In [2]:
import os
import re
import sys
In [3]:
cyrest_folder="/Users/jboucas/py2cytoscape/py2cytoscape/cyrest/"
docs_folder="/Users/jboucas/Desktop/tmp_docs_py2cy/"
In [4]:
files=os.listdir(cyrest_folder)
no_files=["cyrest.py","__init__.py",'base.py']
files=[ s for s in files if s not in no_files ]
files=[ s for s in files if "pyc" not in s ]
files=[ s for s in files if s in ["table.py", ]]
In [18]:
for f in ["cyndex2.py","apply.py","layout.py","styles.py","table.py","session.py","enrichmentmap.py","apps.py","ui.py","collections.py","networks.py"]:
#for f in ["table.py"]:
print f
sys.stdout.flush()
functions={}
mainspace=f.split(".")[0]
print mainspace
with open(cyrest_folder+f, "r") as fin:
funcstring=None
for l in fin:
l_=l.rstrip("\n")
if (" def " in l_) & ("__" not in l_):
fname=re.search('def (.*)\(', l_)
fname=fname.group(1)
func_title="## ***cyclient.%s.%s***" %(mainspace,fname)
#print l_
if "\\" not in l_:
func=re.search('def (.*):', l_)
func=func.group(1)
func="**`cyclient.%s.%s`**" %(mainspace,func)
functions[fname]={'title':func_title,'func':func}
else:
funcstring=l_.strip("\\")
elif funcstring:
funcstring=funcstring+l_
if ":" in funcstring:
func=re.search('def (.*):', funcstring)
func=func.group(1)
funcstring=None
func="**`cyclient.%s.%s`**" %(mainspace,func)
functions[fname]={'title':func_title,'func':func}
with open(cyrest_folder+f, "r") as fin:
collect=False
doc=[]
function_found=False
for l in fin:
l_=l.rstrip("\n")
if (" def " in l_) & ("__" not in l_):
fname=re.search('def (.*)\(', l_)
fname=fname.group(1)
func_title="## ***cyclient.%s.%s***" %(mainspace,fname)
function_found=True
if ('"""' in l_ ) & (len( [s for s in doc if '"""' in s ]) == 0 ) & (function_found):
collect=True
if ('"""' in l_ ) & (len([s for s in doc if '"""' in s ]) == 1 ) & (function_found):
functions[fname]["docs"]=doc
doc=[]
collect=False
if (collect) & (function_found):
doc.append( l_.rstrip("\n") )
with open(docs_folder+f.replace(".py", ".md"), "w") as fout:
valid_functions=functions.keys()
valid_functions=[ s for s in valid_functions if s != "target"]
for docf in valid_functions:
try:
doc_=functions[docf]["docs"][1:]
except:
print f, docf, functions[docf]
doc_=functions[docf]["docs"][1:]
collect=True
description=[]
for s in doc_:
if (":param" not in s) & (collect==True):
desc=s.strip(" ")
if len(desc) > 0:
description.append(desc)
elif ":param" in s:
collect=False
description="\n".join(description)
params=[]
params_={}
pname=None
for p in doc_:
if ":param " in p:
#print p
pname=re.search(':param (.*):', p)
pname=pname.group(1)
params.append(pname)
pdesc=p.split("%s:"%pname)[-1].strip(" ")
params_[pname]=pdesc
elif pname:
pdesc=params_[pname]
pdesc=pdesc+"\n"+p.strip(" ")
params_[pname]=pdesc
params_text=[]
for p in params:
text="* **`%s`** %s" %(p, params_[p])
params_text.append(text)
ftitle=functions[docf]["title"]
func=functions[docf]["func"]
docs_text=ftitle+"\n\n"+func+"\n\n"+description+"\n\n"+"\n".join(params_text)+"\n\n___\n\n"
docs_text=docs_text.replace(":returns:", "* **`returns`**")
print docs_text
fout.write(docs_text)
cyndex2.py
cyndex2
## ***cyclient.cyndex2.saveNetworkToNdex***
**`cyclient.cyndex2.saveNetworkToNdex(suid, body, verbose=None)`**
Save a network/collection to NDEx
* **`suid`** Cytoscape Collection/Subnetwork SUID
* **`body`** Properties required to save network to NDEx.
* **`verbose`** print more
* **`returns`** 200: successful operation; 404: Network does not exist
___
## ***cyclient.cyndex2.getAppInfo***
**`cyclient.cyndex2.getAppInfo(verbose=None)`**
App version and other basic information will be provided.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.cyndex2.updateCurrentNetworkInNdex***
**`cyclient.cyndex2.updateCurrentNetworkInNdex(body, verbose=None)`**
Update current network's record in NDEx
* **`body`** Properties required to update a network record in NDEx.
* **`verbose`** print more
* **`returns`** 200: successful operation; 404: Network does not exist
___
## ***cyclient.cyndex2.getNetworkSummary***
**`cyclient.cyndex2.getNetworkSummary(suid, verbose=None)`**
Returns summary of collection containing the specified network.
* **`suid`** Cytoscape Collection/Subnetwork SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.cyndex2.saveCurrentNetworkToNdex***
**`cyclient.cyndex2.saveCurrentNetworkToNdex(body, verbose=None)`**
Save current network/collection to NDEx
* **`body`** Properties required to save current network to NDEx.
* **`verbose`** print more
* **`returns`** 200: successful operation; 404: Current network does not exist
___
## ***cyclient.cyndex2.updateNetworkInNdex***
**`cyclient.cyndex2.updateNetworkInNdex(suid, body, verbose=None)`**
Update an NDEx network.
* **`suid`** Cytoscape Collection/Subnetwork SUID
* **`body`** Properties required to update a network record in NDEx.
* **`verbose`** print more
* **`returns`** 200: successful operation; 404: Network does not exist
___
## ***cyclient.cyndex2.getCurrentNetworkSummary***
**`cyclient.cyndex2.getCurrentNetworkSummary(verbose=None)`**
Returns summary of collection contains current network.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.cyndex2.createNetworkFromNdex***
**`cyclient.cyndex2.createNetworkFromNdex(body, verbose=None)`**
Import network(s) from NDEx.
* **`body`** Properties required to import network from NDEx.
* **`verbose`** print more
* **`returns`** 200: successful operation; 404: Network does not exist
___
apply.py
apply
## ***cyclient.apply.getLayoutParameters***
**`cyclient.apply.getLayoutParameters(algorithmName, verbose=None)`**
Returns all editable parameters for the Layout algorithm specified by the `algorithmName` parameter.
* **`algorithmName`** Name of the Layout algorithm
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.copyCurrentLayout***
**`cyclient.apply.copyCurrentLayout(sourceViewSUID, targetViewSUID, body, verbose=None)`**
Copy one network view layout onto another, setting the node location and view scale to match. This makes visually comparing networks simple.
* **`sourceViewSUID`** Source network view SUID (or "current")
* **`targetViewSUID`** Target network view SUID (or "current")
* **`body`** Clone the specified network view layout onto another network view -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation; 404: Network View does not exist
___
## ***cyclient.apply.updateLayoutParameters***
**`cyclient.apply.updateLayoutParameters(algorithmName, body, verbose=None)`**
Updates the Layout parameters for the Layout algorithm specified by the `algorithmName` parameter.
* **`algorithmName`** Name of the layout algorithm
* **`body`** A list of Layout Parameters with Values.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.apply.applyStyle***
**`cyclient.apply.applyStyle(styleName, networkId, verbose=None)`**
Applies the Visual Style specified by the `styleName` parameter to the network specified by the `networkId` parameter.
* **`styleName`** Name of the Visual Style
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.getCompatibleColumnDataTypes***
**`cyclient.apply.getCompatibleColumnDataTypes(algorithmName, verbose=None)`**
Returns a list of all compatible column data types for the Layout algorithm specified by the `algorithmName` parameter.
* **`algorithmName`** Name of layout algorithm
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.fitContent***
**`cyclient.apply.fitContent(networkId, verbose=None)`**
Fit the first available Network View for the Network specified by the `networkId` parameter to the current window.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.getStyleNames***
**`cyclient.apply.getStyleNames(verbose=None)`**
Returns a list of all Visual Style names. Style names may not be unique.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.bundleEdge***
**`cyclient.apply.bundleEdge(networkId, verbose=None)`**
Apply edge bundling to the Network specified by the `networkId` parameter. Edge bundling is executed with default parameters; at present, optional parameters are not supported.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.getLayout***
**`cyclient.apply.getLayout(algorithmName, verbose=None)`**
Returns all the details, including names, parameters, and compatible column types for the Layout algorithm specified by the `algorithmName` parameter.
