From 23329d92aad646798328c996564f985ddf1191d3 Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Thu, 31 Dec 2020 16:07:25 +0100 Subject: [PATCH 01/22] Switch to boostrap-v4 branch This branch supports only Bootstrap v4 and does not provide Bootstrap v3 anymore. Some styles and fuctionality might be broken (i.e., use still BS 3) and must be updated in the future. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 8ddb59c..c705151 100644 --- a/package.json +++ b/package.json @@ -68,7 +68,7 @@ "dependencies": { "jstat": "^1.9.3", "jquery-ui": "1.12.1", - "tdp_core": "github:datavisyn/tdp_core#develop" + "tdp_core": "github:datavisyn/tdp_core#bootstrap-v4" }, "optionalDependencies": { "ordino": "github:Caleydo/ordino#develop" From 7720fe4609857d4f01e7a5417fe906e7c3a48164 Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Thu, 31 Dec 2020 16:07:32 +0100 Subject: [PATCH 02/22] Switch ordino to welcome-page branch --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index c705151..e4b9b06 100644 --- a/package.json +++ b/package.json @@ -71,6 +71,6 @@ "tdp_core": "github:datavisyn/tdp_core#bootstrap-v4" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#develop" + "ordino": "github:Caleydo/ordino#welcome-page" } } From 612c4ddc7537d2851d88d5281646df9095ee3011 Mon Sep 17 00:00:00 2001 From: anita-steiner Date: Fri, 12 Feb 2021 19:13:13 +0100 Subject: [PATCH 03/22] changes for release 8.0.0 --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index e8b8d90..71f9686 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "tdp_gene", "description": "", - "version": "8.0.0", + "version": "8.0.1-SNAPSHOT", "author": { "name": "The Caleydo Team", "email": "contact@caleydo.org", @@ -68,9 +68,9 @@ "dependencies": { "jstat": "^1.9.4", "jquery-ui": "1.12.1", - "tdp_core": "^11.0.0" + "tdp_core": "github:datavisyn/tdp_core#develop" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#semver:^9.0.0" + "ordino": "github:Caleydo/ordino#develop" } } From 39b6521719ff5f11a074ee8bd662b8073c4e4857 Mon Sep 17 00:00:00 2001 From: oltionchampari Date: Wed, 3 Mar 2021 09:54:13 +0100 Subject: [PATCH 04/22] Comment out unused extension point --- dist/phovea.js | 12 ++++++------ dist/phovea.js.map | 2 +- src/phovea.ts | 12 ++++++------ 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/dist/phovea.js b/dist/phovea.js index 410f109..ca284db 100644 --- a/dist/phovea.js +++ b/dist/phovea.js @@ -159,12 +159,12 @@ export default function (registry) { idType: 'Ensembl' }); /// #if include('ordino') - registry.push('ordinoStartMenuSection', 'section_species', function () { return import('./menu/SpeciesSelectorMenuSection'); }, { - factory: 'new SpeciesSelectorMenuSection', - name: 'Predefined Datasets', - cssClass: 'speciesSelector', - priority: 10 - }); + // registry.push('ordinoStartMenuSection', 'section_species', function() { return import('./menu/SpeciesSelectorMenuSection'); }, { + // factory: 'new SpeciesSelectorMenuSection', + // name: 'Predefined Datasets', + // cssClass: 'speciesSelector', + // priority: 10 + // }); /// #endif } //# sourceMappingURL=phovea.js.map \ No newline at end of file diff --git a/dist/phovea.js.map b/dist/phovea.js.map index 45da009..5da01a2 100644 --- a/dist/phovea.js.map +++ b/dist/phovea.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/src/phovea.ts b/src/phovea.ts index 5ab50b8..5318912 100644 --- a/src/phovea.ts +++ b/src/phovea.ts @@ -177,12 +177,12 @@ export default function (registry: IRegistry) { }); /// #if include('ordino') - registry.push('ordinoStartMenuSection', 'section_species', function() { return import('./menu/SpeciesSelectorMenuSection'); }, { - factory: 'new SpeciesSelectorMenuSection', - name: 'Predefined Datasets', - cssClass: 'speciesSelector', - priority: 10 - }); + // registry.push('ordinoStartMenuSection', 'section_species', function() { return import('./menu/SpeciesSelectorMenuSection'); }, { + // factory: 'new SpeciesSelectorMenuSection', + // name: 'Predefined Datasets', + // cssClass: 'speciesSelector', + // priority: 10 + // }); /// #endif From ec0ddd6245410c2d4e9901183106f5b360f0f7e8 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 4 May 2021 13:18:53 +0200 Subject: [PATCH 05/22] change hidden class to attr --- dist/views/ACoExpression.js | 8 ++++---- dist/views/ACoExpression.js.map | 2 +- src/views/ACoExpression.ts | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/dist/views/ACoExpression.js b/dist/views/ACoExpression.js index 809ac20..8da7b71 100644 --- a/dist/views/ACoExpression.js +++ b/dist/views/ACoExpression.js @@ -38,7 +38,7 @@ export class ACoExpression extends AD3View { this.$node.classed('multiple', true); this.$errorMessage = this.$node.append('p') .classed('nodata', true) - .classed('hidden', true); + .attr('hidden', true); this.$legend = this.$node.append('div'); // update the refGene select first, then update ref expression data and as last the charts return this.updateRefGeneSelect(this.selection) @@ -152,14 +152,14 @@ export class ACoExpression extends AD3View { const isEmpty = refGene == null || ids.length < 2; const noData = refGeneExpression == null || refGeneExpression.length === 0; if (isEmpty) { - this.$errorMessage.text('Select two or more genes.').classed('hidden', false); + this.$errorMessage.text('Select two or more genes.').attr('hidden', false); this.$node.selectAll('div.plots').remove(); this.color.domain([]); // reset ViewUtils.legend(this.$legend.node(), this.color); return; } if (noData) { - this.$errorMessage.text(this.getNoDataErrorMessage(refGene)).classed('hidden', false); + this.$errorMessage.text(this.getNoDataErrorMessage(refGene)).attr('hidden', false); this.$node.selectAll('div.plots').remove(); this.color.domain([]); // reset ViewUtils.legend(this.$legend.node(), this.color); @@ -171,7 +171,7 @@ export class ACoExpression extends AD3View { return { id, geneName: '', rows: [] }; }); // show/hide message and loading indicator if two less genes are selected - this.$errorMessage.classed('hidden', (data.length > 0)); + this.$errorMessage.attr('hidden', (data.length > 0)); this.setBusy(data.length > 0); const $plots = this.$node.selectAll('div.plots').data(data, (d) => d.id.toString()); const $plotsEnter = $plots.enter().append('div').classed('plots', true); diff --git a/dist/views/ACoExpression.js.map b/dist/views/ACoExpression.js.map index 361dd07..9bacc34 100644 --- a/dist/views/ACoExpression.js.map +++ b/dist/views/ACoExpression.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/views/ACoExpression.ts b/src/views/ACoExpression.ts index 950e67b..8151faf 100644 --- a/src/views/ACoExpression.ts +++ b/src/views/ACoExpression.ts @@ -56,7 +56,7 @@ export abstract class ACoExpression extends AD3View { this.$errorMessage = this.$node.append('p') .classed('nodata', true) - .classed('hidden', true); + .attr('hidden', true); this.$legend = this.$node.append('div'); @@ -194,7 +194,7 @@ export abstract class ACoExpression extends AD3View { const noData = refGeneExpression == null || refGeneExpression.length === 0; if (isEmpty) { - this.$errorMessage.text('Select two or more genes.').classed('hidden', false); + this.$errorMessage.text('Select two or more genes.').attr('hidden', false); this.$node.selectAll('div.plots').remove(); this.color.domain([]); // reset ViewUtils.legend(this.$legend.node(), this.color); @@ -202,7 +202,7 @@ export abstract class ACoExpression extends AD3View { } if (noData) { - this.$errorMessage.text(this.getNoDataErrorMessage(refGene)).classed('hidden', false); + this.$errorMessage.text(this.getNoDataErrorMessage(refGene)).attr('hidden', false); this.$node.selectAll('div.plots').remove(); this.color.domain([]); // reset ViewUtils.legend(this.$legend.node(), this.color); @@ -216,7 +216,7 @@ export abstract class ACoExpression extends AD3View { }); // show/hide message and loading indicator if two less genes are selected - this.$errorMessage.classed('hidden', (data.length > 0)); + this.$errorMessage.attr('hidden', (data.length > 0)); this.setBusy(data.length > 0); const $plots = this.