💥 transformation to FHIR R5 has been officially started.

* root FHIR resources are moved under R4B sub-packages.
* make sure all tests are passing & lintings are fine.

Author: nazrulworld

.gitignore

@@ -106,3 +106,4 @@ ENV/
 # Others
 /pip-wheel-metadata
 /fhir-parser
+.python-version

.travis.yml

@@ -63,6 +63,6 @@ script:
   - pytest tests
   - pytest fhir/resources/DSTU2/tests
   - pytest fhir/resources/STU3/tests
-  - pytest -s --cov=fhir/resources/tests -s --tb=native -v --cov-report term-missing --cov-append fhir/resources/tests
+  - pytest -s --cov=fhir/resources/R4B/tests -s --tb=native -v --cov-report term-missing --cov-append fhir/resources/R4B/tests
 after_success:
   - codecov

fhir/resources/DSTU2/fhirabstractmodel.py

@@ -268,7 +268,6 @@ def dict(
                 if field.outer_type_ != field.type_ and str(
                     field.outer_type_
                 ).startswith("typing.List["):
-
                     children_excludes[field.name] = {
                         "__all__": {FHIR_COMMENTS_FIELD_NAME}
                     }

fhir/resources/DSTU2/fhirtypes.py

@@ -236,7 +236,8 @@ class Oid(ConstrainedStr):
 
 class Markdown(ConstrainedStr):
     """A FHIR string (see above) that may contain markdown syntax for optional processing
-    by a markdown presentation engine, in the GFM extension of CommonMark format (see below)"""
+    by a markdown presentation engine, in the GFM extension of CommonMark format (see below)
+    """
 
     __visit_name__ = "markdown"
     regex = re.compile(r"\s*(\S|\s)*")
@@ -262,7 +263,6 @@ class Date(datetime.date):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod
@@ -309,7 +309,6 @@ class DateTime(datetime.datetime):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod
@@ -351,7 +350,8 @@ class Instant(datetime.datetime):
     use date or dateTime (which can be as precise as instant,
     but is not required to be). instant is a more constrained dateTime
 
-    Note: This type is for system times, not human times (see date and dateTime below)."""
+    Note: This type is for system times, not human times (see date and dateTime below).
+    """
 
     regex = re.compile(
         r"([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|"
@@ -364,7 +364,6 @@ class Instant(datetime.datetime):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod
@@ -389,7 +388,6 @@ class Time(datetime.time):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod

fhir/resources/DSTU2/fhirtypesvalidators.py

@@ -464,22 +464,18 @@ def fhir_model_validator(
 
 
 def fhirprimitiveextension_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
-
     return fhir_model_validator("FHIRPrimitiveExtension", v)
 
 
 def element_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
-
     return fhir_model_validator("Element", v)
 
 
 def resource_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
-
     return fhir_model_validator("Resource", v)
 
 
 def domainresource_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
-
     return fhir_model_validator("DomainResource", v)
 
 

fhir/resources/DSTU2/specimen.py

@@ -134,7 +134,6 @@ class Specimen(DomainResource):
 
 
 class SpecimenCollection(BackboneElement):
-
     resource_type = Field("SpecimenCollection", const=True)
 
     collector: fhirtypes.ReferenceType = Field(

fhir/resources/R4B/__init__.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+from pathlib import Path
+from typing import Any, Dict, Union
+
+from fhir.resources.core.fhirabstractmodel import FHIRAbstractModel
+
+from .fhirtypesvalidators import get_fhir_model_class
+
+__fhir_version__ = "4.3.0"
+
+
+def construct_fhir_element(
+    element_type: str, data: Union[Dict[str, Any], str, bytes, Path]
+) -> FHIRAbstractModel:
+    try:
+        klass = get_fhir_model_class(element_type)
+    except KeyError:
+        raise LookupError(
+            f"'{element_type}' is not valid FHIRModel (element type) name!"
+        )
+    if isinstance(data, (str, bytes)):
+        return klass.parse_raw(data, content_type="application/json")
+    elif isinstance(data, Path):
+        return klass.parse_file(data)
+    return klass.parse_obj(data)
+
+
+__all__ = ["get_fhir_model_class", "construct_fhir_element"]

fhir/resources/account.py fhir/resources/R4B/account.py

@@ -420,7 +420,8 @@ def to_string(cls, value):
 
 class Markdown(ConstrainedStr, Primitive):
     """A FHIR string (see above) that may contain markdown syntax for optional processing
-    by a markdown presentation engine, in the GFM extension of CommonMark format (see below)"""
+    by a markdown presentation engine, in the GFM extension of CommonMark format (see below)
+    """
 
     __visit_name__ = "markdown"
     regex = re.compile(r"\s*(\S|\s)*")
@@ -461,7 +462,6 @@ class Date(datetime.date, Primitive):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod
@@ -516,7 +516,6 @@ class DateTime(datetime.datetime, Primitive):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod
@@ -566,7 +565,8 @@ class Instant(datetime.datetime, Primitive):
     use date or dateTime (which can be as precise as instant,
     but is not required to be). instant is a more constrained dateTime
 
-    Note: This type is for system times, not human times (see date and dateTime below)."""
+    Note: This type is for system times, not human times (see date and dateTime below).
+    """
 
     regex = re.compile(
         r"([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|"
@@ -579,7 +579,6 @@ class Instant(datetime.datetime, Primitive):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod
@@ -612,7 +611,6 @@ class Time(datetime.time, Primitive):
 
     @classmethod
     def __get_validators__(cls) -> "CallableGenerator":
-
         yield cls.validate
 
     @classmethod