def test_cache(self):
records = [{
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:141433"
}]
results_nocache = taxonomy.check(records)
self.assertTrue(results_nocache[0]["annotations"]["aphia"] == 141433)
self.assertFalse(results_nocache[0]["dropped"])
self.assertNotIn(Flag.NOT_MARINE.value, results_nocache[0]["flags"])
results_cache = taxonomy.check(records, self.cache)
self.assertTrue(results_cache[0]["annotations"]["aphia"] == 141433)
self.assertTrue(results_cache[0]["dropped"])
self.assertIn(Flag.NOT_MARINE.value, results_cache[0]["flags"])
def test_name_synonym_accepted_marine_unsure(self):
records = [{"id": 0, "scientificName": "Brockmanniella brockmannii"}]
results = taxonomy.check(records)
self.assertIn("scientificNameID", results[0]["missing"])
self.assertNotIn("scientificName", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertIn(Flag.MARINE_UNSURE.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 971564)
def test_name_invalid(self):
records = [{"id": 0, "scientificName": "Bivalve"}]
results = taxonomy.check(records)
self.assertIn("scientificNameID", results[0]["missing"])
self.assertNotIn("scientificName", results[0]["missing"])
self.assertTrue(results[0]["dropped"])
self.assertIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIsNone(results[0]["annotations"]["aphia"])
self.assertIsNone(results[0]["annotations"]["unaccepted"])
def test_name_valid(self):
records = [{"id": 0, "scientificName": "Abra alba"}]
results = taxonomy.check(records)
self.assertTrue(results[0]["annotations"]["aphia"] == 141433)
self.assertIsNone(results[0]["annotations"]["unaccepted"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn("scientificName", results[0]["missing"])
self.assertIn("scientificNameID", results[0]["missing"])
self.assertTrue(len(results[0]["flags"]) == 0)
def test_name_synonym(self):
records = [{"id": 0, "scientificName": "Orca gladiator"}]
results = taxonomy.check(records)
self.assertTrue(results[0]["annotations"]["aphia"] == 137102)
self.assertTrue(results[0]["annotations"]["unaccepted"] == 384046)
self.assertFalse(results[0]["dropped"])
self.assertNotIn("scientificName", results[0]["missing"])
self.assertIn("scientificNameID", results[0]["missing"])
self.assertTrue(len(results[0]["flags"]) == 0)
def test_name_not_marine(self):
records = [{"id": 0, "scientificName": "Ardea cinerea"}]
results = taxonomy.check(records)
self.assertIn("scientificNameID", results[0]["missing"])
self.assertNotIn("scientificName", results[0]["missing"])
self.assertTrue(results[0]["dropped"])
self.assertIn(Flag.NOT_MARINE.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 212668)
self.assertIsNone(results[0]["annotations"]["unaccepted"])
def test_aphiaid_zero(self):
records = [{
"scientificName": "Phytoplankton color",
"scientificNameID": "urn:lsid:marinespecies.org:taxname:0"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificName", results[0]["missing"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertTrue(results[0]["dropped"])
self.assertIn(Flag.NO_MATCH.value, results[0]["flags"])
def test_unaccepted(self):
records = [{"id": 0, "scientificName": "Dactyliosolen flexuosus"}]
results = taxonomy.check(records)
self.assertNotIn("scientificName", results[0]["missing"])
self.assertIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertNotIn(Flag.MARINE_UNSURE.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 637279)
def test_interim_deleted(self):
records = [{
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:22747"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 22747)
def test_id_invalid(self):
records = [{"scientificNameID": "urn:lsid:itis.gov:itis_tsn:28726"}]
results = taxonomy.check(records)
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertIn("scientificName", results[0]["missing"])
self.assertTrue(results[0]["dropped"])
self.assertIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn("scientificNameID", results[0]["invalid"])
self.assertTrue(len(results[0]["invalid"]) == 1)
self.assertIsNone(results[0]["annotations"]["aphia"])
self.assertIsNone(results[0]["annotations"]["unaccepted"])
def test_id_valid(self):
records = [{
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:141433"
}]
results = taxonomy.check(records)
self.assertTrue(results[0]["annotations"]["aphia"] == 141433)
self.assertIsNone(results[0]["annotations"]["unaccepted"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertIn("scientificName", results[0]["missing"])
self.assertTrue(len(results[0]["flags"]) == 0)
def test_uncertain(self):
records = [{
"scientificNameID": "urn:lsid:marinespecies.org:taxname:835694",
"scientificName": "Operculodinium centrocarpum"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificName", results[0]["missing"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertIn(Flag.MARINE_UNSURE.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 835694)
