# -*- coding: utf-8 -*-
"""Utility functions useful across multiple modules.
"""
"""Copyright 2020-2022 The Cytoscape Consortium
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO
THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import os
LOCAL_BASE_URL = 'http://127.0.0.1:1234/v1'
DEFAULT_BASE_URL = os.environ.get('DEFAULT_BASE_URL') or LOCAL_BASE_URL
# External library imports
import urllib.parse
import re
import sys
from colour import Color
# Internal module imports
from . import tables
from . import cytoscape_system
# Internal module convenience imports
from .exceptions import CyError
from .py4cytoscape_logger import narrate
from .style_visual_props import PROPERTY_NAME_MAP
# print(f'Starting {__name__} module')
# ==============================================================================
# I. Package Utility Functions
# ------------------------------------------------------------------------------
[docs]def cyPalette(name='set1'):
"""Supply a set of colors from Brewer palettes (without requiring rColorBrewer).
Args:
name (str): name of a set of colors (e.g., 'set1', 'burd')
Returns:
list: list of color values in the cy_palette
Raises:
KeyError: if cy_palette name is invalid
Examples:
>>> cyPalette()
['#E41A1C', '#377EB8', '#4DAF4A', '#984EA3', '#FF7F00', '#FFFF33', '#A65628', '#F781BF', '#999999']
>>> cyPalette('burd')
['#053061', '#2166AC', '#4393C3', '#92C5DE', '#D1E5F0', '#F7F7F7', '#FDDBC7', '#F4A582', '#D6604D', '#B2182B', '#67001F']
"""
PALETTES = {
'set1': ['#E41A1C', '#377EB8', '#4DAF4A', '#984EA3', '#FF7F00', '#FFFF33', '#A65628', '#F781BF', '#999999'],
'set2': ['#66C2A5', '#FC8D62', '#8DA0CB', '#E78AC3', '#A6D854', '#FFD92F', '#E5C494', '#B3B3B3'],
'set3': ['#8DD3C7', '#FFFFB3', '#BEBADA', '#FB8072', '#80B1D3', '#FDB462', '#B3DE69', '#FCCDE5', '#D9D9D9',
'#BC80BD', '#CCEBC5', '#FFED6F'],
'reds': ['#FFF5F0', '#FEE0D2', '#FCBBA1', '#FC9272', '#FB6A4A', '#EF3B2C', '#CB181D', '#A50F15', '#67000D'],
'rdbu': ['#67001F', '#B2182B', '#D6604D', '#F4A582', '#FDDBC7', '#F7F7F7', '#D1E5F0', '#92C5DE', '#4393C3',
'#2166AC', '#053061'],
'burd': ['#053061', '#2166AC', '#4393C3', '#92C5DE', '#D1E5F0', '#F7F7F7', '#FDDBC7', '#F4A582', '#D6604D',
'#B2182B', '#67001F']
}
return PALETTES[name]
# ------------------------------------------------------------------------------
def verify_brightness_contrast(bc):
"""Validate and provide user feedback when brightness or contrast is required input.
Args:
bc (int or float): a number between 0 and 100
Returns:
None
Raises:
CyError: if value is invalid
Examples:
>>> verify_brightness_contrast(77)
"""
if not (isinstance(bc, float) or isinstance(bc, int)) or bc < -100 or bc > 100:
raise CyError(f'"{bc}" is invalid. Value must be between -100 and 100).',
caller=sys._getframe(1).f_code.co_name)
def verify_hex_color(color):
"""Validate and provide user feedback when hex color code is required input.
Args:
colors (str): a single value, which is a 6 digit hex value or a color name
Returns:
str: '#' followed by 6 digit hex value
Raises:
CyError: if color is invalid
Examples:
>>> verify_hex_color('#92C5DE')
'#92C5DE'
>>> verify_hex_color('red')
'#FF0000'
"""
try:
if color.startswith('#') and len(color) == 7:
return color
else:
return Color(color).get_hex_l().upper()
except:
raise CyError(
f'"{color}" is not a valid color name (e.g., "red") or a hexadecimal color (has to begin with # and be 7 characters long, e.g., #FF00FF).',
caller=sys._getframe(1).f_code.co_name)
def verify_hex_colors(colors):
"""Validate and provide user feedback when hex color code (or a list of codes) are required input.