$node.selectAll('div.plots').data(data, (d) => d.id.toString()); From 9a056d8abf74315bdfa4eb5986e2c4678cfcafcb Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Wed, 12 May 2021 15:54:24 +0200 Subject: [PATCH 06/22] Remove old extension points and menu code --- dist/common/extensions.d.ts | 21 --- dist/common/extensions.js | 2 - dist/common/extensions.js.map | 1 - dist/common/index.d.ts | 1 - dist/common/index.js | 1 - dist/common/index.js.map | 2 +- dist/index.d.ts | 1 - dist/index.js | 1 - dist/index.js.map | 2 +- dist/menu/ACommonSubSection.d.ts | 30 ---- dist/menu/ACommonSubSection.js | 140 ----------------- dist/menu/ACommonSubSection.js.map | 1 - dist/menu/SpeciesSelectorMenuSection.d.ts | 19 --- dist/menu/SpeciesSelectorMenuSection.js | 132 ---------------- dist/menu/SpeciesSelectorMenuSection.js.map | 1 - dist/menu/index.d.ts | 2 - dist/menu/index.js | 3 - dist/menu/index.js.map | 1 - src/common/extensions.ts | 27 ---- src/common/index.ts | 1 - src/index.ts | 1 - src/menu/ACommonSubSection.ts | 166 -------------------- src/menu/SpeciesSelectorMenuSection.ts | 161 ------------------- src/menu/index.ts | 2 - 24 files changed, 2 insertions(+), 717 deletions(-) delete mode 100644 dist/common/extensions.d.ts delete mode 100644 dist/common/extensions.js delete mode 100644 dist/common/extensions.js.map delete mode 100644 dist/menu/ACommonSubSection.d.ts delete mode 100644 dist/menu/ACommonSubSection.js delete mode 100644 dist/menu/ACommonSubSection.js.map delete mode 100644 dist/menu/SpeciesSelectorMenuSection.d.ts delete mode 100644 dist/menu/SpeciesSelectorMenuSection.js delete mode 100644 dist/menu/SpeciesSelectorMenuSection.js.map delete mode 100644 dist/menu/index.d.ts delete mode 100644 dist/menu/index.js delete mode 100644 dist/menu/index.js.map delete mode 100644 src/common/extensions.ts delete mode 100644 src/menu/ACommonSubSection.ts delete mode 100644 src/menu/SpeciesSelectorMenuSection.ts delete mode 100644 src/menu/index.ts diff --git a/dist/common/extensions.d.ts b/dist/common/extensions.d.ts deleted file mode 100644 index a26684c..0000000 --- a/dist/common/extensions.d.ts +++ /dev/null @@ -1,21 +0,0 @@ -import { IPluginDesc } from 'phovea_core'; -import { INamedSet } from 'tdp_core'; -import { IStartMenuSectionOptions } from 'ordino'; -export declare const EXTENSION_POINT_STARTMENU_SUBSECTION = "ordinoStartMenuSubSection"; -export interface IStartMenuSubSectionDesc extends IPluginDesc { - readonly id: string; - readonly name: string; - readonly cssClass: string; - readonly idType: string; - readonly description: string; - load(): Promise; -} -interface IStartMenuSubSectionPlugin { - desc: IStartMenuSubSectionDesc; - factory(parent: HTMLElement, desc: IStartMenuSubSectionDesc, options: IStartMenuSectionOptions): IStartMenuSubSection; -} -export interface IStartMenuSubSection { - push(namedSet: INamedSet): boolean; - update(): void; -} -export {}; diff --git a/dist/common/extensions.js b/dist/common/extensions.js deleted file mode 100644 index fd1e077..0000000 --- a/dist/common/extensions.js +++ /dev/null @@ -1,2 +0,0 @@ -export const EXTENSION_POINT_STARTMENU_SUBSECTION = 'ordinoStartMenuSubSection'; -//# sourceMappingURL=extensions.js.map \ No newline at end of file diff --git a/dist/common/extensions.js.map b/dist/common/extensions.js.map deleted file mode 100644 index eb5bd91..0000000 --- a/dist/common/extensions.js.map +++ /dev/null @@ -1 +0,0 @@ -{"version":3,"file":"extensions.js","sourceRoot":"","sources":["../../src/common/extensions.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,MAAM,oCAAoC,GAAG,2BAA2B,CAAC"} \ No newline at end of file diff --git a/dist/common/index.d.ts b/dist/common/index.d.ts index 152abd0..2a75e49 100644 --- a/dist/common/index.d.ts +++ b/dist/common/index.d.ts @@ -1,3 +1,2 @@ export * from './Categories'; export * from './common'; -export * from './extensions'; diff --git a/dist/common/index.js b/dist/common/index.js index 6ac3a11..c953841 100644 --- a/dist/common/index.js +++ b/dist/common/index.js @@ -1,4 +1,3 @@ export * from './Categories'; export * from './common'; -export * from './extensions'; //# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/dist/common/index.js.map b/dist/common/index.js.map index cd993bd..c137ea7 100644 --- a/dist/common/index.js.map +++ b/dist/common/index.js.map @@ -1 +1 @@ -{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/common/index.ts"],"names":[],"mappings":"AAAA,cAAc,cAAc,CAAC;AAC7B,cAAc,UAAU,CAAC;AACzB,cAAc,cAAc,CAAC"} \ No newline at end of file +{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/common/index.ts"],"names":[],"mappings":"AAAA,cAAc,cAAc,CAAC;AAC7B,cAAc,UAAU,CAAC"} \ No newline at end of file diff --git a/dist/index.d.ts b/dist/index.d.ts index c31f551..19315ac 100644 --- a/dist/index.d.ts +++ b/dist/index.d.ts @@ -1,4 +1,3 @@ export * from './common'; export * from './provider'; export * from './views'; -export * from './menu'; diff --git a/dist/index.js b/dist/index.js index 694c9b0..9f739af 100644 --- a/dist/index.js +++ b/dist/index.js @@ -1,5 +1,4 @@ export * from './common'; export * from './provider'; export * from './views'; -export * from './menu'; //# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/dist/index.js.map b/dist/index.js.map index 30897a8..123bddc 100644 --- a/dist/index.js.map +++ b/dist/index.js.map @@ -1 +1 @@ -{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,UAAU,CAAC;AACzB,cAAc,YAAY,CAAC;AAC3B,cAAc,SAAS,CAAC;AACxB,cAAc,QAAQ,CAAC"} \ No newline at end of file +{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,UAAU,CAAC;AACzB,cAAc,YAAY,CAAC;AAC3B,cAAc,SAAS,CAAC"} \ No newline at end of file diff --git a/dist/menu/ACommonSubSection.d.ts b/dist/menu/ACommonSubSection.d.ts deleted file mode 100644 index bc910a1..0000000 --- a/dist/menu/ACommonSubSection.d.ts +++ /dev/null @@ -1,30 +0,0 @@ -/** - * Created by Holger Stitz on 10.08.2016. - */ -import { Species } from '../common/common'; -import { IStartMenuSubSection, IStartMenuSubSectionDesc } from '../common/extensions'; -import { IStartMenuSectionOptions } from 'ordino'; -import { NamedSetList } from 'tdp_core'; -import { INamedSet } from 'tdp_core'; -import { ICommonDBConfig } from '../views/ACommonList'; -export declare abstract class ACommonSubSection implements IStartMenuSubSection { - readonly desc: IStartMenuSubSectionDesc; - protected readonly dataSource: ICommonDBConfig; - protected readonly options: IStartMenuSectionOptions; - protected readonly data: NamedSetList; - private readonly idType; - /** - * Set the idType and the default data and build the list - */ - constructor(parent: HTMLElement, desc: IStartMenuSubSectionDesc, dataSource: ICommonDBConfig, options: IStartMenuSectionOptions); - update(): void; - push(namedSet: INamedSet): boolean; - private static panel2NamedSet; - protected loadPanels(): Promise; - protected searchOptions(): any; - protected getDefaultSessionValues(): { - species: string; - }; - private addSearchField; - private static createButton; -} diff --git a/dist/menu/ACommonSubSection.js b/dist/menu/ACommonSubSection.js deleted file mode 100644 index 9f58e0b..0000000 --- a/dist/menu/ACommonSubSection.js +++ /dev/null @@ -1,140 +0,0 @@ -/** - * Created by Holger Stitz on 10.08.2016. - */ -import { SpeciesUtils, Species } from '../common/common'; -import { IDTypeManager, I18nextManager } from 'phovea_core'; -import { NamedSetList } from 'tdp_core'; -import { ENamedSetType, RestStorageUtils } from 'tdp_core'; -import { RestBaseUtils } from 'tdp_core'; -import { FormElementType, FormBuilder } from 'tdp_core'; -import { StoreUtils } from 'tdp_core'; -import { select } from 'd3'; -export class ACommonSubSection { - /** - * Set the idType and the default data and build the list - */ - constructor(parent, desc, dataSource, options) { - this.desc = desc; - this.dataSource = dataSource; - this.options = options; - this.idType = IDTypeManager.getInstance().resolveIdType(desc.idType); - const createSession = (namedSet) => { - if (options.session) { - options.session(this.desc.viewId, { namedSet }, this.getDefaultSessionValues()); - } - else { - console.error('no session factory object given to push new view'); - } - }; - this.data = new NamedSetList(IDTypeManager.getInstance().resolveIdType(desc.idType), createSession, parent.ownerDocument); - parent.appendChild(this.data.node); - // convert all available species to namedsets - const defaultNamedSets = Species.availableSpecies.map((species) => { - return { - name: 'All', - type: ENamedSetType.CUSTOM, - subTypeKey: Species.SPECIES_SESSION_KEY, - subTypeFromSession: true, - subTypeValue: species.value, - description: '', - idType: '', - ids: '', - creator: '' - }; - }); - this.data.push(...defaultNamedSets); - this.loadPanels().then((panels) => this.data.push(...panels)); - this.addSearchField(); - } - update() { - this.data.update(); - } - push(namedSet) { - if (namedSet.idType !