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Major fastpheno refactor: Re-designed ERD to accompany more data (col… #302

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Merged
asherpasha merged 1 commit into from
Mar 16, 2026
Merged

Major fastpheno refactor: Re-designed ERD to accompany more data (col… #302

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105 changes: 62 additions & 43 deletions api/models/fastpheno.py
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Original file line number Diff line number Diff line change
@@ -1,65 +1,84 @@
from datetime import datetime
from api import db
import enum
from sqlalchemy.dialects.mysql import DECIMAL, ENUM
from sqlalchemy.orm import relationship
from sqlalchemy import ForeignKey
from typing import List
from sqlalchemy.dialects.mysql import DECIMAL


class Sites(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "sites"

sites_pk: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
sites_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
site_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False)
site_desc: db.Mapped[str] = db.mapped_column(db.String(99), nullable=True)
children: db.Mapped[List["Trees"]] = relationship()
lat: db.Mapped[float] = db.mapped_column(DECIMAL(15, 12), nullable=False)
lng: db.Mapped[float] = db.mapped_column(DECIMAL(15, 12), nullable=False)
site_desc: db.Mapped[str] = db.mapped_column(db.String(999), nullable=True)


class Flights(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "flights"

flights_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
pilot: db.Mapped[str] = db.mapped_column(db.String(45), nullable=True)
flight_date: db.Mapped[datetime] = db.mapped_column(db.DateTime, nullable=False)
sites_pk: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False)
height: db.Mapped[float] = db.mapped_column(DECIMAL(15, 10), nullable=True)
speed: db.Mapped[float] = db.mapped_column(DECIMAL(15, 10), nullable=True)


class Trees(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "trees"

trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
sites_pk: db.Mapped[int] = db.mapped_column(ForeignKey("sites.sites_pk"))
longitude: db.Mapped[float] = db.mapped_column(db.Float, nullable=False)
latitude: db.Mapped[float] = db.mapped_column(db.Float, nullable=False)
genotype_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=True)
trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
sites_pk: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False)
longitude: db.Mapped[float] = db.mapped_column(DECIMAL(15, 12), nullable=False)
latitude: db.Mapped[float] = db.mapped_column(DECIMAL(15, 12), nullable=False)
tree_site_id: db.Mapped[str] = db.mapped_column(db.String(45), nullable=True)
family_id: db.Mapped[str] = db.mapped_column(db.String(45), nullable=True)
external_link: db.Mapped[str] = db.mapped_column(db.String(200), nullable=True)
tree_given_id: db.Mapped[str] = db.mapped_column(db.String(25), nullable=True)
children: db.Mapped[List["Band"]] = relationship()


class MonthChoices(enum.Enum):
jan = "1"
feb = "2"
mar = "3"
apr = "4"
may = "5"
jun = "6"
jul = "7"
aug = "8"
sep = "9"
oct = "10"
nov = "11"
dec = "12"


class Band(db.Model):
block_num: db.Mapped[int] = db.mapped_column(db.Integer, nullable=True)
seq_id: db.Mapped[str] = db.mapped_column(db.String(25), nullable=True)
x_pos: db.Mapped[int] = db.mapped_column(db.Integer, nullable=True)
y_pos: db.Mapped[int] = db.mapped_column(db.Integer, nullable=True)
height_2022: db.Mapped[str] = db.mapped_column(db.String(10), nullable=True)


class TreesFlightsJoinTbl(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "band"
__tablename__ = "trees_flights_join_tbl"

trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
flights_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
confidence: db.Mapped[float] = db.mapped_column(DECIMAL(8, 5), nullable=True)


trees_pk: db.Mapped[int] = db.mapped_column(ForeignKey("trees.trees_pk"), primary_key=True)
month: db.Mapped[str] = db.mapped_column(ENUM(MonthChoices), nullable=False, primary_key=True)
band: db.Mapped[float] = db.mapped_column(db.String(100), nullable=False, primary_key=True)
class Bands(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "bands"
__table_args__ = (db.Index("bands_flight_band_tree_idx", "flights_pk", "band", "trees_pk"),)

trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
flights_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
band: db.Mapped[str] = db.mapped_column(db.String(20), primary_key=True, nullable=False)
value: db.Mapped[float] = db.mapped_column(DECIMAL(8, 5), nullable=False)


class Pigments(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "pigments"

trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
flights_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
pigment: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
value: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)


class Height(db.Model):
class Unispec(db.Model):
__bind_key__ = "fastpheno"
__tablename__ = "height"
__tablename__ = "unispec"

trees_pk: db.Mapped[int] = db.mapped_column(ForeignKey("trees.trees_pk"), primary_key=True)
month: db.Mapped[str] = db.mapped_column(ENUM(MonthChoices), nullable=False, primary_key=True)
tree_height_proxy: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)
ground_height_proxy: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)
trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
flights_pk: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
pigment: db.Mapped[int] = db.mapped_column(db.Integer, primary_key=True, nullable=False)
value: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)
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