Slurp pipeline

-

src/ontology/mondo-ingest.Makefile

@@ -281,16 +281,17 @@ lexical_matches: mappings/mondo-sources-all-lexical.sssom.tsv
 slurp/:
 	mkdir -p $@
 
-# Feel free to change the signature. Min ID is the next available Mondo ID.
-slurp/%.tsv: components/%.owl tmp/mondo.sssom.tsv reports/mirror-signature-mondo.tsv | slurp/
+# min-id: the next available Mondo ID
+slurp/%.tsv: components/%.owl tmp/mondo.sssom.tsv reports/mirror_signature-mondo.tsv | slurp/
 	python $(SCRIPTSDIR)/migrate.py \
-	-i $< \
-	--mapping-file tmp/mondo.sssom.tsv \
+	--ontology-path components/%.owl \
+	--sssom-map-path tmp/mondo.sssom.tsv \
 	--min-id 123000 \
-	--mondo-terms reports/mirror-signature-mondo.tsv \
-	--output $@
+	--mondo-terms-path reports/mirror_signature-mondo.tsv \
+	--outpath $@
 
 slurp-%: slurp/%.tsv
 
-# TODO: add more ontologies, e.g.: doid, icd10cm, icd10who, ncit, ordo
-slurp: slurp-omim
+# TODO: change to all ontologies when ready
+# slurp-all: slurp-omim slurp-doid slurp-ncit slurp-ordo slurp-icd10cm slurp-icd10who
+slurp-all: slurp-omim

src/scripts/migrate.py

@@ -1,54 +1,72 @@
-"""Migration pipeline
+"""Slurp migration pipeline
 
-#### THIS IS PSEUDO CODE NOT PYTHON OR ANYTHING
-#### THIS IS PSEUDO CODE NOT PYTHON OR ANYTHING
-#### THIS IS PSEUDO CODE NOT PYTHON OR ANYTHING
-#### THIS IS PSEUDO CODE NOT PYTHON OR ANYTHING
-
-TODOs:
+TODO's:
   - add CLI: look to makefile for what to include
 """
-import oakliblib
-import pandas
-
+import os
+from argparse import ArgumentParser
+from typing import Dict
 
-#Inputs:
-source_ontology = ''  #e.g. omim
-sssom_map = ''  # e.g. mondo.sssom.tsv
-min_id = ''
-termlist_mondo = ''
+import oaklib
+import pandas as pd
 
 
-def run(source_ontology = '', sssom_map = '', min_id = '', termlist_mondo = ''):
-    """source_ontology = ''  #e.g. omim
-    sssom_map = ''  # e.g. mondo.sssom.tsv
-    min_id = ''
-    termlist_mondo = ''"""
-    #Outputs:
+def run(ontology_path: str, sssom_map_path: str, min_id: int, mondo_terms_path: str, outpath: str):
+    # TODO: read files
+    source_ontology = ontology_path
+    print(os.path.exists(os.path.join(os.getcwd(), sssom_map_path)))
+    print(os.path.exists(os.path.join(os.getcwd(), mondo_terms_path)))
+    print(os.path.exists(os.path.join(os.getcwd(), ontology_path)))
+    sssom_map = pd.read_csv(sssom_map_path, comment='#', sep='\t')
+    termlist_mondo = pd.read_csv(mondo_terms_path, comment='#', sep='\t')
     data = []
+    # for t in source_ontology:
+    #     if t not in sssom_map['object_id']:
+    #         parents = []
+    #         migrate = True
+    #         for p in oaklib.get_direct_parents(t):
+    #             if p not in sssom_map['object_id']:
+    #                 migrate = False
+    #                 break
+    #             elif sssom_map[sssom_map['object_id']==p]['predicate_id'] = 'skos:exactMatch' \
+    #                 or sssom_map[sssom_map['object_id']==p]['predicate_id'] = 'skos:narrowMatch':
+    #                 # In other words, if the parent is mapped, and the mapping is either exact or narrower
+    #                 parents.append(sssom_map[sssom_map['object_id']==p]['subject_id'])
+    #             else:
+    #                 # Its fine, just continue looking for other parents in this case
+    #         if migrate and parents:
+    #             next_mondo_id = determine_next_available_mondo_id(min_id, termlist_mondo) # satrting from min_id, then counting up and checking if it does not already exist.
+    #             label = oaklib.get_label(t)
+    #             definition = oaklib.get_definition(t)
+    #             data.append({'mondo_id':next_mondo_id, 'xref': t, 'label': label, 'definition': definition})
+    #
+    # pd.DataFrame(data).to_csv(fn, sep="\t")
+    pass
+
 
-    for t in source_ontology:
-        if t not in sssom_map['object_id']:
-            parents = []
-            migrate = True
-            for p in oaklib.get_direct_parents(t):
-                if p not in sssom_map['object_id']:
-                    migrate = False
-                    break
-                elif sssom_map[sssom_map['object_id']==p]['predicate_id'] = 'skos:exactMatch' \
-                    or sssom_map[sssom_map['object_id']==p]['predicate_id'] = 'skos:narrowMatch':
-                    # In other words, if the parent is mapped, and the mapping is either exact or narrower
-                    parents.append(sssom_map[sssom_map['object_id']==p]['subject_id'])
-                else:
-                    # Its fine, just continue looking for other parents in this case
-            if migrate and parents:
-                next_mondo_id = determine_next_available_mondo_id(min_id, termlist_mondo) # satrting from min_id, then counting up and checking if it does not already exist.
-                label = oaklib.get_label(t)
-                definition = oaklib.get_definition(t)
-                data.append({'mondo_id':next_mondo_id, 'xref': t, 'label': label, 'definition': definition})
-
-    pandas.DataFrame(data).to_csv(fn, sep="\t")
+def cli() :
+    """Command line interface."""
+    package_description = \
+        'Slurp pipeline: Integrate new terms from other ontologies into Mondo.'
+    parser = ArgumentParser(description=package_description)
+    parser.add_argument(
+        '-o', '--ontology-path', required=True,
+        help='xxxxxx')
+    parser.add_argument(
+        '-m', '--sssom-map-path', required=True,
+        help='xxxxxx')
+    parser.add_argument(
+        '-i', '--min-id', required=True,
+        help='xxxxxx')
+    parser.add_argument(
+        '-t', '--mondo-terms-path', required=True,
+        help='xxxxxx')
+    parser.add_argument(
+        '-O', '--outpath', required=True,
+        help='xxxxxx')
+    d: Dict = vars(parser.parse_args())
+    return run(**d)
 
 
 if __name__ == '__main__':
-    run()
+    cli()