def __init__(self, db_string, context='cnf', jobs=1, tlim=5000, mlim=2000, flim=1000, separator=" ", join_type="LEFT", verbose=False):
self.databases = db_string.split(os.pathsep)
self.context = context
self.jobs = jobs
self.tlim = tlim # time limit (seconds)
self.mlim = mlim # memory limit (mega bytes)
self.flim = flim # file size limit (mega bytes)
self.separator = separator
self.join_type = join_type
self.verbose = verbose
self.database = Database(self.databases, self.verbose)
def test_create_db(self):
os.remove(self.TDB)
with Database([self.TDB], verbose=True) as db:
assert (Schema.is_database(self.TDB))
assert (len(db.get_databases()) == 1)
assert (len(db.get_features()) == 0)
assert (len(db.get_tables()) == 0)
with Database([self.TDB], verbose=True) as db:
assert (db.dpath(self.TDBN) == self.TDB)
assert (db.dmain(self.TDBN))
assert (len(db.dcontexts(self.TDBN)) == 0)
assert (len(db.dtables(self.TDBN)) == 0)
assert (len(db.dviews(self.TDBN)) == 0)
def test_create_unique_feature(self):
os.remove(self.TDB)
FEAT = "featB"
NAME = self.TDBN + ".features"
with Database([self.TDB], verbose=True) as db:
db.create_feature(FEAT, "empty")
assert (FEAT in db.get_features())
assert ("features" in db.get_tables())
with Database([self.TDB], verbose=True) as db:
assert (db.ftable(FEAT) == NAME)
assert (db.fcolumn(FEAT) == FEAT)
assert (db.fdefault(FEAT) == "empty")
assert (not db.fvirtual(FEAT))
assert (db.fcontext(FEAT) == "cnf")
assert (db.fdatabase(FEAT) == self.TDBN)
def test_create_feature(self):
os.remove(self.TDB)
FEAT = "featA"
NAME = self.TDBN + "." + FEAT
with Database([self.TDB], verbose=True) as db:
db.create_feature(FEAT)
assert (FEAT in db.get_features())
assert (FEAT in db.get_tables())
with Database([self.TDB], verbose=True) as db:
assert (db.ftable(FEAT) == NAME)
assert (db.fcolumn(FEAT) == "value")
assert (db.fdefault(FEAT) == None)
assert (not db.fvirtual(FEAT))
assert (db.fcontext(FEAT) == "cnf")
assert (db.fdatabase(FEAT) == self.TDBN)
def get_features(self, path=None):
if path == None:
return self.database.tables_and_views()
elif path in self.databases:
with Database([path]) as db:
return db.tables_and_views()
else:
return []
def get_virtual_features(self, path=None):
if path == None:
return self.database.views()
elif path in self.databases:
with Database([path]) as db:
return db.views()
else:
return []
def get_feature_info(self, name, path=None):
if path is None:
system_record = self.database.system_record(name)
meta_record = self.database.meta_record(name)
return {**system_record, **meta_record}
else:
with Database(path) as db:
system_record = db.system_record(name)
meta_record = db.meta_record(name)
return {**system_record, **meta_record}
def set_attributes_locked(self, hash, attributes):
self.mutex.acquire()
try:
# create new connection due to limitations of multi-threaded use (cursor initialization issue)
with Database(self.databases) as db:
for attr in attributes:
cmd, name, value = attr[0], attr[1], attr[2]
db.submit('{} INTO {} (hash, value) VALUES ("{}", "{}")'.format(cmd, name, hash, value))
finally:
self.mutex.release()
def test_insert_values(self):
os.remove(self.TDB)
FEAT = "letter"
NAME = self.TDBN + ".features"
with Database([self.TDB], verbose=True) as db:
db.create_feature(FEAT, "empty")
db.set_values(FEAT, "a", ['1', '2', '3'])
db.set_values(FEAT, "b", ['4', '5', '6'])
q = GBDQuery(db)
r = db.query(q.build_query(resolve=[FEAT]))
eprint(r)
assert (r == [('1', 'a'), ('2', 'a'), ('3', 'a'), ('4', 'b'),
('5', 'b'), ('6', 'b')])
r = db.query(q.build_query("{}=a".format(FEAT), resolve=[FEAT]))
assert (r == [('1', 'a'), ('2', 'a'), ('3', 'a')])
def __enter__(self):
self.database = Database(self.databases, self.verbose)
with ExitStack() as stack:
stack.enter_context(self.database)
self._stack = stack.pop_all()
return self
class GbdApi:
# Create a new GbdApi object which operates on the given databases
def __init__(self,
db_string,
jobs=1,
separator=" ",
join_type="LEFT",
verbose=False):
self.databases = db_string.split(":")
self.jobs = jobs
self.mutex = multiprocessing.Lock()
self.separator = separator
self.join_type = join_type
self.verbose = verbose
def __enter__(self):
self.database = Database(self.databases, self.verbose)
with ExitStack() as stack:
stack.enter_context(self.database)
self._stack = stack.pop_all()
return self
def __exit__(self, exc_type, exc, traceback):
self._stack.__exit__(exc_type, exc, traceback)
# Calculate GBD hash
@staticmethod
def hash_file(path):
return gbd_hash(path)
