Merge pull request #310 from AllenNeuralDynamics/release-v0.17.0

Release v0.17.0

src/aind_metadata_service/__init__.py

@@ -1,3 +1,3 @@
 """REST service to retrieve metadata from databases."""
 
-__version__ = "0.16.0"
+__version__ = "0.17.0"

src/aind_metadata_service/mgi/__init__.py

@@ -0,0 +1 @@
+"""Package to handle mgi requests"""

src/aind_metadata_service/mgi/client.py

@@ -0,0 +1,88 @@
+"""Module to handle retrieving information from MGI"""
+
+import logging
+from typing import Any, List, Optional, Union
+
+import requests
+from pydantic import BaseModel, Extra, Field, HttpUrl
+from pydantic_settings import BaseSettings
+
+from aind_metadata_service.response_handler import ModelResponse
+
+
+class MgiSettings(BaseSettings):
+    """Settings required for endpoint"""
+
+    url: HttpUrl = Field(
+        default="https://www.informatics.jax.org//quicksearch/alleleBucket"
+    )
+
+    class Config:
+        """Set env prefix and forbid extra fields."""
+
+        env_prefix = "MGI_"
+        extra = Extra.forbid
+
+
+class MgiSummaryRow(BaseModel):
+    """Model of Summary Row dictionary returned"""
+
+    detailUri: Optional[str] = Field(default=None)
+    featureType: Optional[str] = Field(default=None)
+    strand: Optional[str] = Field(default=None)
+    chromosome: Optional[str] = Field(default=None)
+    stars: Optional[str] = Field(default=None)
+    bestMatchText: Optional[str] = Field(default=None)
+    bestMatchType: Optional[str] = Field(default=None)
+    name: Optional[str] = Field(default=None)
+    location: Optional[str] = Field(default=None)
+    symbol: Optional[str] = Field(default=None)
+
+
+class MgiResponse(BaseModel):
+    """Model for response from MGI"""
+
+    summaryRows: List[MgiSummaryRow]
+    totalCount: Optional[int] = Field(default=None)
+    meta: Optional[Any] = Field(default=None)
+
+
+class MgiClient:
+    """Client to connect to Mgi"""
+
+    def __init__(self, settings: MgiSettings):
+        """Class constructor"""
+
+        self.settings = settings
+
+    def get_allele_info(
+        self, allele_name: str
+    ) -> Union[MgiResponse, ModelResponse]:
+        """
+        Get allele info from mgi endpoint
+        Parameters
+        ----------
+        allele_name : str
+
+        Returns
+        -------
+        MgiResponse
+
+        """
+        try:
+            params = {
+                "queryType": "exactPhrase",
+                "query": allele_name,
+                "submit": "Quick+Search",
+                "startIndex": "0",
+                "results": "1",
+            }
+            response = requests.get(
+                url=self.settings.url.unicode_string(), params=params
+            )
+            response.raise_for_status()
+            response_model = MgiResponse(**response.json())
+            return response_model
+        except Exception as e:
+            logging.exception(e)
+            return ModelResponse.internal_server_error_response()

src/aind_metadata_service/mgi/mapping.py

@@ -0,0 +1,66 @@
+"""Module to handle mapping data from mgi to aind-data-schema models"""
+
+import logging
+import re
+from typing import Union
+
+from aind_data_schema_models.pid_names import PIDName
+from aind_data_schema_models.registries import Registry
+
+from aind_metadata_service.client import StatusCodes
+from aind_metadata_service.mgi.client import MgiResponse
+from aind_metadata_service.response_handler import ModelResponse
+
+
+class MgiMapper:
+    """Class that handles mapping mgi info"""
+
+    DETAIL_URI_PATTERN = re.compile(r"/allele/MGI:(\d+)")
+
+    def __init__(self, mgi_info: Union[MgiResponse, ModelResponse]):
+        """Class constructor"""
+
+        self.mgi_info = mgi_info
+
+    def get_model_response(self) -> ModelResponse:
+        """Get a model response from mgi ingo"""
+
+        try:
+            if isinstance(self.mgi_info, ModelResponse):
+                return self.mgi_info
+
+            if len(self.mgi_info.summaryRows) == 0:
+                return ModelResponse.no_data_found_error_response()
+            first_summary_row = self.mgi_info.summaryRows[0]
+
+            # 4 stars represent an exact match
+            if (
+                first_summary_row.stars != "****"
+                or first_summary_row.bestMatchType != "Synonym"
+            ):
+                return ModelResponse.no_data_found_error_response()
+
+            if (
+                re.match(self.DETAIL_URI_PATTERN, first_summary_row.detailUri)
+                is not None
+            ):
+                registry_identifier = re.match(
+                    self.DETAIL_URI_PATTERN, first_summary_row.detailUri
+                ).group(1)
+            else:
+                registry_identifier = None
+
+            pid_name = PIDName(
+                name=first_summary_row.symbol,
+                abbreviation=None,
+                registry=Registry.MGI,
+                registry_identifier=registry_identifier,
+            )
+
+            model_response = ModelResponse(
+                aind_models=[pid_name], status_code=StatusCodes.DB_RESPONDED
+            )
+            return model_response
+        except Exception as e:
+            logging.exception(e)
+            return ModelResponse.internal_server_error_response()

src/aind_metadata_service/response_handler.py

@@ -15,6 +15,7 @@
 from aind_data_schema.core.rig import Rig
 from aind_data_schema.core.session import Session
 from aind_data_schema.core.subject import Subject
+from aind_data_schema_models.pid_names import PIDName
 from aind_metadata_mapper.core import JobResponse
 from fastapi import Response
 from fastapi.encoders import jsonable_encoder
@@ -37,6 +38,7 @@
     Instrument,
     Rig,
     Session,
+    PIDName,
 )
 
 

src/aind_metadata_service/server.py

@@ -17,6 +17,8 @@
     LabTracksClient,
     LabTracksSettings,
 )
+from aind_metadata_service.mgi.client import MgiClient, MgiSettings
+from aind_metadata_service.mgi.mapping import MgiMapper
 from aind_metadata_service.response_handler import EtlResponse
 from aind_metadata_service.sharepoint.client import (
     SharePointClient,
@@ -65,6 +67,8 @@
     access_token=SMARTSHEET_PROTOCOLS_TOKEN, sheet_id=SMARTSHEET_PROTOCOLS_ID
 )
 
+mgi_settings = MgiSettings()
+
 app = FastAPI()
 
 app.add_middleware(
@@ -90,6 +94,7 @@
 )
 slims_client = SlimsHandler(settings=slims_settings)
 tars_client = TarsClient(azure_settings=tars_settings)
+mgi_client = MgiClient(settings=mgi_settings)
 
 template_directory = os.path.abspath(
     os.path.join(os.path.dirname(__file__), "templates")
@@ -148,6 +153,21 @@ async def retrieve_protocols(
     return model_response.map_to_json_response()
 
 
+@app.get("/mgi_allele/{allele_name}")
+async def retrieve_mgi_allele(
+    allele_name,
+):
+    """Retrieves allele information from mgi"""
+
+    # TODO: We can probably cache the response if it's 200
+    mgi_response = await run_in_threadpool(
+        mgi_client.get_allele_info, allele_name=allele_name
+    )
+    mapper = MgiMapper(mgi_info=mgi_response)
+    model_response = mapper.get_model_response()
+    return model_response.map_to_json_response()
+
+
 @app.get("/perfusions/{subject_id}")
 async def retrieve_perfusions(subject_id):
     """Retrieves perfusion information from smartsheet"""