Do not hardcode location of taxa.yaml file.

Make the scripts/taxa.py script accept a command-line argument
indicating the location of the taxa.yaml file, instead of hardcoding
that location at the beginning of the script. Update the invocations of
that script in the Makefile accordingly.

src/ontology/uberon.Makefile

@@ -1173,7 +1173,7 @@ $(TMPDIR)/composite-%.owl: $(TMPDIR)/collected-%.owl $(TMPDIR)/tax-merges.tsv |
 # Step 2a: The "tax-merges.tsv" file used in the rule above is automatically
 # derived from the list of species in config/taxa.yaml.
 $(TMPDIR)/tax-merges.tsv: $(SCRIPTSDIR)/taxa.py config/taxa.yaml
-	python3 $(SCRIPTSDIR)/taxa.py make-merge-table > $@
+	python3 $(SCRIPTSDIR)/taxa.py make-merge-table config/taxa.yaml > $@
 
 # Step 3: Annotate the result of step 2. This is a separate step only so
 # that we can have explicit rules for composite-metazoan, -vertebrate,
@@ -1329,8 +1329,8 @@ EXTERN_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
 # 1. Prepare the ruleset file.
 # The ruleset file is maintained with the help of the Python script
 # to automatically insert the taxon-specific rules.
-$(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/taxa.py $(BRIDGEDIR)/bridges.rules
-	python3 $(SCRIPTSDIR)/taxa.py make-rules $(BRIDGEDIR)/bridges.rules > $@
+$(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/taxa.py config/taxa.yaml $(BRIDGEDIR)/bridges.rules
+	python3 $(SCRIPTSDIR)/taxa.py make-rules config/taxa.yaml $(BRIDGEDIR)/bridges.rules > $@
 
 # 2. Generate the bridges from the "meta" mapping set and the CL set.
 # Note that merging CL here is not strictly necessary, but doing so

src/scripts/taxa.py

@@ -36,11 +36,7 @@
 import sys
 import yaml
 
-with open('config/taxa.yaml', 'r') as f:
-    taxa = yaml.load(f, yaml.CLoader)
-
-
-def generate_prefix_declarations(f):
+def generate_prefix_declarations(f, taxa):
     """Insert SSSOM/T-OWL prefix declarations for all species."""
     for taxon in taxa['species']:
         for bridge in taxon['bridging']:
@@ -50,13 +46,13 @@ def generate_prefix_declarations(f):
             f.write(f"prefix {prefix}: <{namespace}>\n")
 
 
-def generate_directives(f):
+def generate_directives(f, taxa):
     """Insert SSSOM/T-OWL taxon declarations for all species."""
     for taxon_id in [t['taxon_id'] for t in taxa['species']]:
         f.write(f"declare({taxon_id});\n")
 
 
-def generate_bridging_rules(f):
+def generate_bridging_rules(f, taxa):
     """Insert SSSOM/T-OWL bridging rules for all species."""
     for taxon in taxa['species']:
         taxon_id = taxon['taxon_id']
@@ -78,23 +74,23 @@ def generate_bridging_rules(f):
 """)
 
 
-def process_rule_file(filein, fileout):
+def process_rule_file(filein, fileout, taxa):
     """Insert all SSSOM/T-OWL instructions required to generate
         cross-species bridges.
     """
 
     for line in filein:
         if line.strip() == '%INSERT-TAX-SPECIFIC-PREFIXES':
-            generate_prefix_declarations(fileout)
+            generate_prefix_declarations(fileout, taxa)
         elif line.strip() == '%INSERT-TAX-SPECIFIC-DIRECTIVES':
-            generate_directives(fileout)
+            generate_directives(fileout, taxa)
         elif line.strip() == '%INSERT-TAX-SPECIFIC-BRIDGES':
-            generate_bridging_rules(fileout)
+            generate_bridging_rules(fileout, taxa)
         else:
             fileout.write(line)
 
 
-def generate_merge_table(fileout):
+def generate_merge_table(fileout, taxa):
     """Generates a batch-file for uberon:merge-species."""
     def_link_properties = taxa.get('defaults', {}).get('compositing', {}).get('unfold_over', ['BFO:0000050', 'BFO:0000066'])
     def_preserved_properties = taxa.get('defaults', {}).get('compositing', {}).get('preserve', [])
@@ -108,17 +104,26 @@ def generate_merge_table(fileout):
         fileout.write(f"{taxon_id}\t{label}\t{link_properties}\t{preserved_properties}\n")
 
 
-usage = f"Usage: {sys.argv[0]} <make-rules TEMPLATE> | <make-merge-table>"
+def read_taxa_file(file):
+    with open(file, 'r') as f:
+        return yaml.load(f, yaml.CLoader)
+
+
+usage = f"Usage: {sys.argv[0]} <make-rules TAXA TEMPLATE> | <make-merge-table TAXA>"
 if len(sys.argv) < 2:
     sys.exit(usage)
 
 cmd = sys.argv[1]
 if cmd == 'make-rules':
-    if len(sys.argv) != 3:
+    if len(sys.argv) != 4:
         sys.exit(usage)
-    with open(sys.argv[2], 'r') as fin:
-        process_rule_file(fin, sys.stdout)
+    taxa = read_taxa_file(sys.argv[2])
+    with open(sys.argv[3], 'r') as fin:
+        process_rule_file(fin, sys.stdout, taxa)
 elif cmd == 'make-merge-table':
-    generate_merge_table(sys.stdout)
+    if len(sys.argv) != 3:
+        sys.exit(usage)
+    taxa = read_taxa_file(sys.argv[2])
+    generate_merge_table(sys.stdout, taxa)
 else:
     sys.exit(usage)