diff --git a/package.json b/package.json
index da84eb4c19e0d296aeb11f79c12371889898cfe8..c32a46c131903f5c651d7e401b58fceccac469f5 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,7 @@
"test": "npm run lint && jest",
"build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
"build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
- "build-tsc": "tsc --incremental && tsc --build src/servers --incremental",
+ "build-tsc": "tsc --incremental && tsc --build tsconfig.servers.json --incremental",
"build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
"build-webpack": "webpack --mode production --config ./webpack.config.production.js",
"build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
@@ -24,7 +24,7 @@
"watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
"watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
"watch-tsc": "tsc --watch --incremental",
- "watch-servers": "tsc --build src/servers --watch --incremental",
+ "watch-servers": "tsc --build tsconfig.servers.json --watch --incremental",
"watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
"watch-webpack": "webpack -w --mode development --display minimal",
"watch-webpack-viewer": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.js",
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 02005fd2b90ba61bad0ebbc61bd560dcd1f1b1a9..95ffece477692481de4936337d36dd16ba391071 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -108,6 +108,11 @@ export namespace Field {
return this;
}
+ add(field: Field<K, D>) {
+ this.fields.push(field);
+ return this;
+ }
+
getFields() { return this.fields; }
}
@@ -222,6 +227,8 @@ export namespace Category {
}
export interface Encoder<T = string | Uint8Array> extends EncoderBase {
+ readonly isBinary: boolean,
+
setFilter(filter?: Category.Filter): void,
isCategoryIncluded(name: string): boolean,
setFormatter(formatter?: Category.Formatter): void,
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index 7bafaca3d0ad81fb69b25f6abbd9eed8ac032e74..df5e19b9c0463758b08c9a6b0c2a97c9d8f7cbaa 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -28,6 +28,8 @@ export default class BinaryEncoder implements Encoder<Uint8Array> {
private filter: Category.Filter = Category.DefaultFilter;
private formatter: Category.Formatter = Category.DefaultFormatter;
+ readonly isBinary = true;
+
binaryEncodingProvider: BinaryEncodingProvider | undefined = void 0;
setFilter(filter?: Category.Filter) {
diff --git a/src/mol-io/writer/cif/encoder/text.ts b/src/mol-io/writer/cif/encoder/text.ts
index bfb15d7e21b6314ea9104ae6030468004eb5435f..94049da039901960a2e6e04a37ef0b1a964b3a9f 100644
--- a/src/mol-io/writer/cif/encoder/text.ts
+++ b/src/mol-io/writer/cif/encoder/text.ts
@@ -19,6 +19,8 @@ export default class TextEncoder implements Encoder<string> {
private filter: Category.Filter = Category.DefaultFilter;
private formatter: Category.Formatter = Category.DefaultFormatter;
+ readonly isBinary = false;
+
binaryEncodingProvider = void 0;
setFilter(filter?: Category.Filter) {
diff --git a/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts b/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts
index c76615de78285c00c2db84ff0ee1ea847f5452b3..ae09e71c0a493b45c70a0913dadc1438c5be8277 100644
--- a/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts
+++ b/src/mol-model/structure/export/categories/atom_site_operator_mapping.ts
@@ -6,18 +6,21 @@
import { SymmetryOperator } from '../../../../mol-math/geometry';
import { CifExportContext } from '../mmcif';
-import { StructureElement, StructureProperties as P } from '../../structure';
+import { StructureElement, StructureProperties as P, CifExportCategoryInfo } from '../../structure';
import Unit from '../../structure/unit';
import { Segmentation } from '../../../../mol-data/int';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { Column } from '../../../../mol-data/db';
-export function atom_site_operator_mapping(encoder: CifWriter.Encoder, ctx: CifExportContext) {
+
+export function atom_site_operator_mapping(ctx: CifExportContext): CifExportCategoryInfo | undefined {