* **`algorithmName`** Name of the Layout algorithm
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.layoutList***
**`cyclient.apply.layoutList(verbose=None)`**
Returns all available layouts as a list of layout names.
<h3>Important Note</h3>
This <strong>does not include yFiles layout algorithms</strong>, due to license issues.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.apply.applyLayout***
**`cyclient.apply.applyLayout(algorithmName, networkId, column, verbose=None)`**
Applies the Layout specified by the `algorithmName` parameter to the Network specified by the `networkId` parameter. If the Layout is has an option to use a Column, it can be specified by the `column` parameter.
* **`algorithmName`** Name of layout algorithm
* **`networkId`** SUID of the Network
* **`column`** Name of the Column to be used by the Layout -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
layout.py
layout
styles.py
styles
## ***cyclient.styles.getSingleVisualProperty***
**`cyclient.styles.getSingleVisualProperty(visualProperty, verbose=None)`**
Return the Visual Property specified by the `visualProperty` parameter.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`visualProperty`** ID of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getDefaultValue***
**`cyclient.styles.getDefaultValue(name, vp, verbose=None)`**
Returns the default value for the Visual Property specified by the `name` and `vp` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`name`** Name of the Visual Style containing the Visual Property
* **`vp`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getMappings***
**`cyclient.styles.getMappings(name, verbose=None)`**
Returns a list of all Visual Mappings used in the Visual Style specified by the `name` parameter.
The types of mapping available in Cytoscape are explained in depth [here](http://manual.cytoscape.org/en/stable/Styles.html#how-mappings-work). An example of the data format for each is included below. For additional details, such as what Visual Properties supported by each Mapping, click on the relevant JavaDoc API link.
#### Discrete Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/DiscreteMapping.html)
```
{ "mappingType": "discrete",
"mappingColumn": "interaction",
"mappingColumnType": "String",
"visualProperty": "EDGE_WIDTH",
"map": [
{ "key" : "pd",
"value" : "20"
},
{ "key" : "pp",
"value" : "1.5"
}
]
}```
#### Continuous Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/ContinuousMapping.html)
```
{ "mappingType": "continuous",
"mappingColumn": "Degree",
"mappingColumnType": "Integer",
"visualProperty": "NODE_SIZE",
"points": [
{ "value" : 1,
"lesser" : "20",
"equal" : "20",
"greater" : "20"
},
{ "value" : 20,
"lesser" : "120",
"equal" : "120",
"greater" : "220" }
]
}```
#### Passthrough Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/PassthroughMapping.html)
```
{ "mappingType": "passthrough",
"mappingColumn": "name",
"mappingColumnType": "String",
"visualProperty": "EDGE_LABEL"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`name`** Name of the Visual Style
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getAllDependencies***
**`cyclient.styles.getAllDependencies(name, verbose=None)`**
Returns the status of all the Visual Property Dependencies.
* **`name`** Name of the Visual Style
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getStyleCount***
**`cyclient.styles.getStyleCount(verbose=None)`**
Returns the number of Visual Styles available in the current session
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.updateDependencies***
**`cyclient.styles.updateDependencies(name, body, verbose=None)`**
Sets the value of Visual Property dependencies to the values in the message body.
* **`name`** Name of the Visual Style
* **`body`** A list of dependencies.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.deleteMapping***
**`cyclient.styles.deleteMapping(name, vpName, verbose=None)`**
Deletes the Visual Property mapping specified by the `vpName` and `name` parameters.
* **`name`** Name of the Visual Style containing the Visual Mapping
* **`vpName`** Name of the Visual Property that the Visual Mapping controls
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.getDefaults***
**`cyclient.styles.getDefaults(name, verbose=None)`**
Returns a list of all the default values for the Visual Style specified by the `name` parameter.
* **`name`** Name of the Visual Style
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getVisualProperties***
**`cyclient.styles.getVisualProperties(verbose=None)`**
Get all available Visual Properties.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.updateStyleName***
**`cyclient.styles.updateStyleName(name, body, verbose=None)`**
Updates the name of the Visual Style specified by the `name` parameter.
* **`name`** Original name of the Visual Style
* **`body`** A new name for the Visual Style.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.deleteStyle***
**`cyclient.styles.deleteStyle(name, verbose=None)`**
Deletes the Visual Style specified by the `name` parameter.
* **`name`** Visual Style Name
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.deleteAllStyles***
**`cyclient.styles.deleteAllStyles(verbose=None)`**
Deletes all vision styles except for default style
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.updateMapping***
**`cyclient.styles.updateMapping(name, vp, body, verbose=None)`**
Update the visual mapping specified by the `name` and `vp` parameters.
The types of mapping available in Cytoscape are explained in depth [here](http://manual.cytoscape.org/en/stable/Styles.html#how-mappings-work). An example of the data format for each is included below. For additional details, such as what Visual Properties supported by each Mapping, click on the relevant JavaDoc API link.
#### Discrete Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/DiscreteMapping.html)
```
{ "mappingType": "discrete",
"mappingColumn": "interaction",
"mappingColumnType": "String",
"visualProperty": "EDGE_WIDTH",
"map": [
{ "key" : "pd",
"value" : "20"
},
{ "key" : "pp",
"value" : "1.5"
}
]
}```
#### Continuous Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/ContinuousMapping.html)
```
{ "mappingType": "continuous",
"mappingColumn": "Degree",
"mappingColumnType": "Integer",
"visualProperty": "NODE_SIZE",
"points": [
{ "value" : 1,
"lesser" : "20",
"equal" : "20",
"greater" : "20"
},
{ "value" : 20,
"lesser" : "120",
"equal" : "120",
"greater" : "220" }
]
}```
#### Passthrough Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/PassthroughMapping.html)
```
{ "mappingType": "passthrough",
"mappingColumn": "name",
"mappingColumnType": "String",
"visualProperty": "EDGE_LABEL"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`name`** Name of the Visual Style containing the Visual Mapping
* **`vp`** Name of the Visual Property that the Visual Mapping controls
* **`body`** A list of new mappings.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.getStyle***
**`cyclient.styles.getStyle(name, verbose=None)`**
Visual Style in [Cytoscape.js CSS](http://js.cytoscape.org/#style) format.
* **`name`** Name of the Visual Style
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getStyleNames***
**`cyclient.styles.getStyleNames(verbose=None)`**
Returns a list of all the Visual Style names in the current session.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.createStyle***
**`cyclient.styles.createStyle(body, verbose=None)`**
Creates a new Visual Style using the message body.
Returns the title of the new Visual Style. If the title of the Visual Style already existed in the session, a new one will be automatically generated and returned.
* **`body`** The details of the new Visual Style to be created.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getStyleFull***
**`cyclient.styles.getStyleFull(name, verbose=None)`**
Returns the Visual Style specified by the `name` parameter.
* **`name`** Name of the Visual Style
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.getMapping***
**`cyclient.styles.getMapping(name, vp, verbose=None)`**
Returns the Visual Mapping assigned to the Visual Property specified by the `name` and `vp` parameters.
The types of mapping available in Cytoscape are explained in depth [here](http://manual.cytoscape.org/en/stable/Styles.html#how-mappings-work). An example of the data format for each is included below. For additional details, such as what Visual Properties supported by each Mapping, click on the relevant JavaDoc API link.