== this.idType.id) { - return false; - } - this.data.push(namedSet); - return true; - } - static panel2NamedSet({ id, description, species }) { - return { - type: ENamedSetType.PANEL, - id, - name: id, - description, - subTypeKey: Species.SPECIES_SESSION_KEY, - subTypeFromSession: false, - subTypeValue: species, - idType: '' - }; - } - loadPanels() { - return RestBaseUtils.getTDPData(this.dataSource.db, `${this.dataSource.base}_panel`).then((panels) => { - return panels.map(ACommonSubSection.panel2NamedSet); - }); - } - searchOptions() { - return { - return: 'id', - optionsData: [], - placeholder: `Add ${this.dataSource.name} by Typing or by Dragging a Text File onto the Search Field` - }; - } - getDefaultSessionValues() { - // initialize the session with the selected species - return { - [Species.SPECIES_SESSION_KEY]: SpeciesUtils.getSelectedSpecies() - }; - } - async addSearchField() { - const $searchWrapper = select(this.data.node.parentElement).insert('div', ':first-child').attr('class', 'startMenuSearch'); - const formBuilder = new FormBuilder($searchWrapper); - formBuilder.appendElement({ - id: `search-${this.dataSource.idType}${this.dataSource.entityName}`, - hideLabel: true, - type: FormElementType.SELECT3_MULTIPLE, - attributes: { - style: 'width:100%', - }, - options: this.searchOptions() - }); - const form = await formBuilder.build(); - const $searchButton = ACommonSubSection.createButton($searchWrapper, 'Go'); - const $saveSetButton = ACommonSubSection.createButton($searchWrapper, 'Save'); - const searchField = form.getElementById(`search-${this.dataSource.idType}${this.dataSource.entityName}`); - searchField.on('change', () => { - const state = searchField.hasValue() ? null : 'disabled'; - $searchButton.attr('disabled', state); - $saveSetButton.attr('disabled', state); - }); - $searchButton.on('click', () => { - this.options.session(this.desc.viewId, { - search: { - ids: searchField.value, - type: this.dataSource.tableName - } - }, this.getDefaultSessionValues()); - }); - $saveSetButton.on('click', () => { - StoreUtils.editDialog(null, I18nextManager.getInstance().i18n.t(`tdp:core.editDialog.listOfEntities.default`), async (name, description, isPublic) => { - const idStrings = searchField.value; - const idType = IDTypeManager.getInstance().resolveIdType(this.dataSource.idType); - const ids = await idType.map(idStrings); - const response = await RestStorageUtils.saveNamedSet(name, idType, ids, { - key: Species.SPECIES_SESSION_KEY, - value: SpeciesUtils.getSelectedSpecies() - }, description, isPublic); - this.push(response); - }); - }); - } - static createButton($parent, text) { - return $parent - .append('div') - .append('button') - .classed('btn btn-primary', true) - .attr('disabled', 'disabled') - .text(text); - } -} -//# sourceMappingURL=ACommonSubSection.js.map \ No newline at end of file diff --git a/dist/menu/ACommonSubSection.js.map b/dist/menu/ACommonSubSection.js.map deleted file mode 100644 index 8b0cf7e..0000000 --- a/dist/menu/ACommonSubSection.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/dist/menu/SpeciesSelectorMenuSection.d.ts b/dist/menu/SpeciesSelectorMenuSection.d.ts deleted file mode 100644 index ad38995..0000000 --- a/dist/menu/SpeciesSelectorMenuSection.d.ts +++ /dev/null @@ -1,19 +0,0 @@ -/** - * Created by Holger Stitz on 27.07.2016. - */ -import { IPluginDesc } from 'phovea_core'; -import { IStartMenuSection, IStartMenuSectionOptions } from 'ordino'; -import { INamedSet } from 'tdp_core'; -export declare class SpeciesSelectorMenuSection implements IStartMenuSection { - private readonly parent; - readonly desc: IPluginDesc; - private readonly options; - private readonly subSections; - constructor(parent: HTMLElement, desc: IPluginDesc, options: IStartMenuSectionOptions); - private build; - push(namedSet: INamedSet): boolean; - private buildSpeciesSelection; - private buildEntityTypes; - private buildEntityTypeSelection; - private buildEntryPointList; -} diff --git a/dist/menu/SpeciesSelectorMenuSection.js b/dist/menu/SpeciesSelectorMenuSection.js deleted file mode 100644 index 1fc9738..0000000 --- a/dist/menu/SpeciesSelectorMenuSection.js +++ /dev/null @@ -1,132 +0,0 @@ -/** - * Created by Holger Stitz on 27.07.2016. - */ -import { UserSession } from 'phovea_core'; -import { PluginRegistry } from 'phovea_core'; -import { Species } from '../common/common'; -import { select, event as d3event } from 'd3'; -import * as $ from 'jquery'; -import { EXTENSION_POINT_STARTMENU_SUBSECTION } from '../common/extensions'; -const tabSessionKey = 'entityType'; -const defaultTabSessionValue = 'celllinedb_genes_start'; //ensembl -export class SpeciesSelectorMenuSection { - constructor(parent, desc, options) { - this.parent = parent; - this.desc = desc; - this.options = options; - this.subSections = []; - this.build(); - } - build() { - const $parent = select(this.parent); - $parent.html(''); // remove loading element or previous data - this.buildSpeciesSelection($parent); - this.buildEntityTypes($parent); - } - push(namedSet) { - return this.subSections.some((d) => d.push(namedSet)); - } - buildSpeciesSelection($parent) { - const $speciesSelection = $parent.append('div').classed('species-wrapper', true); - const selectedSpecies = UserSession.getInstance().retrieve(Species.SPECIES_SESSION_KEY, Species.defaultSpecies); - // store default option, if not available - if (!UserSession.getInstance().has(Species.SPECIES_SESSION_KEY)) { - UserSession.getInstance().store(Species.SPECIES_SESSION_KEY, selectedSpecies); - } - const $group = $speciesSelection.selectAll('.species-group').data(Species.availableSpecies); - const group = $group.enter() - .append('div') - .classed('species-group', true) - .attr('data-species', (d) => d.value) - .classed('active', (d) => d.value === selectedSpecies); - const that = this; - group.append('input') - .attr('name', 'species') - .attr('id', (d) => `speciesSelector_${d.value}`) - .attr('type', 'radio') - .attr('checked', (d) => (d.value === selectedSpecies) ? 'checked' : null) - .on('change', function (d) { - UserSession.getInstance().store(Species.SPECIES_SESSION_KEY, d.value); - $group.classed('active', false); - select(this.parentNode).classed('active', true); - that.subSections.forEach((list) => list.update()); - }); - group.append('label') - .attr('for', (d) => `speciesSelector_${d.value}`) - .attr('data-title', (d) => d.name) - .html((d) => { - const className = d.iconClass || ''; - let text = ''; - if (!className) { - text = d.name.substr(0, 1).toUpperCase(); - } - return ``; - }); - } - buildEntityTypes($parent) { - // get start views for entry points and sort them by name ASC - const views = PluginRegistry.getInstance().listPlugins(EXTENSION_POINT_STARTMENU_SUBSECTION).sort((a, b) => a.name.toLowerCase().localeCompare(b.name.toLowerCase())); - if (!UserSession.getInstance().has(tabSessionKey)) { - UserSession.getInstance().store(tabSessionKey, defaultTabSessionValue); - } - this.buildEntityTypeSelection($parent, views); - this.buildEntryPointList($parent, views); - } - buildEntityTypeSelection($parent, views) { - const $entityTypes = $parent.append('ul').classed('nav nav-tabs', true).attr('role', 'tablist'); - $entityTypes - .selectAll('li') - .data(views) - .enter() - .append('li') - .attr('role', 'presentation') - .append('a') - .attr('href', (d) => `#entity_${d.cssClass}`) - .attr('id', (d) => `entityType_${d.cssClass}`) - .text((d) => d.description) - .on('click', function (d) { - d3event.preventDefault(); - UserSession.getInstance().store(tabSessionKey, d.id); - $(this).tab('show').blur(); - }).each(function (d) { - if (d.id === UserSession.getInstance().retrieve(tabSessionKey, defaultTabSessionValue)) { - this.click(); - } - }); - } - buildEntryPointList($parent, views) { - const that = this; - const $entryPoints = $parent.append('div').classed('entry-points-wrapper tab-content', true); - const $items = $entryPoints.selectAll('.item').data(views); - const $enter = $items.enter() - .append('div') - .attr('id', (d) => `entity_${d.cssClass}`) - .attr('class', (d) => d.id === UserSession.getInstance().retrieve(tabSessionKey, defaultTabSessionValue) ? 'active' : '') - .classed('tab-pane', true); - // append initial loading icon --> must be removed by each entry point individually - $enter.append('div').classed('body', true) - .html(` -
