API for tables.

Since Cytoscape.js does not have data type in the spec, it is better to support GraphSON reader when number data type is important:

https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library

Currently, there is no API to enable/disable visual property dependencies, such as Lock node width and height. We need an API to enable/disable these options.

Update the following JavaScript project to test ALL REST API.

• https://github.com/keiono/cy-rest-test

This repository will not be used anymore. Need to move everything to:

https://github.com/idekerlab/cyREST

line 148: 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()

This includes:

• Apply layout
• Apply Visual Style

Currently API documents for Visual Style API is completely broken and cannot generate any API document.

Need some examples to use cy-rest from JavaScript (mainly from node.js).

Cytoscape.js JSON does not have specific format for the view. We need to design how CyNetworkViews are serialized into JSON file.

Add support for Edge Bundling.

Open questions:

• How can we set parameters set via Tunables?

Implement CRUD operations as RESTful API.

Need to add "Rotate" manual layout API.

The docs: http://keiono.github.io/cy-rest/#1288037935
The URL: GET http://example.com/v1/networks/networkId/views/viewId.png
The server replies with Content-Type: application/json but the content itself is a png image. The docs also say that something of Content-Type application/json will be returned.

In contrast, getting the first network view as a png works fine http://keiono.github.io/cy-rest/#144494073

If you want to run cy-rest on a different port, the current workflow of

set a global Cytoscape property from Edit-->Preserences-->Properties... and add a new property port.number"

is rather obscure.

I suggest the following:

• Do not start the server automatically. I don't need it all the time and sometimes I have two instances of Cytoscape open and then I get the error message

    javax.ws.rs.ProcessingException: Failed to start Grizzly HTTP server: Address already in use

• Don't put the global properties in the "cytoscape 3" namespace. Define a seperate "cy-rest" namespace for Edit-->Preserences-->Properties.
• Also make it possible to define the address to bind to. It would be cool if you could control cy-rest from a different computer. The address "localhost" makes this impossible (unless you SSH into the machine first).
• Define a management interface in the OSGi console:

    cy-rest start localhost 1234
    cy-rest start 192.168.1.1 1234
    cy-rest stop
    cy-rest query http://192.168.1.1/v1/networks

Where the last command only supports HTTP GET queries. This should be regarded mostly as a diagnostic tool and not as something to actually work with.

• Define a dialog in the Menu: Apps -> cyREST. Then a window should pop up where you can start and stop the server with parameters described in the previous bullet point. This is for the people who start Cytoscape without a visible OSGi console. The hostname and port fields can be prefilled from the global Cytoscape properties if they are set. If the user uses this method, you can save his choice of host and port as global Cytoscape properties.

Need to support RESTful operations for View objects. This is for setting/getting Visual Property values for the given view object.

Docs URL: http://keiono.github.io/cy-rest/#-875567376
REST URL: v1/networks/networkId/groups/nodeSUID

This always seem to produce a HTTP 404 response.

My curl request:

curl -X GET -v http://localhost:1234/v1/networks/80/groups/90                                                       22:36:25
* Hostname was NOT found in DNS cache
*   Trying ::1...
* connect to ::1 port 1234 failed: Verbindungsaufbau abgelehnt
*   Trying 127.0.0.1...
* Connected to localhost (127.0.0.1) port 1234 (#0)
> GET /v1/networks/80/groups/90 HTTP/1.1
> User-Agent: curl/7.38.0
> Host: localhost:1234
> Accept: */*
> 
< HTTP/1.1 404 Not Found
< Date: Sun, 19 Oct 2014 20:45:58 GMT
< Content-Length: 0
< 
* Connection #0 to host localhost left intact

And I double-checked that network 80 and node 90 (within network 80) do exist.

A minor issue:
http://keiono.github.io/cy-rest/#-1471173272
with the URL
http://localhost:1234/v1/gc
Returns a "HTTP/1.1 204 No Content" on my machine.

The documentation says it should return 200 on success.

Prepare comprehensive tutorial scripts as IPython Notebooks:

• https://github.com/idekerlab/cy-rest-python

Docs: http://keiono.github.io/cy-rest/#-726758156

Path-parameter columnName does not exist.

