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"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into build/test and run the test file directly:
python ../../test/testbabel.py
In both cases, the test file is run directly from the source folder,
and so you can quickly develop the tests and try them out.
"""
import os
import re
import sys
import unittest
from subprocess import Popen, PIPE
def run_exec(*args):
"""Run one of OpenBabel's executables
With two arguments (stdin, commandline) it pipes
the stdin through the executable.
Example: run_exec("CC(=O)Cl", "babel -ismi -oinchi")
Return a tuple (stdout, stderr)
"""
if len(args) == 2:
text, commandline = args
elif len(args) == 1:
text, commandline = "", args[0]
else:
raise Exception("One or two arguments expected")
broken = commandline.encode().split()
exe = executable(broken[0].decode())
# Note that bufsize = -1 means default buffering
# Without this, it's unbuffered and it takes 10x longer on MacOSX
if text:
p = Popen([exe] + broken[1:],
stdin=PIPE, stdout=PIPE, stderr=PIPE, bufsize=1)
stdout, stderr = p.communicate(text.encode())
else:
p = Popen([exe] + broken[1:],
stdout=PIPE, stderr=PIPE, bufsize=-1)
stdout, stderr = p.communicate()
return stdout.decode(), stderr.decode()
def executable(name):
"""Return the full path to an executable"""
suffix = ""
folder = "bin"
if sys.platform == "win32":
suffix = ".exe"
folder = os.path.join(folder, "Release")
return os.path.join("..", folder, name + suffix)
def log(text):
"""Convenience function for debugging tests
The log file (log.txt) is created in build/test
"""
output = open("log.txt", "a")
print >> output, text
output.close()
class BaseTest(unittest.TestCase):
"""A base class for test classes that adds additional
test methods"""
def canFindExecutable(self, name):
fullpath = executable(name)
self.assertTrue(os.path.isfile(fullpath),
"'%s' executable not found at %s" % (name, fullpath))
def canFindFile(self, filename):
self.assertTrue(os.path.isfile(filename),
"Cannot find the file '%s'" % filename)
def getTestFile(self, filename):
here = sys.path[0]
fullpath = os.path.join(here, "files", filename)
self.canFindFile(fullpath)
return fullpath
def assertConverted(self, stderr, N):
"""Assert that N molecules were converted."""
pat = "(-?\d.*) molecule(?:s?) converted"
lines = stderr.split("\n")
convertedline = [line for line in lines if re.match(pat, line)]
if len(convertedline) == 0:
self.fail("Cannot find the number of molecules converted")
conversion_no = int(re.findall(pat, convertedline[0])[0])
self.assertEqual(N, conversion_no,
"Number of molecules converted is %d "
"but should be %d" % (conversion_no, N))
class testBabel(BaseTest):
"""A series of tests relating to the Babel executable"""
def testSMItoInChI(self):
self.canFindExecutable("babel")
output, error = run_exec("CC(=O)Cl", "babel -ismi -oinchi")
self.assertEqual(output.rstrip(), "InChI=1S/C2H3ClO/c1-2(3)4/h1H3")
if __name__ == "__main__":
unittest.main()
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