diff --git a/src/servers/model/local.ts b/src/servers/model/local.ts
index 089706895d8ac9ea0b4e02b171ee9908f8b73882..0aa5ff4f6d966c04a7263998dbcb317617988a55 100644
--- a/src/servers/model/local.ts
+++ b/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
}
];
diff --git a/src/servers/model/server/api-local.ts b/src/servers/model/server/api-local.ts
index 27c9f4250a5ce18d38391889cfe8034dbe259b2b..ff80abade29a011cd23bb5391458e6623685c3d1 100644
--- a/src/servers/model/server/api-local.ts
+++ b/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();
diff --git a/src/servers/model/server/api-web.ts b/src/servers/model/server/api-web.ts
index 297a0c6436f74cdd122517eb2893d0271c099581..9e1e2b4cd42c5f40daeebb29756a498688f82fd1 100644
--- a/src/servers/model/server/api-web.ts
+++ b/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();
});
diff --git a/src/servers/model/server/jobs.ts b/src/servers/model/server/jobs.ts
index f2c77d77dfb86f923ca9080c8c53af7921970d06..adba35f1a0d63269386b218feb9ad258912b2470 100644
--- a/src/servers/model/server/jobs.ts
+++ b/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;
}
diff --git a/src/servers/model/server/landing.ts b/src/servers/model/server/landing.ts
index 2cb4e0aaf3ba22273995bad8ff4953b887fa38c6..1f8af4391a593768dc7b38b689ecb3065deb6509 100644
--- a/src/servers/model/server/landing.ts
+++ b/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>`;