wip model-server

src/apps/model-server-query/index.tsx

@@ -112,7 +112,7 @@ const state: State = {
 
 function formatParams(def: QueryDefinition) {
     const prms = Object.create(null);
-    for (const p of def.params) {
+    for (const p of def.jsonParams) {
         prms[p.name] = p.exampleValues ? p.exampleValues[0] : void 0;
     }
     return JSON.stringify(prms, void 0, 2);

src/servers/model/config.ts

@@ -4,8 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { ModelPropertyProviderConfig } from './property-provider';
-
 const config = {
     /**
      * Determine if and how long to cache entries after a request.
@@ -52,11 +50,11 @@ const config = {
     /**
      * Provide a property config or a path a JSON file with the config.
      */
-    customProperties: <ModelPropertyProviderConfig | string>{
+    customProperties: <import('./property-provider').ModelPropertyProviderConfig | string>{
         sources: [
-            'pdbe',
-            'rcsb',
-            'wwpdb'
+            // 'pdbe',
+            // 'rcsb',
+            // 'wwpdb'
         ],
         params: {
             PDBe: {
@@ -91,10 +89,10 @@ const config = {
      */
     mapFile(source: string, id: string) {
         switch (source.toLowerCase()) {
-            // case 'pdb': return `e:/test/quick/${id}_updated.cif`;
-            case 'pdb': return `e:/test/mol-star/model/out/${id}_updated.bcif`;
-            case 'pdb-bcif': return `c:/test/mol-star/model/out/${id}_updated.bcif`;
-            case 'pdb-cif': return `c:/test/mol-star/model/out/${id}_updated.cif`;
+            case 'pdb': return `e:/test/quick/${id}_updated.cif`;
+            // case 'pdb': return `e:/test/mol-star/model/out/${id}_updated.bcif`;
+            // case 'pdb-bcif': return `c:/test/mol-star/model/out/${id}_updated.bcif`;
+            // case 'pdb-cif': return `c:/test/mol-star/model/out/${id}_updated.cif`;
             default: return void 0;
         }
     }

src/servers/model/query/atoms.ts

@@ -7,6 +7,7 @@
 import { QueryPredicate, StructureElement, StructureProperties as Props } from '../../../mol-model/structure';
 import { AtomsQueryParams } from '../../../mol-model/structure/query/queries/generators';
 import { AtomSiteSchema, AtomSiteSchemaElement } from '../server/api';
+import { ElementSymbol } from '../../../mol-model/structure/model/types';
 
 export function getAtomsTests(params: AtomSiteSchema): Partial<AtomsQueryParams>[] {
     if (!params) return [{ }];
@@ -86,17 +87,17 @@ function atomTest(params: AtomSiteSchemaElement): QueryPredicate | undefined {
 
     if (typeof params.label_atom_id !== 'undefined') {
         props.push(Props.atom.label_atom_id);
-        values.push(+params.label_atom_id);
+        values.push(params.label_atom_id);
     }
 
     if (typeof params.auth_atom_id !== 'undefined') {
         props.push(Props.atom.auth_atom_id);
-        values.push(+params.auth_atom_id);
+        values.push(params.auth_atom_id);
     }
 
     if (typeof params.type_symbol !== 'undefined') {
         props.push(Props.atom.type_symbol);
-        values.push(+params.type_symbol);
+        values.push(ElementSymbol(params.type_symbol));
     }
 
     return andEqual(props, values);

src/servers/model/query/schemas.ts

@@ -1 +1,50 @@
-// TODO
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { CifWriter } from '../../../mol-io/writer/cif';
+
+const InteractionCategories = new Set([
+    'entry',
+    'entity',
+    'exptl',
+    'cell',
+    'symmetry',
+    'struct_conf',
+    'struct_sheet_range',
+    'entity_poly',
+    'struct_asym',
+    'struct_conn',
+    'struct_conn_type',
+    'pdbx_struct_mod_residue',
+    'chem_comp_bond',
+    'atom_sites'
+]);
+
+const AssemblyCategories = new Set([
+    'entry',
+    'entity',
+    'exptl',
+    'cell',
+    'symmetry',
+    'struct_conf',
+    'struct_sheet_range',
+    'entity_poly',
+    'entity_poly_seq',
+    'pdbx_nonpoly_scheme',
+    'struct_asym',
+    'struct_conn',
+    'struct_conn_type',
+    'pdbx_struct_mod_residue',
+    'chem_comp_bond',
+    'atom_sites'
+]);
+
+export const QuerySchemas = {
+    interaction: <CifWriter.Category.Filter>{
+        includeCategory(name) { return InteractionCategories.has(name); },
+        includeField(cat, field) { return true; }
+    }
+}

