Merge branch 'main' into task/fix-release-gates

pyproject.toml

@@ -21,7 +21,7 @@ python = "^3.9"
 geneweaver-core = "^0.9.0a1"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "^0.3.0a11"
+geneweaver-db = "^0.3.0a12"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/api.py

@@ -6,7 +6,7 @@
 from fastapi import APIRouter, FastAPI, Security
 from geneweaver.api import __version__
 from geneweaver.api import dependencies as deps
-from geneweaver.api.controller import genes, genesets, publications
+from geneweaver.api.controller import genes, genesets, publications, species
 from geneweaver.api.core.config import settings
 
 app = FastAPI(
@@ -28,5 +28,6 @@
 api_router.include_router(genesets.router)
 api_router.include_router(genes.router)
 api_router.include_router(publications.router)
+api_router.include_router(species.router)
 
 app.include_router(api_router, prefix=settings.API_PREFIX)

src/geneweaver/api/controller/genes.py

@@ -1,7 +1,7 @@
 """Endpoints related to genes."""
 from typing import Optional
 
-from fastapi import APIRouter, Depends
+from fastapi import APIRouter, Depends, Query
 from geneweaver.api import dependencies as deps
 from geneweaver.api.schemas.apimodels import (
     GeneIdHomologReq,
@@ -10,10 +10,54 @@
     GeneIdMappingResp,
 )
 from geneweaver.api.services import genes as genes_service
+from geneweaver.core.enum import GeneIdentifier, Species
+from typing_extensions import Annotated
+
+from . import message as api_message
 
 router = APIRouter(prefix="/genes", tags=["genes"])
 
 
+@router.get("")
+def get_genes(
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    reference_id: Annotated[
+        Optional[str], Query(description=api_message.GENE_REFERENCE)
+    ] = None,
+    gene_database: Optional[GeneIdentifier] = None,
+    species: Optional[Species] = None,
+    preferred: Annotated[
+        Optional[bool], Query(description=api_message.GENE_PREFERRED)
+    ] = None,
+    limit: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.LIMIT,
+        ),
+    ] = None,
+    offset: Annotated[
+        Optional[int],
+        Query(
+            format="int64",
+            minimum=0,
+            maxiumum=9223372036854775807,
+            description=api_message.OFFSET,
+        ),
+    ] = None,
+) -> dict:
+    """Get geneweaver list of genes."""
+    if limit is None:
+        limit = 100
+
+    response = genes_service.get_genes(
+        cursor, reference_id, gene_database, species, preferred, limit, offset
+    )
+    return response
+
+
 @router.post("/homologs", response_model=GeneIdMappingResp)
 def get_related_gene_ids(
     gene_id_mapping: GeneIdHomologReq,

src/geneweaver/api/controller/message.py

@@ -6,3 +6,9 @@
 UNEXPECTED_ERROR = "Unexpected Error"
 GENE_IDENTIFIER_TYPE_VALUE_ERROR = "Invalid gene identifier type"
 RECORD_NOT_FOUND_ERROR = "Record not found"
+
+##FORM field descriptions
+GENE_REFERENCE = "The reference id to search for"
+GENE_PREFERRED = "Whether to search for preferred genes"
+LIMIT = "The limit of results to return"
+OFFSET = "The offset of results to return"

src/geneweaver/api/controller/species.py

@@ -0,0 +1,24 @@
+"""Endpoints related to species."""
+from typing import Optional
+
+from fastapi import APIRouter, Depends, Query
+from geneweaver.api import dependencies as deps
+from geneweaver.api.services import species as species_service
+from geneweaver.core.enum import GeneIdentifier
+from typing_extensions import Annotated
+
+router = APIRouter(prefix="/species", tags=["species"])
+
+
+@router.get("/")
+def get_species(
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    taxonomy_id: Annotated[
+        Optional[int], Query(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ] = None,
+    reference_gene_id_type: Optional[GeneIdentifier] = None,
+) -> dict:
+    """Get species."""
+    response = species_service.get_species(cursor, taxonomy_id, reference_gene_id_type)
+
+    return response

src/geneweaver/api/services/genes.py

@@ -8,6 +8,40 @@
 from psycopg import Cursor
 
 
+def get_genes(
+    cursor: Cursor,
+    reference_id: Optional[str] = None,
+    gene_database: Optional[GeneIdentifier] = None,
+    species: Optional[Species] = None,
+    preferred: Optional[bool] = None,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> dict:
+    """Get geneweaver genes from DB.
+
+    :param cursor: The database cursor.
+    :param reference_id: The reference id to search for.
+    :param gene_database: The gene database to search for.
+    :param species: The species to search for.
+    :param preferred: Whether to search for preferred genes.
+    :param limit: The limit of results to return.
+    :param offset: The offset of results to return.
+    """
+    if limit is None:
+        limit = 100
+
+    try:
+        gene_list = db_gene.get(
+            cursor, reference_id, gene_database, species, preferred, limit, offset
+        )
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+    return {"genes": gene_list}
+
+
 def get_homolog_ids(
     cursor: Cursor,
     gene_id_list: Iterable,

src/geneweaver/api/services/species.py

@@ -0,0 +1,36 @@
+"""Service functions for Species."""
+
+from typing import Optional
+
+from fastapi.logger import logger
+from geneweaver.core.enum import GeneIdentifier
+from geneweaver.db import species as db_species
+from psycopg import Cursor
+
+
+def get_species(
+    cursor: Cursor,
+    taxonomy_id: Optional[int] = None,
+    reference_gene_id_type: Optional[GeneIdentifier] = None,
+) -> dict:
+    """Get species from DB.
+
+    @param cursor: DB cursor
+    @param taxonomy_id:
+    @param reference_gene_id_type:
+    @return: dictionary response (species).
+    """
+    try:
+        species = db_species.get(cursor, taxonomy_id, reference_gene_id_type)
+        for species_record in species:
+            ref_gene_id_type = species_record.get("reference_gene_identifier", None)
+            if ref_gene_id_type:
+                species_record["reference_gene_identifier"] = GeneIdentifier(
+                    ref_gene_id_type
+                )
+
+        return {"species": species}
+
+    except Exception as err:
+        logger.error(err)
+        raise err

