G3 226 add publication endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.4.0"
+version = "0.5.0a0"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",
@@ -21,7 +21,7 @@ python = "^3.9"
 geneweaver-core = "^0.9.1"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "^0.3.0"
+geneweaver-db = "^0.3.3"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/message.py

@@ -6,6 +6,8 @@
 GENE_IDENTIFIER_TYPE_VALUE_ERROR = "Invalid gene identifier type"
 RECORD_NOT_FOUND_ERROR = "Record not found"
 INVALID_PUBMED_ID_ERROR = "Invalid pubmed id"
+RECORD_EXISTS = "Record already in the system"
+PUBMED_RETRIEVING_ERROR = "Error retrieving publication info from PubMed API"
 
 ##FORM field descriptions
 GENE_REFERENCE = "The reference id to search for"

src/geneweaver/api/controller/publications.py

@@ -2,8 +2,10 @@
 
 from typing import Optional
 
-from fastapi import APIRouter, Depends, HTTPException, Path
+from fastapi import APIRouter, Depends, HTTPException, Path, Security
 from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.apimodels import NewPubmedRecord
+from geneweaver.api.schemas.auth import UserInternal
 from geneweaver.api.services import publications as publication_service
 from geneweaver.core.schema.publication import Publication
 from typing_extensions import Annotated
@@ -33,3 +35,31 @@ def get_publication_by_id(
         raise HTTPException(status_code=404, detail=api_message.RECORD_NOT_FOUND_ERROR)
 
     return response
+
+
+@router.put("/{publication_id}")
+def add_publication(
+    publication_id: Annotated[
+        int, Path(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ],
+    user: UserInternal = Security(deps.full_user),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+) -> NewPubmedRecord:
+    """Add pubmed publication endpoint."""
+    response = publication_service.add_pubmed_record(
+        cursor=cursor, user=user, pubmed_id=publication_id
+    )
+
+    if "error" in response:
+        if response.get("message") == api_message.ACCESS_FORBIDDEN:
+            raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDDEN)
+        elif response.get("message") == api_message.RECORD_EXISTS:
+            raise HTTPException(status_code=412, detail=api_message.RECORD_EXISTS)
+        elif response.get("message") == api_message.PUBMED_RETRIEVING_ERROR:
+            raise HTTPException(
+                status_code=422, detail=api_message.PUBMED_RETRIEVING_ERROR
+            )
+        else:
+            raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
+
+    return response

src/geneweaver/api/dependencies.py

@@ -56,10 +56,8 @@ def cursor(request: Request) -> Generator:
         with conn.cursor(row_factory=dict_row) as cur:
             yield cur
 
-def _get_user_details(
-    cursor: Cursor,
-    user: UserInternal
-) -> UserInternal:
+
+def _get_user_details(cursor: Cursor, user: UserInternal) -> UserInternal:
     """Get the user details.
 
     :param cursor: The database cursor.

src/geneweaver/api/schemas/apimodels.py

@@ -82,3 +82,10 @@ class GeneValueReturn(BaseModel):
     """Model for geneset values endpoint return."""
 
     data: List[GeneValueSchema]
+
+
+class NewPubmedRecord(BaseModel):
+    """Model returned for adding new pubmed info into DB."""
+
+    pub_id: int
+    pubmed_id: int

src/geneweaver/api/services/publications.py

@@ -1,6 +1,10 @@
 """Service functions for publications."""
 
 from fastapi.logger import logger
+from geneweaver.api.controller import message
+from geneweaver.api.schemas.auth import User
+from geneweaver.core.exc import ExternalAPIError
+from geneweaver.core.publication import pubmed
 from geneweaver.db import publication as db_publication
 from psycopg import Cursor
 
@@ -22,17 +26,53 @@ def get_publication(cursor: Cursor, pub_id: int) -> dict:
     return pub
 
 
-def get_publication_by_pubmed_id(cursor: Cursor, pub_med_id: str) -> dict:
+def get_publication_by_pubmed_id(cursor: Cursor, pubmed_id: str) -> dict:
     """Get a publication by Pubmed Id from the DB.
 
     @param cursor: DB cursor
-    @param pub_med_id: pub med identifier
+    @param pubmed_id: pub med identifier
     @return: dictionary response (publication).
     """
     try:
-        pub = db_publication.by_pubmed_id(cursor, pub_med_id)
+        pub = db_publication.by_pubmed_id(cursor, pubmed_id)
         return pub
 