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -13,6 +13,7 @@ import { resolveJob } from './query';
 import { JobManager } from './jobs';
 import { UUID } from '../../../mol-util';
 import { LandingPage } from './landing';
+import { QueryDefinition, normalizeRestQueryParams, normalizeRestCommonParams, QueryList } from './api';
 
 function makePath(p: string) {
     return Config.appPrefix + '/' + p;
@@ -83,21 +84,23 @@ async function processNextJob() {
     }
 }
 
-// function mapQuery(app: express.Express, queryName: string, queryDefinition: QueryDefinition) {
-//     app.get(makePath(':entryId/' + queryName), (req, res) => {
-//         ConsoleLogger.log('Server', `Query '${req.params.entryId}/${queryName}'...`);
-
-//         if (JobManager.size >= Config.maxQueueLength) {
-//             res.status(503).send('Too many queries, please try again later.');
-//             res.end();
-//             return;
-//         }
-
-//         const jobId = JobManager.add('pdb', req.params.entryId, queryName, req.query);
-//         responseMap.set(jobId, res);
-//         if (JobManager.size === 1) processNextJob();
-//     });
-// }
+function mapQuery(app: express.Express, queryName: string, queryDefinition: QueryDefinition) {
+    app.get(makePath('api/v1/:id/' + queryName), (req, res) => {
+        console.log({ queryName, params: req.params, query: req.query });
+        const entryId = req.params.id;
+        const queryParams = normalizeRestQueryParams(queryDefinition, req.query);
+        const commonParams = normalizeRestCommonParams(req.query);
+        const jobId = JobManager.add({
+            sourceId: commonParams.data_source || 'pdb',
+            entryId,
+            queryName: queryName as any,
+            queryParams,
+            options: { modelNums: commonParams.model_nums, binary: commonParams.encoding === 'bcif' }
+        });
+        responseMap.set(jobId, res);
+        if (JobManager.size === 1) processNextJob();
+    });
+}
 
 export function initWebApi(app: express.Express) {
     app.get(makePath('static/:format/:id'), async (req, res) => {
@@ -128,28 +131,28 @@ export function initWebApi(app: express.Express) {
         });
     })
 
-    app.get(makePath('api/v1'), (req, res) => {
-        const query = /\?(.*)$/.exec(req.url)![1];
-        const args = JSON.parse(decodeURIComponent(query));
-        const name = args.name;
-        const entryId = args.id;
-        const queryParams = args.params || { };
-        const jobId = JobManager.add({
-            sourceId: 'pdb',
-            entryId,
-            queryName: name,
-            queryParams,
-            options: { modelNums: args.modelNums, binary: args.binary }
-        });
-        responseMap.set(jobId, res);
-        if (JobManager.size === 1) processNextJob();
-    });
+    // app.get(makePath('api/v1/json'), (req, res) => {
+    //     const query = /\?(.*)$/.exec(req.url)![1];
+    //     const args = JSON.parse(decodeURIComponent(query));
+    //     const name = args.name;
+    //     const entryId = args.id;
+    //     const queryParams = args.params || { };
+    //     const jobId = JobManager.add({
+    //         sourceId: 'pdb',
+    //         entryId,
+    //         queryName: name,
+    //         queryParams,
+    //         options: { modelNums: args.modelNums, binary: args.binary }
+    //     });
+    //     responseMap.set(jobId, res);
+    //     if (JobManager.size === 1) processNextJob();
+    // });
+
+    for (const q of QueryList) {
+        mapQuery(app, q.name, q.definition);
+    }
 
     app.get('*', (req, res) => {
         res.send(LandingPage);
     });
-
-    // for (const q of QueryList) {
-    //     mapQuery(app, q.name, q.definition);
-    // }
 }

src/servers/model/server/api.ts

@@ -1,27 +1,31 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { Queries, Structure, StructureQuery, StructureSymmetry } from '../../../mol-model/structure';
 import { getAtomsTests } from '../query/atoms';
+import { CifWriter } from '../../../mol-io/writer/cif';
+import { QuerySchemas } from '../query/schemas';
 
 export enum QueryParamType {
     JSON,
     String,
     Integer,
-    Float
+    Float,
+    Boolean
 }
 
