model-server: tweak api, added examples to landing page

src/servers/model/local.ts

@@ -19,7 +19,7 @@ let exampleWorkload: LocalInput = [{
         input: 'c:/test/quick/1tqn.cif',
         output: 'c:/test/quick/localapi/1tqn_full.bcif',
         query: 'full',
-        params: { binary: true }
+        params: {}
     }, {
         input: 'c:/test/quick/1cbs_updated.cif',
         output: 'c:/test/quick/localapi/1cbs_ligint.cif',
@@ -29,7 +29,7 @@ let exampleWorkload: LocalInput = [{
         input: 'c:/test/quick/1cbs_updated.cif', // multiple files that are repeated will only be parsed once
         output: 'c:/test/quick/localapi/1cbs_ligint.bcif',
         query: 'residueInteraction',
-        params: { label_comp_id: 'REA', binary: true } // parameters are just a JSON version of the query string
+        params: { label_comp_id: 'REA' } // parameters are just a JSON version of the query string
     }
 ];
 

src/servers/model/server/api-local.ts

@@ -18,7 +18,8 @@ export type LocalInput = {
     output: string,
     query: string,
     modelNums?: number[],
-    params?: any
+    params?: any,
+    binary?: boolean
 }[];
 
 export async function runLocal(input: LocalInput) {
@@ -28,7 +29,12 @@ export async function runLocal(input: LocalInput) {
     }
 
     for (const job of input) {
-        JobManager.add('_local_', job.input, job.query, job.params || { }, job.modelNums, job.output);
+        const binary = /\.bcif/.test(job.output);
+        JobManager.add('_local_', job.input, job.query, job.params || { }, {
+            modelNums: job.modelNums,
+            outputFilename: job.output,
+            binary
+        });
     }
     JobManager.sort();
 

src/servers/model/server/api-web.ts

@@ -133,8 +133,8 @@ export function initWebApi(app: express.Express) {
         const args = JSON.parse(decodeURIComponent(query));
         const name = args.name;
         const entryId = args.id;
-        const params = args.params || { };
-        const jobId = JobManager.add('pdb', entryId, name, params, args.modelNums);
+        const queryParams = args.params || { };
+        const jobId = JobManager.add('pdb', entryId, name, queryParams, { modelNums: args.modelNums, binary: args.binary });
         responseMap.set(jobId, res);
         if (JobManager.size === 1) processNextJob();
     });

src/servers/model/server/jobs.ts

@@ -28,11 +28,12 @@ export interface Job {
     outputFilename?: string
 }
 
-export function createJob(sourceId: '_local_' | string, entryId: string, queryName: string, params: any, modelNums?: number[], outputFilename?: string): Job {
+export function createJob(sourceId: '_local_' | string, entryId: string, queryName: string, queryParams: any,
+        options ?: { modelNums?: number[], outputFilename?: string, binary?: boolean }): Job {
     const queryDefinition = getQueryByName(queryName);
     if (!queryDefinition) throw new Error(`Query '${queryName}' is not supported.`);
 
-    const normalizedParams = normalizeQueryParams(queryDefinition, params);
+    const normalizedParams = normalizeQueryParams(queryDefinition, queryParams);
 
     return {
         id: UUID.create(),
@@ -42,9 +43,9 @@ export function createJob(sourceId: '_local_' | string, entryId: string, queryNa
         entryId,
         queryDefinition,
         normalizedParams,
-        responseFormat: { isBinary: !!params.binary },
-        modelNums,
-        outputFilename
+        responseFormat: { isBinary: !!(options && options.binary) },
+        modelNums: options && options.modelNums,
+        outputFilename: options && options.outputFilename
     };
 }
 
@@ -55,8 +56,9 @@ class _JobQueue {
         return this.list.count;
     }
 
-    add(sourceId: '_local_' | string, entryId: string, queryName: string, params: any, modelNums?: number[], outputFilename?: string) {
-        const job = createJob(sourceId, entryId, queryName, params, modelNums, outputFilename);
+    add(sourceId: '_local_' | string, entryId: string, queryName: string, queryParams: any,
+            options?: { modelNums?: number[], outputFilename?: string, binary?: boolean }) {
+        const job = createJob(sourceId, entryId, queryName, queryParams, options);
         this.list.addLast(job);
         return job.id;
     }

src/servers/model/server/landing.ts

@@ -6,6 +6,45 @@
 
 import Version from '../version'
 
+const examples = [{
+    name: 'Atoms',
+    params: {
+        id: '1cbs',
+        name: 'atoms',
+        params: { atom_site: { label_comp_id: 'ALA' } }
+    }
+}, {
+    name: 'Residue Interaction',
+    params: {
+        id: '1cbs',
+        name: 'residueInteraction',
+        params: {
+            radius: 5,
+            atom_site: { 'label_comp_id': 'REA' }
+        }
+    }
+}, {
+    name: 'Full',
+    params: {
+        id: '1tqn',
+        name: 'full'
+    }
+}, {
+    name: 'Full (binary)',
+    params: {
+        id: '1tqn',
+        name: 'full',
+        binary: true
+    }
+}, {
+    name: 'Full (specific models)',
+    params: {
+        id: '1grm',
+        name: 'full',
+        modelNums: [ 2, 3 ]
+    }
+}];
+
 function create() {
     return `<!DOCTYPE html>
 <html lang="en">
@@ -17,30 +56,35 @@ function create() {
     </head>
     <body>
         <h1>Mol* Model Server ${Version}</h1>
-        <textarea style="height: 280px; width: 600px; font-family: monospace" id="query-text">{
-    "id": "1cbs",
-    "name": "residueInteraction",
-    "params": {
-        "radius": 5,
-        "atom_site": { "label_comp_id": "REA" }
-    }
-}</textarea><br>
+        <select id='example'>
+            <option value='-1'>Select example...</option>
+            ${examples.map((e, i) => `<option value=${i}>${e.name}</option>`)}
+        </select>
+        <br/>
+        <textarea style="height: 280px; width: 600px; font-family: monospace" id="query-text"></textarea><br>
         <button class="button button-primary" style="width: 600px" id="query">Query</button>
         <div id='error' style='color: red; font-weight: blue'></div>
         <div>Static input files available as CIF and BinaryCIF at <a href='ModelServer/static/cif/1cbs' target='_blank'>static/cif/id</a> and <a href='ModelServer/static/bcif/1cbs' target='_blank'>static/bcif/id</a> respectively.</div>
         <script>
-            const err = document.getElementById('error');
+            var Examples = ${JSON.stringify(examples)};
+            var err = document.getElementById('error');
+            var exampleEl = document.getElementById('example'), queryTextEl = document.getElementById('query-text');
+            exampleEl.onchange = function () {
+                var i = +exampleEl.value;
+                if (i < 0) return;
+                queryTextEl.value = JSON.stringify(Examples[i].params, null, 2);
+            };
             document.getElementById('query').onclick = function () {
                 err.innerText = '';
                 try {
-                    var q = JSON.parse(document.getElementById('query-text').value);
+                    var q = JSON.parse(queryTextEl.value);
                     var path = 'ModelServer/api/v1?' + encodeURIComponent(JSON.stringify(q));
                     console.log(path);
                     window.open(path, '_blank');
                 } catch (e) {
                     err.innerText = '' + e;
                 }
-            }
+            };
         </script>
     </body>
 </html>`;