Merge pull request #29 from quantifyearth/mwd-small-updates

Misc small updates

Author: mdales

prepare_species/common.py

@@ -24,7 +24,10 @@
     "full_habitat_code",
     "scientific_name",
     "family_name",
+    "order_name",
     "class_name",
+    "phylum_name",
+    "kingdom_name",
     "threats",
     "category",
     "category_weight",
@@ -225,7 +228,7 @@ def tidy_reproject_save(
         elevation_seperation=ELEVATION_SPREAD,
     )
     os.makedirs(output_directory_path, exist_ok=True)
-    output_path = output_directory_path / f"{grow.id_no}.geojson"
+    output_path = output_directory_path / f"range_T{grow.id_no}A{grow.assessment_id}_{grow.season}.geojson"
     res = gpd.GeoDataFrame(grow.to_frame().transpose(), crs=src_crs, geometry="geometry")
 
     # Ensure proper dtypes for JSON serialization

prepare_species/extract_species_data_psql.py

@@ -46,6 +46,9 @@
     (assessment_supplementary_infos.supplementary_fields->>'ElevationUpper.limit')::numeric AS elevation_upper,
     taxons.scientific_name,
     taxons.family_name,
+    taxons.order_name,
+    taxons.phylum_name,
+    taxons.kingdom_name,
     red_list_category_lookup.code
 FROM
     assessments
@@ -133,7 +136,8 @@ def process_row(
     cursor = connection.cursor()
 
     id_no, assessment_id, assessment_year, possibly_extinct, possibly_extinct_in_the_wild, \
-        elevation_lower, elevation_upper, scientific_name, family_name, category = row
+        elevation_lower, elevation_upper, scientific_name, family_name, \
+        order_name, phylum_name, kingom_name, category = row
 
     report = SpeciesReport(id_no, assessment_id, scientific_name)
     report.has_api_data = True
@@ -212,7 +216,10 @@ def process_row(
             '|'.join(habitats_list),
             scientific_name,
             family_name,
+            order_name,
             class_name,
+            phylum_name,
+            kingom_name,
             json_ready_threats,
             category,
             category_weight,

prepare_species/extract_species_data_redlist.py

@@ -182,6 +182,9 @@ def process_species(
         assessment_year = assessment_dict['assessment_date'].year
         category = assessment_dict['red_list_category']
         family_name = assessment_dict['family_name']
+        order_name = assessment_dict['order_name']
+        phylum_name = assessment_dict['phylum_name']
+        kingdom_name = assessment_dict['kingdom_name']
         possibly_extinct = assessment_dict['possibly_extinct']
         possibly_extinct_in_the_wild = assessment_dict['possibly_extinct_in_the_wild']
         infrarank = assessment_dict['infrarank']
@@ -261,7 +264,10 @@ def process_species(
             '|'.join(habitats_list),
             scientific_name,
             family_name,
+            order_name,
             class_name,
+            phylum_name,
+            kingdom_name,
             json_ready_threats,
             category,
             CATEGORY_WEIGHTS[category],

requirements.txt

@@ -9,7 +9,7 @@ scikit-image
 redlistapi
 boto3
 yirgacheffe>=1.12,<2.0
-aoh[validation]>=2.0.3,<3.0
+aoh[validation]>=2.1.0,<3.0
 
 # Snakemake workflow management
 snakemake>=8.0

threats/threat_processing.py

@@ -25,6 +25,7 @@ def threat_processing_per_species(
         os.makedirs(output_directory_path, exist_ok=True)
 
         taxon_id = data.id_no[0]
+        assessment_id = data.assessment_id[0]
 
         # Due to validation we generate AOHs for many more species than
         # is needed for STAR, but we need to ensure those don't slip into
@@ -54,7 +55,7 @@ def threat_processing_per_species(
 
             threat_dir_path = output_directory_path / str(threat_id)
             os.makedirs(threat_dir_path, exist_ok=True)
-            output_path = threat_dir_path / f"{taxon_id}.tif"
+            output_path = threat_dir_path / f"threat_T{taxon_id}A{assessment_id}.tif"
             per_threat_per_species_score.to_geotiff(output_path)
 
