the resource conveying the essential clinical and
@@ -52,11 +56,13 @@ def __init__(
             :param status: The status of the narrative - whether it's entirely generated (from just the
         defined data or the extensions too), or whether a human authored it and it may
         contain additional data.
+            :param div: The actual narrative content, a stripped down version of XHTML.
         """
         super().__init__(
             id_=id_,
             extension=extension,
             status=status,
+            div=div,
         )
 
     def get_schema(

diff --git a/spark_auto_mapper_fhir/fhir_types/xhtml.py b/spark_auto_mapper_fhir/fhir_types/xhtml.py
@@ -0,0 +1,6 @@
+from typing import Union
+
+from spark_auto_mapper.data_types.text_like_base import AutoMapperTextLikeBase
+from spark_auto_mapper.type_definitions.defined_types import AutoMapperTextInputType
+
+FhirXHtml = Union[AutoMapperTextInputType, AutoMapperTextLikeBase]
diff --git a/spark_auto_mapper_fhir/generator/fhir_xml_schema_parser.py b/spark_auto_mapper_fhir/generator/fhir_xml_schema_parser.py
@@ -129,6 +129,7 @@ class FhirXmlSchemaParser:
         "unsignedInt": "FhirUnsignedInt",
         "uuid": "FhirUuid",
         "oid": "FhirOid",
+        "xhtml": "FhirXHtml",
     }
 
     @staticmethod
@@ -694,7 +695,7 @@ def generate_properties_for_class(
         fhir_properties: List[FhirProperty] = []
         property_: ObjectifiedElement
         for property_ in properties:
-            if hasattr(property_, "ref"):
+            if "ref" in property_.attrib:
                 ref_: str = str(property_.get("ref"))
                 property_name: str = ref_.split(":")[-1]
                 property_type: str = ref_.split(":")[0]

diff --git a/spark_auto_mapper_fhir/value_sets/all_security_labels.py b/spark_auto_mapper_fhir/value_sets/all_security_labels.py
@@ -18,12 +18,6 @@ class AllSecurityLabelsCode(GenericTypeCode):
     def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
-    """
-    http://terminology.hl7.org/CodeSystem/v3-Confidentiality
-    """
-    codeset_v3_Confidentiality: FhirUri = (
-        "http://terminology.hl7.org/CodeSystem/v3-Confidentiality"
-    )
     """
     http://terminology.hl7.org/CodeSystem/v3-ObservationValue
     """
@@ -35,6 +29,12 @@ def __init__(self, value: AutoMapperTextInputType):
     """
     codeset_v3_ActCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
     """
+    http://terminology.hl7.org/CodeSystem/v3-Confidentiality
+    """
+    codeset_v3_Confidentiality: FhirUri = (
+        "http://terminology.hl7.org/CodeSystem/v3-Confidentiality"
+    )
+    """
     http://terminology.hl7.org/CodeSystem/v3-ActUSPrivacyLaw
     """
     codeset_v3_ActUSPrivacyLaw: FhirUri = (

diff --git a/spark_auto_mapper_fhir/value_sets/context_of_use_value_set.py b/spark_auto_mapper_fhir/value_sets/context_of_use_value_set.py
@@ -21,13 +21,13 @@ def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
     """
-    http://terminology.hl7.org/CodeSystem/v3-ActCode
+    http://snomed.info/sct
     """
-    codeset_v3_ActCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
+    codeset_sct: FhirUri = "http://snomed.info/sct"
     """
-    http://nucc.org/provider-taxonomy
+    http://terminology.hl7.org/CodeSystem/v3-ActCode
     """
-    codeset_provider_taxonomy: FhirUri = "http://nucc.org/provider-taxonomy"
+    codeset_v3_ActCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
     """
     urn:iso:std:iso:3166
     """
@@ -37,9 +37,9 @@ def __init__(self, value: AutoMapperTextInputType):
     """
     codeset_m49_htm: FhirUri = "http://unstats.un.org/unsd/methods/m49/m49.htm"
     """
-    http://snomed.info/sct
+    http://nucc.org/provider-taxonomy
     """
-    codeset_sct: FhirUri = "http://snomed.info/sct"
+    codeset_provider_taxonomy: FhirUri = "http://nucc.org/provider-taxonomy"
 
 
 class ContextOfUseValueSetCodeValues:

diff --git a/spark_auto_mapper_fhir/value_sets/data_element_sdc_object_class.py b/spark_auto_mapper_fhir/value_sets/data_element_sdc_object_class.py
@@ -20,10 +20,6 @@ class DataElementSDCObjectClassCode(GenericTypeCode):
     def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
-    """
-    http://loinc.org
-    """
-    codeset_loinc_org: FhirUri = "http://loinc.org"
     """
     http://snomed.info/sct
     """
@@ -32,3 +28,7 @@ def __init__(self, value: AutoMapperTextInputType):
     http://www.nlm.nih.gov/research/umls/rxnorm
     """
     codeset_rxnorm: FhirUri = "http://www.nlm.nih.gov/research/umls/rxnorm"
+    """
+    http://loinc.org
+    """
+    codeset_loinc_org: FhirUri = "http://loinc.org"
diff --git a/spark_auto_mapper_fhir/value_sets/focal_subject_codes.py b/spark_auto_mapper_fhir/value_sets/focal_subject_codes.py
@@ -20,6 +20,10 @@ class FocalSubjectCodesCode(GenericTypeCode):
     def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
+    """
+    http://snomed.info/sct
+    """
+    codeset_sct: FhirUri = "http://snomed.info/sct"
     """
     http://terminology.hl7.org/CodeSystem/v3-RoleCode
     """
@@ -30,10 +34,6 @@ def __init__(self, value: AutoMapperTextInputType):
     codeset_v3_ParticipationType: FhirUri = (
         "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"
     )
-    """
-    http://snomed.info/sct
-    """
-    codeset_sct: FhirUri = "http://snomed.info/sct"
 