#### Discrete Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/DiscreteMapping.html)
```
{ "mappingType": "discrete",
"mappingColumn": "interaction",
"mappingColumnType": "String",
"visualProperty": "EDGE_WIDTH",
"map": [
{ "key" : "pd",
"value" : "20"
},
{ "key" : "pp",
"value" : "1.5"
}
]
}```
#### Continuous Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/ContinuousMapping.html)
```
{ "mappingType": "continuous",
"mappingColumn": "Degree",
"mappingColumnType": "Integer",
"visualProperty": "NODE_SIZE",
"points": [
{ "value" : 1,
"lesser" : "20",
"equal" : "20",
"greater" : "20"
},
{ "value" : 20,
"lesser" : "120",
"equal" : "120",
"greater" : "220" }
]
}```
#### Passthrough Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/PassthroughMapping.html)
```
{ "mappingType": "passthrough",
"mappingColumn": "name",
"mappingColumnType": "String",
"visualProperty": "EDGE_LABEL"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`name`** Name of the Visual Style containing the Visual Property mapping
* **`vp`** Name of the Visual Property that the Visual Mapping controls
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.styles.updateDefaults***
**`cyclient.styles.updateDefaults(name, body, verbose=None)`**
Updates the default values for the Visual Properties in the Visual Style specified by the `name` parameter.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`name`** Name of the Visual Style
* **`body`** A list of Visual Property values to update.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.createMappings***
**`cyclient.styles.createMappings(name, body, verbose=None)`**
Create a new Visual Mapping function and add it to the Visual Style specified by the `name` parameter. Existing mappings in the Visual Style will be overidden by the new mappings created.
The types of mapping available in Cytoscape are explained in depth [here](http://manual.cytoscape.org/en/stable/Styles.html#how-mappings-work). An example of the data format for each is included below. For additional details, such as what Visual Properties supported by each Mapping, click on the relevant JavaDoc API link.
#### Discrete Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/DiscreteMapping.html)
```
{ "mappingType": "discrete",
"mappingColumn": "interaction",
"mappingColumnType": "String",
"visualProperty": "EDGE_WIDTH",
"map": [
{ "key" : "pd",
"value" : "20"
},
{ "key" : "pp",
"value" : "1.5"
}
]
}```
#### Continuous Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/ContinuousMapping.html)
```
{ "mappingType": "continuous",
"mappingColumn": "Degree",
"mappingColumnType": "Integer",
"visualProperty": "NODE_SIZE",
"points": [
{ "value" : 1,
"lesser" : "20",
"equal" : "20",
"greater" : "20"
},
{ "value" : 20,
"lesser" : "120",
"equal" : "120",
"greater" : "220" }
]
}```
#### Passthrough Mapping
[JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/vizmap/mappings/PassthroughMapping.html)
```
{ "mappingType": "passthrough",
"mappingColumn": "name",
"mappingColumnType": "String",
"visualProperty": "EDGE_LABEL"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`name`** Name of the Visual Style
* **`body`** A list of new mappings.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.styles.getRangeValues***
**`cyclient.styles.getRangeValues(vp, verbose=None)`**
Returns a list of all available values for the Visual Property specified by the `vp` parameter.
This method is only for Visual Properties with a Discrete Range, such as NODE_SHAPE or EDGE_LINE_TYPE.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`vp`** ID of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
table.py
table
## ***cyclient.table.import_url***
**`cyclient.table.import_url(self,caseSensitiveNetworkCollectionKeys=None, caseSensitiveNetworkKeys=None,dataTypeList=None,\ DataTypeTargetForNetworkCollection=None,DataTypeTargetForNetworkList=None,\ delimiters=None,delimitersForDataList=None,firstRowAsColumnNames=None,\ KeyColumnForMapping=None,KeyColumnForMappingNetworkList=None,\ keyColumnIndex=None,newTableName=None,startLoadRow=None,\ TargetNetworkCollection=None,TargetNetworkList=None,url=None,\ WhereImportTable=None,verbose=None)`**
Similar to Import Table this uses a long list of input parameters to
specify the attributes of the table, the mapping keys, and the destination
table for the input.
* **`caseSensitiveNetworkCollectionKeys (string, optional)`** Determines wh
ether capitalization is considered in matching and sorting
* **`caseSensitiveNetworkKeys (string, optional)`** Determines whether capi
talization is considered in matching and sorting
* **`dataTypeList (string, optional)`** List of column data types ordered b
y column index (e.g. "string,int,long,double,boolean,intlist" or jus
t "s,i,l,d,b,il")
* **`DataTypeTargetForNetworkCollection (string, optional)`** Select whethe
r to import the data as Node Table Columns, Edge Table Columns, or N
etwork Table Columns
* **`DataTypeTargetForNetworkList (string, optional)`** The data type of th
e targets
* **`delimiters (string, optional)`** The list of delimiters that separate
columns in the table.
* **`delimitersForDataList (string, optional)`** The delimiters between ele
ments of list columns in the table.
* **`firstRowAsColumnNames (string, optional)`** If the first imported row
contains column names, set this to true.
* **`KeyColumnForMapping (string, optional)`** The column in the network to
use as the merge key
* **`KeyColumnForMappingNetworkList (string, optional)`** The column in the
network to use as the merge key
* **`keyColumnIndex (string, optional)`** The column that contains the key
values for this import. These values will be used to match with the
key values in the network.
* **`newTableName (string, optional)`** The title of the new table
* **`startLoadRow (string, optional)`** The first row of the input table to
load. This allows the skipping of headers that are not part of the
import.
* **`TargetNetworkCollection (string, optional)`** The network collection t
o use for the table import
* **`TargetNetworkList (string, optional)`** The list of networks into whic
h the table is imported
* **`url (string)`** The URL of the file or resource that provides the tabl
e or network to be imported.
* **`WhereImportTable (string, optional)`** Determines what network(s) the
imported table will be associated with (if any). A table can be impo
rted into a Network Collection, Selected networks or to an unassigne
d table.
___
## ***cyclient.table.get_column***
**`cyclient.table.get_column(self,column=None,table=None,verbose=None)`**
Get the information about a table column.
* **`column (string, optional)`** Specifies the name of a column in the tab
le
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`returns`** information about a table column
___
## ***cyclient.table.delete_row***
**`cyclient.table.delete_row(self,keyValue=None,table=None,verbose=None)`**
Deletes a row from a table.Requires the table name or SUID and the row key.
* **`keyValue (string)`** Specifies the primary key of a value in the row o
f a table
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.export***
**`cyclient.table.export(self,options=None,OutputFile=None,table=None,verbose=None)`**
Creates a file with name and writes the table there.
* **`options (string, optional)`** The format of the output file.
* **`OutputFile (string, optional)`** The path of the file to export the ta
ble to. Note that the file will be overwritten if it exists.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.loadTableData***
**`cyclient.table.loadTableData(self, df, df_key='index',table="node", table_key_column = "name", network="current",namespace="default",verbose=False)`**
Loads tables into cytoscape.
* **`df`** a pandas dataframe to load
* **`df_key`** key column in df, default="index"
* **`table`** target table, default="node"
* **`table_key_column`** table key column, default="name"
* **`network (string, optional)`** Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
* **`namespace (string, optional)`** Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
* **`verbose`** print more information
* **`returns`** output of put request
___
## ***cyclient.table.rename_column***
**`cyclient.table.rename_column(self,columnName=None,newColumnName=None,table=None,verbose=None)`**
Changes the name of a specified column in the table.
* **`columnName (string)`** The name of the column that will be renamed.
* **`newColumnName (string)`** The new name of the column.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.get_value***
**`cyclient.table.get_value(self,column=None,keyValue=None,table=None,verbose=None)`**
Returns the value from a cell as specified by row and column ids.
* **`column (string, optional)`** Specifies the name of a column in the tab
le
* **`keyValue (string, optional)`** Specifies a row of a table using the pr
imary key as the indentifier
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`returns`** value from a cell as specified by row and column ids
___
## ***cyclient.table.list_rows***
**`cyclient.table.list_rows(self,rowList=None,table=None,verbose=None)`**
Returns the list of primary keys for each of the rows in the specified table.
* **`rowList (string, optional)`** Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.create_table***
**`cyclient.table.create_table(self,keyColumn=None,keyColumnType=None,title=None,verbose=None)`**
Adds a new table to the network.
* **`keyColumn (string, optional)`** Specifies the name of a column in the
table
* **`keyColumnType (string, optional)`** The syntactical type of the value
used in the key
* **`title (string, optional)`** The name of the table used in the current
network
* **`returns`** table SUID
___
## ***cyclient.table.getTableCount***
**`cyclient.table.getTableCount(verbose=None)`**
Returns the number of global tables.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.table.destroy***
**`cyclient.table.destroy(self,table=None,verbose=None)`**
Removes the specified table from the network.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.list_tables***
**`cyclient.table.list_tables(self,includePrivate=None,namespace=None,atype=None,verbose=None)`**
Returns a list of the table SUIDs associated with the passed network parameter.
