Update mutation mapper default PDB url to the new PDB endpoint

[pieterlukasse]

PDB changed its endpoint for serving PDB data from http://www.rcsb.org/pdb/files/ to http://files.rcsb.org/view/ . See also cBioPortal/cbioportal#1434.

So it would be good to update mutationMapper.js code here as follows:

        function delayedInitMutationMapper(el, options, tabs, tabName)
        {
                var mutationMapper = new MutationMapper(options);
                var initialized = false;

@@ -13516,7 +13517,8 @@ function Mutation3dVis(name, options)
                        debug: false,
                        color: "white"
                },
-               pdbUri: "http://www.rcsb.org/pdb/files/", // default PDB database URI
+               //for https, use a proxy since rcsb.org is not serving https and browsers will complain about the mixed https/http content
+               pdbUri: "http://files.rcsb.org/view/",

[pieterlukasse]

@onursumer can it be that this old url is still found in the rc branch? Is this dead code?

[pieterlukasse]

cc @jjgao

[onursumer]

Hi @pieterlukasse, this is the legacy mutation mapper, pretty much dead. We are using the correct url for the latest implementation: https://github.com/cBioPortal/cbioportal-frontend/blob/ad8769543e3642f3d15715305d47b7924043c146/src/shared/components/structureViewer/StructureVisualizer.ts#L71

[pieterlukasse]

Thanks @onursumer . I made 2 PRs to clean this up (they are referenced to this issue).