def test_not_indexed(self):
occurrence = CSVReader("data/occurrence.txt",
delimiter="\t",
quote_char="\"")
with self.assertRaises(RuntimeError):
records = list(
occurrence.get_lines(
"eventID",
"Cruise68:Station593:EventSorbeSledge9887:Subsample16687"))
def test_field_names_dict(self):
names = {"scientificName": 7}
occurrence = CSVReader("data/occurrence.txt",
delimiter="\t",
quote_char="\"",
index_fields=["scientificName"],
field_names=names)
records = list(
occurrence.get_lines("scientificName", "Neomysis integer"))
self.assertTrue(records[0]["scientificName"] == "Neomysis integer")
self.assertTrue(
records[0]["col_6"] == "urn:lsid:marinespecies.org:taxname:120136")
def test_read(self):
occurrence = CSVReader("data/occurrence.txt",
delimiter="\t",
quote_char="\"",
index_fields=["id", "eventID"])
indexes = occurrence.indexes()
self.assertTrue("id" in indexes)
self.assertTrue("eventID" in indexes)
self.assertTrue(
"Cruise68:Station593:EventSorbeSledge9887:Subsample16687" in
indexes["eventID"])
self.assertTrue(
len(indexes["eventID"]
["Cruise68:Station593:EventSorbeSledge9887:Subsample16687"]) ==
39)
records = list(
occurrence.get_lines(
"id",
"Cruise68:Station565:EventSorbeSledge9781:Subsample17409"))
self.assertTrue(len(records) > 0)
self.assertTrue(
records[0]["eventID"] ==
"Cruise68:Station565:EventSorbeSledge9781:Subsample17409")
self.assertTrue(records[0]["scientificNameID"] ==
"urn:lsid:marinespecies.org:taxname:131495")
records = list(
occurrence.get_lines(
"eventID",
"Cruise68:Station622:EventSorbeSledge10018:Subsample15224"))
self.assertTrue(
records[21]["eventID"] ==
"Cruise68:Station622:EventSorbeSledge10018:Subsample15224")
self.assertTrue(records[21]["scientificNameID"] ==
"urn:lsid:marinespecies.org:taxname:120144")
def test_field_names_list(self):
names = [
"id", "basisOfRecord", "occurrenceID", "sex", "lifeStage",
"eventID"
]
occurrence = CSVReader("data/occurrence.txt",
delimiter="\t",
quote_char="\"",
index_fields=["eventID"],
field_names=names)
records = list(
occurrence.get_lines(
"eventID",
"Cruise68:Station593:EventSorbeSledge9887:Subsample16687"))
self.assertTrue(
records[0]["eventID"] ==
"Cruise68:Station593:EventSorbeSledge9887:Subsample16687")
self.assertTrue(records[0]["occurrenceID"] == "Ugenthyperbenthos51168")
self.assertTrue(records[0]["col_6"] == "Sagitta elegans")
