How to use a Cytoscape application from Cyrest ?

[Pascal KREZEL]

Hi, 

Is there a way to use a Cytoscape application from Cyrest ?

From example I would like to use the Community cluster (GLay) from ClusterMaker ?

Pascal

[Scooter Morris]

Hi Pascal,
    Yes, but you should be aware that there are some unfortunate quirks.  You can call apps (clusterMaker2 in particular) using the /v1/commands branch of the REST service.  So, to execute GLay, you would issue the request: http://localhost:1234/v1/commands/cluster/glay?network=yyy&selectedOnly=false where yyy is the name of the network you wish to cluster.  This will result in a plain text response when it's complete.  We're in the process of changing things up so that the command responses are in JSON.

-- scooter

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[Ruth Isserlin]

Hi Scooter, 

There are some quirks with cyrest.  One that I am struggling with right now is I am using this documentation (http://idekerlab.github.io/cyREST/) to find all the cyrest features and I keep forgetting that there are way more that I can use in the command interface.  i realize that the commands available are dependent on the apps that you have installed but it would be helpful to incorporate the set of potentially available commands to this documentation as well (especially the ones that come already installed with cytoscape  like table, network, node,edge, layout....)

I just changed the way I was creating networks because I couldn’t figure out how to create a table from a file and I just found it in the command set :( 

Thanks, 

Ruth 

[Pascal KREZEL]

Hi Scooter,

I followed your explanations and I got an answer:

In: requests.post("http://localhost:1234/v1/commands/clustermaker/glay?network=net&selectedOnly=false")

out: <Response [405]>

How can I read this text file ?

Pascal

Le lundi 7 novembre 2016 18:21:28 UTC+1, Scooter Morris a écrit :

Hi Pascal,
    Yes, but you should be aware that there are some unfortunate quirks.  You can call apps (clusterMaker2 in particular) using the /v1/commands branch of the REST service.  So, to execute GLay, you would issue the request: http://localhost:1234/v1/commands/cluster/glay?network=yyy&selectedOnly=false where yyy is the name of the network you wish to cluster.  This will result in a plain text response when it's complete.  We're in the process of changing things up so that the command responses are in JSON.

-- scooter


On 11/07/2016 12:10 AM, Pascal KREZEL wrote:

Hi, 

Is there a way to use a Cytoscape application from Cyrest ?

From example I would like to use the Community cluster (GLay) from ClusterMaker ?

Pascal

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[Scooter Morris]

Short answer: you can't (remember I said there were some "quirks").  Once the cluster is complete, the network will have a new column (I *think* it's __glay, but you should run a cluster manually to confirm).  That column will assign each node to a cluster number that you can read with CyREST.

-- scooter

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[Pascal KREZEL]

Hi Scooter,

Thank you for your answer.

What should I do to get this column ?

Pascal

[Ruth Isserlin]

Hi Pascal, 

The easiest thing is to get the whole node table:

http://localhost:1234/v1/networks/52/tables/defaultnode/rows/

Where 52 is the network suid. 

Thanks, 

Ruth

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[Pascal KREZEL]

Hi Scooter,

My network in CyREST is named "net".

if I do : 

requests.post("http://localhost:1234/v1/commands/clustermaker/glay?network=net&selectedOnly=false")

nothing happens, there is no new column with the result of GLay.

Is it really possible to get such result ?

Pascal

[Scooter Morris]

Hi Pascal,
    The namespace is actually "cluster", not "clustermaker".  Give this a try:

requests.post("http://localhost:1234/v1/commands/cluster/glay?network=net&selectedOnly=false")

-- scooter

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[Pascal KREZEL]

Hi Scooter;

Thank you for your answer.

I finally succeeded but with GET and not POST : 

                             requests.get("http://localhost:1234/v1/commands/cluster/glay?network=subnet_1&selectedOnly=false")

Thank your for your help.

Pascal

[Pascal KREZEL]

Hi Scooter;

Thank you for your answer.

I finally succeeded but with GET and not POST : 

                             requests.get("http://localhost:1234/v1/commands/cluster/glay?network=subnet_1&selectedOnly=false")

I remarked also an instability in the answer of CyREST. One time, I got the complete action of GLay (with the creation of a new network)  and in a second time I got only the addition of the "_glayClus" column !

Thank your for your help.

Pascal

[Giovanni Urgo]

Hi guys, sorry I was having a similar problem. 

I would like to run Glay clustering from ClusterMaker using R (Rcy3).

Is there any way to do so?? 

Thank you very much !

Giovanni

[Scooter Morris]

Hi Giovani,

   Even easier.  RCy3 has methods called commandRUN and commandPOST that deals with all of the underlying REST calls.   If you look at the help for "cluster glay" you can see:

help cluster glay

This is an implementation of the fast-greedy optimization of of the modularity score, with different corrections on edge density and cluster size.

cluster glay arguments:

clusterAttribute=<String>: Cluster attribute name 

createGroups=true|false: Create groups (metanodes) with results 

network=current|[column:value|network name]: Network to cluster

restoreEdges=true|false: Restore inter-cluster edges after layout 

selectedOnly=true|false: Cluster only selected nodes 

showUI=true|false: Create new clustered network 

undirectedEdges=true|false: Assume edges are undirected

If you just construct the command you want, you can use commandRUN to run it.

-- scooter