From eac4a8988b8573806f80c1f92d93e8907d53f512 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 5 Sep 2019 16:09:05 +0200
Subject: [PATCH] mol-model: added Model.entryId; mol-plugin: toggle validation
tooltip; fixed using correct entryId for various custom properties
---
src/apps/basic-wrapper/index.html | 1 +
src/apps/basic-wrapper/index.ts | 6 +++
.../proteopedia-wrapper/annotation.ts | 2 +-
src/examples/proteopedia-wrapper/helpers.ts | 4 +-
.../structure/mmcif/parser.ts | 2 +
.../pdbe/structure-quality-report.ts | 2 +-
src/mol-model-props/rcsb/assembly-symmetry.ts | 4 +-
src/mol-model/structure/model/model.ts | 1 +
.../structure/structure/properties.ts | 1 +
.../pdbe/structure-quality-report.ts | 53 ++++++++++---------
src/mol-plugin/index.ts | 2 +-
src/mol-plugin/state/transforms/model.ts | 20 ++++---
src/perf-tests/mol-script.ts | 2 +-
.../model/properties/providers/pdbe.ts | 10 ++--
src/servers/model/server/query.ts | 2 +-
15 files changed, 67 insertions(+), 45 deletions(-)
diff --git a/src/apps/basic-wrapper/index.html b/src/apps/basic-wrapper/index.html
index 6c9f2d9d5..cb24e98ba 100644
--- a/src/apps/basic-wrapper/index.html
+++ b/src/apps/basic-wrapper/index.html
@@ -109,6 +109,7 @@
addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());
addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
+ addControl('Validation Tooltip', () => BasicMolStarWrapper.tests.toggleValidationTooltip());
////////////////////////////////////////////////////////
diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
index 4629abcf4..c722e95e4 100644
--- a/src/apps/basic-wrapper/index.ts
+++ b/src/apps/basic-wrapper/index.ts
@@ -17,6 +17,7 @@ import { StateBuilder, StateTransform } from '../../mol-state';
import { StripedResidues } from './coloring';
// import { BasicWrapperControls } from './controls';
import { StaticSuperpositionTestData, buildStaticSuperposition, dynamicSuperpositionTest } from './superposition';
+import { PDBeStructureQualityReport } from '../../mol-plugin/behavior/dynamic/custom-props';
require('mol-plugin/skin/light.scss')
type SupportedFormats = 'cif' | 'pdb'
@@ -152,6 +153,11 @@ class BasicWrapper {
dynamicSuperposition: async () => {
await PluginCommands.State.RemoveObject.dispatch(this.plugin, { state: this.plugin.state.dataState, ref: StateTransform.RootRef });
await dynamicSuperpositionTest(this.plugin, ['1tqn', '2hhb', '4hhb'], 'HEM');
+ },
+ toggleValidationTooltip: async () => {
+ const state = this.plugin.state.behaviorState;
+ const tree = state.build().to(PDBeStructureQualityReport.id).update(PDBeStructureQualityReport, p => ({ ...p, showTooltip: !p.showTooltip }));
+ await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
}
}
}
diff --git a/src/examples/proteopedia-wrapper/annotation.ts b/src/examples/proteopedia-wrapper/annotation.ts
index d628f628a..1d88eae3f 100644
--- a/src/examples/proteopedia-wrapper/annotation.ts
+++ b/src/examples/proteopedia-wrapper/annotation.ts
@@ -27,7 +27,7 @@ export const EvolutionaryConservation = CustomElementProperty.create<number>({
name: 'proteopedia-wrapper-evolutionary-conservation',
display: 'Evolutionary Conservation',
async getData(model: Model) {
- const id = model.label.toLowerCase();
+ const id = model.entryId.toLowerCase();
const req = await fetch(`https://proteopedia.org/cgi-bin/cnsrf?${id}`);
const json = await req.json();
const annotations = (json && json.residueAnnotations) || [];
diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index d8d4f2610..d376596d3 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -18,9 +18,9 @@ export interface ModelInfo {
export namespace ModelInfo {
async function getPreferredAssembly(ctx: PluginContext, model: Model) {
- if (model.label.length <= 3) return void 0;
+ if (model.entryId.length <= 3) return void 0;
try {
- const id = model.label.toLowerCase();
+ const id = model.entryId.toLowerCase();
