Unit testing

- Add: test/ dir, and initialized with the necessary files to test slurp / migrate

.gitignore

@@ -78,3 +78,6 @@ src/scripts/.ipynb_checkpoints/*
 src/ontology/.template.db
 src/mappings/mondo-sources-all-lexical.sssom.tsv
 src/scripts/mondo_unmapped.tsv
+
+# Test
+test/output/

src/ontology/mondo-ingest.Makefile

@@ -496,6 +496,13 @@ update-jinja-sparql-queries:
 	python3 $(SCRIPTSDIR)/ordo_mapping_annotations/create_sparql__ordo_replace_annotation_based_mappings.py
 	python3 $(SCRIPTSDIR)/ordo_mapping_annotations/create_sparql__ordo_mapping_annotations_violation.py
 
+#################
+##### Tests #####
+#################
+.PHONY: tests
+tests:
+	cd ../../; python -m unittest discover
+
 #############################
 ########### Help ############
 #############################
@@ -506,6 +513,9 @@ help:
 	@echo "----------------------------------------"
 	@echo "	Command reference: mondo-ingest"
 	@echo "----------------------------------------"
+	# Tests
+	@echo "tests"
+	@echo "Run all project related (as oppposed to ODK) automated tests. To run ODK tests, use the 'test' goal.\n"
 	# Slurp / migrate
 	@echo "slurp/%.tsv and slurp-%"
 	@echo "For a given ontology, determine all slurpable / migratable terms. That is, terms that are candidates for integration into Mondo.\n"

src/scripts/migrate.py

@@ -10,8 +10,10 @@
 - https://incatools.github.io/ontology-access-kit/intro/tutorial02.html
 """
 import os
+import sys
 from argparse import ArgumentParser
 from glob import glob
+from pathlib import Path
 from typing import Dict, List, Set
 
 import pandas as pd
@@ -20,8 +22,11 @@
 from oaklib.implementations import ProntoImplementation
 from oaklib.types import CURIE, URI
 
-from utils import CACHE_DIR, DOCS_DIR, PREFIX, PROJECT_DIR, Term, _get_all_owned_terms, _get_next_available_mondo_id, \
-    get_mondo_term_ids, _load_ontology, SLURP_DIR
+SCRIPTS_DIR = Path(os.path.abspath(os.path.dirname(__file__)))
+PROJECT_ROOT = SCRIPTS_DIR.parent.parent
+sys.path.insert(0, str(PROJECT_ROOT))
+from src.scripts.utils import CACHE_DIR, DOCS_DIR, PREFIX, PROJECT_DIR, Term, _get_all_owned_terms, \
+    _get_next_available_mondo_id, get_mondo_term_ids, _load_ontology, SLURP_DIR
 
 
 FILENAME_GLOB_PATTERN = '*.tsv'
@@ -50,13 +55,47 @@
     'mondo_id': 'ID', 'mondo_label': 'LABEL', 'xref': 'A oboInOwl:hasDbXref',
     'xref_source': '>A oboInOwl:source SPLIT=|', 'original_label': '', 'definition': 'A IAO:0000115', 'parents': 'SC %'}
 
-def _valid_parent_conditions(
+# TODO: temp term param
+def _valid_parent_conditions(t: Term,
     parents: List[CURIE], mapped: Set[CURIE], excluded: Set[CURIE], obsolete: Set[CURIE]
 ) -> bool:
     """This is an optional, stricter check on slurp candidacy / order.
 
