def test_sql_expression_pk_autoinc_lastinserted(self):
# test that postfetch isn't invoked for a SQL expression
# in a primary key column. the DB either needs to support a lastrowid
# that can return it, or RETURNING. [ticket:3133]
metadata = MetaData()
table = Table(
"sometable",
metadata,
Column("id", Integer, primary_key=True),
Column("data", String),
)
stmt = table.insert().return_defaults().values(id=func.foobar())
compiled = stmt.compile(dialect=sqlite.dialect(), column_keys=["data"])
eq_(compiled.postfetch, [])
eq_(compiled.returning, [])
self.assert_compile(
stmt,
"INSERT INTO sometable (id, data) VALUES "
"(foobar(), ?)",
checkparams={"data": "foo"},
params={"data": "foo"},
dialect=sqlite.dialect(),
)
def get_ips(ids=None, deg=1):
"""
Return a pandas DataFrame with ionization energies for a set of elements.
Args:
ids: list, str or int
A list of atomic number, symbols, element names of a combination of the
above. If nothing is specified all elements are selected.
deg: int or list of int
Degree of ionization, either as int or a list of ints. If a list is
passed then the output will contain ionization energies corresponding
to particalr degrees in columns.
Returns:
df: DataFrame
Pandas DataFrame with atomic numbers, symbols and ionization energies
"""
session = get_session()
engine = get_engine()
if ids is None:
atns = list(range(1, 119))
else:
atns = ids_to_attr(ids, attr="atomic_number")
query = session.query(Element.atomic_number, Element.symbol).filter(
Element.atomic_number.in_(atns))
df = pd.read_sql_query(query.statement.compile(dialect=sqlite.dialect()),
engine)
if isinstance(deg, (list, tuple)):
if all(isinstance(d, int) for d in deg):
for d in deg:
query = (session.query(IonizationEnergy).filter(
IonizationEnergy.degree == d).filter(
IonizationEnergy.atomic_number.in_((atns))))
out = pd.read_sql_query(
query.statement.compile(dialect=sqlite.dialect()), engine)
out = out[["atomic_number", "energy"]]
out.columns = ["atomic_number", "IP{0:d}".format(d)]
df = pd.merge(df, out, on="atomic_number", how="left")
else:
raise ValueError("deg should be a list of ints")
elif isinstance(deg, int):
query = (session.query(IonizationEnergy).filter(
IonizationEnergy.degree == deg).filter(
IonizationEnergy.atomic_number.in_((atns))))
out = pd.read_sql_query(
query.statement.compile(dialect=sqlite.dialect()), engine)
out = out[["atomic_number", "energy"]]
out.columns = ["atomic_number", "IP{0:d}".format(deg)]
df = pd.merge(df, out, on="atomic_number", how="left")
else:
raise ValueError("deg should be an int or a list or tuple of ints")
return df
def fetch_ionization_energies(degree: Union[List[int], int] = 1) -> pd.DataFrame:
"""
Fetch a :py:class:`pandas.DataFrame` with ionization energies for all elements
indexed by atomic number.
Args:
degree: Degree of ionization, either as int or a list of ints. If a list is
passed then the output will contain ionization energies corresponding
to particalr degrees in columns.
