def __get_integer_id(self, cell_value, row_index):
"""
Converts the parsed ID into an integer.
"""
if isinstance(cell_value, int):
result = cell_value
elif isinstance(cell_value, float):
result = int(cell_value)
elif isinstance(cell_value, string_types):
# FIXME: This is highly suspicious - do we really want to parse
# 1.99999 as 1??
if '.' in cell_value:
cell_value = cell_value.split('.')[0]
try:
result = int(cell_value)
except ValueError:
result = None
cell_name = '%s%i' \
% (label_from_number(self.column_index + 1),
row_index + 1)
msg = 'There is a non-number character in row %i. ' \
% (row_index + 1)
error_msg = self.format_log_message(self.SHEET_NAME, cell_name,
msg)
self.add_error(error_msg)
if not result is None:
result = int(cell_value)
return result
def __get_integer_id(self, cell_value, row_index):
"""
Converts the parsed ID into an integer.
"""
if isinstance(cell_value, int):
result = cell_value
elif isinstance(cell_value, float):
result = int(cell_value)
elif isinstance(cell_value, string_types):
# FIXME: This is highly suspicious - do we really want to parse
# 1.99999 as 1??
if '.' in cell_value:
cell_value = cell_value.split('.')[0]
try:
result = int(cell_value)
except ValueError:
result = None
cell_name = '%s%i' \
% (label_from_number(self.column_index + 1),
row_index + 1)
msg = 'There is a non-number character in row %i. ' \
% (row_index + 1)
error_msg = self.format_log_message(self.SHEET_NAME,
cell_name, msg)
self.add_error(error_msg)
if not result is None:
result = int(cell_value)
return result
def __check_for_duplicate_id(self, pool_id, row_index):
"""
Checks whether the current molecule design has been found before.
"""
if pool_id in self.molecule_design_pool_ids:
cell_name = '%s%i' % (label_from_number(self.column_index + 1),
row_index + 1)
msg = 'Duplicate molecule design pool ID %i in row %i!' \
% (pool_id, row_index + 1)
warning_msg = self.format_log_message(self.SHEET_NAME, cell_name,
msg)
self.add_warning(warning_msg)
def __check_for_duplicate_id(self, pool_id, row_index):
"""
Checks whether the current molecule design has been found before.
"""
if pool_id in self.molecule_design_pool_ids:
cell_name = '%s%i' % (label_from_number(self.column_index + 1),
row_index + 1)
msg = 'Duplicate molecule design pool ID %i in row %i!' \
% (pool_id, row_index + 1)
warning_msg = self.format_log_message(self.SHEET_NAME, cell_name,
msg)
self.add_warning(warning_msg)
def get_cell_name(row_index, column_index):
"""
Convenience method deriving an Excel cell label from a row and
column index.
:returns: Cell name.
:rtype: :class:`str`
"""
if row_index is None or column_index is None:
result = None
else:
result = '%s%i' \
% (label_from_number(column_index + 1), row_index + 1)
return result
def get_cell_name(row_index, column_index):
"""
Convenience method deriving an Excel cell label from a row and
column index.
:returns: Cell name.
:rtype: :class:`str`
"""
if row_index is None or column_index is None:
result = None
else:
result = '%s%i' \
% (label_from_number(column_index + 1), row_index + 1)
return result
def __determine_layout_dimension(self):
# Makes sure the layout is in the right position and determines
# the layout dimension.
self.add_debug('Determine layout dimension ...')
first_col_value = self.get_cell_value(self.sheet,
self.TOP_LEFT_POSITION[0] + 1,
self.TOP_LEFT_POSITION[1])
is_layout = first_col_value == 'A'
if not is_layout:
msg = 'Error when trying to locate the layout. Please make sure ' \
'the columns header start in row 2 in column A.'
self.add_error(msg)
return None
row_number = self.get_sheet_row_number(self.sheet)
col_number = self.get_sheet_column_number(self.sheet)
rack_row, rack_column = 0, 0
start_row = self.TOP_LEFT_POSITION[0]
start_column = self.TOP_LEFT_POSITION[1]
# Get number of rows, row labels are alphanumeric.
while True:
row_cell_value = self.get_cell_value(self.sheet,
(start_row + rack_row + 1),
start_column)
if row_cell_value != label_from_number(rack_row + 1):
break
rack_row += 1
if (start_row + rack_row + 1) >= row_number:
break
# Get number of columns, column labels are numbers.
while True:
column_cell_value = self.get_cell_value(
self.sheet, start_row, (start_column + rack_column + 1))
if column_cell_value != (rack_column + 1):
break
rack_column += 1
if (start_column + rack_column + 1) >= col_number:
break
if not (rack_row, rack_column) in self.RACK_SHAPES:
msg = 'Invalid layout block shape (%ix%i).' % (rack_row,
rack_column)
self.add_error(msg)
else:
self.shape = RackShapeParsingContainer(self, rack_row, rack_column)
def get_cell_value(self, sheet, row_index, column_index):
"""
Returns the value of the specified in the given sheet.
