Constants
Contains constants used by the NDEx2 Python Client
- ndex2.constants.ASPECT_ID = 'id'
Key for aspect ID
- ndex2.constants.ASPECT_VALUES = 'v'
Key for aspect values
- ndex2.constants.ATTR_DATATYPE = 'd'
Key for attribute data type
- ndex2.constants.ATTR_NAME = 'n'
Key for attribute name
- ndex2.constants.BOOLEAN_DATATYPE = 'boolean'
Boolean data type for CX
- ndex2.constants.CARTESIAN_LAYOUT_ASPECT = 'cartesianLayout'
Name of opaque aspect containing coordinates of nodes
"cartesianLayout": [ { "node": 0, "x": 25.0, "y": 50.0 }, { "node": 1, "x": -10.0, "y": -200.0 } ]
Note
Although the name implies a cartesian coordinate system, that is actually wrong. The Y access is inverted so lower values of Y are rendered higher on a graph. 0,0 is considered upper left corner, but negative values are allowed
- ndex2.constants.DOUBLE_DATATYPE = 'double'
Double data type for CX
- ndex2.constants.EDGES_ASPECT = 'edges'
Key for nodes attribute
- ndex2.constants.EDGE_ID = '@id'
Key for id of edge
- ndex2.constants.EDGE_INTERACTION = 'i'
Key for edge interaction
- ndex2.constants.EDGE_SOURCE = 's'
Key for edge source
- ndex2.constants.EDGE_TARGET = 't'
Key for edge target
- ndex2.constants.INTEGER_DATATYPE = 'integer'
Integer data type for CX
- ndex2.constants.LAYOUT_NODE = 'node'
Key for node id in
CARTESIAN_LAYOUT_ASPECT
opaque aspect
- ndex2.constants.LAYOUT_X = 'x'
Key for X coordinate in
CARTESIAN_LAYOUT_ASPECT
opaque aspect
- ndex2.constants.LAYOUT_Y = 'y'
Key for Y coordinate in
CARTESIAN_LAYOUT_ASPECT
opaque aspect
- ndex2.constants.LAYOUT_Z = 'z'
Key for Z coordinate in
CARTESIAN_LAYOUT_ASPECT
opaque aspect
- ndex2.constants.LIST_OF_BOOLEAN = 'list_of_boolean'
List of Boolean data type for CX
- ndex2.constants.LIST_OF_DOUBLE = 'list_of_double'
List of Double data type for CX
- ndex2.constants.LIST_OF_INTEGER = 'list_of_integer'
List of Integer data type for CX
- ndex2.constants.LIST_OF_LONG = 'list_of_long'
List of Long data type for CX
- ndex2.constants.LIST_OF_STRING = 'list_of_string'
List of String data type for CX
- ndex2.constants.LONG_DATATYPE = 'long'
Long data type for CX
- ndex2.constants.NET_ATTR_NAME = 'n'
Key for network attribute name
- ndex2.constants.NET_ATTR_VALUE = 'v'
Key for network attribute value
- ndex2.constants.NODES_ASPECT = 'nodes'
Key for nodes attribute
- ndex2.constants.NODE_ATTR_DATATYPE = 'd'
Key for node attribute data type
- ndex2.constants.NODE_ATTR_NAME = 'n'
Key for node attribute name
- ndex2.constants.NODE_ATTR_PROPERTYOF = 'po'
Key for node property of
- ndex2.constants.NODE_ATTR_VALUE = 'v'
Key for node attribute value
- ndex2.constants.NODE_ID = '@id'
Key for id of node
- ndex2.constants.NODE_NAME = 'n'
Key for node name
- ndex2.constants.NODE_REPRESENTS = 'r'
Key for node represents
- ndex2.constants.STRING_DATATYPE = 'string'
String data type for CX
- ndex2.constants.VALID_ATTRIBUTE_DATATYPES = ['boolean', 'double', 'integer', 'long', 'string', 'list_of_boolean', 'list_of_double', 'list_of_integer', 'list_of_long', 'list_of_string']
List of valid attribute data types
Miscellaneous
- class ndex2.util.DataConverter[source]
Base class for subclasses that convert CX data types to/from native data types
- convert_value(value=None, datatype=None)[source]
Defines method to converts value from CX to native data type using datatype as a guide
- Parameters:
value (object) – Value to convert
datatype (str) – CX data type which is one of the following:
ndex2.constants.VALID_ATTRIBUTE_DATATYPES
- Raises:
NotImplementedError – Always raises this error cause subclasses should implement
- Returns:
Always raises
NotImplementedError
- class ndex2.util.PandasDataConverter[source]
Converts CX values to native Python data types via
PandasDataConverter.convert_value()
methodNew in version 3.5.0.
- convert_value(value=None, datatype=None)[source]
Converts value parameter passed in to type based on value of datatype parameter passed in. This is used in data conversion by
to_pandas_dataframe()
New in version 3.5.0.
Conversion rules for different values of datatype parameter:
STRING_DATATYPE
orNone
value is converted by
str
and returned
-
-
INTEGER_DATATYPE
orLONG_DATATYPE
LIST_OF_STRING
,LIST_OF_BOOLEAN
LIST_OF_DOUBLE
,LIST_OF_INTEGER
,LIST_OF_LONG
If value is NOT of type
list
then the value converted as if it’s datatype isSTRING_DATATYPE
. If value is a list, each element is converted as if it’s datatype isSTRING_DATATYPE
and values oflist
are converted to a comma delimitedstr
Example usage:
from ndex2.util import PandasDataConverter converter = PandasDataConverter() # converts number to type str res = converter.convert_value(123, 'string') # would output <class 'str'> print(type(res))
Exceptions
- class ndex2.exceptions.NDExError[source]
Base Exception for all NDEx2 Python Client Exceptions
Warning
Many methods in this code base still incorrectly raise errors not derived from this base class
- class ndex2.exceptions.NDExUnauthorizedError[source]
Raised if unable to authenticate, either due to lack of or invalid credentials.