-export interface QueryParamInfo {
+export interface QueryParamInfo<T extends string | number = string | number> {
     name: string,
     type: QueryParamType,
     description?: string,
     required?: boolean,
     defaultValue?: any,
     exampleValues?: any[],
-    validation?: (v: any) => void
+    validation?: (v: T) => void,
+    supportedValues?: string[]
 }
 
 export interface QueryDefinition<Params = any> {
@@ -30,11 +34,42 @@ export interface QueryDefinition<Params = any> {
     exampleId: string, // default is 1cbs
     query: (params: any, structure: Structure) => StructureQuery,
     description: string,
-    params: QueryParamInfo[],
+    jsonParams: QueryParamInfo[],
+    restParams: QueryParamInfo[],
     structureTransform?: (params: any, s: Structure) => Promise<Structure>,
+    filter?: CifWriter.Category.Filter,
     '@params': Params
 }
 
+export const CommonQueryParamsInfo: QueryParamInfo[] = [
+    { name: 'model_nums', type: QueryParamType.String, description: `A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.` },
+    { name: 'encoding', type: QueryParamType.String, defaultValue: 'cif', description: `Determines the output encoding (text based 'CIF' or binary 'BCIF').`, supportedValues: ['cif', 'bcif'] },
+    { name: 'data_Source', type: QueryParamType.String, defaultValue: '', description: 'Allows to control how the provided data source ID maps to input file (as specified by the server instance config).' }
+];
+
+export interface CommonQueryParamsInfo {
+    model_nums?: number[],
+    encoding?: 'cif' | 'bcif',
+    data_source?: string
+}
+
+export const AtomSiteSchemaElement = {
+    label_entity_id: { type: QueryParamType.String },
+
+    label_asym_id: { type: QueryParamType.String },
+    auth_asym_id: { type: QueryParamType.String },
+
+    label_comp_id: { type: QueryParamType.String },
+    auth_comp_id: { type: QueryParamType.String },
+    label_seq_id: { type: QueryParamType.Integer },
+    auth_seq_id: { type: QueryParamType.Integer },
+    pdbx_PDB_ins_code: { type: QueryParamType.String },
+
+    label_atom_id: { type: QueryParamType.String },
+    auth_atom_id: { type: QueryParamType.String },
+    type_symbol: { type: QueryParamType.String }
+}
+
 export interface AtomSiteSchemaElement {
     label_entity_id?: string,
 
@@ -43,8 +78,8 @@ export interface AtomSiteSchemaElement {
 
     label_comp_id?: string,
     auth_comp_id?: string,
-    label_seq_id?: string,
-    auth_seq_id?: string,
+    label_seq_id?: number,
+    auth_seq_id?: number,
     pdbx_PDB_ins_code?: string,
 
     label_atom_id?: string,
@@ -54,13 +89,23 @@ export interface AtomSiteSchemaElement {
 
 export type AtomSiteSchema = AtomSiteSchemaElement | AtomSiteSchemaElement[]
 
-const AtomSiteTestParams: QueryParamInfo = {
+const AtomSiteTestJsonParam: QueryParamInfo = {
     name: 'atom_site',
     type: QueryParamType.JSON,
     description: 'Object or array of objects describing atom properties. Names are same as in wwPDB mmCIF dictionary of the atom_site category.',
     exampleValues: [{ label_comp_id: 'ALA' }, { label_seq_id: 123, label_asym_id: 'A' }]
 };
 
