From 15471a6af0a9e38ec370221c8c856c5f34f1dbe9 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sat, 29 Sep 2018 18:16:50 +0200
Subject: [PATCH] refactoring CIF exporter
---
src/apps/cif2bcif/converter.ts | 2 +-
src/mol-io/writer/cif.ts | 4 +++
.../pdbe/structure-quality-report.ts | 23 +++++++++-----
src/mol-model-props/rcsb/symmetry.ts | 2 +-
.../structure/export/categories/atom_site.ts | 10 ++++---
.../export/categories/modified-residues.ts | 9 ++++--
.../export/categories/secondary-structure.ts | 15 +++++++---
src/mol-model/structure/export/mmcif.ts | 30 +++++++++----------
.../model/formats/mmcif/bonds/comp.ts | 4 +--
.../model/formats/mmcif/bonds/struct_conn.ts | 7 +++--
.../model/properties/custom/residue.ts | 25 +++++++---------
.../structure/structure/structure.ts | 10 +++++++
src/perf-tests/cif-encoder.ts | 2 +-
src/servers/model/preprocess/converter.ts | 2 +-
src/servers/model/preprocess/preprocess.ts | 2 +-
src/servers/model/server/query.ts | 25 +++++++---------
src/servers/volume/server/query/encode.ts | 10 +++----
17 files changed, 105 insertions(+), 77 deletions(-)
diff --git a/src/apps/cif2bcif/converter.ts b/src/apps/cif2bcif/converter.ts
index b17e126c4..386bba5b5 100644
--- a/src/apps/cif2bcif/converter.ts
+++ b/src/apps/cif2bcif/converter.ts
@@ -27,7 +27,7 @@ async function getCIF(ctx: RuntimeContext, path: string) {
function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
return {
name: cat.name,
- instance: () => ({ data: cat, fields, rowCount: cat.rowCount })
+ instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
};
}
diff --git a/src/mol-io/writer/cif.ts b/src/mol-io/writer/cif.ts
index 84b555a28..c191d8a4b 100644
--- a/src/mol-io/writer/cif.ts
+++ b/src/mol-io/writer/cif.ts
@@ -40,6 +40,10 @@ export namespace CifWriter {
fixedPoint3: E.by(E.fixedPoint(1000)).and(E.delta).and(E.integerPacking),
};
+ export function categoryInstance<Key, Data>(fields: Field<Key, Data>[], source: Category.DataSource): Category.Instance {
+ return { fields, source: [source] };
+ }
+
export function createEncodingProviderFromCifFrame(frame: CifFrame): EncodingProvider {
return {
get(c, f) {
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index 4907860f4..47e874a65 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -28,17 +28,21 @@ const _Descriptor = ModelPropertyDescriptor({
categories: [{
name: 'pdbe_structure_quality_report',
instance(ctx) {
- const issues = StructureQualityReport.get(ctx.model);
- if (typeof ctx.globalCache.pdbe_structure_quality_report !== 'undefined' && ctx.globalCache.pdbe_structure_quality_report !== ctx.model.modelNum) return CifWriter.Category.Empty;
- ctx.globalCache.pdbe_structure_quality_report = ctx.model.modelNum;
- return { fields: _structure_quality_report_fields, rowCount: 1, data: issues ? issues.updated : 'n/a' }
+ const structure = ctx.structures[0];
+ const issues = StructureQualityReport.get(structure.model);
+ return {
+ fields: _structure_quality_report_fields,
+ source: [{ data: issues ? issues.updated : 'n/a', rowCount: 1 }]
+ };
}
}, {
name: 'pdbe_structure_quality_report_issues',
instance(ctx) {
- const issues = StructureQualityReport.get(ctx.model);
- if (!issues || !issues.map) return CifWriter.Category.Empty;
- return ResidueCustomProperty.createCifCategory(ctx, issues.map, _structure_quality_report_issues_fields);
+ return {
+ fields: _structure_quality_report_issues_fields,
+ source: ctx.structures.map(
+ s => ResidueCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
+ };
}
}]
},
@@ -150,6 +154,11 @@ export namespace StructureQualityReport {
return model._dynamicPropertyData.__StructureQualityReport__;
}
+ export function getIssueMap(model: Model): IssueMap | undefined {
+ const data = get(model);
+ return data && data.map;
+ }
+
const _emptyArray: string[] = [];
export function getIssues(e: StructureElement) {
if (!Unit.isAtomic(e.unit)) return _emptyArray;
diff --git a/src/mol-model-props/rcsb/symmetry.ts b/src/mol-model-props/rcsb/symmetry.ts
index c1727ae3a..36bdd5a8e 100644
--- a/src/mol-model-props/rcsb/symmetry.ts
