I will add simple edgelist format support to render function.

cy = CyRestClient(ip="remote.host.org", port="1234", version="v1")
X=cy.network.get_all()
for x in X:
print cy.network.get(x) # okay, we can get the network in json format

The question is how can be obtain the network as a CyNetwork() object instead.
How do I set the ip to "remote.host.org" for the CyNetwork() class? It connects to localhost by default.
Thanks!

When i print the nodes and edges, it shows all the edges, but the render method visualises a blank white screen.
Thank you

I've created a compliance table

@AlexanderPico it would be great if you could add the RCy3 part and add new rows as necessary

I guess @dotasek and @bdemchak might want to drop an eye in there as well

I downloaded the master branch, ran "python setup.py install" using Anaconda3 shell, and saw no errors. Started jupyter notebook from Anaconda3, and attempted to run some examples. 5 of 6 (the 6th could not do a different import) examples all produced they following error traceback:

DeprecationWarning Traceback (most recent call last)
in ()
1 # Boilerplate: Import required packages
----> 2 from py2cytoscape.data.cyrest_client import CyRestClient
3 from py2cytoscape.data.util_network import NetworkUtil as util
4 from py2cytoscape.data.style import StyleUtil as s_util
5 import py2cytoscape.cytoscapejs as renderer

C:\Users\Jeff\Anaconda3\lib\site-packages\py2cytoscape-0.6.1-py3.6.egg\py2cytoscape\data\cyrest_client.py in ()
2
3 import requests
----> 4 from .network_client import NetworkClient
5 from .style_client import StyleClient
6 from .algorithm_client import LayoutClient

C:\Users\Jeff\Anaconda3\lib\site-packages\py2cytoscape-0.6.1-py3.6.egg\py2cytoscape\data\network_client.py in ()
6
7 from . import HEADERS, SUID_LIST
----> 8 from ..util import cytoscapejs as util
9
10 from ..util import util_networkx as nx_util

C:\Users\Jeff\Anaconda3\lib\site-packages\py2cytoscape-0.6.1-py3.6.egg\py2cytoscape\util_init_.py in ()
8 from py2cytoscape.util.util_networkx import from_networkx, to_networkx
9 from py2cytoscape.util.util_graphlab import from_sgraph
---> 10 from py2cytoscape.util.util_igraph import from_igraph
11
12 all = ['from_networkx', 'to_networkx', 'from_igraph']

C:\Users\Jeff\Anaconda3\lib\site-packages\py2cytoscape-0.6.1-py3.6.egg\py2cytoscape\util\util_igraph.py in ()
6 """
7
----> 8 import igraph as ig
9
10 DEF_SCALING = 100.0

C:\Users\Jeff\Anaconda3\lib\site-packages\igraph_init_.py in ()
6 license = "MIT"
7
----> 8 raise DeprecationWarning("To avoid name collision with the igraph project, "
9 "this visualization library has been renamed to "
10 "'jgraph'. Please upgrade when convenient.")

DeprecationWarning: To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient.

Tried uninstalling igraph, and the notebook could not find the module. Reinstalled igraph, and the deprecation warning returned.

I'm trying to set styles using py2cytoscape on a Cytoscape instance running on another url than http://localhost:1234. The CyRestClient provides a way to enter a custom ip/port, but the styles seem to always use the default "localhost".

Small snippet to reproduce (Cytoscape itself should be listening on 172.17.0.1):

from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient(ip='172.17.0.1', port=1234)

style = cy.style.create('basic')
defaults = { 'NODE_SIZE': 12 }
style.update_defaults(defaults)

This gives me an error indicating that it is trying to connect to localhost instead of 172.17.0.1:

ConnectionError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/basic/defaults (Caused by NewConnectionError('<requests.packages.urllib3.connection.HTTPConnection object at 0x7f3eeb6c1860>: Failed to establish a new connection: [Errno 111] Connection refused',))

A workaround is to manually set the BASE_URL:

from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient(ip='172.17.0.1', port=1234)

style = cy.style.create('basic')
style._Style__url = 'http://172.17.0.1:1234/v1/styles/basic/'
defaults = { 'NODE_SIZE': 12 }
style.update_defaults(defaults)

Then it works without error.

readthedocs

• installation
• api docs

installation on Windows

• python-igraph from http://www.lfd.uci.edu/~gohlke/pythonlibs/

I think that

• python-igraph
• scipy

should be moved from install_requires to extras_require.

In trial use, the users would not need these packages. (and these packages are hard to install).

It would be great to have an interface to graph-tool. I would be happy to help.

line 138 of network_client.py: return requests.get(self.__url + '/' + str(id) + '.json').json()
Does not seem to work. networks/52.json does not seem to be supported by CyREST API.
Maybe change it into:
return requests.get(self.__url + '/' + str(id)).json()

The network clone function is pointing to 'add node' instead of clone.

