def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.databasename = "jobs.db"
self.pathdb = self.get_database_user_directory()+"/"+self.databasename
self.log.info(" ==> "+ self.pathdb +"<==");
conn = sqlite3.connect("file:"+self.pathdb,uri=True)
c = conn.cursor()
reqSql = '''CREATE TABLE IF NOT EXISTS jobs
(
jobID INTEGER PRIMARY KEY AUTOINCREMENT,
type text,
state text,
start int,
end int ,
data text,
file text,
preview string,
requestGraph string,
variates string,
nr int
)'''
c.execute(reqSql)
conn.commit()
conn.close()
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.databasename = "endpoints.db"
self.pathdb = self.get_common_user_directory(
) + "/" + self.databasename
self.create_db()
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.databasename = "jobs.db"
self.pathdb = self.get_database_user_directory(
) + "/" + self.databasename
self.log.info(" ==> " + self.pathdb + "<==")
conn = sqlite3.connect("file:" + self.pathdb, uri=True)
c = conn.cursor()
reqSql = '''CREATE TABLE IF NOT EXISTS jobs
(
jobID INTEGER PRIMARY KEY AUTOINCREMENT,
type text,
state text,
start int,
end int ,
data text,
file text,
preview string,
requestGraph string,
nr int
)'''
c.execute(reqSql)
conn.commit()
conn.close()
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.manage_rdf_format = [
'application/rdf+xml', 'owl', 'rdf', 'n3', 'nt', 'json-ld'
]
self.log = logging.getLogger(__name__)
def __init__(self, settings, session, path, preview_limit):
ParamManager.__init__(self, settings, session)
self.timestamp = str(time.time())
self.path = path
# The name should not contain extension as dots are not allowed in rdf names
self.name = os.path.splitext(os.path.basename(path))[0]
# FIXME check name uniqueness as we remove extension (collision if uploading example.tsv and example.txt)
self.preview_limit = preview_limit
self.forced_column_types = ['entity']
self.category_values = defaultdict(set)
self.type_dict = {
'numeric' : 'xsd:decimal',
'text' : 'xsd:string',
'category': ':',
'taxon': ':',
'ref': ':',
'strand': ':',
'start': 'xsd:decimal',
'end': 'xsd:decimal',
'entity' : ':',
'entitySym' : ':',
'entity_start' : ':',
'entityGoterm' : ''}
self.delims = {
'numeric' : ('', ''),
'text' : ('"', '"'),
'category': (':', ''),
'taxon': (':', ''),
'ref': (':', ''),
'strand': (':', ''),
'start' : ('', ''),
'end' : ('', ''),
'entity' : (':', ''),
'entitySym' : (':', ''),
'entity_start' : (':', ''),
'entityGoterm' : ('"', '"')}
self.metadatas = {
'loadDate': '',
'username': getpass.getuser(),
'fileName': self.name,
'version': get_distribution('Askomics').version,
'server': '',
'graphName':''}
self.log = logging.getLogger(__name__)
self.reset_cache()
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.database_path = self.get_param("askomics.database_path")
# Create tables
self.create_user_table()
self.create_galaxy_table()
self.create_integration_table()
self.create_query_table()
self.create_endpoints_table()
def __init__(self, settings, session,
name = None, endpoint = None,
username=None, password=None,
urlupdate=None):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.name = name
self.endpoint = endpoint
self.username = username
self.password = password
self.urlupdate = urlupdate
self.allowUpdate = False
def __init__(self, settings, session, name = None, endpoint = None ,username=None, password=None,urlupdate=None,auth='Basic'):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.name = name
self.endpoint = endpoint
self.username = username
self.password = password
self.urlupdate = urlupdate
self.auth = auth
self.allowUpdate = False
if self.auth != 'Basic' and self.auth != 'Digest':
raise ValueError("Invalid Auth parameter :"+self.auth)
def __init__(self, settings, session):
'''
Manage Modules Askomics
'''
ParamManager.__init__(self, settings, session)
'''
All modules have to be composed with thes keys
'''
self.latt = ['module', 'comment', 'version', 'owl', 'rdf']
self.moduleFiles = {}
self.graph_modules = "askomics:graph:module"
self.modulesdir = 'askomics/static/modules/'
self.data = {}
def __init__(self, settings, session):
'''
Manage Modules Askomics
'''
ParamManager.__init__(self, settings, session)
'''
All modules have to be composed with thes keys
'''
self.latt = ['module','comment','version','owl','rdf']
self.moduleFiles = {}
self.graph_modules="askomics:graph:module"
self.modulesdir='askomics/static/modules/'
self.data = {}
def __init__(self, settings, session, type_dict=None, delims=None):
#FIXME: Can we get dict()s from config ?