+++ b/src/mol-model-props/rcsb/symmetry.ts
@@ -22,7 +22,7 @@ const { str, int, float, Aliased, Vector, List } = Column.Schema;
function getInstance(name: keyof AssemblySymmetry.Schema): (ctx: CifExportContext) => CifWriter.Category.Instance<any, any> {
return function(ctx: CifExportContext) {
- const assemblySymmetry = AssemblySymmetry.get(ctx.model);
+ const assemblySymmetry = AssemblySymmetry.get(ctx.structures[0].model);
return assemblySymmetry ? Category.ofTable(assemblySymmetry.db[name]) : CifWriter.Category.Empty;
}
}
diff --git a/src/mol-model/structure/export/categories/atom_site.ts b/src/mol-model/structure/export/categories/atom_site.ts
index e80212e10..b908c7a00 100644
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/src/mol-model/structure/export/categories/atom_site.ts
@@ -51,12 +51,14 @@ const atom_site_fields = CifWriter.fields<StructureElement, Structure>()
export const _atom_site: CifCategory<CifExportContext> = {
name: 'atom_site',
- instance({ structure }: CifExportContext) {
+ instance({ structures }: CifExportContext) {
return {
fields: atom_site_fields,
- data: structure,
- rowCount: structure.elementCount,
- keys: () => structure.elementLocations()
+ source: structures.map(s => ({
+ data: s,
+ rowCount: s.elementCount,
+ keys: () => s.elementLocations()
+ }))
};
}
}
diff --git a/src/mol-model/structure/export/categories/modified-residues.ts b/src/mol-model/structure/export/categories/modified-residues.ts
index 52886186c..0ca4666ce 100644
--- a/src/mol-model/structure/export/categories/modified-residues.ts
+++ b/src/mol-model/structure/export/categories/modified-residues.ts
@@ -27,7 +27,9 @@ const pdbx_struct_mod_residue_fields: CifField<number, StructureElement[]>[] = [
CifField.str('details', (i, xs) => xs[i].unit.model.properties.modifiedResidues.details.get(P.residue.label_comp_id(xs[i]))!)
];
-function getModifiedResidues({ model, structure }: CifExportContext): StructureElement[] {
+function getModifiedResidues({ structures }: CifExportContext): StructureElement[] {
+ // TODO: can different models have differnt modified residues?
+ const structure = structures[0], model = structure.model;
const map = model.properties.modifiedResidues.parentId;
if (!map.size) return [];
@@ -54,6 +56,9 @@ export const _pdbx_struct_mod_residue: CifCategory<CifExportContext> = {
name: 'pdbx_struct_mod_residue',
instance(ctx) {
const residues = getModifiedResidues(ctx);
- return { fields: pdbx_struct_mod_residue_fields, data: residues, rowCount: residues.length };
+ return {
+ fields: pdbx_struct_mod_residue_fields,
+ source: [{ data: residues, rowCount: residues.length }]
+ };
}
}
\ No newline at end of file
diff --git a/src/mol-model/structure/export/categories/secondary-structure.ts b/src/mol-model/structure/export/categories/secondary-structure.ts
index afd936db2..2f0b3950a 100644
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/src/mol-model/structure/export/categories/secondary-structure.ts
@@ -18,7 +18,10 @@ export const _struct_conf: CifCategory<CifExportContext> = {
name: 'struct_conf',
instance(ctx) {
const elements = findElements(ctx, 'helix');
- return { fields: struct_conf_fields, data: elements, rowCount: elements.length };
+ return {
+ fields: struct_conf_fields,
+ source: [{ data: elements, rowCount: elements.length }]
+ };
}
};
@@ -26,7 +29,10 @@ export const _struct_sheet_range: CifCategory<CifExportContext> = {
name: 'struct_sheet_range',
instance(ctx) {
const elements = (findElements(ctx, 'sheet') as SSElement<SecondaryStructure.Sheet>[]).sort(compare_ssr);
- return { fields: struct_sheet_range_fields, data: elements, rowCount: elements.length };
+ return {
+ fields: struct_sheet_range_fields,
+ source: [{ data: elements, rowCount: elements.length }]
+ };
}
};
@@ -63,11 +69,12 @@ interface SSElement<T extends SecondaryStructure.Element> {
}
function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContext, kind: SecondaryStructure.Element['kind']) {
- const { key, elements } = ctx.model.properties.secondaryStructure;
+ // TODO: encode secondary structure for different models?
