Test New REST on Stage

[everbeek]

Deploy new REST API usage to the Biomixer stage URL. Paul has informed me that the bioportal stage has the new URL format, so I can do this.

See #268, and #317.

Bugs:

[Don't Fix, Inherent to Choosel] in IE, at concepts such as http://stage.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F14734007#visualization , the large concept expansion takes forever to complete.

[Don't Fix, Inherent to Choosel] in IE, clicking to hide nodes by ontology take inordinately long. I believe there is an existing bug or this. This will probably best be fixed during the D3 implementation, when this will probably be implemented in a way that makes this very fast.

[No Replicate] -changing concepts in the tree on the side doesn't always trigger a proper refresh of the visualization. This is likely a bug that needs to be fixed on Bioportal side.

[everbeek]

I checked the embed URL, and it looks right: http://stage.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F82968002#visualization

Also tested the embed URL with our internal test URL and that worked, so things look fine for stage deployment.

[everbeek]

Compare live and stage, stage being the newer version: Live: http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F82968002#visualization and my fave class: http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F368597006#visualization

Stage: http://stage.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F82968002#visualization and my fave class: http://stage.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F368597006#visualization

Additional test points: -correct nodes should be included (no extra, and none missing...hard to verify because old and new REST have different backing data, and the old calls are structured differently, and often trickle in over minutes...) -both the is-a and part-of links should be populated properly (can find part-of in basic concept data on bioportal) e.g. see has_part entry here: http://purl.bioontology.org/ontology/SNOMEDCT/35146001 -layouts in general should work -node expansions via the node drop downs (but only do 'Concept' expansions! Mappings aren't done yet) -when expanding nodes, there should be the warning when there are more than 20 to be loaded. Both options should work. [http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F14734007#visualization ; notably, when the 20 to 60 nodes are added, the radial layout does some interesting helpful things, and inverted radial becomes very useless]

All the other stuff that applied to the other view you recently tested, as follows: -overall loading of view should be similar, though it may take a different amount of time -view should still take up all available room in the browser window -view should work for most central ontology [sometimes private ones can sometimes leak their acronym via mapping REST calls, so you won't find one easily] -variable node coloration, relative node sizing, and relative arc sizing should still work -hover over for nodes and arcs should have correct contents -popups should still become opaque and stay open when directly hovered. -popups should still be text selectable. -popups should not fall off the screen or cover the origin node. -node interactions such as dragging should work smoothly

From the side panel: -layout resetting should work -the ontology filter should still work -arc styles and colors editing should still work

[everbeek]

Pushed it up.