From 03f47b457bef22c88dfbb16300fde090750a881b Mon Sep 17 00:00:00 2001
From: Matt Garber <matthew.garber@childrens.harvard.edu>
Date: Fri, 9 Aug 2024 09:27:22 -0400
Subject: [PATCH] Added convenience subtables

This adds two derived tables, mrrel_is_a, and mrconso_drugs,
in order to speed up long queries in vocab lookup scenarios.

It also bumps the version as part of the library 3.0 cutover,
and moves the version definition to __init__.
---
 README.md                                 | 11 +++++++++++
 cumulus_library_umls/__init__.py          |  1 +
 cumulus_library_umls/umls/umls_builder.py | 23 ++++++++++++++++++-----
 pyproject.toml                            |  6 +++---
 4 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index bf32867..b954b82 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,17 @@ Note: This study is explicitly namespaced in its own schema, `umls`. Make sure y
 database is not using this schema for another use. Do not create tables inside this
 schema by another means.
 
+## Additional custom tables
+
+The following tables are a derived from the primary tables, and are included here as a 
+convenience to avoid having to compute these on a repeated basis
+
+- **mrrel_is_a** a subset of the relationships in mrrel, including only those that define
+that concept A is a member of concept B (i.e. is a child, or is explicitly marked as
+being a tradename/member belonging to the parent concept).
+- **mrconso_drugs** a subset of the entity list in mrconso, limited to vocabularies
+specifically dealing with drug identifiers (i.e. SNOMED, RxNorm, etc.)
+
 ## Licensing details
 
 The `cumulus-library-umls` study is provided as a convenience to install the
diff --git a/cumulus_library_umls/__init__.py b/cumulus_library_umls/__init__.py
index e69de29..5becc17 100644
--- a/cumulus_library_umls/__init__.py
+++ b/cumulus_library_umls/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.0.0"
diff --git a/cumulus_library_umls/umls/umls_builder.py b/cumulus_library_umls/umls/umls_builder.py
index f7ab343..ecd4626 100644
--- a/cumulus_library_umls/umls/umls_builder.py
+++ b/cumulus_library_umls/umls/umls_builder.py
@@ -1,7 +1,7 @@
 import pathlib
 
 import pandas
-from cumulus_library import base_table_builder, base_utils, databases
+from cumulus_library import base_table_builder, base_utils, study_manifest
 from cumulus_library.apis import umls
 from cumulus_library.template_sql import base_templates
 
@@ -145,10 +145,9 @@ def create_parquet(
 
     def prepare_queries(
         self,
-        cursor: databases.DatabaseCursor,
-        schema: str,
+        config: base_utils.StudyConfig,
+        manifest: study_manifest.StudyManifest,
         *args,
-        config=base_utils.StudyConfig,
         **kwargs,
     ):
         download_path = pathlib.Path(__file__).resolve().parent / "downloads"
@@ -184,7 +183,7 @@ def prepare_queries(
                     )
                     self.queries.append(
                         base_templates.get_ctas_from_parquet_query(
-                            schema_name=schema,
+                            schema_name=config.schema,
                             table_name=f"umls__{file.stem}",
                             local_location=parquet_path / f"{file.stem}.parquet",
                             remote_location=remote_path,
@@ -193,3 +192,17 @@ def prepare_queries(
                         )
                     )
                     progress.advance(task)
+
+        # Section for resuable cross-study helper tables
+        self.queries.append(
+            """CREATE TABLE umls__mrrel_is_a AS
+SELECT * FROM umls.mrrel
+WHERE REL = 'CHD' 
+OR RELA in ('isa','tradename_of','has_tradename','has_basis_of_strength_substance')"""
+        )
+        self.queries.append(
+            """CREATE TABLE umls__mrconso_drugs AS
+SELECT * FROM umls.mrconso
+WHERE SAB in ('ATC','CVX','DRUGBANK','GS','MMSL','MMX','MTHCMSFRFMTHSPL','NDDF',
+    'RXNORM','SNOMEDCT_US','USP','VANDF')"""
+        )
diff --git a/pyproject.toml b/pyproject.toml
index a4916a2..ab0c563 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,9 +1,8 @@
 [project]
-version = "0.2.0"
 name = "cumulus-library-umls"
-requires-python = ">= 3.10"
+requires-python = ">= 3.11"
 dependencies = [
-    "cumulus-library >= 2.3",
+    "cumulus-library >= 3.0",
 ]
 description = "A Unified Medical Language System® Metathesaurus study for the Cumulus project"
 readme = "README.md"
@@ -15,6 +14,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
+dynamic=["version"]
 [project.optional-dependencies]
 dev = [
     "ruff == 0.2.1",