+ const { key, elements } = ctx.structures[0].model.properties.secondaryStructure;
const ssElements: SSElement<any>[] = [];
- for (const unit of ctx.structure.units) {
+ for (const unit of ctx.structures[0].units) {
// currently can only support this for "identity" operators.
if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index bd774b605..a5924f652 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -8,32 +8,30 @@
import { CifWriter } from 'mol-io/writer/cif'
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif'
import { Structure } from '../structure'
-import { Model } from '../model'
import { _atom_site } from './categories/atom_site';
import CifCategory = CifWriter.Category
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
import { _pdbx_struct_mod_residue } from './categories/modified-residues';
export interface CifExportContext {
- structure: Structure,
- model: Model,
- localCache: any,
- /** useful when exporting multiple models at the same time */
- globalCache: any
+ structures: Structure[],
+ cache: any
}
export namespace CifExportContext {
- export function create(structures: Structure | Structure[]): CifExportContext[] {
- const globalCache = Object.create(null);
- if (Array.isArray(structures)) return structures.map(structure => ({ structure, model: structure.models[0], localCache: Object.create(null), globalCache }));
- return [{ structure: structures, model: structures.models[0], localCache: Object.create(null), globalCache }];
+ export function create(structures: Structure | Structure[]): CifExportContext {
+ return {
+ structures: Array.isArray(structures) ? structures : [structures],
+ cache: Object.create(null)
+ };
}
}
function copy_mmCif_category(name: keyof mmCIF_Schema): CifCategory<CifExportContext> {
return {
name,
- instance({ model }) {
+ instance({ structures }) {
+ const model = structures[0].model;
if (model.sourceData.kind !== 'mmCIF') return CifCategory.Empty;
const table = model.sourceData.data[name];
if (!table || !table._rowCount) return CifCategory.Empty;
@@ -44,9 +42,9 @@ function copy_mmCif_category(name: keyof mmCIF_Schema): CifCategory<CifExportCon
const _entity: CifCategory<CifExportContext> = {
name: 'entity',
- instance({ structure, model}) {
- const keys = Structure.getEntityKeys(structure);
- return CifCategory.ofTable(model.entities.data, keys);
+ instance({ structures}) {
+ const keys = Structure.getEntityKeys(structures[0]);
+ return CifCategory.ofTable(structures[0].model.entities.data, keys);
}
}
@@ -103,13 +101,13 @@ export const mmCIF_Export_Filters = {
}
/** Doesn't start a data block */
-export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: { skipCategoryNames?: Set<string>, exportCtx?: CifExportContext[] }) {
+export function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: { skipCategoryNames?: Set<string>, exportCtx?: CifExportContext }) {
const first = Array.isArray(structures) ? structures[0] : (structures as Structure);
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 && params.exportCtx ? params.exportCtx : CifExportContext.create(structures);
