Percent grass curing from CWFIS (bcgov#3385)

Co-authored-by: Conor Brady <con.brad@gmail.com>

.github/workflows/deployment.yml

@@ -175,6 +175,12 @@ jobs:
           oc login "${{ secrets.OPENSHIFT_CLUSTER }}" --token="${{ secrets.OC4_DEV_TOKEN }}"
           PROJ_DEV="e1e498-dev" bash openshift/scripts/oc_provision_viirs_snow_cronjob.sh ${SUFFIX} apply
 
+      - name: GRASS CURING cronjob
+        shell: bash
+        run: |
+          oc login "${{ secrets.OPENSHIFT_CLUSTER }}" --token="${{ secrets.OC4_DEV_TOKEN }}"
+          PROJ_DEV="e1e498-dev" bash openshift/scripts/oc_provision_grass_curing_cronjob.sh ${SUFFIX} apply
+
   # TODO: Delete once pmtiles has run for some time
   # deploy-tileserv:
   #   name: Deploy tileserv to Dev

api/alembic/versions/2b3755392ad8_percent_grass_curing.py

@@ -0,0 +1,41 @@
+"""Percent grass curing
+
+Revision ID: 2b3755392ad8
+Revises: 5845f568a975
+Create Date: 2024-02-01 16:45:05.914743
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from app.db.models.common import TZTimeStamp
+
+# revision identifiers, used by Alembic.
+revision = '2b3755392ad8'
+down_revision = '5845f568a975'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic ###
+    op.create_table('percent_grass_curing',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('station_code', sa.Integer(), nullable=False),
+    sa.Column('percent_grass_curing', sa.Float(), nullable=False),
+    sa.Column('for_date', TZTimeStamp(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    comment='Record containing information about percent grass curing from the CFWIS.'
+    )
+    op.create_index(op.f('ix_percent_grass_curing_for_date'), 'percent_grass_curing', ['for_date'], unique=False)
+    op.create_index(op.f('ix_percent_grass_curing_id'), 'percent_grass_curing', ['id'], unique=False)
+    op.create_index(op.f('ix_percent_grass_curing_station_code'), 'percent_grass_curing', ['station_code'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic ###
+    op.drop_index(op.f('ix_percent_grass_curing_station_code'), table_name='percent_grass_curing')
+    op.drop_index(op.f('ix_percent_grass_curing_id'), table_name='percent_grass_curing')
+    op.drop_index(op.f('ix_percent_grass_curing_for_date'), table_name='percent_grass_curing')
+    op.drop_table('percent_grass_curing')
+    # ### end Alembic commands ###

api/app/db/crud/grass_curing.py

@@ -0,0 +1,28 @@
+""" CRUD operations relating to processing grass curing
+"""
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.sql import func
+from app.db.models.grass_curing import PercentGrassCuring
+
+
+async def save_percent_grass_curing(session: AsyncSession, percent_grass_curing: PercentGrassCuring):
+    """ Add a new PercentGrassCuring record.
+
+    :param session: A session object for asynchronous database access.
+    :type session: AsyncSession
+    :param percent_grass_curing: The record to be saved.
+    :type percent_grass_curing: PercentGrassCuring
+    """
+    session.add(percent_grass_curing)
+
+
+async def get_last_percent_grass_curing_for_date(session: AsyncSession):
+    """ Get the last date for which a PercentGrassCuring record exists.
+    
+    :param session: A session object for asynchronous database access.
+    :type session: AsyncSession
+    """
+    stmt = select(func.max(PercentGrassCuring.for_date))
+    result = await session.execute(stmt)
+    return result.scalar()

api/app/db/models/__init__.py

@@ -17,3 +17,4 @@
                                                  ClassifiedHfi, RunTypeEnum, ShapeTypeEnum, FuelType, HighHfiArea, RunParameters)
 from app.db.models.morecast_v2 import MorecastForecastRecord
 from app.db.models.snow import ProcessedSnow, SnowSourceEnum
+from app.db.models.grass_curing import PercentGrassCuring