* **`includePrivate (string, optional)`** A boolean value determining wheth
er to return private as well as public tables
* **`namespace (string, optional)`** An optional argument to contrain outpu
t to a single namespace, or ALL
* **`atype (string, optional)`** One of ''network'', ''node'', ''edge'', ''u
nattached'', ''all'', to constrain the type of table listed
* **`returns`** list of the table SUIDs associated with the passed network parameter.
___
## ***cyclient.table.create_column***
**`cyclient.table.create_column(self,columnName=None,listType=None,table=None,ntype=None,verbose=None)`**
Appends an additional column of attribute values to the current table.
* **`columnName (string, optional)`** The new column name
* **`listType (string, optional)`** Can be one of integer, long, double, or
string.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`ntype (string, optional)`** Can be one of integer, long, double, string
, or list.
___
## ***cyclient.table.list_columns***
**`cyclient.table.list_columns(self,table=None,verbose=None)`**
Returns the list of columns in the table.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`returns`** list of columns in the table.
___
## ***cyclient.table.delete_column***
**`cyclient.table.delete_column(self,column=None,table=None,verbose=None)`**
Remove a column from a table, specified by its name. Returns the name of
the column removed.
* **`column (string, optional)`** Specifies the name of a column in the tab
le
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.set_title***
**`cyclient.table.set_title(self,table=None,title=None,verbose=None)`**
Changes the visible identifier of a single table.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`title (string, optional)`** The name of the table used in the current
network
___
## ***cyclient.table.getTable***
**`cyclient.table.getTable(self, columns=None, table=None, network = "current", namespace='default', verbose=VERBOSE)`**
Gets tables from cytoscape.
* **`table`** table to retrieve eg. node
* **`columns`** columns to retrieve in list format
* **`network (string, optional)`** Specifies a network by name, or by
SUID if the prefix SUID: is used. The keyword CURRENT, or a blank
value can also be used to specify the current network.
* **`namespace (string, optional)`** Node, Edge, and Network objects support
the default, local, and hidden namespaces. Root networks also support the
shared namespace. Custom namespaces may be specified by Apps.
* **`returns`** a pandas dataframe
___
## ***cyclient.table.get_row***
**`cyclient.table.get_row(self,keyValue=None,table=None,verbose=None)`**
Returns the values in each column of a row of a table.
* **`keyValue (string, optional)`** Specifies a row of a table using the pr
imary key as the indentifier
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`returns`** values in each column of a row of a table
___
## ***cyclient.table.import_file***
**`cyclient.table.import_file(self,caseSensitiveNetworkCollectionKeys=None, caseSensitiveNetworkKeys=None,dataTypeList=None,\ DataTypeTargetForNetworkCollection=None,DataTypeTargetForNetworkList=None,\ delimiters=None,delimitersForDataList=None,afile=None,firstRowAsColumnNames=None,\ KeyColumnForMapping=None,KeyColumnForMappingNetworkList=None,keyColumnIndex=None,\ newTableName=None,startLoadRow=None,TargetNetworkCollection=None,\ TargetNetworkList=None,WhereImportTable=None,verbose=None)`**
This uses a long list of input parameters to specify the attributes of
the table, the mapping keys, and the destination table for the input.
* **`caseSensitiveNetworkCollectionKeys (string, optional)`** Determines wh
ether capitalization is considered in matching and sorting
* **`caseSensitiveNetworkKeys (string, optional)`** Determines whether capi
talization is considered in matching and sorting
* **`dataTypeList (string, optional)`** List of column data types ordered b
y column index (e.g. "string,int,long,double,boolean,intlist" or jus
t "s,i,l,d,b,il")
* **`DataTypeTargetForNetworkCollection (string, optional)`** Select whethe
r to import the data as Node Table Columns, Edge Table Columns, or N
etwork Table Columns
* **`DataTypeTargetForNetworkList (string, optional)`** The data type of th
e targets
* **`delimiters (string, optional)`** The list of delimiters that separate
columns in the table.
* **`delimitersForDataList (string, optional)`** The delimiters between ele
ments of list columns in the table.
* **`afile (string)`** The path to the file that contains the table or netwo
rk to be imported.
* **`firstRowAsColumnNames (string, optional)`** If the first imported row
contains column names, set this to true.
* **`KeyColumnForMapping (string, optional)`** The column in the network to
use as the merge key
* **`KeyColumnForMappingNetworkList (string, optional)`** The column in the
network to use as the merge key
* **`keyColumnIndex (string, optional)`** The column that contains the key
values for this import. These values will be used to match with the
key values in the network.
* **`newTableName (string, optional)`** The title of the new table
* **`startLoadRow (string, optional)`** The first row of the input table to
load. This allows the skipping of headers that are not part of the
import.
* **`TargetNetworkCollection (string, optional)`** The network collection t
o use for the table import
* **`TargetNetworkList (string, optional)`** The list of networks into whic
h the table is imported
* **`WhereImportTable (string, optional)`** Determines what network(s) the
imported table will be associated with (if any). A table can be impo
rted into a Network Collection, Selected networks or to an unassigne
d table.
___
## ***cyclient.table.merge***
**`cyclient.table.merge(self,DataTypeTargetForNetworkCollection=None, dataTypeTargetForNetworkList=None,mergeType=None,SourceMergeColumns=None,\ SourceMergeKey=None,SourceTable=None,TargetKeyNetworkCollection=None,\ TargetMergeKey=None,TargetNetworkCollection=None,TargetNetworkList=None,\ UnassignedTable=None,WhereMergeTable=None,verbose=None)`**
Merge tables together joining around a designated key column. Depending
on the arguments, might merge into multiple local tables.
* **`DataTypeTargetForNetworkCollection (string, optional)`** The collectio
n of networks where the merged table will reside
* **`dataTypeTargetForNetworkList (string, optional)`**
* **`mergeType (string, optional)`** A choice between ''Copy Columns'' and
''Link To Columns'' that determines if replicates are created
* **`SourceMergeColumns (string, optional)`** A list of columns that will b
e brought into the merged table
* **`SourceMergeKey (string, optional)`** The name of the columns that exis
ts in both tables and is used to correlate rows
* **`SourceTable (string, optional)`** The name of the table used as the ba
se data in the merge
* **`TargetKeyNetworkCollection (string, optional)`** The name of the prima
ry column about which the merge is made
* **`TargetMergeKey (string, optional)`**
* **`TargetNetworkCollection (string, optional)`** The group of networks th
at will be merged into the source table
* **`TargetNetworkList (string, optional)`** The list of networks where the
merged table will be added
* **`UnassignedTable (string, optional)`**
* **`WhereMergeTable (string, optional)`** The destination path of the resu
ltant merged table. The choices are ''Network Collection'', ''Select
ed Networks'', or ''All Unassigned Tables''.
___
## ***cyclient.table.add_row***
**`cyclient.table.add_row(self,keyValue=None,table=None,verbose=None)`**
Appends an additional row of empty cells to the current table.
* **`keyValue (string, optional)`** Specifies the primary key of a value in
the row of a table Note that network, node, and edge tables must ha
ve Long values as keys
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
___
## ***cyclient.table.set_values***
**`cyclient.table.set_values(self,columnName=None,rowList=None,table=None,value=None,verbose=None)`**
Set all the values in the specified list of rows with a single value.
* **`columnName (string, optional)`** Specifies the name of a column in the
table
* **`rowList (string, optional)`** Specifies a list of rows. The pattern CO
LUMN:VALUE sets this parameter to any rows that contain the specifie
d column value; if the COLUMN prefix is not used, the NAME column is
matched by default. A list of COLUMN:VALUE pairs of the format COLU
MN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.
This parameter can also be set to all to include all rows.
* **`table (string, optional)`** Specifies a table by table name. If the pr
efix SUID: is used, the table corresponding the SUID will be returne
d.
* **`value (string, optional)`** The value to set the columns in the select
ed rows to. This should be a string value, which will be converted t
o the appropriate column type.
___
session.py
session
## ***cyclient.session.save_as***
**`cyclient.session.save_as(self, session_file, verbose=False)`**
Saves the current session as a new file.
* **`session_file`** The path to the file where the current session
must be saved to.
* **`verbose`** print more
___
## ***cyclient.session.runGarbageCollection***
**`cyclient.session.runGarbageCollection(verbose=None)`**
Manually call Java's System.gc() to free up unused memory. This process happens automatically, but may be useful to call explicitly for testing or evaluation purposes.