Returns:
df (pandas.DataFrame): ionization energies, indexed by atomic number
"""
# validate degree
if isinstance(degree, (list, tuple, set)):
if not all(isinstance(d, int) for d in degree) or any(d <= 0 for d in degree):
raise ValueError("degree should be a list of positive ints")
elif isinstance(degree, int):
if degree <= 0:
raise ValueError(f"degree should be positive")
degree = [degree]
else:
raise ValueError(
f"degree should be either a positive int or a collection of positive ints, got: {degree}"
)
session = get_session()
engine = get_engine()
query = session.query(Element.atomic_number).order_by("atomic_number")
df = pd.read_sql_query(query.statement.compile(dialect=sqlite.dialect()), engine)
for d in degree:
query = session.query(IonizationEnergy).filter(IonizationEnergy.degree == d)
energies = pd.read_sql_query(
query.statement.compile(dialect=sqlite.dialect()), engine
)
df = pd.merge(
df,
energies.loc[:, ["atomic_number", "energy"]].rename(
columns={"energy": "IE{0:d}".format(d)}
),
on="atomic_number",
how="left",
)
return df.set_index("atomic_number")
class SQLite(Resource):
def autocommit_off(self) -> None:
# default is off
pass
def create_column_metadata_set(self, cursor: Cursor) -> List[ColumnMetadata]:
raise NotImplementedError
DIALECT = sqlite.dialect(paramstyle='named')
@classmethod
def create_connection_maker(
cls,
host: Optional[str] = None,
port: Optional[int] = None,
user_name: Optional[str] = None,
password: Optional[str] = None,
engine_kwargs: Dict[str, Any] = None,
) -> ConnectionMaker:
def connect(_: Optional[str] = None): # type: ignore
return sqlite3.connect(':memory:')
return connect
def get_field_from_value(self, value: Any) -> Field:
return super().get_field_from_value(value)
def get(self):
t_i = time.time()
offset = 0
limit = 1000
args = parser.parse_args()
logger.debug(args)
if args['offset']!=None: offset = args['offset']
if args['limit']!=None and args['limit'] < 1000: limit = args['limit'] # TODO: make max limit a config option
with orm.get_session() as sess:
q = sess.query(Event)
if args['type']!=None: q = q.filter_by(type=args['type'])
if args['src']!=None: q = q.filter_by(src_abbr=args['src'])
if args['reverse']==None: # cant offset when reversed
q = q.filter(Event.id >= offset)
else:
q = q.order_by(Event.id.desc())
q = q.limit(limit)
result = default_ok_result.copy()
qstring = str(q.statement.compile(dialect=sqlite.dialect(),
compile_kwargs={"literal_binds": True})).replace('\n','')
logger.debug("DB Query: {}".format(qstring))
es = q.all()
logger.debug('queried db in {} seconds.'.format(time.time()-t_i))
result.update({'offset': offset, 'next_offset': (es[-1].id+1 if len(es)>0 else offset), 'results': [e.getDict() for e in es]})
return result
def get_sql(self, query):
print("QUERY:", query)
self._set_fields()
tree = parser.parse(query)
rtree = resolver(tree)
print("REPR:", repr(rtree))
visited = (self.visit(rtree))
print("VISITED:", visited)
self.make_joins()
columns = self.get_columns()
print("COLUMNS:", columns)
s = select(columns)
for join in self.joins:
s = s.select_from(join)
if self.where:
print("WHERE:", self.where)
for where in self.where:
s = s.where(where)
s = s.where(visited)
if self.having is not None:
s = s.having(self.having)
if self.group_by is not None:
s = s.group_by(self.group_by)
print(s)
print(s.compile().params)
return str(
s.compile(compile_kwargs={"literal_binds": True},
dialect=sqlite.dialect()))
async def test_pagination(database, notes, notes_data):
await database.connect()
# Create table
dialect = sqlite.dialect()
create_query = str(CreateTable(notes).compile(dialect=dialect))
await database.execute(query=create_query)
# Insert
query = notes.insert()
await database.execute_many(query=query, values=notes_data)
# Fetch multiple rows
query = notes.select()
pagination = CursorPagination(database, query)
paginated = await pagination.page(PAGE_PARAMS)
assert len(paginated.edges) == PAGE_PARAMS.first
assert paginated.page_info.has_next_page == True
assert paginated.page_info.has_previous_page == False
searched = await pagination.page(SEARCH_PARAMS)
assert len(searched.edges) == 1
filtered = await pagination.page(FILTER_PARAMS)
actual = [e.node["completed"] for e in filtered.edges]
expected = [True] * FILTER_PARAMS.first
assert actual == expected
drop_query = str(DropTable(notes).compile(dialect=dialect))
await drop_db(database, drop_query)
def find_by_pkg_name(session, package_name, version=None):
"""
Find a package by name. If version is `None`, returns all versions.
