initial commit as place to keep project creation bash scripts for now.

dev/rfp_source_bcdata.R

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+#' Load bcdata layers to a geopackage.
+#'
+#' This function loads bcdata layers to a `background_layers.gpkg` with the specified watershed groups. The update
+#' option can be set to update an existing geopackage if it exists.
+#'
+#' @param watershed_groups A character vector of watershed group codes. Double quoted list of single quoted values. Default is NULL.
+#' @param update A logical indicating whether to update the GeoPackage file. Default is FALSE.
+#'
+#' @return Invisible NULL. The function is called for its side effects.
+#' @importFrom reticulate use_condaenv
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' rfp_source_bcdata(watershed_groups = c("ADMS", "BULK"))
+#' }
+rfp_source_bcdata <- function(watershed_groups = NULL, update = FALSE) {
+  # Construct the path to the script within the installed package
+  scriptPath <- system.file("extdata", "rfp_source_bcdata.sh", package = "rfp")
+
+  # Check if the script exists to avoid errors
+  if(!file.exists(scriptPath)) {
+    stop("Script 'rfp_source_bcdata.sh' not found in the package.")
+  }
+
+  if(update){
+    update <-  "update"
+  }else{
+    update <- ""
+  }
+
+  # Convert watershed_groups to a single, comma-separated string
+  watershed_groups <- paste(shQuote(watershed_groups, type = "sh"), collapse = " ")
+
+  # Prepare the arguments for the script
+  args <- c(watershed_groups, update)
+
+  # Call the bash script with arguments
+  system2("bash", args = c(scriptPath, watershed_groups, update))
+
+  invisible(NULL)
+}
+
+
+

inst/extdata/rfp_qgis_create_bcfishpass.sh

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+#!/bin/bash
+set -euxo pipefail
+
+
+# check that the name of the new directory for the project is provided as argument
+if [ $# -eq 0 ]
+  then
+    echo "No arguments supplied - provide name of new project directory to be placed in ~Projects/gis/"
+    exit 1
+fi
+
+echo 'Generating QGIS project in Projects/gis/: '$1
+
+
+# ---------------
+# create directory for project and move the files in and copy in a qlr template (works relative to location dragged from when we reference gpkg) along with the directories for info ignored on phones
+
+mkdir ~/Projects/gis/$1
+mv background_layers.gpkg* ~/Projects/gis/$1/
+mv habitat_lateral.tif ~/Projects/gis/$1/
+cp ../../data/qgis/bcfishpass_mobile.qgs ~/Projects/gis/$1/$1.qgs
+cp ../../data/qgis/form_pscis.gpkg ~/Projects/gis/$1/
+cp ../../data/qgis/form_fiss_site.gpkg ~/Projects/gis/$1/
+mkdir -p ~/Projects/gis/$1/ignore_mobile/photos
+touch ~/Projects/gis/$1/ignore_mobile/photos/photos.txt
+cp -R ../../data/methods ~/Projects/gis/$1/ignore_mobile/methods
+cp -R ../../data/templates ~/Projects/gis/$1/ignore_mobile/templates

