def makeBundle(self, localParentPath, subDirList):
""" Bundle the subdirectories of the input parent directory path.
Args:
localParentPath (str): local parent directory path containing the bundling targets
subDirList (list, str): list of subdirectories of the parent path to be bundled
Returns:
(bool): True for success or False otherwise
"""
fileU = FileUtil()
dirPathList = [os.path.join(localParentPath, subDir) for subDir in subDirList]
okT = fileU.bundleTarfile(self.__localStashTarFilePath, dirPathList, mode="w:gz", recursive=True)
return okT
def buildDependenices(self, ccUrlTarget, birdUrlTarget, **kwargs):
"""Convenience method to build configuration and static dependencies for the chemical search services.
Args:
ccUrlTarget (str): path to source concatenated chemical component definition file
birdUrlTarget (str): path to the source concatenated BIRD definition file
Other options are propagated to configurations of the wrapped classes in __bootstrapConfig()
"""
try:
okT = False
ok1 = self.setConfig(ccUrlTarget=ccUrlTarget,
birdUrlTarget=birdUrlTarget,
**kwargs)
useCache = kwargs.get("useCache", False)
ok2 = self.updateChemCompIndex(useCache=useCache)
ok3 = self.updateSearchIndex(useCache=useCache)
ok4 = self.updateSearchMoleculeProvider(useCache=useCache)
okBuild = ok1 and ok2 and ok3 and ok4
if okBuild:
fileU = FileUtil()
dirPathList = [
os.path.join(self.__cachePath, subDir)
for subDir in ["chem_comp", "oe_mol", "config"]
]
okT = fileU.bundleTarfile(self.__dependTarFilePath,
dirPathList,
mode="w:gz",
recursive=True)
#
return okT and okBuild
except Exception as e:
logger.exception("Failing build with %r and %r with %s",
ccUrlTarget, birdUrlTarget, str(e))
return False
class FileUtilTests(unittest.TestCase):
def setUp(self):
self.__verbose = True
self.__pathPdbxDictionaryFile = os.path.join(TOPDIR, "rcsb",
"mock-data",
"dictionaries",
"mmcif_pdbx_v5_next.dic")
self.__pathTaxonomyFile = os.path.join(TOPDIR, "rcsb", "mock-data",
"NCBI", "names.dmp.gz")
self.__zipFileUrl = "https://inventory.data.gov/dataset/794cd3d7-4d28-4408-8f7d-84b820dbf7f2/resource/6b78ec0c-4980-4ad8-9cbd-2d6eb9eda8e7/download/myfoodapediadata.zip"
self.__xzFile = os.path.join(TOPDIR, "rcsb", "mock-data",
"MOCK_MODBASE_MODELS",
"NP_001030614.1_1.pdb.xz")
#
self.__ftpFileUrl = "ftp://ftp.wwpdb.org/pub/pdb/data/component-models/complete/chem_comp_model.cif.gz"
self.__httpsFileUrl = "https://ftp.wwpdb.org/pub/pdb/data/component-models/complete/chem_comp_model.cif.gz"
#
self.__workPath = os.path.join(HERE, "test-output")
self.__inpDirPath = os.path.join(HERE, "test-data")
self.__fileU = FileUtil()
self.__startTime = time.time()
logger.debug("Running tests on version %s", __version__)
logger.debug("Starting %s at %s", self.id(),
time.strftime("%Y %m %d %H:%M:%S", time.localtime()))
def tearDown(self):
endTime = time.time()
logger.debug("Completed %s at %s (%.4f seconds)", self.id(),
time.strftime("%Y %m %d %H:%M:%S", time.localtime()),
endTime - self.__startTime)
def testTarBundling(self):
"""Test case for tarfile bundling and unbundling"""
try:
tP = os.path.join(self.__workPath, "t0.tar.gz")
dirPath = os.path.join(self.__inpDirPath, "topdir")
ok = self.__fileU.bundleTarfile(tP, [dirPath],
mode="w:gz",
recursive=True)
self.assertTrue(ok)
numBytes = self.__fileU.size(tP)
self.assertGreaterEqual(numBytes, 250)
#
md5 = self.__fileU.hash(tP, hashType="md5")
self.assertTrue(md5 is not None)
#
ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)
self.assertTrue(ok)
#
tP = os.path.join(self.__workPath, "t1.tar.gz")
dirPathList = [
os.path.join(self.__inpDirPath, "topdir", "subdirA"),
os.path.join(self.__inpDirPath, "topdir", "subdirB")
]
ok = self.__fileU.bundleTarfile(tP,
dirPathList,
mode="w:gz",
recursive=True)
self.assertTrue(ok)
#
ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)
self.assertTrue(ok)
tP = os.path.join(self.__workPath, "t2.tar")
dirPathList = [
os.path.join(self.__inpDirPath, "topdir", "subdirA"),
os.path.join(self.__inpDirPath, "topdir", "subdirB")
]
ok = self.__fileU.bundleTarfile(tP,
dirPathList,
mode="w",
recursive=True)
self.assertTrue(ok)
#
ok = self.__fileU.unbundleTarfile(tP, dirPath=self.__workPath)
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testGetFile(self):
"""Test case for a local files and directories"""
try:
remoteLocator = self.__pathPdbxDictionaryFile
fn = self.__fileU.getFileName(remoteLocator)
# _, fn = os.path.split(remoteLocator)
lPath = os.path.join(self.__workPath, fn)
ok = self.__fileU.get(remoteLocator, lPath)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertTrue(ok)
ok = self.__fileU.isLocal(lPath)
self.assertTrue(ok)
tPath = self.__fileU.getFilePath(lPath)
