remove genomic table stuff

Author: jsstevenson

compose.yaml

@@ -14,7 +14,6 @@ services:
         read_only: true
         bind:
           create_host_path: false
-      - ./uta-setup.sql:/docker-entrypoint-initdb.d/uta-setup.sql
     ports:
       - 127.0.0.1:5432:5432
 

pyproject.toml

@@ -49,7 +49,7 @@ dev = [
 ]
 tests = ["pytest", "pytest-cov", "pytest-asyncio", "mock"]
 docs = [
-    "sphinx==6.1.3",
+    "sphinx==6.2.1",
     "sphinx-autodoc-typehints==1.22.0",
     "sphinx-autobuild==2021.3.14",
     "sphinx-copybutton==0.5.2",

src/cool_seq_tool/sources/uta_database.py

@@ -132,52 +132,6 @@ async def execute_query(
             )
             raise
 
-    async def create_genomic_table(self) -> None:
-        """Create the derived ``genomic`` table in the current schema if needed."""
-        create_genomic_table = """
-            CREATE TABLE IF NOT EXISTS genomic AS
-                SELECT
-                    t.hgnc,
-                    aes.alt_ac,
-                    aes.alt_aln_method,
-                    aes.alt_strand,
-                    ae.start_i AS alt_start_i,
-                    ae.end_i AS alt_end_i
-                FROM transcript t
-                JOIN exon_set tes
-                    ON t.ac = tes.tx_ac
-                   AND tes.alt_aln_method = 'transcript'
-                JOIN exon_set aes
-                    ON t.ac = aes.tx_ac
-                   AND aes.alt_aln_method <> 'transcript'
-                JOIN exon te
-                    ON tes.exon_set_id = te.exon_set_id
-                JOIN exon ae
-                    ON aes.exon_set_id = ae.exon_set_id
-                   AND te.ord = ae.ord
-                LEFT JOIN exon_aln ea
-                    ON te.exon_id = ea.tx_exon_id
-                   AND ae.exon_id = ea.alt_exon_id;
-        """
-        await self.execute_query(create_genomic_table)
-
-        indexes = [
-            """
-            CREATE INDEX IF NOT EXISTS alt_pos_index
-            ON genomic (alt_ac, alt_start_i, alt_end_i);
-            """,
-            """
-            CREATE INDEX IF NOT EXISTS gene_alt_index
-            ON genomic (hgnc, alt_ac);
-            """,
-            """
-            CREATE INDEX IF NOT EXISTS alt_ac_index
-            ON genomic (alt_ac);
-            """,
-        ]
-        for create_index in indexes:
-            await self.execute_query(create_index)
-
     async def get_alt_ac_start_or_end(
         self, tx_ac: str, tx_exon_start: int, tx_exon_end: int, gene: str | None
     ) -> GenomicAlnData:
@@ -678,6 +632,11 @@ async def get_gene_from_ac(
         >>> result
         ['BRCA1']
 
+        This function performs a relatively expensive condition check and is expected to
+        be relatively slow (~100ms under ideal conditions). If users need a more efficient
+        lookup of this form, they should either create their own materialized views/indices,
+        or lobby for their inclusion in a new UTA release.
+
         :param ac: NC accession, e.g. ``"NC_000001.11"``
         :param start_pos: Start position change
         :param end_pos: End position change
@@ -1028,9 +987,7 @@ def _normalize_uta_db_url(db_url: str) -> str:
     )
 
 
-async def create_uta_connection_pool(
-    db_url: str | None = None, initialize_genomic_table: bool = True
-) -> AsyncConnectionPool:
+async def create_uta_connection_pool(db_url: str | None = None) -> AsyncConnectionPool:
     """Create and initialize a UTA connection pool.
 
     Connection parameters are resolved in the following order:
@@ -1041,13 +998,23 @@ async def create_uta_connection_pool(
     3. If not provided, fall back to environment variable ``UTA_DB_URL``
     4. If not declared, then use default value
 
-    After opening the pool, a one-time initialization step is performed to ensure that
-    required genomic tables are present.
+    Connection strings are expected to look like this:
+
+    .. note::
 
-    :param db_url: PostgreSQL connection URI (e.g., ``postgresql://user@host:port/db?options=-csearch_path%3Duta_schema,public``).
-        If not provided, resolved from environment or defaults.
-    :param initialize_genomic_table: whether to attempt initialization of the ``genomic``
-        table which is used/managed by coolseqtool.
+       Connection strings are expected to look like this:
+
+          postgresql://user@host:port/db?options=-csearch_path%3Duta_schema,public
+
+       For example, this is the default:
+
+          postgresql://anonymous@localhost:5432/uta?options=-csearch_path%3Duta_20241220,public
+
+       However, biocommons-style connection strings are presently supported, although they are considered deprecated:
+
+          postgresql://anonymous@localhost:5432/uta/uta_20241220
+
+    :param db_url: PostgreSQL connection URI If not provided, resolved from environment or defaults.
     :return: An open ``AsyncConnectionPool`` configured for the UTA database
     """
     if "UTA_DB_PROD" in os.environ:
@@ -1061,20 +1028,6 @@ async def create_uta_connection_pool(
     )
     pool = AsyncConnectionPool(conninfo=db_url, open=False)
     await pool.open()
-    if initialize_genomic_table:
-        warnings.warn(
-            "Genomic table initialization during connection pool construction is deprecated and subject to deletion in future releases. Users should perform this operation manually using `UtaRepository.create_genomic_table()`.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        try:
-            async with pool.connection() as conn:
-                await UtaRepository(conn).create_genomic_table()
-        # catch all exceptions -- this is probably a critical error, it's good to
-        # close the pool first
-        except:
-            await pool.close()
-            raise
     return pool