Parameters
----------
session : :class:`sqlalchemy.orm.session.Session`
package_name : str
The NuGet name of the package - the "id" tag in the NuSpec file.
version : str
The version of the package to download. If `None`, then return all
versions.
Returns
-------
results : list of :class:`Version`
"""
logger.debug("db.find_by_pkg_name('%s', version='%s')" %
(package_name, version))
query = (session.query(Version).join(Package).filter(
Package.name == package_name))
stmt = query.statement.compile(dialect=sqlite.dialect(),
compile_kwargs={"literal_binds": True})
logger.debug(stmt)
if version:
query = query.filter(Version.version == version)
query.order_by(desc(Version.version))
results = query.all()
logger.info("Found %d results." % len(results))
logger.debug(results)
return results
def index():
conn = db.session()
if request.method == 'GET':
bookmarks = conn.query(Bookmark).join(
User, Bookmark.user_id == User.id).order_by(Bookmark.id).all()
if request.method == 'POST':
query = request.form['search']
bookmarks = conn.query(Bookmark).join(
User, Bookmark.user_id == User.id).filter(
Bookmark.title.like(f"%{query}%"),
Bookmark.private == 0).all()
from sqlalchemy.dialects import sqlite
print(
conn.query(Bookmark).join(
User, Bookmark.user_id == User.id).filter(
Bookmark.title.like(f"%{query}%")).statement.compile(
dialect=sqlite.dialect()))
page = request.args.get(get_page_parameter(), type=int, default=1)
res = bookmarks[(page - 1) * 10:page * 10]
pagination = Pagination(page=page,
total=len(bookmarks),
per_page=10,
css_framework='bootstrap4')
return render_template('bookmark/index.html',
bookmarks=res,
pagination=pagination)
def create_index(table: Table):
creates = {}
for index in table.indexes:
index: Index
stmt = CreateIndex(index).compile(dialect=sqlite.dialect())
stmt = str(stmt).replace('INDEX', 'INDEX IF NOT EXISTS').strip()
creates[index.name] = stmt
return creates
def test_process_bind_param_none(self):
"""Assert UUIDs with other dialects are hex-encoded strings of length 32."""
guid = models.GUID()
dialect = sqlite.dialect()
result = guid.process_bind_param(None, dialect)
self.assertTrue(result is None)
def test_load_dialect_impl_other(self):
"""Assert with dialects other than PostgreSQL, a CHAR type is used."""
guid = models.GUID()
dialect = sqlite.dialect()
result = guid.load_dialect_impl(dialect)
self.assertTrue(isinstance(result, CHAR))
def pprint(query_or_sql, engine):
if isinstance(query_or_sql, Query):
sql = query_or_sql.statement.compile(dialect=sqlite.dialect())
else:
sql = query_or_sql
result_proxy = engine.execute(sql)
p_table = from_db_cursor(result_proxy.cursor)
print(p_table)
def test_generic_now(self):
assert isinstance(func.now().type, sqltypes.DateTime)
for ret, dialect in [('CURRENT_TIMESTAMP', sqlite.dialect()),
('now()', postgresql.dialect()),
('now()', mysql.dialect()),
('CURRENT_TIMESTAMP', oracle.dialect())]:
self.assert_compile(func.now(), ret, dialect=dialect)
def log_query(self, q):
"""
Log Query
:param q: Query
"""
query_str =str(q.statement.compile(dialect=sqlite.dialect()))
log.debug(query_str)
def test_load_dialect_impl_other(self):
"""Assert with dialects other than PostgreSQL, a CHAR type is used."""
guid = models.GUID()
dialect = sqlite.dialect()
result = guid.load_dialect_impl(dialect)
self.assertTrue(isinstance(result, CHAR))
def test_process_bind_param_none(self):
"""Assert UUIDs with other dialects are hex-encoded strings of length 32."""
guid = models.GUID()
dialect = sqlite.dialect()
result = guid.process_bind_param(None, dialect)
self.assertTrue(result is None)
def test_process_result_string(self):
"""Assert when the result value is a string, a native UUID is returned."""