Args:
colors (str or list): a single value or a list of colors, which are 6 digit hex values
Returns:
str or list: colors as '#' followed by 6 digit hex value
Raises:
CyError: if color is invalid
Examples:
>>> verify_hex_colors('#92C5DE')
'#92C5DE'
>>> verify_hex_colors(['#053061', '#2166AC', '#4393C3', '#92C5DE', '#D1E5F0', '#F7F7F7', '#FDDBC7', '#F4A582', '#D6604D', '#B2182B', '#67001F'])
['#053061', '#2166AC', '#4393C3', '#92C5DE', '#D1E5F0', '#F7F7F7', '#FDDBC7', '#F4A582', '#D6604D', '#B2182B', '#67001F']
>>> verify_hex_colors(['red', 'blue', '#4393C3'])
['#FF0000', '#0000FF', '#4393C3']
"""
if colors is None: return None
if isinstance(colors, list):
return [verify_hex_color(c) for c in colors]
else:
return verify_hex_color(colors)
def verify_opacity(opacity, max_opacity=100):
"""Validate and provide user feedback when opacity is required input.
Args:
opacity (int or float): a number between 0 and a max
Returns:
int or float: validated opacity
Raises:
CyError: if opacity is invalid
Examples:
>>> verify_opacity(77)
"""
if not (isinstance(opacity, float) or isinstance(opacity, int)) or opacity < 0 or opacity > max_opacity:
raise CyError(f'"{opacity}" is not a valid opacity (has to be an integer between 0 and {max_opacity}).',
caller=sys._getframe(1).f_code.co_name)
return opacity
def verify_opacities(opacities):
"""Validate and provide user feedback when opacity is required input.
Args:
opacities (int, float or list): a single value or a list of values, all of which are integers or floats
Returns:
str or list: verified opacities
Raises:
CyError: if opacity is invalid
Examples:
>>> verify_opacities(177)
>>> verify_opacities([177, 200])
"""
if opacities is None: return None
if isinstance(opacities, list):
return [verify_opacity(opacity, max_opacity=255) for opacity in opacities]
else:
return verify_opacity(opacities, max_opacity=255)
def verify_dimensions(dimension, sizes):
"""Validate and provide user feedback when dimensions is required input.
Args:
dimension (str): name of the sizes being examined (e.g., 'width')
sizes (int, float or list): a single value or a list of values, all of which are integers or floats
Returns:
list: verified dimensions
Raises:
CyError: if size is invalid
Examples:
>>> verify_dimensions('width', 50)
>>> verify_dimensions('width', [10, 20])
"""
def verify_dimension(dimension, size):
if not isinstance(size, float) and not isinstance(size, int):
raise CyError(f'Illegal {dimension} "{size}". It needs to be a number.',
caller=sys._getframe(2).f_code.co_name)
return size
if sizes is None: return None
if isinstance(sizes, list):
return [verify_dimension(dimension, size) for size in sizes]
else:
return verify_dimension(dimension, sizes)
def verify_slot(slot):
"""Validate and provide user feedback when slot is required input.
Args:
slot (int or float): a slot number between 1 and 9
Returns:
None
Raises:
CyError: if slot is invalid
Examples:
>>> verify_slot(5)
"""
if not (isinstance(slot, float) or isinstance(slot, int)) or slot < 1 or slot > 9:
raise CyError(f'slot must be an integer between 1 and 9', caller=sys._getframe(1).f_code.co_name)
def verify_unique(value, existing_values):
if value in existing_values:
raise CyError(f'{value} is not unique. Please provide a unique value.', caller=sys._getframe(1).f_code.co_name)
def verify_positive(number):
"""Validate and provide user feedback when positive number is required input.
