fix: lint ruff errors

src/api/create.py

@@ -9,6 +9,7 @@
 import numpy as np
 import pandas as pd
 import pyarrow.parquet as pq
+from psycopg2.extras import Json
 from sqlalchemy import MetaData, create_engine, text
 from sqlalchemy_utils.functions import (
     create_database,
@@ -17,7 +18,6 @@
 )
 from sqlmodel import SQLModel
 from tqdm import tqdm
-from psycopg2.extras import Json
 
 # Do not remove. Sqlalchemy needs this import to create tables
 from . import models  # noqa: F401
@@ -36,14 +36,16 @@ class Context(str, Enum):
     DQV = "http://www.w3.org/ns/dqv#"
     SDMX = "http://purl.org/linked-data/sdmx/2009/measure#"
 
+
 base_context = {
-    "dct": Context.DCT, 
+    "dct": Context.DCT,
     "schema": Context.SCHEMA,
-    "dqv": Context.DQV, 
-    "sdmx-measure": Context.SDMX, 
-    "dcat": Context.DCAT, 
+    "dqv": Context.DQV,
+    "sdmx-measure": Context.SDMX,
+    "dcat": Context.DCAT,
 }
 
+
 class URLType(Enum):
     """Enum type for different types of storage endpoint"""
 
@@ -130,9 +132,8 @@ def create_cpf_summary(self, data_path: Path):
         dfs = [pd.read_parquet(path) for path in paths]
         df = pd.concat(dfs).reset_index(drop=True)
         df["context"] = [Json(base_context)] * len(df)
-        df = df.drop_duplicates(subset=['name'])
+        df = df.drop_duplicates(subset=["name"])
         df.to_sql("cpf_summary", self.uri, if_exists="append")
-
 
     def create_scenarios(self, data_path: Path):
         """Create the scenarios metadata table"""
@@ -238,7 +239,15 @@ def create_sources(self, data_path: Path):
             + ".zarr/"
             + source_metadata["name"]
         )
-        column_names = ["uuid", "shot_id", "name", "description", "quality", "url", "context"]
+        column_names = [
+            "uuid",
+            "shot_id",
+            "name",
+            "description",
+            "quality",
+            "url",
+            "context",
+        ]
         source_metadata = source_metadata[column_names]
         source_metadata.to_sql("sources", self.uri, if_exists="append", index=False)
 

src/api/crud.py

@@ -67,7 +67,7 @@ def apply_filters(query: Query, filters: str) -> Query:
 def apply_sorting(query: Query, sort: t.Optional[str] = None) -> Query:
     if sort is None:
         return query
-    
+
     if sort.startswith("-"):
         sort = sort[1:]
         order = desc(column(sort))

src/api/main.py

@@ -1,15 +1,14 @@
 import datetime
 import io
+import json
 import os
+import re
 import uuid
 from typing import List, Optional
 
 import pandas as pd
 import sqlmodel
 import ujson
-import re
-import json
-
 from fastapi import (
     Depends,
     FastAPI,
@@ -22,8 +21,6 @@
 from fastapi.encoders import jsonable_encoder
 from fastapi.exceptions import RequestValidationError
 from fastapi.responses import JSONResponse
-
-
 from fastapi.staticfiles import StaticFiles
 from fastapi.templating import Jinja2Templates
 from fastapi_pagination import add_pagination
@@ -36,12 +33,10 @@
 
 from . import crud, graphql, models
 from .database import get_db
-from .models import CPFSummaryModel, ScenarioModel, ShotModel, SignalModel, SourceModel
 
 templates = Jinja2Templates(directory="src/api/templates")
 
 
-
 class JSONLDGraphQL(GraphQL):
     async def process_result(
         self, request: Request, result: ExecutionResult
@@ -196,24 +191,24 @@ def __init__(
 
 class CustomJSONResponse(JSONResponse):
     """
-    serializes the result of a database query (a dictionary) into a JSON-readable format 
+    serializes the result of a database query (a dictionary) into a JSON-readable format
     """
-    
+
     media_type = "application/json"
- 
-    def render(self, content)-> bytes:
+
+    def render(self, content) -> bytes:
         """
         renders the output of the request
         """
         content = self.convert_to_jsonld_terms(content)
         extracted_dict = {}
         edited_content = self.extract_meta_key(content, extracted_dict)
-        
+
         # merge content with extracted context by placing context at the top
         merged_content = {**extracted_dict, **edited_content}
-       
+
         return json.dumps(merged_content).encode()
-    
+
     def convert_to_jsonld_terms(self, items):
         """
         Replaces '__' with ':', and [A-Za-z_] with [@A-Za-z] in the mapping of terms (column names) to
@@ -222,7 +217,6 @@ def convert_to_jsonld_terms(self, items):
         if not isinstance(items, dict):
             return items
         for key, val in list(items.items()):
-
             # Recursive key modification if value is a dictionary or list object
             if isinstance(val, list):
                 items[key] = [self.convert_to_jsonld_terms(item) for item in val]
@@ -237,9 +231,9 @@ def convert_to_jsonld_terms(self, items):
 
     def extract_meta_key(self, content, extracted_dict):
         """
-            Extract keys and values of @context and @type from the dictionary to 
-            return them at the top of the dictionary as one entity for the whole dictionary, 
-            rather than each for each item since they contain the same key and values
+        Extract keys and values of @context and @type from the dictionary to
+        return them at the top of the dictionary as one entity for the whole dictionary,
+        rather than each for each item since they contain the same key and values
         """
         target_keys = ["@context", "@type", "dct:title"]
         for k, v in list(content.items()):
@@ -255,7 +249,6 @@ def extract_meta_key(self, content, extracted_dict):
                         self.extract_meta_key(item, extracted_dict)
         # return popped content
         return content
-
 
 
 def apply_pagination(
@@ -306,18 +299,19 @@ def query_aggregate(
     "/json/shots",
     description="Get information about experimental shots",
     response_model=CursorPage[models.ShotModel],
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_shots(
     db: Session = Depends(get_db), params: QueryParams = Depends()
 ) -> CursorPage[models.ShotModel]:
     if params.sort is None:
         params.sort = "shot_id"
 
