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test_tsindex.py
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test_tsindex.py
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# -*- coding: utf-8 -*-
from collections import namedtuple
import sqlalchemy as sa
from sqlalchemy.orm import sessionmaker
import os
import re
import requests
import tempfile
import uuid
from unittest import mock, TestCase
from obspy.clients.filesystem.tsindex import Client, Indexer, \
TSIndexDatabaseHandler
from obspy import read
from obspy import UTCDateTime
def get_test_data_filepath():
package_dir = os.path.abspath(os.path.dirname(__file__))
# TODO It perhaps shouldn't be the case, but the string here has to end
# in a forward slash. We should fix this in the future.
filepath = os.path.join(package_dir, 'data', 'tsindex_data/')
return filepath
def get_test_client():
filepath = get_test_data_filepath()
db_path = os.path.join(filepath, 'timeseries.sqlite')
client = Client(db_path,
datapath_replace=("^",
filepath))
return client
class ClientTestCase(TestCase):
def test_bad_sqlitdb_filepath(self):
"""
Checks that an error is raised when an invalid path is provided to
a SQLite database
"""
self.assertRaisesRegex(OSError,
"^Database path.*does not exist.$",
Client,
"/some/bad/path/timeseries.sqlite")
def test_get_waveforms(self):
filepath = get_test_data_filepath()
client = get_test_client()
expected_stream = \
read(
filepath + os.path.join(
'IU', '2018', '001',
'IU.ANMO.10.BHZ.2018.001_first_minute.mseed'),
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 5))
returned_stream = client.get_waveforms(
"IU", "ANMO", "10", "BHZ",
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 5))
returned_stream.sort()
expected_stream.sort()
for t1, t2 in zip(returned_stream, expected_stream):
self.assertListEqual(list(t1.data), list(t2.data))
# wildcard request spanning multiple files
expected_stream1 = \
read(
filepath + os.path.join(
'CU', '2018', '001',
'CU.TGUH.00.BHZ.2018.001_first_minute.mseed'),
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 3, 1))
expected_stream2 = \
read(
filepath + os.path.join(
'IU', '2018', '001',
'IU.ANMO.10.BHZ.2018.001_first_minute.mseed'),
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 3, 1))
expected_stream3 = \
read(
filepath + os.path.join(
'IU', '2018', '001',
'IU.COLA.10.BHZ.2018.001_first_minute.mseed'),
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 3, 1))
expected_stream = \
expected_stream1 + expected_stream2 + expected_stream3
returned_stream = client.get_waveforms(
"*", "*", "10,00", "BHZ",
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 3, 1))
returned_stream.sort()
expected_stream.sort()
self.assertEqual(len(returned_stream), len(expected_stream))
for t1, t2 in zip(returned_stream, expected_stream):
self.assertListEqual(list(t1.data), list(t2.data))
# request resulting in no data
returned_stream = client.get_waveforms(
"XX", "XXX", "XX", "XXX",
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 3, 1))
self.assertListEqual(returned_stream.traces, [])
def test_get_waveforms_bulk(self):
filepath = get_test_data_filepath()
client = get_test_client()
expected_stream1 = \
read(
filepath +
'CU/2018/001/CU.TGUH.00.BHZ.2018.001_first_minute.mseed',
starttime=UTCDateTime(2018, 1, 1, 0, 0, 1),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 7))
expected_stream2 = \
read(
filepath +
'IU/2018/001/IU.ANMO.10.BHZ.2018.001_first_minute.mseed',
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 5))
expected_stream = expected_stream1 + expected_stream2