* **`verbose`** print more
* **`returns`** 204: Successful Garbage Collection
___
## ***cyclient.session.getSessionName***
**`cyclient.session.getSessionName(verbose=None)`**
Returns the file name for the current Cytoscape session.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.session.getSessionFromFile***
**`cyclient.session.getSessionFromFile(file, verbose=None)`**
Loads a session from a local file and returns the session file name
* **`file`** Session file location as an absolute path
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.session.deleteSession***
**`cyclient.session.deleteSession(verbose=None)`**
This deletes the current session and initializes a new one. A message is returned to indicate the success of the deletion.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.session.createSessionFile***
**`cyclient.session.createSessionFile(file, verbose=None)`**
Saves the current session to a file. If successful, the session file location will be returned.
* **`file`** Session file location as an absolute path
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.session.new***
**`cyclient.session.new(self, verbose=False)`**
Destroys the current session and creates a new, empty one.
* **`wid`** Window ID
* **`verbose`** print more
___
## ***cyclient.session.save***
**`cyclient.session.save(self, session_file, verbose=False)`**
Saves the current session to an existing file, which will be replaced.
If this is a new session that has not been saved yet, use 'save as'
instead.
* **`session_file`** The path to the file where the current session
must be saved to.
* **`verbose`** print more
___
## ***cyclient.session.open***
**`cyclient.session.open(self, session_file=None,session_url=None, verbose=False)`**
Opens a session from a local file or URL.
* **`session_file`** The path to the session file (.cys) to be loaded.
* **`session_url`** A URL that provides a session file.
* **`verbose`** print more
___
enrichmentmap.py
enrichmentmap
## ***cyclient.enrichmentmap.getExpressionDataForNode***
**`cyclient.enrichmentmap.getExpressionDataForNode(network, node, verbose=None)`**
* **`network`** Network name or SUID
* **`node`** Node SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.enrichmentmap.getExpressionDataForNetwork***
**`cyclient.enrichmentmap.getExpressionDataForNetwork(network, verbose=None)`**
* **`network`** Network name or SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.enrichmentmap.getModelData***
**`cyclient.enrichmentmap.getModelData(network, verbose=None)`**
* **`network`** Network name or SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
apps.py
apps
## ***cyclient.apps.getAppList***
**`cyclient.apps.getAppList(verbose=None)`**
Returns installed Cytoscape Apps that have CyREST accessible Functions or Commands, as a list of App names.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
ui.py
ui
## ***cyclient.ui.updatePanelStatus***
**`cyclient.ui.updatePanelStatus(body, verbose=None)`**
Updates the status(es) of available CytoPanels.
* **`body`** A list of CytoPanels with states.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.ui.getAllPanelStatus***
**`cyclient.ui.getAllPanelStatus(verbose=None)`**
Returns all CytoPanels and their statuses.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.ui.getPanelStatus***
**`cyclient.ui.getPanelStatus(panelName, verbose=None)`**
Returns the status of the CytoPanel specified by the `panelName` parameter.
* **`panelName`** Name of the CytoPanel
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.ui.getDesktop***
**`cyclient.ui.getDesktop(verbose=None)`**
Returns the status of the Desktop
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.ui.updateLodState***
**`cyclient.ui.updateLodState(verbose=None)`**
Switch between full graphics details <---> fast rendering mode.
Returns a success message.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
collections.py
collections
## ***cyclient.collections.getCollectionCount***
**`cyclient.collections.getCollectionCount(verbose=None)`**
Returns a count of all root networks.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
networks.py
networks
## ***cyclient.networks.getView***
**`cyclient.networks.getView(networkId, viewId, objectType, objectId, verbose=None)`**
Gets a list of Visual Properties for the Object specified by the `objectId` and `objectType` parameters in the Network View specified by the `viewId` and `networkId` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`objectType`** Type of Object
* **`objectId`** SUID of the Object
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getColumnNames***
**`cyclient.networks.getColumnNames(networkId, tableType, verbose=None)`**
Returns all the columns in the table specified by the `networkId` and `tableType` parameters.
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table Type
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.updateTable***
**`cyclient.networks.updateTable(networkId, tableType, body, class, verbose=None)`**
Updates the table specified by the `tableType` and `networkId` parameters. New columns will be created if they do not exist in the target table.
Current limitations:
* Numbers are handled as Double
* List column is not supported in this version
* **`networkId`** SUID containing the table
* **`tableType`** Type of table
* **`body`** The data with which to update the table.
* **`class`** None -- Not required, can be None
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.createNetworkFromSelected***
**`cyclient.networks.createNetworkFromSelected(networkId, title, verbose=None)`**
Creates new sub-network from current selection, with the name specified by the `title` parameter.
Returns the SUID of the new sub-network.
* **`networkId`** SUID of the network containing the selected nodes and edges
* **`title`** Name for the new sub-network -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNodeCount***
**`cyclient.networks.getNodeCount(networkId, verbose=None)`**
Returns the number of nodes in the network specified by the `networkId` parameter.
* **`networkId`** SUID of the network containing the nodes
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.collapseGroup***
**`cyclient.networks.collapseGroup(networkId, groupNodeId, verbose=None)`**
Collapses the group specified by the `groupNodeId` and `networkId` parameters.
* **`networkId`** SUID of the Network
* **`groupNodeId`** SUID of the Node representing the Group
* **`verbose`** print more
* **`returns`** 204: Group collapsed; 500: Failed to collapse group
___
## ***cyclient.networks.getEdge***
**`cyclient.networks.getEdge(networkId, edgeId, verbose=None)`**
Returns an edge with its associated row data.
* **`networkId`** SUID of the network containing the edge
* **`edgeId`** SUID of the edge
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getTables***
**`cyclient.networks.getTables(networkId, verbose=None)`**
Returns every table in the network specified by the `networkId` parameter.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getFirstImageAsSvg***
**`cyclient.networks.getFirstImageAsSvg(networkId, h, verbose=None)`**
Returns an SVG image of the first available Network View for the Network specified by the `networkId` parameter.
Default size is 600 px
* **`networkId`** SUID of the Network
* **`h`** Height of the image. Width is set automatically -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: SVG image stream.
___
## ***cyclient.networks.getRows***
**`cyclient.networks.getRows(networkId, tableType, verbose=None)`**
Returns all rows from the table specified by `networkId` and `tableType` parameters. Returns a JSON representation of an array of rows.
```
[
{
"SUID": 101,
"gene_name": "brca1",
"exp": 0.1
},
{
"SUID": 102,
"gene_name": "brca2",
"exp": 0.2
}
]
```
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table Type
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteGroup***
**`cyclient.networks.deleteGroup(networkId, groupNodeId, verbose=None)`**
Deletes the group specified by the `groupNodeId` and `networkId` parameters. The nodes and edges that the group contained will remain present in the network, however the node used to identify the Group will be deleted.
* **`networkId`** SUID of the Network
* **`groupNodeId`** SUID of the Node representing the Group
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getSelectedNodes***
**`cyclient.networks.getSelectedNodes(networkId, verbose=None)`**
Gets the selected nodes in the network specified by the `networkId` parameter. The results are presented as a list of SUIDs.
* **`networkId`** SUID of the network containing the nodes
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.setCurrentNetworkView***
**`cyclient.networks.setCurrentNetworkView(body, verbose=None)`**
Sets the current Network View.
* **`body`** SUID of the Network View -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.expandGroup***
**`cyclient.networks.expandGroup(networkId, groupNodeId, verbose=None)`**
Expands the group specified by the `groupNodeId` and `networkId` parameters.
* **`networkId`** SUID of the Network
* **`groupNodeId`** SUID of the Node representing the Group
* **`verbose`** print more
* **`returns`** 204: Group expanded; 500: Failed to expand group
___
## ***cyclient.networks.setSelectedEdges***
**`cyclient.networks.setSelectedEdges(networkId, body, verbose=None)`**
Sets as selected the edges specified by the `suids` and `networkId` parameters.
Returns a list of selected SUIDs.
* **`networkId`** SUID of the network containing the edges
* **`body`** Array of edge SUIDs to select -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getEdgeDirected***
**`cyclient.networks.getEdgeDirected(networkId, edgeId, verbose=None)`**
Returns true if the edge specified by the `edgeId` and `networkId` parameters is directed.
