From 5395d337d1e0979e1619a77670461a051cfdca82 Mon Sep 17 00:00:00 2001 From: Vanessa Stoiber <52395160+dvvanessastoiber@users.noreply.github.com> Date: Thu, 24 Nov 2022 09:35:31 +0100 Subject: [PATCH] Release 16.2.1 (#808) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Moritz Heckmann Co-authored-by: dvmoritzschoefl <77104411+dvmoritzschoefl@users.noreply.github.com> Co-authored-by: Michael Puehringer Co-authored-by: dvtschachinger Co-authored-by: Holger Stitz Co-authored-by: Michael Pühringer <51900829+puehringer@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: dvzacharycutler Co-authored-by: oltionchampari Co-authored-by: Christian Bors Co-authored-by: dvflorianengertsberger <87969942+dvflorianengertsberger@users.noreply.github.com> Co-authored-by: Zach Cutler <87644761+dvzacharycutler@users.noreply.github.com> Co-authored-by: anita-steiner <> Co-authored-by: Anita Steiner Co-authored-by: dvdanielamoitzi <57343176+dvdanielamoitzi@users.noreply.github.com> Co-authored-by: Christian Bors <84898946+dvchristianbors@users.noreply.github.com> Co-authored-by: Markus Vogl <80687597+dvmarkusvogl@users.noreply.github.com> Co-authored-by: Champari Oltion <51322092+oltionchampari@users.noreply.github.com> --- .gitignore | 2 +- README.md | 4 ++-- dist/lineup/ARankingView.d.ts.map | 2 +- dist/lineup/ARankingView.js | 23 +++++++++++++---------- dist/lineup/ARankingView.js.map | 2 +- dist/lineup/Ranking.d.ts.map | 2 +- dist/lineup/Ranking.js | 12 ++++++++++-- dist/lineup/Ranking.js.map | 2 +- dist/lineup/internal/ScoreUtils.d.ts.map | 2 +- dist/lineup/internal/ScoreUtils.js | 11 +++++++---- dist/lineup/internal/ScoreUtils.js.map | 2 +- dist/lineup/panel/PanelTab.js | 2 +- dist/vis/bar/BarVis.d.ts.map | 2 +- dist/vis/bar/BarVis.js | 1 - dist/vis/bar/BarVis.js.map | 2 +- dist/vis/general/layoutUtils.d.ts | 2 +- dist/vis/general/layoutUtils.d.ts.map | 2 +- dist/vis/general/layoutUtils.js.map | 2 +- dist/vis/scatter/ScatterVis.d.ts.map | 2 +- dist/vis/scatter/ScatterVis.js | 1 - dist/vis/scatter/ScatterVis.js.map | 2 +- dist/vis/strip/StripVis.d.ts.map | 2 +- dist/vis/strip/StripVis.js | 1 - dist/vis/strip/StripVis.js.map | 2 +- dist/vis/violin/ViolinVis.d.ts.map | 2 +- dist/vis/violin/ViolinVis.js | 1 - dist/vis/violin/ViolinVis.js.map | 2 +- package.json | 12 ++++++------ src/lineup/ARankingView.ts | 23 +++++++++++++---------- src/lineup/Ranking.tsx | 11 +++++++++-- src/lineup/internal/ScoreUtils.ts | 11 +++++++---- src/lineup/panel/PanelTab.ts | 2 +- src/vis/bar/BarVis.tsx | 3 +-- src/vis/general/layoutUtils.ts | 2 +- src/vis/scatter/ScatterVis.tsx | 3 +-- src/vis/strip/StripVis.tsx | 3 +-- src/vis/violin/ViolinVis.tsx | 3 +-- tdp_core/security/manager.py | 17 ++++++++++++++--- 38 files changed, 106 insertions(+), 76 deletions(-) diff --git a/.gitignore b/.gitignore index 11f2280db..32be9923e 100644 --- a/.gitignore +++ b/.gitignore @@ -41,4 +41,4 @@ node_modules/ !.yarn/versions # env -/env/ \ No newline at end of file +/.venv*/ \ No newline at end of file diff --git a/README.md b/README.md index b01d6b7ce..387ba886c 100644 --- a/README.md +++ b/README.md @@ -16,8 +16,8 @@ cd tdp_core yarn install # Backend -python3 -m venv env # create a new virutal environment -source env/bin/activate # active it +python3 -m venv .venv # create a new virtual environment +source .venv/bin/activate # active it make develop # install all dependencies ``` diff --git a/dist/lineup/ARankingView.d.ts.map b/dist/lineup/ARankingView.d.ts.map index 126cb6aac..55d5bab96 100644 --- a/dist/lineup/ARankingView.d.ts.map +++ b/dist/lineup/ARankingView.d.ts.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/lineup/ARankingView.js b/dist/lineup/ARankingView.js index 53a11ad8d..bf4122d35 100644 --- a/dist/lineup/ARankingView.js +++ b/dist/lineup/ARankingView.js @@ -244,16 +244,17 @@ export class ARankingView extends AView { */ init(params, onParameterChange) { return super.init(params, onParameterChange).then(() => { - if (!WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { - // inject stats - const base = params.querySelector('form') || params; - base.insertAdjacentHTML('beforeend', `
