mol-model-props refactoring

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 }

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);
 }

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'
+export * from './structure/unit/rings'
+export * from './export/mmcif'

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(/\..+/, '');
+}

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'
     ],
 

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)
     });
 }
 

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,

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);

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"],