const entries = getEntries(ctx);
if (entries.length === 0) return;
- encoder.writeCategory(Category, entries, { ignoreFilter: true });
+ return [Category, entries, { ignoreFilter: true }];
}
+export const AtomSiteOperatorMappingCategoryName = 'molstar_atom_site_operator_mapping';
+
export const AtomSiteOperatorMappingSchema = {
molstar_atom_site_operator_mapping: {
label_asym_id: Column.Schema.Str(),
diff --git a/src/mol-model/structure/export/categories/utils.ts b/src/mol-model/structure/export/categories/utils.ts
index 4f500efbf56d9dfe93322614ca74b4b1d1958e47..4914c55046862c591099a844cde401b1893600af 100644
--- a/src/mol-model/structure/export/categories/utils.ts
+++ b/src/mol-model/structure/export/categories/utils.ts
@@ -14,6 +14,7 @@ import { sortArray } from '../../../../mol-data/util';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { CifExportContext } from '../mmcif';
import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { CifCategory, CifField, getCifFieldType } from '../../../../mol-io/reader/cif';
export function getModelMmCifCategory<K extends keyof mmCIF_Schema>(model: Model, name: K): mmCIF_Database[K] | undefined {
if (!MmcifFormat.is(model.sourceData)) return;
@@ -58,4 +59,41 @@ export function copy_mmCif_category(name: keyof mmCIF_Schema, condition?: (struc
return CifWriter.Category.ofTable(table);
}
};
+}
+
+export function copy_source_mmCifCategory(encoder: CifWriter.Encoder, ctx: CifExportContext, category: CifCategory): CifWriter.Category<CifExportContext> | undefined {
+ if (!MmcifFormat.is(ctx.firstModel.sourceData)) return;
+
+ const fs = CifWriter.fields<number, undefined>();
+ if (encoder.isBinary) {
+ for (const f of category.fieldNames) {
+ // TODO: this could be optimized
+ const field = classifyField(f, category.getField(f)!);
+ fs.add(field);
+ }
+ } else {
+ for (const f of category.fieldNames) {
+ const field = category.getField(f)!;
+ fs.str(f, row => field.str(row));
+ }
+ }
+
+ const fields = fs.getFields();
+ return {
+ name: category.name,
+ instance() {
+ return { fields, source: [{ data: void 0, rowCount: category.rowCount }] };
+ }
+ };
+}
+
+function classifyField(name: string, field: CifField): CifWriter.Field {
+ const type = getCifFieldType(field);
+ if (type['@type'] === 'str') {
+ return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
+ } else if (type['@type'] === 'float') {
+ return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, typedArray: Float64Array });
+ } else {
+ return CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, typedArray: Int32Array });
+ }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index c6368925dfc083010e5e77665404c76db48e3668..725a1923979f2d40f2303d3adc298fbd4fd9243e 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -13,10 +13,11 @@ import CifCategory = CifWriter.Category
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
import { Model } from '../model';
-import { getUniqueEntityIndicesFromStructures, copy_mmCif_category } from './categories/utils';
+import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
import { CustomPropertyDescriptor } from '../common/custom-property';
import { atom_site_operator_mapping } from './categories/atom_site_operator_mapping';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
export interface CifExportContext {
structures: Structure[],
@@ -24,6 +25,10 @@ export interface CifExportContext {
cache: any
}
+export type CifExportCategoryInfo =
+ | [CifWriter.Category, any /** context */, CifWriter.Encoder.WriteCategoryOptions]
+ | [CifWriter.Category, any /** context */]
+
export namespace CifExportContext {
export function create(structures: Structure | Structure[]): CifExportContext {
const structureArray = Array.isArray(structures) ? structures : [structures];
@@ -99,8 +104,8 @@ export const mmCIF_Export_Filters = {
}
};
-function encodeCustomProp(customProp: CustomPropertyDescriptor, ctx: CifExportContext, encoder: CifWriter.Encoder, params: encode_mmCIF_categories_Params) {
