Merge pull request #26 from TheJacksonLaboratory/G3-153-publication-f…

…or-geneset

G3-153 publication by geneset id

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.2.0a3"
+version = "0.2.0a4"
 description = "description"
 authors = ["Jax Computational Sciences <[email protected]>"]
 packages = [

src/geneweaver/api/controller/genesets.py

@@ -10,6 +10,7 @@
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.auth import UserInternal
 from geneweaver.api.services import geneset as genset_service
+from geneweaver.api.services import publications as publication_service
 from geneweaver.core.enum import GeneIdentifier
 from geneweaver.db import geneset as db_geneset
 from typing_extensions import Annotated
@@ -122,3 +123,36 @@ def get_geneset_metadata(
             raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
 
     return response
+
+
+@router.get("/{geneset_id}/publication")
+def get_publication_for_geneset(
+    geneset_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> dict:
+    """Get the publication associated with the geneset."""
+    geneset_resp = genset_service.get_geneset_metadata(cursor, geneset_id, user, True)
+
+    if "error" in geneset_resp:
+        if geneset_resp.get("message") == api_message.ACCESS_FORBIDDEN:
+            raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN)
+        else:
+            raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
+
+    geneset = geneset_resp.get("geneset")
+    if geneset is None:
+        raise HTTPException(status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR)
+
+    pub_id = geneset.get("publication_id")
+    if pub_id is None:
+        raise HTTPException(status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR)
+
+    pub_resp = publication_service.get_publication(cursor, pub_id)
+
+    if pub_resp.get("publication") is None:
+        raise HTTPException(status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR)
+
+    return pub_resp

tests/controllers/test_genesets.py

@@ -3,10 +3,12 @@
 
 import pytest
 
-from tests.data import test_geneset_data
+from tests.data import test_geneset_data, test_publication_data
 
 geneset_by_id_resp = test_geneset_data.get("geneset_by_id_resp")
 geneset_w_gene_id_type_resp = test_geneset_data.get("geneset_w_gene_id_type_resp")
+geneset_metadata_w_pub_info = test_geneset_data.get("geneset_metadata_w_pub_info")
+publication_by_id_resp = test_publication_data.get("publication_by_id")
 
 
 @patch("geneweaver.api.services.geneset.get_geneset")
@@ -79,3 +81,63 @@ def test_invalid_gene_type_id(mock_service_get_geneset_w_gene_id_type, client):
 
     assert "ctx" in response.json()["detail"][0]
     assert response.status_code == 422
+
+
+@patch("geneweaver.api.services.geneset.get_geneset_metadata")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+def test_get_geneset_metadata(mock_genset_is_readable, mock_get_genenset, client):
+    """Test get geneset metadata."""
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset.return_value = geneset_by_id_resp
+    response = client.get("/api/genesets/1234/metadata")
+
+    assert response.status_code == 200
+    assert response.json() == geneset_by_id_resp
+
+
+@patch("geneweaver.api.services.geneset.get_geneset_metadata")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+def test_get_geneset_metadata_w_publication(
+    mock_genset_is_readable, mock_get_genenset, client
+):
+    """Test get geneset ID data response."""
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset.return_value = geneset_metadata_w_pub_info
+
+    response = client.get("/api/genesets/1234/metadata?include_pub_info=true")
+    assert response.status_code == 200
+    assert response.json() == geneset_metadata_w_pub_info
+
+
+@patch("geneweaver.api.services.geneset.get_geneset_metadata")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+@patch("geneweaver.api.services.publications.get_publication")
+def test_publication_for_geneset(
+    mock_pub_service_call, mock_genset_is_readable, mock_get_genenset_metadata, client
+):
+    """Test valid url request to get publication for a geneset."""
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset_metadata.return_value = geneset_metadata_w_pub_info
+
+    mock_pub_service_call.return_value = publication_by_id_resp
+
+    response = client.get("/api/genesets/1234/publication")
+
+    assert response.status_code == 200
+    assert response.json() == publication_by_id_resp
+
+
+@patch("geneweaver.api.services.geneset.get_geneset_metadata")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+@patch("geneweaver.api.services.publications.get_publication")
+def test_publication_not_found_for_geneset(
+    mock_pub_service_call, mock_genset_is_readable, mock_get_genenset_metadata, client
+):
+    """Test get publication for a geneset with not found record."""
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset_metadata.return_value = geneset_by_id_resp.get("geneset")
+    mock_pub_service_call.return_value = {"publication": None}
+
+    response = client.get("/api/genesets/1234/publication")
+
+    assert response.status_code == 404