I'll add a function for this type of snippet.

chart_entry = 'barchart: attributelist="ld20t14,ld20t16,ld20t20,ld20t24,ld20t28,ld20t32,ld20t36,ld20t40,ld20t44,ld20t48,ld20t52,ld20t56,ld20t60,ld20t64,ld20t68,ld20t72" colorlist="up:red,zero:red,down:red" showlabels="false"'

target_row_url = BASE_URL + "networks/" + str(pathway_suid) + "/tables/defaultnode/columns/KEGG"
res2 = requests.get(target_row_url)
matched = json.loads(res2.content)["values"]

df2 = pd.DataFrame(columns=["id", "chart"]);
df2["id"] = matched
df2["chart"] = chart_entry

data = json.loads(df2.to_json(orient="records"))

chart_data = {
    "key": "KEGG",
    "dataKey": "id",
    "data": data
}

requests.put(update_table_url, data=json.dumps(chart_data), headers=HEADERS)

For large networks, cytoscape is not creating network views and, therefore, no image is possible to be downloaded.

If clicking in the "create view" button in cytoscape, it works as expected.

• merge pull requests if added value

migrate to cytoscape automation repo

How does this library work?
It could be an amazing library if there was a proper documentation.

What is 'cyjs'? Does that need to imported separately?

I've found if I start up my Cytoscape instance the code present in this branch cannot connect to it

https://github.com/cytoscape/py2cytoscape/tree/develop/py2cytoscape/cyrest

Hi there, I tried to list commands from py2cytoscape as shown in docs:

>>> from py2cytoscape import cyrest
>>> cytoscape=cyrest.cyclient()
>>> cytoscape.commands.list()

but I am getting ImportError: cannot import name 'cyrest' as py2cytoscape is essentially empty. I tried with both: the latest version installed using pip3 and using latest version from develop branch. I can run:

from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient()

as shown in Readme. Could you help me understand why are there two different ways to initialize the REST API client? And why the REST client (in the second example) resides in the data submodule?

docs table does not get parsed

Hello,

I recently discovered that if a user installs igraph, you will get a warning telling that igraph is now changed to jgraph. So py2cytoscape doesn't work then since it uses igraph.
When the import in util/util_igraph.py is changed to jgraph instead of igraph it works.

Kind regards,
Sven

I would like to offer a feature like this issue title.
"sif like pandas dataframe" is 3 column dataframe.

• 1st column is source node
• 2nd column interaction type
• 3rd column is target node

sys.path.insert(0,"/home/user/.local/lib/python2.7/site-packages/py2cytoscape-0.6.2-py2.7.egg/py2cytoscape")
import cyrest as cyrest

Step 1: Create py2cytoscape client

cy=cyrest.cyclient()
cy.status()
cy.version()
print cy.commands.list()
cy.commands.namespace("session")
cy.commands.command("session", "new")
cy.session.new()

Output:
CyREST online!
cytoscapeVersion 3.5.1
apiVersion v1
Available namespaces:
command
edge
group
layout
network
node
session
table
view
vizmap

<Response [405]> 405

HTTP ERROR 405

Problem accessing /v1/commands/session/new. Reason:

    Method Not Allowed

I would like to render cytoscapejs HTML outside of IPython notebook (i.e. in my own webapp). Unfortunately, the function py2cytoscape.cytoscapejs.viewer.render does not return HTML, it calls display(HTML(html_string)), then returns None. This means (AFAIK), I cannot directly access the HTML that is generated from this function.

I suggest that there be two functions in py2cytoscape.cytoscapejs.viewer, one to render HTML from a graph, and another to both render and display the result in IPython notebook. Or even more simply, the function could remain as is, but just return the html string from the rendered template (but I am not sure if this would interfere with usage in ipynb).

Another possible approach would be to allow the caller to select the IPython frontend that is called by display and return the DisplayHandle object used by IPython, which might let the user control how and where the HTML is rendered. But I think the first approach is simpler and more flexible.

I'm looking over the code in base.py and there's a few things I noticed about error handling, particularly linked to the code here:

There doesn't appear to be an exception thrown when an error condition is encountered. From what I can see, the response for the method is set to the error code.

What I think of when reporting an error is to raise an exception. If a CI Error can be found, it should be parsed and included in the exception:

raise CIError(parsedErrorMessage)

I could also be missing some critical information about how this is executed; if this is the case, please let me know where to look.

• not forgetting to mention the CyREST F1000 paper
• add links to cytoscape automation on the readthedocs

The 201 HTTP code appears to be treated as an error here:

This is a successful created response; shouldn't this be treated as a successful request?

• basic structure for documentation of new function as one goes along
• full docs will be added once decision is made on which functions to deprecate

Currently, Multigraphs are not supported in py2cytoscape. They should be supported by using "interaction" edge column in Cytoscape.

