Merge pull request #103 from SnowEx/break_up_tables

Refactor table to object mapping into dedicated classes.

snowexsql/api.py

@@ -1,16 +1,16 @@
 import logging
 from contextlib import contextmanager
-from sqlalchemy.sql import func
+
+import geoalchemy2.functions as gfunc
 import geopandas as gpd
-from shapely.geometry import box
 from geoalchemy2.shape import from_shape
-import geoalchemy2.functions as gfunc
 from geoalchemy2.types import Raster
+from shapely.geometry import box
+from sqlalchemy.sql import func
 
-from snowexsql.db import get_db
-from snowexsql.data import PointData, LayerData, ImageData
 from snowexsql.conversions import query_to_geopandas, raster_to_rasterio
-
+from snowexsql.db import get_db
+from snowexsql.tables import ImageData, LayerData, PointData
 
 LOG = logging.getLogger(__name__)
 DB_NAME = 'snow:[email protected]/snowex'

snowexsql/conversions.py

@@ -3,17 +3,14 @@
 filetypes, datatypes, etc. Many tools here will be useful for most end users
 of the database.
 """
-from os.path import basename, dirname, join
 
 import geopandas as gpd
 import pandas as pd
-import numpy as np
-import rasterio
 from geoalchemy2.shape import to_shape
 from rasterio import MemoryFile
 from sqlalchemy.dialects import postgresql
 
-from .data import PointData
+from snowexsql.tables import PointData
 
 
 def points_to_geopandas(results):

snowexsql/db.py

@@ -4,10 +4,11 @@
 """
 
 import json
+
 from sqlalchemy import MetaData, create_engine
 from sqlalchemy.orm import sessionmaker
 
-from .data import Base
+from snowexsql.tables import Base
 
 
 def initialize(engine):

snowexsql/tables/__init__.py

@@ -0,0 +1,16 @@
+from .base import Base, Measurement, SingleLocationData, SnowData
+from .image_data import ImageData
+from .layer_data import LayerData
+from .point_data import PointData
+from .site_data import SiteData
+
+__all__ = [
+    'Base',
+    'ImageData',
+    'LayerData',
+    'Measurement',
+    'PointData',
+    'SingleLocationData',
+    'SiteData'
+    'SnowData',
+]

snowexsql/tables/base.py

@@ -0,0 +1,51 @@
+"""
+Module contains all the data models for the database. Classes here actually
+represent tables where columns are mapped as attributed. Any class inheriting
+from Base is a real table in the database. This is called Object Relational
+Mapping in the sqlalchemy or ORM.
+"""
+
+from geoalchemy2 import Geometry
+from sqlalchemy import Column, Date, DateTime, Float, Integer, String, Time
+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.sql import func
+
+Base = declarative_base()
+
+
+class SnowData(object):
+    """
+    Base class for which all data will have these attributes
+    """
+    site_name = Column(String(250))
+    date = Column(Date)
+    time_created = Column(DateTime(timezone=True), server_default=func.now())
+    time_updated = Column(DateTime(timezone=True), onupdate=func.now())
+    id = Column(Integer, primary_key=True)
+    doi = Column(String(50))
+    date_accessed = Column(Date)
+
+
+class SingleLocationData(SnowData):
+    """
+    Base class for points and profiles
+    """
+    latitude = Column(Float)
+    longitude = Column(Float)
+    northing = Column(Float)
+    easting = Column(Float)
+    elevation = Column(Float)
+    utm_zone = Column(Integer)
+    geom = Column(Geometry("POINT"))
+    time = Column(Time(timezone=True))
+    site_id = Column(String(50))
+
+
+class Measurement(object):
+    """
+    Base Class providing attributes required for a measurement of any kind
+    """
+    instrument = Column(String(50))
+    type = Column(String(50))
+    units = Column(String(50))
+    observers = Column(String(100))

snowexsql/tables/image_data.py

@@ -0,0 +1,14 @@
+from geoalchemy2 import Raster
+from sqlalchemy import Column, String
+
+from .base import Base, Measurement, SnowData
+
+
+class ImageData(SnowData, Measurement, Base):
+    """
+    Class representing the images table. This table holds all images/rasters
+    """
+    __tablename__ = 'images'
+    __table_args__ = {"schema": "public"}
+    raster = Column(Raster)
+    description = Column(String(1000))

snowexsql/tables/layer_data.py

@@ -0,0 +1,25 @@
+from sqlalchemy import Column, Float, String
+
+from .base import Base, Measurement, SingleLocationData
+
+
+class LayerData(SingleLocationData, Measurement, Base):
+    """
+    Class representing the layers table. This table holds all layers or
+    profile data. Here a single data entry is a single value at depth in the
+    snowpack and a single coordinate pair.  e.g. SMP profiles, Hand hardness,
+    temperature etc...
+    """
+    __tablename__ = 'layers'
+    __table_args__ = {"schema": "public"}
+
+    depth = Column(Float)
+    site_id = Column(String(50))
+    pit_id = Column(String(50))
+    bottom_depth = Column(Float)
+    comments = Column(String(1000))
+    sample_a = Column(String(20))
+    sample_b = Column(String(20))
+    sample_c = Column(String(20))
+    value = Column(String(50))
+    flags = Column(String(20))

snowexsql/tables/point_data.py

@@ -0,0 +1,17 @@
+from sqlalchemy import Column, Float, Integer, String
+
+from .base import Base, Measurement, SingleLocationData
+
+
+class PointData(SingleLocationData, Measurement, Base):
+    """
+    Class representing the points table. This table holds all point data.
+    Here a single data entry is a single coordinate pair with a single value
+    e.g. snow depths
+    """
+    __tablename__ = 'points'
+    __table_args__ = {"schema": "public"}
+
+    version_number = Column(Integer)
+    equipment = Column(String(50))
+    value = Column(Float)

snowexsql/tables/site_data.py

@@ -0,0 +1,28 @@
+from sqlalchemy import Column, Float, String
+
+from .base import Base, SingleLocationData
+
+
+class SiteData(SingleLocationData, Base):
+    """
+    Table for storing pit site meta data, This table doesn't represent any
+    main data record but only support data for each site
+    """
+    __tablename__ = 'sites'
+    __table_args__ = {"schema": "public"}
+
+    pit_id = Column(String(50))
+    slope_angle = Column(Float)
+    aspect = Column(Float)
+    air_temp = Column(Float)
+    total_depth = Column(Float)
+    weather_description = Column(String(500))
+    precip = Column(String(100))
+    sky_cover = Column(String(100))
+    wind = Column(String(100))
+    ground_condition = Column(String(100))
+    ground_roughness = Column(String(100))
+    ground_vegetation = Column(String(100))
+    vegetation_height = Column(String(100))
+    tree_canopy = Column(String(100))
+    site_notes = Column(String(1000))

tests/test_db.py

@@ -1,12 +1,10 @@
-from os import remove
-from os.path import dirname, join
+from os.path import join
 
 import pytest
-from sqlalchemy import MetaData, Table, inspect
+from sqlalchemy import Table
 
-from snowexsql.data import ImageData, LayerData, PointData, SiteData
 from snowexsql.db import *
-
+from snowexsql.tables import ImageData, LayerData, PointData, SiteData
 from .sql_test_base import DBSetup