rcsb provider: remove mmtf support, always use https

RCSB redirects calls from http to https, but the redirection is not handled by the Streamer code.
MMTF support has now been removed from RCSB. Default to bfic for compatibility and log warnings.

src/datasource/rcsb-datasource.ts

@@ -5,15 +5,12 @@
  */
 
 import { Log, DatasourceRegistry } from '../globals'
-import { getProtocol } from '../utils'
 import { getFileInfo } from '../loader/loader-utils'
 import Datasource from './datasource'
 
 const baseUrl = '//files.rcsb.org/download/'
-const mmtfBaseUrl = '//mmtf.rcsb.org/v1.0/'
-const mmtfFullUrl = mmtfBaseUrl + 'full/'
-const mmtfReducedUrl = mmtfBaseUrl + 'reduced/'
 const bcifBaseUrl = '//models.rcsb.org/'
+const protocol = 'https:'
 
 class RcsbDatasource extends Datasource {
   getUrl (src: string) {
@@ -22,35 +19,32 @@ class RcsbDatasource extends Datasource {
     // XXXX defaults to XXXX.cif
     const info = getFileInfo(src)
     const pdbid = info.name.indexOf('_') > -1 ? info.name : info.name.substring(0, 4) // Allow extended pdb codes and alphafold codes
-    let url
     if ([ 'pdb', 'cif' ].includes(info.ext) &&
         (info.compressed === false || info.compressed === 'gz')
     ) {
-      url = baseUrl + info.path
-    } else if (info.ext === 'mmtf') {
-      Log.warn('MMTF files distribution is discontinued by RCSB PDB as of July 2, 2024.\n Consider using bcif format instead. See https://www.rcsb.org/news/65a1af31c76ca3abcc925d0c for the deprecation notice')
+      return protocol + baseUrl + info.path
+    }
+
+    if (info.ext === 'mmtf') {
+      Log.warn('MMTF files distribution has been discontinued by RCSB PDB as of July 2024.\n Defaulting to bcif format instead. See https://www.rcsb.org/news/65a1af31c76ca3abcc925d0c for the deprecation notice')
       if (info.base.endsWith('.bb')) {
-        url = mmtfReducedUrl + pdbid
-      } else {
-        url = mmtfFullUrl + pdbid
+        Log.warn('Backbone only files are not available from RCSB PDB anymore.')
       }
-    } else if (info.ext === 'bcif' &&
-        (info.compressed === false || info.compressed === 'gz')
-    ) {
-      url = bcifBaseUrl + info.path
-    } else if (!info.ext) {
+      info.ext = ''
+    }
+
+    if (!info.ext) {
       Log.warn('mmCif files available from RCSB PDB lack connectivity information.\n Consider using PDBe as the data provider for using "Updated mmCif files" that contain residues connectivity records.')
-      url = bcifBaseUrl + pdbid + '.bcif.gz'
     } else {
       Log.warn('unsupported ext', info.ext)
-      url = bcifBaseUrl + pdbid + '.bcif.gz'
     }
-    return getProtocol() + url
+
+    return protocol + bcifBaseUrl + pdbid + '.bcif.gz'
   }
 
   getExt (src: string) {
     const ext = getFileInfo(src).ext
-    return ext ? ext : 'mmtf'
+    return ext ? ext : 'bcif'
   }
 }