Args:
number (int or float): a number greater than 0
Returns:
None
Raises:
CyError: if number is invalid
Examples:
>>> verify_positive(5)
"""
if not (isinstance(number, float) or isinstance(number, int)):
raise CyError(f'Value must be a positive number.', caller=sys._getframe(1).f_code.co_name)
if number <= 0:
raise CyError(f'{number} is invalid. Number must be positive', caller=sys._getframe(1).f_code.co_name)
def verify_non_negative(number):
"""Validate and provide user feedback when a non-negative number is required input.
Args:
number (int or float): a number greater than or equal to 0
Returns:
None
Raises:
CyError: if number is invalid
Examples:
>>> verify_non_negative(5)
"""
if not (isinstance(number, float) or isinstance(number, int)):
raise CyError(f'Value must be a non-negative number.', caller=sys._getframe(1).f_code.co_name)
if number <= 0:
raise CyError(f'{number} is invalid. Number must be greater than or equal to 0',
caller=sys._getframe(1).f_code.co_name)
def verify_font_style(style):
"""Validate and provide user feedback when font style is required input.
Args:
font_style (str): a font style ['plain', 'bold', 'italic', 'bolditalic']
Returns:
None
Raises:
CyError: if style is invalid
Examples:
>>> verify_font_style('plain')
"""
valid_styles = ['plain', 'bold', 'italic', 'bolditalic']
if style not in valid_styles:
raise CyError(f'{style} is invalid. Use {valid_styles}', caller=sys._getframe(1).f_code.co_name)
def verify_canvas(canvas):
"""Validate acceptable canvas
Args:
canvas (str): a canvas ['foreground', 'background']
Returns:
None
Raises:
CyError: if canvas is invalid
Examples:
>>> verify_canvas('foreground')
"""
valid_canvases = ['foreground', 'background']
if canvas not in valid_canvases:
raise CyError(f'{canvas} is invalid. Use {valid_canvases}', caller=sys._getframe(1).f_code.co_name)
def verify_node_shapes(shapes, valid_shapes):
"""Validate list of proposed shapes for nodes
Args:
shapes (list or str): shapes (e.g., 'RECTANGLE', 'HEXAGON')
valid_shapes (list): a list of valid shapes
Returns:
list or str: shape(s), updated old shape names to new ones
Raises:
CyError: if a shape is invalid
Examples:
>>> verify_node_shapes('RECTANGLE', styles.get_node_shapes())
['RECTANGLE']
>>> verify_node_shapes(['RECTANGLE', 'DIAMOND'], styles.get_node_shapes())
['RECTANGLE', 'DIAMOND']
"""
def verify_node_shape(shape, valid_shapes):
shape = 'ROUND_RECTANGLE' if shape == 'round_rect' else shape
shape = 'RECTANGLE' if shape == 'rect' else shape.upper()
if shape in valid_shapes:
return shape
raise CyError(
f'"{shape}" is not a valid shape. Please note that some older shapes are no longer available. For valid ones check get_node_shapes().',
caller=sys._getframe(2).f_code.co_name)
if shapes is None: return None
if isinstance(shapes, list):
return [verify_node_shape(shape, valid_shapes) for shape in shapes]
else:
return verify_node_shape(shapes, valid_shapes)
def verify_edge_shapes(shapes, valid_shapes, style_name, style_authority):
"""Validate list of proposed shapes for edges
Args:
shapes (list or str): line styles (e.g., 'ZIGZAG', 'SOLID')
valid_line_styles (list): a list of valid shapes
style_name (str): name of the style being validated
style_authority (str): plausible function for getting list of valid shapes
Returns:
list or str: the style
Raises:
CyError: if a style is invalid
Examples:
>>> verify_edge_shapes('SOLID', styles.get_line_styles(), 'line style', 'get_line_styles')
['SOLID']
>>> verify_edge_shapes(['SOLID', 'ZIGZAG'], styles.get_line_styles(), 'line style', 'get_line_styles')
['SOLID', 'ZIGZAG']
"""
def verify_edge_shape(shape, valid_shapes, style_name, style_authority):
shape = shape.upper()
if shape in valid_shapes:
return shape
raise CyError(f'"{shape}" is not a valid {style_name}. For valid ones check {style_authority}().',
caller=sys._getframe(2).f_code.co_name)
if shapes is None: return None
if isinstance(shapes, list):
return [verify_edge_shape(shape, valid_shapes, style_name, style_authority) for shape in shapes]