def test_id_non_existing(self):
records = [{
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:99999999"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertIn("scientificName", results[0]["missing"])
self.assertTrue(results[0]["dropped"])
self.assertIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn("scientificNameID", results[0]["invalid"])
self.assertIsNone(results[0]["annotations"]["aphia"])
self.assertIsNone(results[0]["annotations"]["unaccepted"])
def test_paraphyletic(self):
records = [{
"scientificNameID": "urn:lsid:marinespecies.org:taxname:794",
"scientificName": "Turbellaria"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificName", results[0]["missing"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertNotIn(Flag.MARINE_UNSURE.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 794)
def test_nomen_dubium(self):
records = [{
"scientificNameID": "urn:lsid:marinespecies.org:taxname:130270",
"scientificName": "Magelona minuta"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificName", results[0]["missing"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertNotIn(Flag.MARINE_UNSURE.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 130270)
def test_taxon_inquirendum(self):
records = [{
"id":
0,
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:133144"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 133144)
def test_whitespace(self):
records = [{
"scientificName":
"Illex illecebrosus",
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:153087 "
}]
results = taxonomy.check(records)
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertNotIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 153087)
def test_annotations_resolvable(self):
records = [{
"scientificName": "Hyalinia crystallina Muller, 1774",
"phylum": "Mollusca",
"class": "Gastropoda Cuvier, 1797",
"order": "Stylommatophora",
"family": "Zonitidae Mörch, 1864",
"genus": "Hyalinia Agassiz, 1837"
}]
results = taxonomy.check(records)
self.assertIn(Flag.WORMS_ANNOTATION_RESOLVABLE.value,
results[0]["flags"])
self.assertIsNotNone(results[0]["annotations"]["aphia"])
def test_id_synonym(self):
records = [{
"id":
0,
"scientificNameID":
"urn:lsid:marinespecies.org:taxname:384046"
}]
results = taxonomy.check(records)
self.assertTrue(results[0]["annotations"]["aphia"] == 137102)
self.assertTrue(results[0]["annotations"]["unaccepted"] == 384046)
self.assertFalse(results[0]["dropped"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertIn("scientificName", results[0]["missing"])
self.assertTrue(len(results[0]["flags"]) == 0)
def test_nomen_nudum(self):
records = [{
"id": 0,
"scientificNameID": "urn:lsid:marinespecies.org:taxname:152230",
"scientificName": "Coelenterata tissue"
}]
results = taxonomy.check(records)
self.assertNotIn("scientificName", results[0]["missing"])
self.assertNotIn("scientificNameID", results[0]["missing"])
self.assertFalse(results[0]["dropped"])
self.assertNotIn(Flag.NO_MATCH.value, results[0]["flags"])
self.assertIn(Flag.MARINE_UNSURE.value, results[0]["flags"])
self.assertIn(Flag.NO_ACCEPTED_NAME.value, results[0]["flags"])
self.assertTrue(results[0]["annotations"]["aphia"] == 152230)
def test_annotations(self):
records = [
{
"scientificName": "NA",
"scientificNameID": "NA",
"phylum": "Ciliophora",
"class": "Ciliatea",
"order": "NA",
"family": "NA",
"genus": "NA"
},
{
"scientificName": "**non-current code** Antennarius sp.",
"scientificNameID": None,
"phylum": "Chordata",
"class": "Actinopterygii",
"order": "Lophiiformes",
"family": "Antennariidae",
"genus": "Antennarius"
},
{
"scientificName": "Vinundu guellemei",
"scientificNameID": None,
"phylum": None,
"class": None,
"order": None,
"family": None,
"genus": None
},
{
"scientificName": "unknown fish [, 1998]"
},
]
results = taxonomy.check(records)
self.assertIn(Flag.WORMS_ANNOTATION_UNRESOLVABLE.value,
results[0]["flags"])
self.assertIsNone(results[0]["annotations"]["aphia"])
self.assertIn(Flag.WORMS_ANNOTATION_REJECT_AMBIGUOUS.value,
results[1]["flags"])
self.assertIsNone(results[1]["annotations"]["aphia"])
self.assertIn(Flag.WORMS_ANNOTATION_RESOLVABLE_HUMAN.value,
results[2]["flags"])
self.assertEquals(results[2]["annotations"]["aphia"], 1060834)
self.assertIn(Flag.WORMS_ANNOTATION_RESOLVABLE_LOSS.value,
results[3]["flags"])
self.assertEquals(results[3]["annotations"]["aphia"], 11676)
def test_annotations(self):
records = [{
"id": 0,
"scientificName": "Brachiolaria"
}, {
"id": 1,
"scientificName": "Cercocebus sanjei"
}, {
"id": 2,
"scientificName": "**non-current code** ??"
}]
results = taxonomy.check(records)
self.assertIn(Flag.WORMS_ANNOTATION_REJECT_GROUPING.value,
results[0]["flags"])
self.assertIn(Flag.WORMS_ANNOTATION_REJECT_HABITAT.value,
results[1]["flags"])
self.assertIn(Flag.WORMS_ANNOTATION_NO_BIOTA.value,
results[2]["flags"])
