class GenAPI(object):
"""
Python module that leverages Genesis PyAPI (Python API for accsess to DictyExpress database).
It supports connection to the server and data retrieval functionalities.
"""
def __init__(self, email=DEFAULT_EMAIL, password=DEFAULT_PASSWD, url=DEFAULT_URL):
self._gen = Genesis(email, password, url)
self.email = email
def fetch_etc_objects(self, callback=lambda: None):
""" Function downloads all available :obj:`GenData` etc objects from DictyExpress database.
Returns:
:obj:`list`: of :obj:`GenData` objects
"""
cbc = CallBack(1, callback)
try:
list_of_experiments = self._gen.api.data.get(case_ids__contains='5535115cfad58d5e03006217', status='done',
type__startswith='data:etc:')['objects']
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError('Server not accessible, check your connection.') from e
cbc()
store_experiments = [GenData(exp, self._gen) for exp in list_of_experiments]
cbc.end()
return store_experiments
def download_etc_data(self, gen_data_id, callback=lambda: None):
""" Function downloads etc data of a chosen experiment from the server.
Args:
gen_data_id (str): id of :obj:`GenData` object to download.
Returns:
:obj:`dict`: data in json like format
"""
cbc = CallBack(3, callback, callbacks=70)
try:
response = next(self._gen.download([gen_data_id], 'output.etcfile'))
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError('Server not accessible, check your connection.') from e
cbc()
if not response.ok:
response.raise_for_status()
response_gzipped = io.BytesIO(response.content)
cbc()
response_content = io.TextIOWrapper(gzip.GzipFile(fileobj=response_gzipped), encoding="utf-8")
cbc()
try:
json_object = json.load(response_content)
except ValueError as e:
raise ValueError('Downloaded data is not a valid JSON') from e
cbc.end()
return json_object
def etc_to_table(self, etc_json, time_var=False, callback=lambda: None):
""" Converts data from Json to :obj:`Orange.data.table`
Args:
etc_json (dict): Data in json like format
time_var (bool): Create column of time points. Default is set to False.
Returns:
:obj:`Orange.data.Table`
"""
cbc = CallBack(2, callback, callbacks=30)
variables = []
time_point = 1
for time in etc_json['etc']['timePoints']:
var = ContinuousVariable('TP ' + str(time_point))
var.attributes['Time'] = str(time)
variables.append(var)
time_point += 1
meta_attr = StringVariable.make('Gene')
domain = Domain(variables, metas=[meta_attr])
cbc()
table = []
for row in etc_json['etc']['genes']:
gene_expression = [exp for exp in etc_json['etc']['genes'][row]]
gene_expression.append(row)
table.append(gene_expression)
orange_table = Table(domain, table)
if time_var:
orange_table = transpose_table(orange_table)
cbc()
cbc.end()
return orange_table
class GenAPI:
"""Python module that leverages Genesis PyAPI (Python API for accsess to DictyExpress database).
It supports connection to the server and data retrieval functionalities.
"""
def __init__(self,
email=DEFAULT_EMAIL,
password=DEFAULT_PASSWD,
url=DEFAULT_URL):
self._gen = Genesis(email, password, url)
self.email = email
self._data_endpoint = url + '/data/'
@staticmethod
def clear_cache():
with requests_cache.enabled(cache_name=GENAPI_CACHE,
backend=CACHE_BACKEND):
requests_cache.clear()
def get_cached_ids(self):
with requests_cache.enabled(cache_name=GENAPI_CACHE,
backend=CACHE_BACKEND):
cached_object = requests_cache.get_cache()
responses = [
cached_object.get_response(response)
for response in cached_object.responses
]
gen_ids = []
for url in [response.url for response in responses]:
gen_id = re.search(r'{}(.*?)/'.format(self._data_endpoint),
url)
if gen_id is not None:
gen_ids.append(gen_id.group(1))
return gen_ids
def fetch_etc_objects(self, *args, **kwargs):
"""Function downloads all available :obj:`GenData` etc objects from DictyExpress database.
:rtype: list of GenData objects
"""
with requests_cache.enabled(cache_name=GENAPI_CACHE,
backend=CACHE_BACKEND):
try:
# Note: this is hardcoded for now. When we port this module to Resolwe platform
# data retrieval will be different
list_of_experiments = self._gen.api.data.get(
case_ids__contains='5535115cfad58d5e03006217',
status='done',
type__startswith='data:etc:')['objects']
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError(
'Server not accessible, check your connection.') from e
store_experiments = [
GenData(exp, self._gen) for exp in list_of_experiments
]
return store_experiments
def download_etc_data(self, gen_data_id, *args, **kwargs):
"""Function downloads etc data of a chosen experiment from the server.
:param gen_data_id: id of GeneData object
:type gen_data_id: str
:rtype: data in json like format
"""
table_name = kwargs.get("table_name", '')
with requests_cache.enabled(cache_name=GENAPI_CACHE,
backend=CACHE_BACKEND):
try:
response = next(
self._gen.download([gen_data_id], 'output.etcfile'))
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError(
'Server not accessible, check your connection.') from e
return response_to_json(response), table_name
class GenAPI:
def __init__(self,
email=DEFAULT_EMAIL,
password=DEFAULT_PASSWD,
url=DEFAULT_URL):
""" Python module that leverages Genesis PyAPI (Python API for accsess to DictyExpress database).