else:
return verify_edge_shape(shapes, valid_shapes, style_name, style_authority)
def verify_bools(bool_values):
"""Validate list of boolean values
Args:
(list or str): boolean values (e.g., True or False)
Returns:
list or str: the style
Raises:
CyError: if a style is invalid
Examples:
>>> verify_bools(True)
True
>>> verify_bools('True')
'True'
>>> verify_bools([True, False])
[True, False]
"""
def verify_bool(bool_value):
if isinstance(bool_value, bool):
return bool_value
elif isinstance(bool_value, str) and bool_value.upper() in {'TRUE', 'FALSE'}:
return bool_value
raise CyError(f'"{bool_value}" is not a valid boolean. It must be either true or false.',
caller=sys._getframe(2).f_code.co_name)
if bool_values is None: return None
if isinstance(bool_values, list):
return [verify_bool(bool_value) for bool_value in bool_values]
else:
return verify_bool(bool_values)
def verify_strs(str_values):
"""Validate list of string values
Args:
(list or str): string values (e.g., 'happy'
Returns:
list or str: the style
Raises:
CyError: if a style is invalid
Examples:
>>> verify_strs('happy')
'happy'
>>> verify_bools(['happy', 'sad'])
['happy', 'sad']
"""
def verify_str(str_value):
if isinstance(str_value, str):
return str_value
raise CyError(f'"{str_value}" is not a valid string.',
caller=sys._getframe(2).f_code.co_name)
if str_values is None: return None
if isinstance(str_values, list):
return [verify_str(str_value) for str_value in str_values]
else:
return verify_str(str_values)
def normalize_rotation(degree):
"""Validates and fixes rotation values from -180 to +180 range to match GUI
Args:
degree (int or float): an angle in degrees
Returns:
int or float: angle normalized to [-180..+180]
Raises:
CyError: if angle is invalid
Examples:
>>> normalize_rotation(200)
"""
if not (isinstance(degree, float) or isinstance(degree, int)):
raise CyError(f'Angle must be a number.', caller=sys._getframe(1).f_code.co_name)
while degree < -180:
degree += 360
while degree > 180:
degree -= 360
return degree
[docs]def node_name_to_node_suid(node_names, network=None, base_url=DEFAULT_BASE_URL, *, unique_list=False):
"""Translate one node name or a list of node names into a list of SUIDs.
List can contain either names or SUIDs. If the list contains all SUIDs and no names, the list
is returned.
If a name occurs multiple times in the list and unique_list=True, a different SUID is returned
for each name instance, provided that the network has enough same-named edges. If not, an error is returned.
If a name occures multiple times but unique_list=False, a list of SUIDs is returned for each name instance. If there
is only one name, the SUID is returned as a scalar.
Args:
node_names (str or list): an node name or a list of node names
network (SUID or str or None): Name or SUID of a network. Default is the
"current" network active in Cytoscape.
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
unique_list (bool): True if duplicate node names refer to different nodes; False if it doesn't matter
Returns:
list: [<SUID or SUID list corresponding to each name>] or None if node_names is None
Raises:
CyError: if network name or SUID doesn't exist
requests.exceptions.RequestException: if can't connect to Cytoscape or Cytoscape returns an error
Examples:
>>> node_name_to_node_suid('YDR277C')
[1022]
>>> node_name_to_node_suid(['YDR277C', 'YDL194W'], network='myNetwork')
[1022, 1023]
>>> node_name_to_node_suid('YDR277C, YDL194W', network='myNetwork')
[1022, 1023]
>>> node_name_to_node_suid([1022, 1023], network='myNetwork')
[1022, 1023]
>>> node_name_to_node_suid(['YDR277C', 'YDR277C'], network='myNetwork', unique_list=True)
[1022, 1024]
>>> node_name_to_node_suid(['YDR277C', 'YDR277C', 'YDL194W'], network='myNetwork')
[[1022, 1024], [1022, 1024], 1023]
Note:
To identify a node whose name contains a comma, use '\\\\' to escape the comma. For example,
'node1, node\\\\,2' identifies 'node1' and 'node,2'.