* **`networkId`** SUID of the network containing the edge
* **`edgeId`** SUID of the edge
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getRow***
**`cyclient.networks.getRow(networkId, tableType, primaryKey, verbose=None)`**
Gets a row matching the value specified by the `primaryKey` parameter from the table specified by the `tableType` and `networkId` parameters.
Data is represented by column names and their values.
```json
{
"name": "Hodor 1",
"value": 0.11,
"matched": false
...
}
```
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table type
* **`primaryKey`** Primary key of the row Object, normally an SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getCurrentNetworkView***
**`cyclient.networks.getCurrentNetworkView(verbose=None)`**
Returns the current Network View.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getImageAsSvg***
**`cyclient.networks.getImageAsSvg(networkId, viewId, h, verbose=None)`**
Returns an SVG image of the Network View specified by the `viewId` and `networkId` parameters.
Default size is 600 px.
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`h`** Height of the image. Width is set automatically -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: SVG image stream.
___
## ***cyclient.networks.getGroup***
**`cyclient.networks.getGroup(networkId, groupNodeId, verbose=None)`**
Returns the group specified by the `groupNodeId` and `networkId` parameters.
* **`networkId`** SUID of the Network
* **`groupNodeId`** SUID of the Node representing the Group
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkPointer***
**`cyclient.networks.getNetworkPointer(networkId, nodeId, verbose=None)`**
If the node specified by the `nodeId` and `networkId` parameters has an associated nested network, returns the SUID of the nested network.
* **`networkId`** SUID of the network containing the node
* **`nodeId`** SUID of the node
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getAllGroups***
**`cyclient.networks.getAllGroups(networkId, verbose=None)`**
Returns a list of all the groups in the network specified by the `networkId` parameter.
* **`networkId`** Network SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getImageAsPdf***
**`cyclient.networks.getImageAsPdf(networkId, viewId, verbose=None)`**
Returns a PDF of the Network View specified by the `viewId` and `networkId` parameters.
Default size is 500 px.
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`verbose`** print more
* **`returns`** 200: PDF image stream.
___
## ***cyclient.networks.putSingleVisualPropertyValueBypass***
**`cyclient.networks.putSingleVisualPropertyValueBypass(networkId, viewId, objectType, objectId, visualProperty, body, verbose=None)`**
Bypasses the Visual Style of the object specified by the `objectId` and `objectType` parameters, in the Network View specified by the `viewId` and `networkId` parameters. The Visual Property included in the message body will be used instead of the definition provided by the Visual Style.
Examples of Visual Properties:
```
{
"visualProperty": "NODE_BORDER_WIDTH",
"value": 2
}
```
```
{
"visualProperty": "EDGE_TRANSPARENCY",
"value": 170
}```
```
{
"visualProperty": "NETWORK_BACKGROUND_PAINT",
"value": "#000000"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** Network SUID
* **`viewId`** Network View SUID
* **`objectType`** Type of Object
* **`objectId`** SUID of the Object
* **`visualProperty`** Name of the Visual Property
* **`body`** A Visual Property and its value.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getNetworkViewAsCx***
**`cyclient.networks.getNetworkViewAsCx(networkId, viewId, verbose=None)`**
Returns the Network View specified by the `viewId` and `networkId` parameters in [CX format](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#cytoscape-cx)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.deleteAllNodes***
**`cyclient.networks.deleteAllNodes(networkId, verbose=None)`**
Delete all the nodes from the network specified by the `networkId` parameter.
* **`networkId`** SUID of the network to delete nodes from
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getNeighbours***
**`cyclient.networks.getNeighbours(networkId, nodeId, verbose=None)`**
Returns the neighbors of the node specified by the `nodeId` and `networkId` parameters as a list of SUIDs.
* **`networkId`** SUID of the network containing the node.
* **`nodeId`** SUID of the node
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.setSelectedNodes***
**`cyclient.networks.setSelectedNodes(networkId, body, verbose=None)`**
Sets as selected the nodes specified by the `suids` and `networkId` parameters.
Returns a list of selected SUIDs.
* **`networkId`** SUID of the network containing the nodes
* **`body`** Array of node SUIDs to select -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkCount***
**`cyclient.networks.getNetworkCount(verbose=None)`**
Returns the number of networks in current Cytoscape session.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getViews***
**`cyclient.networks.getViews(networkId, viewId, objectType, visualProperty, verbose=None)`**
Returns a list of all Visual Property values for the Visual Property specified by the `visualProperty` and `objectType` parameters, in the Network View specified by the `viewId` and `networkId` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`objectType`** Type of Object
* **`visualProperty`** Name of the Visual Property -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getSelectedEdges***
**`cyclient.networks.getSelectedEdges(networkId, verbose=None)`**
Gets the selected edges in the network specified by the `networkId` parameter. The results are presented as a list of SUIDs.
* **`networkId`** SUID of the network containing the edges
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteFirstNetworkView***
**`cyclient.networks.deleteFirstNetworkView(networkId, verbose=None)`**
Deletes the first available Network View for the Network specified by the `networkId` parameter. Cytoscape can have multiple views per network model, but this feature is not exposed in the Cytoscape GUI. GUI access is limited to the first available view only.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.deleteNetworkVisualProp***
**`cyclient.networks.deleteNetworkVisualProp(networkId, viewId, visualProperty, verbose=None)`**
Deletes the bypass Visual Property specificed by the `visualProperty`, `viewId`, and `networkId` parameters. When this is done, the Visual Property will be defined by the Visual Style
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`visualProperty`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getFirstImageAsPng***
**`cyclient.networks.getFirstImageAsPng(networkId, h, verbose=None)`**
Returns a PNG image of the first available Network View for the Network specified by the `networkId` parameter.
Default size is 600 px
* **`networkId`** SUID of the Network
* **`h`** Height of the image. Width is set automatically -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: PNG image stream.
___
## ***cyclient.networks.getColumnValues***
**`cyclient.networks.getColumnValues(networkId, tableType, columnName, verbose=None)`**
Returns all the values for the column specified by the `columnType` parameter, in the table specified by the `networkId` and `tableType` parameters.
* **`networkId`** SUID of the Network
* **`tableType`** Type of Table
* **`columnName`** Name of the Column
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getEdgeCount***
**`cyclient.networks.getEdgeCount(networkId, verbose=None)`**
Returns the number of edges in the network specified by the `networkId` parameter.
* **`networkId`** SUID of the network containing the edges
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.updateNetworkView***
**`cyclient.networks.updateNetworkView(networkId, viewId, bypass, body, verbose=None)`**
Updates the Visual Properties in the Network View specified by the `viewId` and `networkId` parameters.
Example Visual Properties:
```
{
"visualProperty": "NETWORK_BACKGROUND_PAINT",
"value": "#000000"
}```
```
{
"visualProperty": "NETWORK_CENTER_X_LOCATION",
"value": 250
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
Note that this sets the Visual Properties temporarily unless the `bypass` parameter is set to `true`. If the `bypass` parameter is set to `true`, the Visual Style will be overridden by these Visual Property values. If the `bypass` parameter is not used or is set to `false`, any Visual Properties set will return to those defined in the Visual Style if the Network View is updated.
* **`networkId`** Network SUID
* **`viewId`** Network View SUID
* **`bypass`** Bypass the Visual Style with these properties -- Not required, can be None
* **`body`** A list of Visual Properties and their values.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getCell***
**`cyclient.networks.getCell(networkId, tableType, primaryKey, columnName, verbose=None)`**
Return the value of a cell specified by the `primaryKey` and `columnName` parameters in the table specified by the `tableType` and `networkId` parameters.
Returns a JSON representation of a String, Boolean, Number, or List.
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table type
* **`primaryKey`** Primary key of the row Object, normally an SUID
* **`columnName`** Name of the Column
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getEdges***
**`cyclient.networks.getEdges(networkId, column, query, verbose=None)`**
Returns a list of all edges in the network specified by the `networkId` parameter as SUIDs.
If the `column` and `query` parameters are specified, the results will be limited to rows in the edge table where the value in the column specified by the `column` parameter matches the value specified by the `query` parameter.
