Merge pull request #89 from TheJacksonLaboratory/G3-325-api-genset-en…

…dpoint-update

G3 325 api genset endpoint update

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.8.0a2"
+version = "0.8.0a3"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",
@@ -20,7 +20,7 @@ python = "^3.9"
 geneweaver-core = "^0.10.0a3"
 fastapi = {extras = ["all"], version = "^0.111.0"}
 uvicorn = {extras = ["standard"], version = "^0.30.0"}
-geneweaver-db = "0.5.0a15"
+geneweaver-db = "0.5.0a16"
 psycopg-pool = "^3.1.7"
 requests = "^2.32.3"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/genesets.py

@@ -1,7 +1,7 @@
 """Endpoints related to genesets."""
 
 import json
-import time
+from datetime import date, datetime
 from tempfile import TemporaryDirectory
 from typing import Optional, Set
 
@@ -13,7 +13,7 @@
 from geneweaver.api.services import geneset as genset_service
 from geneweaver.api.services import publications as publication_service
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
-from geneweaver.core.schema.score import GenesetScoreType
+from geneweaver.core.schema.score import GenesetScoreType, ScoreType
 from typing_extensions import Annotated
 
 from . import message as api_message
@@ -69,6 +69,29 @@ def get_visible_genesets(
     with_publication_info: Annotated[
         bool, Query(description=api_message.ONLY_MY_GS)
     ] = True,
+    score_type: Optional[ScoreType] = None,
+    size_less_than: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.GENESET_SIZE,
+        ),
+    ] = None,
+    size_greater_than: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.GENESET_SIZE,
+        ),
+    ] = None,
+    created_after: Annotated[date, Query(description=api_message.CREATE_DATE)] = None,
+    created_before: Annotated[date, Query(description=api_message.CREATE_DATE)] = None,
+    updated_after: Annotated[date, Query(description=api_message.UPDATE_DATE)] = None,
+    updated_before: Annotated[date, Query(description=api_message.UPDATE_DATE)] = None,
     limit: Annotated[
         Optional[int],
         Query(
@@ -104,6 +127,13 @@ def get_visible_genesets(
         with_publication_info=with_publication_info,
         ontology_term=ontology_term,
         only_my_genesets=only_my_genesets,
+        score_type=score_type,
+        lte_count=size_less_than,
+        gte_count=size_greater_than,
+        created_after=created_after,
+        created_before=created_before,
+        updated_after=updated_after,
+        updated_before=updated_before,
         limit=limit,
         offset=offset,
     )
@@ -190,7 +220,8 @@ def get_export_geneset_by_id_type(
     gene_id_type: Optional[GeneIdentifier] = None,
 ) -> StreamingResponse:
     """Export geneset into JSON file. Search by ID and optional gene identifier type."""
-    timestr = time.strftime("%Y%m%d-%H%M%S")
+    current_datetime = datetime.now()
+    timestr = current_datetime.strftime("%Y%m%d-%H%M%S")
 
     # Validate gene identifier type
     if gene_id_type:

src/geneweaver/api/controller/message.py

@@ -29,3 +29,6 @@
 )
 CHECK_DB_HEALTH = "Check DB health flag"
 ONTOLOGY_ID = "Ontology term reference ID"
+CREATE_DATE = "Create date limit (before or after). E.g. 2024-08-01"
+UPDATE_DATE = "Update date limit (before or after). E.g. 2023-07-01"
+GENESET_SIZE = "Geneset size (Genes count)"

src/geneweaver/api/services/geneset.py

@@ -1,13 +1,14 @@
 """Service functions for dealing with genesets."""
 
+from datetime import date
 from typing import Iterable, Optional, Set
 
 from fastapi.logger import logger
 from geneweaver.api.controller import message
 from geneweaver.api.core.exceptions import UnauthorizedException
 from geneweaver.api.schemas.auth import AppRoles, User
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
-from geneweaver.core.schema.score import GenesetScoreType
+from geneweaver.core.schema.score import GenesetScoreType, ScoreType
 from geneweaver.db import gene as db_gene
 from geneweaver.db import geneset as db_geneset
 from geneweaver.db import geneset_value as db_geneset_value
@@ -90,9 +91,16 @@ def get_visible_genesets(
     gene_id_type: Optional[GeneIdentifier] = None,
     search_text: Optional[str] = None,
     ontology_term: Optional[str] = None,
+    with_publication_info: bool = True,
+    score_type: Optional[ScoreType] = None,
+    lte_count: Optional[int] = None,
+    gte_count: Optional[int] = None,
+    created_after: Optional[date] = None,
+    created_before: Optional[date] = None,
+    updated_after: Optional[date] = None,
+    updated_before: Optional[date] = None,
     limit: Optional[int] = None,
     offset: Optional[int] = None,
-    with_publication_info: bool = True,
 ) -> dict:
     """Get genesets from the database.
 
