Merge pull request #56 from TheJacksonLaboratory/G3-280-db-ontology-b…

…y-geneset

G3-282 DB implementation ontology by geneset

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-db"
-version = "0.5.0a8"
+version = "0.5.0a9"
 description = "Database Interaction Services for GeneWeaver"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"

src/geneweaver/db/aio/ontology.py

@@ -0,0 +1,32 @@
+"""Database code for interacting with ontologies."""
+
+from typing import List, Optional
+
+from geneweaver.db.query import ontology as ontology_query
+from psycopg import AsyncCursor
+from psycopg.rows import Row
+
+
+async def by_geneset(
+    cursor: AsyncCursor,
+    geneset_id: int,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> List[Row]:
+    """Get geneset ontologies from the database.
+
+    :param cursor: An async database cursor.
+    :param geneset_id: Show only results for this geneset identifier
+    :param limit: Limit the number of results.
+    :param offset: Offset the results.
+    @return:
+    """
+    await cursor.execute(
+        *ontology_query.by_geneset(
+            geneset_id=geneset_id,
+            limit=limit,
+            offset=offset,
+        )
+    )
+
+    return await cursor.fetchall()

src/geneweaver/db/ontology.py

@@ -0,0 +1,32 @@
+"""Database code for interacting with ontologies."""
+
+from typing import List, Optional
+
+from geneweaver.db.query import ontology as ontology_query
+from psycopg import Cursor
+from psycopg.rows import Row
+
+
+def by_geneset(
+    cursor: Cursor,
+    geneset_id: int,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> List[Row]:
+    """Get geneset ontologies from the database.
+
+    :param cursor: A database cursor.
+    :param geneset_id: Show only results for this geneset identifier
+    :param limit: Limit the number of results.
+    :param offset: Offset the results.
+    @return:
+    """
+    cursor.execute(
+        *ontology_query.by_geneset(
+            geneset_id=geneset_id,
+            limit=limit,
+            offset=offset,
+        )
+    )
+
+    return cursor.fetchall()

src/geneweaver/db/query/ontology.py

@@ -0,0 +1,43 @@
+"""Query generation functions for ontologies."""
+
+from typing import Optional, Tuple
+
+from geneweaver.db.utils import limit_and_offset
+from psycopg.sql import SQL, Composed
+
+
+def by_geneset(
+    geneset_id: int,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> Tuple[Composed, dict]:
+    """Create a psycopg query to get genesets ontologies.
+
+    :param geneset_id: The geneset identifier to search for.
+    :param limit: The limit of results to return.
+    :param offset: The offset of results to return.
+
+    :return: A query (and params) that can be executed on a cursor.
+    """
+    query = SQL("SELECT")
+    query_fields = (
+        SQL("geneset.gs_id AS geneset_id")
+        + SQL(",ontology.ont_ref_id AS ontology_id")
+        + SQL(",ontology.ont_name AS name")
+        + SQL(",ontology.ont_description as description")
+        + SQL(",ontologydb.ontdb_name as source_ontology")
+    )
+    query = (
+        query
+        + query_fields
+        + SQL("FROM geneset")
+        + SQL("JOIN geneset_ontology ON geneset.gs_id = geneset_ontology.gs_id")
+        + SQL("JOIN ontology ON geneset_ontology.ont_id = ontology.ont_id")
+        + SQL("JOIN ontologydb ON ontology.ontdb_id = ontologydb.ontdb_id")
+        + SQL("WHERE geneset.gs_id = %(gs_id)s")
+    ).join(" ")
+    params = {"gs_id": geneset_id}
+
+    query = limit_and_offset(query, limit, offset).join(" ")
+
+    return query, params

tests/unit/ontology/__init__.py

@@ -0,0 +1 @@
+"""Tests for the ontology db module."""

