From d4df628a6d14b689d76448d160b37c9dae895649 Mon Sep 17 00:00:00 2001
From: elpamart <elena.palao@vizzuality.com>
Date: Thu, 21 Sep 2023 16:41:39 +0200
Subject: [PATCH] add pipe for ingesting the biodiversity indicator data

---
 data/h3_data_importer/Makefile           | 12 ++++++++++++
 data/preprocessing/README.md             | 11 +++++++++++
 data/preprocessing/biodiversity/Makefile |  1 +
 3 files changed, 24 insertions(+)

diff --git a/data/h3_data_importer/Makefile b/data/h3_data_importer/Makefile
index 16aeb16f2..e5164ba7e 100644
--- a/data/h3_data_importer/Makefile
+++ b/data/h3_data_importer/Makefile
@@ -21,6 +21,7 @@ WORKDIR_DEFORESTATION=data/hansen_loss
 WORKDIR_GHG=data/forest_ghg
 WORKDIR_WOODPULP=data/woodpulp
 WORKING_NATURAL_CROP_CONVERSION=data/natural_crop_conversion
+WORKDIR_BIODIVERSITY=data/biodiversity
 
 CHECKSUMS_PATH=data_checksums
 
@@ -52,6 +53,7 @@ indicators:
 	make convert-forestGHG
 	make convert-satDeforestation
 	make convert-naturalCropConversion
+	make convert-biodiversity
 contextual-layers: convert-hdi-contextual convert-blue-water-contextual
 
 
@@ -234,6 +236,16 @@ convert-naturalCropConversion: download-naturalCropConversion
 	python raster_folder_to_h3_table.py $(WORKING_NATURAL_CROP_CONVERSION) h3_grid_natural_crop_conversion_global indicator NECR 2022 --h3-res=6 --thread-count=$(PARALLELIZATION_FACTOR)
 
 
+download-biodiversity:
+	# download and check
+	mkdir -p $(WORKDIR_BIODIVERSITY)
+	aws s3 sync $(AWS_S3_BUCKET_URL)/processed/biodiversity $(WORKDIR_BIODIVERSITY)
+	cd $(WORKDIR_BIODIVERSITY) && sha256sum --check ../../$(CHECKSUMS_PATH)/biodiversity
+
+convert-biodiversity: download-biodiversity
+	@echo "Converting biodiversity data... "
+	python raster_folder_to_h3_table.py $(WORKDIR_BIODIVERSITY) h3_grid_biodiversity_global indicator BL_LUC_S 2022 --h3-res=6 --thread-count=$(PARALLELIZATION_FACTOR)
+
 
 ##################################
 #        Satelligence data       #
diff --git a/data/preprocessing/README.md b/data/preprocessing/README.md
index aec6bf489..12318ba8e 100644
--- a/data/preprocessing/README.md
+++ b/data/preprocessing/README.md
@@ -59,3 +59,14 @@ make all
 
 Read more about this pipeline in the [natural_crop_conversion/README.md](natural_crop_conversion/README.md) file.
 
+### Biodiversity
+
+It contains the computation of the biodiversity - forest landscape integrity loss dataset .
+
+To run the pipeline, `cd biodiversity` and
+
+```bash
+make all
+```
+
+Read more about this pipeline in the [biodiversity/README.md](biodiversity/README.md) file.
diff --git a/data/preprocessing/biodiversity/Makefile b/data/preprocessing/biodiversity/Makefile
index 11a26c7fd..ca5f6d561 100644
--- a/data/preprocessing/biodiversity/Makefile
+++ b/data/preprocessing/biodiversity/Makefile
@@ -15,6 +15,7 @@ download_forest_landscape_integrity_loss:
 		"gs://landgriffon-gee-bucket/landscape_indicators_20230821/natural_crop_flii_loss_by_human_lu_50km_1000m.tif" \
 		$(data_dir)
 
+# TODO- Review resampling method. We can use max resampling method to be conservative as the most intact areas are the most important to avoid.
 resample_forest_landscape_integrity_loss:
 	rio warp \
 		$(data_dir)/natural_crop_flii_loss_by_human_lu_50km_1000m.tif \