guid = models.GUID()
uuid = uuid4()
result = guid.process_result_value(str(uuid), sqlite.dialect())
self.assertTrue(isinstance(result, UUID))
self.assertEqual(uuid, result)
def test_process_result_short_string(self):
"""Assert when the result value is a short string, a native UUID is returned."""
guid = models.GUID()
uuid = uuid4()
result = guid.process_result_value(str(uuid).replace("-", ""), sqlite.dialect())
self.assertTrue(isinstance(result, UUID))
self.assertEqual(uuid, result)
def test_generic_random(self):
assert func.random().type == sqltypes.NULLTYPE
assert isinstance(func.random(type_=Integer).type, Integer)
for ret, dialect in [('random()', sqlite.dialect()),
('random()', postgresql.dialect()),
('rand()', mysql.dialect()),
('random()', oracle.dialect())]:
self.assert_compile(func.random(), ret, dialect=dialect)
def test_process_bind_param_str_other(self):
"""Assert UUIDs with other dialects are hex-encoded strings of length 32."""
guid = models.GUID()
uuid = uuid4()
dialect = sqlite.dialect()
result = guid.process_bind_param(str(uuid), dialect)
self.assertEqual(32, len(result))
self.assertEqual(str(uuid).replace("-", ""), result)
def test_generic_now(self):
assert isinstance(func.now().type, sqltypes.DateTime)
for ret, dialect in [
('CURRENT_TIMESTAMP', sqlite.dialect()),
('now()', postgresql.dialect()),
('now()', mysql.dialect()),
('CURRENT_TIMESTAMP', oracle.dialect())
]:
self.assert_compile(func.now(), ret, dialect=dialect)
def test_process_bind_param_str_other(self):
"""Assert UUIDs with other dialects are hex-encoded strings of length 32."""
guid = models.GUID()
uuid = uuid4()
dialect = sqlite.dialect()
result = guid.process_bind_param(str(uuid), dialect)
self.assertEqual(32, len(result))
self.assertEqual(str(uuid).replace("-", ""), result)
def log_query(q):
"""Log Query
:param q: Query
"""
statement = q.statement.compile(dialect=sqlite.dialect())
if statement.params:
query_str = '{0}\n{1}'.format(statement, statement.params)
else:
query_str = str(statement)
log.debug(query_str)
def test_generic_random(self):
assert func.random().type == sqltypes.NULLTYPE
assert isinstance(func.random(type_=Integer).type, Integer)
for ret, dialect in [
('random()', sqlite.dialect()),
('random()', postgresql.dialect()),
('rand()', mysql.dialect()),
('random()', oracle.dialect())
]:
self.assert_compile(func.random(), ret, dialect=dialect)
def test_nextval_unsupported(self):
"""test next_value() used on non-sequence platform
raises NotImplementedError."""
s = Sequence("my_seq")
d = sqlite.dialect()
assert_raises_message(
NotImplementedError,
"Dialect 'sqlite' does not support sequence increments.",
s.next_value().compile,
dialect=d)
def stringify_query(query, kwargs):
"""
Sample usage:
print stringify_query(session.query(model).filter_by(**kwargs), kwargs)
"""
from sqlalchemy.dialects import sqlite
s = str(query.statement.compile(dialect=sqlite.dialect()))
for key in kwargs:
s = s.replace('?', '\'' + str(kwargs[key]) + '\'', 1)
pass
return s
def log_query(q):
"""Log Query
:param q: Query
"""
statement = q.statement.compile(dialect=sqlite.dialect())
if statement.params:
query_str = '{0}\n{1}'.format(statement, statement.params)
else:
query_str = str(statement)
log.debug(query_str)
def test_nextval_unsupported(self):
"""test next_value() used on non-sequence platform
raises NotImplementedError."""