     except Exception as err:
         logger.error(err)
         raise err
+
+
+def add_pubmed_record(cursor: Cursor, user: User, pubmed_id: str) -> dict:
+    """Add pubmed publication to the DB given pub-med id.
+
+    @param cursor: DB cursor
+    @param user: logged-in user
+    @param pubmed_id: pubmed id
+    @return:
+    """
+    try:
+        # check logged-in user
+        if user is None or user.id is None:
+            return {"error": True, "message": message.ACCESS_FORBIDDEN}
+        # check publication is not already in the DB
+        pub = db_publication.by_pubmed_id(cursor, pubmed_id)
+        if pub:
+            return {"pubmed_id": pubmed_id, "pub_id": pub.get("id")}
+
+        # retrieve publication info to be stored
+        pub_record = pubmed.get_publication(pubmed_id=pubmed_id)
+        # persist publication in DB
+        results = db_publication.add(cursor, pub_record)
+
+        if results is None:
+            return {"error": True, "message": message.UNEXPECTED_ERROR}
+
+        return {"pubmed_id": pubmed_id, "pub_id": results.get("pub_id")}
+
+    except ExternalAPIError as err:
+        logger.error(err)
+        return {"error": True, "message": message.PUBMED_RETRIEVING_ERROR}
+
+    except Exception as err:
+        logger.error(err)
+        raise err

tests/controllers/test_publications.py

@@ -8,6 +8,8 @@
 
 publication_by_id_resp = test_publication_data.get("publication_by_id")
 publication_by_pubmed_id_resp = test_publication_data.get("publication_by_pubmed_id")
+add_pubmed_info = test_publication_data.get("add_pubmed_info")
+add_pubmed_resp = test_publication_data.get("add_pubmed_resp")
 
 
 @patch("geneweaver.api.services.publications.get_publication")
@@ -65,3 +67,46 @@ def test_invalid_pub_id_type(mock_pub_service_call, client):
 
     response = client.get(url="/api/publications/werte123")
     assert response.status_code == 422
+
+
+@patch("geneweaver.api.services.publications.add_pubmed_record")
+def test_add_pubmed_valid_url_req(mock_pub_service_call, client):
+    """Test valid url request to add pubmed record."""
+    mock_pub_service_call.return_value = add_pubmed_resp
+
+    response = client.put(url="/api/publications/1234")
+
+    assert response.status_code == 200
+    assert response.json() == add_pubmed_resp
+
+
+@patch("geneweaver.api.services.publications.add_pubmed_record")
+def test_add_pubmed_valid_errors(mock_pub_service_call, client):
+    """Test error codes adding pubmed record."""
+    mock_pub_service_call.return_value = {
+        "error": True,
+        "message": message.ACCESS_FORBIDDEN,
+    }
+    response = client.put(url="/api/publications/1234")
+    assert response.status_code == 403
+
+    mock_pub_service_call.return_value = {
+        "error": True,
+        "message": message.RECORD_EXISTS,
+    }
+    response = client.put(url="/api/publications/1234")
+    assert response.status_code == 412
+
+    mock_pub_service_call.return_value = {
+        "error": True,
+        "message": message.PUBMED_RETRIEVING_ERROR,
+    }
+    response = client.put(url="/api/publications/1234")
+    assert response.status_code == 422
+
+    mock_pub_service_call.return_value = {
+        "error": True,
+        "message": message.UNEXPECTED_ERROR,
+    }
+    response = client.put(url="/api/publications/1234")
+    assert response.status_code == 500

tests/data/__init__.py

@@ -99,6 +99,8 @@
     "publication_by_pubmed_id": json.loads(publications_json).get(
         "publication_by_pubmed_id"
     ),
+    "add_pubmed_info": json.loads(publications_json).get("add_pubmed_info"),
+    "add_pubmed_resp": json.loads(publications_json).get("add_pubmed_resp"),
 }
 
 # Json web token keys data

tests/data/publications.json

@@ -22,5 +22,20 @@
       "month": "Jan",
       "year": 2008,
       "id": 1234
+  },
+  "add_pubmed_info": {
+    "pubmed_id": 1234,
+    "authors": "D Nadeau, C Marchand",
+    "title": "Change in the kinetics of sulphacetamide tissue distribution in Walker tumor-bearing rats.",
+    "abstract": "The effect of Walker tumor on sulphacetamide distribution was studied in rats 21 days after tumor implantation in a hind leg. After oral administration of sulphacetamide (5 and 20 min), the concentration of the drug was found to be lower in the plasma and liver of tumor-bearing rats when compared with that of control group. However, 90 min after sulphacetamide administration, the concentration of the drug in these same tissues was found to be higher in tumor-bearing rats than in control animals. Whereas the tumor had no apparent effect on sulphacetamide concentration in the brain, drug concentrations in the fat tissue of tumor-bearing rats were constantly higher than those of control animals. These changes in sulphacentamide disposition kinetics could be explained in part by delay in gastrointestinal absorption of the drug. Contrary to what was observed after oral administration, constantly higher drug concentrations were found in the plasma of tumor-bearing rats after iv injection of sulphacetamide. Furthermore, the half-life of sulphacetamide in these same animals was much higher than in control animals. It is concluded that, in Walker tumor-bearing rats, there are changes in the kinetics of sulphacetamide which are functions of the route of administration of the drug.",
+    "journal": "Drug metabolism and disposition: the biological fate of chemicals",
+    "volume": "3",
+    "pages": "565-76",
+    "month": null,
+    "year": 1975
+  },
+  "add_pubmed_resp": {
+    "pubmed_id": 1234,
+    "pub_id": 79325
   }
 }

