just convert from bulk file (ask me for it)

ops/.gitignore

@@ -1,3 +1,4 @@
 node_modules/
 package-lock.json
 molecules/
+bulk.sdf

ops/fetch.molecules.js

@@ -1,4 +1,3 @@
-const request = require('request');
 const fs = require('fs');
 const renderer = require('sdftosvg');
 
@@ -6,40 +5,78 @@ const SVG_OPTS = {
     backgroundColor: 'none',
 }
 
-function fetch(i) {
+function convert(i) {
+    const output = `./../client/assets/molecules/${i}.svg`;
+
     return new Promise((resolve, reject) => {
-        const url = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${i}/record/SDF/?record_type=2d&response_type=save&response_basename=Structure2D_CID_2519`;
-        const output = `./../client/assets/molecules/${i}.svg`;
-
-        request(url, function cb(err, res, body) {
-            if (err) reject(err);
-
-            // write file
-            fs.writeFile(`./molecules/Structure2D_CID_${i}.sdf`, body, function written(err) {
-                if (err) reject(err);
-            });
-
+        fs.readFile(`./molecules/mol${i}`, 'utf8', function rfCb(err, sdf) {
+            if (err) return reject(err);
             // write svg
-            renderer.renderSdfToSvg(body, SVG_OPTS, function(err, svg) {
-                if (err) reject(err);
+            renderer.renderSdfToSvg(sdf, SVG_OPTS, function(err, svg) {
+                if (err) return reject(err);
                 fs.writeFile(output, svg, function written(err) {
                     if (err) reject(err);
                     resolve();
                 });
             });
-        });
+        })
     });
 }
 
 async function loop() {
     for (var i = 10000; i >= 0; i--) {
         try {
-            await fetch(i);
+            await convert(i);
             console.log('finished record', i);
         } catch (e) {
-            console.error(e);
+            console.error('record error', i, e);
         }
     }
 }
 
 loop();
+
+// const request = require('request');
+// const fs = require('fs');
+// const renderer = require('sdftosvg');
+
+// const SVG_OPTS = {
+//     backgroundColor: 'none',
+// }
+
+// function fetch(i) {
+//     return new Promise((resolve, reject) => {
+//         const url = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${i}/record/SDF/?record_type=2d&response_type=save&response_basename=Structure2D_CID_2519`;
+//         const output = `./../client/assets/molecules/${i}.svg`;
+
+//         request(url, function cb(err, res, body) {
+//             if (err) reject(err);
+
+//             // write file
+//             fs.writeFile(`./molecules/Structure2D_CID_${i}.sdf`, body, function written(err) {
+//                 if (err) reject(err);
+//             });
+
+//             // write svg
+//             renderer.renderSdfToSvg(body, SVG_OPTS, function(err, svg) {
+//                 if (err) reject(err);
+//                 fs.writeFile(output, svg, function written(err) {
+//                     if (err) reject(err);
+//                     resolve();
+//                 });
+//             });
+//         });
+//     });
+// }
+
+// async function loop() {
+//     for (var i = 10000; i >= 0; i--) {
+//         try {
+//             await fetch(i);
+//             console.log('finished record', i);
+//         } catch (e) {
+//             console.error(e);
+//         }
+//     }
+// }
+

ops/package.json

@@ -4,6 +4,7 @@
   "description": "",
   "main": "index.js",
   "scripts": {
+    "split:molecules": "cd molecules; csplit -f mol bulk.sdf /\$\$\$\$/ {*} --suppress-matched -z",
     "migrate": "knex migrate:latest",
     "migrate:make": "knex migrate:make --",
     "test": "echo \"Error: no test specified\" && exit 1"