Converts the passed cell value either into
a ascii string (if basestring) or a number (if non_string).
"""
cell_value = sheet.cell_value(row_index, column_index)
cell_name = '%s%i' % (label_from_number(column_index + 1),
row_index + 1)
sheet_name = self.get_sheet_name(sheet)
conv_value = None
if isinstance(cell_value, string_types):
try:
conv_value = ascii_native_(cell_value)
except UnicodeEncodeError:
msg = 'Unknown character in cell %s (sheet "%s"). Remove ' \
'or replace the character, please.' \
% (cell_name, sheet_name)
self.add_error(msg)
else:
if conv_value == '':
conv_value = None
else:
# Try to convert to an int or float.
try:
conv_value = int(conv_value)
except ValueError:
try:
conv_value = float(conv_value)
except ValueError:
pass
elif isinstance(cell_value, (float, int)):
if is_valid_number(value=cell_value, is_integer=True):
conv_value = int(cell_value)
else:
conv_value = cell_value
else:
msg = 'There is some unknown content in cell %s (sheet %s).' \
% (cell_name, sheet_name)
self.add_error(msg)
return conv_value
def __parse_layout_shape(self, start_row, start_col):
"""
Determines the dimensions of plate layout definition.
"""
rack_row = 0
rack_col = 0
# Get number of rows, row labels are alphanumeric.
while rack_row + start_row + 2 < self._row_number:
row_value = self._get_cell_value(start_row + rack_row + 1,
start_col)
if row_value != label_from_number(rack_row + 1):
break
rack_row += 1
# Get number of columns, column labels are numbers.
while start_col + rack_col + 1 < self._col_number:
col_value = self._get_cell_value(start_row,
start_col + rack_col + 1)
if col_value != rack_col + 1:
break
rack_col += 1
if not (rack_row, rack_col) in self._parser.allowed_rack_dimensions:
msg = 'Invalid layout block shape (%ix%i). Make sure you ' \
'have placed an "%s" maker, too.' % (rack_row, rack_col,
self._END_MARKER)
self._create_error(msg, self._get_cell_name(start_row, start_col))
result = None
else:
shape = RackShapeParsingContainer(self._parser, rack_row,
rack_col)
result = shape
if self._parser.HAS_COMMON_LAYOUT_DIMENSION:
if self._parser.shape is None:
self._parser.shape = shape
elif not shape == self._parser.shape:
msg = 'There are 2 different layout shapes in the file ' \
'(%s and %s). For this parser, all layout ' \
'dimensions have to be the same.' \
% (shape, self._parser.shape)
self._create_error(msg)
result = None
return result
def __determine_layout_dimension(self):
# Makes sure the layout is in the right position and determines
# the layout dimension.
self.add_debug('Determine layout dimension ...')
first_col_value = self.get_cell_value(self.sheet,
self.TOP_LEFT_POSITION[0] + 1, self.TOP_LEFT_POSITION[1])
is_layout = first_col_value == 'A'
if not is_layout:
msg = 'Error when trying to locate the layout. Please make sure ' \
'the columns header start in row 2 in column A.'
self.add_error(msg)
return None
row_number = self.get_sheet_row_number(self.sheet)
col_number = self.get_sheet_column_number(self.sheet)
rack_row, rack_column = 0, 0
start_row = self.TOP_LEFT_POSITION[0]
start_column = self.TOP_LEFT_POSITION[1]
# Get number of rows, row labels are alphanumeric.
while True:
row_cell_value = self.get_cell_value(self.sheet,
(start_row + rack_row + 1), start_column)
if row_cell_value != label_from_number(rack_row + 1):
break
rack_row += 1
if (start_row + rack_row + 1) >= row_number:
break
# Get number of columns, column labels are numbers.
while True:
column_cell_value = self.get_cell_value(self.sheet, start_row,
(start_column + rack_column + 1))
if column_cell_value != (rack_column + 1):
break
rack_column += 1
if (start_column + rack_column + 1) >= col_number:
break
if not (rack_row, rack_column) in self.RACK_SHAPES:
msg = 'Invalid layout block shape (%ix%i).' % (rack_row,
rack_column)
self.add_error(msg)
else:
self.shape = RackShapeParsingContainer(self, rack_row, rack_column)
def get_cell_value(self, sheet, row_index, column_index):
"""
Returns the value of the specified in the given sheet.
Converts the passed cell value either into
a ascii string (if basestring) or a number (if non_string).