* **`networkId`** SUID of the network containing the edges
* **`column`** The name of the column that will be queried for matches. -- Not required, can be None
* **`query`** The value to be matched. -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.createNetworkView***
**`cyclient.networks.createNetworkView(networkId, verbose=None)`**
Creates a new Network View for the Network specified by the `networkId` parameter.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 201: Network View SUID
___
## ***cyclient.networks.getNetwork***
**`cyclient.networks.getNetwork(networkId, verbose=None)`**
Returns the Network specified by the `networkId` parameter with all associated tables in [Cytoscape.js](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#cytoscape-js-json) format
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkViewCount***
**`cyclient.networks.getNetworkViewCount(networkId, verbose=None)`**
Returns a count of the Network Views available for the Network specified by the `networkId` parameter.
Cytoscape can have multiple views per network model, but this feature is not exposed in the Cytoscape GUI. GUI access is limited to the first available view only.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.updateView***
**`cyclient.networks.updateView(networkId, viewId, objectType, objectId, bypass, body, verbose=None)`**
Updates the Visual Properties in the object specified by the `objectId` and `objectType` parameters in the Network View specified by the `viewId` and `networkId` parameters.
Examples of Visual Properties:
```
{
"visualProperty": "NODE_BORDER_WIDTH",
"value": 2
}
```
```
{
"visualProperty": "EDGE_TRANSPARENCY",
"value": 170
}```
```
{
"visualProperty": "NETWORK_BACKGROUND_PAINT",
"value": "#000000"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
Note that this sets the Visual Properties temporarily unless the `bypass` parameter is set to `true`. If the `bypass` parameter is set to `true`, the Visual Style will be overridden by these Visual Property values. If the `bypass` parameter is not used or is set to `false`, any Visual Properties set will return to those defined in the Visual Style if the Network View is updated.
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`objectType`** Type of Object
* **`objectId`** SUID of the Object
* **`bypass`** Bypass the Visual Style with these Visual Properties -- Not required, can be None
* **`body`** A list of Visual Properties and their values.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.deleteAllNetworkViews***
**`cyclient.networks.deleteAllNetworkViews(networkId, verbose=None)`**
Deletes all Network Views available in the Network specified by the `networkId` parameter. Cytoscape can have multiple views per network model, but this feature is not exposed in the Cytoscape GUI. GUI access is limited to the first available view only.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getSingleVisualPropertyValueBypass***
**`cyclient.networks.getSingleVisualPropertyValueBypass(networkId, viewId, objectType, objectId, visualProperty, verbose=None)`**
Gets the bypass Visual Property specified by the `visualProperty` parameter from the object specified by the `objectId` and `objectType` parameters in the Network View Specified by the `viewId` and `networkId` parameters. The response is the Visual Property that is used in place of the definition provided by the Visual Style.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** Network SUID
* **`viewId`** Network View SUID
* **`objectType`** Type of Object
* **`objectId`** SUID of the Object
* **`visualProperty`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkVisualProp***
**`cyclient.networks.getNetworkVisualProp(networkId, viewId, visualProperty, verbose=None)`**
Gets the Network Visual Property specificed by the `visualProperty`, `viewId`, and `networkId` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`visualProperty`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkVisualProps***
**`cyclient.networks.getNetworkVisualProps(networkId, viewId, verbose=None)`**
Returns a list of the Visual Properties for the Network View specified by the `viewId` and `networkId` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteNode***
**`cyclient.networks.deleteNode(networkId, nodeId, verbose=None)`**
Deletes the node specified by the `nodeId` and `networkId` parameters.
* **`networkId`** SUID of the network containing the node.
* **`nodeId`** SUID of the node
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.createGroup***
**`cyclient.networks.createGroup(networkId, body, verbose=None)`**
Create a new group in the network specified by the parameter `networkId`. The contents are specified the message body.
* **`networkId`** SUID of the Network
* **`body`** New Group name and contents
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getFirstNetworkView***
**`cyclient.networks.getFirstNetworkView(networkId, file, verbose=None)`**
This returns the first view of the network. Cytoscape can have multiple views per network model, but this feature is not exposed in the Cytoscape GUI. GUI access is limited to the first available view only.
If the `file` parameter is left unspecified, the response will contain data in [Cytoscape.js](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#cytoscape-js-json) format.
If the `file` parameter is specified, the Network View will be written to a file, and the response will contain the location of the file in the following format:
```
{
"file": "/media/HD1/myFiles/networkView.sif"
}
```
The format of the output file is defined by the extension of the `file` parameter.
* **`networkId`** SUID of the Network
* **`file`** A path to a file relative to the current directory. The format of the file written is defined by the file extension.
| Extension | Details |
| ----------- | -----------|
| .cys | Cytoscape Style format |
| .xml/.xgmml | [XGMML](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html?highlight=xgmml#xgmml-format) format |
| .nnf | [NNF](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#nnf) format |
| .sif | [SIF](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#sif-format) format |
| .cyjs | [Cytoscape.js](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#cytoscape-js-json) format |
-- Not required, can be None
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.deleteColumn***
**`cyclient.networks.deleteColumn(networkId, tableType, columnName, verbose=None)`**
Deletes the column specified by the `columnName` parameter from the table speficied by the `tableType` and `networkId` parameters.
* **`networkId`** SUID of the network containing the table from which to delete the column
* **`tableType`** Table Type from which to delete the column
* **`columnName`** Name of the column to delete
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.createNode***
**`cyclient.networks.createNode(networkId, body, verbose=None)`**
Adds new nodes to the network specified by the `networkId` parameter. The `name` column will be populated by the contents of the message body.
* **`networkId`** SUID of the network containing the node.
* **`body`** Array of new node names
* **`verbose`** print more
* **`returns`** 201: ; 412:
___
## ***cyclient.networks.getNeighborsSelected***
**`cyclient.networks.getNeighborsSelected(networkId, verbose=None)`**
Returns the neighbors of the nodes currently selected in the network specified by the `networkId` parameter as a list of SUIDs.
Note that this does not include the nodes in the original selection.
* **`networkId`** SUID of the network
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getImageAsPng***
**`cyclient.networks.getImageAsPng(networkId, viewId, h, verbose=None)`**
Returns a PNG image of the Network View specified by the `viewId` and `networkId` parameters.
Default size is 600 px.
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`h`** Height of the image. Width is set automatically -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: PNG image stream.
___
## ***cyclient.networks.getAdjEdges***
**`cyclient.networks.getAdjEdges(networkId, nodeId, verbose=None)`**
Returns a list of connected edges as SUIDs for the node specified by the `nodeId` and `networkId` parameters.
* **`networkId`** SUID of the network containing the node
* **`nodeId`** SUID of the node
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkVisualPropBypass***
**`cyclient.networks.getNetworkVisualPropBypass(networkId, viewId, visualProperty, verbose=None)`**
Gets the bypass Visual Property specified by the `visualProperty`, `viewId`, and `networkId` parameters. The response is the Visual Property that is used in place of the definition provided by the Visual Style.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`visualProperty`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.createColumn***
**`cyclient.networks.createColumn(networkId, tableType, body, verbose=None)`**
Creates a new, empty column in the table specified by the `tableType` parameter, in the network specified by the `networkId` parameter.
This resource can also accept an array of new columns to create multiple columns.
* **`networkId`** SUID of the Network
* **`tableType`** Table Type
* **`body`** New Column Info
* **`verbose`** print more
* **`returns`** 201: Column(s) createed; 412: Could not process column JSON
___
## ***cyclient.networks.setCurrentNetwork***
**`cyclient.networks.setCurrentNetwork(body, verbose=None)`**
Sets the current network.
* **`body`** SUID of the Network -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getNetworkView***
**`cyclient.networks.getNetworkView(networkId, viewId, file, verbose=None)`**
Gets the Network View specified by the `viewId` and `networkId` parameters.
If the `file` parameter is left unspecified, the response will contain data in [Cytoscape.js](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#cytoscape-js-json) format.
If the `file` parameter is specified, the Network View will be written to a file, and the response will contain the location of the file in the following format:
```
{
"file": "/media/HD1/myFiles/networkView.sif"
}
```
The format of the output file is defined by the extension of the `file` parameter.
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`file`** A path to a file relative to the current directory. The format of the file written is defined by the file extension.
| Extension | Details |
| ----------- | -----------|
| .cys | Cytoscape Style format |
| .xml/.xgmml | [XGMML](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html?highlight=xgmml#xgmml-format) format |
| .nnf | [NNF](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#nnf) format |
| .sif | [SIF](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#sif-format) format |
| .cyjs | [Cytoscape.js](http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#cytoscape-js-json) format |
-- Not required, can be None
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getTable***
**`cyclient.networks.getTable(networkId, tableType, verbose=None)`**
Returns the table specified by the `networkId` and 'tableType' parameters.
