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matthiaskoenig / cy3sbml

cy3sbml: SBML for Cytoscape 3
GNU Lesser General Public License v3.0
13 stars 2 forks source link

REST API (Java via bundles & python via REST) #18

Open matthiaskoenig opened 9 years ago

matthiaskoenig commented 9 years ago

Providing API for other apps like cy3fluxviz.

matthiaskoenig commented 8 years ago

See the cyREST example. Provide REST functionality for the API analog to cyREST.

matthiaskoenig commented 8 years ago

Stable interfaces matter, stable services matter.

matthiaskoenig commented 8 years ago

see the commands interface & cyREST https://groups.google.com/forum/#!topic/cytoscape-app-dev/kyv_2ddE6-w Create example for SBML loading and visualization from python notebook.

matthiaskoenig commented 8 years ago

Some things which should be supported:

ext -> cy3sbml
> load SBML
> create and apply style
> create subnetwork
> create image
> set node images (via id mapping)
> get SBMLManager content
cy3sbml --> ext
> node selection listener (get some event)

The main idea is the support of visualization from within different programming frameworks. Via sending/receiving REST commands the both way communication can be implemented.

matthiaskoenig commented 8 years ago

As part of the API also the export interfaces have to be defined. This will remove the current problems with 

[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml,  has 1,  private references [org.sbml.jsbml], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.biomodel,  has 1,  private references [uk.ac.ebi.biomodels.ws], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.chebi,  has 1,  private references [uk.ac.ebi.chebi.webapps.chebiWS.model], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.gui,  has 1,  private references [org.identifiers.registry.data], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.layout,  has 3,  private references [org.sbml.jsbml.ext.qual, org.sbml.jsbml, org.sbml.jsbml.ext.layout], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.mapping,  has 1,  private references [org.sbml.jsbml], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.ols,  has 2,  private references [uk.ac.ebi.pride.utilities.ols.web.service.model, org.identifiers.registry.data], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.oven,  has 1,  private references [javax.xml.stream], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.uniprot,  has 1,  private references [uk.ac.ebi.kraken.interfaces.uniprot], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.util,  has 6,  private references [org.sbml.jsbml.ext.qual, org.sbml.jsbml.ext.fbc, org.sbml.jsbml.ext.comp, org.sbml.jsbml.ext.groups, org.sbml.jsbml, org.w3c.dom], 
[WARNING] Bundle org.cysbml:cy3sbml:bundle:0.3.0 : Export org.cy3sbml.validator,  has 2,  private references [org.sbml.jsbml, javax.xml.stream],
matthiaskoenig commented 6 years ago

With cytoscape 3.6 the new automatization API is available. This will simplify the implementation of the API and automatization tasks (which can be called from python).