const src = await ctx.runTask(ctx.fetch({ url: `https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/${id}` })) as string;
const json = JSON.parse(src);
const data = json && json[id];
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 6d4647644..2ec01ddd4 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -217,6 +217,7 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIn
return {
id: UUID.create22(),
+ entryId: entry,
label: label.join(' | '),
entry,
sourceData: format,
@@ -253,6 +254,7 @@ function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatD
return {
id: UUID.create22(),
+ entryId: entry,
label: label.join(' | '),
entry,
sourceData: format,
diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index ada52bbb5..7cc742b66 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/src/mol-model-props/pdbe/structure-quality-report.ts
@@ -98,7 +98,7 @@ export namespace StructureQualityReport {
{
const url = mapUrl(model);
const dataStr = await fetch({ url }).runInContext(ctx) as string;
- const data = JSON.parse(dataStr)[model.label.toLowerCase()];
+ const data = JSON.parse(dataStr)[model.entryId.toLowerCase()];
if (!data) return false;
info = PropertyWrapper.createInfo();
issueMap = createIssueMapFromJson(model, data);
diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index bdf36072c..d87065908 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -264,8 +264,8 @@ export namespace AssemblySymmetry {
db = createDatabaseFromCif(model)
} else {
let result: AssemblySymmetryGraphQL.Query
- console.log('model.label.toLowerCase()', model.label.toLowerCase())
- const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.label.toLowerCase() };
+ console.log('model.entryId.toLowerCase()', model.entryId.toLowerCase())
+ const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.entryId.toLowerCase() };
try {
console.log('foo', client)
result = await client.request<AssemblySymmetryGraphQL.Query>(ctx || RuntimeContext.Synchronous, query, variables);
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 22d1ae04e..de0649f49 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -23,6 +23,7 @@ import { ModelFormat } from '../../../mol-model-formats/structure/format';
*/
export interface Model extends Readonly<{
id: UUID,
+ entryId: string,
label: string,
/** the name of the entry/file/collection the model is part of */
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 046c32f78..5ca9b5caa 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -139,6 +139,7 @@ const unit = {
operator_name: p(l => l.unit.conformation.operator.name),
model_index: p(l => l.unit.model.modelNum),
model_label: p(l => l.unit.model.label),
+ model_entry_id: p(l => l.unit.model.entryId),
hkl: p(l => l.unit.conformation.operator.hkl),
spgrOp: p(l => l.unit.conformation.operator.spgrOp),
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
index 91bf463a6..0b937d954 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
@@ -14,13 +14,13 @@ import { PluginBehavior } from '../../../behavior';
import { ThemeDataContext } from '../../../../../mol-theme/theme';
import { CustomPropertyRegistry } from '../../../../../mol-model-props/common/custom-property-registry';
-export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean }>({
+export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'pdbe-structure-quality-report-prop',
category: 'custom-props',
display: { name: 'PDBe Structure Quality Report' },
- ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
+ ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
private attach = StructureQualityReport.createAttachTask(
- m => `https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${m.label.toLowerCase()}`,
+ m => `https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${m.entryId.toLowerCase()}`,
this.ctx.fetch
);
@@ -32,9 +32,27 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
attach: this.attach
}
+ private labelPDBeValidation = (loci: Loci): string | undefined => {