`); - const container = base.lastElementChild; - container.appendChild(this.stats); - if (this.options.enableSidePanel === 'top') { - container.classList.add('d-flex', 'flex-row', 'align-items-center', 'gap-3'); - container.insertAdjacentElement('afterbegin', this.panel.node); - } + if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { + return; // do nothing when feature flag is enabled + } + // inject stats + const base = params.querySelector('form') || params; + base.insertAdjacentHTML('beforeend', `
`); + const container = base.lastElementChild; + container.appendChild(this.stats); + if (this.options.enableSidePanel === 'top') { + container.classList.add('d-flex', 'flex-row', 'align-items-center', 'gap-3'); + container.insertAdjacentElement('afterbegin', this.panel.node); } }); } @@ -524,6 +525,7 @@ export class ARankingView extends AView { * @returns {Promise<{col: Column; loaded: Promise}>} */ async addTrackedScoreColumn(score, position) { + // skip provenance impl when feature flag is enabled if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { return this.addScoreColumn(score, position); } @@ -538,6 +540,7 @@ export class ARankingView extends AView { * @returns {Promise} */ async removeTrackedScoreColumn(columnId) { + // skip provenance impl when feature flag is enabled if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { const column = this.provider.find(columnId); return column.removeMe(); diff --git a/dist/lineup/ARankingView.js.map b/dist/lineup/ARankingView.js.map index 282ae6c5f..0d5541abc 100644 --- a/dist/lineup/ARankingView.js.map +++ b/dist/lineup/ARankingView.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/lineup/Ranking.d.ts.map b/dist/lineup/Ranking.d.ts.map index bf13e36ee..d9784ad50 100644 --- a/dist/lineup/Ranking.d.ts.map +++ b/dist/lineup/Ranking.d.ts.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/lineup/Ranking.js b/dist/lineup/Ranking.js index 7c4011512..35aa41a88 100644 --- a/dist/lineup/Ranking.js +++ b/dist/lineup/Ranking.js @@ -27,6 +27,7 @@ import { ErrorAlertHandler } from '../base/ErrorAlertHandler'; import { useAsync } from '../hooks/useAsync'; import { StructureImageColumn, StructureImageFilterDialog, StructureImageRenderer } from './structureImage'; import TDPLocalDataProvider from './provider/TDPLocalDataProvider'; +import { WebpackEnv } from '../base'; const defaults = { itemName: 'item', itemNamePlural: 'items', @@ -331,10 +332,17 @@ onAddScoreColumn, }) { onUpdateEntryPoint?.(namedSet); }); panelRef.current.on(LineUpPanelActions.EVENT_ADD_TRACKED_SCORE_COLUMN, async (_event, scoreName, scoreId, p) => { - const storedParams = await AttachemntUtils.externalize(p); // TODO: do we need this? const pluginDesc = PluginRegistry.getInstance().getPlugin(EXTENSION_POINT_TDP_SCORE_IMPL, scoreId); const plugin = await pluginDesc.load(); - const params = await AttachemntUtils.resolveExternalized(storedParams); + let params; + // skip attachment utils call when feature flag is enabled + if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { + params = p; + } + else { + const storedParams = await AttachemntUtils.externalize(p); // TODO: do we need this? + params = await AttachemntUtils.resolveExternalized(storedParams); + } const score = plugin.factory(params, pluginDesc); const scores = Array.isArray(score) ? score : [score]; const results = await Promise.all(scores.map((s) => addScoreColumn(s))); diff --git a/dist/lineup/Ranking.js.map b/dist/lineup/Ranking.js.map index 381d16739..b018d4a8c 100644 --- a/dist/lineup/Ranking.js.map +++ b/dist/lineup/Ranking.