s = Sequence("my_seq")
d = sqlite.dialect()
assert_raises_message(
NotImplementedError,
"Dialect 'sqlite' does not support sequence increments.",
s.next_value().compile,
dialect=d
)
def retrieve_stations_data(self, station: models.Station,
template_for_lines):
# print(template_for_lines)
session = self.Session()
engine = self.engine
dict_with_relevant_to_station_help_ids = {
helper.id: helper.observable_id
for helper in station.helper
}
sql = session.query(models.Observations). \
filter(models.Observations.helper_observable_id.in_(list(dict_with_relevant_to_station_help_ids)))
sql_literal = str(
sql.statement.compile(dialect=sqlite.dialect(),
compile_kwargs={"literal_binds": True}))
df = pd.read_sql_query(sql_literal, engine)
df['helper_observable_id'] = df['helper_observable_id']. \
apply(lambda x: dict_with_relevant_to_station_help_ids[x])
df.drop('id', axis=1, inplace=True)
df = df.pivot_table(index=df.timestamp,
columns='helper_observable_id',
values='value',
aggfunc='first')
df.reset_index(inplace=True)
df["timestamp"] = df["timestamp"].apply(lambda x: pd.to_datetime(x))
df.set_index(keys=["timestamp"], drop=False, inplace=True)
station_df = copy.deepcopy(df)
# Convert values to Measurement objects
observables_list = list(df)
observables_list.remove('timestamp')
table = str.maketrans(dict.fromkeys('#*\"'))
for observable in observables_list:
df[observable] = df[observable].apply(lambda x: Measurement(x))
try:
station_df[observable] = station_df[observable].apply(
lambda x: str(x).translate(table))
except Exception as e:
print(observable, e.args)
# TODO: This is soooooo dangerous. Please re-implement......
station_df = station_df.replace('None', np.nan)
# station_df = station_df.fillna('---')
# print(station_df)
zip_argument = map(lambda x: "df." + x, template_for_lines)
zip_argument = ",".join(zip_argument)
zip_argument = eval("zip(%s)" % zip_argument)
return Station(station, df=station_df), zip_argument
def test_sqlite_in_with_multiple_columns():
vals = (
(1, '1'),
(2, '2'),
)
cols = table.c.id, table.c.a
select_in = sa.select(cols).where(sa.tuple_(*cols).in_(vals))
select_and = sa.select(cols).where(
sa.or_(
sa.and_(col == value for col, value in zip(cols, vs))
for vs in vals))
compiled_in = select_in.compile(dialect=sqlite.dialect())
compiled_and = select_and.compile(dialect=sqlite.dialect())
assert str(compiled_in) == str(compiled_and)
update_in = table.update().where(sa.tuple_(*cols).in_(vals))
update_and = table.update().where(
sa.or_(
sa.and_(col == value for col, value in zip(cols, vs))
for vs in vals))
compiled_in = update_in.compile(dialect=sqlite.dialect())
compiled_and = update_and.compile(dialect=sqlite.dialect())
assert str(compiled_in) == str(compiled_and)
def test_sqlite_in_with_multiple_columns():
vals = (
(1, '1'),
(2, '2'),
)
cols = table.c.id, table.c.a
select_in = sa.select(cols).where(sa.tuple_(*cols).in_(vals))
select_and = sa.select(cols).where(sa.or_(
sa.and_(col == value for col, value in zip(cols, vs))
for vs in vals
))
compiled_in = select_in.compile(dialect=sqlite.dialect())
compiled_and = select_and.compile(dialect=sqlite.dialect())
assert str(compiled_in) == str(compiled_and)
update_in = table.update().where(sa.tuple_(*cols).in_(vals))
update_and = table.update().where(sa.or_(
sa.and_(col == value for col, value in zip(cols, vs))
for vs in vals
))
compiled_in = update_in.compile(dialect=sqlite.dialect())
compiled_and = update_and.compile(dialect=sqlite.dialect())
assert str(compiled_in) == str(compiled_and)
def schema():
parser = argparse.ArgumentParser(
description="Generate different schema documents")
parser.add_argument(
"schema",
metavar="<SCHEMA>",
type=str,
choices=("openapi", "dsl", "sql"),
default="openapi",
help=
("The schema to generate: 'openapi' for the complete web OpenAPI/Swagger schema,"
" 'dsl' for the JSON schema for the DSL, 'sql' for the database schema."