for (const cat of Categories) {
if (_params.skipCategoryNames && _params.skipCategoryNames.has(cat.name)) continue;
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
index 7aab5ed22..430480733 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/comp.ts
@@ -26,10 +26,10 @@ export namespace ComponentBond {
categories: [{
name: 'chem_comp_bond',
instance(ctx) {
- const chem_comp_bond = getChemCompBond(ctx.model);
+ const chem_comp_bond = getChemCompBond(ctx.structures[0].model);
if (!chem_comp_bond) return CifWriter.Category.Empty;
- const comp_names = getUniqueResidueNames(ctx.structure);
+ const comp_names = getUniqueResidueNames(ctx.structures[0]);
const { comp_id, _rowCount } = chem_comp_bond;
const indices: number[] = [];
for (let i = 0; i < _rowCount; i++) {
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
index 3296debca..486c071a1 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds/struct_conn.ts
@@ -31,10 +31,11 @@ export namespace StructConn {
categories: [{
name: 'struct_conn',
instance(ctx) {
- const struct_conn = getStructConn(ctx.model);
+ const structure = ctx.structures[0], model = structure.model;
+ const struct_conn = getStructConn(model);
if (!struct_conn) return CifWriter.Category.Empty;
- const strConn = get(ctx.model);
+ const strConn = get(model);
if (!strConn || strConn.entries.length === 0) return CifWriter.Category.Empty;
const foundAtoms = new Set<ElementIndex>();
@@ -45,7 +46,7 @@ export namespace StructConn {
for (let i = 0, _i = partners.length; i < _i; i++) {
const atom = partners[i].atomIndex;
if (foundAtoms.has(atom)) continue;
- if (hasAtom(ctx.structure, atom)) {
+ if (hasAtom(structure, atom)) {
foundAtoms.add(atom);
} else {
hasAll = false;
diff --git a/src/mol-model/structure/model/properties/custom/residue.ts b/src/mol-model/structure/model/properties/custom/residue.ts
index 0b9b480b7..ba79b8d7b 100644
--- a/src/mol-model/structure/model/properties/custom/residue.ts
+++ b/src/mol-model/structure/model/properties/custom/residue.ts
@@ -7,7 +7,6 @@
import { ResidueIndex } from '../../indexing';
import { Unit, Structure, StructureElement } from '../../../structure';
import { Segmentation } from 'mol-data/int';
-import { CifExportContext } from '../../../export/mmcif';
import { UUID } from 'mol-util';
import { CifWriter } from 'mol-io/writer/cif';
@@ -20,25 +19,23 @@ export interface ResidueCustomProperty<T = any> {
export namespace ResidueCustomProperty {
export interface ExportCtx<T> {
- exportCtx: CifExportContext,
elements: StructureElement[],
property(index: number): T
};
- function getExportCtx<T>(exportCtx: CifExportContext, prop: ResidueCustomProperty<T>): ExportCtx<T> {
- if (exportCtx.localCache[prop.id]) return exportCtx.localCache[prop.id];
- const residueIndex = exportCtx.model.atomicHierarchy.residueAtomSegments.index;
- const elements = getStructureElements(exportCtx.structure, prop);
- return {
- exportCtx,
- elements,
- property: i => prop.get(residueIndex[elements[i].element])!