api/app/db/models/grass_curing.py

@@ -0,0 +1,18 @@
+from app.db.models import Base
+from sqlalchemy import (Column, Float, Integer, Sequence)
+from app.db.models.common import TZTimeStamp
+
+
+class PercentGrassCuring(Base):
+    """ Daily percent grass curing per weather station. """
+    __tablename__ = 'percent_grass_curing'
+    __table_args__ = (
+        {'comment': 'Record containing information about percent grass curing from the CFWIS.'}
+    )
+
+    id = Column(Integer, Sequence('percent_grass_curing_id_seq'),
+                primary_key=True, nullable=False, index=True)
+    station_code = Column(Integer, nullable=False, index=True)
+    percent_grass_curing = Column(Float, nullable=False, index=False)
+    for_date = Column(TZTimeStamp, nullable=False, index=True)
+

api/app/jobs/grass_curing.py

@@ -0,0 +1,156 @@
+from affine import Affine
+from datetime import date
+from osgeo import gdal
+import asyncio
+import logging
+import math
+import numpy as np
+import os
+import requests
+import sys
+import tempfile
+import xml.etree.ElementTree as ET
+from app import configure_logging
+from app.db.crud.grass_curing import get_last_percent_grass_curing_for_date, save_percent_grass_curing
+from app.db.database import get_async_read_session_scope, get_async_write_session_scope
+from app.geospatial import WGS84
+from app.db.models.grass_curing import PercentGrassCuring
+from app.rocketchat_notifications import send_rocketchat_notification
+from app.stations import get_stations_asynchronously
+
+logger = logging.getLogger(__name__)
+
+GRASS_CURING_FILE_NAME_3978 = "grass_curing_epsg_3978.tif"
+GRASS_CURING_FILE_NAME_4326 = "grass_curing_epsg_4326.tif"
+GRASS_CURING_COVERAGE_ID = "public:pc_current"
+WCS_URL = "https://cwfis.cfs.nrcan.gc.ca/geoserver/public/wcs"
+
+
+class OwsException(Exception):
+    """ Raise when OWS service returns an exception report."""
+
+
+class GrassCuringJob():
+    """ Job that downloads and processes percent grass curing data from the CWFIS. """
+
+    async def _get_grass_curing_wcs_raster(self, path: str):
+        """ Gets the current percent grass curing as a tif from the CFWIS Web Coverage Service. """
+        session = requests.session()
+        param_dict= {
+            "service": "WCS",
+            "version": "2.0.0",
+            "request": "GetCoverage",
+            "format": "image/geotiff",
+            "coverageId": GRASS_CURING_COVERAGE_ID
+        }
+        response = session.get(WCS_URL, params = param_dict)
+        # Check HTTP response code for error condition
+        response.raise_for_status()
+        # GeoServer can return an exception report as xml within a 200 response. Check if we have a content type header 
+        # of application/xml and check if an exception is present.
+        if "Content-Type" in response.headers and response.headers["Content-Type"] == "application/xml":
+            root_element = ET.fromstring(response.content)
+            if "ExceptionReport" in root_element.tag:
+                message = f"GeoServer returned an exception when attempting to download percent grass curing from URL: {response.request.url}"
+                logger.error(message)
+                raise OwsException(message)
+        file_path = os.path.join(path, GRASS_CURING_FILE_NAME_3978)
+        with open(file_path, 'wb') as file:
+            file.write(response.content)
+
+
+    def _reproject_to_epsg_4326(self, path: str):
+        """ Transforms coordinates in source_file geotiff to EPSG:3005 (BC Albers),
+        writes to newly created geotiff called <new_filename>.tif
+
+        :param path: A path to a temporary directory containing the percent grass curing tif.
+        """
+        destination_path = f"{path}/{GRASS_CURING_FILE_NAME_4326}"
+        source_path = f"{path}/{GRASS_CURING_FILE_NAME_3978}"
+        source_data = gdal.Open(source_path, gdal.GA_ReadOnly)
+        gdal.Warp(destination_path, source_data, dstSRS=WGS84)
+        del source_data
+
+
+    def _yield_value_for_stations(self, data_source, stations):
+        """ Given a list of stations, and a gdal dataset, yield the grass curing value for each station
+
+        :param data_source: A gdal representation of a raster image of percent grass curing.
+        :param stations: A list of weather station objects.
+        :return: A tuple of a weather station code and the percent grass curing at its location.
+        """
+        raster_band = data_source.GetRasterBand(1)
+        data_np_array = raster_band.ReadAsArray()
+        data_np_array = np.array(data_np_array)
+        forward_transform = Affine.from_gdal(*data_source.GetGeoTransform())
+        reverse_transform = ~forward_transform
+        for station in stations:
+            longitude = station.long
+            latitude = station.lat
+            px, py = reverse_transform * (longitude, latitude)
+            px = math.floor(px)
+            py = math.floor(py)
+            yield (station.code, data_np_array[py][px])
+
+
+    async def _get_last_for_date(self):
+        """ Get the date of the most recently processed percent grass curing data."""
+        async with get_async_read_session_scope() as session:
+            result =  await get_last_percent_grass_curing_for_date(session)
+            return result
+
+
+    async def _process_grass_curing(self):
+        """ Download and process percent grass curing data. """
+        async with get_async_write_session_scope() as session:
+            today = date.today()
+            logger.info(f"Starting collection of percent grass curing data from CWFIS for {today}.")
+            with tempfile.TemporaryDirectory() as temp_dir:
+                await self._get_grass_curing_wcs_raster(temp_dir)
+                self._reproject_to_epsg_4326(temp_dir)
+
+                # Open the reprojected grass curing data
+                raster = gdal.Open(f"{temp_dir}/{GRASS_CURING_FILE_NAME_4326}")
+                stations = await get_stations_asynchronously()
+                for station, value in self._yield_value_for_stations(raster, stations):
+                    percent_grass_curing = PercentGrassCuring(for_date=today,
+                                                                percent_grass_curing=value,
+                                                                station_code=station )
+                    await save_percent_grass_curing(session, percent_grass_curing)
+        logger.info(f"Finished processing percent grass curing data from CFWIS for {today}.")
+
+
+    async def _run_grass_curing(self):
+        """ Entry point for running the job. """   
+        last_processed = await self._get_last_for_date()
+        if last_processed is None or last_processed.date() < date.today():
+            await self._process_grass_curing()
+        else:
+            logger.info(f"Percent grass curing processing is up to date as of {date.today()}")
+
+
+def main():
+    """ Kicks off asynchronous processing of VIIRS snow coverage data.
+    """
+    try:
+        # We don't want gdal to silently swallow errors.
+        gdal.UseExceptions()
+        logger.debug('Begin processing VIIRS snow coverage data.')
+
+        bot = GrassCuringJob()
+        loop = asyncio.new_event_loop()
+        asyncio.set_event_loop(loop)
+        loop.run_until_complete(bot._run_grass_curing())
+
+        # Exit with 0 - success.
+        sys.exit(os.EX_OK)
+    except Exception as exception:
+        # Exit non 0 - failure.
+        logger.error("An error occurred while processing CWFIS grass curing data.", exc_info=exception)
+        rc_message = ':scream: Encountered an error while processing CWFIS grass curing data.'
+        send_rocketchat_notification(rc_message, exception)
+        sys.exit(os.EX_SOFTWARE)
+
+if __name__ == '__main__':
+    configure_logging()
+    main()

