def get_plugin_and_folder(inputzip=None, inputdir=None, inputfile=None):
""" Main function. """
if (inputzip and inputdir) \
or (inputzip and inputfile) \
or (inputdir and inputfile):
raise MQ2Exception('You must provide either a zip file or a '
'directory or an input file as input.')
if not inputzip and not inputdir and not inputfile:
raise MQ2Exception('You must provide either a zip file or a '
'directory or an input file as input.')
# retrieve input: file, directory, zip
if inputzip:
tmp_folder = set_tmp_folder()
extract_zip(inputzip, tmp_folder)
elif inputfile:
tmp_folder = inputfile
else:
tmp_folder = inputdir
# retrieve the plugins
plugins = load('MQ2.plugins', subclasses=PluginInterface)
LOG.debug('Plugin loaded: %s' % [plugin.name for plugin in plugins])
# keep only the plugins that will work
plugins = [plugin for plugin in plugins if plugin.is_applicable()]
LOG.debug('Plugin applicable: %s' % [plugin.name for plugin in plugins])
# keep only the plugins that have the file(s) they need
if inputfile:
plugins = [
plugin for plugin in plugins if plugin.valid_file(tmp_folder)
]
else:
plugins = [
plugin for plugin in plugins if plugin.get_files(tmp_folder)
]
LOG.debug('Plugin w/ valid input: %s' %
[plugin.name for plugin in plugins])
if len(plugins) > 1:
raise MQ2Exception('Your dataset contains valid input for '
'several plugins.')
if len(plugins) == 0:
raise MQ2Exception('Invalid dataset: your input cannot not be '
'processed by any of the current plugins.')
plugin = plugins[0]
return (plugin, tmp_folder)
def get_plugin_and_folder(inputzip=None, inputdir=None, inputfile=None):
""" Main function. """
if (inputzip and inputdir) \
or (inputzip and inputfile) \
or (inputdir and inputfile):
raise MQ2Exception('You must provide either a zip file or a '
'directory or an input file as input.')
if not inputzip and not inputdir and not inputfile:
raise MQ2Exception('You must provide either a zip file or a '
'directory or an input file as input.')
# retrieve input: file, directory, zip
if inputzip:
tmp_folder = set_tmp_folder()
extract_zip(inputzip, tmp_folder)
elif inputfile:
tmp_folder = inputfile
else:
tmp_folder = inputdir
# retrieve the plugins
plugins = load('MQ2.plugins', subclasses=PluginInterface)
LOG.debug('Plugin loaded: %s' % [plugin.name for plugin in plugins])
# keep only the plugins that will work
plugins = [plugin for plugin in plugins if plugin.is_applicable()]
LOG.debug('Plugin applicable: %s' % [plugin.name for plugin in plugins])
# keep only the plugins that have the file(s) they need
if inputfile:
plugins = [plugin for plugin in plugins
if plugin.valid_file(tmp_folder)]
else:
plugins = [plugin for plugin in plugins
if plugin.get_files(tmp_folder)]
LOG.debug('Plugin w/ valid input: %s' %
[plugin.name for plugin in plugins])
if len(plugins) > 1:
raise MQ2Exception('Your dataset contains valid input for '
'several plugins.')
if len(plugins) == 0:
raise MQ2Exception('Invalid dataset: your input cannot not be '
'processed by any of the current plugins.')
plugin = plugins[0]
return (plugin, tmp_folder)
def get_mapqtl_session(session_id):
""" Retrieve the list of MapQTL session available.
@param session_id the session identifier uniquely identifying the
MapQTL zip file and the JoinMap map file. The session identifier
also uniquely identifies the folder in which are the files uploaded.
"""
folder = os.path.join(UPLOAD_FOLDER, session_id)
tmp_folder = None
sessions = []
try:
tmp_folder = set_tmp_folder()
extract_zip(os.path.join(folder, 'input.zip'), tmp_folder)
filelist = []
for root, dirs, files in os.walk(tmp_folder):
for filename in files:
if filename.startswith('Session') \
and filename.endswith('.mqo'):
session = filename.split()[1].strip()
if session not in sessions:
sessions.append(session)
except IOError, err:
raise MQ2NoSuchSessionException(err)
def get_mapqtl_session(session_id):
""" Retrieve the list of MapQTL session available.
@param session_id the session identifier uniquely identifying the
MapQTL zip file and the JoinMap map file. The session identifier
also uniquely identifies the folder in which are the files uploaded.
"""
folder = os.path.join(UPLOAD_FOLDER, session_id)
tmp_folder = None
sessions = []
try:
tmp_folder = set_tmp_folder()
extract_zip(os.path.join(folder, 'input.zip'), tmp_folder)
filelist = []
for root, dirs, files in os.walk(tmp_folder):
for filename in files:
if filename.startswith('Session') \
and filename.endswith('.mqo'):
session = filename.split()[1].strip()
if session not in sessions:
sessions.append(session)
except IOError, err:
raise MQ2NoSuchSessionException(err)