# Import data from CSV file
def import_file(self, path, key, source, target):
if not self.feature_exists(target):
print("Feature {} does not exist. Import canceled.".format(target))
with open(path, newline='') as csvfile:
csvreader = csv.DictReader(csvfile,
delimiter=self.separator,
quotechar='\'')
lst = [(row[key].strip(), row[source].strip()) for row in csvreader
if row[source] and row[source].strip()]
print("Inserting {} values into group {}".format(len(lst), target))
self.database.bulk_insert(target, lst)
# Initialize table 'local' with instances found under given path
def init_database(self, path=None):
eprint('Initializing local path entries {} using {} cores'.format(
path, self.jobs))
if self.jobs == 1 and multiprocessing.cpu_count() > 1:
eprint("Activate parallel initialization using --jobs={}".format(
multiprocessing.cpu_count()))
benchmark_administration.remove_benchmarks(self.database)
benchmark_administration.register_benchmarks(self, self.database, path,
self.jobs)
def bootstrap(self, named_algo, hashes):
bootstrap.bootstrap(self, self.database, named_algo, hashes, self.jobs)
def get_databases(self):
return self.databases
# Get all features (or those of given db)
def get_features(self, path=None):
if path == None:
return self.database.tables_and_views()
elif path in self.databases:
with Database([path]) as db:
return db.tables_and_views()
else:
return []
# Get all material features (or those of given db)
def get_material_features(self, path=None):
if path == None:
return self.database.tables()
elif path in self.databases:
with Database([path]) as db:
return db.tables()
else:
return []
# Get all virtual features (or those of given db)
def get_virtual_features(self, path=None):
if path == None:
return self.database.views()
elif path in self.databases:
with Database([path]) as db:
return db.views()
else:
return []
# Check for existence of given feature
def feature_exists(self, name):
return name in self.database.tables()
# Creates the given feature
def create_feature(self, name, default_value=None):
self.database.create_table(name, default_value)
# Removes the given feature
def remove_feature(self, name):
self.database.delete_table(name)
# Rename the given feature
def rename_feature(self, old_name, new_name):
self.database.rename_table(old_name, new_name)
def get_feature_size(self, name):
if not name in self.get_features():
raise ValueError("Attribute '{}' is not available".format(name))
return self.database.table_size(name)
# Retrieve information about a specific feature
def get_feature_info(self, name, path=None):
if path is None:
system_record = self.database.system_record(name)
meta_record = self.database.meta_record(name)
return {**system_record, **meta_record}
else:
with Database(path) as db:
system_record = db.system_record(name)
meta_record = db.meta_record(name)
return {**system_record, **meta_record}
def meta_set(self, feature, meta_feature, value):
self.database.meta_set(feature, meta_feature, value)
# clears sepcified meta-features of feature,
# or clears all meta-features if meta_feature is not specified
def meta_clear(self, feature, meta_feature=None):
self.database.meta_clear(feature, meta_feature)
def callback_set_attributes_locked(self, arg):
self.set_attributes_locked(arg['hashvalue'], arg['attributes'])
def set_attributes_locked(self, hash, attributes):
self.mutex.acquire()
try:
# create new connection due to limitations of multi-threaded use (cursor initialization issue)
with Database(self.databases) as db:
for attr in attributes:
cmd, name, value = attr[0], attr[1], attr[2]
db.submit(
'{} INTO {} (hash, value) VALUES ("{}", "{}")'.format(
cmd, name, hash, value))
finally:
self.mutex.release()
# Set the attribute value for the given hashes
def set_attribute(self, feature, value, hash_list, force):
if not feature in self.get_material_features():
raise ValueError(
"Attribute '{}' is not available (or virtual)".format(feature))
values = ', '.join(
['("{}", "{}")'.format(hash, value) for hash in hash_list])
if self.database.table_unique(feature):
if force:
self.database.submit(
'DELETE FROM {} WHERE hash IN ("{}")'.format(
feature, '", "'.join(hash_list)))
try:
self.database.submit(
'REPLACE INTO {} (hash, value) VALUES {}'.format(
feature, values))
except sqlite3.IntegrityError as err:
#thrown if existing value is not the default value or equal to the value to be set
#requires the unique on insert-triggers introduced in version 3.0.9
eprint(str(err) + ": Use the force!")