expected_stream.sort()
# assert equal
bulk_request = [
("CU", "TGUH", "00", "BHZ",
UTCDateTime(2018, 1, 1, 0, 0, 1),
UTCDateTime(2018, 1, 1, 0, 0, 7)),
("IU", "ANMO", "10", "BHZ",
UTCDateTime(2018, 1, 1, 0, 0, 0),
UTCDateTime(2018, 1, 1, 0, 0, 5)),
]
returned_stream = client.get_waveforms_bulk(bulk_request)
returned_stream.sort()
self.assertEqual(len(returned_stream), len(expected_stream))
for t1, t2 in zip(returned_stream, expected_stream):
self.assertListEqual(list(t1.data), list(t2.data))
# assert not equal with a non-equivalent request
bulk_request = [
("IU", "ANMO", "10", "BHZ",
UTCDateTime(2018, 1, 1, 0, 0, 0),
UTCDateTime(2018, 1, 1, 0, 0, 5)),
]
returned_stream = client.get_waveforms_bulk(bulk_request)
returned_stream.sort()
self.assertNotEqual(len(returned_stream), len(expected_stream))
for t1, t2 in zip(returned_stream, expected_stream):
self.assertRaises(AssertionError,
self.assertListEqual,
list(t1.data), list(t2.data))
# request resulting in no data
returned_stream = client.get_waveforms(
"XX", "XXX", "XX", "XXX",
starttime=UTCDateTime(2018, 1, 1, 0, 0, 0),
endtime=UTCDateTime(2018, 1, 1, 0, 0, 3, 1))
self.assertListEqual(returned_stream.traces, [])
def test_get_nslc(self):
client = get_test_client()
# test using actual sqlite3 test database
expected_nslc = [(u'CU', u'TGUH', u'00', u'BHZ')]
actual_nslc = client.get_nslc("I*,CU",
"ANMO,COL?,T*",
"00,10",
"BHZ",
"2018-01-01T00:00:00.000000",
"2018-01-01T00:00:00.019499")
self.assertListEqual(actual_nslc, expected_nslc)
actual_nslc = client.get_nslc("CU",
"ANMO,COL?,T*")
self.assertListEqual(actual_nslc, expected_nslc)
# test using mocked client._get_summary_rows method for more diversity
NamedRow = namedtuple('NamedRow',
['network', 'station', 'location', 'channel',
'earliest', 'latest'])
mocked_summary_rows = [NamedRow("AK", "ANM", "", "VM2",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991"),
NamedRow("AK", "ANM", "", "VM3",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991"),
NamedRow("AK", "ANM", "", "VM4",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991"),
NamedRow("XX", "ANM", "", "VM5",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991"),
NamedRow("N4", "H43A", "", "VM2",
"2018-08-10T21:09:39.000000",
"2018-08-10T22:09:28.890415"),
NamedRow("N4", "H43A", "", "VM3",
"2018-08-10T21:09:39.000000",
"2018-08-10T22:09:28.890415")]
client._get_summary_rows = \
mock.MagicMock(return_value=mocked_summary_rows)
expected_nslc = [("AK", "ANM", "", "VM2"),
("AK", "ANM", "", "VM3"),
("AK", "ANM", "", "VM4"),
("N4", "H43A", "", "VM2"),
("N4", "H43A", "", "VM3"),
("XX", "ANM", "", "VM5")]
self.assertEqual(client.get_nslc("AK,N4,XX",
"ANM,H43A",
"",
"VM2,VM3,VM4,VM5",
"2018-08-10T21:09:39.000000",
"2018-08-10T22:09:28.890415"),
expected_nslc)
def test_get_availability_extent(self):
client = get_test_client()
# test using actual sqlite test database
expected_nslc = [(u'IU', u'ANMO', u'10', u'BHZ',
UTCDateTime(2018, 1, 1, 0, 0, 0, 19500),
UTCDateTime(2018, 1, 1, 0, 0, 59, 994536)),
(u'IU', u'COLA', u'10', u'BHZ',
UTCDateTime(2018, 1, 1, 0, 0, 0, 19500),
UTCDateTime(2018, 1, 1, 0, 0, 59, 994538))]
actual_avail_extents = client.get_availability_extent(
"I*",
"ANMO,COL?,T*",
"00,10",
"BHZ",
"2018-01-01T00:00:00.000000",
"2018-12-31T00:00:00.000000")
self.assertListEqual(actual_avail_extents, expected_nslc)
actual_avail_extents = client.get_availability_extent("I*")
self.assertListEqual(actual_avail_extents, expected_nslc)
# test using mocked client._get_summary_rows method for more diversity
NamedRow = namedtuple('NamedRow',
['network', 'station', 'location', 'channel',
'earliest', 'latest'])
mocked_summary_rows = [NamedRow("AK", "ANM", "", "VM2",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991"),
NamedRow("AK", "ANM", "", "VM3",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991"),
NamedRow("AK", "ANM", "", "VM5",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:15:39.999991"),
NamedRow("N4", "H43A", "", "VM2",
"2018-08-10T21:09:39.000000",
"2018-08-10T22:09:28.890415"),
NamedRow("N4", "H43A", "", "VM3",
"2018-08-10T21:09:39.000000",
"2018-08-10T22:09:28.890415"),
NamedRow("XX", "ANM", "", "VM4",
"2018-08-10T21:52:50.000000",
"2018-08-10T22:12:39.999991")]
client._get_summary_rows = \
mock.MagicMock(return_value=mocked_summary_rows)
expected_avail_extents = \
[("AK", "ANM", "", "VM2",
UTCDateTime("2018-08-10T21:52:50.000000"),
UTCDateTime("2018-08-10T22:12:39.999991")),
("AK", "ANM", "", "VM3",
UTCDateTime("2018-08-10T21:52:50.000000"),
UTCDateTime("2018-08-10T22:12:39.999991")),
("AK", "ANM", "", "VM5",
UTCDateTime("2018-08-10T21:52:50.000000"),
UTCDateTime("2018-08-10T22:15:39.999991")),
("N4", "H43A", "", "VM2",
UTCDateTime("2018-08-10T21:09:39.000000"),
UTCDateTime("2018-08-10T22:09:28.890415")),
("N4", "H43A", "", "VM3",
UTCDateTime("2018-08-10T21:09:39.000000"),
UTCDateTime("2018-08-10T22:09:28.890415")),
("XX", "ANM", "", "VM4",
UTCDateTime("2018-08-10T21:52:50.000000"),
UTCDateTime("2018-08-10T22:12:39.999991"))]
self.assertListEqual(client.get_availability_extent(
"AK,N4",
"ANM,H43A", "",
"VM2,VM3,VM4,VM5",
"2018-08-10T21:09:39.000000",
"2018-08-10T22:09:28.890415"),
expected_avail_extents)
def test__are_timespans_adjacent(self):
client = get_test_client()
sample_rate = 40
# sample_period = 1/40 = 0.025 sec = 25000 ms
# and tolerance = 0.5 so an adjacent sample is +/-0.0125 sec = 12500 ms
# 1 sample period later
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 50000),
UTCDateTime(2018, 8, 10, 22, 0, 0, 75000))
self.assertTrue(client._are_timespans_adjacent(ts1, ts2, sample_rate))
# 1ms after nearest tolerance boundary (next sample - 12500ms)
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 37501),
UTCDateTime(2018, 8, 10, 22, 0, 0, 75000))
self.assertTrue(client._are_timespans_adjacent(ts1, ts2, sample_rate))
# exactly on nearest tolerance boundary (next sample - 12500ms)
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 37500),
UTCDateTime(2018, 8, 10, 22, 0, 0, 75000))
self.assertFalse(client._are_timespans_adjacent(ts1, ts2, sample_rate))
# 1ms before nearest tolerance boundary (next sample - 12500ms)
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 37499),
UTCDateTime(2018, 8, 10, 22, 0, 0, 75000))
self.assertFalse(client._are_timespans_adjacent(ts1, ts2, sample_rate))
# 1ms after farthest tolerance boundary (next sample + 12500ms)
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 62501),
UTCDateTime(2018, 8, 10, 22, 0, 0, 100000))
self.assertFalse(client._are_timespans_adjacent(ts1, ts2, sample_rate))
# on farthest tolerance boundary (next sample + 12500ms)
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 62500),
UTCDateTime(2018, 8, 10, 22, 0, 0, 100000))
self.assertFalse(client._are_timespans_adjacent(ts1, ts2, sample_rate))
# 1ms before farthest tolerance boundary (next sample + 12500ms)
ts1 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 0),
UTCDateTime(2018, 8, 10, 22, 0, 0, 25000))
ts2 = \
client._create_timespan(UTCDateTime(2018, 8, 10, 22, 0, 0, 62499),
UTCDateTime(2018, 8, 10, 22, 0, 0, 100000))
self.assertTrue(client._are_timespans_adjacent(ts1, ts2, sample_rate))
def test_get_availability(self):
client = get_test_client()
# test using actual sqlite test database
expected_avail = [(u'IU', u'ANMO', u'10', u'BHZ',
UTCDateTime(2018, 1, 1, 0, 0, 0, 19500),
UTCDateTime(2018, 1, 1, 0, 0, 59, 994536)),
(u'IU', u'COLA', u'10', u'BHZ',
UTCDateTime(2018, 1, 1, 0, 0, 0, 19500),
UTCDateTime(2018, 1, 1, 0, 0, 59, 994538))]
actual_avail = client.get_availability(
"IU",
"ANMO,COLA",
"10",
"BHZ",
"2018-01-01",
"2018-12-31")
self.assertListEqual(actual_avail, expected_avail)
actual_avail = client.get_availability("IU",
"ANMO,COLA")
self.assertListEqual(actual_avail, expected_avail)
# test using mocked client._get_summary_rows method for more diversity
NamedRow = namedtuple('NamedRow',
['network', 'station', 'location', 'channel',
'samplerate', 'starttime', 'endtime',
'timespans'])
# Each row contains one gap. The first rows latest time is adjacent
# to the second rows earliest time. The third row overlaps with the
# second row.
mocked_tsindex_rows = \
[
# 2018-08-10T22:00:54 to 2018-08-10T22:15:53
# 2018-08-10T22:05:54 to 2018-08-10T22:20:53 (MERGE)
NamedRow(
network=u'AK', station=u'BAGL',
location=u'', channel=u'LCC',
starttime=u'2018-08-10T22:00:54.000000',
endtime=u'2018-08-10T22:20:53.000000',
samplerate=1.0,
timespans=u'[1533938454.000000:1533939353.000000],'
u'[1533938754.000000:1533939653.000000]'),
# 2018-08-10T22:20:53.999000 to 2018-08-12T22:20:53 (JOIN)
# 2018-08-12T23:20:53 to 2018-09-01T23:20:53
NamedRow(
network=u'AK', station=u'BAGL',
location=u'', channel=u'LCC',
starttime=u'2018-08-10T22:20:53.999000',
endtime=u'2018-09-01T23:20:53.000000',
samplerate=1.0,
timespans=u'[1533939653.999000:1534112453.000000],'
u'[1534116053.000000:1535844053.000000]'),
# (MERGE IF INCL SAMPLE RATE IS TRUE)
# 2018-08-27T00:00:00 to 2018-09-11T00:00:00
NamedRow(network=u'AK', station=u'BAGL',
location=u'', channel=u'LCC',
starttime=u'2018-08-27T00:00:00.000000',
endtime=u'2018-09-11T00:00:00.000000',
samplerate=10.0,
timespans=u'[1535328000.0:1536624000.0]')
]
client._get_tsindex_rows = \
mock.MagicMock(return_value=mocked_tsindex_rows)
expected_unmerged_avail = [("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 10, 22, 15, 53)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 10, 22, 5, 54),
UTCDateTime(2018, 8, 12, 22, 20, 53)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 12, 23, 20, 53),
UTCDateTime(2018, 9, 1, 23, 20, 53)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 27, 0, 0),
UTCDateTime(2018, 9, 11, 0, 0, 0))]
# test default options
self.assertListEqual(client.get_availability(
"AK",
"BAGL",
"",
"LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 10, 22, 9, 28, 890415)),
expected_unmerged_avail)
# test merge overlap false
self.assertListEqual(client.get_availability(
"AK",
"BAGL",
"--",
"LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 10, 22, 9, 28, 890415),
merge_overlap=False),
expected_unmerged_avail)
# test merge overlap true
expected_merged_avail = [("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 12, 22, 20, 53)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 12, 23, 20, 53),
UTCDateTime(2018, 9, 11, 0, 0, 0))]
self.assertListEqual(
client.get_availability(
"AK",
"BAGL",
"--",
"LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 10, 22, 9, 28, 890415),
merge_overlap=True),
expected_merged_avail)
# test include_sample_rate true
expected_incl_sr_avail = \
[("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 12, 22, 20, 53), 1.0),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 12, 23, 20, 53),
UTCDateTime(2018, 9, 1, 23, 20, 53), 1.0),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 27, 0, 0),
UTCDateTime(2018, 9, 11, 0, 0, 0), 10.0)]
self.assertListEqual(
client.get_availability(
"AK",
"BAGL",
"--",
"LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 10, 22, 9, 28, 890415),
merge_overlap=True,
include_sample_rate=True),
expected_incl_sr_avail)
def test_get_availability_percentage(self):
client = get_test_client()
mock_availability_output = [("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 8, 12, 22, 20, 53)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 8, 12, 23, 20, 53),
UTCDateTime(2018, 9, 11, 0, 0, 0))]
client.get_availability = mock.MagicMock(
return_value=mock_availability_output)
avail_percentage = client.get_availability_percentage(
"AK",
"BAGL",
"--",
"LCC",
UTCDateTime(2018, 8, 10, 22, 0, 54),
UTCDateTime(2018, 9, 11, 0, 0, 0))
expected_avail_percentage = (0.998659490472, 1)
self.assertAlmostEqual(avail_percentage[0],
expected_avail_percentage[0])
self.assertEqual(avail_percentage[1],
expected_avail_percentage[1])
self.assertIsInstance(avail_percentage, tuple)
mock_availability_output = [("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 1, 1),
UTCDateTime(2018, 1, 2)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 1, 3),
UTCDateTime(2018, 1, 4)),
("AK", "BAGL", "", "LCC",
UTCDateTime(2018, 1, 5),
UTCDateTime(2018, 1, 6))]
client.get_availability = mock.MagicMock(
return_value=mock_availability_output)
avail_percentage = client.get_availability_percentage(
"AK",
"BAGL",
"--",
"LCC",
UTCDateTime(2018, 1, 1),
UTCDateTime(2018, 1, 6))
expected_avail_percentage = (0.6, 2)
self.assertAlmostEqual(avail_percentage[0],
expected_avail_percentage[0])
self.assertEqual(avail_percentage[1],
expected_avail_percentage[1])
self.assertIsInstance(avail_percentage, tuple)
# Test for over extending time span
avail_percentage = client.get_availability_percentage(
"AK",
"BAGL",
"--",
"LCC",
UTCDateTime(2017, 12, 31),
UTCDateTime(2018, 1, 7))
expected_avail_percentage = (0.4285714, 4)
self.assertAlmostEqual(avail_percentage[0],
expected_avail_percentage[0])
self.assertEqual(avail_percentage[1],
expected_avail_percentage[1])
self.assertIsInstance(avail_percentage, tuple)
def test_has_data(self):
client = get_test_client()
self.assertTrue(client.has_data())
self.assertTrue(client.has_data(starttime=UTCDateTime(2017, 12, 31),
endtime=UTCDateTime(2018, 1, 7)))
self.assertFalse(client.has_data(starttime=UTCDateTime(1970, 12, 31),
endtime=UTCDateTime(2013, 1, 7)))
def purge(dir, pattern):
"""
Delete a file matching a pattern from the OS.
"""
for f in os.listdir(dir):
if re.search(pattern, f):
os.remove(os.path.join(dir, f))
class IndexerTestCase(TestCase):
def test_bad_rootpath(self):
"""
Checks that an error is raised when an invalid path is provided to
a data
"""
filepath = get_test_data_filepath()
database = os.path.join(filepath,
'timeseries.sqlite')
# test that a bad leap second file path raises an error
self.assertRaisesRegex(OSError,
"^Root path.*does not exists.$",
Indexer,
"/some/bad/path",
database=database,
filename_pattern="*.mseed",
parallel=2)
def test_bad_sqlitdb_filepath(self):
"""
Checks that an error is raised when an invalid path is provided to
a SQLite database
"""
filepath = get_test_data_filepath()
self.assertRaisesRegex(OSError,
"^Database path.*does not exist.$",
Indexer,
filepath,
database='/some/bad/path/',
filename_pattern="*.mseed")
def test_bad_database(self):
"""
Checks that an error is raised when an invalid database is provided.
The database must be a TSIndexDatabaseHandler or a str, otherwise
a ValueError is raised.
"""
filepath = get_test_data_filepath()
self.assertRaisesRegex(ValueError,
"^Database must be a string or "
"TSIndexDatabaseHandler object.$",
Indexer,
filepath,
database=None,
filename_pattern="*.mseed")
def test_download_leap_seconds_file(self):
filepath = get_test_data_filepath()
database = os.path.join(filepath, 'timeseries.sqlite')
indexer = Indexer(filepath,
database=database)
# mock actually downloading the file since this requires a internet
# connection
indexer._download = mock.MagicMock(return_value=requests.Response())
# create a empty leap-seconds.list file
test_file = os.path.join(
os.path.dirname(database), "leap-seconds.list")
file_path = indexer.download_leap_seconds_file(test_file)
# assert that the file was put in the same location as the
# sqlite db
self.assertTrue(os.path.isfile(file_path))
self.assertEqual(file_path, test_file)
os.remove(test_file)
def test_download_leap_seconds_file_no_path_given(self):
filepath = get_test_data_filepath()
database = os.path.join(filepath, 'timeseries.sqlite')
indexer = Indexer(filepath,
database=database)
# mock actually downloading the file since this requires a internet
# connection
indexer._download = mock.MagicMock(return_value=requests.Response())
file_path = indexer.download_leap_seconds_file()
self.assertEqual(
os.path.normpath(file_path),
os.path.normpath(os.path.join(os.path.dirname(database),
"leap-seconds.list")))
# assert that the file was put in the same location as the
# sqlite db
self.assertTrue(os.path.isfile(file_path))
os.remove(file_path)
def test__get_leap_seconds_file(self):
filepath = get_test_data_filepath()
database = os.path.join(filepath, 'timeseries.sqlite')
indexer = Indexer(filepath,
database=database)
# test that a bad leap second file path raises an error
self.assertRaisesRegex(OSError,
"^No leap seconds file exists at.*$",
Indexer,
filepath,
database=database,
leap_seconds_file="/some/bad/path/")
self.assertRaisesRegex(OSError,
"^No leap seconds file exists at.*$",
indexer._get_leap_seconds_file,
"/some/bad/path/")
# test search
# create a empty leap-seconds.list file
test_file = os.path.normpath(os.path.join(
os.path.dirname(database), "leap-seconds.list"))
open(test_file, 'a').close()
file_path = os.path.normpath(indexer._get_leap_seconds_file("SEARCH"))
self.assertEqual(file_path, test_file)
os.remove(test_file)
def test_build_file_list(self):
filepath = get_test_data_filepath()
database = os.path.join(filepath, 'timeseries.sqlite')
indexer = Indexer(filepath,
database=database,
filename_pattern="*.mseed")
# test for relative paths
file_list = indexer.build_file_list(relative_paths=True,
reindex=True)
file_list.sort()
self.assertEqual(len(file_list), 3)
self.assertEqual(os.path.normpath(
'CU/2018/001/CU.TGUH.00.BHZ.2018.001_first_minute.mseed'),
file_list[0])
self.assertEqual(os.path.normpath(
'IU/2018/001/IU.ANMO.10.BHZ.2018.001_first_minute.mseed'),
file_list[1])
self.assertEqual(os.path.normpath(
'IU/2018/001/IU.COLA.10.BHZ.2018.001_first_minute.mseed'),
file_list[2])
# case where the root path is outside of the absolute
# data path, to assert that already indexed files are still skipped
indexer = Indexer(tempfile.mkdtemp(),
database=TSIndexDatabaseHandler(database=database),
filename_pattern="*.mseed")
self.assertRaisesRegex(OSError,
"^No files matching filename.*$",
indexer.build_file_list,
reindex=True)
# test for absolute paths
# this time pass a TSIndexDatabaseHandler instance as the database
indexer = Indexer(filepath,
database=TSIndexDatabaseHandler(database=database),
filename_pattern="*.mseed",
leap_seconds_file=None)
file_list = indexer.build_file_list(reindex=True)
file_list.sort()
self.assertEqual(len(file_list), 3)
self.assertNotEqual(os.path.normpath(
'CU/2018/001/CU.TGUH.00.BHZ.2018.001_first_minute.mseed'),
file_list[0])
self.assertIn(os.path.normpath(
'CU/2018/001/CU.TGUH.00.BHZ.2018.001_first_minute.mseed'),
file_list[0])
self.assertNotEqual(os.path.normpath(
'IU/2018/001/IU.ANMO.10.BHZ.2018.001_first_minute.mseed'),
file_list[1])
self.assertIn(os.path.normpath(
'IU/2018/001/IU.ANMO.10.BHZ.2018.001_first_minute.mseed'),
file_list[1])
self.assertNotEqual(os.path.normpath(
'IU/2018/001/IU.COLA.10.BHZ.2018.001_first_minute.mseed'),
file_list[2])
self.assertIn(os.path.normpath(
'IU/2018/001/IU.COLA.10.BHZ.2018.001_first_minute.mseed'),
file_list[2])
# test that already indexed files (relative and absolute) get skipped.
self.assertRaisesRegex(OSError,
"^No unindexed files matching filename.*$",
indexer.build_file_list,
reindex=False,
relative_paths=False)
self.assertRaisesRegex(OSError,
"^No unindexed files matching filename.*$",
indexer.build_file_list,
reindex=False,
relative_paths=True)
# for this test mock an unindexed file ('data.mseed') to ensure that
# it gets added when reindex is True
mocked_files = [
'CU/2018/001/'
'CU.TGUH.00.BHZ.2018.001_first_minute.mseed',
'IU/2018/001/'
'IU.ANMO.10.BHZ.2018.001_first_minute.mseed',
'IU/2018/001/'
'IU.COLA.10.BHZ.2018.001_first_minute.mseed',
'data.mseed'
]
for i in range(len(mocked_files)):
mocked_files[i] = os.path.normpath(mocked_files[i])
indexer._get_rootpath_files = mock.MagicMock(return_value=mocked_files)
self.assertEqual(indexer.build_file_list(
reindex=False,
relative_paths=False),
['data.mseed'])
def test_run_bad_index_cmd(self):
"""
Checks that an OSError is raised when there is an error running a
index_cmd. (such as no command found.)
"""
filepath = get_test_data_filepath()
indexer = Indexer(filepath,
filename_pattern="*.mseed",
index_cmd="some_bad_command"
)
self.assertRaisesRegex(OSError,
"^Required program.* is not installed.*$",
indexer.run)
def test_run(self):
my_uuid = uuid.uuid4().hex
fname = 'test_timeseries_{}'.format(my_uuid)
filepath = get_test_data_filepath()
database = '{}{}.sqlite'.format(filepath, fname)
try:
indexer = Indexer(filepath,
database=database,
filename_pattern="*.mseed",
parallel=2)
if indexer._is_index_cmd_installed():
indexer.run(relative_paths=True)
keys = ['network', 'station', 'location', 'channel',
'quality', 'starttime', 'endtime', 'samplerate',
'filename', 'byteoffset', 'bytes', 'hash',
'timeindex', 'timespans', 'timerates', 'format']
NamedRow = namedtuple('NamedRow',
keys)
expected_tsindex_data = \
[
NamedRow(
"CU", "TGUH", "00", "BHZ", "M",
"2018-01-01T00:00:00.000000",
"2018-01-01T00:01:00.000000", 40.0,
"CU/2018/001/"
"CU.TGUH.00.BHZ.2018.001_first_minute.mseed",
0, 4096, "aaaac5315f84cdd174fd8360002a1e3a",
"1514764800.000000=>0,latest=>1",
"[1514764800.000000:1514764860.000000]", None, None),
NamedRow(
"IU", "ANMO", "10", "BHZ", "M",
"2018-01-01T00:00:00.019500",
"2018-01-01T00:00:59.994536", 40.0,
"IU/2018/001/"
"IU.ANMO.10.BHZ.2018.001_first_minute.mseed",
0, 2560, "36a771ca1dc648c505873c164d8b26f2",
"1514764800.019500=>0,latest=>1",
"[1514764800.019500:1514764859.994536]", None, None),
NamedRow(
"IU", "COLA", "10", "BHZ", "M",
"2018-01-01T00:00:00.019500",
"2018-01-01T00:00:59.994538", 40.0,
"IU/2018/001/"
"IU.COLA.10.BHZ.2018.001_first_minute.mseed",
0, 5120, "4ccbb97573ca00ef8c2c4f9c01d27ddf",
"1514764800.019500=>0,latest=>1",
"[1514764800.019500:1514764859.994538]", None, None)]
db_handler = TSIndexDatabaseHandler(database=database)
tsindex_data = db_handler._fetch_index_rows([("I*,C*", "*",
"0?,1?", "*",
"2018-01-01",
"2018-02-01")])
for i in range(0, len(expected_tsindex_data)):
for j in range(0, len(keys)):
self.assertEqual(getattr(expected_tsindex_data[i],
keys[j]),
getattr(tsindex_data[i], keys[j]))
self.assertEqual(len(tsindex_data), len(expected_tsindex_data))
finally:
purge(filepath, '^{}.*$'.format(fname))
class TSIndexDatabaseHandlerTestCase(TestCase):
def test_bad_sqlitdb_filepath(self):
"""
Checks that an error is raised when an invalid path is provided to
a SQLite database
"""
filepath = get_test_data_filepath()
self.assertRaisesRegex(OSError,
"^Database path.*does not exist.$",
Indexer,
filepath,
database='/some/bad/path/',
filename_pattern="*.mseed",
parallel=2)
def test__fetch_summary_rows(self):
# test with actual sqlite3 database that is missing a summary table
# a temporary summary table gets created at runtime
filepath = get_test_data_filepath()
db_path = os.path.join(filepath, 'timeseries.sqlite')
request_handler = TSIndexDatabaseHandler(db_path)
keys = ['network', 'station', 'location', 'channel',
'earliest', 'latest']
NamedRow = namedtuple('NamedRow',
keys)
expected_ts_summary_data = \
[NamedRow(
"CU", "TGUH", "00", "BHZ",
"2018-01-01T00:00:00.000000",
"2018-01-01T00:01:00.000000"),
NamedRow(
"IU", "ANMO", "10", "BHZ",
"2018-01-01T00:00:00.019500",
"2018-01-01T00:00:59.994536")]
ts_summary_data = request_handler._fetch_summary_rows(
[("I*,CU",
"ANMO,T*",
"00,10",
"BHZ",
"2018-01-01T00:00:00.000000",
"2018-12-31T00:00:00.000000")])
for i in range(0, len(expected_ts_summary_data)):
for j in range(0, len(keys)):
self.assertEqual(getattr(expected_ts_summary_data[i], keys[j]),
getattr(ts_summary_data[i], keys[j]))
# test for case where query returns no results
ts_summary_data = request_handler._fetch_summary_rows(
[("XX",
"ANMO,T*",
"00,10",
"BHZ",
"2018-01-01T00:00:00.000000",
"2018-12-31T00:00:00.000000")])
self.assertEqual(ts_summary_data, [])
def test_get_tsindex_summary_cte(self):
# test with actual sqlite3 database that is missing a summary table
# a tsindex summary CTE gets created using the tsindex at runtime
filepath = get_test_data_filepath()
db_path = os.path.join(filepath, 'timeseries.sqlite')
# supply an existing session
engine = sa.create_engine("sqlite:///{}".format(db_path))
session = sessionmaker(bind=engine)
request_handler = TSIndexDatabaseHandler(session=session)
ts_summary_cte = request_handler.get_tsindex_summary_cte()
expected_ts_summary_data = \
[("CU", "TGUH", "00", "BHZ",
"2018-01-01T00:00:00.000000",
"2018-01-01T00:01:00.000000"),
("IU", "ANMO", "10", "BHZ",
"2018-01-01T00:00:00.019500",
"2018-01-01T00:00:59.994536"),
("IU", "COLA", "10", "BHZ",
"2018-01-01T00:00:00.019500",
"2018-01-01T00:00:59.994538")]
query_results = (session().query(ts_summary_cte))
for idx, r in enumerate(query_results):
result = r[:6] # ignore updt date
self.assertEqual(result, expected_ts_summary_data[idx])