"""
return _item_to_suid(node_names, 'node', network=network, base_url=base_url, unique_list=unique_list)
[docs]def node_suid_to_node_name(node_suids, network=None, base_url=DEFAULT_BASE_URL):
"""Translate one node SUID or a list of node SUIDs into a list of names.
List can contain a mixture of names and SUIDs. If it does, only the SUIDs are translated,
but all entries are returned. If the list contains all names and no SUIDs, the list is returned.
Args:
node_suids (SUID or list): an edge SUID or a list of edge SUIDs
network (SUID or str or None): Name or SUID of a network. Default is the
"current" network active in Cytoscape.
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
Returns:
list: [<name corresponding to each SUID>] or None if node_suids is None
Raises:
CyError: if network name or SUID doesn't exist
requests.exceptions.RequestException: if can't connect to Cytoscape or Cytoscape returns an error
Examples:
>>> node_suid_to_node_name(1022)
['YDR277C']
>>> node_suid_to_node_name([1022, 1023], network='myNetwork')
['YDR277C', 'YDL194W']
>>> node_suid_to_node_name(['YDR277C', 'YDL194W'], network='myNetwork')
['YDR277C', 'YDL194W']
>>> node_suid_to_node_name('YDR277C, YDL194W', network='myNetwork')
['YDR277C', 'YDL194W']
"""
if node_suids is None: return None
node_suids = normalize_list(node_suids)
df = tables.get_table_columns('node', ['name'], 'default', network, base_url=base_url)
all_names = df['name'].values
test_present = [x in all_names for x in node_suids]
if not False in test_present:
return node_suids
all_suids_list = df.index.tolist()
try:
# map all SUIDS into column names ... all SUIDs *must* be actual SUIDs
node_names = [all_names[all_suids_list.index(node_suid)] for node_suid in node_suids]
return node_names
except Exception as e:
raise CyError(f'Invalid node SUID in list: {node_suids}')
[docs]def edge_name_to_edge_suid(edge_names, network=None, base_url=DEFAULT_BASE_URL, *, unique_list=False):
"""Translate one edge name or a list of edge names into a list of SUIDs.
List can contain either names or SUIDs. If the list contains all SUIDs and no names, the list
is returned.
If a name occurs multiple times in the list and unique_list=True, a different SUID is returned
for each name instance, provided that the network has enough same-named edges. If not, an error is returned.
If a name occures multiple times but unique_list=False, a list of SUIDs is returned for each name instance. If there
is only one name, the SUID is returned as a scalar.
Args:
edge_names (str or list): an edge name or a list of edge names
network (SUID or str or None): Name or SUID of a network. Default is the
"current" network active in Cytoscape.
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
unique_list (bool): True if duplicate edge names refer to different edges; False if it doesn't matter
Returns:
list: [<SUID or SUID listcorresponding to each name>] or None if edge_names is None
Raises:
CyError: if network name or SUID doesn't exist
requests.exceptions.RequestException: if can't connect to Cytoscape or Cytoscape returns an error
Examples:
>>> edge_name_to_edge_suid('YDR277C (pp) YDL194W')
[1022]
>>> edge_name_to_edge_suid(1022)
[1022]
>>> edge_name_to_edge_suid(['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W'], network='myNetwork')
[1022, 1023]
>>> edge_name_to_edge_suid('YDR277C (pp) YDL194W, YDR277C (pp) YDR206W', network='myNetwork')
[1022, 1023]
>>> edge_name_to_edge_suid([1022, 1023], network='myNetwork')
[1022, 1023]
>>> edge_name_to_edge_suid(['YDR277C (pp) YDL194W', 'YDR277C (pp) YDL194W'], network='myNetwork', unique_list=True)
[1022, 1024]
>>> edge_name_to_edge_suid(['YDR277C (pp) YDL194W', 'YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W'], network='myNetwork')
[[1022, 1024], [1022, 1024], 1023]
Note:
To identify a node whose name contains a comma, use '\\\\' to escape the comma. For example,
'node1 (pd) node\\\\,2' identifies 'node1 (pd) node,2'.