else:
try:
self.database.submit(
'INSERT INTO {} (hash, value) VALUES {}'.format(
feature, values))
except Exception as err:
#thrown if hash+value combination is already set
#requires the unique constraint introduced in version 3.0.9
eprint(err)
# Remove the attribute value for the given hashes
def remove_attributes(self, feature, hash_list):
if not feature in self.get_material_features():
raise ValueError(
"Attribute '{}' is not available (or virtual)".format(feature))
self.database.submit("DELETE FROM {} WHERE hash IN ('{}')".format(
feature, "', '".join(hash_list)))
def set_tag(self, tag_feature, tag_value, hash_list):
self.database.set_tag(tag_feature, tag_value, hash_list)
def search(self, feature, hashvalue):
if not feature in self.get_features():
raise ValueError("Attribute '{}' is not available".format(feature))
return self.database.value_query(
"SELECT value FROM {} WHERE hash = '{}'".format(
feature, hashvalue))
def query_search(self,
query=None,
hashes=[],
resolve=[],
collapse="GROUP_CONCAT",
group_by="hash"):
try:
sql = search.build_query(query, hashes, resolve or [], collapse,
group_by or "hash", self.join_type)
return self.database.query(sql)
except sqlite3.OperationalError as err:
raise ValueError("Query error in database '{}': {}".format(
self.databases, err))
except tatsu.exceptions.FailedParse as err:
raise ValueError("Query error in parser: {}.".format(err.message))
def calculate_par2_score(self, query, feature):
info = self.database.meta_record(feature)
if not "timeout" in info:
eprint(
"Time-limit 'timeout' missing in meta-record of table '{}'.".
format(feature))
eprint("Unable to calculate score.")
return
if not "memout" in info:
eprint(
"Memory-limit 'memout' missing in meta-record of table '{}'.".
format(feature))
if not "machine" in info:
eprint(
"Machine-id 'machine' missing in meta-record of table '{}'.".
format(feature))
timeout = int(info["timeout"])
times = self.query_search(query, [], [feature])
score = 0
penalized = set()
for time in times:
if is_number(time[1]):
score += int(time[1])
else:
score += 2 * timeout
penalized.add(time[1])
print(score / len(times))
print(penalized)
class GBD:
# Create a new GBD object which operates on the given databases
def __init__(self, db_string, context='cnf', jobs=1, tlim=5000, mlim=2000, flim=1000, separator=" ", join_type="LEFT", verbose=False):
self.databases = db_string.split(os.pathsep)
self.context = context
self.jobs = jobs
self.tlim = tlim # time limit (seconds)
self.mlim = mlim # memory limit (mega bytes)
self.flim = flim # file size limit (mega bytes)
self.separator = separator
self.join_type = join_type
self.verbose = verbose
self.database = Database(self.databases, self.verbose)
def __enter__(self):
with ExitStack() as stack:
stack.enter_context(self.database)
self._stack = stack.pop_all()
return self
def __exit__(self, exc_type, exc, traceback):
self._stack.__exit__(exc_type, exc, traceback)
def get_limits(self) -> dict():
return { 'tlim': self.tlim, 'mlim': self.mlim, 'flim': self.flim }
def get_databases(self):
return list(self.database.get_databases())
def get_database_path(self, dbname):
return self.database.dpath(dbname)
# Get all features
def get_features(self, dbname=None):
return self.database.get_features(tables=True, views=True, database=dbname)
# Get all material features
def get_material_features(self, dbname=None):
return self.database.get_features(tables=True, views=False, database=dbname)
# Get all virtual features
def get_virtual_features(self, dbname=None):
return self.database.get_features(tables=False, views=True, database=dbname)
# Check for existence of given feature
def feature_exists(self, name):
return name in self.get_features()
# Creates the given feature
def create_feature(self, name, default_value=None):
if not self.feature_exists(name):
self.database.create_feature(name, default_value)
else:
raise GBDException("Feature '{}' does already exist".format(name))
# Removes the given feature
def delete_feature(self, name):
if self.feature_exists(name):
self.database.delete_feature(name)
else:
raise GBDException("Feature '{}' does not exist or is virtual".format(name))
# Rename the given feature
def rename_feature(self, old_name, new_name):
if not self.feature_exists(old_name):
raise GBDException("Feature '{}' does not exist or is virtual".format(old_name))
elif self.feature_exists(new_name):
raise GBDException("Feature '{}' does already exist".format(new_name))
else:
self.database.rename_feature(old_name, new_name)
# Retrieve information about a specific feature
def get_feature_info(self, name):
return self.database.feature_info(name)
# Set the attribute value for the given hashes
def set_attribute(self, feature, value, query, hashes=[], force=False):
if not feature in self.get_material_features():
raise GBDException("Feature '{}' missing or virtual".format(feature))
hash_list = hashes
if query:
hash_list = [hash[0] for hash in self.query_search(query, hashes)]
try:
self.database.set_values(feature, value, hash_list)
except Exception as err:
raise GBDException(str(err))
# Remove the attribute value for the given hashes
def remove_attributes(self, feature, hash_list):
if not feature in self.get_material_features():
raise GBDException("Feature '{}' not found".format(feature))
self.database.delete_hashes(feature, hash_list)
def query_search(self, gbd_query=None, hashes=[], resolve=[], collapse="GROUP_CONCAT", group_by="hash"):
try:
query_builder = GBDQuery(self.database, self.join_type, collapse)
sql = query_builder.build_query(gbd_query, hashes, resolve or [], group_by or "hash")
return self.database.query(sql)
except sqlite3.OperationalError as err:
raise GBDException("Database Operational Error: {}".format(str(err)))
except tatsu.exceptions.FailedParse as err:
raise GBDException("Parser Error: {}".format(str(err)))