),
)
parser.add_argument(
"outfile",
metavar="<FILE>",
nargs="?",
type=argparse.FileType("w"),
default=sys.stdout,
help="The file to use. <stdout> if not specified.",
)
parser.add_argument(
"-r",
"--raw",
action="store_true",
help="Do not pretty print the generated JSON.",
)
args = parser.parse_args()
if args.schema == "openapi":
json_schema = get_openapi(
title=app.title,
version=app.version,
openapi_version=app.openapi_version,
description=app.description,
routes=app.routes,
)
_print_json(json_schema, args.outfile, args.raw)
elif args.schema == "dsl":
json_schema = JobModel.schema()
_print_json(json_schema, args.outfile, args.raw)
elif args.schema == "sql":
for tbl in db.__all__:
print(
CreateTable(getattr(
db, tbl).__table__).compile(dialect=sqlite.dialect()),
file=args.outfile,
)
def ORM2SQL(self, statement):
"""
:param statement:
:return:
"""
query = statement.compile(dialect=sqlite.dialect())
query_str = str(query)
query_paras: dict = query.params
query_raw_sql = query_str.replace('?', r"%r") % tuple(
query_paras.values())
# print("==query_raw_sql==↓:")
# print(query_raw_sql)
# print("==query_raw_sql==↑:")
return query_raw_sql
def __init__(self, uri):
parsed = urlparse.urlparse(uri)
args = []
if parsed.scheme in ("sqlite", "sqlite3"):
args.append("sqlite3")
if not parsed.path:
args.append(":memory:")
else:
args.append(parsed.path)
from sqlalchemy.dialects.sqlite import dialect
self.dialect = dialect()
self.pool = adbapi.ConnectionPool(*args, cp_min=1, cp_max=1)
def test_sql_expression_pk_autoinc_lastinserted(self):
# test that postfetch isn't invoked for a SQL expression
# in a primary key column. the DB either needs to support a lastrowid
# that can return it, or RETURNING. [ticket:3133]
metadata = MetaData()
table = Table(
"sometable",
metadata,
Column("id", Integer, primary_key=True),
Column("data", String),
)
stmt = table.insert().return_defaults().values(id=func.foobar())
compiled = stmt.compile(dialect=sqlite.dialect(), column_keys=["data"])
eq_(compiled.postfetch, [])
eq_(compiled.returning, [])
self.assert_compile(
stmt,
"INSERT INTO sometable (id, data) VALUES " "(foobar(), ?)",
checkparams={"data": "foo"},
params={"data": "foo"},
dialect=sqlite.dialect(),
)
class SQLite(Resource):
DIALECT = sqlite.dialect(paramstyle='named')
@classmethod
def create_connection_maker(
cls,
host: Optional[str] = None,
port: Optional[int] = None,
user_name: Optional[str] = None,
password: Optional[str] = None,
engine_kwargs: Dict[str, Any] = None,
) -> ConnectionMaker:
def connect(): # type: ignore
return sqlite3.connect(':memory:')
return connect
def artists():
# If the user not specifically define 'false' for force (which is the
# default) value, then the attempt will be treated as if it were defined as
# 'true'. Eg. force=yes or force=1 and even force=fasle (mistyped value)
# will be treated as force=true
force = request.args.get('force')
force = True if force is not None and force != 'false' else False
# Get and set each parameter's value
asked = {}
for parameter, getter in PARAMETERS.items():
try:
asked[parameter] = getter(request.args.get(parameter), force)
except ParamError as error:
return error.jsonify()
# Store values more than once locally
count = asked['count']
start = (asked['start'] - START) * count
weights = asked['sort']
distance = Artist.distance(asked['latitude'],
asked['longitude']).label('distance')
# Do the query
query = session.query(Artist, distance).filter(
true() if asked['gender'] == 'both' else Artist.gender
== asked['gender'], Artist.rate <= asked['rate'],
Artist.age.between(asked['youngest'], asked['oldest']),