+export const AtomSiteTestRestParams = (function() {
+    const params: QueryParamInfo[] = [];
+    for (const k of Object.keys(AtomSiteSchemaElement)) {
+        const p = (AtomSiteSchemaElement as any)[k] as QueryParamInfo;
+        p.name = k;
+        params.push(p);
+    }
+    return params;
+})();
+
 const RadiusParam: QueryParamInfo = {
     name: 'radius',
     type: QueryParamType.Float,
@@ -83,8 +128,9 @@ const QueryMap = {
     'atoms': Q<{ atom_site: AtomSiteSchema }>({
         niceName: 'Atoms',
         description: 'Atoms satisfying the given criteria.',
-        query: p => Queries.combinators.merge(getAtomsTests(p.atom_site).map(test => Queries.generators.atoms(test))),
-        params: [ AtomSiteTestParams ]
+        query: p => Queries.combinators.merge(getAtomsTests(p).map(test => Queries.generators.atoms(test))),
+        jsonParams: [ AtomSiteTestJsonParam ],
+        restParams: AtomSiteTestRestParams
     }),
     'symmetryMates': Q<{ radius: number }>({
         niceName: 'Symmetry Mates',
@@ -93,7 +139,7 @@ const QueryMap = {
         structureTransform(p, s) {
             return StructureSymmetry.builderSymmetryMates(s, p.radius).run();
         },
-        params: [ RadiusParam ]
+        jsonParams: [ RadiusParam ]
     }),
     'assembly': Q<{ name: string }>({
         niceName: 'Assembly',
@@ -102,7 +148,7 @@ const QueryMap = {
         structureTransform(p, s) {
             return StructureSymmetry.buildAssembly(s, '' + (p.name || '1')).run();
         },
-        params: [{
+        jsonParams: [{
             name: 'name',
             type: QueryParamType.String,
             defaultValue: '1',
@@ -110,11 +156,11 @@ const QueryMap = {
             description: 'Assembly name.'
         }]
     }),
-    'residueInteraction': Q<{ atom_site: AtomSiteSchema, radius: number }>({
+    'residueInteraction': Q<AtomSiteSchema & { radius: number }>({
         niceName: 'Residue Interaction',
         description: 'Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.',
         query(p) {
-            const tests = getAtomsTests(p.atom_site);
+            const tests = getAtomsTests(p);
             const center = Queries.combinators.merge(tests.map(test => Queries.generators.atoms({
                 ...test,
                 entityTest: test.entityTest
@@ -126,17 +172,21 @@ const QueryMap = {
         structureTransform(p, s) {
             return StructureSymmetry.builderSymmetryMates(s, p.radius).run();
         },
-        params: [ AtomSiteTestParams, RadiusParam ]
+        jsonParams: [ AtomSiteTestJsonParam, RadiusParam ],
+        restParams: [ ...AtomSiteTestRestParams, RadiusParam ],
+        filter: QuerySchemas.interaction
     }),
-    'residueSurroundings': Q<{ atom_site: AtomSiteSchema, radius: number }>({
+    'residueSurroundings': Q<AtomSiteSchema & { radius: number }>({
         niceName: 'Residue Surroundings',
         description: 'Identifies all residues within the given radius from the source residue.',
         query(p) {
-            const tests = getAtomsTests(p.atom_site);
+            const tests = getAtomsTests(p);
             const center = Queries.combinators.merge(tests.map(test => Queries.generators.atoms(test)));
             return Queries.modifiers.includeSurroundings(center, { radius: p.radius, wholeResidues: true });
         },
-        params: [ AtomSiteTestParams, RadiusParam ]
+        jsonParams: [ AtomSiteTestJsonParam, RadiusParam ],
+        restParams: [ ...AtomSiteTestRestParams, RadiusParam ],
+        filter: QuerySchemas.interaction
     })
 };
 
@@ -159,36 +209,45 @@ export const QueryList = (function () {
     for (let q of QueryList) {
         const m = q.definition;
         m.name = q.name;
-        m.params = m.params || [];
+        m.jsonParams = m.jsonParams || [];
+        m.restParams = m.restParams || m.jsonParams;
     }
 })();
 
-// function _normalizeQueryParams(params: { [p: string]: string }, paramList: QueryParamInfo[]): { [p: string]: string | number | boolean } {
-//     const ret: any = {};
-//     for (const p of paramList) {
-//         const key = p.name;
-//         const value = params[key];
-//         if (typeof value === 'undefined' || (typeof value !== 'undefined' && value !== null && value['length'] === 0)) {
-//             if (p.required) {
-//                 throw `The parameter '${key}' is required.`;
-//             }
-//             if (typeof p.defaultValue !== 'undefined') ret[key] = p.defaultValue;
-//         } else {
-//             switch (p.type) {
-//                 case QueryParamType.JSON: ret[key] = JSON.parse(value); break;
-//                 case QueryParamType.String: ret[key] = value; break;
-//                 case QueryParamType.Integer: ret[key] = parseInt(value); break;
-//                 case QueryParamType.Float: ret[key] = parseFloat(value); break;
-//             }
-
-//             if (p.validation) p.validation(ret[key]);
-//         }
-//     }
-
-//     return ret;
-// }
-
-export function normalizeQueryParams(query: QueryDefinition, params: any) {
-    return params;
-    // return _normalizeQueryParams(params, query.params);
+function _normalizeQueryParams(params: { [p: string]: string }, paramList: QueryParamInfo[]): { [p: string]: string | number | boolean } {
+    const ret: any = {};
+    for (const p of paramList) {
+        const key = p.name;
+        const value = params[key];
+        if (typeof value === 'undefined' || (typeof value !== 'undefined' && value !== null && value['length'] === 0)) {
+            if (p.required) {
+                throw `The parameter '${key}' is required.`;
+            }
+            if (typeof p.defaultValue !== 'undefined') ret[key] = p.defaultValue;
+        } else {
+            switch (p.type) {
+                case QueryParamType.JSON: ret[key] = JSON.parse(value); break;
+                case QueryParamType.String: ret[key] = value; break;
+                case QueryParamType.Integer: ret[key] = parseInt(value); break;
+                case QueryParamType.Float: ret[key] = parseFloat(value); break;
+            }
+
+            if (p.validation) p.validation(ret[key]);
+        }
+    }
+
+    return ret;
+}
+
+export function normalizeRestQueryParams(query: QueryDefinition, params: any) {
+    // return params;
+    return _normalizeQueryParams(params, query.restParams);
+}
+
+export function normalizeRestCommonParams(params: any): CommonQueryParamsInfo {
+    return {
+        model_nums: params.model_nums ? ('' + params.model_nums).split(',').map(n => n.trim()).filter(n => !!n).map(n => +n) : void 0,
+        data_source: params.data_source,
+        encoding: ('' + params.encoding).toLocaleLowerCase() === 'bcif' ? 'bcif' : 'cif'
+    };
 }