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/lineup/internal/ScoreUtils.d.ts.map b/dist/lineup/internal/ScoreUtils.d.ts.map index 5f357b40e..4de6a27a8 100644 --- a/dist/lineup/internal/ScoreUtils.d.ts.map +++ b/dist/lineup/internal/ScoreUtils.d.ts.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/lineup/internal/ScoreUtils.js b/dist/lineup/internal/ScoreUtils.js index d8f09b02b..fafe53104 100644 --- a/dist/lineup/internal/ScoreUtils.js +++ b/dist/lineup/internal/ScoreUtils.js @@ -10,13 +10,17 @@ export class ScoreUtils { const pluginDesc = PluginRegistry.getInstance().getPlugin(EXTENSION_POINT_TDP_SCORE_IMPL, scoreId); const plugin = await pluginDesc.load(); let view; + let params; if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { view = await inputs[0].v; + // disable eslint because it is unclear how to avoid the eslint warning and destructure `params` from the `parameter` object with `let` variable `params` in this case + // eslint-disable-next-line prefer-destructuring + params = parameter.params; } else { view = await inputs[0].v.then((vi) => vi.getInstance()); + params = await AttachemntUtils.resolveExternalized(parameter.params); } - const params = await AttachemntUtils.resolveExternalized(parameter.params); const score = plugin.factory(params, pluginDesc); const scores = Array.isArray(score) ? score : [score]; const results = await Promise.all(scores.map((s) => view.addTrackedScoreColumn(s))); @@ -47,10 +51,9 @@ export class ScoreUtils { }); } static async pushScoreAsync(graph, provider, scoreName, scoreId, params) { + // skip attachment utils + provenance impl and add score directly when feature flag is enabled if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { - const storedParams = await AttachemntUtils.externalize(params); - const toStoreParams = { id: scoreId, params: storedParams }; - return ScoreUtils.addScoreImpl([provider], toStoreParams); + return ScoreUtils.addScoreImpl([provider], { id: scoreId, params }); } const storedParams = await AttachemntUtils.externalize(params); const currentParams = { id: scoreId, params, storedParams }; diff --git a/dist/lineup/internal/ScoreUtils.js.map b/dist/lineup/internal/ScoreUtils.js.map index e645598c7..6c067dc8a 100644 --- a/dist/lineup/internal/ScoreUtils.js.map +++ b/dist/lineup/internal/ScoreUtils.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/lineup/panel/PanelTab.js b/dist/lineup/panel/PanelTab.js index 6c91ef544..ae17a8547 100644 --- a/dist/lineup/panel/PanelTab.js +++ b/dist/lineup/panel/PanelTab.js @@ -16,7 +16,7 @@ export class PanelTab extends EventHandler { this.options = { faIcon: 'fas fa-sliders-h', title: I18nextManager.getInstance().i18n.t('tdp:core.lineup.LineupPanelActions.rankingPanelTabTitle'), - width: '24em', + width: '26em', order: 0, }; this.node = parent.ownerDocument.createElement('div'); diff --git a/dist/vis/bar/BarVis.d.ts.map b/dist/vis/bar/BarVis.d.ts.map index b4292cb7b..61f48b2f1 100644 --- a/dist/vis/bar/BarVis.d.ts.map +++ b/dist/vis/bar/BarVis.d.ts.map @@ -1 +1 @@ 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\ No newline at end of file +{"version":3,"file":"BarVis.d.ts","sourceRoot":"","sources":["../../../src/vis/bar/BarVis.