@@ -110,6 +118,13 @@ def get_visible_genesets(
     :param search_text: Return genesets that match this search text (using PostgreSQL
                         full-text search).
     :param ontology_term: Show only results associated with this ontology term.
+    :param score_type: Show only results with given score type.
+    :param lte_count: less than or equal geneset count.
+    :param gte_count: greater than or equal geneset count.
+    :param updated_before: Show only results updated before this date.
+    :param updated_after: Show only results updated after this date.
+    :param created_before: Show only results created before this date.
+    :param created_after: Show only results updated before this date.
     :param limit: Limit the number of results.
     :param offset: Offset the results.
     :param with_publication_info: Include publication info in the return.
@@ -134,6 +149,13 @@ def get_visible_genesets(
             search_text=search_text,
             with_publication_info=with_publication_info,
             ontology_term=ontology_term,
+            score_type=score_type,
+            lte_count=lte_count,
+            gte_count=gte_count,
+            created_after=created_after,
+            created_before=created_before,
+            updated_after=updated_after,
+            updated_before=updated_before,
             limit=limit,
             offset=offset,
         )

tests/controllers/test_genesets.py

@@ -3,6 +3,7 @@
 import json
 from unittest.mock import patch
 
+import pytest
 from geneweaver.api.controller import message
 
 from tests.data import test_geneset_data, test_ontology_data, test_publication_data
@@ -398,3 +399,71 @@ def test_delete_geneset_ontology_terms_errors(mock_delete_genenset_onto_terms, c
     }
     response = client.delete("/api/genesets/1234/ontologies/D001921")
     assert response.status_code == 404
+
+
+@pytest.mark.parametrize("score_type", ["1", "binary"])
+@patch("geneweaver.api.services.geneset.get_visible_genesets")
+def test_get_geneset_by_score_type(mock_get_visible_genesets, score_type, client):
+    """Test get geneset  data response."""
+    mock_get_visible_genesets.return_value = geneset_by_id_resp.get("geneset")
+
+    response = client.get("/api/genesets?score_type=" + score_type)
+    assert response.status_code == 200
+    assert response.json() == geneset_by_id_resp.get("geneset")
+
+
+@patch("geneweaver.api.services.geneset.get_visible_genesets")
+def test_get_geneset_by_create_date(mock_get_visible_genesets, client):
+    """Test get geneset  data response."""
+    mock_get_visible_genesets.return_value = geneset_by_id_resp.get("geneset")
+
+    response = client.get(
+        "/api/genesets?created_after=2023-08-01&created_before=2024-07-01"
+    )
+    assert response.status_code == 200
+    assert response.json() == geneset_by_id_resp.get("geneset")
+
+
+@patch("geneweaver.api.services.geneset.get_visible_genesets")
+def test_get_geneset_by_update_date(mock_get_visible_genesets, client):
+    """Test get geneset  data response."""
+    mock_get_visible_genesets.return_value = geneset_by_id_resp.get("geneset")
+
+    response = client.get(
+        "/api/genesets?updated_after=2023-08-01&updated_before=2024-07-01"
+    )
+    assert response.status_code == 200
+    assert response.json() == geneset_by_id_resp.get("geneset")
+
+
+@pytest.mark.parametrize("score_type", ["2342", "test"])
+def test_invalid_score_type(score_type, client):
+    """Test general get geneset data no parameters -- default limit."""
+    response = client.get("/api/genesets?score_type=" + score_type)
+    assert response.status_code == 422
+
+
+@pytest.mark.parametrize("created_before", ["20-23-20", "08-01-2023", "80/01/2022"])
+@pytest.mark.parametrize("created_after", ["20-23-20", "08-01-2023", "80/01/2022"])
+def test_invalid_create_date_params(created_before, created_after, client):
+    """Test general get geneset data no parameters -- default limit."""
+    response = client.get(
+        "/api/genesets?created_before="
+        + created_before
+        + ",created_after="
+        + created_after
+    )
+    assert response.status_code == 422
+
+
+@pytest.mark.parametrize("updated_before", ["20-23-20", "08-01-2023", "80/01/2022"])
+@pytest.mark.parametrize("updated_after", ["20-23-20", "08-01-2023", "80/01/2022"])
+def test_invalid_update_date_params(updated_before, updated_after, client):
+    """Test general get geneset data no parameters -- default limit."""
+    response = client.get(
+        "/api/genesets?created_before="
+        + updated_before
+        + ",created_after="
+        + updated_after
+    )
+    assert response.status_code == 422

tests/services/test_genset.py

@@ -1,5 +1,6 @@
 """Tests for geneset Service."""
 
+import datetime
 from unittest.mock import patch
 
 import pytest
@@ -8,7 +9,7 @@
 from geneweaver.api.schemas.auth import AppRoles, User
 from geneweaver.api.services import geneset
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species
-from geneweaver.core.schema.score import GenesetScoreType
+from geneweaver.core.schema.score import GenesetScoreType, ScoreType
 
 from tests.data import test_geneset_data
 
@@ -258,7 +259,14 @@ def test_visible_geneset_all_expected_parameters(mock_db_geneset):
         abbreviation="test",
         publication_id=123,
         pubmed_id="p123",
+        score_type=ScoreType("p-value"),
+        lte_count=50,
+        gte_count=5,
         gene_id_type=GeneIdentifier(5),
+        created_before=datetime.datetime(2024, 7, 31),
+        created_after=datetime.datetime(2008, 7, 31),
+        updated_before=datetime.datetime(2024, 7, 31),
+        updated_after=datetime.datetime(2023, 7, 31),
         limit=10,
         offset=0,
         with_publication_info=True,