- - Loading... -
- `); - $enter.selectAll('div.body') - .each(function (desc) { - const elem = this; - desc.load().then((i) => { - elem.innerHTML = ''; //clear loading - if (i.factory) { - return i.factory(elem, desc, that.options); - } - console.log(`No viewId and/or factory method found for '${i.desc.id}'`); - return null; - }).then((instance) => { - if (instance) { - that.subSections.push(instance); - } - }); - }); - } -} -//# sourceMappingURL=SpeciesSelectorMenuSection.js.map \ No newline at end of file diff --git a/dist/menu/SpeciesSelectorMenuSection.js.map b/dist/menu/SpeciesSelectorMenuSection.js.map deleted file mode 100644 index cedb16c..0000000 --- a/dist/menu/SpeciesSelectorMenuSection.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/dist/menu/index.d.ts b/dist/menu/index.d.ts deleted file mode 100644 index 490875d..0000000 --- a/dist/menu/index.d.ts +++ /dev/null @@ -1,2 +0,0 @@ -export * from './SpeciesSelectorMenuSection'; -export * from './ACommonSubSection'; diff --git a/dist/menu/index.js b/dist/menu/index.js deleted file mode 100644 index 223a014..0000000 --- a/dist/menu/index.js +++ /dev/null @@ -1,3 +0,0 @@ -export * from './SpeciesSelectorMenuSection'; -export * from './ACommonSubSection'; -//# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/dist/menu/index.js.map b/dist/menu/index.js.map deleted file mode 100644 index fdbee2e..0000000 --- a/dist/menu/index.js.map +++ /dev/null @@ -1 +0,0 @@ -{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/menu/index.ts"],"names":[],"mappings":"AAAA,cAAc,8BAA8B,CAAC;AAC7C,cAAc,qBAAqB,CAAC"} \ No newline at end of file diff --git a/src/common/extensions.ts b/src/common/extensions.ts deleted file mode 100644 index 09d7a07..0000000 --- a/src/common/extensions.ts +++ /dev/null @@ -1,27 +0,0 @@ - -import {IPluginDesc} from 'phovea_core'; -import {INamedSet} from 'tdp_core'; -import {IStartMenuSectionOptions} from 'ordino'; - -export const EXTENSION_POINT_STARTMENU_SUBSECTION = 'ordinoStartMenuSubSection'; - -export interface IStartMenuSubSectionDesc extends IPluginDesc { - readonly id: string; - readonly name: string; - readonly cssClass: string; - readonly idType: string; - readonly description: string; - - load(): Promise; -} - -interface IStartMenuSubSectionPlugin { - desc: IStartMenuSubSectionDesc; - - factory(parent: HTMLElement, desc: IStartMenuSubSectionDesc, options: IStartMenuSectionOptions): IStartMenuSubSection; -} - -export interface IStartMenuSubSection { - push(namedSet: INamedSet): boolean; - update(): void; -} diff --git a/src/common/index.ts b/src/common/index.ts index 152abd0..2a75e49 100644 --- a/src/common/index.ts +++ b/src/common/index.ts @@ -1,3 +1,2 @@ export * from './Categories'; export * from './common'; -export * from './extensions'; diff --git a/src/index.ts b/src/index.ts index c31f551..19315ac 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,4 +1,3 @@ export * from './common'; export * from './provider'; export * from './views'; -export * from './menu'; diff --git a/src/menu/ACommonSubSection.ts b/src/menu/ACommonSubSection.ts deleted file mode 100644 index 6e6555d..0000000 --- a/src/menu/ACommonSubSection.ts +++ /dev/null @@ -1,166 +0,0 @@ -/** - * Created by Holger Stitz on 10.08.2016. - */ - -import {SpeciesUtils, Species} from '../common/common'; -import {IDTypeManager, IDType, I18nextManager} from 'phovea_core'; -import {IStartMenuSubSection, IStartMenuSubSectionDesc} from '../common/extensions'; -import {IStartMenuSectionOptions} from 'ordino'; -import {NamedSetList} from 'tdp_core'; -import {ENamedSetType, INamedSet, RestStorageUtils} from 'tdp_core'; -import {RestBaseUtils} from 'tdp_core'; -import {FormElementType, FormBuilder} from 'tdp_core'; -import {StoreUtils} from 'tdp_core'; -import {select, Selection} from 'd3'; -import {ICommonDBConfig} from '../views/ACommonList'; -import {FormSelect3} from 'tdp_core'; -import {IForm} from 'tdp_core'; - -export abstract class ACommonSubSection implements IStartMenuSubSection { - protected readonly data: NamedSetList; - private readonly idType: IDType; - - /** - * Set the idType and the default data and build the list - */ - constructor(parent: HTMLElement, public readonly desc: IStartMenuSubSectionDesc, protected readonly dataSource: ICommonDBConfig, protected readonly options: IStartMenuSectionOptions) { - this.idType = IDTypeManager.getInstance().resolveIdType(desc.idType); - const createSession = (namedSet: INamedSet) => { - if (options.session) { - options.session((this.desc).viewId, {namedSet}, this.getDefaultSessionValues()); - } else { - console.error('no session factory object given to push new view'); - } - }; - this.data = new NamedSetList(IDTypeManager.getInstance().resolveIdType(desc.idType), createSession, parent.ownerDocument); - - parent.appendChild(this.data.node); - - // convert all available species to namedsets - const defaultNamedSets = Species.availableSpecies.map((species) => { - return { - name: 'All', - type: ENamedSetType.CUSTOM, - subTypeKey: Species.SPECIES_SESSION_KEY, - subTypeFromSession: true, - subTypeValue: species.value, - description: '', - idType: '', - ids: '', - creator: '' - }; - }); - - this.data.push(...defaultNamedSets); - this.loadPanels().then((panels) => this.data.push(...panels)); - - this.addSearchField(); - } - - update() { - this.data.update(); - } - - push(namedSet: INamedSet) { - if (namedSet.idType !== this.idType.id) { - return false; - } - this.data.push(namedSet); - return true; - } - - private static panel2NamedSet({id, description, species}: { id: string, description: string, species: string }): INamedSet { - return { - type: ENamedSetType.PANEL, - id, - name: id, - description, - subTypeKey: Species.SPECIES_SESSION_KEY, - subTypeFromSession: false, - subTypeValue: species, - idType: '' - }; - } - - protected loadPanels(): Promise { - return RestBaseUtils.getTDPData(this.dataSource.db, `${this.dataSource.base}_panel`).then((panels: { id: string, description: string, species: string }[]) => { - return panels.map(ACommonSubSection.panel2NamedSet); - }); - } - - protected searchOptions(): any { - return { - return: 'id', - optionsData: [], - placeholder: `Add ${this.dataSource.name} by Typing or by Dragging a Text File onto the Search Field` - }; - } - - protected getDefaultSessionValues() { - // initialize the session with the selected species - return { - [Species.SPECIES_SESSION_KEY]: SpeciesUtils.getSelectedSpecies() - }; - } - - private async addSearchField() { - const $searchWrapper = select(this.data.node.parentElement!).insert('div', ':first-child').attr('class', 'startMenuSearch'); - - const formBuilder = new FormBuilder($searchWrapper); - formBuilder.appendElement({ - id: `search-${this.dataSource.idType}${this.dataSource.entityName}`, - hideLabel: true, - type: FormElementType.SELECT3_MULTIPLE, - attributes: { - style: 'width:100%', - }, - options: this.searchOptions() - }); - - const form: IForm = await formBuilder.build(); - - const $searchButton = ACommonSubSection.createButton($searchWrapper, 'Go'); - const $saveSetButton = ACommonSubSection.createButton($searchWrapper, 'Save'); - - const searchField = form.getElementById(`search-${this.dataSource.idType}${this.dataSource.entityName}`); - - searchField.on('change', () => { - const state = (searchField).hasValue() ? null : 'disabled'; - $searchButton.attr('disabled', state); - $saveSetButton.attr('disabled', state); - }); - - $searchButton.on('click', () => { - this.options.session((this.desc).viewId, { - search: { - ids: searchField.value, - type: this.dataSource.tableName - } - }, this.getDefaultSessionValues()); - }); - - $saveSetButton.on('click', () => { - StoreUtils.editDialog(null, I18nextManager.getInstance().i18n.t(`tdp:core.editDialog.listOfEntities.default`), async (name, description, isPublic) => { - const idStrings = searchField.value; - - const idType = IDTypeManager.getInstance().resolveIdType(this.dataSource.idType); - const ids = await idType.map(idStrings); - - const response = await RestStorageUtils.saveNamedSet(name, idType, ids, { - key: Species.SPECIES_SESSION_KEY, - value: SpeciesUtils.getSelectedSpecies() - }, description, isPublic); - this.push(response); - }); - }); - } - - private static createButton($parent: Selection, text: string): Selection { - return $parent - .append('div') - .append('button') - .classed('btn btn-primary', true) - .attr('disabled', 'disabled') - .text(text); - } -} diff --git a/src/menu/SpeciesSelectorMenuSection.ts b/src/menu/SpeciesSelectorMenuSection.ts deleted file mode 100644 index 7168903..0000000 --- a/src/menu/SpeciesSelectorMenuSection.ts +++ /dev/null @@ -1,161 +0,0 @@ -/** - * Created by Holger Stitz on 27.07.2016. - */ - -import {UserSession} from 'phovea_core'; -import {IPluginDesc, PluginRegistry} from 'phovea_core'; -import {Species} from '../common/common'; -import {select, event as d3event, Selection} from 'd3'; -import * as $ from 'jquery'; -import {IStartMenuSection, IStartMenuSectionOptions} from 'ordino'; -import {INamedSet} from 'tdp_core'; -import { - EXTENSION_POINT_STARTMENU_SUBSECTION, IStartMenuSubSection, - IStartMenuSubSectionDesc -} from '../common/extensions'; - - -const tabSessionKey = 'entityType'; -const defaultTabSessionValue = 'celllinedb_genes_start'; //ensembl - -export class SpeciesSelectorMenuSection implements IStartMenuSection { - - private readonly subSections: IStartMenuSubSection[] = []; - - constructor(private readonly parent: HTMLElement, public readonly desc: IPluginDesc, private readonly options:IStartMenuSectionOptions) { - this.build(); - } - - private build() { - const $parent = select(this.parent); - $parent.html(''); // remove loading element or previous data - - this.buildSpeciesSelection($parent); - this.buildEntityTypes($parent); - } - - push(namedSet: INamedSet) { - return this.subSections.some((d) => d.push(namedSet)); - } - - private buildSpeciesSelection($parent: Selection) { - const $speciesSelection = $parent.append('div').classed('species-wrapper', true); - - const selectedSpecies = UserSession.getInstance().retrieve(Species.SPECIES_SESSION_KEY, Species.defaultSpecies); - - // store default option, if not available - if(!UserSession.getInstance().has(Species.SPECIES_SESSION_KEY)) { - UserSession.getInstance().store(Species.SPECIES_SESSION_KEY, selectedSpecies); - } - - const $group = $speciesSelection.selectAll('.species-group').data(Species.availableSpecies); - const group = $group.enter() - .append('div') - .classed('species-group', true) - .attr('data-species', (d) => d.value) - .classed('active', (d) => d.value === selectedSpecies); - - const that = this; - group.append('input') - .attr('name', 'species') - .attr('id', (d) => `speciesSelector_${d.value}`) - .attr('type', 'radio') - .attr('checked', (d) => (d.value === selectedSpecies) ? 'checked' : null) - .on('change', function(d) { - UserSession.getInstance().store(Species.SPECIES_SESSION_KEY, d.value); - - $group.classed('active', false); - select(this.parentNode).classed('active', true); - that.subSections.forEach((list) => list.update()); - }); - - group.append('label') - .attr('for', (d) => `speciesSelector_${d.value}`) - .attr('data-title', (d) => d.name) - .html((d) => { - const className = d.iconClass || ''; - let text = ''; - - if(!className) { - text = d.name.substr(0, 1).toUpperCase(); - } - - return ``; - }); - - } - - private buildEntityTypes($parent: Selection) { - // get start views for entry points and sort them by name ASC - const views = PluginRegistry.getInstance().listPlugins(EXTENSION_POINT_STARTMENU_SUBSECTION).sort((a,b) => a.name.toLowerCase().localeCompare(b.name.toLowerCase())); - - if(!UserSession.getInstance().has(tabSessionKey)) { - UserSession.getInstance().store(tabSessionKey, defaultTabSessionValue); - } - - this.buildEntityTypeSelection($parent, views); - this.buildEntryPointList($parent, views); - } - - private buildEntityTypeSelection($parent: Selection, views: IStartMenuSubSectionDesc[]): void { - const $entityTypes = $parent.append('ul').classed('nav nav-tabs', true).attr('role', 'tablist'); - - $entityTypes - .selectAll('li') - .data(views) - .enter() - .append('li') - .attr('role', 'presentation') - .append('a') - .attr('href', (d) => `#entity_${d.cssClass}`) - .attr('id', (d) => `entityType_${d.cssClass}`) - .text((d) => d.description) - .on('click', function(d) { - (d3event).preventDefault(); - UserSession.getInstance().store(tabSessionKey, d.id); - $(this).tab('show').blur(); - }).each(function(this: HTMLElement, d) { - if (d.id === UserSession.getInstance().retrieve(tabSessionKey, defaultTabSessionValue)) { - this.click(); - } - }); - } - - private buildEntryPointList($parent: Selection, views: IStartMenuSubSectionDesc[]): void { - const that = this; - const $entryPoints = $parent.append('div').classed('entry-points-wrapper tab-content', true); - - const $items = $entryPoints.selectAll('.item').data(views); - const $enter = $items.enter() - .append('div') - .attr('id', (d) => `entity_${d.cssClass}`) - .attr('class', (d) => d.id === UserSession.getInstance().retrieve(tabSessionKey, defaultTabSessionValue)? 'active' : '') - .classed('tab-pane', true); - - // append initial loading icon --> must be removed by each entry point individually - $enter.append('div').classed('body', true) - .html(` -
- - Loading... -
- `); - - $enter.selectAll('div.body') - .each(function (this: HTMLElement, desc) { - const elem = this; - desc.load().then((i) => { - elem.innerHTML = ''; //clear loading - if (i.factory) { - return i.factory(elem, desc, that.options); - } - console.log(`No viewId and/or factory method found for '${i.desc.id}'`); - return null; - }).then((instance: IStartMenuSubSection) => { - if (instance) { - that.subSections.push(instance); - } - }); - }); - } -} diff --git a/src/menu/index.ts b/src/menu/index.ts deleted file mode 100644 index 490875d..0000000 --- a/src/menu/index.ts +++ /dev/null @@ -1,2 +0,0 @@ -export * from './SpeciesSelectorMenuSection'; -export * from './ACommonSubSection'; From 25acf32070d0eabd31154ba50157a05fec85980e Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Wed, 19 May 2021 14:04:37 +0200 Subject: [PATCH 07/22] switch branches --- package.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 09313b0..a19d42d 100644 --- a/package.json +++ b/package.json @@ -68,9 +68,9 @@ "dependencies": { "jstat": "^1.9.4", "jquery-ui": "1.12.1", - "tdp_core": "github:datavisyn/tdp_core#bootstrap-v4" + "tdp_core": "github:datavisyn/tdp_core#vstoiber/bootstrap_v5" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#welcome-page" + "ordino": "github:Caleydo/ordino#vstoiber/bootstrap_v5" } } From 56bdcd6a5bc8e00bf12161417fc6fdf4e33e4d8b Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Wed, 19 May 2021 14:31:38 +0200 Subject: [PATCH 08/22] Add missing dependencies to package.json --- package.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index 09313b0..e10fc54 100644 --- a/package.json +++ b/package.json @@ -52,8 +52,9 @@ "dist": "mkdir lib && cd dist && tar cvzf ../lib/tdp_gene.tar.gz *" }, "devDependencies": { - "@types/jest": "~26.0.20", "@types/d3": "~3.5.36", + "@types/jest": "~26.0.20", + "@types/jquery": "~3.5.5", "identity-obj-proxy": "~3.0.0", "jest": "~26.6.3", "jest-raw-loader": "~1.0.1", @@ -66,7 +67,9 @@ "typescript": "~3.9.7" }, "dependencies": { + "d3": "~3.5.17", "jstat": "^1.9.4", + "jquery": "~3.5.1", "jquery-ui": "1.12.1", "tdp_core": "github:datavisyn/tdp_core#bootstrap-v4" }, From 32eee622edaee204b65a79140ae825bc0e794c33 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 20 May 2021 09:56:02 +0200 Subject: [PATCH 09/22] btn-close --- dist/views/AOncoPrint.js | 2 +- src/views/AOncoPrint.ts | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dist/views/AOncoPrint.js b/dist/views/AOncoPrint.js index ab6cf85..c2142ff 100644 --- a/dist/views/AOncoPrint.js +++ b/dist/views/AOncoPrint.js @@ -196,7 +196,7 @@ export class AOncoPrint extends AView { // append the legend for missing values $mutLegend.append('li').attr('data-mut', Categories.unknownMutationValue).text('Missing Values'); $node.append('div').attr('class', 'alert alert-info alert-dismissible').attr('role', 'alert').html(` - +

Please note:

  • The indicated copy number states are only estimates, which can be affected by sample purity, ploidy, and other factors.
