Issue#378 update cytoscape.js version

[JingVT]

Update Cytoscape.js to v3.2.17. For compatibility, we need to upgrade cytoscape-context-menus to version 3.0.6 as well.

Task list for making sure all features related to Cytoscape.js work properly:

• [X] Change Layout on Graph Visualization page
  • [X] Layout Selections -- Circle, Grid, Concentric, Spring Embedder, Tree, cola.
  • Fixed issue #396. Refer: https://github.com/cytoscape/cytoscape.js/issues/1533
  • [X] cola settings
• [X] Use Layout Editor on Graph Visualization page
  • [X] Edit selected nodes or Edit selected edges
  • Fixed issue #398. Refer: http://js.cytoscape.org/#cy.on, where "- events: A space separated list of event names."
  • [X] Arrange nodes
  • Fixed issue #402. Refer: https://github.com/cytoscape/cytoscape.js/issues/1533
• [X] Popup for node or edge
  • Fixed issue #400. Refer: https://github.com/cytoscape/cytoscape.js/issues/1537
  • Cytoscape.js V3 has removed 'cy' prefix on event fields. This pull request changed all cyTarget to Target in graphs_page.js.
• [X] Nodes with multiple background images mentioned in issue #378 For Example: the node with background-image: Pigeon_silhouette_4874 and background-color: rgb(137,208,245). Before Upgrade Cytoscape.js (i.e. v2.7): After Upgrade Cytoscape.js (i.e. v3.2.17):

• [X] Support "z-compound-depth" and "z-index-compare" attributes mentioned in issue #295 Before Upgrade Cytoscape.js (i.e. v2.7): After Upgrade Cytoscape.js (i.e. v3.2.17):

  • Label on the top of edges, see "G1 Pathway"
  • Exported json file has "z-compound-depth" attribute

  

• [X] Search or Filter nodes and edges
• [X] Remove applyMax functions in graphs_page.js which have been deprecated.
  • Fixed issue #405

Useful Reference: Announcing Cytoscape.js 3.0.0

[JingVT]

Possible issue:

Solution:
uninstall bower: sudo npm -g uninstall bower check if it is still here which bower if it will show you something like /usr/local/bin/bower then rm <path from previous command> set npm registry URL： npm config set registry="http://registry.npmjs.org/" install bower: sudo npm -g install bower

[JingVT]

Update cytoscape: bower update cytoscape-context-menus bower update cytoscape