def notest_queue():
"""
Testing PyChemiaQueue :
"""
if not HAS_PYMONGO or not HAS_GRIDFS:
print('PyChemiaQueue was disabled')
return
print("Testing PyChemiaQueue")
source = 'pychemia/test/data/vasp_01'
destination = tempfile.mkdtemp()
print('Destination: %s' % destination)
st = pychemia.code.vasp.read_poscar(source + os.sep + 'POSCAR')
print('Structure: \n%s' % st)
vi = pychemia.code.vasp.read_incar(source + os.sep + 'INCAR')
print('VASP Input: \n%s' % vi)
pq = pychemia.db.PyChemiaQueue()
files = [source + os.sep + 'KPOINTS']
entry_id = pq.new_entry(structure=st,
variables=vi,
code='vasp',
files=files)
nfiles = pq.db.fs.files.count()
print('Number of files: ', nfiles)
pychemia.code.vasp.write_from_queue(pq, entry_id, destination)
for i in os.listdir(source):
assert hashfile(source + os.sep + i) == hashfile(destination + os.sep +
i)
print('Files in source and destination are identical')
print(
'Adding the same entry again and testing that the number of files is unchanged'
)
entry_id = pq.new_entry(structure=st,
variables=vi,
code='vasp',
files=files)
assert nfiles == pq.db.fs.files.count()
print('The number of files remains the same ', nfiles)
shutil.rmtree(destination)
def notest_queue():
"""
Testing PyChemiaQueue :
"""
if not HAS_PYMONGO or not HAS_GRIDFS:
print('PyChemiaQueue was disabled')
return
print("Testing PyChemiaQueue")
source = 'pychemia/test/data/vasp_01'
destination = tempfile.mkdtemp()
print('Destination: %s' % destination)
st = pychemia.code.vasp.read_poscar(source + os.sep + 'POSCAR')
print('Structure: \n%s' % st)
vi = pychemia.code.vasp.read_incar(source + os.sep + 'INCAR')
print('VASP Input: \n%s' % vi)
pq = pychemia.db.PyChemiaQueue()
files = [source + os.sep + 'KPOINTS']
entry_id = pq.new_entry(structure=st, variables=vi, code='vasp', files=files)
nfiles = pq.db.fs.files.count()
print('Number of files: ', nfiles)
pychemia.code.vasp.write_from_queue(pq, entry_id, destination)
for i in os.listdir(source):
assert hashfile(source + os.sep + i) == hashfile(destination + os.sep + i)
print('Files in source and destination are identical')
print('Adding the same entry again and testing that the number of files is unchanged')
entry_id = pq.new_entry(structure=st, variables=vi, code='vasp', files=files)
assert nfiles == pq.db.fs.files.count()
print('The number of files remains the same ', nfiles)
shutil.rmtree(destination)
def add_file(self, entry_id, location, filepath):
assert (os.path.isfile(filepath))
hashcode = hashfile(filepath)
rf = open(filepath, 'rb')
filename = os.path.basename(filepath)
length = os.path.getsize(filepath)
existing = self.db.fs.files.find_one({'hash': hashcode, 'length': length, 'filename': filename})
if existing is None:
file_id = self.fs.put(rf, filename=os.path.basename(filename), hash=hashcode)
print('New file ', file_id)
self.db.pychemia_entries.update({'_id': entry_id}, {'$addToSet': {location + '.files': {'file_id': file_id,
'name': filename,
'hash': hashcode}}})
else:
file_id = existing['_id']
print('File already present ', file_id)
self.db.pychemia_entries.update({'_id': entry_id}, {'$addToSet': {location + '.files': {'file_id': file_id,
'name': filename,
'hash': hashcode}}})
def add_file(self, entry_id, location, filepath):
assert (os.path.isfile(filepath))
hashcode = hashfile(filepath)
rf = open(filepath, 'rb')
filename = os.path.basename(filepath)
length = os.path.getsize(filepath)
existing = self.db.fs.files.find_one({'hash': hashcode, 'length': length, 'filename': filename})
if existing is None:
file_id = self.fs.put(rf, filename=os.path.basename(filename), hash=hashcode)
print(('New file ', file_id))
self.db.pychemia_entries.update({'_id': entry_id}, {'$addToSet': {location + '.files': {'file_id': file_id,
'name': filename,
'hash': hashcode}}})
else:
file_id = existing['_id']
print(('File already present ', file_id))
self.db.pychemia_entries.update({'_id': entry_id}, {'$addToSet': {location + '.files': {'file_id': file_id,
'name': filename,
'hash': hashcode}}})