src/servers/model/server/jobs.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { UUID } from '../../../mol-util';
-import { getQueryByName, normalizeQueryParams, QueryDefinition, QueryName, QueryParams } from './api';
+import { getQueryByName, QueryDefinition, QueryName, QueryParams } from './api';
 import { LinkedList } from '../../../mol-data/generic';
 
 export interface ResponseFormat {
@@ -40,7 +40,7 @@ export function createJob<Name extends QueryName>(definition: JobDefinition<Name
     const queryDefinition = getQueryByName(definition.queryName);
     if (!queryDefinition) throw new Error(`Query '${definition.queryName}' is not supported.`);
 
-    const normalizedParams = normalizeQueryParams(queryDefinition, definition.queryParams);
+    const normalizedParams = definition.queryParams;
     const sourceId = definition.sourceId || '_local_';
     return {
         id: UUID.create22(),

src/servers/model/server/query.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -22,7 +22,8 @@ import { createModelPropertiesProviderFromConfig, ModelPropertiesProvider } from
 export interface Stats {
     structure: StructureWrapper,
     queryTimeMs: number,
-    encodeTimeMs: number
+    encodeTimeMs: number,
+    resultSize: number
 }
 
 const perf = new PerformanceMonitor();
@@ -56,7 +57,8 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
         const queries = structures.map(s => job.queryDefinition.query(job.normalizedParams, s));
         const result: Structure[] = [];
         for (let i = 0; i < structures.length; i++) {
-            result.push(await StructureSelection.unionStructure(StructureQuery.run(queries[i], structures[i], Config.maxQueryTimeInMs)));
+            const s = await StructureSelection.unionStructure(StructureQuery.run(queries[i], structures[i], Config.maxQueryTimeInMs))
+            if (s.elementCount > 0) result.push(s);
         }
         perf.end('query');
 
@@ -74,15 +76,16 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
         encoder.writeCategory(_model_server_result, job);
         encoder.writeCategory(_model_server_params, job);
 
-        // encoder.setFilter(mmCIF_Export_Filters.onlyPositions);
-        encode_mmCIF_categories(encoder, result);
-        // encoder.setFilter();
+        if (job.queryDefinition.filter) encoder.setFilter(job.queryDefinition.filter);
+        if (result.length > 0) encode_mmCIF_categories(encoder, result);
+        if (job.queryDefinition.filter) encoder.setFilter();
         perf.end('encode');
 
         const stats: Stats = {
             structure: wrappedStructure,
             queryTimeMs: perf.time('query'),
-            encodeTimeMs: perf.time('encode')
+            encodeTimeMs: perf.time('encode'),
+            resultSize: result.reduce((n, s) => n + s.elementCount, 0)
         };
 
         encoder.writeCategory(_model_server_stats, stats);
@@ -151,7 +154,8 @@ const _model_server_stats_fields: CifField<number, Stats>[] = [
     // int32<Stats>('attach_props_time_ms', ctx => ctx.structure.info.attachPropsTime | 0),
     int32<Stats>('create_model_time_ms', ctx => ctx.structure.info.createModelTime | 0),
     int32<Stats>('query_time_ms', ctx => ctx.queryTimeMs | 0),
-    int32<Stats>('encode_time_ms', ctx => ctx.encodeTimeMs | 0)
+    int32<Stats>('encode_time_ms', ctx => ctx.encodeTimeMs | 0),
+    int32<Stats>('element_count', ctx => ctx.resultSize | 0),
 ];
 
 const _model_server_result: CifWriter.Category<Job> = {

src/servers/model/version.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export default '0.8.0';
+export default '0.9.0';