diff --git a/src/mol-model-props/common/wrapper.ts b/src/mol-model-props/common/wrapper.ts
new file mode 100644
index 0000000000000000000000000000000000000000..6265ca85049af7cc2af6316b22e4dbe4a0bc8677
--- /dev/null
+++ b/src/mol-model-props/common/wrapper.ts
@@ -0,0 +1,56 @@
+/**
+ * Copyright (c) 2018 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';
+import { Model } from 'mol-model/structure';
+import { CifExportContext } from 'mol-model/structure';
+import { dateToUtcString } from 'mol-util/date';
+
+interface PropertyWrapper<Data> {
+ info: PropertyWrapper.Info,
+ data: Data
+}
+
+namespace PropertyWrapper {
+ export interface Info {
+ timestamp_utc: string
+ }
+
+ export function createInfo(): Info {
+ return { timestamp_utc: dateToUtcString(new Date()) };
+ }
+
+ export function defaultInfoCategory(name: string, getter: (model: Model) => PropertyWrapper<unknown> | undefined): CifWriter.Category<CifExportContext> {
+ return {
+ name,
+ instance(ctx) {
+ const prop = getter(ctx.firstModel);
+ if (!prop) return CifWriter.Category.Empty;
+ return {
+ fields: _info_fields,
+ source: [{ data: prop.info.timestamp_utc, rowCount: 1 }]
+ };
+ }
+ }
+ }
+
+ const _info_fields: CifWriter.Field<number, string>[] = [
+ CifWriter.Field.str('updated_datetime_utc', (_, date) => date)
+ ];
+
+ export function tryGetInfoFromCif(categoryName: string, model: Model): Info | undefined {
+ if (model.sourceData.kind !== 'mmCIF' || !model.sourceData.frame.categoryNames.includes(categoryName)) {
+ return;
+ }
+
+ const timestampField = model.sourceData.frame.categories[categoryName].getField('updated_datetime_utc');
+ if (!timestampField || timestampField.rowCount === 0) return;
+
+ return { timestamp_utc: timestampField.str(0) || dateToUtcString(new Date()) };
+ }
+}
+
+export { PropertyWrapper }
\ No newline at end of file
diff --git a/src/mol-model-props/index.ts b/src/mol-model-props/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index 47e874a65c56e610f236f202acdccd7b6d4eab04..d69524a6ab5b22957568a9ef7f973d49c728d633 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -4,111 +4,51 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { CifWriter } from 'mol-io/writer/cif';
-import { Model, ModelPropertyDescriptor, ResidueIndex, Unit, ResidueCustomProperty, StructureProperties as P } from 'mol-model/structure';
-import { residueIdFields } from 'mol-model/structure/export/categories/atom_site';
-import CifField = CifWriter.Field;
-import { mmCIF_residueId_schema } from 'mol-io/reader/cif/schema/mmcif-extras';
import { Column, Table } from 'mol-data/db';
import { toTable } from 'mol-io/reader/cif/schema';
+import { mmCIF_residueId_schema } from 'mol-io/reader/cif/schema/mmcif-extras';
+import { CifWriter } from 'mol-io/writer/cif';
+import { Model, ModelPropertyDescriptor, ResidueCustomProperty, ResidueIndex, StructureProperties as P, Unit } from 'mol-model/structure';
+import { residueIdFields } from 'mol-model/structure/export/categories/atom_site';
import { StructureElement } from 'mol-model/structure/structure';
-
-
-import { QuerySymbolRuntime } from 'mol-script/runtime/query/compiler';
import { CustomPropSymbol } from 'mol-script/language/symbol';
import Type from 'mol-script/language/type';
-
-type IssueMap = ResidueCustomProperty<string[]>
-
-const _Descriptor = ModelPropertyDescriptor({
- isStatic: false,
- name: 'structure_quality_report',
- cifExport: {
- prefix: 'pdbe',
- categories: [{
- name: 'pdbe_structure_quality_report',
- instance(ctx) {
- 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) {
- return {
- fields: _structure_quality_report_issues_fields,
- source: ctx.structures.map(
- s => ResidueCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
- };
- }
- }]
- },
- symbols: {
- issueCount: QuerySymbolRuntime.Dynamic(CustomPropSymbol('pdbe', 'structure-quality.issue-count', Type.Num),
- ctx => StructureQualityReport.getIssues(ctx.element).length),
- // TODO: add (hasIssue :: IssueType(extends string) -> boolean) symbol
- }
-})
-
-type ExportCtx = ResidueCustomProperty.ExportCtx<string[]>
-const _structure_quality_report_issues_fields: CifField<number, ExportCtx>[] = [
- CifField.index('id'),
