From faab5cb3627732a360ed5061dacba73b975fd6a0 Mon Sep 17 00:00:00 2001
From: Kasra Farmer <kasra.keshavarz@usask.ca>
Date: Tue, 15 Nov 2022 18:14:04 -0600
Subject: [PATCH] Iss12 (#13)

* updating exactextractr dependency version as well as updating Graham's local cache files

* correcting subsetting address file for the output tif

* correcting variables in GSDE's example
---
 assets/renv.lock   |  8 ++++----
 example/gsde.sh    | 44 ++++++++++++++++++++++++++++++++++++++++++++
 landsat/landsat.sh |  2 +-
 3 files changed, 49 insertions(+), 5 deletions(-)
 create mode 100755 example/gsde.sh

diff --git a/assets/renv.lock b/assets/renv.lock
index 31b071c..b68df67 100644
--- a/assets/renv.lock
+++ b/assets/renv.lock
@@ -110,15 +110,15 @@
     },
     "exactextractr": {
       "Package": "exactextractr",
-      "Version": "0.9.0",
+      "Version": "0.9.1",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "isciences",
       "RemoteRepo": "exactextractr",
-      "RemoteRef": "6d02446438991c3d6a8017474200aaf23fc7a695",
-      "RemoteSha": "6d02446438991c3d6a8017474200aaf23fc7a695",
-      "Hash": "c22e1f368bc1d3083f3ad82ee8134344",
+      "RemoteRef": "f875cea876f0f9746f741e5559fce0e044fae8b8",
+      "RemoteSha": "f875cea876f0f9746f741e5559fce0e044fae8b8",
+      "Hash": "dc114ab271000cfc3e72331d5212f2c2",
       "Requirements": [
         "Rcpp",
         "raster",
diff --git a/example/gsde.sh b/example/gsde.sh
new file mode 100755
index 0000000..e92cfb5
--- /dev/null
+++ b/example/gsde.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+# Geospatial Dataset Processing Workflow
+# Copyright (C) 2022, University of Saskatchewan
+#
+# This file is part of the Geospatial Dataset Processing Workflow
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# This is a simple example to extract common statistics for the 
+# pfaf 71 - Saskatchewan-Nelson System Shapefiles of MERIT-Basins -
+# from the GSDE rasters.
+
+# Always call the script in the root directory of this repository
+cd ..
+echo "The current directory is: $(pwd)"
+
+# first download a sample shapefile - could be any shapefile
+wget -m -nd -nv -q -A "cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.*" \
+     "http://hydrology.princeton.edu/data/mpan/MERIT_Basins/MERIT_Hydro_v07_Basins_v01_bugfix1/pfaf_level_02/"; 
+
+# implement subsetting and zonal statistics
+./extract-gis.sh --dataset="GSDE" \
+  --dataset-dir="/project/rpp-kshook/Model_Output/GSDE/download/gsde-30sec/" \
+  --variable="BD" \
+  --shape-file="$(pwd)/cat_pfaf_71_MERIT_Hydro_v07_Basins_v01_bugfix1.shp" \
+  --print-geotiff=true \
+  --output-dir="$HOME/scratch/depth-to-bedrock-test/" \
+  --prefix="dtb_" \
+  --stat="mean,min,max" \
+  --email="you@company.ca" \ 
+  -j;
+
diff --git a/landsat/landsat.sh b/landsat/landsat.sh
index 8856608..82beb9e 100755
--- a/landsat/landsat.sh
+++ b/landsat/landsat.sh
@@ -243,7 +243,7 @@ if [[ "$printGeotiff" == "true" ]]; then
   echo "$(logDate)$(basename $0): subsetting GeoTIFFs under $outputDir"
   for var in "${variables[@]}"; do
     # subset based on lat and lon values
-    subset_geotiff "${geotiffDir}/${var}.tif" "${outputDir}/${prefix}${var}.tif"
+    subset_geotiff "${cache}/${var}/${var}.tif" "${outputDir}/${prefix}${var}.tif"
   done
 fi