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table type
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.createEdge***
**`cyclient.networks.createEdge(networkId, body, verbose=None)`**
Add new edge(s) to the network. Body should include an array of new node names.
Returns and array of objects with fields itentifying the SUIDs of the new edges along with source and target SUIDs.
* **`networkId`** SUID of the network to add edges to.
* **`body`** Array of new edges
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getAllNetworkViews***
**`cyclient.networks.getAllNetworkViews(networkId, verbose=None)`**
Returns an array of all network views belonging to the network specified by the `networkId` paramter. The response is a list of Network SUIDs.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** 200: An array of Network View SUIDs
___
## ***cyclient.networks.updateColumnName***
**`cyclient.networks.updateColumnName(networkId, tableType, body, verbose=None)`**
Renames an existing column in the table specified by the `tableType` and `networkId` parameters.
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table Type
* **`body`** Old and new column name
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getCurrentNetwork***
**`cyclient.networks.getCurrentNetwork(verbose=None)`**
Returns the current network.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.updateViews***
**`cyclient.networks.updateViews(networkId, viewId, objectType, bypass, body, verbose=None)`**
Updates multiple node or edge Visual Properties as defined by the `objectType` parameter, in the Network View specified by the `viewId` and `networkId` parameters.
Examples of Visual Properties:
```
{
"visualProperty": "NODE_BORDER_WIDTH",
"value": 2
}
```
```
{
"visualProperty": "NODE_BORDER_PAINT",
"value": "#CCCCCC"
}
```
```
{
"visualProperty": "EDGE_TRANSPARENCY",
"value": 170
}```
```
{
"visualProperty": "EDGE_PAINT",
"value": "#808080"
}```
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
Note that this sets the Visual Properties temporarily unless the `bypass` parameter is set to `true`. If the `bypass` parameter is set to `true`, the Visual Style will be overridden by these Visual Property values. If the `bypass` parameter is not used or is set to `false`, any Visual Properties set will return to those defined in the Visual Style if the Network View is updated.
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`objectType`** Type of Object
* **`bypass`** Bypass the Visual Style with these Visual Properties -- Not required, can be None
* **`body`** A list of Objects with Visual Properties.
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getNodes***
**`cyclient.networks.getNodes(networkId, column, query, verbose=None)`**
Returns a list of all nodes in the network specified by the `networkId` parameter as SUIDs.
If the `column` and `query` parameters are specified, the results will be limited to rows in the node table where the value in the column specified by the `column` parameter matches the value specified by the `query` parameter.
* **`networkId`** SUID of the network containing the nodes
* **`column`** The name of the column that will be queried for matches. -- Not required, can be None
* **`query`** The value to be matched. -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.putNetworkVisualPropBypass***
**`cyclient.networks.putNetworkVisualPropBypass(networkId, viewId, visualProperty, body, verbose=None)`**
Bypasses the Visual Style of the Network with the Visual Property specificed by the `visualProperty`, `viewId`, and `networkId` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`visualProperty`** Name of the Visual Property
* **`body`** A Visual Property and its value.
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteNetwork***
**`cyclient.networks.deleteNetwork(networkId, verbose=None)`**
Deletes the network specified by the `networkId` parameter.
* **`networkId`** SUID of the network to delete
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getSingleVisualPropertyValue***
**`cyclient.networks.getSingleVisualPropertyValue(networkId, viewId, objectType, objectId, visualProperty, verbose=None)`**
Gets the Visual Property specificed by the `visualProperty` parameter for the node or edge specified by the `objectId` parameter in the Network View specified by the `viewId` and `networkId` parameters.
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`objectType`** Type of Object
* **`objectId`** SUID of the Object
* **`visualProperty`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteAllGroups***
**`cyclient.networks.deleteAllGroups(networkId, verbose=None)`**
Deletes all groups in the network specified by `networkId` parameter. The nodes and edges that the groups contained will remain present in the network, however the nodes used to identify the Groups will be deleted.
* **`networkId`** SUID of the Network
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.deleteEdge***
**`cyclient.networks.deleteEdge(networkId, edgeId, verbose=None)`**
Deletes the edge specified by the `edgeId` and `networkId` parameters.
* **`networkId`** SUID of the network containing the edge.
* **`edgeId`** SUID of the edge
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getFirstImageAsPdf***
**`cyclient.networks.getFirstImageAsPdf(networkId, h, verbose=None)`**
Returns a PDF of the first available Network View for the Network specified by the `networkId` parameter.
Default size is 600 px
* **`networkId`** SUID of the Network
* **`h`** Height of the image. Width is set automatically -- Not required, can be None
* **`verbose`** print more
* **`returns`** 200: PDF image stream.
___
## ***cyclient.networks.getTableAsCsv***
**`cyclient.networks.getTableAsCsv(networkId, tableType, verbose=None)`**
Returns a CSV representation of the table specified by the `networkId` and `tableType` parameters. All column names are included in the first row.
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table type
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getTableAsTsv***
**`cyclient.networks.getTableAsTsv(networkId, tableType, verbose=None)`**
Returns a TSV (tab delimited text) representation of the table specified by the `networkId` and `tableType` parameters. All column names are included in the first row.
* **`networkId`** SUID of the network containing the table
* **`tableType`** Table type
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.updateColumnValues***
**`cyclient.networks.updateColumnValues(networkId, tableType, columnName, default, body, verbose=None)`**
Sets the values for cells in the table specified by the `tableType` and `networkId` parameters.
If the 'default` parameter is not specified, the message body should consist of key-value pairs with which to set values.
If the `default` parameter is specified, its value will be used for every cell in the column. This is useful to set columns like "selected."
* **`networkId`** SUID of the network containing the table
* **`tableType`** The type of table
* **`columnName`** Name of the column in which to set values
* **`default`** Default Value. If this value is provided, all cells will be set to this. -- Not required, can be None
* **`body`** Array of SUID Keyed values
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getEdgeComponent***
**`cyclient.networks.getEdgeComponent(networkId, edgeId, type, verbose=None)`**
Returns the SUID of the source or target node of the edge specified by the `edgeId` and `networkId` parameters.
Return values can be in one of two formats, depending on the value specified in the `type` parameter:
```
{
"source": 101
}
```
```
{
"target": 102
}
```
* **`networkId`** SUID of the network containing the edge
* **`edgeId`** SUID of the edge
* **`type`** The node type to return
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.getGroupCount***
**`cyclient.networks.getGroupCount(networkId, verbose=None)`**
Returns the number of groups in the network
* **`networkId`** Network SUID
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteSingleVisualPropertyValueBypass***
**`cyclient.networks.deleteSingleVisualPropertyValueBypass(networkId, viewId, objectType, objectId, visualProperty, verbose=None)`**
Deletes the bypass Visual Property specified by the `visualProperty` parameter from the object specified by the `objectId` and `objectType` parameters in the Network View Specified by the `viewId` and `networkId` parameters. When this is done, the Visual Property will be defined by the Visual Style
Additional details on common Visual Properties can be found in the [Basic Visual Lexicon JavaDoc API](http://chianti.ucsd.edu/cytoscape-3.6.1/API/org/cytoscape/view/presentation/property/BasicVisualLexicon.html)
* **`networkId`** SUID of the Network
* **`viewId`** SUID of the Network View
* **`objectType`** Type of Object
* **`objectId`** SUID of Object
* **`visualProperty`** Name of the Visual Property
* **`verbose`** print more
* **`returns`** 200: successful operation
___
## ***cyclient.networks.deleteAllEdges***
**`cyclient.networks.deleteAllEdges(networkId, verbose=None)`**
Delete all the edges from the network specified by the `networkId` parameter.
* **`networkId`** SUID of the network to delete edges from
* **`verbose`** print more
* **`returns`** default: successful operation
___
## ***cyclient.networks.getNode***
**`cyclient.networks.getNode(networkId, nodeId, verbose=None)`**
Returns a node with its associated row data.
* **`networkId`** SUID of the network containing the node
* **`nodeId`** SUID of the node
* **`verbose`** print more
* **`returns`** 200: successful operation
___
In [ ]:
Content source: idekerlab/py2cytoscape
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