Update data table method does not work if the data key is set to DataFrame's Index.

The edge get function is pointing to 'add' instead of get.

Within groups, the url may be incorrectly rooted at 'commands/edge'

This may be leftover from a cut-and-paste.

There seem to be two libraries in here to use:

https://github.com/cytoscape/py2cytoscape/tree/develop/py2cytoscape/cyrest
https://github.com/cytoscape/py2cytoscape/tree/develop/py2cytoscape/data

Which one is actually active? Seems like cyrest is slightly newer and more featured, but I'm not sure which one to use.

Thanks!

window gets hidden but it does not get sent to the results panel as described in the swagger

The input csv format is

Hi,

(If I got it right) it seems after using a map function there is an access by index which throws an error in python 3.x as map no longer returns a list.

`
if layout is not None:
pos = map(lambda position:
{'x': position[0]*scale, 'y': position[1]*scale},
layout.values())

nodes = g.nodes()
if isinstance(g, nx.MultiDiGraph) or isinstance(g, nx.MultiGraph):
    edges = g.edges(data=True, keys=True)
    edge_builder = __build_multi_edge
else:
    edges = g.edges(data=True)
    edge_builder = __build_edge

# Map network table data
cygraph[DATA] = __map_table_data(g.graph.keys(), g.graph)

for i, node_id in enumerate(nodes):
    new_node = __create_node(g.node[node_id], node_id)
    if layout is not None:
        new_node['position'] = pos[i]

`

I'm trying to use py2cytoscape to create network on Cytoscape. However, "lock width and height" is always applied on Cytoscape network Node-Style after I run the program, I tried to add some statements like " 'NODE_LOCK_NODE_WIDTH_AND_HEIGHT': False " or "'NODE_VISUAL_PROPERTY_DEPENDENCY': False" to basic_settings dict to avoid locking, but all of them don't work. Could someone tell me how to update default setting to make height and width unlocked?

In addition, it seems that py2cytoscape is still python2 incompatible when I install it by command "pip install py2cytoscape"(Issue #63 has talked about this). I was wondering when will it be updated in master branch.

Cytoscape:

CyRest:

Java:

Code:

 network_style = cy.style.create('Mapping Style') 
 basic_settings = {
    'NODE_WIDTH': 80,
    'NODE_HEIGHT': 35,
    'NODE_BORDER_WIDTH': 0,
    'NODE_VISUAL_DEPENDENCY': False,

    'EDGE_WIDTH': 1,
    'EDGE_TRANSPARENCY': 255,
    'EDGE_STROKE_UNSELECTED_PAINT': '#848484',
    'NETWORK_BACKGROUND_PAINT': '#FFFFFF'}

network_style.update_defaults(basic_settings)

error:

I tried to control (cyREST + Cytoscape 3.5.1 [Java SE 8u131]) from Bash on Ubuntu on Windows.

The error, and how to reproduce it

In [1]: from py2cytoscape.data.cyrest_client import CyRestClient

In [2]: cy = CyRestClient()

In [3]: cy.session.delete()

In [4]: yeast_net = cy.network.create_from('./galFiltered.sif')
---------------------------------------------------------------------------
HTTPError                                 Traceback (most recent call last)
<ipython-input-4-629751329a66> in <module>()
----> 1 yeast_net = cy.network.create_from('./galFiltered.sif')

/usr/local/lib/python2.7/dist-packages/py2cytoscape/data/network_client.pyc in create_from(self, locations, collection)
     55         res = self.session.post(self.__url, data=json.dumps(location_list),
     56                                 params=parameters, headers=HEADERS)
---> 57         check_response(res)
     58         res = res.json()
     59

/usr/local/lib/python2.7/dist-packages/py2cytoscape/data/cynetwork.pyc in check_response(res)
    372                                        % list(err_info.keys()))
    373         exc.args += (err_msg,)
--> 374         raise exc

HTTPError: (u'500 Server Error: Internal Server Error for url: http://localhost:1234/v1/networks?source=url&collection=Created+from+resources', u'Could not load networks from given locations.')

The environment

knishida@DESKTOP-ETL8RDS ~> python2 --version
Python 2.7.12
knishida@DESKTOP-ETL8RDS ~> pip2 list |grep py2
DEPRECATION: The default format will switch to columns in the future. You can use --format=(legacy|columns) (or define a format=(legacy|columns) in your pip.conf under the [list] section) to disable this warning.
py2cytoscape (0.6.2)
knishida@DESKTOP-ETL8RDS ~> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.2 LTS
Release:        16.04
Codename:       xenial
knishida@DESKTOP-ETL8RDS ~>

In [1]: from py2cytoscape.data.cyrest_client import CyRestClient
In [2]: cy = CyRestClient()
---------------------------------------------------------------------------
JSONDecodeError                           Traceback (most recent call last)
<ipython-input-5-226b69f7d760> in <module>()
----> 1 cy = CyRestClient()