"""
return _item_to_suid(edge_names, 'edge', network=network, base_url=base_url, unique_list=unique_list)
[docs]def edge_suid_to_edge_name(edge_suids, network=None, base_url=DEFAULT_BASE_URL):
"""Translate one edge SUID or a list of edge SUIDs into a list of names.
List can contain a mixture of names and SUIDs. If it does, only the SUIDs are translated,
but all entries are returned. If the list contains all names and no SUIDs, the list is returned.
Args:
edge_suids (SUID or list): an edge SUID or a list of edge SUIDs
network (SUID or str or None): Name or SUID of a network. Default is the
"current" network active in Cytoscape.
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
Returns:
list: [<name corresponding to each SUID>] or None if edge_suids is None
Raises:
CyError: if network name or SUID doesn't exist
requests.exceptions.RequestException: if can't connect to Cytoscape or Cytoscape returns an error
Examples:
>>> edge_suid_to_edge_name(1022)
['YDR277C (pp) YDL194W']
>>> edge_suid_to_edge_name('1022, 1023')
['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W']
>>> edge_suid_to_edge_name([1022, 1023], network='myNetwork')
['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W']
>>> edge_suid_to_edge_name(['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W'], network='myNetwork')
['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W']
"""
if edge_suids is None: return None
edge_suids = normalize_list(edge_suids)
df = tables.get_table_columns('edge', ['name'], 'default', network, base_url=base_url)
all_names = df['name'].values
test = [edge_suid in all_names for edge_suid in edge_suids]
if not False in test: return edge_suids # the list already had valid names
all_suids_list = df.index.tolist()
try:
# map all SUIDS into column names ... all SUIDs *must* be actual SUIDs
edge_names = [all_names[all_suids_list.index(edge_suid)] for edge_suid in edge_suids]
return edge_names
except Exception as e:
raise CyError(f'Invalid edge SUID in list: {edge_suids}')
# ------------------------------------------------------------------------------
# TODO: R had netowrk=network, which looks like a typo
[docs]def table_column_exists(table_column, table, network=None, base_url=DEFAULT_BASE_URL):
"""Checks to see if a particular column name exists in the specific table.
Args:
table_column (str): name of column within table
table (str): name of table to check (e.g., 'node', 'edge', 'network')
network (SUID or str or None): Name or SUID of a network. Default is the
"current" network active in Cytoscape.
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
Returns:
bool: True if column exists, False if not
Raises:
CyError: if table or network name or SUID doesn't exist
requests.exceptions.RequestException: if can't connect to Cytoscape or Cytoscape returns an error
Examples:
>>> table_column_exists('YDL194W', 'node')
True
>>> table_column_exists('bogus', 'edge', network='myNetwork')
False
"""
if table_column not in tables.get_table_column_names(table, network=network, base_url=base_url):
narrate('Column ' + table_column + ' does not exist in the ' + table + ' table.')
return False
return True
# ------------------------------------------------------------------------------
def check_supported_versions(cyrest=1, cytoscape=3.6, base_url=DEFAULT_BASE_URL, caller=None, test_cytoscape=None):
"""Checks to see if min supported versions of api and cytoscape are running.
