app.py

# -*- coding: utf-8 -*-
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""An example of showing species richness from GBIF data."""

import os

# +
import altair as alt
import numpy as np
import pandas as pd
import pydeck as pdk
import streamlit as st

import ibis
from ibis import _
# -

# SETTING PAGE CONFIG TO WIDE MODE AND ADDING A TITLE AND FAVICON
st.set_page_config(layout="wide", page_title="GBIF Biodiversity Demo", page_icon=":butterfly:")



# +
# LOAD DATA ONCE
@st.cache_resource
def load_data():
    con = ibis.duckdb.connect()
    con.raw_sql('''
    INSTALL httpfs;
    LOAD httpfs;
    SET s3_url_style='path';
    SET s3_endpoint='minio.carlboettiger.info';
    CREATE VIEW gb AS SELECT * FROM read_parquet('s3://shared-data/gbif_gb/**');
    ''')

    hzoom = "h3z" + str(6)
    
    data =  (
        con.table("gb").
        select(_[hzoom], _.species, _.year).
        distinct().
        group_by([_[hzoom], _.year]).
        aggregate(n = _.count()).
        mutate(color = 255 * _.n / _.n.max()).
        to_pandas()
    )
    return data


@st.cache_data
def filterdata(df, year):
    return df[df.year == year]



# -

def map(data, lat, lon, zoom):
    st.write(
        pdk.Deck(
            map_style="mapbox://styles/mapbox/light-v9",
            initial_view_state={
                "latitude": lat,
                "longitude": lon,
                "zoom": zoom,
                "pitch": 50,
            },
            layers=[
                pdk.Layer(
                    "H3HexagonLayer",
                    data,
                    pickable=True,
                    stroked=True,
                    filled=True,
                    extruded=True,
                    elevation_scale=200,
                    get_elevation='color',
                    get_hexagon="h3z6", # set by zoom
                    get_fill_color="[color, 30, color]",
                    get_line_color=[255, 255, 255],
                    line_width_min_pixels=2,
                ),
            ],
        )
    )


# CALCULATE MIDPOINT FOR GIVEN SET OF DATA
@st.cache_data
def mpoint(lat, lon):
    return (np.average(lat), np.average(lon))


# LAYING OUT THE TOP SECTION OF THE APP
row1_1, row1_2 = st.columns((2, 3))

# SEE IF THERE'S A QUERY PARAM IN THE URL (e.g. ?pickup_hour=2)
# THIS ALLOWS YOU TO PASS A STATEFUL URL TO SOMEONE WITH A SPECIFIC HOUR SELECTED,
# E.G. https://share.streamlit.io/streamlit/demo-uber-nyc-pickups/main?pickup_hour=2
if not st.session_state.get("url_synced", False):
    try:
        year = int(st.query_params["year"][0])
        st.session_state["year"] = year
        st.session_state["url_synced"] = True
    except KeyError:
        pass


# IF THE SLIDER CHANGES, UPDATE THE QUERY PARAM
def update_query_params():
    year_selected = st.session_state["year"]
    st.query_params["year"]=year_selected


with row1_1:
    st.title("GBIF Species Richness")
    year_selected = st.slider(
        "Select year", 2015, 2023, key="year", on_change=update_query_params
    )


with row1_2:
    st.write(
    """
    ##
    By sliding the slider on the left you can view different slices of time and explore different trends.
    """
    )

# +
# LAYING OUT THE MIDDLE SECTION OF THE APP WITH THE MAPS
# -

# SETTING THE ZOOM LOCATIONS
midpoint =  (52.0, -1.0)  #mpoint(data["lat"], data["lon"])
# STREAMLIT APP LAYOUT
data = load_data()

st.write(
    f"""**Large Map**"""
)
map(filterdata(data, year_selected), midpoint[0], midpoint[1], 4)