- if (!customProp.cifExport || customProp.cifExport.categories.length === 0) return;
+function getCustomPropCategories(customProp: CustomPropertyDescriptor, ctx: CifExportContext, params?: encode_mmCIF_categories_Params): CifExportCategoryInfo[] {
+ if (!customProp.cifExport || customProp.cifExport.categories.length === 0) return [];
const prefix = customProp.cifExport.prefix;
const cats = customProp.cifExport.categories;
@@ -114,14 +119,21 @@ function encodeCustomProp(customProp: CustomPropertyDescriptor, ctx: CifExportCo
ctx.cache[propId + '__ctx'] = propCtx;
}
}
+
+ const ret: CifExportCategoryInfo[] = [];
for (const cat of cats) {
- if (params.skipCategoryNames && params.skipCategoryNames.has(cat.name)) continue;
+ if (params?.skipCategoryNames?.has(cat.name)) continue;
if (cat.name.indexOf(prefix) !== 0) throw new Error(`Custom category '${cat.name}' name must start with prefix '${prefix}.'`);
- encoder.writeCategory(cat, propCtx);
+ ret.push([cat, propCtx]);
}
+ return ret;
}
-type encode_mmCIF_categories_Params = { skipCategoryNames?: Set<string>, exportCtx?: CifExportContext }
+type encode_mmCIF_categories_Params = {
+ skipCategoryNames?: Set<string>,
+ exportCtx?: CifExportContext,
+ copyAllCategories?: boolean
+}
/** Doesn't start a data block */
export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: encode_mmCIF_categories_Params) {
@@ -129,30 +141,95 @@ export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures:
const models = first.models;
if (models.length !== 1) throw 'Can\'t export stucture composed from multiple models.';
- const _params = params || { };
- const ctx: CifExportContext = params && params.exportCtx ? params.exportCtx : CifExportContext.create(structures);
+ const ctx: CifExportContext = params?.exportCtx || CifExportContext.create(structures);
+ if (params?.copyAllCategories && MmcifFormat.is(models[0].sourceData)) {
+ encode_mmCIF_categories_copyAll(encoder, ctx);
+ } else {
+ console.log('default');
+ encode_mmCIF_categories_default(encoder, ctx, params);
+ }
+}
+
+function encode_mmCIF_categories_default(encoder: CifWriter.Encoder, ctx: CifExportContext, params?: encode_mmCIF_categories_Params) {
for (const cat of Categories) {
- if (_params.skipCategoryNames && _params.skipCategoryNames.has(cat.name)) continue;
+ if (params?.skipCategoryNames && params?.skipCategoryNames.has(cat.name)) continue;
encoder.writeCategory(cat, ctx);
}
- if ((!_params.skipCategoryNames || !_params.skipCategoryNames.has('atom_site')) && encoder.isCategoryIncluded('atom_site')) {
- atom_site_operator_mapping(encoder, ctx);
+ if (!params?.skipCategoryNames?.has('atom_site') && encoder.isCategoryIncluded('atom_site')) {
+ const info = atom_site_operator_mapping(ctx);
+ if (info) encoder.writeCategory(info[0], info[1], info[2]);
}
- for (const customProp of models[0].customProperties.all) {
- encodeCustomProp(customProp, ctx, encoder, _params);
+ const _params = params || { };
+ for (const customProp of ctx.firstModel.customProperties.all) {
+ for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
+ encoder.writeCategory(cat, propCtx);
+ }
}
- const structureCustomProps = new Set<CustomPropertyDescriptor>();
for (const s of ctx.structures) {
if (!s.hasCustomProperties) continue;
- for (const p of s.customPropertyDescriptors.all) structureCustomProps.add(p);
+ for (const customProp of s.customPropertyDescriptors.all) {
+ for (const [cat, propCtx] of getCustomPropCategories(customProp, ctx, _params)) {
+ encoder.writeCategory(cat, propCtx);
+ }
+ }
}
- structureCustomProps.forEach(customProp => encodeCustomProp(customProp, ctx, encoder, _params));
}
+function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExportContext) {
+ const providedCategories = new Map<string, CifExportCategoryInfo>();
+
+ for (const cat of Categories) {
+ providedCategories.set(cat.name, [cat, ctx]);
+ }
+
+ const mapping = atom_site_operator_mapping(ctx);
+ if (mapping) providedCategories.set(mapping[0].name, mapping);
+
+ for (const customProp of ctx.firstModel.customProperties.all) {