- ...residueIdFields<number, ExportCtx>((i, d) => d.elements[i]),
- CifField.int<number, ExportCtx>('pdbx_PDB_model_num', (i, d) => P.unit.model_num(d.elements[i])),
- CifField.str<number, ExportCtx>('issues', (i, d) => d.property(i).join(','))
-];
-
-const _structure_quality_report_fields: CifField<number, string>[] = [
- CifField.str('updated_datetime_utc', (_, date) => date)
-];
-
-function createIssueMapFromJson(modelData: Model, data: any): IssueMap | undefined {
- const ret = new Map<ResidueIndex, string[]>();
- if (!data.molecules) return;
-
- for (const entity of data.molecules) {
- const entity_id = entity.entity_id.toString();
- for (const chain of entity.chains) {
- const asym_id = chain.struct_asym_id.toString();
- for (const model of chain.models) {
- const model_id = model.model_id.toString();
- if (+model_id !== modelData.modelNum) continue;
-
- for (const residue of model.residues) {
- const auth_seq_id = residue.author_residue_number, ins_code = residue.author_insertion_code || '';
- const idx = modelData.atomicHierarchy.index.findResidue(entity_id, asym_id, auth_seq_id, ins_code);
- ret.set(idx, residue.outlier_types);
- }
- }
- }
- }
-
- return ResidueCustomProperty.fromMap(ret, Unit.Kind.Atomic);
-}
-
-function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>): IssueMap | undefined {
- const ret = new Map<ResidueIndex, string[]>();
- const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issues, pdbx_PDB_model_num, _rowCount } = data;
-
- for (let i = 0; i < _rowCount; i++) {
- if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue;
- const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
- ret.set(idx, issues.value(i));
- }
-
- return ResidueCustomProperty.fromMap(ret, Unit.Kind.Atomic);
-}
+import { QuerySymbolRuntime } from 'mol-script/runtime/query/compiler';
+import { PropertyWrapper } from '../common/wrapper';
+import CifField = CifWriter.Field;
export namespace StructureQualityReport {
- export interface Data {
- updated: string,
- map: IssueMap | undefined
+ export type IssueMap = ResidueCustomProperty<string[]>
+ export type Property = PropertyWrapper<IssueMap | undefined>
+
+ export function get(model: Model): Property | undefined {
+ // must be defined before the descriptor so it's not undefined.
+ return model._dynamicPropertyData.__StructureQualityReport__;
}
- export const Descriptor = _Descriptor;
+ export const Descriptor = ModelPropertyDescriptor({
+ isStatic: false,
+ name: 'structure_quality_report',
+ cifExport: {
+ prefix: 'pdbe',
+ categories: [
+ PropertyWrapper.defaultInfoCategory('pdbe_structure_quality_report', StructureQualityReport.get),
+ {
+ name: 'pdbe_structure_quality_report_issues',
+ instance(ctx) {
+ return {
+ fields: _structure_quality_report_issues_fields,
+ source: ctx.structures.map(s => ResidueCustomProperty.getCifDataSource(s, StructureQualityReport.getIssueMap(s.model), ctx.cache))
+ };
+ }
+ }]
+ },
+ symbols: {
+ issueCount: QuerySymbolRuntime.Dynamic(CustomPropSymbol('pdbe', 'structure-quality.issue-count', Type.Num),
+ ctx => StructureQualityReport.getIssues(ctx.element).length),
+ // TODO: add (hasIssue :: IssueType(extends string) -> boolean) symbol
+ }
+ });
export const Schema = {
pdbe_structure_quality_report: {
@@ -122,49 +62,96 @@ export namespace StructureQualityReport {
}
}
+ function getCifData(model: Model) {
+ if (model.sourceData.kind !== 'mmCIF') throw new Error('Data format must be mmCIF.');
+ return toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues);
+ }
+
export async function attachFromCifOrApi(model: Model, params: {
// provide JSON from api
PDBe_apiSourceJson?: (model: Model) => Promise<any>
}) {
if (get(model)) return true;
- let issueMap, updated = `${new Date().toISOString().replace(/T/, ' ').replace(/\..+/, '')}`;
- if (model.sourceData.kind === 'mmCIF' && model.sourceData.frame.categoryNames.includes('pdbe_structure_quality_report')) {
- const data = toTable(Schema.pdbe_structure_quality_report_issues, model.sourceData.frame.categories.pdbe_structure_quality_report_issues);
- const f = model.sourceData.frame.categories['pdbe_structure_quality_report'].getField('updated_datetime_utc');