     # This script generates a bunch of rasters, but snakemake needs one

workflow/rules/aoh.smk

@@ -53,7 +53,7 @@ def aoh_species_inputs(wildcards):
         / "species-info"
         / wildcards.taxa
         / SCENARIO
-        / f"{wildcards.species_id}.geojson",
+        / f"range_{wildcards.species_id}.geojson",
         # Base layers (precious - won't trigger rebuilds)
         "habitat_sentinel": ancient(
             DATADIR / "habitat_layers" / SCENARIO / ".habitat_complete"
@@ -88,11 +88,11 @@ rule generate_aoh:
         unpack(aoh_species_inputs),
     output:
         # Only declare JSON as output - TIF is optional (not created for empty AOHs)
-        metadata=DATADIR / "aohs" / SCENARIO / "{taxa}" / "{species_id}_all.json",
+        metadata=DATADIR / "aohs" / SCENARIO / "{taxa}" / "aoh_{species_id}.json",
     params:
         habitat_dir=DATADIR / "habitat_layers" / SCENARIO,
     log:
-        DATADIR / "logs" / "aoh" / "{taxa}" / "{species_id}_all.log",
+        DATADIR / "logs" / "aoh" / "{taxa}" / "{species_id}.log",
     resources:
         # Limit concurrent AOH jobs if needed (e.g., for memory)
         aoh_slots=1,
@@ -126,7 +126,7 @@ def get_species_ids_for_taxa(wildcards):
         taxa=wildcards.taxa
     ).output[0]
     geojson_dir = Path(checkpoint_output).parent
-    return [p.stem for p in geojson_dir.glob("*.geojson")]
+    return [p.stem[6:] for p in geojson_dir.glob("range_*.geojson")]
 
 
 def get_all_aoh_metadata_for_taxa(wildcards):
@@ -135,7 +135,7 @@ def get_all_aoh_metadata_for_taxa(wildcards):
     """
     species_ids = get_species_ids_for_taxa(wildcards)
     return [
-        DATADIR / "aohs" / SCENARIO / wildcards.taxa / f"{sid}_all.json"
+        DATADIR / "aohs" / SCENARIO / wildcards.taxa / f"aoh_{sid}.json"
         for sid in species_ids
     ]
 

workflow/rules/threats.smk

@@ -39,9 +39,9 @@ def get_star_species_for_taxa(wildcards):
 
     star_species = []
     for geojson_path in geojson_dir.glob("*.geojson"):
-        species_id = geojson_path.stem
+        species_id = geojson_path.stem[6:]
         aoh_path = (
-            DATADIR / "aohs" / SCENARIO / wildcards.taxa / f"{species_id}_all.tif"
+            DATADIR / "aohs" / SCENARIO / wildcards.taxa / f"aoh_{species_id}.tif"
         )
 
         # Check if species should be in STAR and has an AOH
@@ -88,8 +88,8 @@ rule generate_threat_rasters:
         / "species-info"
         / "{taxa}"
         / SCENARIO
-        / "{species_id}.geojson",
-        aoh=DATADIR / "aohs" / SCENARIO / "{taxa}" / "{species_id}_all.tif",
+        / "range_{species_id}.geojson",
+        aoh=DATADIR / "aohs" / SCENARIO / "{taxa}" / "aoh_{species_id}.tif",
     output:
         # Sentinel file since actual outputs depend on species' threats
         sentinel=DATADIR / "threat_rasters" / "{taxa}" / ".{species_id}_complete",

workflow/rules/validation.smk

@@ -96,7 +96,8 @@ rule validate_gbif_occurrences:
         gbif_data=lambda wildcards: DATADIR
         / "validation"
         / "occurrences"
-        / wildcards.taxa,
+        / wildcards.taxa
+        / "points.csv",
         species_data=lambda wildcards: DATADIR
         / "species-info"
         / wildcards.taxa
@@ -106,7 +107,7 @@ rule validate_gbif_occurrences:
         DATADIR / "logs" / "validate_gbif_{taxa}.log",
     shell:
         """
-        aoh-validate-occurrences \
+        aoh-validate-occurences \
             --gbif_data_path {params.gbif_data} \
             --species_data {params.species_data} \
             --aoh_results {params.aoh_results} \