self.type_dict = {
'Numeric' : 'xsd:decimal',
'Text' : 'xsd:string',
'Category': ':',
'Entity' : ':'} if type_dict is None else type_dict
self.delims = {
'Numeric' : ('', ''),
'Text' : ('"', '"'),
'Category': (':', ''),
'Entity' : (':', '')} if delims is None else delims
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
def __init__(self,
settings,
session,
name=None,
endpoint=None,
username=None,
password=None,
urlupdate=None):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.name = name
self.endpoint = endpoint
self.username = username
self.password = password
self.urlupdate = urlupdate
self.allowUpdate = False
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.ldap_server = self.settings['askomics.ldap_host']
self.ldap_port = self.settings['askomics.ldap_port']
# self.ldap_bind_dn = self.settings['askomics.ldap_bind_dn']
# self.ldap_bind_passwd = self.settings['askomics.ldap_bind_passwd']
self.ldap_user_search_base = self.settings['askomics.ldap_user_search_base']
self.ldap_user_filter = self.settings['askomics.ldap_user_filter']
self.ldap_username_attr = self.settings['askomics.ldap_username_attr']
self.ldap_email_attr = self.settings['askomics.ldap_email_attr']
self.username = None
self.password = None
self.email = None
def __init__(self, settings, session, username, email, password, password2):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.username = str(username)
self.email = str(email)
self.passwd = str(password)
self.passwd2 = str(password2)
self.admin = False
self.blocked = True
self.galaxy = False
# concatenate askmics salt, password and random salt and hash it with sha512 function
# see --"https://en.wikipedia.org/wiki/Salt_(cryptography)"-- for more info about salt
alpabet = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
self.randomsalt = ''.join(random.choice(alpabet) for i in range(20))
salted_pw = self.settings["askomics.salt"] + self.passwd + self.randomsalt
self.sha256_pw = hashlib.sha512(salted_pw.encode('utf8')).hexdigest()
def __init__(self, settings, session, username, email, password, password2):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.username = str(username)
self.email = str(email)
self.passwd = str(password)
self.passwd2 = str(password2)
self.admin = False
self.blocked = True
self.galaxy = False
# concatenate askmics salt, password and random salt and hash it with sha256 function
# see --"https://en.wikipedia.org/wiki/Salt_(cryptography)"-- for more info about salt
alpabet = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
self.randomsalt = ''.join(random.choice(alpabet) for i in range(20))
salted_pw = self.settings["askomics.salt"] + self.passwd + self.randomsalt
self.sha256_pw = hashlib.sha256(salted_pw.encode('utf8')).hexdigest()
def __init__(self, settings, session, path, uri_set=None):
ParamManager.__init__(self, settings, session)
self.timestamp = datetime.datetime.now().isoformat()
self.path = path
self.metadatas = {}
# The name should not contain extension as dots are not allowed in rdf names
# self.name = os.path.splitext(os.path.basename(path))[0]
self.name = os.path.basename(path)
self.alphanum_name = re.sub('[^0-9a-zA-Z]+', '_', self.name)
self.graph = 'askomics:unkown:uri:graph'
if 'graph' in self.session:
self.graph = self.session['graph']
# Graph name can't contain any non alphanumeric characters. replace all with _
self.graph = self.graph + ':' + self.alphanum_name + '_' + self.timestamp
self.log = logging.getLogger(__name__)
self.reset_cache()
self.uri = {}
pref_uri = "http://semanticweb.org/askomics/entity/"
if self.is_defined('askomics.prefix'):
pref_uri = self.get_param("askomics.prefix")
self.uri = [ pref_uri for idx in range(20) ]
if uri_set != None:
for idx,uri in uri_set.items():
if uri:
# uri have to end with # or /
if not uri.endswith('#') and not uri.endswith('/'):
uri = uri + "/"
self.uri[int(idx)] = uri
else:
self.uri[int(idx)] = self.get_param("askomics.prefix")
def __init__(self, settings, session, path, uri_set=None):
ParamManager.__init__(self, settings, session)
self.timestamp = datetime.datetime.now().isoformat()
self.path = path
self.metadatas = {}
# The name should not contain extension as dots are not allowed in rdf names
# self.name = os.path.splitext(os.path.basename(path))[0]
self.name = os.path.basename(path)
self.alphanum_name = re.sub('[^0-9a-zA-Z]+', '_', self.name)
self.graph = 'askomics:unkown:uri:graph'
if 'graph' in self.session:
self.graph = self.session['graph']
# Graph name can't contain any non alphanumeric characters. replace all with _
self.graph = self.graph + ':' + self.alphanum_name + '_' + self.timestamp
self.log = logging.getLogger(__name__)
self.reset_cache()
self.uri = {}
pref_uri = "http://semanticweb.org/askomics/entity/"
if self.is_defined('askomics.prefix'):
pref_uri = self.get_param("askomics.prefix")
self.uri = [pref_uri for idx in range(20)]
if uri_set != None:
for idx, uri in uri_set.items():
if uri:
# uri have to end with # or /
if not uri.endswith('#') and not uri.endswith('/'):
uri = uri + "/"
self.uri[int(idx)] = uri
else:
self.uri[int(idx)] = self.get_param("askomics.prefix")
def __init__(self, settings, session, path):
ParamManager.__init__(self, settings, session)
self.timestamp = datetime.datetime.now().isoformat()
self.path = path
# The name should not contain extension as dots are not allowed in rdf names
self.name = os.path.splitext(os.path.basename(path))[0]
# FIXME check name uniqueness as we remove extension (collision if uploading example.tsv and example.txt)
self.log = logging.getLogger(__name__)
self.metadatas = {
'loadDate': '',
'username': getpass.getuser(),
'fileName': self.name,
'version': get_distribution('Askomics').version,
'server': '',
'graphName':''}
self.reset_cache()
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.manage_rdf_format = ['application/rdf+xml','owl','rdf','n3','nt','json-ld']
self.log = logging.getLogger(__name__)
def __init__(self, settings, session, url, apikey):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.url = url
self.apikey = apikey
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
def __init__(self, settings, session, auth_type='local'):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.auth_type = auth_type
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.databasename = "endpoints.db"
self.pathdb = self.get_common_user_directory()+"/"+self.databasename
self.create_db()
def __init__(self, settings, session, dico={}):
ParamManager.__init__(self, settings, session)
CounterManager.__init__(self, dico)
self.log = logging.getLogger(__name__)
def __init__(self, settings, session):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
def __init__(self, settings, session, url, apikey):
ParamManager.__init__(self, settings, session)
self.log = logging.getLogger(__name__)
self.url = url
self.apikey = apikey
