From 9bd082cecc1de214abf3169883e6e899bab6fd5d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adrien=20Wehrl=C3=A9?=
 <44843368+AdrienWehrle@users.noreply.github.com>
Date: Sun, 26 Apr 2020 15:44:49 +0200
Subject: [PATCH] S3_wrapper.sh Near Real-Time (NRT) over a list of arctic
 regions (#37)

---
 S3_NRT.sh | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 S3_NRT.sh

diff --git a/S3_NRT.sh b/S3_NRT.sh
new file mode 100644
index 0000000..f2bd200
--- /dev/null
+++ b/S3_NRT.sh
@@ -0,0 +1,67 @@
+#!/usr/bin/env bash
+
+# Wrapper for running SICE pipeline Near Real-Time (NRT) 
+
+# example of cron job:
+# m h  dom mon dow   command
+# 00 12 * * * /bin/bash -c "/path/to/wrapper/S3_NRT.sh" > /path/to/log/log_NRT.txt
+
+# use SNAP gpt
+export PATH=/srv/home/8675309/local/snap/bin:${PATH}
+
+# activate SICE anaconda virtual environment
+. /srv/home/8675309/local/anaconda/envs/SICE/bin/activate
+
+set -o errexit
+set -o nounset
+set -o pipefail
+set -x
+
+red='\033[0;31m'; orange='\033[0;33m'; green='\033[0;32m'; nc='\033[0m' # No Color
+log_info() { echo -e "${green}[$(date --iso-8601=seconds)] [INFO] ${@}${nc}"; }
+log_warn() { echo -e "${orange}[$(date --iso-8601=seconds)] [WARN] ${@}${nc}"; }
+log_err() { echo -e "${red}[$(date --iso-8601=seconds)] [ERR] ${@}${nc}" 1>&2; }
+
+# change directory to the current folder
+cd "${0%/*}"
+
+### dev
+# SEN3_source=./SEN3
+# proc_root=./out
+# mosaic_root=./mosaic
+
+LD_LIBRARY_PATH=. # SNAP requirement
+
+date=$(date -d '-2days' "+%Y-%m-%d")
+year=$(date "+%Y")
+
+declare -a regions=("Greenland" "Iceland" "Svalbard" "NovayaZemlya" "SevernayaZemlya" "FransJosefLand" "NorthernArcticCanada" "SouthernArcticCanada" "JanMayen" "Norway" "Beaufort")
+
+for region in "${regions[@]}"; do
+
+  # CREODIAS
+  SEN3_local=/eodata/Sentinel-3
+  SEN3_source=/sice-data/SICE/${region}/S3
+  proc_root=/sice-data/SICE/${region}/proc
+  mosaic_root=/sice-data/SICE/${region}/mosaic
+
+  mkdir -p /sice-data/SICE/${region}
+
+  ### Fetch one day of OLCI & SLSTR scenes over Greenland
+  ## Use local files (PTEP, DIAS, etc.)
+  ./dhusget_wrapper.sh -d ${date} -l ${SEN3_local} -o ${SEN3_source}/${year}/${date} \
+                       -f ${region} -u <user> -p <password>
+
+  # SNAP: Reproject, calculate reflectance, extract bands, etc.
+  ./S3_proc.sh -i ${SEN3_source}/${year}/${date} -o ${proc_root}/${date} -X S3.xml -t
+
+  # Run the Simple Cloud Detection Algorithm (SCDA)
+  python ./SCDA.py ${proc_root}/${date}
+
+  # Mosaic
+  ./dm.sh ${date} ${proc_root}/${date} ${mosaic_root}
+
+  # SICE
+  python ./sice.py ${mosaic_root}/${date}
+
+done