Merge pull request #41 from icanbwell/add_dstu2_schemas

Add dstu2 schemas

.github/workflows/build_and_test.yml

@@ -19,24 +19,6 @@ jobs:
         with:
           python-version: '3.7'
 
-      - name: Set cache permissions
-        run: |
-          mkdir ~/.local && mkdir ~/.local/share && mkdir ~/.local/share/virtualenvs
-          chown -R $(whoami) ~/.local/share/virtualenvs/
-
-      - name: Cache pip dependencies
-        uses: actions/cache@v2
-        env:
-          cache-name: cache-pip-deps-warehouse-p
-        with:
-          path: ~/.local/share/virtualenvs/
-          key: ${{ runner.os }}-${{ env.CACHE_SEED }}-${{ github.job }}-${{ env.cache-name }}-${{ hashFiles('Pipfile.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ env.CACHE_SEED }}-${{ github.job }}-${{ env.cache-name }}-
-            ${{ runner.os }}-${{ env.CACHE_SEED }}-${{ github.job }}-
-            ${{ runner.os }}-${{ env.CACHE_SEED }}-
-            ${{ runner.os }}-
-
       - name: pre-commit
         run: make run-pre-commit
 

Makefile

@@ -69,3 +69,10 @@ schema-stu3:
 	docker-compose run --rm --name sfs_shell dev python3 spark_fhir_schemas/stu3/generate_schema.py && \
 	make run-pre-commit
 	make run-pre-commit
+
+.PHONY:schema-dstu2
+schema-dstu2:
+	docker-compose run --rm --name sfs_shell dev python3 spark_fhir_schemas/dstu2/generate_schema_file.py && \
+	docker-compose run --rm --name sfs_shell dev python3 spark_fhir_schemas/dstu2/generate_schema.py && \
+	make run-pre-commit
+	make run-pre-commit

Pipfile

@@ -10,12 +10,12 @@ pyspark = ">=3.1.1"
 setuptools=">=60.9.3"
 wheel=">=0.37.1"
 twine=">=3.8.0"
-pre-commit=">=2.18.0"
-autoflake=">=1.4"
-flake8 = ">=4.0.1"
-mypy = "==0.942"
-pytest = ">=7.1.1"
-black = ">=22.1.0"
+pre-commit=">=2.20.0"
+autoflake=">=1.5.3"
+flake8 = ">=5.0.4"
+mypy = "==0.971"
+pytest = ">=7.1.2"
+black = ">=22.8.0"
 importlib-metadata = ">=4.0.1"
 py4j = "==0.10.9.5" # https://spark.apache.org/docs/latest/api/python/getting_started/install.html#dependencies
 pyspark="==3.3.0"  # should match the version of spark we use for testing
@@ -26,6 +26,9 @@ sphinx-autoapi="==1.8.4"
 sphinx-rtd-theme="==0.5.2"
 myst-parser="==0.15.1"
 pipenv-setup = ">=3.2.0"
+lxml="==4.9.1"
+jinja2="==3.1.2"
+jsonpickle="==2.2.0"
 
 [requires]
 python_version = "3.7"