Extracts numerics from api, major and patch cytoscape versions before making comparison, per semantic versioning @ https://semver.org/
Args:
cyrest (int): minimum CyREST version
cytoscape (float or str): minimum Cytoscape version ... should be str if version > 3.9
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
Returns:
None or Str: Str is explanation if error was found: otherwise, None
Raises:
AttributeError: if required version can't be parsed
Examples:
>>> check_supported_versions(1, 3.7)
>>> check_supported_versions(1, '3.10')
>>> check_supported_versions(1, '3.10.0')
"""
if isinstance(cytoscape, float): cytoscape = str(cytoscape)
v = cytoscape_system.cytoscape_version_info(base_url=base_url)
v_api_str = v['apiVersion']
v_cy_str = v['cytoscapeVersion'] if test_cytoscape is None else test_cytoscape
v_api_num = int(re.match('v([0-9]+)$', v_api_str).group(1))
# Check the CyREST version
if cyrest > v_api_num:
return 'CyREST API version %d or greater is required. You are currently working with version %d.' % (cyrest, v_api_num)
# Check the Cytoscape version
re_v_cytoscape = re.match('^([0-9]+)\\.([0-9]+)\\.([0-9]+).*$', v_cy_str)
v_cytoscape_major = int(re_v_cytoscape.group(1))
v_cytoscape_minor = int(re_v_cytoscape.group(2))
v_cytoscape_patch = int(re_v_cytoscape.group(3))
re_cytoscape = re.match('^([0-9]+)\\.([0-9]+)?(\\.[0-9]+)?(-.*)*$', cytoscape)
required_cytoscape_major = int(re_cytoscape.group(1))
required_cytoscape_minor = int(re_cytoscape.group(2))
if re_cytoscape.group(3) is None:
required_cytoscape_patch = 0
else:
required_cytoscape_patch = int(re_cytoscape.group(3)[1:]) # Strip leading '.' and take the rest
if v_cytoscape_major > required_cytoscape_major or \
(v_cytoscape_major == required_cytoscape_major and v_cytoscape_minor > required_cytoscape_minor) or \
(v_cytoscape_major == required_cytoscape_major and v_cytoscape_minor == required_cytoscape_minor and v_cytoscape_patch >= required_cytoscape_patch):
return None
else:
return f'Cytoscape version {cytoscape} or greater is required. You are currently working with version {v_cy_str}.'
[docs]def verify_supported_versions(cyrest=1, cytoscape=3.6, base_url=DEFAULT_BASE_URL, caller=None):
"""Throws exception if min supported versions of api and cytoscape are not running.
Extracts numerics from api and major cytoscape versions before making comparison.
Args:
cyrest (int): minimum CyREST version
cytoscape (float or str): minimum Cytoscape version ... should be str if version > 3.9
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
caller (str): name of function in which error is to be reported
Returns:
None
Raises:
CyError: if required version is greater than current version
AttributeError: if required version can't be parsed
Examples:
>>> verify_supported_versions(1, 3.7)
>>> verify_supported_versions(1, '3.10')
>>> verify_supported_versions(1, '3.10.1')
"""
nogo = check_supported_versions(cyrest=cyrest, cytoscape=cytoscape, base_url=base_url)
if nogo:
if caller is None: caller = sys._getframe(1).f_code.co_name
raise CyError(f'Function not run due to unsupported version: {nogo}', caller=caller)
def normalize_list(entity):
# Return a Python list of strings given a Python list, a string list of strings, a string list of ints, or a scalar
if isinstance(entity, str): # If it's a string, it could be names, SUIDs, or whatever
scalar_list = str.split(entity, ',')
try:
return [int(x) for x in scalar_list] # for each entry, see if it's a number
except:
return [str.strip(x) for x in scalar_list] # for each entry, get rid of leading/trialing spaces
elif not isinstance(entity, list): # If it's not a string, it could be int, int64 or whatever
