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dictionaries. Each dictionary corresponds to one experiment.
.. doctest::
from bioservices import GeneProf
g = GeneProf(verbose=False)
experiments = g.get_list_experiments(with_outputs=True)
"""
frmt = self._check_format(frmt)
params = {}
for key in kargs.keys():
if key not in ["with_ats", "with_samples", "with_inputs",
"with_outputs", "with_workflow", "with_all_data",
"only_user_experiments", "key"]:
raise BioServicesError("invalid parameter (%s) provided" % key)
params[key] = kargs.get(key)
params = self._clean_parameters(params)
res =self.http_get("exp/list." + frmt, frmt=frmt, params=params)
if frmt == "json":
try:
res = res['experiments']
except:
pass
return res
s.list("hsa") # returns the entire list of human genes
s.list("T01001") # same as above
s.list("hsa:10458+ece:Z5100") # returns the list of a human gene and an E.coli O157 gene
s.list("cpd:C01290+gl:G00092")# returns the list of a compound entry and a glycan entry
s.list("C01290+G00092") # same as above
"""
url = "list"
if query:
#can be something else than a database so we can not use checkDB
#self._checkDB(database, mode="list")
url += "/" + query
if organism:
if organism not in self.organismIds:
self.logging.error("""Invalid organism provided (%s). See the organismIds attribute""" % organism)
raise BioServicesError("Not a valid organism")
if query not in ["pathway", "module"]:
self.logging.error("""
If organism is set, then the first argument
(database) must be either 'pathway' or 'module'. You provided %s""" % query)
raise
url += "/" + organism
res = self.http_get(url, "txt")
return res
def _check_id(self, Id):
try:
Id = int(Id)
except:
pass
if Id not in self.ids_exp and Id not in self.rigid_ids_exp:
raise BioServicesError("Incorrect ids provides. See ids and rigid_ids attributes.")
def _check_kargs(self, kargs, valid_keys):
for key in kargs.keys():
if key not in valid_keys:
raise BioServicesError("invalid parameter (%s) provided" % key)
def _check_reference(self, ref):
if ref not in self.valid_species:
raise BioServicesError("Incorrect reference. check attribute :attr:`valid_species`.")