spark_fhir_schemas/dstu2/backbone_elements/allergyintolerancereaction.py

@@ -0,0 +1,273 @@
+from typing import Union, List, Optional
+
+from pyspark.sql.types import StructType, StructField, StringType, ArrayType, DataType
+
+
+# This file is auto-generated by generate_schema so do not edit manually
+# noinspection PyPep8Naming
+class AllergyIntoleranceReactionSchema:
+    """
+    Risk of harmful or undesirable, physiological response which is unique to an
+    individual and associated with exposure to a substance.
+    """
+
+    # noinspection PyDefaultArgument
+    @staticmethod
+    def get_schema(
+        max_nesting_depth: Optional[int] = 6,
+        nesting_depth: int = 0,
+        nesting_list: List[str] = [],
+        max_recursion_limit: Optional[int] = 2,
+        include_extension: Optional[bool] = False,
+        extension_fields: Optional[List[str]] = [
+            "valueBoolean",
+            "valueCode",
+            "valueDate",
+            "valueDateTime",
+            "valueDecimal",
+            "valueId",
+            "valueInteger",
+            "valuePositiveInt",
+            "valueString",
+            "valueTime",
+            "valueUnsignedInt",
+            "valueUri",
+            "valueQuantity",
+        ],
+        extension_depth: int = 0,
+        max_extension_depth: Optional[int] = 2,
+    ) -> Union[StructType, DataType]:
+        """
+        Risk of harmful or undesirable, physiological response which is unique to an
+        individual and associated with exposure to a substance.
+
+
+            id: None
+            extension: May be used to represent additional information that is not part of the basic
+        definition of the element. In order to make the use of extensions safe and
+        manageable, there is a strict set of governance  applied to the definition and
+        use of extensions. Though any implementer is allowed to define an extension,
+        there is a set of requirements that SHALL be met as part of the definition of
+        the extension.
+            modifierExtension: May be used to represent additional information that is not part of the basic
+        definition of the element, and that modifies the understanding of the element
+        that contains it. Usually modifier elements provide negation or qualification.
+        In order to make the use of extensions safe and manageable, there is a strict
+        set of governance applied to the definition and use of extensions. Though any
+        implementer is allowed to define an extension, there is a set of requirements
+        that SHALL be met as part of the definition of the extension. Applications
+        processing a resource are required to check for modifier extensions.
+            substance: Identification of the specific substance considered to be responsible for the
+        Adverse Reaction event. Note: the substance for a specific reaction may be
+        different to the substance identified as the cause of the risk, but must be
+        consistent with it. For instance, it may be a more specific substance (e.g. a
+        brand medication) or a composite substance that includes the identified
+        substance. It must be clinically safe to only process the
+        AllergyIntolerance.substance and ignore the
+        AllergyIntolerance.event.substance.
+            certainty: Statement about the degree of clinical certainty that the specific substance
+        was the cause of the manifestation in this reaction event.
+            manifestation: Clinical symptoms and/or signs that are observed or associated with the
+        adverse reaction event.
+            description: Text description about the reaction as a whole, including details of the
+        manifestation if required.
+            onset: Record of the date and/or time of the onset of the Reaction.
+            severity: Clinical assessment of the severity of the reaction event as a whole,
+        potentially considering multiple different manifestations.
+            exposureRoute: Identification of the route by which the subject was exposed to the substance.
+            note: Additional text about the adverse reaction event not captured in other fields.
+        """
+        # id
+        from spark_fhir_schemas.dstu2.simple_types.id import idSchema
+
+        # extension
+        from spark_fhir_schemas.dstu2.complex_types.extension import ExtensionSchema
+
+        # substance
+        from spark_fhir_schemas.dstu2.complex_types.codeableconcept import (
+            CodeableConceptSchema,
+        )
+
+        # certainty
+        # type = code
+        # onset
+        from spark_fhir_schemas.dstu2.simple_types.datetime import dateTimeSchema
+
+        # note
+        from spark_fhir_schemas.dstu2.complex_types.annotation import AnnotationSchema
+
+        if (
+            max_recursion_limit
+            and nesting_list.count("AllergyIntoleranceReaction") >= max_recursion_limit
+        ) or (max_nesting_depth and nesting_depth >= max_nesting_depth):
+            return StructType([StructField("id", StringType(), True)])
+        # add my name to recursion list for later
+        my_nesting_list: List[str] = nesting_list + ["AllergyIntoleranceReaction"]
+        schema = StructType(
+            [
+                # None
+                StructField(
+                    "id",
+                    idSchema.get_schema(
+                        max_nesting_depth=max_nesting_depth,
+                        nesting_depth=nesting_depth + 1,
+                        nesting_list=my_nesting_list,
+                        max_recursion_limit=max_recursion_limit,
+                        include_extension=include_extension,
+                        extension_fields=extension_fields,
+                        extension_depth=extension_depth + 1,
+                        max_extension_depth=max_extension_depth,
+                    ),
+                    True,
+                ),
+                # May be used to represent additional information that is not part of the basic
+                # definition of the element. In order to make the use of extensions safe and
+                # manageable, there is a strict set of governance  applied to the definition and
+                # use of extensions. Though any implementer is allowed to define an extension,
+                # there is a set of requirements that SHALL be met as part of the definition of
+                # the extension.
+                StructField(
+                    "extension",
+                    ArrayType(
+                        ExtensionSchema.get_schema(
+                            max_nesting_depth=max_nesting_depth,
+                            nesting_depth=nesting_depth + 1,
+                            nesting_list=my_nesting_list,
+                            max_recursion_limit=max_recursion_limit,
+                            include_extension=include_extension,
+                            extension_fields=extension_fields,
+                            extension_depth=extension_depth + 1,
+                            max_extension_depth=max_extension_depth,
