Open matthiaskoenig opened 9 years ago
See the cyREST example. Provide REST functionality for the API analog to cyREST.
Stable interfaces matter, stable services matter.
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.
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.
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],
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).
Providing API for other apps like cy3fluxviz.