01_load.R

# Copyright 2024 Province of British Columbia
# 
# 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.


# Script purpose  ---------------------------------------------------------

# This script uses the bcgroundwater R package (https://github.com/bcgov/bcgroundwater)
# to download groundwater level data from the B.C. Data Catalogue 
# (https://catalogue.data.gov.bc.ca/dataset/57c55f10-cf8e-40bb-aae0-2eff311f1685), 
# provided under the Open Government Licence - British Columbia.
# The data is generated through the B.C. Ministry of Environment's
# Provincial Groundwater Observation Well Network Monitoring Program
# (https://www2.gov.bc.ca/gov/content?id=B03D0994BB5C4F98B6F7D4FD8610C836).
#
# Groundwater well attribute data and Natural Resource (NR) Regions are also
# sourced from the B.C. Data Catalogue, both released udner the Open Government
# Licence - British Columbia.
# Groundwater Wells: 
# https://catalogue.data.gov.bc.ca/dataset/e4731a85-ffca-4112-8caf-cb0a96905778
# Natural Resource (NR) Regions: 
# https://catalogue.data.gov.bc.ca/dataset/dfc492c0-69c5-4c20-a6de-2c9bc999301f



# Load required packages and download well metadata --------------------

## Source package libraries and the bcdc_map() function
if (!exists(".header_sourced")) source("header.R")
source("func.R")

if(!dir.exists('data'))dir.create("data", showWarnings = FALSE)


library(bcdata)

# Retrieve data directly from BC Data Catalogue.
obs_wells_in = bcdc_get_data('e4731a85-ffca-4112-8caf-cb0a96905778') %>% 
  filter(!is.na(WELL_TAG_NUMBER),
         !is.na(WELL_STATUS)) %>% 
  collect() %>% 
  setNames(snakecase::to_snake_case(colnames(.)))


##Filter out observations with no observation well status or number (the vast majority!)
#Join the natural resource region names etc. to data

obs_wells = obs_wells_in %>% 
  # filter(!is.na(observation_well_status)) %>% 
  # filter(!is.na(observation_well_number)) %>% 
  st_join(bcmaps::nr_regions()) %>% 
  #Make column names 'R-friendly'
  setNames(snakecase::to_snake_case(colnames(.))) %>% 
  #Narrow down columns.
  dplyr::select(observation_well_number, ems_id, 
                well_tag_number, construction_end_date, #general_remarks, other_information,
                observation_well_status, aquifer_type = aquifer_material,
                aquifer_id, total_depth_drilled,
                finished_well_depth, static_water_level, region_name, feature_area_sqm) %>% 
  # Clean up natural resource region name and aquifer type text fields.
  mutate(region_name = str_remove_all(region_name, " Natural Resource Region"),
         region_name = str_replace(region_name, "-", " / "),
         aquifer_type = case_when(
           aquifer_type == "Unconsolidated" ~ "Sand and Gravel",
           is.na(aquifer_type) ~ "Unknown",
           T ~ aquifer_type
         )) %>% 
  #Make aquifer type into an ordered factor.
  mutate(aquifer_type = factor(aquifer_type, levels = c("Bedrock","Sand and Gravel","Unknown"))) %>% 
  #Remove any duplicated observation well numbers.
  filter(!duplicated(observation_well_number))



# Download all observation well data   --------------------------------------------

# Download all data for wells from https://www.env.gov.bc.ca/wsd/data_searches/obswell/map/data/
# If the url for a given well doesn't work, the code creates an empty data.frame to 
# make sure such a result can still be combined with the successful data reading attempts. In this way,
# the function does not break if one or more wells has no available data to download.

wells_data_raw = obs_wells$observation_well_number %>% 
  map( ~ {
    tryCatch(read_csv(paste0("https://www.env.gov.bc.ca/wsd/data_searches/obswell/map/data/OW",.x,"-data.csv")), 
             #If the url for this repetition doesn't exist / work, we create an empty data.frame to 
             # make sure such a result can still be combined with the successful data reading attempts.
             error = function(e) data.frame(Time = structure(numeric(0), 
                                                             tzone = "UTC", 
                                                             class = c("POSIXct","POSIXt")), 
                                            Value = numeric(0), 
                                            Approval = character(0), 
                                            myLocation = character(0)))
    
  }) %>% 
  bind_rows()



# Save raw data objects in tmp directory ----------------------------------

save(obs_wells, file = "./tmp/well_location_data.RData")
save(wells_data_raw, file = "./tmp/raw_well_data.RData")