    • diff --git a/src/views/AOncoPrint.ts b/src/views/AOncoPrint.ts index b3106eb..4235795 100644 --- a/src/views/AOncoPrint.ts +++ b/src/views/AOncoPrint.ts @@ -249,7 +249,7 @@ export abstract class AOncoPrint extends AView { $mutLegend.append('li').attr('data-mut', Categories.unknownMutationValue ).text('Missing Values'); $node.append('div').attr('class', 'alert alert-info alert-dismissible').attr('role', 'alert').html(` - +

    Please note:

    • The indicated copy number states are only estimates, which can be affected by sample purity, ploidy, and other factors.
      • From b18ec2517a67a0dd6de297b6cf6ca3688aa560ba Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 20 May 2021 10:20:54 +0200 Subject: [PATCH 10/22] update close button --- dist/views/AOncoPrint.js | 2 +- src/views/AOncoPrint.ts | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/dist/views/AOncoPrint.js b/dist/views/AOncoPrint.js index c2142ff..83c2680 100644 --- a/dist/views/AOncoPrint.js +++ b/dist/views/AOncoPrint.js @@ -196,7 +196,7 @@ export class AOncoPrint extends AView { // append the legend for missing values $mutLegend.append('li').attr('data-mut', Categories.unknownMutationValue).text('Missing Values'); $node.append('div').attr('class', 'alert alert-info alert-dismissible').attr('role', 'alert').html(` - +

      Please note:

      • The indicated copy number states are only estimates, which can be affected by sample purity, ploidy, and other factors.
        • diff --git a/src/views/AOncoPrint.ts b/src/views/AOncoPrint.ts index 4235795..b174568 100644 --- a/src/views/AOncoPrint.ts +++ b/src/views/AOncoPrint.ts @@ -249,7 +249,7 @@ export abstract class AOncoPrint extends AView { $mutLegend.append('li').attr('data-mut', Categories.unknownMutationValue ).text('Missing Values'); $node.append('div').attr('class', 'alert alert-info alert-dismissible').attr('role', 'alert').html(` - +

        Please note:

        • The indicated copy number states are only estimates, which can be affected by sample purity, ploidy, and other factors.
          • From 40628b4a89729189e4445c03f339e0b799080ef8 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Mon, 31 May 2021 15:43:08 +0200 Subject: [PATCH 11/22] fix oncoprint view --- dist/views/AOncoPrint.js | 4 ++-- src/views/AOncoPrint.ts | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/dist/views/AOncoPrint.js b/dist/views/AOncoPrint.js index 83c2680..0ac26d3 100644 --- a/dist/views/AOncoPrint.js +++ b/dist/views/AOncoPrint.js @@ -138,7 +138,7 @@ export class AOncoPrint extends AView { super.init(params, onParameterChange); // inject stats const base = params.querySelector('form') || params; - base.insertAdjacentHTML('beforeend', `
          + base.insertAdjacentHTML('beforeend', `
          `); let s = 0; @@ -196,7 +196,7 @@ export class AOncoPrint extends AView { // append the legend for missing values $mutLegend.append('li').attr('data-mut', Categories.unknownMutationValue).text('Missing Values'); $node.append('div').attr('class', 'alert alert-info alert-dismissible').attr('role', 'alert').html(` - +

          Please note:

          • The indicated copy number states are only estimates, which can be affected by sample purity, ploidy, and other factors.
            • diff --git a/src/views/AOncoPrint.ts b/src/views/AOncoPrint.ts index b174568..f8d6cbe 100644 --- a/src/views/AOncoPrint.ts +++ b/src/views/AOncoPrint.ts @@ -178,7 +178,7 @@ export abstract class AOncoPrint extends AView { // inject stats const base = params.querySelector('form') || params; - base.insertAdjacentHTML('beforeend', `
            + base.insertAdjacentHTML('beforeend', `
            `); let s = 0; @@ -249,7 +249,7 @@ export abstract class AOncoPrint extends AView { $mutLegend.append('li').attr('data-mut', Categories.unknownMutationValue ).text('Missing Values'); $node.append('div').attr('class', 'alert alert-info alert-dismissible').attr('role', 'alert').html(` - +

            Please note:

            • The indicated copy number states are only estimates, which can be affected by sample purity, ploidy, and other factors.
              • From 530c277e417d5ce70505774ddeaff311d2335f8b Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Wed, 7 Jul 2021 12:17:54 +0200 Subject: [PATCH 12/22] prepare release 9.0.0-alpha.0 --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index e10fc54..ed3e1d8 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "tdp_gene", "description": "", - "version": "7.0.2-SNAPSHOT", + "version": "9.0.0-alpha.0", "author": { "name": "The Caleydo Team", "email": "contact@caleydo.org", @@ -71,9 +71,9 @@ "jstat": "^1.9.4", "jquery": "~3.5.1", "jquery-ui": "1.12.1", - "tdp_core": "github:datavisyn/tdp_core#bootstrap-v4" + "tdp_core": "12.0.0-alpha.0" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#welcome-page" + "ordino": "10.0.0-alpha.0" } } From 361abe672d5edce64de482b4a72c8da92accec14 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 8 Jul 2021 09:35:13 +0200 Subject: [PATCH 13/22] reset repo to use bootstrap branches --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index ed3e1d8..4521983 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "tdp_gene", "description": "", - "version": "9.0.0-alpha.0", + "version": "8.0.1-SNAPSHOT", "author": { "name": "The Caleydo Team", "email": "contact@caleydo.org", @@ -71,9 +71,9 @@ "jstat": "^1.9.4", "jquery": "~3.5.1", "jquery-ui": "1.12.1", - "tdp_core": "12.0.0-alpha.0" + "tdp_core": "github:datavisyn/tdp_core#bootstrap-v4" }, "optionalDependencies": { - "ordino": "10.0.0-alpha.0" + "ordino": "github:Caleydo/ordino#welcome-page" } } From 9a25d7625ada16b6a619a48073e4a6b76dc35b0c Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Mon, 2 Aug 2021 22:05:36 +0200 Subject: [PATCH 14/22] Fix spacing of expression plot --- dist/scss/components/_expression_vs_copynumber.scss | 6 +++++- dist/views/AExpressionVsCopyNumber.js | 2 +- src/scss/components/_expression_vs_copynumber.scss | 6 +++++- src/views/AExpressionVsCopyNumber.ts | 2 +- 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/dist/scss/components/_expression_vs_copynumber.scss b/dist/scss/components/_expression_vs_copynumber.scss index 595919d..72a6878 100644 --- a/dist/scss/components/_expression_vs_copynumber.scss +++ b/dist/scss/components/_expression_vs_copynumber.scss @@ -11,7 +11,7 @@ stroke: $core_color_almost_black; shape-rendering: crispEdges; } - + .mark { fill: $core_color_almost_black; fill-opacity: 0.8; @@ -53,6 +53,10 @@ overflow-x: hidden; text-overflow: ellipsis; } + + &:empty { + display: none; + } } .spearmancoeff { diff --git a/dist/views/AExpressionVsCopyNumber.js b/dist/views/AExpressionVsCopyNumber.js index 00587e7..bd19e67 100644 --- a/dist/views/AExpressionVsCopyNumber.js +++ b/dist/views/AExpressionVsCopyNumber.js @@ -14,7 +14,7 @@ const spearmancoeffTitle = 'Spearman Coefficient: '; export class AExpressionVsCopyNumber extends AD3View { constructor() { super(...arguments); - this.margin = { top: 40, right: 5, bottom: 50, left: 50 }; + this.margin = { top: 40, right: 5, bottom: 50, left: 90 }; this.width = 280 - this.margin.left - this.margin.right; this.height = 320 - this.margin.top - this.margin.bottom; this.x = d3.scale.linear(); diff --git a/src/scss/components/_expression_vs_copynumber.scss b/src/scss/components/_expression_vs_copynumber.scss index 595919d..72a6878 100644 --- a/src/scss/components/_expression_vs_copynumber.scss +++ b/src/scss/components/_expression_vs_copynumber.scss @@ -11,7 +11,7 @@ stroke: $core_color_almost_black; shape-rendering: crispEdges; } - + .mark { fill: $core_color_almost_black; fill-opacity: 0.8; @@ -53,6 +53,10 @@ overflow-x: hidden; text-overflow: ellipsis; } + + &:empty { + display: none; + } } .spearmancoeff { diff --git a/src/views/AExpressionVsCopyNumber.ts b/src/views/AExpressionVsCopyNumber.ts index cf92ea9..7e55790 100644 --- a/src/views/AExpressionVsCopyNumber.ts +++ b/src/views/AExpressionVsCopyNumber.ts @@ -16,7 +16,7 @@ import {jStat} from 'jstat'; const spearmancoeffTitle = 'Spearman Coefficient: '; export abstract class AExpressionVsCopyNumber extends AD3View { - private readonly margin = {top: 40, right: 5, bottom: 50, left: 50}; + private readonly margin = {top: 40, right: 5, bottom: 50, left: 90}; private readonly width = 280 - this.margin.left - this.margin.right; private readonly height = 320 - this.margin.top - this.margin.bottom; From 4d65f98edcb52eabb37519ade48b3e9da688ea3a Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Wed, 4 Aug 2021 09:59:02 +0200 Subject: [PATCH 15/22] switch to merged branches --- package.