Updated retrieval code.

rules/retrieve.smk

@@ -325,8 +325,8 @@ if config["enable"]["retrieve"] and any(c in ["UA", "MD"] for c in config["count
 
     rule retrieve_gdp_uamd:
         output:
-            "data/GDP_per_capita_PPP_1990_2015_v2.nc",
-            "data/ppp_2013_1km_Aggregated.tif",
+            gdp="data/GDP_per_capita_PPP_1990_2015_v2.nc",
+            ppp="data/ppp_2013_1km_Aggregated.tif",
         log:
             "logs/retrieve_gdp_uamd.log",
         resources:

scripts/determine_availability_matrix_MD_UA.py

@@ -49,6 +49,7 @@ def get_wdpa_layer_name(wdpa_fn, layer_substring):
         gpd.read_file(snakemake.input.regions).set_index("name").rename_axis("bus")
     )
     buses = regions.index
+    buses = regions.loc[regions["country"].isin(["UA", "MD"])].index.values
 
     excluder = atlite.ExclusionContainer(crs=3035, res=100)
 

scripts/retrieve_gdp_uamd.py

@@ -9,41 +9,26 @@
 import logging
 from pathlib import Path
 
-from _helpers import retrieve_file
+from _helpers import configure_logging, retrieve_file, set_scenario_config
 
 logger = logging.getLogger(__name__)
 
 
-def retrieve(url, destination):
-
-    logger.info(f"Downloading file from '{url}'.")
-    retrieve_file(url, destination)
-    logger.info("File downloaded and validated.")
-
-
 if __name__ == "__main__":
     if "snakemake" not in globals():
         from _helpers import mock_snakemake
 
         snakemake = mock_snakemake("retrieve_gdp_uamd")
-        rootpath = ".."
-    else:
-        rootpath = "."
-
-datasets = [
-    # GDP_PPP_30arcsec_v3.nc: raw dataset. Available at: [M. Kummu, M. Taka, J. H. A. Guillaume. (2020), Data from: Gridded global datasets for Gross Domestic Product and Human Development Index over 1990-2015, Dryad, Dataset. doi: https://doi.org/10.5061/dryad.dk1j0]
-    (
-        "https://datadryad.org/stash/downloads/file_stream/241947",
-        "GDP_per_capita_PPP_1990_2015_v2.nc",
-    ),
-    # ppp_2020_1km_Aggregated.tif: raw dataset. Available at: https://data.humdata.org/dataset/
-    (
-        "https://data.worldpop.org/GIS/Population/Global_2000_2020/2020/0_Mosaicked/ppp_2020_1km_Aggregated.tif",
-        "ppp_2020_1km_Aggregated.tif",
-    ),
-]
+    configure_logging(snakemake)
+    set_scenario_config(snakemake)
+
+dict_urls = dict(
+    {
+        "gdp": "https://datadryad.org/stash/downloads/file_stream/241947",
+        "ppp": "https://github.com/ecohealthalliance/sars_cov_risk/releases/download/v2.0.1/ppp_2020_1km_Aggregated.tif",
+    }
+)
 
 # Download and validate each dataset
-for url, filename in datasets:
-    file_path = rootpath / "data" / filename
-    retrieve(url, file_path)
+for key, path in snakemake.output.items():
+    retrieve_file(dict_urls[key], path)