+ if (!this.params.showTooltip) return void 0;
+
+ switch (loci.kind) {
+ case 'element-loci':
+ const e = loci.elements[0];
+ const u = e.unit;
+ if (!u.model.customProperties.has(StructureQualityReport.Descriptor)) return void 0;
+
+ const se = StructureElement.Location.create(u, u.elements[OrderedSet.getAt(e.indices, 0)]);
+ const issues = StructureQualityReport.getIssues(se);
+ if (issues.length === 0) return 'PDBe Validation: No Issues';
+ return `PDBe Validation: ${issues.join(', ')}`;
+
+ default: return void 0;
+ }
+ }
+
register(): void {
this.ctx.customModelProperties.register(this.provider);
- this.ctx.lociLabels.addProvider(labelPDBeValidation);
+ this.ctx.lociLabels.addProvider(this.labelPDBeValidation);
this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('pdbe-structure-quality-report', {
label: 'PDBe Structure Quality Report',
@@ -45,37 +63,22 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
})
}
- update(p: { autoAttach: boolean }) {
+ update(p: { autoAttach: boolean, showTooltip: boolean }) {
let updated = this.params.autoAttach !== p.autoAttach
this.params.autoAttach = p.autoAttach;
+ this.params.showTooltip = p.showTooltip;
this.provider.defaultSelected = p.autoAttach;
return updated;
}
unregister() {
- console.log('unregister')
this.ctx.customModelProperties.unregister(StructureQualityReport.Descriptor.name);
- this.ctx.lociLabels.removeProvider(labelPDBeValidation);
+ this.ctx.lociLabels.removeProvider(this.labelPDBeValidation);
this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('pdbe-structure-quality-report')
}
},
params: () => ({
- autoAttach: PD.Boolean(false)
+ autoAttach: PD.Boolean(false),
+ showTooltip: PD.Boolean(true)
})
-});
-
-function labelPDBeValidation(loci: Loci): string | undefined {
- switch (loci.kind) {
- case 'element-loci':
- const e = loci.elements[0];
- const u = e.unit;
- if (!u.model.customProperties.has(StructureQualityReport.Descriptor)) return void 0;
-
- const se = StructureElement.Location.create(u, u.elements[OrderedSet.getAt(e.indices, 0)]);
- const issues = StructureQualityReport.getIssues(se);
- if (issues.length === 0) return 'PDBe Validation: No Issues';
- return `PDBe Validation: ${issues.join(', ')}`;
-
- default: return void 0;
- }
-}
\ No newline at end of file
+});
\ No newline at end of file
diff --git a/src/mol-plugin/index.ts b/src/mol-plugin/index.ts
index 209daad2c..5dffcda53 100644
--- a/src/mol-plugin/index.ts
+++ b/src/mol-plugin/index.ts
@@ -66,7 +66,7 @@ export const DefaultPluginSpec: PluginSpec = {
PluginSpec.Behavior(PluginBehaviors.Camera.FocusLociOnSelect, { minRadius: 8, extraRadius: 4 }),
// PluginSpec.Behavior(PluginBehaviors.Labels.SceneLabels),
PluginSpec.Behavior(PluginBehaviors.CustomProps.MolstarSecondaryStructure, { autoAttach: true }),
- PluginSpec.Behavior(PluginBehaviors.CustomProps.PDBeStructureQualityReport, { autoAttach: true }),
+ PluginSpec.Behavior(PluginBehaviors.CustomProps.PDBeStructureQualityReport, { autoAttach: true, showTooltip: true }),
PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBAssemblySymmetry, { autoAttach: true }),
PluginSpec.Behavior(StructureRepresentationInteraction)
],
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 6df5fc2fe..2b4136293 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -228,12 +228,12 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
if (model.symmetry.assemblies.length === 0) {
if (id !== 'deposited') {
- plugin.log.warn(`Model '${a.data.label}' has no assembly, returning deposited structure.`);
+ plugin.log.warn(`Model '${a.data.entryId}' has no assembly, returning deposited structure.`);
}
} else {
asm = ModelSymmetry.findAssembly(model, id || '');
if (!asm) {
- plugin.log.warn(`Model '${a.data.label}' has no assembly called '${id}', returning deposited structure.`);
+ plugin.log.warn(`Model '${a.data.entryId}' has no assembly called '${id}', returning deposited structure.`);
}
}