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 804629a..392adcc 100644 --- a/package.json +++ b/package.json @@ -71,9 +71,9 @@ "jstat": "^1.9.4", "jquery": "~3.5.1", "jquery-ui": "1.12.1", - "tdp_core": "github:datavisyn/tdp_core#vstoiber/bootstrap_v5" + "tdp_core": "github:datavisyn/tdp_core#bootstrap-v5" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#vstoiber/bootstrap_v5" + "ordino": "github:Caleydo/ordino#bootstrap-v5" } } From 233dcdfb16fa46efb05ba7d746fe55f76123704c Mon Sep 17 00:00:00 2001 From: anita-steiner Date: Wed, 11 Aug 2021 10:16:12 +0200 Subject: [PATCH 16/22] change dependencies --- package.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index 392adcc..cc29ea0 100644 --- a/package.json +++ b/package.json @@ -71,9 +71,9 @@ "jstat": "^1.9.4", "jquery": "~3.5.1", "jquery-ui": "1.12.1", - "tdp_core": "github:datavisyn/tdp_core#bootstrap-v5" + "tdp_core": "github:datavisyn/tdp_core#develop" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#bootstrap-v5" + "ordino": "github:Caleydo/ordino#develop" } } From a5a9574f2f36fce212bf1d29c7ca397e4008b89b Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Thu, 12 Aug 2021 12:29:01 +0200 Subject: [PATCH 17/22] Fix axis margin of co-expression plot --- dist/views/ACoExpression.js | 2 +- src/views/ACoExpression.ts | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/dist/views/ACoExpression.js b/dist/views/ACoExpression.js index 8da7b71..39f37bd 100644 --- a/dist/views/ACoExpression.js +++ b/dist/views/ACoExpression.js @@ -21,7 +21,7 @@ const spearmancoeffTitle = 'Spearman Coefficient: '; export class ACoExpression extends AD3View { constructor() { super(...arguments); - this.margin = { top: 40, right: 5, bottom: 50, left: 50 }; + this.margin = { top: 40, right: 5, bottom: 50, left: 90 }; this.width = 280 - this.margin.left - this.margin.right; this.height = 320 - this.margin.top - this.margin.bottom; this.refGene = null; diff --git a/src/views/ACoExpression.ts b/src/views/ACoExpression.ts index 8151faf..341ad81 100644 --- a/src/views/ACoExpression.ts +++ b/src/views/ACoExpression.ts @@ -32,7 +32,7 @@ export interface IGeneOption extends IFormSelectOption { const spearmancoeffTitle = 'Spearman Coefficient: '; export abstract class ACoExpression extends AD3View { - private readonly margin = {top: 40, right: 5, bottom: 50, left: 50}; + private readonly margin = {top: 40, right: 5, bottom: 50, left: 90}; private readonly width = 280 - this.margin.left - this.margin.right; private readonly height = 320 - this.margin.top - this.margin.bottom; @@ -446,4 +446,3 @@ export interface ICoExprDataFormat { geneName: string; rows: ICoExprDataFormatRow[]; } - From 6b286d8c48bc4347c499c003f19c1043e3eddd3d Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 31 Aug 2021 11:08:36 +0200 Subject: [PATCH 18/22] fix oncoprint formelement --- dist/views/AOncoPrint.js | 10 ++++++---- dist/views/AOncoPrint.js.map | 2 +- src/views/AOncoPrint.ts | 27 +++++++++++++++++---------- 3 files changed, 24 insertions(+), 15 deletions(-) diff --git a/dist/views/AOncoPrint.js b/dist/views/AOncoPrint.js index 0ac26d3..8fe0989 100644 --- a/dist/views/AOncoPrint.js +++ b/dist/views/AOncoPrint.js @@ -134,11 +134,14 @@ export class AOncoPrint extends AView { this.manuallyResorted = false; this.scaleFactor = ''; } - init(params, onParameterChange) { - super.init(params, onParameterChange); + async init(params, onParameterChange) { + await super.init(params, onParameterChange); // inject stats + console.log(params); const base = params.querySelector('form') || params; - base.insertAdjacentHTML('beforeend', `
              + const test = params.getElementsByTagName('form'); + console.log(test); + base.insertAdjacentHTML('afterbegin', `
              `); let s = 0; @@ -155,7 +158,6 @@ export class AOncoPrint extends AView { s = Math.max(s - 1, 0); scaleElem.dataset.scale = this.node.dataset.scale = 's'.repeat(s); }); - return Promise.resolve(); } initImpl() { super.initImpl(); diff --git a/dist/views/AOncoPrint.js.map b/dist/views/AOncoPrint.js.map index 3486cfd..d4ccba5 100644 --- a/dist/views/AOncoPrint.js.map +++ b/dist/views/AOncoPrint.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/views/AOncoPrint.ts b/src/views/AOncoPrint.ts index f8d6cbe..1281c3b 100644 --- a/src/views/AOncoPrint.ts +++ b/src/views/AOncoPrint.ts @@ -171,16 +171,25 @@ export abstract class AOncoPrint extends AView { */ private manuallyResorted: boolean = false; - private scaleFactor: '' | 's' | 'ss' | 'sss' = ''; - - init(params: HTMLElement, onParameterChange: (name: string, value: any, previousValue: any) => Promise) { - super.init(params, onParameterChange); + async init(params: HTMLElement, onParameterChange: (name: string, value: any, previousValue: any) => Promise) { + await super.init(params, onParameterChange); // inject stats - const base = params.querySelector('form') || params; - base.insertAdjacentHTML('beforeend', `
              -
              -
              `); + console.log(params); + const base = params.querySelector('form')|| params; + const test = params.getElementsByTagName('form'); + console.log(test); + base.insertAdjacentHTML('afterbegin', ` +
              + +
              +
              +
              +
              +
              + +
              `); + let s = 0; const scaleElem = base.lastElementChild!; @@ -196,8 +205,6 @@ export abstract class AOncoPrint extends AView { s = Math.max(s - 1, 0); scaleElem.dataset.scale = this.node.dataset.scale = 's'.repeat(s); }); - - return Promise.resolve(); } protected initImpl() { From 0890211b0a2dd327c44534049010eb0f78a51227 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 31 Aug 2021 11:16:59 +0200 Subject: [PATCH 19/22] remove logs --- dist/views/AOncoPrint.d.ts | 1 - dist/views/AOncoPrint.js | 17 ++++++++++------- dist/views/AOncoPrint.js.map | 2 +- src/views/AOncoPrint.ts | 3 --- 4 files changed, 11 insertions(+), 12 deletions(-) diff --git a/dist/views/AOncoPrint.d.ts b/dist/views/AOncoPrint.d.ts index 3181c17..fc1b7b0 100644 --- a/dist/views/AOncoPrint.d.ts +++ b/dist/views/AOncoPrint.d.ts @@ -32,7 +32,6 @@ export declare abstract class AOncoPrint extends AView { * @type {boolean} */ private manuallyResorted; - private scaleFactor; init(params: HTMLElement, onParameterChange: (name: string, value: any, previousValue: any) => Promise): Promise; protected initImpl(): Promise; protected parameterChanged(name: string): void; diff --git a/dist/views/AOncoPrint.js b/dist/views/AOncoPrint.js index 8fe0989..1ffc8b2 100644 --- a/dist/views/AOncoPrint.js +++ b/dist/views/AOncoPrint.js @@ -132,18 +132,21 @@ export class AOncoPrint extends AView { * @type {boolean} */ this.manuallyResorted = false; - this.scaleFactor = ''; } async init(params, onParameterChange) { await super.init(params, onParameterChange); // inject stats - console.log(params); const base = params.querySelector('form') || params; - const test = params.getElementsByTagName('form'); - console.log(test); - base.insertAdjacentHTML('afterbegin', `
              -
              -
              `); + base.insertAdjacentHTML('afterbegin', ` +
              + +
              +
              +
              +
              +
              + +
              `); let s = 0; const scaleElem = base.lastElementChild; scaleElem.firstElementChild.addEventListener('click', (e) => { diff --git a/dist/views/AOncoPrint.js.map b/dist/views/AOncoPrint.js.map index d4ccba5..2e886ec 100644 --- a/dist/views/AOncoPrint.js.map +++ b/dist/views/AOncoPrint.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/views/AOncoPrint.ts b/src/views/AOncoPrint.ts index 1281c3b..c2844cf 100644 --- a/src/views/AOncoPrint.ts +++ b/src/views/AOncoPrint.ts @@ -175,10 +175,7 @@ export abstract class AOncoPrint extends AView { await super.init(params, onParameterChange); // inject stats - console.log(params); const base = params.querySelector('form')|| params; - const test = params.getElementsByTagName('form'); - console.log(test); base.insertAdjacentHTML('afterbegin', `