- }
+ function getExportCtx<T>(prop: ResidueCustomProperty<T>, structure: Structure): ExportCtx<T> {
+ const residueIndex = structure.model.atomicHierarchy.residueAtomSegments.index;
+ const elements = getStructureElements(structure, prop);
+ return { elements, property: i => prop.get(residueIndex[elements[i].element])! };
}
- export function createCifCategory<T>(ctx: CifExportContext, prop: ResidueCustomProperty<T>, fields: CifWriter.Field<number, ExportCtx<T>>[]): CifWriter.Category.Instance {
- const data = getExportCtx(ctx, prop);
- return { fields, data, rowCount: data.elements.length };
+ export function getCifDataSource<T>(structure: Structure, prop: ResidueCustomProperty<T> | undefined, cache: any): CifWriter.Category.Instance['source'][0] {
+ if (!prop) return { rowCount: 0 };
+ if (cache && cache[prop.id]) return cache[prop.id];
+ const data = getExportCtx(prop, structure);
+ const ret = { data, rowCount: data.elements.length };
+ if (cache) cache[prop.id] = ret;
+ return ret;
}
class FromMap<T> implements ResidueCustomProperty<T> {
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index b93f7e96c..7f41cc5fc 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -38,6 +38,7 @@ class Structure {
unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
carbohydrates?: Carbohydrates,
models?: ReadonlyArray<Model>,
+ model?: Model,
hashCode: number,
elementCount: number,
polymerResidueCount: number,
@@ -128,6 +129,15 @@ class Structure {
return this._props.models;
}
+ /** If the structure is based on a single model, return it. Otherwise throw an exception. */
+ get model(): Model {
+ if (this._props.model) return this._props.model;
+ const models = this.models;
+ if (models.length > 1) throw new Error('The structre is based on multiple models.');
+ this._props.model = models[0];
+ return this._props.model;
+ }
+
hasElement(e: StructureElement) {
if (!this.unitMap.has(e.unit.id)) return false;
return SortedArray.has(this.unitMap.get(e.unit.id).elements, e.element);
diff --git a/src/perf-tests/cif-encoder.ts b/src/perf-tests/cif-encoder.ts
index f8f2ab18c..59f0eb3f6 100644
--- a/src/perf-tests/cif-encoder.ts
+++ b/src/perf-tests/cif-encoder.ts
@@ -23,7 +23,7 @@ function getCat(name: string): CifWriter.Category {
return {
name,
instance(ctx: { fields: CifWriter.Field[], rowCount: number }) {
- return { data: void 0, fields: ctx.fields, rowCount: ctx.rowCount };
+ return { fields: ctx.fields, source: [{ rowCount: ctx.rowCount }] };
}
};
}
diff --git a/src/servers/model/preprocess/converter.ts b/src/servers/model/preprocess/converter.ts
index 66d77fcb4..0ef1bb1b5 100644
--- a/src/servers/model/preprocess/converter.ts
+++ b/src/servers/model/preprocess/converter.ts
@@ -12,7 +12,7 @@ import { Task } from 'mol-task';
function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
return {
name: cat.name,
- instance: () => ({ data: cat, fields, rowCount: cat.rowCount })
+ instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
};
}
diff --git a/src/servers/model/preprocess/preprocess.ts b/src/servers/model/preprocess/preprocess.ts
index 371ae472a..187a017b7 100644
--- a/src/servers/model/preprocess/preprocess.ts
+++ b/src/servers/model/preprocess/preprocess.ts
@@ -36,7 +36,7 @@ export async function preprocessFile(filename: string, propertyProvider?: ModelP
}
}
-function encode(structure: Structure, header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, exportCtx: CifExportContext[], writer: Writer) {
+function encode(structure: Structure, header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, exportCtx: CifExportContext, writer: Writer) {
const skipCategoryNames = new Set<string>(categories.map(c => c.name));
encoder.startDataBlock(header);
for (const cat of categories) {
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 09603e183..0c80ae56c 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -70,8 +70,8 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
perf.start('encode');
encoder.startDataBlock(sourceStructures[0].models[0].label.toUpperCase());
- encoder.writeCategory(_model_server_result, [job]);
- encoder.writeCategory(_model_server_params, [job]);
+ encoder.writeCategory(_model_server_result, job);
+ encoder.writeCategory(_model_server_params, job);
// encoder.setFilter(mmCIF_Export_Filters.onlyPositions);
encode_mmCIF_categories(encoder, result);