@@ -533,8 +533,12 @@ const CustomModelProperties = PluginStateTransform.BuiltIn({
});
async function attachModelProps(model: Model, ctx: PluginContext, taskCtx: RuntimeContext, names: string[]) {
for (const name of names) {
- const p = ctx.customModelProperties.get(name);
- await p.attach(model).runInContext(taskCtx);
+ try {
+ const p = ctx.customModelProperties.get(name);
+ await p.attach(model).runInContext(taskCtx);
+ } catch (e) {
+ ctx.log.warn(`Error attaching model prop '${name}': ${e}`);
+ }
}
}
@@ -558,8 +562,12 @@ const CustomStructureProperties = PluginStateTransform.BuiltIn({
});
async function attachStructureProps(structure: Structure, ctx: PluginContext, taskCtx: RuntimeContext, names: string[]) {
for (const name of names) {
- const p = ctx.customStructureProperties.get(name);
- await p.attach(structure).runInContext(taskCtx);
+ try {
+ const p = ctx.customStructureProperties.get(name);
+ await p.attach(structure).runInContext(taskCtx);
+ } catch (e) {
+ ctx.log.warn(`Error attaching structure prop '${name}': ${e}`);
+ }
}
}
diff --git a/src/perf-tests/mol-script.ts b/src/perf-tests/mol-script.ts
index 0ff78a678..3c9d21c48 100644
--- a/src/perf-tests/mol-script.ts
+++ b/src/perf-tests/mol-script.ts
@@ -69,7 +69,7 @@ export async function testQ() {
await StructureQualityReport.attachFromCifOrApi(structure.models[0], {
PDBe_apiSourceJson: async model => {
- const rawData = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.label.toLowerCase()}`, { timeout: 1500 });
+ const rawData = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${model.entryId.toLowerCase()}`, { timeout: 1500 });
return await rawData.json();
}
})
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index 7935d4a49..3cdf25817 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -40,14 +40,14 @@ namespace residuewise_outlier_summary {
// This is for "testing" purposes and should probably only read
// a single file with the appropriate prop in the "production" version.
return async (model: Model) => {
- const key = `${model.label[1]}${model.label[2]}`;
+ const key = `${model.entryId[1]}${model.entryId[2]}`;
if (!json.has(key)) {
const fn = path.join(pathPrefix, `${key}.json`);
if (!fs.existsSync(fn)) json.set(key, { });
// TODO: use async readFile?
else json.set(key, JSON.parse(fs.readFileSync(fn, 'utf8')));
}
- return json.get(key)![model.label.toLowerCase()] || { };
+ return json.get(key)![model.entryId.toLowerCase()] || { };
}
}
}
@@ -74,15 +74,15 @@ function apiQueryProvider(urlPrefix: string, cache: any) {
return async (model: Model) => {
try {
if (cache[cacheKey]) return cache[cacheKey];
- const rawData = await fetchRetry(`${urlPrefix}/${model.label.toLowerCase()}`, 1500, 5);
+ const rawData = await fetchRetry(`${urlPrefix}/${model.entryId.toLowerCase()}`, 1500, 5);
// TODO: is this ok?
if (rawData.status !== 200) return { };
- const json = (await rawData.json())[model.label.toLowerCase()] || { };
+ const json = (await rawData.json())[model.entryId.toLowerCase()] || { };
cache[cacheKey] = json;
return json;
} catch (e) {
// TODO: handle better
- ConsoleLogger.warn('Props', `Count not retrieve prop @${`${urlPrefix}/${model.label.toLowerCase()}`}`);
+ ConsoleLogger.warn('Props', `Count not retrieve prop @${`${urlPrefix}/${model.entryId.toLowerCase()}`}`);
return { };
}
}
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 9bbcf807c..726e74a96 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -72,7 +72,7 @@ export async function resolveJob(job: Job): Promise<CifWriter.Encoder<any>> {
ConsoleLogger.logId(job.id, 'Query', 'Query finished.');
perf.start('encode');
- encoder.startDataBlock(sourceStructures[0].models[0].label.toUpperCase());
+ encoder.startDataBlock(sourceStructures[0].models[0].entryId.toUpperCase());
encoder.writeCategory(_model_server_result, job);
encoder.writeCategory(_model_server_params, job);
--
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