def _get_connection(self, name):
""" Create a connection object to CubicWeb instance.
"""
if self.connection is None:
url = self.conf[name]["url"]
login, password = ask_credential()
self.connection = CWInstanceConnection(
url, login, password, verify=True,
server_root="/home/{0}".format(login))
return self.connection
url = "https://metagen.partenaires.cea.fr/metagen"
#############################################################################
# SNP information
# ---------------
# Define the RQL request
rql = ("Any SP, SM, CN, GN Where S is Snp, S rs_id 'rs75684916', "
"S position SP, S maf SM, S snp_chromosome C, C name CN, "
"S snp_genes G, G hgnc_name GN")
# Ask for login & password
login, password = ask_credential()
# Define a connection: disable the security certificate check
connection = CWInstanceConnection(url, login, password, verify=False)
# Execute the request
rset = connection.execute(rql)
pprint(rset)
info = {"rs75684916": {}}
for position, maf, chr_name, gene_name in rset:
info["rs75684916"]["position"] = position
info["rs75684916"]["maf"] = maf
info["rs75684916"]["chr_name"] = chr_name
info["rs75684916"].setdefault("gene_names", {})[gene_name] = {}
print("Information about SNP 'rs75684916': ")
pprint(info)
#############################################################################
# Add Gene information
#############################################################################
# Get some PLINK data
# -------------------
#
# We want to download the QC Gentic PLINK data available in IMAGEN.
# Define CubicWeb service url
url = "https://imagen2.cea.fr/database"
# Ask for login & password
print(url)
login, password = ask_credential()
# Define a connection
connection = CWInstanceConnection(url,
login,
password,
verify=True,
server_root="/home/{0}".format(login))
# Define the RQL request
rql = "Any G Where G is GenomicMeasure, G label 'QC_Genetics'"
# Create a persistent temporary directory
tmp_dir = os.path.join(os.sep, "tmp", "cwbrowser_data")
if not os.path.isdir(tmp_dir):
os.mkdir(tmp_dir)
# Execute the request
rset = connection.execute_with_sync(rql, sync_dir=tmp_dir, nb_tries=5)
pprint(rset)
# Define CubicWeb service url
url = "https://metagen.partenaires.cea.fr/metagen"
#############################################################################
# For one gene
# ------------
# Define the RQL request
rql = "Any I Where X is Gene, X hgnc_name 'BRCA2', X gene_snps S, S rs_id I"
# Ask for login & password
login, password = ask_credential()
# Define a connection: disable the security certificate check
connection = CWInstanceConnection(url, login, password, verify=False)
# Execute the request
rset = connection.execute(rql)
pprint(rset[:10])
print("...")
print("Number of SNPs associated to 'BRCA2': ", len(rset))
#############################################################################
# For a list of genes
# -------------------
# Define the RQL request
rql = ("Any N, I Where X is Gene, X hgnc_name IN ('BRCA2', 'TOMM22P2'), "
"X hgnc_name N, X gene_snps S, S rs_id I")
url = "https://imagen2.cea.fr/database"
#############################################################################
# List RAW types
# --------------
#
# We first list all the available RAW data types.
# Define the RQL request
rql = "DISTINCT Any L ORDERBY L Where S is Scan, S label L"
# Ask for login & password
login, password = ask_credential()
# Define a connection
connection = CWInstanceConnection(url, login, password, verify=True,
server_root="/home/{0}".format(login))
# Execute the request
rset = connection.execute(rql)
pprint(rset)
#############################################################################
# Get T1 data
# -----------
#
# We want to list all the available T1 data and associated subjects.
# Define the RQL request
rql = ("Any S, C Where S is Scan, S subject SU, SU code_in_study C, S label "
"'ADNI_MPRAGE'")
return snp_data
#############################################################################
# Get some PLINK data
# -------------------
#
# We want to download the QC Gentic PLINK data available in IMAGEN.
# Define CubicWeb service url
url = "https://imagen2.cea.fr/database"
# Ask for login & password
print(url)
login, password = ask_credential()
# Define a connection
connection = CWInstanceConnection(url, login, password, verify=True,
server_root="/home/{0}".format(login))
# Define the RQL request
rql = "Any G Where G is GenomicMeasure, G label 'QC_Genetics'"
# Create a persistent temporary directory
tmp_dir = os.path.join(os.sep, "tmp", "cwbrowser_data")
if not os.path.isdir(tmp_dir):
os.mkdir(tmp_dir)
# Execute the request
rset = connection.execute_with_sync(rql, sync_dir=tmp_dir, nb_tries=5)
pprint(rset)
# Unzip the downloaded file
zip_file = rset[0][0]
#############################################################################
# List questionnaires
# -------------------
#
# We first list all the available questionnaires.
# Define the RQL request
rql = "DISTINCT Any QN ORDERBY QN Where Q is Questionnaire, Q name QN"
# Ask for login & password
login, password = ask_credential()
# Define a connection
connection = CWInstanceConnection(url,
login,
password,
verify=True,
server_root="/home/{0}".format(login))
# Execute the request
rset = connection.execute(rql)
pprint(rset)
#############################################################################
# Get the 'PSYTOOLS-adsr-youth' questionnaire
# -------------------------------------------
#
# We want to get all the available 'PSYTOOLS-adsr-youth' questionnaire data.
# We ask the system for all the subjects and all the timepoints.
# Define the RQL request