# Note that list could contain strings with leading/trailing spaces. Caller will likely think this is an error.
return [entity]
else:
return entity
def prep_post_query_lists(cmd_list=None, cmd_by_col=None):
# Return 'selected' or a comma-separated list of strings as either 'x,y,x' or 'col:x,col:y,col:z'
if cmd_list is None:
cmd_list_ready = 'selected'
else:
cmd_list_normal = normalize_list(cmd_list)
if cmd_by_col is None:
cmd_list_normal = [f'{cmd}' for cmd in cmd_list_normal]
else:
cmd_list_normal = [f'{cmd_by_col}:{cmd}' for cmd in cmd_list_normal]
cmd_list_ready = ','.join(cmd_list_normal)
return cmd_list_ready
def parse_edges(edge_list):
# Convert edge list into list of parts: ["xxx (pp) yyy", "zzz (pp) aaa"] into [("xxx", "pp", "yyy"), ("zzz", "pp", "aaa")]
def split_edge(edge):
res = re.match('(.*) \((.*)\) (.*)', edge)
return (res.group(1), res.group(2), res.group(3))
return [split_edge(x) for x in edge_list]
[docs]def build_url(base_url=DEFAULT_BASE_URL, command=None):
"""Append a command (if it exists) to a base URL.
Args:
base_url (str): Ignore unless you need to specify a custom domain,
port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
and the latest version of the CyREST API supported by this version of py4cytoscape.
command (str): the command (if any) to append to the base_url
Returns:
str: URL composed of base and URL-encoded command
Raises:
none
Examples:
>>> build_url()
'http://127.0.0.1:1234/v1'
>>> build_url('collections/1043355/tables/default')
'http://127.0.0.1:1234/v1/collections/1043355/tables/default'
"""
if command is not None:
return base_url + "/" + urllib.parse.quote(command)
else:
return base_url
# Figure out which kind of visual style mapping is being used
def normalize_mapping(mapping_type, visual_prop_name, supported_mappings, long_name=True):
if mapping_type in ['continuous', 'c', 'interpolate']:
mapped = ('continuous', 'c')
elif mapping_type in ['discrete', 'd', 'lookup']:
mapped = ('discrete', 'd')
elif mapping_type in ['passthrough', 'p']:
mapped = ('passthrough', 'p')
else:
mapped = ('?', '?')
if mapped[1] in supported_mappings:
return mapped[0 if long_name else 1]
else:
raise CyError(
f'mapping_type "{mapping_type}" for property "{visual_prop_name}" not recognized ... must be "{supported_mappings}"')
def normalize_prop_name(prop_name):
if prop_name is None:
raise CyError(f'Invalid visual property ... visual_property must be non-null')
# Convert white space to '_' and uppercase everything (e.g., 'edge color' -> 'EDGE_COLOR')
visual_prop_name = re.sub('\\s+', '_', prop_name).upper()
if visual_prop_name in PROPERTY_NAME_MAP: visual_prop_name = PROPERTY_NAME_MAP[visual_prop_name]
return visual_prop_name
def _item_to_suid(item_names, table_name, network=None, base_url=DEFAULT_BASE_URL, unique_list=False):
# Translate a list of node or edge names into a list of SUIDs ... account for duplicatated names if list is unique
if item_names is None: return None
item_names = normalize_list(item_names)
df = tables.get_table_columns(table_name, ['name'], 'default', network, base_url=base_url)
# Check all item names to see if they're all valid SUIDs ... if so, we're already done
all_suids = df.index
try:
item_names = [int(i) for i in item_names]
found_valid_suids = [i in all_suids for i in item_names]
if False not in found_valid_suids:
return item_names
except:
pass
# map all names into SUIDs ... all names *must* be actual names ... and must be str() to match the 'name' column
item_names = [str(item_name) for item_name in item_names]
item_name_to_suid_list = {item_name: list(df[df.name.eq(item_name)].index.values) for item_name in item_names}
try:
if unique_list:
suid_list = [item_name_to_suid_list[item_name].pop(0) for item_name in item_names]
else:
suid_list = [item_name_to_suid_list[item_name] for item_name in item_names]
suid_list = [s[0] if len(s) <= 1 else s for s in
suid_list] # return scalar if len(list) = 1, blow up if len(list) = 0
except:
raise CyError(f'Invalid name in {table_name} name list: {item_names}')
return suid_list