+                        )
+                    ),
+                    True,
+                ),
+                # May be used to represent additional information that is not part of the basic
+                # definition of the element, and that modifies the understanding of the element
+                # that contains it. Usually modifier elements provide negation or qualification.
+                # In order to make the use of extensions safe and manageable, there is a strict
+                # set of governance applied to the definition and use of extensions. Though any
+                # implementer is allowed to define an extension, there is a set of requirements
+                # that SHALL be met as part of the definition of the extension. Applications
+                # processing a resource are required to check for modifier extensions.
+                StructField(
+                    "modifierExtension",
+                    ArrayType(
+                        ExtensionSchema.get_schema(
+                            max_nesting_depth=max_nesting_depth,
+                            nesting_depth=nesting_depth + 1,
+                            nesting_list=my_nesting_list,
+                            max_recursion_limit=max_recursion_limit,
+                            include_extension=include_extension,
+                            extension_fields=extension_fields,
+                            extension_depth=extension_depth + 1,
+                            max_extension_depth=max_extension_depth,
+                        )
+                    ),
+                    True,
+                ),
+                # Identification of the specific substance considered to be responsible for the
+                # Adverse Reaction event. Note: the substance for a specific reaction may be
+                # different to the substance identified as the cause of the risk, but must be
+                # consistent with it. For instance, it may be a more specific substance (e.g. a
+                # brand medication) or a composite substance that includes the identified
+                # substance. It must be clinically safe to only process the
+                # AllergyIntolerance.substance and ignore the
+                # AllergyIntolerance.event.substance.
+                StructField(
+                    "substance",
+                    CodeableConceptSchema.get_schema(
+                        max_nesting_depth=max_nesting_depth,
+                        nesting_depth=nesting_depth + 1,
+                        nesting_list=my_nesting_list,
+                        max_recursion_limit=max_recursion_limit,
+                        include_extension=include_extension,
+                        extension_fields=extension_fields,
+                        extension_depth=extension_depth + 1,
+                        max_extension_depth=max_extension_depth,
+                    ),
+                    True,
+                ),
+                # Statement about the degree of clinical certainty that the specific substance
+                # was the cause of the manifestation in this reaction event.
+                StructField("certainty", StringType(), True),
+                # Clinical symptoms and/or signs that are observed or associated with the
+                # adverse reaction event.
+                StructField(
+                    "manifestation",
+                    ArrayType(
+                        CodeableConceptSchema.get_schema(
+                            max_nesting_depth=max_nesting_depth,
+                            nesting_depth=nesting_depth + 1,
+                            nesting_list=my_nesting_list,
+                            max_recursion_limit=max_recursion_limit,
+                            include_extension=include_extension,
+                            extension_fields=extension_fields,
+                            extension_depth=extension_depth + 1,
+                            max_extension_depth=max_extension_depth,
+                        )
+                    ),
+                    True,
+                ),
+                # Text description about the reaction as a whole, including details of the
+                # manifestation if required.
+                StructField("description", StringType(), True),
+                # Record of the date and/or time of the onset of the Reaction.
+                StructField(
+                    "onset",
+                    dateTimeSchema.get_schema(
+                        max_nesting_depth=max_nesting_depth,
+                        nesting_depth=nesting_depth + 1,
+                        nesting_list=my_nesting_list,
+                        max_recursion_limit=max_recursion_limit,
+                        include_extension=include_extension,
+                        extension_fields=extension_fields,
+                        extension_depth=extension_depth + 1,
+                        max_extension_depth=max_extension_depth,
+                    ),
+                    True,
+                ),
+                # Clinical assessment of the severity of the reaction event as a whole,
+                # potentially considering multiple different manifestations.
+                StructField("severity", StringType(), True),
+                # Identification of the route by which the subject was exposed to the substance.
+                StructField(
+                    "exposureRoute",
+                    CodeableConceptSchema.get_schema(
+                        max_nesting_depth=max_nesting_depth,
+                        nesting_depth=nesting_depth + 1,
+                        nesting_list=my_nesting_list,
+                        max_recursion_limit=max_recursion_limit,
+                        include_extension=include_extension,
+                        extension_fields=extension_fields,
+                        extension_depth=extension_depth + 1,
+                        max_extension_depth=max_extension_depth,
+                    ),
+                    True,
+                ),
+                # Additional text about the adverse reaction event not captured in other fields.
+                StructField(
+                    "note",
+                    AnnotationSchema.get_schema(
+                        max_nesting_depth=max_nesting_depth,
+                        nesting_depth=nesting_depth + 1,
+                        nesting_list=my_nesting_list,
+                        max_recursion_limit=max_recursion_limit,
+                        include_extension=include_extension,
+                        extension_fields=extension_fields,
+                        extension_depth=extension_depth + 1,
+                        max_extension_depth=max_extension_depth,
+                    ),
+                    True,
+                ),
+            ]
+        )
+        if not include_extension:
+            schema.fields = [
+                c
+                if c.name != "extension"
+                else StructField("extension", StringType(), True)
+                for c in schema.fields
+            ]
+
+        return schema