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")