+ for (const info of getCustomPropCategories(customProp, ctx)) {
+ providedCategories.set(info[0].name, info);
+ }
+ }
+
+ for (const s of ctx.structures) {
+ if (!s.hasCustomProperties) continue;
+ for (const customProp of s.customPropertyDescriptors.all) {
+ for (const info of getCustomPropCategories(customProp, ctx)) {
+ providedCategories.set(info[0].name, info);
+ }
+ }
+ }
+
+ const handled = new Set<string>();
+
+ const data = (ctx.firstModel.sourceData as MmcifFormat).data;
+ for (const catName of data.frame.categoryNames) {
+ handled.add(catName);
+
+ if (providedCategories.has(catName)) {
+ const info = providedCategories.get(catName)!;
+ encoder.writeCategory(info[0], info[1], info[2]);
+ } else {
+ if ((data.db as any)[catName]) {
+ const cat = copy_mmCif_category(catName as any);
+ encoder.writeCategory(cat, ctx);
+ } else {
+ const cat = copy_source_mmCifCategory(encoder, ctx, data.frame.categories[catName]);
+ if (cat) encoder.writeCategory(cat);
+ }
+ }
+ }
+
+ providedCategories.forEach((info, name) => {
+ if (!handled.has(name)) encoder.writeCategory(info[0], info[1], info[2]);
+ });
+}
+
+
function to_mmCIF(name: string, structure: Structure, asBinary = false) {
const enc = CifWriter.createEncoder({ binary: asBinary });
enc.startDataBlock(name);
diff --git a/src/servers/common/swagger-ui/index.ts b/src/servers/common/swagger-ui/index.ts
index 1c0348a7c61a47bf8d4db60546f0af4b16ff4cbb..20366f824f6c92c6017c06200317656d2fe65d76 100644
--- a/src/servers/common/swagger-ui/index.ts
+++ b/src/servers/common/swagger-ui/index.ts
@@ -5,11 +5,11 @@
*/
import * as express from 'express';
-import * as fs from 'fs';
import { getAbsoluteFSPath } from 'swagger-ui-dist';
import { ServeStaticOptions } from 'serve-static';
import { interpolate } from '../../../mol-util/string';
import { Handler } from 'express-serve-static-core';
+import IndexTemplate from './indexTemplate';
export function swaggerUiAssetsHandler(options?: ServeStaticOptions): Handler {
const opts = options || {};
@@ -25,8 +25,7 @@ export interface SwaggerUIOptions {
}
function createHTML(options: SwaggerUIOptions) {
- const htmlTemplate = fs.readFileSync(`${__dirname}/indexTemplate.html`).toString();
- return interpolate(htmlTemplate, options);
+ return interpolate(IndexTemplate, options);
}
export function swaggerUiIndexHandler(options: SwaggerUIOptions): express.Handler {
diff --git a/src/servers/common/swagger-ui/indexTemplate.html b/src/servers/common/swagger-ui/indexTemplate.ts
similarity index 80%
rename from src/servers/common/swagger-ui/indexTemplate.html
rename to src/servers/common/swagger-ui/indexTemplate.ts
index 92869e8c5713a1f663fccefd9484562096cae5b1..5c6a1d3b0cb7d5f2e79d730a1a9aac77ca01f505 100644
--- a/src/servers/common/swagger-ui/indexTemplate.html
+++ b/src/servers/common/swagger-ui/indexTemplate.ts
@@ -1,10 +1,10 @@
-<!DOCTYPE html>
+export default `<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
- <title>${title}</title>
- <link rel="stylesheet" type="text/css" href="${apiPrefix}/swagger-ui.css" >
- ${shortcutIconLink}
+ <title>\${title}</title>
+ <link rel="stylesheet" type="text/css" href="\${apiPrefix}/swagger-ui.css" >
+ \${shortcutIconLink}
<style>
html
@@ -30,8 +30,8 @@
<body>
<div id="swagger-ui"></div>
- <script src="${apiPrefix}/swagger-ui-bundle.js"> </script>
- <script src="${apiPrefix}/swagger-ui-standalone-preset.js"> </script>
+ <script src="\${apiPrefix}/swagger-ui-bundle.js"> </script>
+ <script src="\${apiPrefix}/swagger-ui-standalone-preset.js"> </script>
<script>
function HidePlugin() {
// this plugin overrides some components to return nothing
@@ -44,7 +44,7 @@
}
window.onload = function () {
var ui = SwaggerUIBundle({
- url: '${openapiJsonUrl}',
+ url: '\${openapiJsonUrl}',
validatorUrl: null,
docExpansion: 'list',
dom_id: '#swagger-ui',
@@ -63,4 +63,4 @@
}
</script>
</body>
-</html>
\ No newline at end of file
+</html>`;
\ No newline at end of file
diff --git a/src/servers/model/server/api-local.ts b/src/servers/model/server/api-local.ts
index c94230dd4a41c22c266515cb24d87f1c6f032610..9235932a2440e54257e7a3a30997eab1d7616e62 100644