The REST call actually expects a JSON object with two fields: old_name and new_name that contain the column names.

If table includes non-English UTF-8 chars, they cannot be decoded. Need to specify encoding when returning non-English chars.

Add GraphSON writer. This is useful when using external tools such as graph databases supporting Tinkerpop Blueprints:

https://github.com/tinkerpop/blueprints

Need to add "Scaling" function API.

In current version, updating Table data requires the following steps:

1. Create new columns one-by-one
2. Prepare data to be PUT:
   • mapping key name in target table
   • mapping key in the data to be posted
   • Actual key-value pairs
3. Call PUT method

This is not intuitive. We need a simplified method to batch-update table.

Hey,
Can I find API docs anywhere? Or even just a list of possible endpoints?
Am happy to help generate one, if it doesn't exist, if you point me in the right direction, as well :)
thanks!
Rishi

Please use our new repo.

Used URL:
http://example.com/v1/networks/ (docs: http://keiono.github.io/cy-rest/#-1099067042)
with GET parameters "column" and "query".

This request will fail (HTTP 500) if at least one of the network collections doesn't have a network table with the specified column, even though other network collections do have that column in their network tables.

I therefore suggest that network collections which don't have the specified column are ignored for the search.

Implement CRUD operations for default values of Visual Style.

Need an API to get current network view as image.

Currently, there is no way to create new List column. We need to support it by adding new option in POST Column API. The new POST format will be:

{
    "name": COL_NAME,
    "type": COL_TYPE,
    "immutable": (optional),
    "isList": (optional.  If true, create as List)
{

App "fails to start" according to cytoscape app-manager. Screenshot of app manager attached.

OS X 10.8.3, Cytoscape 3.1.1. Tried both pre-alpha builds; neither works.

Clean and deploy py2cytoscape library and make it available to pip command.

https://github.com/idekerlab/py2cytoscape

Utility for JavaScript should be deployed to NPM repository and we need to add it to BioJS registry.

It should be possible to save and load sessions via cy-rest.
This could be especially handy when several sessions have to be created automatically.

Add comprehensive examples for R users. Scripts and Markdown documents will be maintained here:

• https://github.com/idekerlab/cy-rest-R

Write a complete user documentation in the Wiki.

"Fit network view to current window" is a useful feature for everyone. This should be included in the first release.

Current POST method for column accepts single entry only. This should accept both multiple columns and single column.

Docs: http://keiono.github.io/cy-rest/#1469098445
The curl command I have tried: curl -X DELETE -v http://localhost:1234/v1/networks/80/groups/115/
and I am very certain that network 80 and group 115 exist.

I get a HTTP 500 error for this. Complete HTTP conversation:

> DELETE /v1/networks/80/groups/115/ HTTP/1.1
> User-Agent: curl/7.38.0
> Host: localhost:1234
> Accept: */*
> 
< HTTP/1.1 500 Request failed.
< Content-Type: text/html;charset=ISO-8859-1
< Date: Sun, 19 Oct 2014 20:36:25 GMT
< Connection: close
< Content-Length: 1033
< 
<html><head><title>Grizzly 2.3.16</title><style><!--div.header {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#003300;font-size:22px;-moz-border-radius-topleft: 10px;border-top-left-radius: 10px;-moz-border-radius-topright: 10px;border-top-right-radius: 10px;padding-left: 5px}div.body {font-family:Tahoma,Arial,sans-serif;color:black;background-color:#FFFFCC;font-size:16px;padding-top:10px;padding-bottom:10px;padding-left:10px}div.footer {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#666633;font-size:14px;-moz-border-radius-bottomleft: 10px;border-bottom-left-radius: 10px;-moz-border-radius-bottomright: 10px;border-bottom-right-radius: 10px;padding-left: 5px}BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;}B {font-family:Tahoma,Arial,sans-serif;color:black;}A {color : black;}HR {color : #999966;}--></style> </head><body><div class="header">Request failed.</div><div class="body">Request failed.</div><div class="footer">Grizzly 2.3.16</div></bod* Closing connection 0
y></html>