self.assertEqual(lPath, tPath)
ok = self.__fileU.remove(lPath)
self.assertTrue(ok)
dPath = os.path.join(self.__workPath, "tdir")
ok = self.__fileU.mkdir(dPath)
self.assertTrue(ok)
ok = self.__fileU.remove(dPath)
self.assertTrue(ok)
ok = self.__fileU.remove(";lakdjf")
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testMoveAndCopyFile(self):
"""Test case for copying ("put") and moving ("replace") local files"""
try:
remoteLocator = self.__pathPdbxDictionaryFile
fn = self.__fileU.getFileName(remoteLocator)
# _, fn = os.path.split(remoteLocator)
lPath = os.path.join(self.__workPath, fn)
ok = self.__fileU.get(remoteLocator, lPath)
self.assertTrue(ok)
# Test copy file
dPath2 = os.path.join(self.__workPath, "tdir")
ok = self.__fileU.mkdir(dPath2)
self.assertTrue(ok)
lPath2 = os.path.join(dPath2, fn)
ok = self.__fileU.put(lPath, lPath2)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath2)
self.assertTrue(ok)
# Remove copied file (to test moving file next)
ok = self.__fileU.remove(lPath2)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath2)
self.assertFalse(ok)
# Test move file
ok = self.__fileU.replace(lPath, lPath2)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertFalse(ok)
ok = self.__fileU.exists(lPath2)
self.assertTrue(ok)
# Now clean up files and dirs
ok = self.__fileU.remove(lPath)
self.assertTrue(ok)
ok = self.__fileU.remove(dPath2)
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testZipUrl(self):
"""Test case for downloading remote zip file and extracting contents."""
try:
remoteLocator = self.__zipFileUrl
# fn = self.__fileU.getFileName(remoteLocator)
ok = self.__fileU.isLocal(remoteLocator)
self.assertFalse(ok)
#
lPath = os.path.join(self.__workPath,
self.__fileU.getFileName(self.__zipFileUrl))
ok = self.__fileU.get(remoteLocator, lPath)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertTrue(ok)
ok = self.__fileU.isLocal(lPath)
self.assertTrue(ok)
tPath = self.__fileU.getFilePath(lPath)
self.assertEqual(lPath, tPath)
fp = self.__fileU.uncompress(lPath, outputDir=self.__workPath)
ok = fp.endswith("Food_Display_Table.xlsx")
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testFtpUrl(self):
"""Test case for downloading remote file ftp protocol and extracting contents."""
try:
remoteLocator = self.__ftpFileUrl
# fn = self.__fileU.getFileName(remoteLocator)
ok = self.__fileU.isLocal(remoteLocator)
self.assertFalse(ok)
#
dirPath = os.path.join(self.__workPath, "chem_comp_models")
lPath = os.path.join(dirPath,
self.__fileU.getFileName(self.__ftpFileUrl))
ok = self.__fileU.get(remoteLocator, lPath)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertTrue(ok)
ok = self.__fileU.isLocal(lPath)
self.assertTrue(ok)
tPath = self.__fileU.getFilePath(lPath)
self.assertEqual(lPath, tPath)
fp = self.__fileU.uncompress(lPath, outputDir=dirPath)
ok = fp.endswith("chem_comp_model.cif")
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testRemote(self):
"""Test case remote status"""
try:
remoteLocator = self.__httpsFileUrl
ok = self.__fileU.isLocal(remoteLocator)
self.assertFalse(ok)
#
ok = self.__fileU.exists(remoteLocator)
self.assertTrue(ok)
size = self.__fileU.size(remoteLocator)
self.assertGreaterEqual(size, 1000)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
@unittest.skip("DrugBank example -- skipping")
def testGetDrugBankUrl(self):
"""Test case for downloading drugbank master xml file"""
try:
remoteLocator = "https://www.drugbank.ca/releases/latest/downloads/all-full-database"
un = "username"
pw = "password"
# fn = self.__fileU.getFileName(remoteLocator)
ok = self.__fileU.isLocal(remoteLocator)
self.assertFalse(ok)
#
lPath = os.path.join(self.__workPath, "db-download.zip")
ok = self.__fileU.get(remoteLocator,
lPath,
username=un,
password=pw)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertTrue(ok)
ok = self.__fileU.isLocal(lPath)
self.assertTrue(ok)
tPath = self.__fileU.getFilePath(lPath)
self.assertEqual(lPath, tPath)
self.__fileU.uncompress(lPath, outputDir=self.__workPath)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
def testXzFile(self):
"""Test case for extracting contents from xz file"""
try:
remoteLocator = self.__xzFile
fn = self.__fileU.getFileName(remoteLocator)
lPath = os.path.join(self.__workPath, fn)
ok = self.__fileU.get(remoteLocator, lPath)
self.assertTrue(ok)
ok = self.__fileU.exists(lPath)
self.assertTrue(ok)
ok = self.__fileU.isLocal(lPath)
self.assertTrue(ok)
tPath = self.__fileU.getFilePath(lPath)
self.assertEqual(lPath, tPath)
fp = self.__fileU.uncompress(lPath, outputDir=self.__workPath)
ok = fp.endswith(".pdb")
self.assertTrue(ok)
except Exception as e:
logger.exception("Failing with %s", str(e))
self.fail()