--- a/src/servers/model/server/api-local.ts
+++ b/src/servers/model/server/api-local.ts
@@ -13,11 +13,11 @@ import { Job, JobEntry, JobManager } from './jobs';
import { resolveJob } from './query';
import { StructureCache } from './structure-wrapper';
-
export type Entry<Q extends QueryName = QueryName> = {
input: string,
query: Q,
modelNums?: number[],
+ copyAllCategories?: boolean,
params?: QueryParams<Q>,
}
@@ -43,6 +43,7 @@ export async function runLocal(input: LocalInput) {
queryName: q.query,
queryParams: q.params || { },
modelNums: q.modelNums,
+ copyAllCategories: !!q.copyAllCategories
})),
writer: job.asTarGz
? new TarballFileResultWriter(job.output, job.gzipLevel)
diff --git a/src/servers/model/server/api-schema.ts b/src/servers/model/server/api-schema.ts
index e2071c4d7c5262afcafcb1d9ca340d58f272ddc0..34b532020f9b1e5b6a312d8e14102454f740698c 100644
--- a/src/servers/model/server/api-schema.ts
+++ b/src/servers/model/server/api-schema.ts
@@ -52,7 +52,7 @@ function getPaths() {
const queryManyExample: MultipleQuerySpec = {
queries: [
{ entryId: '1cbs', query: 'residueInteraction', params: { atom_site: [{ label_comp_id: 'REA' }], radius: 5 } },
- { entryId: '1tqn', query: 'full' }
+ { entryId: '1tqn', query: 'full', copy_all_categories: true }
],
encoding: 'cif',
asTarGz: false
@@ -174,7 +174,12 @@ function getParamInfo(info: QueryParamInfo) {
description: info.description,
required: !!info.required,
schema: {
- type: info.type === QueryParamType.String ? 'string' : info.type === QueryParamType.Integer ? 'integer' : 'number',
+ type: info.type === QueryParamType.String
+ ? 'string' : info.type === QueryParamType.Integer
+ ? 'integer'
+ : info.type === QueryParamType.Boolean
+ ? 'boolean'
+ : 'number',
enum: info.supportedValues ? info.supportedValues : void 0,
default: info.defaultValue
},
diff --git a/src/servers/model/server/api-web-multiple.ts b/src/servers/model/server/api-web-multiple.ts
index f073af8a1477ca3da41a17bbbe213ac763efd40e..c6ad015f3589dcb0d88e502cd47eaadec3cd08db 100644
--- a/src/servers/model/server/api-web-multiple.ts
+++ b/src/servers/model/server/api-web-multiple.ts
@@ -11,7 +11,8 @@ export interface MultipleQueryEntry<Name extends QueryName = QueryName> {
entryId: string,
query: Name,
params?: QueryParams<Name>,
- model_nums?: number[]
+ model_nums?: number[],
+ copy_all_categories?: boolean
}
export interface MultipleQuerySpec {
diff --git a/src/servers/model/server/api-web.ts b/src/servers/model/server/api-web.ts
index d92ce1d89c081427b1e60c22bb48a5b4a62c408b..3ce061a5fadadcf8bf69b93fd13be88f38026ba4 100644
--- a/src/servers/model/server/api-web.ts
+++ b/src/servers/model/server/api-web.ts
@@ -63,7 +63,8 @@ function mapQuery(app: express.Express, queryName: string, queryDefinition: Quer
entryId,
queryName: queryName as any,
queryParams,
- modelNums: commonParams.model_nums
+ modelNums: commonParams.model_nums,
+ copyAllCategories: !!commonParams.copy_all_categories
})],
writer: createResultWriter(res, commonParams.encoding === 'bcif', entryId, queryName),
options: { binary: commonParams.encoding === 'bcif' }
@@ -134,7 +135,8 @@ function createMultiJob(spec: MultipleQuerySpec, res: express.Response) {
entryId: q.entryId,
queryName: q.query,
queryParams: q.params || { },
- modelNums: q.model_nums
+ modelNums: q.model_nums,
+ copyAllCategories: !!q.copy_all_categories
})),
writer,
options: { binary: spec.encoding?.toLowerCase() === 'bcif', tarball: spec.asTarGz }
diff --git a/src/servers/model/server/api.ts b/src/servers/model/server/api.ts
index e2a797be53d2fcf670349c7543ce4f5ec63e6468..fd2861dd7b06259266a3c8ca7447207f22965d6d 100644
--- a/src/servers/model/server/api.ts
+++ b/src/servers/model/server/api.ts
@@ -13,6 +13,7 @@ export enum QueryParamType {
JSON,
String,
Integer,
+ Boolean,
Float
}
@@ -44,12 +45,14 @@ export interface QueryDefinition<Params = any> {
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: 'copy_all_categories', type: QueryParamType.Boolean, defaultValue: false, description: 'If true, copy all categories from the input file.' },