inst/extdata/rfp_source_aws.sh

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+#!/bin/bash
+set -euxo pipefail
+
+# ---------------
+# extract layers from aws to load to background_layers.gpkg within digital field projects
+
+# usage: specify watershed groups of interest as a comma separated, single quoted string
+# eg
+# test with ./rfp_sources_aws.sh "'PARS'" &>log.txt
+# ---------------
+
+
+# check that watershed group code is provided as argument
+if [ $# -eq 0 ]
+  then
+    echo "No arguments supplied - provide list of watershed_group_code values for watersheds of interest"
+    exit 1
+fi
+
+
+# Name of the file
+GPKG="background_layers.gpkg"
+
+# name the sources file
+SOURCES="rfp_source_aws.txt"
+
+# Check if the GPKG IS NOT there
+if [[ ! -f $GPKG ]]; then
+  # If the file exists, ask the user if they wish to remove it
+  echo "There should already be a file called $GPKG. Please provide."
+  exit 1
+else
+echo 'Updateing project area from watershed group boundaries: '$1
+    rm -f aoi.geojson
+    bcdata dump WHSE_BASEMAPPING.FWA_WATERSHED_GROUPS_POLY \
+        --query "WATERSHED_GROUP_CODE in ($1)" -l > aoi.geojson
+        ogr2ogr -f GPKG background_layers.gpkg \
+            -update \
+            -overwrite \
+            -t_srs EPSG:3005 \
+            -nln fwa_watershed_groups_poly \
+            aoi.geojson
+fi
+
+# get bounding box of project area in BC Albers and WGS84 (lon/lat)
+BOUNDS=$(fio info background_layers.gpkg --layer fwa_watershed_groups_poly --bounds)
+BOUNDS_LL=$(echo "[$BOUNDS]" | tr ' ', ',' | rio transform --src_crs EPSG:3005 --dst_crs EPSG:4326 | tr -d '[] ')
+
+
+# ---------------
+# lateral habitat
+# ---------------
+# should be able to pipe $(fio cat aoi.geojson --dst_crs EPSG:3005) to rio mask for a one liner,
+# but this works fine
+echo 'Clipping lateral habitat tiff to project area'
+ogr2ogr -f GeoJSON aoi_alb.geojson -t_srs EPSG:3005 aoi.geojson
+
+rio mask /vsicurl/https://bcfishpass.s3.us-west-2.amazonaws.com/habitat_lateral.tif \
+  habitat_lateral.tif \
+  --crop \
+  --geojson-mask aoi_alb.geojson
+
+rm aoi_alb.geojson
+
+# ---------------
+# bcfishpass releated data sources archived to flatgeobuf on s3 for fast retrieval
+# (and with watershed group code included, no spatial query for clipping required)
+# ---------------
+echo 'Getting bcfishpass and supporting layers from s3'
+
+# get a list of the aws layers to update
+FGB_SOURCES=$(grep -v '^#' $SOURCES)
+
+for layer in $FGB_SOURCES; do
+  ogr2ogr \
+    -f GPKG background_layers.gpkg \
+    -update \
+    -overwrite \
+    -nln $layer \
+    -t_srs EPSG:3005 \
+    -dim XY \
+    -spat $BOUNDS \
+    -spat_srs EPSG:3005 \
+    -where "watershed_group_code in ($1)" \
+    /vsicurl/https://newgraph.s3.us-west-2.amazonaws.com/$layer.fgb \
+    $layer
+done
+
+# ---------------
+# model parameters
+# ---------------
+echo 'Getting model parameter info from aws'
+
+# update the model info used to create the crossings and streams layers
+CSVS=("parameters_habitat_method" "parameters_habitat_thresholds")
+
+for layer in "${CSVS[@]}"; do
+  ogr2ogr \
+    -f GPKG background_layers.gpkg \
+    -update \
+    -overwrite \
+    -nln $layer \
+    /vsicurl/https://newgraph.s3.us-west-2.amazonaws.com/$layer.csv
+done
+
+# ---------------
+# named streams
+# ---------------
+echo 'Getting named streams from fwapg feature service'
+ogr2ogr -f GPKG background_layers.gpkg \
+    -update \
+    -overwrite \
+    -t_srs EPSG:3005 \
+    -nln fwa_named_streams \
+    -clipsrc aoi.geojson \
+    -clipsrclayer aoi \
+    "https://features.hillcrestgeo.ca/fwa/collections/whse_basemapping.fwa_named_streams/items.json?bbox=$BOUNDS_LL"
+    # "http://www.a11s.one:9000/collections/whse_basemapping.fwa_named_streams/items.json?bbox=$BOUNDS_LL"
+
+
+echo 'Creating a record of the layers that were loaded'
+# create a record of the layers that were loaded
+# Get the current date and time
+TIMESTAMP=$(date '+%Y-%m-%d %H:%M')
+
+# Header for the CSV file
+echo "timestamp,content,watershed_groups,source" > temp.csv
+
+# Use awk to process the text file line by line
+awk -v timestamp="$TIMESTAMP" -v watershed_groups="$1" -v source="$SOURCES" '!/^#/ && NF > 0 {print timestamp "," $0 "," watershed_groups "," source}' $SOURCES >> temp.csv
+
+# Append the temporary CSV file to the GeoPackage
+ogr2ogr -append -f "GPKG" $GPKG temp.csv -nln rfp_tracking
+
+# Remove the temporary CSV file
+rm temp.csv
+
+
+
+
+