/Users/kozo2/miniconda3/lib/python3.6/site-packages/py2cytoscape/data/cyrest_client.py in __init__(self, ip, port, version)
     17 
     18         self.network = NetworkClient(self.__url)
---> 19         self.style = StyleClient(self.__url)
     20         self.layout = LayoutClient(self.__url)
     21         self.edgebundling = EdgeBundlingClient(self.__url)

/Users/kozo2/miniconda3/lib/python3.6/site-packages/py2cytoscape/data/style_client.py in __init__(self, url)
     14         self.__url_apply = url + 'apply/styles/'
     15 
---> 16         self.vps = VisualProperties(url)
     17 
     18     def create(self, name=None, original_style=None):

/Users/kozo2/miniconda3/lib/python3.6/site-packages/py2cytoscape/data/style_client.py in __init__(self, url)
     71     def __init__(self, url):
     72         self.__url = url + 'styles/visualproperties'
---> 73         self.__convert_to_dict()
     74 
     75     def __convert_to_dict(self):

/Users/kozo2/miniconda3/lib/python3.6/site-packages/py2cytoscape/data/style_client.py in __convert_to_dict(self)
     74 
     75     def __convert_to_dict(self):
---> 76         vps = requests.get(self.__url).json()
     77         vp_dict = {}
     78         node_vps = []

/Users/kozo2/miniconda3/lib/python3.6/site-packages/requests/models.py in json(self, **kwargs)
    848                     # used.
    849                     pass
--> 850         return complexjson.loads(self.text, **kwargs)
    851 
    852     @property

/Users/kozo2/miniconda3/lib/python3.6/json/__init__.py in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    352             parse_int is None and parse_float is None and
    353             parse_constant is None and object_pairs_hook is None and not kw):
--> 354         return _default_decoder.decode(s)
    355     if cls is None:
    356         cls = JSONDecoder

/Users/kozo2/miniconda3/lib/python3.6/json/decoder.py in decode(self, s, _w)
    337 
    338         """
--> 339         obj, end = self.raw_decode(s, idx=_w(s, 0).end())
    340         end = _w(s, end).end()
    341         if end != len(s):

/Users/kozo2/miniconda3/lib/python3.6/json/decoder.py in raw_decode(self, s, idx)
    355             obj, end = self.scan_once(s, idx)
    356         except StopIteration as err:
--> 357             raise JSONDecodeError("Expecting value", s, err.value) from None
    358         return obj, end

JSONDecodeError: Expecting value: line 1 column 1 (char 0)

You can reproduce this error with

• Cytoscape 3.5.1
• py2cytoscape 121224f
• macOS Sierra
• Miniconda3

Trying to run the basic notebook - basic1.ipynb and get the following error. I read thru your issues and saw there was a related error with styles and used that code in an initial cell of notebook to get it to run, but unable.
thx for any help you might offer. Looks like an amazing library. We are trying to create a network graph in a notebook happy to show you when done.

ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<requests.packages.urllib3.connection.HTTPConnection object at 0x11896a080>: Failed to establish a new connection: [Errno 61] Connection refused',))

I tried to implement session save method (currently marked as "pass" in the package" without success. I posted the question here 20 days ago and have not got a reply. Could anyone help? Based on the Cy-REST documentation, this seems to be straightforward, if we have it implemented in the next release, it will be greatly appreciated. Thanks!
idekerlab/cyREST#34

I've found if I start up my Cytoscape instance not on port 1234, the code present in this branch can connect to it, but any other commands do not work.

https://github.com/cytoscape/py2cytoscape/tree/develop/py2cytoscape/data

Specifically this command doesn't work:

cy.style.apply(style=mystyle, network=network1)

It seems that the styles apply is hardcoded with the port.

just as this title

Hi. I was wondering if it made sense to make igraph an optional dependency? It can be a pain in the neck to install on some systems and as far as I can tell, it's only relevant for from_igraph() in util_igraph.py. People might be perfectly happy with using only pure-Python NetworkX. You could wrap the import in a try statement like this:

try:
   import igraph as ig
except Exception as error:   
   print(str(error))
   print("py2cytoscape: Error importing igraph. You won't be able to import from igraph.")
   ig = None

def from_igraph(igraph_network, layout=None, scale=DEF_SCALING):
   if ig == None:
      raise ImportError('igraph not found')
   ....

PS: Love this library. Keep up the good work!

Need to add test cases for the following:

• All graph types (Graph, DiGraph, MultiGraph, MultiDiGraph)
• Adj matrix
• File format conversions (GraphML-->cyjs)

Here is an example:

http://nbviewer.ipython.org/gist/keiono/6c6c427c6dead80a6481

For the first two cases, it works fine, but fails for the last one.