Amend tests to reflect changes in EFO

opentargets · Nov 17, 2022 · c4f12e7 · c4f12e7
1 parent 88eb3a3
commit c4f12e7
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Showing 3 changed files with 11 additions and 14 deletions.
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -19,5 +19,5 @@ def test_file_batch_input(rootdir):
     ])
     assert result.exit_code == 0
     output = open('/tmp/ontoma-1.txt').read()
-    assert 'EFO_0000270' in output
+    assert 'MONDO_0004979' in output
     # assert 'MONDO_0002279' in output  # Related synonyms are not processed by this version.
diff --git a/tests/test_ontoma.py b/tests/test_ontoma.py
@@ -4,21 +4,18 @@
 def test_find_term_asthma(ontclient):
     assert_result_ot_label(
         ontclient.find_term('asthma'),
-        ['EFO_0000270']
+        ['MONDO_0004979']
     )
 
 
 def test_is_included(ontclient):
-    assert ontclient.filter_identifiers_by_efo_current(['ORDO:354']) == ['ORDO:354']
-    # FIXME: This represents a term which is in EFO, but perhaps should not be considered by OnToma, because this is
-    # FIXME: a body part rather than a disease/drug response/etc.
-    assert ontclient.filter_identifiers_by_efo_current(['UBERON:0000310']) == ['UBERON:0000310']
+    assert ontclient.filter_identifiers_by_efo_current(['MONDO:0018149']) == ['MONDO:0018149']
 
 
 def test_suggest_hp_term_not_excluded(ontclient):
     assert_result_ot_label(
         ontclient.find_term('hypogammaglobulinemia'),
-        ['Orphanet_183669']
+        ['MONDO_0015977']
     )
 
 
@@ -29,7 +26,7 @@ def test_catch_ordo(ontclient):
     )
     assert_result_ot_label(
         ontclient.find_term('OMIM:208250', code=True),
-        {'EFO_0009028', 'MONDO_0008828'}
+        {'EFO_0009028'}
     )
 
 
@@ -42,5 +39,5 @@ def test_query_comma(ontclient):
 def test_find_term_alzheimer(ontclient):
     assert_result_ot_label(
         ontclient.find_term('alzheimer\'s disease'),
-        ['EFO_0000249']
+        ['MONDO_0004975']
     )
diff --git a/tests/test_phewascat.py b/tests/test_phewascat.py
@@ -4,14 +4,14 @@
 def test_find_term_asthma(ontclient):
     assert_result_ot_label(
         ontclient.find_term('asthma'),
-        ['EFO_0000270']
+        ['MONDO_0004979']
     )
 
 
 def test_efo_direct_match(ontclient):
-    # The test deliberately expects no results, since a match from “Dementias” to “EFO_0004718” is a fuzzy one and
-    # cannot be assumed of high quality.
-    assert not ontclient.find_term('Dementias')
+    # The test deliberately expects no results, since a match from “Xeroderma Pigmentosa” to “MONDO_0019600” is a fuzzy
+    # one and cannot be assumed of high quality.
+    assert not ontclient.find_term('Xeroderma Pigmentosa')
 
 
 def test_otzooma_mappings_whitespace(ontclient):
@@ -24,7 +24,7 @@ def test_otzooma_mappings_whitespace(ontclient):
 def test_efo_match_with_apostrophe(ontclient):
     assert_result_ot_label(
         ontclient.find_term('Alzheimer\'s disease'),
-        ['EFO_0000249']
+        ['MONDO_0004975']
     )