-    query = crud.select_query(models.ShotModel, params.fields, params.filters, params.sort)
-
-    return paginate(db, query)
+    query = crud.select_query(
+        models.ShotModel, params.fields, params.filters, params.sort
+    )
 
+    return paginate(db, query)
 
 
 @app.get("/json/shots/aggregate")
@@ -335,7 +329,7 @@ def get_shots_aggregate(
     "/json/shots/{shot_id}",
     description="Get information about a single experimental shot",
     response_model=models.ShotModel,
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_shot(db: Session = Depends(get_db), shot_id: int = None) -> models.ShotModel:
     shot = crud.get_shot(shot_id)
@@ -347,7 +341,7 @@ def get_shot(db: Session = Depends(get_db), shot_id: int = None) -> models.ShotM
     "/json/shots/{shot_id}/signals",
     description="Get information all signals for a single experimental shot",
     response_model=CursorPage[models.SignalModel],
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_signals_for_shot(
     db: Session = Depends(get_db),
@@ -362,21 +356,26 @@ def get_signals_for_shot(
 
     # Get signals for this shot
     params.filters.append(f"shot_id$eq:{shot['shot_id']}")
-    query = crud.select_query(models.SignalModel, params.fields, params.filters, params.sort)
+    query = crud.select_query(
+        models.SignalModel, params.fields, params.filters, params.sort
+    )
     return paginate(db, query)
 
+
 @app.get(
     "/json/signals",
     description="Get information about specific signals.",
     response_model=CursorPage[models.SignalModel],
-    response_class=CustomJSONResponse
-    )
+    response_class=CustomJSONResponse,
+)
 def get_signals(
     db: Session = Depends(get_db), params: QueryParams = Depends()
-    ) -> CursorPage[models.SignalModel]:
+) -> CursorPage[models.SignalModel]:
     if params.sort is None:
         params.sort = "uuid"
-    query = crud.select_query(models.SignalModel, params.fields, params.filters, params.sort)
+    query = crud.select_query(
+        models.SignalModel, params.fields, params.filters, params.sort
+    )
 
     return paginate(db, query)
 
@@ -397,23 +396,23 @@ def get_signals_aggregate(
     description="Get information about a single signal",
     response_model_exclude_unset=True,
     response_model=models.SignalModel,
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_signal(
-    db: Session = Depends(get_db), uuid_: uuid.UUID = None) -> models.SignalModel:
+    db: Session = Depends(get_db), uuid_: uuid.UUID = None
+) -> models.SignalModel:
     signal = crud.get_signal(uuid_)
     signal = crud.execute_query_one(db, signal)
 
     return signal
 
 
-
 @app.get(
     "/json/signals/{uuid_}/shot",
     description="Get information about the shot for a single signal",
     response_model_exclude_unset=True,
     response_model=models.ShotModel,
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_shot_for_signal(
     db: Session = Depends(get_db), uuid_: uuid.UUID = None
@@ -429,7 +428,7 @@ def get_shot_for_signal(
     "/json/cpf_summary",
     description="Get descriptions of CPF summary variables.",
     response_model=CursorPage[models.CPFSummaryModel],
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_cpf_summary(
     db: Session = Depends(get_db), params: QueryParams = Depends()
@@ -447,37 +446,43 @@ def get_cpf_summary(
     "/json/scenarios",
     description="Get information on different scenarios.",
     response_model=CursorPage[models.ScenarioModel],
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_scenarios(
     db: Session = Depends(get_db), params: QueryParams = Depends()
 ) -> CursorPage[models.ScenarioModel]:
     if params.sort is None:
         params.sort = "id"
 
-    query = crud.select_query(models.ScenarioModel, params.fields, params.filters, params.sort)
+    query = crud.select_query(
+        models.ScenarioModel, params.fields, params.filters, params.sort
+    )
     return paginate(db, query)
 
 
 @app.get(
     "/json/sources",
     description="Get information on different sources.",
     response_model=CursorPage[models.SourceModel],
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_sources(
     db: Session = Depends(get_db), params: QueryParams = Depends()
 ) -> CursorPage[models.SourceModel]:
     if params.sort is None:
         params.sort = "name"
 
-    query = crud.select_query(models.SourceModel, params.fields, params.filters, params.sort)
+    query = crud.select_query(
+        models.SourceModel, params.fields, params.filters, params.sort
+    )
     return paginate(db, query)
 
 
-@app.get("/json/sources/aggregate",
-        response_model=models.SourceModel,
-        response_class=CustomJSONResponse)
+@app.get(
+    "/json/sources/aggregate",
+    response_model=models.SourceModel,
+    response_class=CustomJSONResponse,
+)
 def get_sources_aggregate(
     request: Request,
     response: Response,
@@ -492,7 +497,7 @@ def get_sources_aggregate(
     "/json/sources/{name}",
     description="Get information about a single signal",
     response_model=models.SourceModel,
-    response_class=CustomJSONResponse
+    response_class=CustomJSONResponse,
 )
 def get_single_source(
     db: Session = Depends(get_db), name: str = None
@@ -501,6 +506,7 @@ def get_single_source(
     source = db.execute(source).one()[0]
     return source
 
+
 def ndjson_stream_query(db, query):
     STREAM_SIZE = 1000
     offset = 0