api/app/tests/jobs/test_grass_curing.py

@@ -0,0 +1,43 @@
+""" Unit testing for CWFIS grass curing data processing """
+
+import os
+import pytest
+from datetime import datetime
+from pytest_mock import MockerFixture
+from app.jobs import grass_curing
+from app.jobs.grass_curing import GrassCuringJob
+
+
+def test_grass_curing_job_fail(mocker: MockerFixture,
+                                 monkeypatch):
+    """
+    Test that when the bot fails, a message is sent to rocket-chat, and our exit code is 1.
+    """
+
+    async def mock__run_grass_curing(self):
+        raise OSError("Error")
+
+    monkeypatch.setattr(GrassCuringJob, '_run_grass_curing', mock__run_grass_curing)
+    rocket_chat_spy = mocker.spy(grass_curing, 'send_rocketchat_notification')
+
+    with pytest.raises(SystemExit) as excinfo:
+        grass_curing.main()
+    # Assert that we exited with an error code.
+    assert excinfo.value.code == os.EX_SOFTWARE
+    # Assert that rocket chat was called.
+    assert rocket_chat_spy.call_count == 1
+
+
+def test_grass_curing_job_exits_without_error_when_no_work_required(monkeypatch):
+    """ Test that grass_curing_job exits without error when no data needs to be processed.
+    """
+    async def mock__get_last_for_date(self):
+        return datetime.now()
+
+    monkeypatch.setattr(GrassCuringJob, '_get_last_for_date', mock__get_last_for_date)
+
+    with pytest.raises(SystemExit) as excinfo:
+        grass_curing.main()
+    # Assert that we exited with an error code.
+    assert excinfo.value.code == os.EX_OK
+