@@ -84,7 +84,7 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
encodeTimeMs: perf.time('encode')
};
- encoder.writeCategory(_model_server_stats, [stats]);
+ encoder.writeCategory(_model_server_stats, stats);
encoder.encode();
ConsoleLogger.logId(job.id, 'Query', 'Encoded.');
return encoder;
@@ -101,9 +101,9 @@ function getEncodingProvider(structure: StructureWrapper) {
function doError(job: Job, e: any) {
const encoder = CifWriter.createEncoder({ binary: job.responseFormat.isBinary, encoderName: `ModelServer ${Version}` });
- encoder.writeCategory(_model_server_result, [job]);
- encoder.writeCategory(_model_server_params, [job]);
- encoder.writeCategory(_model_server_error, ['' + e]);
+ encoder.writeCategory(_model_server_result, job);
+ encoder.writeCategory(_model_server_params, job);
+ encoder.writeCategory(_model_server_error, '' + e);
encoder.encode();
return encoder;
}
@@ -155,12 +155,12 @@ const _model_server_stats_fields: CifField<number, Stats>[] = [
const _model_server_result: CifWriter.Category<Job> = {
name: 'model_server_result',
- instance: (job) => ({ data: job, fields: _model_server_result_fields, rowCount: 1 })
+ instance: (job) => CifWriter.categoryInstance(_model_server_result_fields,{ data: job, rowCount: 1 })
};
const _model_server_error: CifWriter.Category<string> = {
name: 'model_server_error',
- instance: (message) => ({ data: message, fields: _model_server_error_fields, rowCount: 1 })
+ instance: (message) => CifWriter.categoryInstance(_model_server_error_fields, { data: message, rowCount: 1 })
};
const _model_server_params: CifWriter.Category<Job> = {
@@ -170,17 +170,12 @@ const _model_server_params: CifWriter.Category<Job> = {
for (const k of Object.keys(job.normalizedParams)) {
params.push([k, JSON.stringify(job.normalizedParams[k])]);
}
- return {
- data: params,
-
- fields: _model_server_params_fields,
- rowCount: params.length
- }
+ return CifWriter.categoryInstance(_model_server_params_fields, { data: params, rowCount: params.length });
}
};
const _model_server_stats: CifWriter.Category<Stats> = {
name: 'model_server_stats',
- instance: (stats) => ({ data: stats, fields: _model_server_stats_fields, rowCount: 1 })
+ instance: (stats) => CifWriter.categoryInstance(_model_server_stats_fields, { data: stats, rowCount: 1 })
}
\ No newline at end of file
diff --git a/src/servers/volume/server/query/encode.ts b/src/servers/volume/server/query/encode.ts
index a754ef489..f456c9edf 100644
--- a/src/servers/volume/server/query/encode.ts
+++ b/src/servers/volume/server/query/encode.ts
@@ -102,7 +102,7 @@ const _volume_data_3d_info: CifWriter.Category<ResultContext> = {
sampledValuesInfo: result.query.data.header.sampling[result.query.samplingInfo.sampling.index].valuesInfo[result.channelIndex]
};
- return { data: ctx, fields: _volume_data_3d_info_fields, rowCount: 1 }
+ return { fields: _volume_data_3d_info_fields, source: [{ data: ctx, rowCount: 1 }] }
}
};
@@ -136,7 +136,7 @@ const _volume_data_3d: CifWriter.Category<ResultContext> = {
}
const fields = [CifWriter.Field.float('values', _volume_data_3d_number, { encoder, typedArray, digitCount: 6 })];
- return { data, fields, rowCount: data.length };
+ return CifWriter.categoryInstance(fields, { data, rowCount: data.length });
}
}
@@ -174,12 +174,12 @@ const _density_server_result_fields = [
const _density_server_result: CifWriter.Category<Data.QueryContext> = {
name: 'density_server_result',
- instance: ctx => ({ data: ctx, fields: _density_server_result_fields, rowCount: 1 })
+ instance: ctx => CifWriter.categoryInstance(_density_server_result_fields, { data: ctx, rowCount: 1 })
}
function write(encoder: CifWriter.Encoder, query: Data.QueryContext) {
encoder.startDataBlock('SERVER');
- encoder.writeCategory(_density_server_result, [query]);
+ encoder.writeCategory(_density_server_result, query);
switch (query.kind) {
case 'Data':
@@ -189,7 +189,7 @@ function write(encoder: CifWriter.Encoder, query: Data.QueryContext) {
const header = query.data.header;
for (let i = 0; i < header.channels.length; i++) {
encoder.startDataBlock(header.channels[i]);
- const ctx: ResultContext[] = [{ query, channelIndex: i }];
+ const ctx: ResultContext = { query, channelIndex: i };
encoder.writeCategory(_volume_data_3d_info, ctx);
encoder.writeCategory(_volume_data_3d, ctx);
--
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