     For a term to be immediately migratable, it must either (a) have no parents, or (b) all of its parents must be
     mapped, obsolete, or excluded"""
+    # TODO: save curie and why it was a candidate
+    # - save which cases did not occur at the end
+    # if all([x in mapped for x in parents]):
+    #     print(t.curie)
+    # elif all([x in excluded for x in parents]):
+    #     print(t.curie)
+    # elif all([x in obsolete for x in parents]):
+    #     print(t.curie)
+    # elif all([x not in mapped for x in parents]):
+    #     print(t.curie)
+    # elif all([x not in excluded for x in parents]):
+    #     print(t.curie)
+    # elif all([x not in obsolete for x in parents]):
+    #     print(t.curie)
+    # # 1 but not all parent is mapped
+    # elif any([x in mapped for x in parents]) and not all([x in mapped for x in parents]):
+    #     print(t.curie)
+    # # 1 but not all parent is excluded
+    # elif any([x in excluded for x in parents]) and not all([x in excluded for x in parents]):
+    #     print(t.curie)
+    # # 1 but not all parent is obsolete
+    # elif any([x in obsolete for x in parents]) and not all([x in obsolete for x in parents]):
+    #     print(t.curie)
+    # elif all([x in y for y in [mapped, excluded, obsolete] for x in parents]):  # does this make sense
+    # at least 1 parent that is all of mapped, excluded, and obsolete
+    if any([(x in mapped) and (x in excluded) and (x in obsolete) for x in parents]):
+        print(t.curie)
+    # all parents are all of mapped, excluded, and obsolete
+    elif all([(x in mapped) and (x in excluded) and (x in obsolete) for x in parents]):
+        print(t.curie)
+    # no parents mapped, exlcuded, or obsolete
+    elif all([(x not in mapped) and (x not in excluded) and (x not in obsolete) for x in parents]):
+        print(t.curie)
     return not parents or all([(x in mapped) or (x in excluded) or (x in obsolete) for x in parents])
 
 
@@ -115,14 +154,49 @@ def slurp(
     # `reports/%_term_exclusions.txt`), and (iii) must not be deprecated / obsolete. Then, unless
     # `parent_conditions_off`, will also (iv) `_check_parent_conditions()`.
     terms_to_slurp: List[Dict[str, str]] = []
-    slurp_candidates = [t for t in slurp_candidates if _valid_parent_conditions(
+    # TODO: temp term param
+    slurp_candidates = [t for t in slurp_candidates if _valid_parent_conditions(t,
         t.direct_owned_parent_curies, mapped, excluded, obsolete)] if not parent_conditions_off else slurp_candidates
     for t in slurp_candidates:
         if t.curie in slurp_id_map:
             mondo_id = slurp_id_map[t.curie]
         else:
             next_mondo_id, mondo_term_ids = _get_next_available_mondo_id(next_mondo_id, max_id, mondo_term_ids)
             mondo_id = 'MONDO:' + str(next_mondo_id).zfill(7)  # leading 0-padding
+        qualified_parents = [p for p in t.direct_owned_parent_curies
+                             if p in match_types and match_types[p] in ['skos:exactMatch', 'skos:narrowMatch']]
+        qualified_mondo_paents = [mondo_id_map[p] for p in qualified_parents if p in mondo_id_map]
+
+        # TODO: temp: obsolete mondo parents
+        mondo_parents = {}
+        for parent_curie in t.direct_owned_parent_curies:
+            parent: Dict = sssom_df[sssom_df['object_id'] == parent_curie].to_dict('records')[0]
+            mondo_parents[parent['subject_id']] = parent['subject_label']
+        osbsolete_status_mondo_parents = [x.startswith('obsolete') for x in list(mondo_parents.values())]
+        # some parents obsolete
+        if any(osbsolete_status_mondo_parents) and not all(osbsolete_status_mondo_parents):
+            print(t.curie)
+        # all parents obsolete
+        elif all(osbsolete_status_mondo_parents):
+            print(t.curie)
+        # no parents obsolete
+        elif not any(osbsolete_status_mondo_parents):
+            print(t.curie)
+
+        # TODO: temp: qualified parents
+        # all parents qualified
+        if len(qualified_parents) > 0 and len(qualified_mondo_paents) == len(t.direct_owned_parent_curies):
+            print(t.curie)
+        # but not all parents are qualified
+        elif len(qualified_parents) > 0 and len(qualified_mondo_paents) != len(t.direct_owned_parent_curies):
+            print(t.curie)
+        # has parents but none of them are qualified
+        elif len(qualified_parents) == 0 and len(t.direct_owned_parent_curies) > 0:
+            print(t.curie)
+        # no parents
+        elif not t.direct_owned_parent_curies:
+            print(t.curie)
+
         mondo_label = t.label.lower() if t.label else ''
         qualified_parents = [p for p in t.direct_owned_parent_curies
                              if p in match_types and match_types[p] in ['skos:exactMatch', 'skos:narrowMatch']]

test/__init__.py

@@ -0,0 +1 @@
+"""Unit tests"""