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,KAAK,MAAM,OAAO,CAAC;AAI/B,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,UAAU,EAAoB,MAAM,eAAe,CAAC;AAU5F,UAAU,WAAW;IACnB,MAAM,EAAE,UAAU,CAAC;IACnB,aAAa,CAAC,EAAE;QACd,KAAK,CAAC,EAAE;YACN,MAAM,CAAC,EAAE,OAAO,CAAC;YACjB,eAAe,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;SACnC,CAAC;QACF,SAAS,CAAC,EAAE;YACV,MAAM,CAAC,EAAE,OAAO,CAAC;YACjB,eAAe,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;SACnC,CAAC;QACF,SAAS,CAAC,EAAE;YACV,MAAM,CAAC,EAAE,OAAO,CAAC;YACjB,eAAe,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;SACnC,CAAC;QACF,YAAY,CAAC,EAAE;YACb,MAAM,CAAC,EAAE,OAAO,CAAC;YACjB,eAAe,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;SACnC,CAAC;QACF,OAAO,CAAC,EAAE;YACR,MAAM,CAAC,EAAE,OAAO,CAAC;YACjB,eAAe,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;SACnC,CAAC;KACH,CAAC;IACF,UAAU,CAAC,EAAE;QACX,OAAO,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;QAC1B,QAAQ,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;QAC3B,UAAU,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;QAC7B,WAAW,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;KAC/B,CAAC;IACF,OAAO,EAAE,SAAS,EAAE,CAAC;IACrB,mBAAmB,CAAC,EAAE,MAAM,IAAI,CAAC;IACjC,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,iBAAiB,CAAC,EAAE,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,IAAI,CAAC;IAC5C,WAAW,CAAC,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;KAAE,CAAC;IACzC,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,SAAS,EAAE,CAAC,MAAM,EAAE,UAAU,KAAK,IAAI,CAAC;IACxC,MAAM,EAAE,MAAM,CAAC;IACf,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AASD,wBAAgB,MAAM,CAAC,EACrB,MAAM,EACN,aAAa,EACb,UAAU,EACV,OAAO,EACP,SAAS,EACT,MAAM,EACN,iBAA8B,EAC9B,WAAgB,EAChB,YAAiB,EACjB,WAAmB,EACnB,eAAuB,EACvB,mBAAgC,GACjC,EAAE,WAAW,eAgLb"} \ No newline at end of file diff --git a/dist/vis/bar/BarVis.js b/dist/vis/bar/BarVis.js index 216891369..83d838670 100644 --- a/dist/vis/bar/BarVis.js +++ b/dist/vis/bar/BarVis.js @@ -98,7 +98,6 @@ export function BarVis({ config, optionsConfig, extensions, columns, setConfig, autosize: true, grid: { rows: finalTraces.rows, columns: finalTraces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, barmode: config.groupType === EBarGroupingType.STACK ? 'stack' : 'group', dragmode: false, }; diff --git a/dist/vis/bar/BarVis.js.map b/dist/vis/bar/BarVis.js.map index aaf9ec442..f7913c102 100644 --- a/dist/vis/bar/BarVis.js.map +++ b/dist/vis/bar/BarVis.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/vis/general/layoutUtils.d.ts b/dist/vis/general/layoutUtils.d.ts index 1f88b8af5..3cb585f8f 100644 --- a/dist/vis/general/layoutUtils.d.ts +++ b/dist/vis/general/layoutUtils.d.ts @@ -13,7 +13,7 @@ export declare function columnNameWithDescription(col: ColumnInfo): string; * @param layout the current layout to be changed. Typed to any because the plotly types complain.p * @returns the changed layout */ -export declare function beautifyLayout(traces: PlotlyInfo, layout: Plotly.Layout): Plotly.Layout; +export declare function beautifyLayout(traces: PlotlyInfo, layout: Partial): Partial; export declare function resolveColumnValues(columns: VisColumn[]): Promise<({ resolvedValues: (import("../interfaces").VisNumericalValue | import("../interfaces").VisCategoricalValue)[]; type: import("../interfaces").EColumnTypes.NUMERICAL; diff --git a/dist/vis/general/layoutUtils.d.ts.map b/dist/vis/general/layoutUtils.d.ts.map index cb3aa9979..938f1d7e2 100644 --- a/dist/vis/general/layoutUtils.d.ts.map +++ b/dist/vis/general/layoutUtils.d.ts.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/vis/scatter/ScatterVis.js b/dist/vis/scatter/ScatterVis.js index 68718d8c3..109a2be66 100644 --- a/dist/vis/scatter/ScatterVis.js +++ b/dist/vis/scatter/ScatterVis.js @@ -67,7 +67,6 @@ export function ScatterVis({ config, optionsConfig, extensions, columns, shapes autosize: true, grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, dragmode: config.dragMode, }; return beautifyLayout(traces, innerLayout); diff --git a/dist/vis/scatter/ScatterVis.js.map b/dist/vis/scatter/ScatterVis.js.map index 21bbcc983..16467203c 100644 --- a/dist/vis/scatter/ScatterVis.js.map +++ b/dist/vis/scatter/ScatterVis.