 
 class FocalSubjectCodesCodeValues:

diff --git a/spark_auto_mapper_fhir/value_sets/observation_reference_range_applies_to_codes.py b/spark_auto_mapper_fhir/value_sets/observation_reference_range_applies_to_codes.py
@@ -19,14 +19,14 @@ class ObservationReferenceRangeAppliesToCodesCode(GenericTypeCode):
     def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
-    """
-    http://terminology.hl7.org/CodeSystem/v3-Race
-    """
-    codeset_v3_Race: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-Race"
     """
     http://snomed.info/sct
     """
     codeset_sct: FhirUri = "http://snomed.info/sct"
+    """
+    http://terminology.hl7.org/CodeSystem/v3-Race
+    """
+    codeset_v3_Race: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-Race"
 
 
 class ObservationReferenceRangeAppliesToCodesCodeValues:

diff --git a/spark_auto_mapper_fhir/value_sets/participation_role_type.py b/spark_auto_mapper_fhir/value_sets/participation_role_type.py
@@ -32,42 +32,42 @@ class ParticipationRoleTypeCode(GenericTypeCode):
     def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
-    """
-    http://dicom.nema.org/resources/ontology/DCM
-    """
-    codeset_DCM: FhirUri = "http://dicom.nema.org/resources/ontology/DCM"
     """
     http://terminology.hl7.org/CodeSystem/v3-ParticipationFunction
     """
     codeset_v3_ParticipationFunction: FhirUri = (
         "http://terminology.hl7.org/CodeSystem/v3-ParticipationFunction"
     )
     """
+    http://terminology.hl7.org/CodeSystem/v3-ParticipationType
+    """
+    codeset_v3_ParticipationType: FhirUri = (
+        "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"
+    )
+    """
+    http://terminology.hl7.org/CodeSystem/extra-security-role-type
+    """
+    codeset_extra_security_role_type: FhirUri = (
+        "http://terminology.hl7.org/CodeSystem/extra-security-role-type"
+    )
+    """
     http://terminology.hl7.org/CodeSystem/contractsignertypecodes
     """
     codeset_contractsignertypecodes: FhirUri = (
         "http://terminology.hl7.org/CodeSystem/contractsignertypecodes"
     )
     """
-    http://terminology.hl7.org/CodeSystem/v3-RoleCode
-    """
-    codeset_v3_RoleCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-RoleCode"
-    """
     http://terminology.hl7.org/CodeSystem/v3-RoleClass
     """
     codeset_v3_RoleClass: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-RoleClass"
     """
-    http://terminology.hl7.org/CodeSystem/extra-security-role-type
+    http://dicom.nema.org/resources/ontology/DCM
     """
-    codeset_extra_security_role_type: FhirUri = (
-        "http://terminology.hl7.org/CodeSystem/extra-security-role-type"
-    )
+    codeset_DCM: FhirUri = "http://dicom.nema.org/resources/ontology/DCM"
     """
-    http://terminology.hl7.org/CodeSystem/v3-ParticipationType
+    http://terminology.hl7.org/CodeSystem/v3-RoleCode
     """
-    codeset_v3_ParticipationType: FhirUri = (
-        "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"
-    )
+    codeset_v3_RoleCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-RoleCode"
 
 
 class ParticipationRoleTypeCodeValues:

diff --git a/spark_auto_mapper_fhir/value_sets/provenance_activity_type.py b/spark_auto_mapper_fhir/value_sets/provenance_activity_type.py
@@ -22,28 +22,28 @@ class ProvenanceActivityTypeCode(GenericTypeCode):
     def __init__(self, value: AutoMapperTextInputType):
         super().__init__(value=value)
 
-    """
-    http://terminology.hl7.org/CodeSystem/v3-ParticipationType
-    """
-    codeset_v3_ParticipationType: FhirUri = (
-        "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"
-    )
     """
     http://terminology.hl7.org/CodeSystem/v3-DataOperation
     """
     codeset_v3_DataOperation: FhirUri = (
         "http://terminology.hl7.org/CodeSystem/v3-DataOperation"
     )
     """
+    http://terminology.hl7.org/CodeSystem/v3-ActCode
+    """
+    codeset_v3_ActCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
+    """
     http://terminology.hl7.org/CodeSystem/v3-DocumentCompletion
     """
     codeset_v3_DocumentCompletion: FhirUri = (
         "http://terminology.hl7.org/CodeSystem/v3-DocumentCompletion"
     )
     """
-    http://terminology.hl7.org/CodeSystem/v3-ActCode
+    http://terminology.hl7.org/CodeSystem/v3-ParticipationType
     """
-    codeset_v3_ActCode: FhirUri = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
+    codeset_v3_ParticipationType: FhirUri = (
+        "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"
+    )
 
 
 class ProvenanceActivityTypeCodeValues: