Updated database access code

Author: davenquinn

.idea/inspectionProfiles/Project_Default.xml

@@ -1,4 +1,6 @@
 import logging
+from dotenv import load_dotenv
+
 
 disable_loggers = ["macrostrat.database.utils"]
 
@@ -8,3 +10,5 @@ def pytest_configure():
     for logger_name in disable_loggers:
         logger = logging.getLogger(logger_name)
         logger.disabled = True
+
+    load_dotenv()

services/column-footprint-editor/conftest.py

@@ -8,6 +8,7 @@
 from .home import HomePage
 from .project import ProjectsAPI
 from .voronoi import VoronoiTesselator
+from ..settings import DATABASE
 
 middleware = [
     Middleware(
@@ -36,6 +37,5 @@
 async def startup_event():
     from ..database import Database
 
-    # TODO: don't create tables on startup
-    db = Database()
+    db = Database(DATABASE)
     db.create_project_table()

services/column-footprint-editor/macrostrat/column_footprint_editor/api/__init__.py

@@ -4,8 +4,8 @@
 from starlette.endpoints import HTTPEndpoint
 from starlette.responses import JSONResponse
 
-from ..database import Database
 from ..project import Project
+from ..settings import DATABASE
 
 
 class ColumnGroups(HTTPEndpoint):
@@ -20,7 +20,7 @@ async def get(self, request):
         """
 
         project_id = request.path_params["project_id"]
-        project = Project(project_id)
+        project = Project(DATABASE, project_id)
 
         if "id" in request.query_params:
             id_ = request.query_params["id"]
@@ -29,7 +29,7 @@ async def get(self, request):
             )
 
             try:
-                df = Database().exec_query(sql)
+                df = project.db.exec_query(sql)
                 col_groups = df.to_dict(orient="records")
 
                 return JSONResponse({"status": "success", "data": col_groups})
@@ -53,7 +53,7 @@ async def post(self, request):
             :col_group,:col_group_name,:color
         )  """
 
-        project = Project(request.path_params["project_id"])
+        project = Project(DATABASE, request.path_params["project_id"])
 
         res = await request.json()
 
@@ -82,7 +82,7 @@ async def put(self, request):
                 color = :color
             WHERE cg.id = :col_group_id
          """
-        project = Project(request.path_params["project_id"])
+        project = Project(DATABASE, request.path_params["project_id"])
 
         res = await request.json()
 

services/column-footprint-editor/macrostrat/column_footprint_editor/api/column_groups.py

@@ -1,13 +1,15 @@
 import json
-import simplejson
 from pathlib import Path
+
+import simplejson
 from starlette.endpoints import HTTPEndpoint
 from starlette.responses import JSONResponse, PlainTextResponse
 
 from .utils import clean_change_set
 from ..database import Database
 from ..project import Project
 from ..project.importer import ProjectImporter
+from ..settings import DATABASE
 
 here = Path(__file__).parent / ".."
 procedures = here / "database" / "procedures"
@@ -18,8 +20,7 @@
 class Lines(HTTPEndpoint):
     async def get(self, request):
         project_id = request.path_params["project_id"]
-        project = Project(project_id)
-        db = Database(project)
+        project = Project(DATABASE, project_id)
 
         if "id" in request.query_params:
             id_ = request.query_params["id"]
@@ -41,7 +42,7 @@ async def get(self, request):
         q = queries / "get-linework.sql"
         sql = open(q).read()
 
-        df = db.exec_query(sql)
+        df = project.db.exec_query(sql)
 
         lines = []
         for i in range(0, len(df["lines"])):
@@ -72,7 +73,7 @@ async def put(self, request):
         data = await request.json()
 
         project_id = data["project_id"]
-        project = Project(project_id)
+        project = Project(DATABASE, project_id)
         db = Database(project)
 
         new_change_set = clean_change_set(data["change_set"])
@@ -107,13 +108,12 @@ async def put(self, request):
 class Points(HTTPEndpoint):
     async def get(self, request):
         project_id = request.path_params["project_id"]
-        project = Project(project_id)
-        db = Database(project)
+        project = Project(DATABASE, project_id)
 
         q = queries / "get-points.sql"
         sql = open(q).read()
 
-        df = db.exec_query(sql)
+        df = project.db.exec_query(sql)
         cols = df.to_dict(orient="records")
         cols = json.loads(simplejson.dumps(cols, ignore_nan=True))
 
@@ -159,7 +159,7 @@ async def get_line(request):
 
     sql = f"SELECT ST_AsGeoJSON(((ST_Dump(ST_Boundary({location_parser}))).geom))"
 
-    db = Database()
+    db = Database(DATABASE)
     df = db.exec_query(sql, params={"location": data})
     location = json.loads(df.to_dict(orient="records")[0]["st_asgeojson"])
 
@@ -169,13 +169,12 @@ async def get_line(request):
 async def geometries(request):
 
     project_id = request.path_params["project_id"]
-    project = Project(project_id)
-    db = Database(project)
+    project = Project(DATABASE, project_id)
 
     q = queries / "get-topology-columns.sql"
     sql = open(q).read()
 
-    df = db.exec_query(sql)
+    df = project.db.exec_query(sql)
     cols = df.to_dict(orient="records")
     cols = json.loads(simplejson.dumps(cols, ignore_nan=True))
 

services/column-footprint-editor/macrostrat/column_footprint_editor/api/geometries.py