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/vis/strip/StripVis.d.ts.map b/dist/vis/strip/StripVis.d.ts.map index 6e4ca3e50..d245af370 100644 --- a/dist/vis/strip/StripVis.d.ts.map +++ b/dist/vis/strip/StripVis.d.ts.map @@ -1 +1 @@ -{"version":3,"file":"StripVis.d.ts","sourceRoot":"","sources":["../../../src/vis/strip/StripVis.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,KAAK,MAAM,OAAO,CAAC;AAI/B,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,eAAe,CAAC;AAU5E,UAAU,aAAa;IACrB,MAAM,EAAE,YAAY,CAAC;IACrB,UAAU,CAAC,EAAE;QACX,OAAO,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;QAC1B,QAAQ,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;QAC3B,UAAU,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;QAC7B,WAAW,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC;KAC/B,CAAC;IACF,OAAO,EAAE,SAAS,EAAE,CAAC;IACrB,SAAS,EAAE,CAAC,MAAM,EAAE,UAAU,KAAK,IAAI,CAAC;IACxC,MAAM,EAAE,MAAM,CAAC;IACf,iBAAiB,CAAC,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,IAAI,CAAC;IAC1C,mBAAmB,CAAC,EAAE,MAAM,IAAI,CAAC;IACjC,QAAQ,CAAC,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;KAAE,CAAC;IACtC,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,eAAe,CAAC,EAAE,OAAO,CAAC;CAC3B;AASD,wBAAgB,QAAQ,CAAC,EACvB,MAAM,EACN,UAAU,EACV,OAAO,EACP,SAAS,EACT,iBAA8B,EAC9B,QAAa,EACb,MAAM,EACN,WAAmB,EACnB,eAAuB,EACvB,mBAAgC,GACjC,EAAE,aAAa,eAsGf"} \ No newline at end of file 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diff --git a/dist/vis/strip/StripVis.js b/dist/vis/strip/StripVis.js index d9dd7f961..454aa0448 100644 --- a/dist/vis/strip/StripVis.js +++ b/dist/vis/strip/StripVis.js @@ -58,7 +58,6 @@ export function StripVis({ config, extensions, columns, setConfig, selectionCall autosize: true, grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, dragmode: 'select', }; return beautifyLayout(traces, innerLayout); diff --git a/dist/vis/strip/StripVis.js.map b/dist/vis/strip/StripVis.js.map index 1852176d3..70ddda35f 100644 --- a/dist/vis/strip/StripVis.js.map +++ b/dist/vis/strip/StripVis.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/dist/vis/violin/ViolinVis.d.ts.map b/dist/vis/violin/ViolinVis.d.ts.map index 3c6b51ec9..f1bce641d 100644 --- a/dist/vis/violin/ViolinVis.d.ts.map +++ b/dist/vis/violin/ViolinVis.d.ts.map @@ -1 +1 @@ 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a/dist/vis/violin/ViolinVis.js b/dist/vis/violin/ViolinVis.js index f6d387827..5b338ac3c 100644 --- a/dist/vis/violin/ViolinVis.js +++ b/dist/vis/violin/ViolinVis.js @@ -58,7 +58,6 @@ export function ViolinVis({ config, optionsConfig, extensions, columns, setConfi autosize: true, grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, }; return beautifyLayout(traces, innerLayout); }, [traces]); diff --git a/dist/vis/violin/ViolinVis.js.map b/dist/vis/violin/ViolinVis.js.map index 5fc42c379..2fad93524 100644 --- a/dist/vis/violin/ViolinVis.js.map +++ b/dist/vis/violin/ViolinVis.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/package.json b/package.json index 8eaf96242..7a3453069 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "tdp_core", "description": "Target discovery platform for exploring rankings of genes, disease models, and other entities.", - "version": "16.2.0", + "version": "16.2.1", "author": { "name": "datavisyn GmbH", "email": "contact@datavisyn.io", @@ -53,20 +53,20 @@ "webpack:prod": "visyn_scripts build --mode production --env