- updated = f ? f.str(0) : updated;
+ let issueMap: IssueMap | undefined;
+ let info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
+ if (info) {
+ const data = getCifData(model);
issueMap = createIssueMapFromCif(model, data);
} else if (params.PDBe_apiSourceJson) {
const data = await params.PDBe_apiSourceJson(model);
if (!data) return false;
+ info = PropertyWrapper.createInfo();
issueMap = createIssueMapFromJson(model, data);
} else {
return false;
}
model.customProperties.add(Descriptor);
- (model._dynamicPropertyData.__StructureQualityReport__ as Data) = {
- updated,
- map: issueMap
- };
+ set(model, { info, data: issueMap });
return true;
}
- export function get(model: Model): Data | undefined {
- return model._dynamicPropertyData.__StructureQualityReport__;
+ function set(model: Model, prop: Property) {
+ (model._dynamicPropertyData.__StructureQualityReport__ as Property) = prop;
}
export function getIssueMap(model: Model): IssueMap | undefined {
- const data = get(model);
- return data && data.map;
+ const prop = get(model);
+ return prop && prop.data;
}
const _emptyArray: string[] = [];
export function getIssues(e: StructureElement) {
if (!Unit.isAtomic(e.unit)) return _emptyArray;
- const issues = StructureQualityReport.get(e.unit.model);
- if (!issues || !issues.map) return _emptyArray;
+ const prop = StructureQualityReport.get(e.unit.model);
+ if (!prop || !prop.data) return _emptyArray;
const rI = e.unit.residueIndex[e.element];
- return issues.map.has(rI) ? issues.map.get(rI)! : _emptyArray;
+ return prop.data.has(rI) ? prop.data.get(rI)! : _emptyArray;
}
+}
+
+type ExportCtx = ResidueCustomProperty.ExportCtx<string[]>
+const _structure_quality_report_issues_fields: CifField<number, ExportCtx>[] = [
+ CifField.index('id'),
+ ...residueIdFields<number, ExportCtx>((i, d) => d.elements[i]),
+ CifField.int<number, ExportCtx>('pdbx_PDB_model_num', (i, d) => P.unit.model_num(d.elements[i])),
+ CifField.str<number, ExportCtx>('issues', (i, d) => d.property(i).join(','))
+];
+
+function createIssueMapFromJson(modelData: Model, data: any): StructureQualityReport.IssueMap | undefined {
+ const ret = new Map<ResidueIndex, string[]>();
+ if (!data.molecules) return;
+
+ for (const entity of data.molecules) {
+ const entity_id = entity.entity_id.toString();
+ for (const chain of entity.chains) {
+ const asym_id = chain.struct_asym_id.toString();
+ for (const model of chain.models) {
+ const model_id = model.model_id.toString();
+ if (+model_id !== modelData.modelNum) continue;
+
+ for (const residue of model.residues) {
+ const auth_seq_id = residue.author_residue_number, ins_code = residue.author_insertion_code || '';
+ const idx = modelData.atomicHierarchy.index.findResidue(entity_id, asym_id, auth_seq_id, ins_code);
+ ret.set(idx, residue.outlier_types);
+ }
+ }
+ }
+ }
+
+ return ResidueCustomProperty.fromMap(ret, Unit.Kind.Atomic);
+}
+
+function createIssueMapFromCif(modelData: Model, data: Table<typeof StructureQualityReport.Schema.pdbe_structure_quality_report_issues>): StructureQualityReport.IssueMap | undefined {
+ const ret = new Map<ResidueIndex, string[]>();
+ const { label_entity_id, label_asym_id, auth_seq_id, pdbx_PDB_ins_code, issues, pdbx_PDB_model_num, _rowCount } = data;
+
+ for (let i = 0; i < _rowCount; i++) {
+ if (pdbx_PDB_model_num.value(i) !== modelData.modelNum) continue;
+ const idx = modelData.atomicHierarchy.index.findResidue(label_entity_id.value(i), label_asym_id.value(i), auth_seq_id.value(i), pdbx_PDB_ins_code.value(i));
+ ret.set(idx, issues.value(i));
+ }
+
+ return ResidueCustomProperty.fromMap(ret, Unit.Kind.Atomic);
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure.ts b/src/mol-model/structure/structure.ts
index a6a25607900a4ac9912f878f6ac5ddc9abf9541b..46dbdecdcc8a9aec23583dc4fab0a5d3fe79bc97 100644
--- a/src/mol-model/structure/structure.ts
+++ b/src/mol-model/structure/structure.ts
@@ -12,4 +12,5 @@ import { Link } from './structure/unit/links'
import StructureProperties from './structure/properties'
export { StructureElement, Link, Structure, Unit, StructureSymmetry, StructureProperties }
-export * from './structure/unit/rings'
\ No newline at end of file
