Move all URLs to a separate file & improve getbin method

src/URLs.ts

@@ -0,0 +1,3 @@
+export const RCSB_FILES_URL = "https://files.rcsb.org/view/";
+export const NCBI_PUBCHEM_URL = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/";
+export const RCSB_MMTF_URL = "https://mmtf.rcsb.org/v1.0/full/";

src/autoload.ts

@@ -4,6 +4,7 @@
 import { SurfaceType } from "./ProteinSurface4";
 import { get, specStringToObject } from "./utilities";
 import { CC } from "./colors";
+import { NCBI_PUBCHEM_URL, RCSB_FILES_URL } from "./URLs";
 
 export var autoinit = false;
 export var processing_autoinit = false;
@@ -40,12 +41,12 @@
 
             type = null;
             if (viewerdiv.dataset.pdb) {
-                datauri.push("https://files.rcsb.org/view/" + viewerdiv.dataset.pdb + ".pdb");
+                datauri.push(RCSB_FILES_URL + viewerdiv.dataset.pdb + ".pdb");
                 datatypes.push("pdb");
             } else if (viewerdiv.dataset.cid) {
                 //this doesn't actually work since pubchem does have CORS enabled
                 datatypes.push("sdf");
-                datauri.push("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + viewerdiv.dataset.cid +
+                datauri.push(NCBI_PUBCHEM_URL + viewerdiv.dataset.cid +
                     "/SDF?record_type=3d");
             }
             else if (viewerdiv.dataset.href || viewerdiv.dataset.url) {
@@ -67,15 +68,15 @@
             var divdata = viewerdiv.dataset;
             for (i in divdata) {
                 if ((i.substring(0, 3) === "pdb" && (i !== "pdb"))) {
-                    datauri.push("https://files.rcsb.org/view/" + divdata[i] + ".pdb");
+                    datauri.push(RCSB_FILES_URL + divdata[i] + ".pdb");
                     datatypes.push('pdb');
 
                 } else if (i.substring(0, 4) === "href" && (i !== "href")) {
                     uri = divdata[i];
                     datauri.push(uri);
                     datatypes.push(uri.substring(uri.lastIndexOf('.') + 1));
                 } else if (i.substring(0, 3) === "cid" && (i !== "cid")) {
-                    datauri.push("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + divdata[i] + "/SDF?record_type=3d");
+                    datauri.push(NCBI_PUBCHEM_URL + divdata[i] + "/SDF?record_type=3d");
                     datatypes.push('sdf');
                 }
             }

src/utilities.ts

@@ -1,5 +1,6 @@
 //a collection of miscellaneous utility functions
 
+import { NCBI_PUBCHEM_URL, RCSB_FILES_URL, RCSB_MMTF_URL } from "./URLs";
 import { builtinGradients, Gradient } from "./Gradient";
 import { VolumeData } from "./VolumeData";
 import { builtinColorSchemes, CC, elementColors, htmlColors, Color } from "./colors";
@@ -350,14 +351,15 @@
  * @param uri URL
  * @param callback Function to call with data 
  */
-export function get(uri, callback?) {
-    var promise = fetch(uri).then(checkStatus).then((response) => response.text());
+export function get(uri:string, callback?) {
+    const promise = fetch(uri).then(checkStatus).then((response) => response.text());
     if (callback)
         return promise.then(callback);
-    else
-        return promise;
+    return promise;
 }
 
+
+type RequestMethod = "GET"|"POST"|"PUT"|"DELETE"|"HEAD"|"OPTIONS"|"PATCH";
 /**
  * Download binary data (e.g. a gzipped file) into an array buffer and provide
  * arraybuffer to callback.
@@ -367,19 +369,14 @@
  * @param {string} [postdata] - data for POST request
  * @return {Promise}
  */
-export function getbin(uri, callback?, request?, postdata?) {
-    var promise;
-    if (request == "POST") {
-        promise = fetch(uri, { method: 'POST', body: postdata })
+
+export function getbin(uri:string, callback?, request?: RequestMethod, postdata?) {
+    const promise = fetch(uri, { method: request || "GET", body: postdata })
             .then((response) => checkStatus(response))
             .then((response) => response.arrayBuffer());
-    } else {
-        promise = fetch(uri).then((response) => checkStatus(response))
-            .then((response) => response.arrayBuffer());
-    }
-
+
     if (callback) return promise.then(callback);
-    else return promise;
+    return promise;
 };
 
 
@@ -420,13 +417,14 @@
         }
     }
     if (query.substring(0, 5) === 'mmtf:') {
-        pdbUri = options && options.pdbUri ? options.pdbUri : "https://mmtf.rcsb.org/v1.0/full/";
+        pdbUri = options && options.pdbUri ? options.pdbUri : RCSB_MMTF_URL;
         query = query.substring(5).toUpperCase();
         uri = pdbUri + query;
         if (options && typeof options.noComputeSecondaryStructure === 'undefined') {
             //when fetch directly from pdb, trust structure annotations
             options.noComputeSecondaryStructure = true;
         }
+
         promise = new Promise(function (resolve) {
             getbin(uri)
                 .then(function (ret) {
@@ -454,21 +452,21 @@
                 return;
             }
             if (type == 'mmtf') {
-                mmtfUri = options && options.mmtfUri ? options.mmtfUri : 'https://mmtf.rcsb.org/v1.0/full/';
+                mmtfUri = options && options.mmtfUri ? options.mmtfUri : RCSB_MMTF_URL;
                 uri = mmtfUri + query.toUpperCase();
             }
             else {
-                pdbUri = options && options.pdbUri ? options.pdbUri : "https://files.rcsb.org/view/";
+                pdbUri = options && options.pdbUri ? options.pdbUri : RCSB_FILES_URL;
                 uri = pdbUri + query + "." + type;
             }
 
         } else if (query.substring(0, 4) == 'cid:') {
             type = "sdf";
             query = query.substring(4);
             if (!query.match(/^[0-9]+$/)) {
-                alert("Wrong Compound ID"); return;
+                return alert("Wrong Compound ID"); 
             }
-            uri = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + query +
+            uri = NCBI_PUBCHEM_URL + query +
                 "/SDF?record_type=3d";
         } else if (query.substring(0, 4) == 'url:') {
             uri = query.substring(4);
@@ -480,15 +478,16 @@
             viewer.zoomTo();
             viewer.render();
         };
+
         promise = new Promise(function (resolve) {
-            if (type == 'mmtf') { //binary data
+            if (type === 'mmtf') { //binary data
                 getbin(uri)
                     .then(function (ret) {
                         handler(ret);
                         resolve(m);
                     }).catch(function () {
                         //if mmtf server is being annoying, fallback to text
-                        pdbUri = options && options.pdbUri ? options.pdbUri : "https://files.rcsb.org/view/";
+                        pdbUri = options && options.pdbUri ? options.pdbUri : RCSB_FILES_URL;
                         uri = pdbUri + query + ".pdb";
                         type = "pdb";
                         console.log("falling back to pdb format");
@@ -520,7 +519,8 @@
         });
         return m;
     }
-    else return promise;
+
+    return promise;
 };