workspace_mode=single" }, "dependencies": { + "@emotion/react": "^11.0.0", "@fortawesome/fontawesome-free": "^6.1.1", "@fortawesome/fontawesome-svg-core": "^6.1.2", "@fortawesome/free-regular-svg-icons": "^6.1.2", "@fortawesome/free-solid-svg-icons": "^6.1.2", "@fortawesome/react-fontawesome": "^0.2.0", + "@mantine/core": "^5.0.0", + "@mantine/form": "^5.0.0", + "@mantine/hooks": "^5.0.0", "@popperjs/core": "^2.9.3", "@types/bootstrap": "~5.0.15", "@types/d3v3": "npm:@types/d3@~3.5.36", "@types/d3v7": "npm:@types/d3@^7.4.0", "@types/jquery": "~3.5.5", - "@emotion/react": "^11.0.0", - "@mantine/core": "^5.0.0", - "@mantine/form": "^5.0.0", - "@mantine/hooks": "^5.0.0", "@types/papaparse": "~5.3.0", "@types/plotly.js-dist-min": "^2.3.0", "@types/react": "^16.9.23", @@ -99,7 +99,7 @@ "select2": "~4.0.13", "select2-bootstrap-theme": "0.1.0-beta.9", "use-deep-compare-effect": "^1.8.0", - "visyn_scripts": "^1.0.1" + "visyn_scripts": "^1.1.1" }, "devDependencies": { "@babel/core": "^7.17.7", diff --git a/src/lineup/ARankingView.ts b/src/lineup/ARankingView.ts index 1dd59ca9f..e565e24b3 100644 --- a/src/lineup/ARankingView.ts +++ b/src/lineup/ARankingView.ts @@ -322,16 +322,17 @@ export abstract class ARankingView extends AView { */ init(params: HTMLElement, onParameterChange: (name: string, value: any, previousValue: any) => Promise) { return super.init(params, onParameterChange).then(() => { - if (!WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { - // inject stats - const base = params.querySelector('form') || params; - base.insertAdjacentHTML('beforeend', `
`); - const container = base.lastElementChild!; - container.appendChild(this.stats); - if (this.options.enableSidePanel === 'top') { - container.classList.add('d-flex', 'flex-row', 'align-items-center', 'gap-3'); - container.insertAdjacentElement('afterbegin', this.panel.node); - } + if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { + return; // do nothing when feature flag is enabled + } + // inject stats + const base = params.querySelector('form') || params; + base.insertAdjacentHTML('beforeend', `
`); + const container = base.lastElementChild!; + container.appendChild(this.stats); + if (this.options.enableSidePanel === 'top') { + container.classList.add('d-flex', 'flex-row', 'align-items-center', 'gap-3'); + container.insertAdjacentElement('afterbegin', this.panel.node); } }); } @@ -634,6 +635,7 @@ export abstract class ARankingView extends AView { * @returns {Promise<{col: Column; loaded: Promise}>} */ async addTrackedScoreColumn(score: IScore, position?: number): Promise { + // skip provenance impl when feature flag is enabled if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { return this.addScoreColumn(score, position); } @@ -650,6 +652,7 @@ export abstract class ARankingView extends AView { * @returns {Promise} */ async removeTrackedScoreColumn(columnId: string): Promise { + // skip provenance impl when feature flag is enabled if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { const column = this.provider.find(columnId); return column.removeMe(); diff --git a/src/lineup/Ranking.tsx b/src/lineup/Ranking.tsx index 9a59df5fc..493a79340 100644 --- a/src/lineup/Ranking.tsx +++ b/src/lineup/Ranking.tsx @@ -54,6 +54,7 @@ import { ErrorAlertHandler } from '../base/ErrorAlertHandler'; import { useAsync } from '../hooks/useAsync'; import { StructureImageColumn, StructureImageFilterDialog, StructureImageRenderer } from './structureImage'; import TDPLocalDataProvider from './provider/TDPLocalDataProvider'; +import { WebpackEnv } from '../base'; export interface IScoreResult { instance: ILazyLoadedColumn; @@ -450,10 +451,16 @@ export function Ranking({ ); panelRef.current.on(LineUpPanelActions.EVENT_ADD_TRACKED_SCORE_COLUMN, async (_event, scoreName: string, scoreId: string, p: any) => { - const storedParams = await AttachemntUtils.externalize(p); // TODO: do we need this? const pluginDesc = PluginRegistry.getInstance().getPlugin(EXTENSION_POINT_TDP_SCORE_IMPL, scoreId); const plugin = await pluginDesc.load(); - const params = await AttachemntUtils.resolveExternalized(storedParams); + let params; + // skip attachment utils call when feature flag is enabled + if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { + params = p; + } else { + const storedParams = await AttachemntUtils.externalize(p); // TODO: do we need this? + params = await AttachemntUtils.resolveExternalized(storedParams); + } const score: IScore | IScore[] = plugin.factory(params, pluginDesc); const scores = Array.isArray(score) ? score : [score]; const results = await Promise.all(scores.map((s) => addScoreColumn(s))); diff --git a/src/lineup/internal/ScoreUtils.ts b/src/lineup/internal/ScoreUtils.ts index 14fb9a2e9..c08081525 100644 --- a/src/lineup/internal/ScoreUtils.ts +++ b/src/lineup/internal/ScoreUtils.ts @@ -17,12 +17,16 @@ export class ScoreUtils { const pluginDesc = PluginRegistry.getInstance().getPlugin(EXTENSION_POINT_TDP_SCORE_IMPL, scoreId); const plugin = await pluginDesc.load(); let view; + let params; if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { view = await inputs[0].v; + // disable eslint because it is unclear how to avoid the eslint warning and destructure `params` from the `parameter` object with `let` variable `params` in this case + // eslint-disable-next-line prefer-destructuring + params = parameter.params; } else { view = await inputs[0].v.then((vi) => vi.getInstance()); + params = await AttachemntUtils.resolveExternalized(parameter.params); } - const params = await AttachemntUtils.resolveExternalized(parameter.params); const score: IScore | IScore[] = plugin.factory(params, pluginDesc); const scores = Array.isArray(score) ? score : [score]; @@ -78,10 +82,9 @@ export class ScoreUtils { } static async pushScoreAsync(graph: ProvenanceGraph, provider: IObjectRef, scoreName: string, scoreId: string, params: any) { + // skip attachment utils + provenance impl and add score directly when feature flag is enabled if (WebpackEnv.ENABLE_EXPERIMENTAL_REPROVISYN_FEATURES) { - const storedParams = await AttachemntUtils.externalize(params); - const toStoreParams = { id: scoreId, params: storedParams }; - return ScoreUtils.addScoreImpl([provider], toStoreParams); + return ScoreUtils.addScoreImpl([provider], { id: scoreId, params }); } const storedParams = await AttachemntUtils.externalize(params); const currentParams = { id: scoreId, params, storedParams }; diff --git a/src/lineup/panel/PanelTab.ts b/src/lineup/panel/PanelTab.ts index 5049cec31..922264456 100644 --- a/src/lineup/panel/PanelTab.ts +++ b/src/lineup/panel/PanelTab.ts @@ -18,7 +18,7 @@ export class PanelTab extends EventHandler { readonly options: IPanelTabDesc = { faIcon: 'fas fa-sliders-h', title: I18nextManager.getInstance().i18n.t('tdp:core.lineup.LineupPanelActions.rankingPanelTabTitle'), - width: '24em', + width: '26em', order: 0, }; diff --git a/src/vis/bar/BarVis.tsx b/src/vis/bar/BarVis.tsx index 5eed63a76..7f1417502 100644 --- a/src/vis/bar/BarVis.tsx +++ b/src/vis/bar/BarVis.tsx @@ -160,7 +160,7 @@ export function BarVis({ return null; } - const innerLayout: Plotly.Layout = { + const innerLayout: Partial = { showlegend: true, legend: { // @ts-ignore @@ -173,7 +173,6 @@ export function BarVis({ autosize: true, grid: { rows: finalTraces.rows, columns: finalTraces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, barmode: config.groupType === EBarGroupingType.STACK ? 