It supports connection to the server and data retrieval functionalities.
Args:
email (str):
password (str):
url (str):
"""
self._gen = Genesis(email, password, url)
self.email = email
self._data_endpoint = url + '/data/'
def get_cached_ids(self):
with requests_cache.enabled(cache_name=cache_name,
backend=cache_backend):
cached_object = requests_cache.core.get_cache()
responses = [
cached_object.get_response_and_time(response)
for response in cached_object.responses
]
gen_ids = []
for url in [response.url for response, _ in responses]:
gen_id = re.search(r'{}(.*?)/'.format(self._data_endpoint),
url)
if gen_id is not None:
gen_ids.append(gen_id.group(1))
return gen_ids
def fetch_etc_objects(self, **kwargs):
""" Function downloads all available :obj:`GenData` etc objects from DictyExpress database.
Returns:
:obj:`list`: :obj:`GenData` objects
"""
callback = kwargs.get("progress_callback", None)
with requests_cache.enabled(cache_name=cache_name,
backend=cache_backend):
try:
# Note: this is hardcoded for now. When we port this module to Resolwe platform
# data retrieval will be different
list_of_experiments = self._gen.api.data.get(
case_ids__contains='5535115cfad58d5e03006217',
status='done',
type__startswith='data:etc:')['objects']
if callback:
callback.emit()
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError(
'Server not accessible, check your connection.') from e
store_experiments = [
GenData(exp, self._gen) for exp in list_of_experiments
]
if callback:
callback.emit()
return store_experiments
def download_etc_data(self, gen_data_id, **kwargs):
""" Function downloads etc data of a chosen experiment from the server.
Args:
gen_data_id (str): id of :obj:`GenData` object to download.
Returns:
:obj:`dict`: data in json like format
"""
callback = kwargs.get("progress_callback", None)
table_name = kwargs.get("table_name", '')
with requests_cache.enabled(cache_name=cache_name,
backend=cache_backend):
try:
response = next(
self._gen.download([gen_data_id], 'output.etcfile'))
# TODO: maybe edit Genesis module to support callback?
if callback:
callback.emit()
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError(
'Server not accessible, check your connection.') from e
return response_to_json(response), table_name
class GenAPI(object):
"""
Python module that leverages Genesis PyAPI (Python API for accsess to DictyExpress database).
It supports connection to the server and data retrieval functionalities.
"""
def __init__(self,
email=DEFAULT_EMAIL,
password=DEFAULT_PASSWD,
url=DEFAULT_URL):
self._gen = Genesis(email, password, url)
self.email = email
def fetch_etc_objects(self, callback=lambda: None):
""" Function downloads all available :obj:`GenData` etc objects from DictyExpress database.
Returns:
:obj:`list`: of :obj:`GenData` objects
"""
cbc = CallBack(1, callback)
try:
list_of_experiments = self._gen.api.data.get(
case_ids__contains='5535115cfad58d5e03006217',
status='done',
type__startswith='data:etc:')['objects']
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError(
'Server not accessible, check your connection.') from e
cbc()
store_experiments = [
GenData(exp, self._gen) for exp in list_of_experiments
]
cbc.end()
return store_experiments
def download_etc_data(self, gen_data_id, callback=lambda: None):
""" Function downloads etc data of a chosen experiment from the server.
Args:
gen_data_id (str): id of :obj:`GenData` object to download.
Returns:
:obj:`dict`: data in json like format
"""
cbc = CallBack(3, callback, callbacks=70)
try:
response = next(self._gen.download([gen_data_id],
'output.etcfile'))
except requests.exceptions.ConnectionError as e:
raise requests.exceptions.ConnectionError(
'Server not accessible, check your connection.') from e
cbc()
if not response.ok:
response.raise_for_status()
response_gzipped = io.BytesIO(response.content)
cbc()
response_content = io.TextIOWrapper(
gzip.GzipFile(fileobj=response_gzipped), encoding="utf-8")
cbc()
try:
json_object = json.load(response_content)
except ValueError as e:
raise ValueError('Downloaded data is not a valid JSON') from e
cbc.end()
return json_object
def etc_to_table(self, etc_json, time_var=False, callback=lambda: None):
""" Converts data from Json to :obj:`Orange.data.table`
Args:
etc_json (dict): Data in json like format
time_var (bool): Create column of time points. Default is set to False.
Returns:
:obj:`Orange.data.Table`
"""
cbc = CallBack(2, callback, callbacks=30)
variables = []
time_point = 1
for time in etc_json['etc']['timePoints']:
var = ContinuousVariable('TP ' + str(time_point))
var.attributes['Time'] = str(time)
variables.append(var)
time_point += 1
meta_attr = StringVariable.make('Gene')
domain = Domain(variables, metas=[meta_attr])
cbc()
table = []
for row in etc_json['etc']['genes']:
gene_expression = [exp for exp in etc_json['etc']['genes'][row]]
gene_expression.append(row)
table.append(gene_expression)
orange_table = Table(domain, table)
if time_var:
orange_table = transpose_table(orange_table)
cbc()
cbc.end()
return orange_table