def write_config(self, fp=None):
if fp is None:
fp = os.path.join(click.get_app_dir('datafs'), 'config.yml')
with open_filelike(fp, 'w+') as f:
f.write(yaml.dump(self.config))
def hash_file(f):
'''
Utility function for hashing file contents
Overload this function to change the file equality checking algorithm
Parameters
----------
f: file-like
File-like object or file path from which to compute checksum value
Returns
-------
checksum: dict
dictionary with {'algorithm': 'md5', 'checksum': hexdigest}
'''
md5 = hashlib.md5()
with open_filelike(f, 'rb') as f_obj:
for chunk in iter(lambda: f_obj.read(128 * md5.block_size), b''):
md5.update(chunk)
return {'algorithm': 'md5', 'checksum': md5.hexdigest()}
def get_api(profile=None, config_file=None, requirements=None):
'''
Generate a datafs.DataAPI object from a config profile
``get_api`` generates a DataAPI object based on a
pre-configured datafs profile specified in your datafs
config file.
To create a datafs config file, use the command line
tool ``datafs configure --helper`` or export an existing
DataAPI object with
:py:meth:`datafs.ConfigFile.write_config_from_api`
Parameters
----------
profile : str
(optional) name of a profile in your datafs config
file. If profile is not provided, the default
profile specified in the file will be used.
config_file : str or file
(optional) path to your datafs configuration file.
By default, get_api uses your OS's default datafs
application directory.
Examples
--------
The following specifies a simple API with a MongoDB
manager and a temporary storage service:
.. code-block:: python
>>> try:
... from StringIO import StringIO
... except ImportError:
... from io import StringIO
...
>>> import tempfile
>>> tempdir = tempfile.mkdtemp()
>>>
>>> config_file = StringIO("""
... default-profile: my-data
... profiles:
... my-data:
... manager:
... class: MongoDBManager
... kwargs:
... database_name: 'MyDatabase'
... table_name: 'DataFiles'
...
... authorities:
... local:
... service: OSFS
... args: ['{}']
... """.format(tempdir))
>>>
>>> # This file can be read in using the datafs.get_api helper function
...
>>>
>>> api = get_api(profile='my-data', config_file=config_file)
>>> api.manager.create_archive_table(
... 'DataFiles',
... raise_on_err=False)
>>>
>>> archive = api.create(
... 'my_first_archive',
... metadata = dict(description = 'My test data archive'),
... raise_on_err=False)
>>>
>>> with archive.open('w+') as f:
... res = f.write(u'hello!')
...
>>> with archive.open('r') as f:
... print(f.read())
...
hello!
>>>
>>> # clean up
...
>>> archive.delete()
>>> import shutil
>>> shutil.rmtree(tempdir)
'''
config = ConfigFile(config_file=config_file)
config.read_config()
if profile is None:
profile = config.config['default-profile']
profile_config = config.get_profile_config(profile)
default_versions = {}
if requirements is None:
requirements = config.config.get('requirements', None)
if requirements is not None and not os.path.isfile(requirements):
for reqline in re.split(r'[\r\n;]+', requirements):
if re.search(r'^\s*$', reqline):
continue
archive, version = _parse_requirement(reqline)
default_versions[archive] = version
else:
if requirements is None:
requirements = 'requirements_data.txt'
if os.path.isfile(requirements):
with open_filelike(requirements, 'r') as reqfile:
for reqline in reqfile.readlines():
if re.search(r'^\s*$', reqline):
continue
archive, version = _parse_requirement(reqline)
default_versions[archive] = version
api = APIConstructor.generate_api_from_config(profile_config)
api.default_versions = default_versions
APIConstructor.attach_manager_from_config(api, profile_config)
APIConstructor.attach_services_from_config(api, profile_config)
APIConstructor.attach_cache_from_config(api, profile_config)
return api
def read_config(self):
with open_filelike(self.config_file, 'r') as f:
config = yaml.load(f)
self.parse_configfile_contents(config)