              From c9c1703e93c67ea2276a4b1888ae4be004b52c9b Mon Sep 17 00:00:00 2001 From: Holger Stitz Date: Mon, 13 Sep 2021 21:10:43 +0200 Subject: [PATCH 20/22] Fix parameter desc typings Switch from `IFormSelectDesc` to `IFormElementDesc` because we are using other form elements than selects --- dist/views/ACoExpression.d.ts | 8 ++++++-- dist/views/ACoExpression.js.map | 2 +- dist/views/AExpressionVsCopyNumber.d.ts | 5 ++--- dist/views/AExpressionVsCopyNumber.js | 5 +---- dist/views/AExpressionVsCopyNumber.js.map | 2 +- src/views/ACoExpression.ts | 6 +++--- src/views/AExpressionVsCopyNumber.ts | 7 ++----- 7 files changed, 16 insertions(+), 19 deletions(-) diff --git a/dist/views/ACoExpression.d.ts b/dist/views/ACoExpression.d.ts index 43a6f6b..ddaccdf 100644 --- a/dist/views/ACoExpression.d.ts +++ b/dist/views/ACoExpression.d.ts @@ -1,4 +1,8 @@ -import { IFormSelectDesc, IFormSelectOption } from 'tdp_core'; +/** + * Created by Holger Stitz on 12.08.2016. + */ +import { IFormElementDesc } from 'tdp_core'; +import { IFormSelectOption } from 'tdp_core'; import * as d3 from 'd3'; import { Range } from 'phovea_core'; import { AD3View } from 'tdp_core'; @@ -23,7 +27,7 @@ export declare abstract class ACoExpression extends AD3View { private readonly xAxis; private readonly yAxis; protected initImpl(): Promise; - protected getParameterFormDescs(): IFormSelectDesc[]; + protected getParameterFormDescs(): IFormElementDesc[]; parameterChanged(name: string): void; selectionChanged(): void; private updateRefGeneSelect; diff --git a/dist/views/ACoExpression.js.map b/dist/views/ACoExpression.js.map index 9bacc34..b4ab508 100644 --- a/dist/views/ACoExpression.js.map +++ b/dist/views/ACoExpression.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/dist/views/AExpressionVsCopyNumber.d.ts b/dist/views/AExpressionVsCopyNumber.d.ts index 9d5ff9e..1cb4f03 100644 --- a/dist/views/AExpressionVsCopyNumber.d.ts +++ b/dist/views/AExpressionVsCopyNumber.d.ts @@ -2,8 +2,7 @@ * Created by Holger Stitz on 21.07.2016. */ import { Range } from 'phovea_core'; -import { IFormSelectDesc } from 'tdp_core'; -import { AD3View } from 'tdp_core'; +import { IFormElementDesc, AD3View } from 'tdp_core'; export declare abstract class AExpressionVsCopyNumber extends AD3View { private readonly margin; private readonly width; @@ -25,7 +24,7 @@ export declare abstract class AExpressionVsCopyNumber extends AD3View { value: string; data: any; }[]; - protected getParameterFormDescs(): IFormSelectDesc[]; + protected getParameterFormDescs(): IFormElementDesc[]; parameterChanged(name: string): void; selectionChanged(): void; /** diff --git a/dist/views/AExpressionVsCopyNumber.js b/dist/views/AExpressionVsCopyNumber.js index bd19e67..27a8946 100644 --- a/dist/views/AExpressionVsCopyNumber.js +++ b/dist/views/AExpressionVsCopyNumber.js @@ -2,12 +2,9 @@ * Created by Holger Stitz on 21.07.2016. */ import { FormSubtype } from '../provider/forms'; -import { ErrorAlertHandler } from 'tdp_core'; +import { ErrorAlertHandler, FormElementType, ResolveUtils, AD3View } from 'tdp_core'; import * as d3 from 'd3'; import { SelectionUtils, SelectOperation } from 'phovea_core'; -import { FormElementType } from 'tdp_core'; -import { ResolveUtils } from 'tdp_core'; -import { AD3View } from 'tdp_core'; import { ViewUtils } from './ViewUtils'; import { jStat } from 'jstat'; const spearmancoeffTitle = 'Spearman Coefficient: '; diff --git a/dist/views/AExpressionVsCopyNumber.js.map b/dist/views/AExpressionVsCopyNumber.js.map index defc1db..4d0ef2f 100644 --- a/dist/views/AExpressionVsCopyNumber.js.map +++ b/dist/views/AExpressionVsCopyNumber.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/views/ACoExpression.ts b/src/views/ACoExpression.ts index 341ad81..05fe867 100644 --- a/src/views/ACoExpression.ts +++ b/src/views/ACoExpression.ts @@ -1,9 +1,9 @@ /** * Created by Holger Stitz on 12.08.2016. */ -import {ISelection} from 'tdp_core'; +import {ISelection, IFormElementDesc} from 'tdp_core'; import {ResolveUtils} from 'tdp_core'; -import {FormElementType, IFormSelectDesc, IFormSelectElement, IFormSelectOption} from 'tdp_core'; +import {FormElementType, IFormSelectElement, IFormSelectOption} from 'tdp_core'; import {ErrorAlertHandler} from 'tdp_core'; import * as d3 from 'd3'; import {Range} from 'phovea_core'; @@ -75,7 +75,7 @@ export abstract class ACoExpression extends AD3View { }); } - protected getParameterFormDescs(): IFormSelectDesc[] { + protected getParameterFormDescs(): IFormElementDesc[] { return [ { type: FormElementType.SELECT, diff --git a/src/views/AExpressionVsCopyNumber.ts b/src/views/AExpressionVsCopyNumber.ts index 7e55790..23cb8f3 100644 --- a/src/views/AExpressionVsCopyNumber.ts +++ b/src/views/AExpressionVsCopyNumber.ts @@ -4,12 +4,9 @@ import {Range} from 'phovea_core'; import {FormSubtype} from '../provider/forms'; -import {ErrorAlertHandler} from 'tdp_core'; +import {ErrorAlertHandler, IFormElementDesc, FormElementType, ResolveUtils, AD3View} from 'tdp_core'; import * as d3 from 'd3'; import {SelectionUtils, SelectOperation} from 'phovea_core'; -import {FormElementType, IFormSelectDesc} from 'tdp_core'; -import {ResolveUtils} from 'tdp_core'; -import {AD3View} from 'tdp_core'; import {ViewUtils} from './ViewUtils'; import {jStat} from 'jstat'; @@ -38,7 +35,7 @@ export abstract class AExpressionVsCopyNumber extends AD3View { protected abstract getExpressionValues(): {name: string, value: string, data: any}[]; protected abstract getCopyNumberValues(): {name: string, value: string, data: any}[]; - protected getParameterFormDescs(): IFormSelectDesc[] { + protected getParameterFormDescs(): IFormElementDesc[] { return [ { type: FormElementType.SELECT, From 5d509cd3c07f3d1447fbb17f1fb73c439f563006 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Tue, 21 Sep 2021 15:45:09 +0200 Subject: [PATCH 21/22] add panelAddColumnBtnOptions --- dist/views/ACommonList.js | 3 +++ dist/views/ACommonList.js.map | 2 +- src/views/ACommonList.ts | 3 +++ 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/dist/views/ACommonList.js b/dist/views/ACommonList.js index 4cf56d6..bb85ce8 100644 --- a/dist/views/ACommonList.js +++ b/dist/views/ACommonList.js @@ -13,6 +13,9 @@ export class ACommonList extends AStartList { subType: { key: Species.SPECIES_SESSION_KEY, value: SpeciesUtils.getSelectedSpecies() + }, + panelAddColumnBtnOptions: { + btnClass: 'btn-primary' } }, options)); this.dataSource = dataSource; diff --git a/dist/views/ACommonList.js.map b/dist/views/ACommonList.js.map index 89ea753..0234c2b 100644 --- a/dist/views/ACommonList.js.map +++ b/dist/views/ACommonList.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/src/views/ACommonList.ts b/src/views/ACommonList.ts index 017d2bc..6672c80 100644 --- a/src/views/ACommonList.ts +++ b/src/views/ACommonList.ts @@ -36,6 +36,9 @@ export abstract class ACommonList extends AStartList { subType: { key: Species.SPECIES_SESSION_KEY, value: SpeciesUtils.getSelectedSpecies() + }, + panelAddColumnBtnOptions: { + btnClass: 'btn-primary' } }, options)); From d87535928129d9b73612ec14f41ca59cf6065814 Mon Sep 17 00:00:00 2001 From: dvvanessastoiber Date: Thu, 7 Oct 2021 09:36:51 +0200 Subject: [PATCH 22/22] prepare release_9.0.0 --- package.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package.json b/package.json index cc29ea0..18fa552 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "tdp_gene", "description": "", - "version": "8.0.1-SNAPSHOT", + "version": "9.0.0", "author": { "name": "The Caleydo Team", "email": "contact@caleydo.org", @@ -71,9 +71,9 @@ "jstat": "^1.9.4", "jquery": "~3.5.1", "jquery-ui": "1.12.1", - "tdp_core": "github:datavisyn/tdp_core#develop" + "tdp_core": "^12.1.0" }, "optionalDependencies": { - "ordino": "github:Caleydo/ordino#develop" + "ordino": "github:Caleydo/ordino#semver:^10.0.0" } }