tests/controllers/test_genes.py

@@ -2,7 +2,10 @@
 import json
 from unittest.mock import patch
 
-from tests.data import test_gene_homolog_data, test_gene_mapping_data
+from tests.data import test_gene_homolog_data, test_gene_mapping_data, test_genes_data
+
+# genes
+genes_list_10 = test_genes_data.get("genes_list_10")
 
 # gene homolog ids test data
 gene_ids_homolog_req_1 = test_gene_homolog_data.get(
@@ -144,3 +147,36 @@ def test_gene_aon_mapping_invalid_post_data_(client):
         url="/api/genes/mapping/aon", data=json.dumps({"test": "test"})
     )
     assert response.status_code == 422
+
+
+@patch("geneweaver.api.services.genes.get_genes")
+def test_valid_gene_get_req(mock_gene_call, client):
+    """Test valid get genes request."""
+    mock_gene_call.return_value = genes_list_10
+
+    response = client.get(url="/api/genes")
+
+    print(response)
+    assert response.status_code == 200
+    assert response.json() == genes_list_10
+
+    response = client.get(url="/api/genes?limit=10")
+    assert response.status_code == 200
+    assert response.json() == genes_list_10
+
+
+@patch("geneweaver.api.services.genes.get_genes")
+def test_invalid_param_gene_get_req(mock_gene_call, client):
+    """Test invalid get genes request parameters."""
+    mock_gene_call.return_value = genes_list_10
+
+    response = client.get(url="/api/genes?limit=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?offset=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?gene_database=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?species=abc")
+    assert response.status_code == 422
+    response = client.get(url="/api/genes?preferred=abc")
+    assert response.status_code == 422

tests/controllers/test_species.py

@@ -0,0 +1,43 @@
+"""Tests for species API."""
+from unittest.mock import patch
+
+from tests.data import test_species_data
+
+species_no_params = test_species_data.get("species_no_parameters")
+species_by_taxonomy_id_10090 = test_species_data.get("species_by_taxonomy_id_10090")
+species_by_gene_id_type_flybase = test_species_data.get(
+    "species_by_gene_id_type_flybase"
+)
+
+
+@patch("geneweaver.api.services.species.get_species")
+def test_valid_species_url_req(mock_species_service_call, client):
+    """Test valid url request to get species."""
+    mock_species_service_call.return_value = species_no_params
+
+    response = client.get(url="/api/species")
+
+    assert response.status_code == 200
+    assert response.json() == species_no_params
+
+
+@patch("geneweaver.api.services.species.get_species")
+def test_species_url_taxonomy_req(mock_species_service_call, client):
+    """Test valid url request to get species."""
+    mock_species_service_call.return_value = species_by_taxonomy_id_10090
+
+    response = client.get(url="/api/species?taxonomy_id=10090")
+
+    assert response.status_code == 200
+    assert response.json() == species_by_taxonomy_id_10090
+
+
+@patch("geneweaver.api.services.species.get_species")
+def test_valid_species_url_gene_id_type_req(mock_species_service_call, client):
+    """Test valid url request to get species."""
+    mock_species_service_call.return_value = species_by_gene_id_type_flybase
+
+    response = client.get(url="/api/species?gene_id_type=14")
+
+    assert response.status_code == 200
+    assert response.json() == species_by_gene_id_type_flybase

tests/data/__init__.py

@@ -3,6 +3,8 @@
 import importlib.resources
 import json
 
+from geneweaver.core.enum import GeneIdentifier
+
 ## Load test data
 # Opening JSON files
 geneset_response_json = importlib.resources.read_text(
@@ -24,6 +26,9 @@
     "tests.data", "security_jwt_RS256_keys.json"
 )
 
+species_json = importlib.resources.read_text("tests.data", "species.json")
+
+genes_json = importlib.resources.read_text("tests.data", "genes.json")
 
 ## laod and returns JSON string as a dictionary
 
@@ -88,8 +93,39 @@
     ),
 }
 
-# Json web token keys data =
+# Json web token keys data
 test_jwt_keys_data = {
     "test_private_key": json.loads(jwt_test_keys_json).get("private_key"),
     "test_public_key": json.loads(jwt_test_keys_json).get("public_key"),
 }
+
+
+## Species test data
+test_species_data = {
+    "species_no_parameters": json.loads(species_json).get("species_no_parameters"),
+    "species_by_taxonomy_id_10090": json.loads(species_json).get(
+        "species_by_taxonomy_id_10090"
+    ),
+    "species_by_gene_id_type_flybase": json.loads(species_json).get(
+        "species_by_gene_id_type_flybase"
+    ),
+}
+
+
+## geneweaver genes test data
+test_genes_data = {
+    "genes_list_10": json.loads(genes_json).get("genes_list_10"),
+}
+
+def get_species_db_resp(species_data: dict) -> dict:
+    """Get species data as returned by DB."""
+    species = species_data.get("species")
+    for species_record in species:
+        ref_gene_id_type = species_record.get("reference_gene_identifier", None)
+        if ref_gene_id_type:
+            species_record["reference_gene_identifier"] = GeneIdentifier(
+                ref_gene_id_type
+            ).as_int()
+
+    return species
+