{ 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',
+ copy_all_categories?: boolean
data_source?: string
}
@@ -234,6 +237,7 @@ function _normalizeQueryParams(params: { [p: string]: string }, paramList: Query
case QueryParamType.String: el = value; break;
case QueryParamType.Integer: el = parseInt(value); break;
case QueryParamType.Float: el = parseFloat(value); break;
+ case QueryParamType.Boolean: el = Boolean(+value); break;
}
if (p.validation) p.validation(el);
@@ -260,6 +264,7 @@ 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,
+ copy_all_categories: Boolean(params.copy_all_categories),
encoding: ('' + params.encoding).toLocaleLowerCase() === 'bcif' ? 'bcif' : 'cif'
};
}
\ No newline at end of file
diff --git a/src/servers/model/server/jobs.ts b/src/servers/model/server/jobs.ts
index 62919e74704116b32b2c4576291c355031cc7645..49c512e5bbfacc9bd8476e20d63460efe092f594 100644
--- a/src/servers/model/server/jobs.ts
+++ b/src/servers/model/server/jobs.ts
@@ -40,7 +40,8 @@ export interface JobEntry {
queryDefinition: QueryDefinition,
normalizedParams: any,
- modelNums?: number[]
+ modelNums?: number[],
+ copyAllCategories: boolean
}
interface JobEntryDefinition<Name extends QueryName> {
@@ -48,7 +49,8 @@ interface JobEntryDefinition<Name extends QueryName> {
entryId: string,
queryName: Name,
queryParams: QueryParams<Name>,
- modelNums?: number[]
+ modelNums?: number[],
+ copyAllCategories: boolean
}
export function JobEntry<Name extends QueryName>(definition: JobEntryDefinition<Name>): JobEntry {
@@ -65,7 +67,8 @@ export function JobEntry<Name extends QueryName>(definition: JobEntryDefinition<
entryId: definition.entryId,
queryDefinition,
normalizedParams,
- modelNums: definition.modelNums
+ modelNums: definition.modelNums,
+ copyAllCategories: !!definition.copyAllCategories
};
}
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 4b08c065bec5c1d48945f3fd44166bdac3eb590e..ce6c67924673a7ca35d2400826ed2b7471b60391 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -163,7 +163,7 @@ async function resolveJobEntry(entry: JobEntry, structure: StructureWrapper, enc
const queries = structures.map(s => entry.queryDefinition.query(entry.normalizedParams, s));
const result: Structure[] = [];
for (let i = 0; i < structures.length; i++) {
- const s = await StructureSelection.unionStructure(StructureQuery.run(queries[i], structures[i], { timeoutMs: Config.queryTimeoutMs }));
+ const s = StructureSelection.unionStructure(StructureQuery.run(queries[i], structures[i], { timeoutMs: Config.queryTimeoutMs }));
if (s.elementCount > 0) result.push(s);
}
perf.end('query');
@@ -178,9 +178,9 @@ async function resolveJobEntry(entry: JobEntry, structure: StructureWrapper, enc
encoder.writeCategory(_model_server_result, entry);
encoder.writeCategory(_model_server_params, entry);
- if (entry.queryDefinition.filter) encoder.setFilter(entry.queryDefinition.filter);
- if (result.length > 0) encode_mmCIF_categories(encoder, result);
- if (entry.queryDefinition.filter) encoder.setFilter();
+ if (!entry.copyAllCategories && entry.queryDefinition.filter) encoder.setFilter(entry.queryDefinition.filter);
+ if (result.length > 0) encode_mmCIF_categories(encoder, result, { copyAllCategories: entry.copyAllCategories });
+ if (!entry.copyAllCategories && entry.queryDefinition.filter) encoder.setFilter();
perf.end('encode');
const stats: Stats = {
diff --git a/src/servers/tsconfig.json b/tsconfig.servers.json
similarity index 85%
rename from src/servers/tsconfig.json
rename to tsconfig.servers.json
index a1d79bbde5f0134635cfaee4ed2ce53063d373c8..343cb7b047808a8ba0aa24d9b872bcc3a40f9770 100644
--- a/src/servers/tsconfig.json
+++ b/tsconfig.servers.json
@@ -16,8 +16,8 @@
"noEmitHelpers": true,
"jsx": "react",
"lib": [ "es6", "dom", "esnext.asynciterable", "es2016" ],
- "rootDir": "../../src",
- "outDir": "../../lib/servers"
+ "rootDir": "src",
+ "outDir": "lib/servers"
},
- "include": [ "**/*" ]
+ "include": [ "src/servers/**/*" ]
}
\ No newline at end of file