# -*- coding: utf-8 -*-
"""Utility functions useful across multiple modules.
"""
"""Copyright 2020 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.
"""
DEFAULT_BASE_URL: str = 'http://127.0.0.1:1234/v1'
# External library imports
import urllib.parse
import re
import sys
# Internal module imports
from . import tables
from . import cytoscape_system
# Internal module convenience imports
from .exceptions import CyError
from .py4cytoscape_logger import narrate
# ==============================================================================
# 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 palette
Raises:
KeyError: if 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_hex_colors(colors):
"""Validate and provide user feedback when hex color codes (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:
None
Raises:
CyError: if color is invalid
Examples:
>>> verify_hex_colors('#92C5DE')
>>> verify_hex_colors(['#053061', '#2166AC', '#4393C3', '#92C5DE', '#D1E5F0', '#F7F7F7', '#FDDBC7', '#F4A582', '#D6604D', '#B2182B', '#67001F'])
"""
if colors is None: return
if not isinstance(colors, list): colors = [colors]
for color in colors:
if not color.startswith('#') or len(color) != 7:
raise CyError(f'"{color}" is not a valid hexadecimal color (has to begin with # and be 7 characters long, for example: #FF00FF).', caller=sys._getframe(1).f_code.co_name)
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:
None
Raises:
CyError: if opacity is invalid
Examples:
>>> verify_opacities(177)
>>> verify_opacities([177, 200])
"""
if opacities is None: return
if not isinstance(opacities, list): opacities = [opacities]
for opacity in opacities:
if not (isinstance(opacity, float) or isinstance(opacity, int)) or opacity < 0 or opacity > 255:
raise CyError(f'"{opacity}" is not a valid opacity (has to be an integer between 0 and 255).', caller=sys._getframe(1).f_code.co_name)
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:
None
Raises:
CyError: if size is invalid
Examples:
>>> verify_dimensions('width', 50)
>>> verify_dimensions('width', [10, 20])
"""
if sizes is None: return
if not isinstance(sizes, list): sizes = [sizes]
for size in sizes:
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(1).f_code.co_name)
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)
[docs]def node_name_to_node_suid(node_names, network=None, base_url=DEFAULT_BASE_URL):
"""Translate one node name or a list of node names into a list of SUIDs.
List can contain a mixture of names and SUIDs. If it does, only the names are translated,
but all entries are returned. If the list contains all SUIDs and no names, the list is returned.
If a name maps to multiple SUIDs, a list of SUIDs are returned instead of a single SUID.
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.
Returns:
list: [<SUID or SUID list corresponding to each name>]
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', 'AXD206W'], network='myNetwork')
[1022, [1099, 1100]]
"""
if node_names is None: return None
# TODO: Should this be a simple conversion, or a split(',')??
if isinstance(node_names, str): node_names = [node_names]
df = tables.get_table_columns('node', ['name'], 'default', network=network, base_url=base_url)
all_suids = df.index
test_present = [x in all_suids for x in node_names]
if not False in test_present:
return node_names
# map all node names into SUIDs ... all names *must* be actual names ... for names mapping to multiple SUIDs, return a SUID list
node_suids = [list(df[df.name.eq(node_name)].index.values) for node_name in node_names]
if True in [True if len(x) == 0 else False for x in node_suids]:
raise CyError(f'Invalid name in node name list: {node_names}')
node_suids = [x[0] if len(x) == 1 else x for x in node_suids]
return node_suids
[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>]
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']
"""
if node_suids is None: return None
if isinstance(node_suids, str): node_suids = [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):
"""Translate one edge name or a list of edge names into a list of SUIDs.
List can contain a mixture of names and SUIDs. If it does, only the names are translated,
but all entries are returned. If the list contains all SUIDs and no names, the list is returned.
If a name maps to multiple SUIDs, a list of SUIDs are returned instead of a single SUID.
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.
Returns:
list: [<SUID or SUID list corresponding to each name>]
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(['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W'], network='myNetwork')
[1022, 1023]
>>> edge_name_to_edge_suid(['YDR277C (pp) YDL194W', 'YDR277C (pp) AXD206W'], network='myNetwork')
[1022, [1099, 1100]]
"""
if edge_names is None: return None
if isinstance(edge_names, str): edge_names = [edge_names]
df = tables.get_table_columns('edge', ['name'], 'default', network, base_url=base_url)
all_suids = df.index
test_present = [x in all_suids for x in edge_names]
if not False in test_present:
return edge_names
# map all edge names into SUIDs ... all names *must* be actual names ... for names mapping to multiple SUIDs, return a SUID list
edge_suids = [list(df[df.name.eq(edge_name)].index.values) for edge_name in edge_names]
if True in [True if len(x) == 0 else False for x in edge_suids]:
raise CyError(f'Invalid edge name in list: {edge_names}')
edge_suids = [x[0] if len(x) == 1 else x for x in edge_suids]
return edge_suids
[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>]
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], network='myNetwork')
['YDR277C (pp) YDL194W', 'YDR277C (pp) YDR206W']
"""
if edge_suids is None: return None
if isinstance(edge_suids, str): edge_suids = [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
# ------------------------------------------------------------------------------
[docs]def verify_supported_versions(cyrest=1, cytoscape=3.6, base_url=DEFAULT_BASE_URL):
"""Checks to see if min supported versions of api and cytoscape are running.
Extracts numerics from api and major cytoscape versions before making comparison.
Args:
cyrest (int): minimum CyREST version
cytoscape (float): minimum Cytoscape version
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
Raises:
none
Examples:
>>> verify_supported_versions(1, 3.7)
"""
v = cytoscape_system.cytoscape_version_info(base_url=base_url)
v_api_str = v['apiVersion']
v_cy_str = v['cytoscapeVersion']
v_api_num = int(re.match('v([0-9]+)$', v_api_str).group(1))
v_cy_num = float(re.match('([0-9]+\\.[0-9]+)\\..*$', v_cy_str).group(1))
nogo = None
if cyrest > v_api_num:
nogo = 'CyREST API version %d or greater is required. You are currently working with version %d.' % (cyrest, v_api_num)
if cytoscape > v_cy_num:
nogo = 'Cytoscape version %0.2g or greater is required. You are currently working with version %0.2g.' % (cytoscape, v_cy_num)
if nogo: raise CyError(f'Function not run due to unsupported version: {nogo}')
[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