literal_column(distance.name) <= asked['radius']).order_by(
(asc if asked['order'] == 'asc' else desc
)((weights['age'] * Artist.age) +
(weights['gender'] * Artist.gender) +
(weights['rate'] * Artist.rate) +
(weights['distance'] * literal_column(distance.name)))).slice(
start, start + count)
# If debugging mode is on print the compiled SQL(ite) query
if app.debug:
print('\n',
str(query.statement.compile(dialect=sqlite.dialect())),
'parameters:',
asked,
sep='\n',
end='\n\n')
# Return serialised and jsonified result
return jsonify([artist.serialise(distance) for artist, distance in query])
class SQLite(Resource):
def create_column_metadata_set(self, cursor: Cursor) -> List[ColumnMetadata]:
raise NotImplementedError
DIALECT = sqlite.dialect(paramstyle='named')
@classmethod
def create_connection_maker(
cls,
host: Optional[str] = None,
port: Optional[int] = None,
user_name: Optional[str] = None,
password: Optional[str] = None,
engine_kwargs: Dict[str, Any] = None,
) -> ConnectionMaker:
def connect(_: Optional[str] = None): # type: ignore
return sqlite3.connect(':memory:')
return connect
def fetch_electronegativities(scales: List[str] = None) -> pd.DataFrame:
"""
Fetch electronegativity scales for all elements as :py:class:`pandas.DataFrame`
Args:
scales: list of scale names, defaults to all available scales
Returns:
df (pandas.DataFrame): Pandas DataFrame with the contents of the table
"""
session = get_session()
engine = get_engine()
query = session.query(Element.atomic_number).order_by("atomic_number")
df = pd.read_sql_query(query.statement.compile(dialect=sqlite.dialect()), engine)
scales = [
"allen",
"allred-rochow",
"cottrell-sutton",
"ghosh",
"gordy",
"li-xue",
"martynov-batsanov",
"mulliken",
"nagle",
"pauling",
"sanderson",
]
for scale in scales:
scale_name = "-".join(s.capitalize() for s in scale.split("-"))
df.loc[:, scale_name] = [
element(int(row.atomic_number)).electronegativity(scale=scale)
for _, row in df.iterrows()
]
return df.set_index("atomic_number")
def rlist(dbtype, tablename):
lkup, dbsess = obtain_lkup(dbtype)
if (lkup is None):
return render_template("errors/error.html",
error_title="Lookup Failure",
error_message="Unknown Database")
display_tablename = lkup[tablename].model.rlist_dis
if (lkup[tablename].lsform == rstruct.all_only):
# Get all matches
mobj = getMatch(lkup, tablename)
columnHead = mobj[0]
match = mobj[1]
prikey_match = mobj[2]
return render_template('res/datalist0.html', dbtype = dbtype,\
colNum=len(columnHead),matches=match,\
columnHead=columnHead, tablename=tablename,\
prikeyMatch=prikey_match,\
data_table_name=display_tablename)
else:
resls_form = lkup[tablename].lsform() #creates an LS FORM
resls_form = regenerateForm(lkup, resls_form, None)
if resls_form.validate_on_submit():
q = resls_form.getrawquery()
elif (session.get('query') is not None
and session.get('param') is not None):
# previous query is inplace
q = session['query']
qp = json.loads(session['param'])
# THIS IS VERY DANGEROUS ! VULNERABLE TO SQLI -- ToraNova
# But I have no choice to use this for the sake of convenience
# Please look into
# https://stackoverflow.com/questions/14845196/dynamically-constructing-filters-in-sqlalchemy
q = dbsess.query(lkup[tablename].model).from_statement(
text(q)).params(qp)
else:
# await user query
crawq = "No Queries. Hit 'Query' to start"
return render_template('res/datalist1.html',
dbtype=dbtype,
colNum=0,
matches=[],
columnHead=[],
tablename=tablename,
prikeyMatch=[],
data_table_name=display_tablename,
form=resls_form,
dqstr=crawq)
#session['query'] = str(q.with_labels().statement)