+export * from './structure/unit/rings'
+export * from './export/mmcif'
\ No newline at end of file
diff --git a/src/mol-util/date.ts b/src/mol-util/date.ts
new file mode 100644
index 0000000000000000000000000000000000000000..90d03997b579862440fc0dc3a30c8663a6ee48cc
--- /dev/null
+++ b/src/mol-util/date.ts
@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export function dateToUtcString(date: Date) {
+ return date.toISOString().replace(/T/, ' ').replace(/\..+/, '');
+}
\ No newline at end of file
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index 1bf830d00639fd568c5adebbe8d9bbda7da03cbd..ae25a2e55d07f23948ae0fe754e333e8082f1830 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -51,7 +51,7 @@ const config = {
* Paths (relative to the root directory of the model server) to JavaScript files that specify custom properties
*/
customPropertyProviders: [
- // './properties/pdbe',
+ './properties/pdbe',
// './properties/rcsb'
],
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index 751bab2ea6fc56fdf99220976bb905aa930f1b86..bec1c19332f271950b78eb2086eca8d27fdff77b 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -10,9 +10,13 @@ import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-r
import { fetchRetry } from '../../utils/fetch-retry';
import { UUID } from 'mol-util';
+const USE_FILE_SOURCE = false;
+
export function PDBe_structureQualityReport(model: Model, cache: any) {
return StructureQualityReport.attachFromCifOrApi(model, {
- PDBe_apiSourceJson: residuewise_outlier_summary.getDataFromFile
+ PDBe_apiSourceJson: USE_FILE_SOURCE
+ ? residuewise_outlier_summary.getDataFromFile
+ : residuewise_outlier_summary.getDataFromApiProvider(cache)
});
}
diff --git a/src/servers/model/server/jobs.ts b/src/servers/model/server/jobs.ts
index 4019cc654b401c4d7c4f951d14e363e271406226..7697d30c52260acf5d6ba729eb2c6b4a63b3d048 100644
--- a/src/servers/model/server/jobs.ts
+++ b/src/servers/model/server/jobs.ts
@@ -41,12 +41,12 @@ export function createJob<Name extends QueryName>(definition: JobDefinition<Name
if (!queryDefinition) throw new Error(`Query '${definition.queryName}' is not supported.`);
const normalizedParams = normalizeQueryParams(queryDefinition, definition.queryParams);
-
+ const sourceId = definition.sourceId || '_local_';
return {
id: UUID.create(),
datetime_utc: `${new Date().toISOString().replace(/T/, ' ').replace(/\..+/, '')}`,
- key: `${definition.sourceId}/${definition.entryId}`,
- sourceId: definition.sourceId || '_local_',
+ key: `${sourceId}/${definition.entryId}`,
+ sourceId,
entryId: definition.entryId,
queryDefinition,
normalizedParams,
diff --git a/src/servers/model/test.ts b/src/servers/model/test.ts
index c346381c4da729d786751bcf30f6a4b95a49633b..3e1cc6d9e7e5b0ac0be920df3fbb0ed4bf7d8108 100644
--- a/src/servers/model/test.ts
+++ b/src/servers/model/test.ts
@@ -42,19 +42,19 @@ if (!fs.existsSync(outPath)) fs.mkdirSync(outPath);
async function run() {
try {
// const testFile = '1crn.cif'
- const testFile = '1grm_updated.cif'
- // const request = createJob({
- // entryId: path.join(examplesPath, testFile),
- // queryName: 'full',
- // queryParams: { }
- // });
+ const testFile = '1cbs_updated.cif'
const request = createJob({
entryId: path.join(examplesPath, testFile),
- queryName: 'atoms',
- queryParams: {
- atom_site: { label_comp_id: 'ALA' }
- }
+ queryName: 'full',
+ queryParams: { }
});
+ // const request = createJob({
+ // entryId: path.join(examplesPath, testFile),
+ // queryName: 'atoms',
+ // queryParams: {
+ // atom_site: { label_comp_id: 'ALA' }
+ // }
+ // });
const encoder = await resolveJob(request);
const writer = wrapFile(path.join(outPath, testFile));
encoder.writeTo(writer);
diff --git a/tsconfig.json b/tsconfig.json
index d68886f2655f80a6b402a75e583cec8fdbe969b1..31421faf7852e8d4f240815c857b7b047af3467a 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -21,7 +21,7 @@
"mol-io": ["./mol-io"],
"mol-math": ["./mol-math"],
"mol-model": ["./mol-model"],
- "mol-model-props": ["./mol-model-props"],
+ "mol-model-props": ["./mol-model-props", "./mol-model-props/index.ts"],
"mol-ql": ["./mol-ql"],
"mol-script": ["./mol-script"],
"mol-task": ["./mol-task", "./mol-task/index.ts"],