added filter to only have MONDO terms in validate result

.gitignore

@@ -136,4 +136,4 @@ tests/input/example-relation-graph.tsv.gz
 **/__pycache__/**
 tmp/*
 !tmp/.keep
-!tmp/mondo_validate.tsv
+!tmp/mondo_validate*

Makefile

@@ -29,9 +29,12 @@ tmp/mondo.db:
 tmp/mondo_lexmatch.sssom.tsv: tmp/mondo.db
 	runoak -i sqlite:$< lexmatch -o $@ -R $(RULES_FILE)
 
-tmp/mondo_validate.tsv: tmp/mondo.db
+tmp/mondo_validate_full.tsv: tmp/mondo.db
 	runoak -i sqlite:$< validate -o $@
 
+tmp/mondo_validate.tsv: tmp/mondo_validate_full.tsv
+	mondoqc validate $< -o $@
+
 lexmatch: tmp/mondo_lexmatch.sssom.tsv
 validate: tmp/mondo_validate.tsv
 clear-tmp:

src/mondolib/cli.py

@@ -36,9 +36,10 @@ def main(verbose: int, quiet: bool):
 
 @main.command("validate")
 @click.argument("input")
-def click_validate(input: str):
+@click.option("-o", "--output", help="Output file path")
+def click_validate(input: str, output:str):
     """Run the mondolib's demo command."""
-    validate(input)
+    validate(input, output)
 
 
 if __name__ == "__main__":

src/mondolib/main.py

@@ -1,14 +1,17 @@
 """Main python file."""
+import pandas as pd
 
 
 def demo():
     """Define API."""
     print("Hello, World!")
 
 
-def validate(input: str):
+def validate(input: str, output: str):
     """Validate."""
-    print(input)
+    df = pd.read_csv(input, sep="\t", index_col=None)
+    mondo_df = df.loc[df["subject"].str.startswith("MONDO:")]
+    mondo_df.to_csv(output, sep="\t", index=False)
 
 
 def update():