'stack' : 'group', dragmode: false, }; diff --git a/src/vis/general/layoutUtils.ts b/src/vis/general/layoutUtils.ts index 70b3dd5cd..3f508369d 100644 --- a/src/vis/general/layoutUtils.ts +++ b/src/vis/general/layoutUtils.ts @@ -20,7 +20,7 @@ export function columnNameWithDescription(col: ColumnInfo) { * @param layout the current layout to be changed. Typed to any because the plotly types complain.p * @returns the changed layout */ -export function beautifyLayout(traces: PlotlyInfo, layout: Plotly.Layout) { +export function beautifyLayout(traces: PlotlyInfo, layout: Partial) { const layoutEdit = layout; layoutEdit.annotations = []; traces.plots.forEach((t, i) => { diff --git a/src/vis/scatter/ScatterVis.tsx b/src/vis/scatter/ScatterVis.tsx index 475f7c9fb..ac824537a 100644 --- a/src/vis/scatter/ScatterVis.tsx +++ b/src/vis/scatter/ScatterVis.tsx @@ -111,7 +111,7 @@ export function ScatterVis({ return null; } - const innerLayout: Plotly.Layout = { + const innerLayout: Partial = { showlegend: true, legend: { // @ts-ignore @@ -128,7 +128,6 @@ export function ScatterVis({ autosize: true, grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, dragmode: config.dragMode, }; diff --git a/src/vis/strip/StripVis.tsx b/src/vis/strip/StripVis.tsx index 91e642cc8..b0de62770 100644 --- a/src/vis/strip/StripVis.tsx +++ b/src/vis/strip/StripVis.tsx @@ -88,7 +88,7 @@ export function StripVis({ return null; } - const innerLayout: Plotly.Layout = { + const innerLayout: Partial = { showlegend: true, legend: { // @ts-ignore @@ -101,7 +101,6 @@ export function StripVis({ autosize: true, grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, dragmode: 'select', }; diff --git a/src/vis/violin/ViolinVis.tsx b/src/vis/violin/ViolinVis.tsx index ae27f0536..2b5dbf982 100644 --- a/src/vis/violin/ViolinVis.tsx +++ b/src/vis/violin/ViolinVis.tsx @@ -92,7 +92,7 @@ export function ViolinVis({ return null; } - const innerLayout: Plotly.Layout = { + const innerLayout: Partial = { showlegend: true, legend: { // @ts-ignore @@ -105,7 +105,6 @@ export function ViolinVis({ autosize: true, grid: { rows: traces.rows, columns: traces.cols, xgap: 0.3, pattern: 'independent' }, shapes: [], - violingap: 0, }; return beautifyLayout(traces, innerLayout); diff --git a/tdp_core/security/manager.py b/tdp_core/security/manager.py index e16e304cf..8e7406a03 100644 --- a/tdp_core/security/manager.py +++ b/tdp_core/security/manager.py @@ -115,7 +115,17 @@ def _delegate_stores_until_not_none(self, store_method_name: str, *args): @property def current_user(self) -> Optional[User]: try: - return self.load_from_request(get_request()) + req = get_request() + # Fetch the existing user from the request if there is any + try: + user = req.state.user + if user: + return user + except (KeyError, AttributeError): + pass + # If there is no user, try to load it from the request and store it in the request + user = req.state.user = self.load_from_request(get_request()) + return user except HTTPException: return None except Exception: @@ -182,7 +192,8 @@ def init_app(self, app: FastAPI): async def refresh_token_middleware(request: Request, call_next): response = await call_next(request) try: - user = self.current_user + # Use the cached user from the request, to only refresh a token if the user was actually requested. This avoids calling load_from_request for every request. + user = request.state.user if user and user.access_token: exp_timestamp = access_token_to_payload(user.access_token)["exp"] target_timestamp = datetime.timestamp( @@ -191,7 +202,7 @@ async def refresh_token_middleware(request: Request, call_next): if target_timestamp > exp_timestamp: access_token, payload = user_to_access_token(user) add_access_token_to_response(response, access_token) - except (RuntimeError, KeyError): + except (RuntimeError, KeyError, AttributeError): # Case where there is not a valid JWT. Just return the original respone pass finally: