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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Part of pymzml test cases
"""
import os
from pymzml.utils.GSGW import GSGW
import unittest
import zlib
import struct
class GSGWTest(unittest.TestCase):
"""
TODO: Write messages for assertions
"""
def setUp(self):
self.paths = [os.path.join(os.path.dirname(__file__), "data", "unittest.mzml")]
self.Writer = GSGW(
self.paths[0],
max_idx=80,
max_idx_len=8,
max_offset_len=8,
output_path=os.path.abspath(
os.path.join(".", "tests", "data", "unittest.mzml")
),
)
def tearDown(self):
"""
"""
self.Writer.close()
os.remove(os.path.abspath(os.path.join(".", "tests", "data", "unittest.mzml")))
def test_init(self):
self.assertEqual(self.Writer.crc32, 0)
self.assertEqual(self.Writer.crc32, 0)
self.assertEqual(
self.Writer.file_name,
os.path.abspath(
os.path.join(
# os.path.dirname(__file__),
# 'Test',
"tests",
"data",
"unittest.mzml",
)
),
)
def test_write_gen_header_index(self):
self.Writer._write_gen_header(Index=True)
self.Writer.close()
file = open(self.paths[0], "rb")
header = file.read()
file.close()
# Normal stuff
self.assertEqual(header[:2], b"\x1f\x8b") # Gzip magic bytes
self.assertEqual(header[2], 8) # comp
self.assertEqual(header[3], 16) # comment flags set
# self.assertEqual(header[5:9], b'') # time, how to check?
self.assertEqual(header[8], 2) # xfl
self.assertEqual(header[9], 3) # os
# extra field with index
self.assertEqual(header[10:12], b"FU") # magic index bytes
self.assertEqual(header[12], 1) # version
def test_write_gen_header_no_index(self):
self.Writer._write_gen_header(Index=False)
self.Writer.close()
file = open(self.paths[0], "rb")
header = file.read()
file.close()
# Normal stuff
self.assertEqual(header[:2], b"\x1f\x8b")
self.assertEqual(header[2], 8) # comp
self.assertEqual(header[3], 0) # comment flags set
# self.assertEqual(header[5:9], b'') # time, how to check?
self.assertEqual(header[8], 2) # xfl
self.assertEqual(header[9], 3) # os
self.assertEqual(len(header), 10)
def test_allocate_index_bytes(self):
self.Writer._allocate_index_bytes()
self.Writer.close()
file = open(self.paths[0], "rb")
data = file.read()
print(data, data[1], len(data))
file.close()
max_idx_num = 80
max_idx = 8
max_offset = 8
self.assertEqual(len(data), ((max_idx + max_offset) * max_idx_num) + 1)
self.assertEqual(len(data), max_idx_num * (max_idx + max_offset) + 1)
def test_write_data(self):
test_string = b"AAAAAAAAbbbbbbbbCCCCCCCC"
self.Writer._write_data(test_string)
self.Writer.close()
Decomp = zlib.decompressobj(-zlib.MAX_WBITS)
file = open(
os.path.join(os.path.dirname(__file__), "data", "unittest.mzml"), "rb"
)
data = file.read()
file.close()
compData = data[:-8]
crc = struct.unpack("<L", data[-8:-4])[0]
isize = struct.unpack("<L", data[-4:])[0]
self.assertEqual(Decomp.decompress(compData), test_string)
self.assertEqual(crc, zlib.crc32(test_string))
self.assertEqual(isize, len(test_string) % 2 ** 32)
def test_add_data(self):
test_string = b"AAAAAAAAbbbbbbbbCCCCCCCCdddddddd"
self.Writer.add_data(test_string, 1)
self.Writer.close()
file = open(self.paths[0], "rb")
data = file.read()
file.close()
index = self.Writer.index
self.assertIn(1, index)
test_file = os.path.join(
os.path.dirname(__file__),
"data",
"uncompressed",
"CF_07062012_pH8_2_3A.mzML",
)
self.Writer = GSGW(test_file, max_idx=80, max_idx_len=8, max_offset_len=8)
self.Writer.add_data(test_string, "a")
self.Writer.close()
file = open(self.paths[0], "rb")
data = file.read()
file.close()
index = self.Writer.index
self.assertIn("a", index)
def test_write_index(self):
test_string = b"AAAAAAAAbbbbbbbbCCCCCCCCdddddddd"
# with int as id
# TODO assertions
self.Writer.add_data(test_string, 1)
self.Writer.write_index()
self.Writer.close()
file = open(self.paths[0], "rb")
data = file.read()
file.close()
index = data[
15 : 15 + (80 * 16) + 1
] # dont read header (first 15 bytes) and read idx_num * (idx_len + offset_len bytes) and zero termination
identifier = index[:8].decode("latin-1")
offset = index[8:16].decode("latin-1")
self.assertEqual(identifier.strip("\xAC"), "1")
self.assertIsInstance(offset.strip("\xAC"), str)
if __name__ == "__main__":
unittest.main(verbosity=3)
|
