Replace core__medicationrequest code with core__medication code (#276)

* Delete current medication request builder code

* Rename medication to medicationrequest

* Replace core__medicationrequest code with core__medication code

- core__medication no longer exists.
- core__medicationrequest now has all the "abstract where medications
  come from" logic that core__medication had and no longer retricts
  itself to just RxNorm.

Changes to the field list for core__medicationrequest:
- Dropped `dosageInstruction_text`, since no one was using it and the
  ETL strips the text anyway.
- Add reported_ref (to match reportedBoolean).
- Add category_display.

CONTRIBUTING.md

@@ -48,3 +48,20 @@ cumulus-library generate-sql \
   --target core \
   --target discovery
 ```
+
+## Rebuilding the Markdown table docs
+
+We keep some generated documentation in git,
+to help us keep our docs in sync with table changes.
+This is stored in `docs/core-study-details.md`
+
+You can regenerate these yourself when you make changes to table layout:
+1. Rebuild the `core` study in Athena.
+1. Run `generate-md` against Athena:
+```sh
+cumulus-library generate-md --target core [database args pointing at your athena db]
+```
+
+Then take the contents of `cumulus_library/studies/core/core_generated.md`
+and paste them into `docs/core-study-details.md`
+(being careful to not erase any manually entered descriptions).

cumulus_library/.sqlfluff

@@ -162,6 +162,10 @@ schema =
             'category': {
                 'code': True, 'system': True, 'display': False
             },
+            'reportedBoolean': True,
+            'reportedReference': {
+                'reference': True
+            },
             'dosageInstruction': {
                 'text': True,
             },

cumulus_library/studies/core/builder_medicationrequest.py

@@ -1,7 +1,4 @@
-"""Module for extracting US core extensions from medicationrequests
-
-Note: This module assumes that you have already run builder_medication,
-as it leverages the core__medication table for data population"""
+"""Module for generating core medicationrequest table"""
 
 from cumulus_library import base_table_builder, base_utils
 from cumulus_library.studies.core.core_templates import core_templates
@@ -14,34 +11,60 @@
         "intent": [],
         "authoredOn": [],
         "reportedBoolean": [],
+        "reportedReference": sql_utils.REFERENCE,
         "subject": sql_utils.REFERENCE,
         "encounter": sql_utils.REFERENCE,
-        "dosageInstruction": ["text"],
+        "medicationReference": sql_utils.REFERENCE,
     }
 }
 
 
 class MedicationRequestBuilder(base_table_builder.BaseTableBuilder):
-    display_text = "Creating MedicationRequest tables..."
+    display_text = "Creating MedicationRequest table..."
 
     def prepare_queries(
         self,
         *args,
         config: base_utils.StudyConfig,
         **kwargs,
-    ):
-        """constructs queries related to patient extensions of interest
+    ) -> None:
+        """Constructs queries related to medication requests
 
         :param config: A study config object
         """
         code_sources = [
+            sql_utils.CodeableConceptConfig(
+                source_table="medication",
+                column_hierarchy=[("code", dict)],
+                target_table="core__medication_dn_code",
+            ),
+            sql_utils.CodeableConceptConfig(
+                source_table="medicationrequest",
+                column_hierarchy=[("medicationCodeableConcept", dict)],
+                target_table="core__medicationrequest_dn_inline_code",
+            ),
+            sql_utils.CodeableConceptConfig(
+                source_table="medicationrequest",
+                column_hierarchy=[("contained", list), ("code", dict)],
+                target_table="core__medicationrequest_dn_contained_code",
+                expected={
+                    "code": sql_utils.CODEABLE_CONCEPT,
+                    "id": {},
+                    "resourceType": {},
+                },
+                extra_fields=[
+                    ("id", "contained_id"),
+                    ("resourceType", "resource_type"),
+                ],
+            ),
             sql_utils.CodeableConceptConfig(
                 source_table="medicationrequest",
-                source_id="id",
                 column_hierarchy=[("category", list)],
                 target_table="core__medicationrequest_dn_category",
             ),
         ]
         self.queries += sql_utils.denormalize_complex_objects(config.db, code_sources)
         validated_schema = sql_utils.validate_schema(config.db, expected_table_cols)
-        self.queries.append(core_templates.get_core_template("medicationrequest", validated_schema))
+        self.queries += [
+            core_templates.get_core_template("medicationrequest", validated_schema),
+        ]