openshift/scripts/oc_deploy_to_production.sh

@@ -55,6 +55,8 @@ echo C-Haines
 PROJ_TARGET=${PROJ_TARGET} bash $(dirname ${0})/oc_provision_c_haines_cronjob.sh prod ${RUN_TYPE}
 echo VIIRS Snow
 PROJ_TARGET=${PROJ_TARGET} bash $(dirname ${0})/oc_provision_viirs_snow_cronjob.sh prod ${RUN_TYPE}
+echo Grass Curing
+PROJ_TARGET=${PROJ_TARGET} bash $(dirname ${0})/oc_provision_grass_curing_cronjob.sh prod ${RUN_TYPE}
 echo BC FireWeather cronjobs
 echo "Run forecast at 8h30 PDT and 16h30 PDT (so before and after noon)"
 PROJ_TARGET=${PROJ_TARGET} SCHEDULE="30 * * * *" bash $(dirname ${0})/oc_provision_wfwx_noon_forecasts_cronjob.sh prod ${RUN_TYPE}

openshift/scripts/oc_provision_grass_curing_cronjob.sh

@@ -0,0 +1,58 @@
+#!/bin/sh -l
+#
+source "$(dirname ${0})/common/common"
+
+#%
+#% OpenShift Deploy Helper
+#%
+#%   Intended for use with a pull request-based pipeline.
+#%   Suffixes incl.: pr-###.
+#%
+#% Usage:
+#%
+#%    ${THIS_FILE} [SUFFIX] [apply]
+#%
+#% Examples:
+#%
+#%   Provide a PR number. Defaults to a dry-run.
+#%   ${THIS_FILE} pr-0
+#%
+#%   Apply when satisfied.
+#%   ${THIS_FILE} pr-0 apply
+#%
+
+# Target project override for Dev or Prod deployments
+#
+PROJ_TARGET="${PROJ_TARGET:-${PROJ_DEV}}"
+
+# Specify a default schedule to run daily at 5am-ish
+SCHEDULE="${SCHEDULE:-$((3 + $RANDOM % 54)) 5 * * *}"
+
+# Process template
+OC_PROCESS="oc -n ${PROJ_TARGET} process -f ${TEMPLATE_PATH}/grass_curing.cronjob.yaml \
+-p JOB_NAME=grass-curing-${APP_NAME}-${SUFFIX} \
+-p APP_LABEL=${APP_NAME}-${SUFFIX} \
+-p NAME=${APP_NAME} \
+-p SUFFIX=${SUFFIX} \
+-p SCHEDULE=\"${SCHEDULE}\" \
+-p POSTGRES_DATABASE=${POSTGRES_DATABASE:-${APP_NAME}} \
+-p POSTGRES_USER=wps-crunchydb-${SUFFIX} \
+-p POSTGRES_WRITE_HOST=wps-crunchydb-${SUFFIX}-primary \
+-p POSTGRES_READ_HOST=wps-crunchydb-${SUFFIX}-primary \
+-p CRUNCHYDB_USER=wps-crunchydb-${SUFFIX}-pguser-wps-crunchydb-${SUFFIX} \
+${PROJ_TOOLS:+ "-p PROJ_TOOLS=${PROJ_TOOLS}"} \
+${IMAGE_REGISTRY:+ "-p IMAGE_REGISTRY=${IMAGE_REGISTRY}"}"
+
+# Apply template (apply or use --dry-run)
+#
+OC_APPLY="oc -n ${PROJ_TARGET} apply -f -"
+[ "${APPLY}" ] || OC_APPLY="${OC_APPLY} --dry-run"
+
+# Execute commands
+#
+eval "${OC_PROCESS}"
+eval "${OC_PROCESS} | ${OC_APPLY}"
+
+# Provide oc command instruction
+#
+display_helper "${OC_PROCESS} | ${OC_APPLY}"