@@ -1,12 +1,13 @@
-from os import error
-
 import json
+from os import error
 from pathlib import Path
+
 from starlette.endpoints import HTTPEndpoint
 from starlette.responses import JSONResponse
 
 from ..database import Database
 from ..project import Project
+from ..settings import DATABASE
 
 here = Path(__file__).parent / ".."
 procedures = here / "database" / "procedures"
@@ -18,7 +19,7 @@ class ProjectsAPI(HTTPEndpoint):
 
     async def get(self, request):
         """endpoint to get availble projects"""
-        db = Database()
+        db = Database(DATABASE)
 
         project_data = db.get_project_info()
 
@@ -58,7 +59,7 @@ async def put(self, request):
     async def post(self, request):
         res = await request.json()
 
-        db = Database()
+        db = Database(DATABASE)
         next_id = db.get_next_project_id()
 
         params = res["data"]

services/column-footprint-editor/macrostrat/column_footprint_editor/api/project.py

@@ -1,12 +1,13 @@
-from collections import defaultdict
-
 import json
+from collections import defaultdict
 from pathlib import Path
+
 from starlette.endpoints import HTTPEndpoint
 from starlette.responses import JSONResponse
 
 from ..database import Database
 from ..project import Project
+from ..settings import DATABASE
 
 here = Path(__file__).parent / ".."
 procedures = here / "database" / "procedures"
@@ -112,30 +113,28 @@ def tesselate(self, db: Database, points, radius, quad_segs):
 
     async def put(self, request):
         project_id = request.path_params["project_id"]
-        project = Project(project_id)
-        db = Database(project)
+        project = Project(DATABASE, project_id)
 
         data = await request.json()
         points = data["points"]
         radius = data["radius"]
         quad_segs = data["quad_segs"]
 
-        polygons = self.tesselate(db, points, radius, quad_segs)
+        polygons = self.tesselate(project.db, points, radius, quad_segs)
 
         return JSONResponse({"Status": "Success", "polygons": polygons})
 
     async def post(self, request):
         project_id = request.path_params["project_id"]
-        project = Project(project_id)
-        db = Database(project)
+        project = Project(DATABASE, project_id)
 
         data = await request.json()
         points = data["points"]
 
         radius = data["radius"]
         quad_segs = data["quad_segs"]
 
-        polygons = self.tesselate(db, points, radius, quad_segs)
+        polygons = self.tesselate(project.db, points, radius, quad_segs)
         ## dump each polygon to multilinestring and insert!!
         sql = open(self.dump_voronoi_to_lines).read()
 

services/column-footprint-editor/macrostrat/column_footprint_editor/api/voronoi.py

@@ -1,11 +1,9 @@
 from macrostrat.database import Database as BaseDatabase
 from macrostrat.database.utils import get_sql_text
 from pathlib import Path
-from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker
 
 from .sql_formatter import SqlFormatter
-from ..settings import DATABASE
 from ..utils import run_topology_command, delete_config
 
 here = Path(__file__).parent
@@ -30,11 +28,10 @@ class Database(BaseDatabase):
     Database class with built in SQL Formatter
     """
 
-    def __init__(self, project=None):
+    def __init__(self, url, project=None):
         self.project_id = getattr(project, "id", None)
-        super().__init__(DATABASE, echo_sql=True)
+        super().__init__(url)
 
-        self.engine = create_engine(DATABASE, echo=True)
         self.Session = sessionmaker(bind=self.engine)
         # self.config = config_check(project)
         self.formatter = SqlFormatter(self.project_id)
@@ -110,7 +107,7 @@ def redump_linework_from_edge(self):
         self.run_sql_file(redump_linework_sql)
 
     def remove_project(self, params={}):
-        run_topology_command(self.project_id, "delete")  # delete topology
+        run_topology_command(self, self.project_id, "delete")  # delete topology
         self.run_sql_file(remove_project_schema, params={"project_id": self.project_id})
         delete_config(self.project_id)  # remove config file
 

services/column-footprint-editor/macrostrat/column_footprint_editor/database/__init__.py

@@ -1,5 +1,6 @@
 import requests
 from pathlib import Path
+from psycopg2.sql import Identifier
 
 from mapboard.topology_manager.database import _get_instance_params
 from ..database import Database
@@ -12,24 +13,27 @@
 class Project:
     """Helper class to pass around project attributes"""
 
-    def __init__(self, id_: int = None, name: str = "", description: str = "") -> None:
+    def __init__(
+        self, db_url: str, id_: int = None, *, name: str = "", description: str = ""
+    ) -> None:
         self.id = id_
         self.name = name
         self.description = description
-        self.db = Database(self)
+        self.db = Database(db_url, project=self)
 
         params = _get_instance_params(
             data_schema=f"project_{self.id}_data",
             topo_schema=f"project_{self.id}_topology",
             tolerance=0.0001,
         )
-        params["project_schema"] = f"project_{self.id}"
+        params["project_schema"] = Identifier(f"project_{self.id}")
 
         self.db.instance_params = params
 
         self.base_url = IMPORTER_API
 
     def create_new_project(self):
+        self.db.create_project_table()
         if not self.project_in_db():
             self.id = self.db.get_next_project_id()
             self.insert_project_info()

services/column-footprint-editor/macrostrat/column_footprint_editor/project/__init__.py

@@ -1,8 +1,9 @@
 import json
+
 import requests
 
 from . import Project
-from ..settings import IMPORTER_API
+from ..settings import IMPORTER_API, DATABASE
 
 
 class ProjectImporter:
@@ -22,7 +23,7 @@ class ProjectImporter:
     """
 
     def __init__(self, project_id: int, name: str, description: str):
-        self.project = Project(project_id, name, description)
+        self.project = Project(DATABASE, project_id, name=name, description=description)
         self.db = self.project.db
         self.base_url = IMPORTER_API