sco query non trans; curie resolution

Makefile

@@ -1,6 +1,6 @@
 .PHONY: all clean tests dep_check
 
-all: clean dep_check tests target/sco.tsv
+all: clean dep_check tests target/envo_sco.tsv
 
 clean:
 	rm -rf downloads/*
@@ -17,5 +17,5 @@ downloads/envo.owl:
 	# --location (-L) pursues redirects
 	curl --location http://purl.obolibrary.org/obo/envo.owl -o $@
 
-target/sco.tsv: downloads/envo.owl
+target/envo_sco.tsv: downloads/envo.owl
 	robot query --input $< --query sparql/sco.sparql $@

hident/hident.py

@@ -1,4 +1,25 @@
+import logging
+import click
+import click_log
+
+logger = logging.getLogger(__name__)
+click_log.basic_config(logger)
+
+
+@click.command()
+@click_log.simple_verbosity_option(logger)
+@click.option('--termlist', type=click.Path(exists=True), required=True, help="headerless list of term ids")
+@click.option('--sco_table', type=click.Path(exists=True), required=True, help="subclass table from sparql/sco.sparql")
+def hident(termlist, sco_file):
+    logger.info(termlist)
+    logger.info(sco_file)
+
+
 def set_to_sorted_list(term_set: set[str]) -> list[str]:
     listified = list(term_set)
     listified.sort()
     return listified
+
+
+if __name__ == "__main__":
+    hident()

pyproject.toml

@@ -6,10 +6,16 @@ authors = ["Mark A. Miller <[email protected]>"]
 
 [tool.poetry.dependencies]
 python = "^3.9"
+click = "^8.0.3"
+click-log = "^0.3.2"
+prefixcommons = "^0.1.9"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.scripts]
+hident = 'hident.hident:hident'

sparql/sco.sparql

@@ -1,11 +1,13 @@
 prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix ENVO: <http://purl.obolibrary.org/obo/ENVO_>
 select
 ?sub ?super
 where
 {
-    ?sub rdfs:subClassOf+ ?super
+    ?sub rdfs:subClassOf ?super
     filter(isuri(?super))
     filter(isuri(?sub))
 }
 #limit 3
+# also try a sco+ query?
 

tests/data/termlist.txt

@@ -0,0 +1,5 @@
+ENVO:00001998
+ENVO:00002232
+ENVO:00002263
+ENVO:00005779
+ENVO:01001841