tests/unit/ontology/test_by_geneset.py

@@ -0,0 +1,87 @@
+"""Test the ontology.by_geneset db function."""
+
+import pytest
+from geneweaver.db.aio.ontology import (
+    by_geneset as async_get_ontology_by_gs_id,
+)
+from geneweaver.db.ontology import by_geneset
+
+from tests.unit.testing_utils import (
+    async_create_execute_raises_error_test,
+    async_create_fetchall_raises_error_test,
+    create_execute_raises_error_test,
+    create_fetchall_raises_error_test,
+)
+
+
+@pytest.mark.parametrize("geneset_id", [12345])
+@pytest.mark.parametrize("limit", [None, 1, 10])
+@pytest.mark.parametrize("offset", [None, 1, 10])
+@pytest.mark.parametrize(
+    "ontologies_resp",
+    [
+        ["a", "b", "c"],
+        ["d", "e", "f"],
+        ["g", "h", "i"],
+    ],
+)
+def test_get_ontology_by_gs_id(geneset_id, limit, offset, ontologies_resp, cursor):
+    """Test the ontology.get_ontology_by_gs_id function."""
+    cursor.fetchall.return_value = ontologies_resp
+
+    result = by_geneset(
+        cursor=cursor,
+        geneset_id=geneset_id,
+        limit=limit,
+        offset=offset,
+    )
+    assert result == ontologies_resp
+    assert cursor.execute.call_count == 1
+    assert cursor.fetchone.call_count == 0
+    assert cursor.fetchall.call_count == 1
+
+
+@pytest.mark.parametrize("geneset_id", [12345])
+@pytest.mark.parametrize("limit", [None, 1, 10])
+@pytest.mark.parametrize("offset", [None, 1, 10])
+@pytest.mark.parametrize(
+    "ontologies_resp",
+    [
+        ["a", "b", "c"],
+        ["d", "e", "f"],
+        ["g", "h", "i"],
+    ],
+)
+async def test_async_get_ontology_by_gs_id(
+    geneset_id,
+    limit,
+    offset,
+    ontologies_resp,
+    async_cursor,
+):
+    """Test the async ontology.get_ontology_by_gs_id function."""
+    async_cursor.fetchall.return_value = ontologies_resp
+
+    result = await async_get_ontology_by_gs_id(
+        cursor=async_cursor,
+        geneset_id=geneset_id,
+        limit=limit,
+        offset=offset,
+    )
+    assert result == ontologies_resp
+    assert async_cursor.execute.call_count == 1
+    assert async_cursor.fetchone.call_count == 0
+    assert async_cursor.fetchall.call_count == 1
+
+
+test_get_execute_raises_error = create_execute_raises_error_test(by_geneset, 1)
+
+test_get_fetchall_raises_error = create_fetchall_raises_error_test(by_geneset, 1)
+
+test_get_execute_raises_error = async_create_execute_raises_error_test(
+    async_get_ontology_by_gs_id, 1
+)
+
+test_async_get_fetchall_raises_error = async_create_fetchall_raises_error_test(
+    async_get_ontology_by_gs_id, 1
+)

tests/unit/query/ontology/__init__.py

@@ -0,0 +1 @@
+"""Test the sql generation code for ontologies."""

tests/unit/query/ontology/test_by_geneset.py

@@ -0,0 +1,23 @@
+"""Test the ontology.by_geneset query generation function."""
+
+import pytest
+from geneweaver.db.query.ontology import by_geneset
+
+
+@pytest.mark.parametrize("geneset_id", [12345])
+@pytest.mark.parametrize("limit", [None, 1, 10])
+@pytest.mark.parametrize("offset", [None, 1, 10])
+def test_all_kwargs(geneset_id, limit, offset):
+    """Test all the kwarg combinations for query.ontology.by_geneset."""
+    query, params = by_geneset(
+        geneset_id=geneset_id,
+        limit=limit,
+        offset=offset,
+    )
+
+    assert "gs_id" in params
+
+    str_query = str(query)
+
+    for key in ["ontology_id", "name", "description", "source_ontology"]:
+        assert key in str_query