# SPECIAL THANKS TO
# https://stackoverflow.com/questions/4617291/how-do-i-get-a-raw-compiled-sql-query-from-a-sqlalchemy-expression
# crawq = str(q.statement.compile(compile_kwargs={"literal_binds": True}))
crawq = q.statement.compile(dialect=sqlite.dialect(paramstyle="named"))
crawq_str = str(crawq)
# Thanks again to
# https://stackoverflow.com/questions/11875770/how-to-overcome-datetime-datetime-not-json-serializable
crawq_params = json.dumps(crawq.params, cls=ExtendedEncoder)
session['query'] = crawq_str
session['param'] = crawq_params
# FOR LS FORM SESSION/QUERY READY
rawlist = q.all()
try:
mobj = getMatch(lkup, tablename, rawlist)
columnHead = mobj[0]
match = mobj[1]
prikey_match = mobj[2]
except Exception as e:
crawq = "Expired Query. Hit Query to start again"
columnHead = []
match = []
prikey_match = []
return render_template('res/datalist1.html', dbtype = dbtype,\
colNum=len(columnHead),matches=match,\
columnHead=columnHead, tablename=tablename,\
prikeyMatch=prikey_match,\
data_table_name=display_tablename,
form = resls_form, dqstr = crawq)
def test_match_1(self):
self.assert_compile(self.table1.c.myid.match('somstr'),
"mytable.myid MATCH ?",
dialect=sqlite.dialect())
expression2 = user_table.c.username.in_(["wendy", "mary", "ed"])
compiled=expression2.compile()
print("expression2 : {}".format(expression2))
print("xpression2.compile().params : {}".format(compiled.params))
print("-" * 80)
"""
heading = "Building expressions using SQL Expression."
print_output(number, code, heading)
#Dialect differences
print("Dialect Differences.")
print("-" * 80)
expression = user_table.c.username == 'ed'
print(expression.compile(dialect=mysql.dialect()))
print(expression.compile(dialect=postgresql.dialect()))
print(expression.compile(dialect=sqlite.dialect()))
print("-" * 80)
#Expressions as an object - BinaryExpression object.
print("Expression as an object - BinaryExpression object.")
print("-" * 80)
print("expression : {}".format(expression))
print("type(expression) : {}".format(type(expression)))
print("expression.left : {}".format(expression.left))
print("expression.right : {}".format(expression.right))
print("expression.operator : {}".format(expression.operator))
print("-" * 80)
#Compiling expressions
print("Parameters of expressions")
print("-" * 80)
expression2 = user_table.c.username.in_(["wendy", "mary", "ed"])
compiled = expression2.compile()
def test_mac_load_dialect_impl(self):
dialect = self.mac.load_dialect_impl(sqlite.dialect())
self.assertEqual(type(dialect), sqlite.CHAR)
def test_process_result_value_with_value(self):
bind = self.inet.process_result_value(1.0, sqlite.dialect())
self.assertEqual(bind, 1.0)
def test_process_bind_param_with_value(self):
bind = self.inet.process_bind_param("foo", sqlite.dialect())
self.assertEqual(bind, "foo")
def test_inet_load_dialect_impl_sqlite(self):
dialect = self.inet.load_dialect_impl(sqlite.dialect())
self.assertEqual(type(dialect), sqlite.CHAR)
def test_process_result_value_none(self):
"""Assert when the result value is None, None is returned."""
guid = models.GUID()
self.assertTrue(guid.process_result_value(None, sqlite.dialect()) is None)
from sqlalchemy.dialects import sqlite, mysql
__all__ = ['sqlite_dialect', 'mysql_dialect', 'create_table_sql', 'sqlite3']
sqlite_dialect = sqlite.dialect()
mysql_dialect = mysql.dialect()
def create_table_sql(table, dialect):
from sqlalchemy.schema import CreateTable
return str(CreateTable(table).compile(dialect=dialect)).strip()
def sqlite3(db_file, command):
import subprocess
return subprocess.check_output(['sqlite3', db_file, command])