tests/services/test_publications.py

@@ -2,12 +2,20 @@
 
 from unittest.mock import patch
 
+import pytest
+from geneweaver.api.controller import message
+from geneweaver.api.schemas.auth import User
 from geneweaver.api.services import publications as pub_service
+from geneweaver.core.exc import ExternalAPIError
 
 from tests.data import test_publication_data
 
 publication_by_id_resp = test_publication_data.get("publication_by_id")
 publication_by_pubmed_id_resp = test_publication_data.get("publication_by_pubmed_id")
+add_pubmed_info = test_publication_data.get("add_pubmed_info")
+add_pubmed_resp = test_publication_data.get("add_pubmed_resp")
+mock_user = User()
+mock_user.id = 1
 
 
 @patch("geneweaver.api.services.publications.db_publication")
@@ -28,3 +36,85 @@ def test_get_publication_by_pubmed_id(mock_db_publication):
     response = pub_service.get_publication_by_pubmed_id(None, "17931734")
 
     assert response == publication_by_id_resp
+
+
+@patch("geneweaver.api.services.publications.db_publication")
+def test_get_publication_errors(mock_db_publication):
+    """Test get publication by ID data response structure."""
+    # unexpected error
+    mock_db_publication.by_pubmed_id.side_effect = Exception()
+    with pytest.raises(expected_exception=Exception):
+        pub_service.get_publication_by_pubmed_id(cursor=None, pubmed_id=1234)
+
+    # unexpected error
+    mock_db_publication.by_id.side_effect = Exception()
+    with pytest.raises(expected_exception=Exception):
+        pub_service.get_publication(cursor=None, pub_id=123)
+
+
+@patch("geneweaver.api.services.publications.pubmed")
+@patch("geneweaver.api.services.publications.db_publication")
+def test_add_pubmed_publication(mock_db_publication, mock_pubmed):
+    """Test persisting non-existing pubmed publication."""
+    mock_pubmed.get_publication.return_value = add_pubmed_info
+    mock_db_publication.by_pubmed_id.return_value = None
+    mock_db_publication.add.return_value = {"pub_id": add_pubmed_resp.get("pub_id")}
+
+    # adding pubmed info
+    response = pub_service.add_pubmed_record(
+        cursor=None, user=mock_user, pubmed_id=1234
+    )
+    assert response == add_pubmed_resp
+
+    # pubmed found in DB
+    mock_db_publication.by_pubmed_id.return_value = publication_by_pubmed_id_resp
+    pubmed_svc_rsp = {
+        "pub_id": publication_by_pubmed_id_resp.get("id"),
+        "pubmed_id": publication_by_pubmed_id_resp.get("pubmed_id"),
+    }
+    response = pub_service.add_pubmed_record(
+        cursor=None, user=mock_user, pubmed_id=17931734
+    )
+    assert response.get("error") is None
+    assert response == pubmed_svc_rsp
+
+
+@patch("geneweaver.api.services.publications.pubmed")
+@patch("geneweaver.api.services.publications.db_publication")
+def test_add_pubmed_publication_errors(mock_db_publication, mock_pubmed):
+    """Test errors adding pubmed info."""
+    mock_pubmed.get_publication.return_value = add_pubmed_info
+    mock_db_publication.by_pubmed_id.return_value = None
+    mock_db_publication.add.return_value = {"pub_id": add_pubmed_resp.get("pub_id")}
+
+    # user is not logged-in
+    response = pub_service.add_pubmed_record(cursor=None, user=None, pubmed_id=1234)
+    assert response.get("error") is True
+    assert response.get("message") == message.ACCESS_FORBIDDEN
+
+    # Error retrieving pubmed info
+    mock_db_publication.by_pubmed_id.return_value = None
+    mock_pubmed.get_publication.side_effect = ExternalAPIError()
+    response = pub_service.add_pubmed_record(
+        cursor=None, user=mock_user, pubmed_id=1234
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.PUBMED_RETRIEVING_ERROR
+
+    # No record returned by DB call
+    mock_pubmed.get_publication.side_effect = None
+    mock_pubmed.get_publication.return_value = add_pubmed_info
+    mock_db_publication.by_pubmed_id.return_value = None
+    mock_db_publication.add.return_value = None
+    response = pub_service.add_pubmed_record(
+        cursor=None, user=mock_user, pubmed_id=1234
+    )
+    assert response.get("error") is True
+    assert response.get("message") == message.UNEXPECTED_ERROR
+
+    # unexpected error
+    mock_db_publication.add.side_effect = Exception()
+    with pytest.raises(expected_exception=Exception):
+        response = pub_service.add_pubmed_record(
+            cursor=None, user=mock_user, pubmed_id=1234
+        )