"""
cell_value = sheet.cell_value(row_index, column_index)
cell_name = '%s%i' % (label_from_number(column_index + 1),
row_index + 1)
sheet_name = self.get_sheet_name(sheet)
conv_value = None
if isinstance(cell_value, string_types):
try:
conv_value = ascii_native_(cell_value)
except UnicodeEncodeError:
msg = 'Unknown character in cell %s (sheet "%s"). Remove ' \
'or replace the character, please.' \
% (cell_name, sheet_name)
self.add_error(msg)
else:
if conv_value == '':
conv_value = None
else:
# Try to convert to an int or float.
try:
conv_value = int(conv_value)
except ValueError:
try:
conv_value = float(conv_value)
except ValueError:
pass
elif isinstance(cell_value, (float, int)):
if is_valid_number(value=cell_value, is_integer=True):
conv_value = int(cell_value)
else:
conv_value = cell_value
else:
msg = 'There is some unknown content in cell %s (sheet %s).' \
% (cell_name, sheet_name)
self.add_error(msg)
return conv_value
def __parse_layout_shape(self, start_row, start_col):
"""
Determines the dimensions of plate layout definition.
"""
rack_row = 0
rack_col = 0
# Get number of rows, row labels are alphanumeric.
while rack_row + start_row + 2 < self._row_number:
row_value = self._get_cell_value(start_row + rack_row + 1,
start_col)
if row_value != label_from_number(rack_row + 1):
break
rack_row += 1
# Get number of columns, column labels are numbers.
while start_col + rack_col + 1 < self._col_number:
col_value = self._get_cell_value(start_row,
start_col + rack_col + 1)
if col_value != rack_col + 1:
break
rack_col += 1
if not (rack_row, rack_col) in self._parser.allowed_rack_dimensions:
msg = 'Invalid layout block shape (%ix%i). Make sure you ' \
'have placed an "%s" maker, too.' % (rack_row, rack_col,
self._END_MARKER)
self._create_error(msg, self._get_cell_name(start_row, start_col))
result = None
else:
shape = RackShapeParsingContainer(self._parser, rack_row, rack_col)
result = shape
if self._parser.HAS_COMMON_LAYOUT_DIMENSION:
if self._parser.shape is None:
self._parser.shape = shape
elif not shape == self._parser.shape:
msg = 'There are 2 different layout shapes in the file ' \
'(%s and %s). For this parser, all layout ' \
'dimensions have to be the same.' \
% (shape, self._parser.shape)
self._create_error(msg)
result = None
return result
def get_label(cls, row_index, column_index):
"""
Return the label for the given row and column indices.
:param row_index: The row index (0-based) of the rack position.
:type row_index: :class:`int`
:param column_index: The column index (0-based) of the rack position.
:type column_index: :class:`int`
:raises TypeError: If one of the indices is not an non-negative integer.
:raises ValueError: If there is not rack position for these indices in
the DB.
"""
if not cls.is_positive_integer(row_index):
raise ValueError('The row index must be a non-negative integer ' \
'(obtained: %s).' % (row_index))
if not cls.is_positive_integer(column_index):
raise ValueError('The column index must be a non-negative ' \
'integer (obtained: %s).' % (column_index))
return '%s%d' % (label_from_number(row_index + 1), column_index + 1)
db_name = 'buffalo_backup'
db_string = "postgresql+psycopg2://%(db_user)s:%(db_password)s" \
"@%(db_server)s:%(db_port)s/%(db_name)s" % locals()
engine = create_engine(db_string)
metadata = create_metadata(engine)
sess = Session()
max_row_number = 32
max_col_number = 48
pos_map = dict()
for r in range(max_row_number):
row_letter = label_from_number(r + 1)
for c in range(max_col_number):
label = '%s%i' % (row_letter, c + 1)
rack_pos = RackPosition(row_index=r, column_index=c, label=label)
pos_map[label] = rack_pos
sess.add(rack_pos)
print '%i rack positions have been created.' % (len(pos_map))
print 'Done processing.'
if COMMIT:
sess.commit()
else:
sess.rollback()
def test_basic(self):
assert 'AG' == label_from_number(33)
def label(self):
"""
The label for this rack position.
"""
return '%s%d' % (label_from_number(self.row_index + 1),
self.column_index + 1)
def test_basic(self):
assert 'AG' == label_from_number(33)
db_name = 'buffalo_backup'
db_string = "postgresql+psycopg2://%(db_user)s:%(db_password)s" \
"@%(db_server)s:%(db_port)s/%(db_name)s" % locals()
engine = create_engine(db_string)
metadata = create_metadata(engine)
sess = Session()
max_row_number = 32
max_col_number = 48
pos_map = dict()
for r in range(max_row_number):
row_letter = label_from_number(r + 1)
for c in range(max_col_number):
label = '%s%i' % (row_letter, c + 1)
rack_pos = RackPosition(row_index=r, column_index=c, label=label)
pos_map[label] = rack_pos
sess.add(rack_pos)
print '%i rack positions have been created.' % (len(pos_map))
print 'Done processing.'
if COMMIT:
sess.commit()
else:
sess.rollback()
def label(self):
"""
The label for this rack position.
"""
return '%s%d' % (label_from_number(self.row_index + 1),
self.column_index + 1)
