Feat import errors#53
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* Feat import errors (#53) * chore: delete AppModal.jsx and rename AppModal2 to AppModal * feat: import Errors install react-toastify * feat: implement react-toastify toast notification on wrong file types * merge 'main' into 'development' * fix: linter errors * chore: update dependencies 2021-06-09 (#65) * fix: linter errors * chore: update babel * chore: update eslint * chore: update css packages - tailwindcss - postcss - autoprefixer - css-loader - mini-css-extract-plugin * chore: update @testing-library/jest-dom@5.13.0 * chore: update nanoid@3.1.23, react-toastify@7.0.4 * chore: update mobx@6.3.2, mobx-react@7.2.0 * chore: vite migration (#66) * chore: migrate from webpack to vitejs * chore: remove unused root index.jsx * fix: favicon is served from root * fix: serve icons from /public * chore: ignore public/ and index.html * fix: remove redundant svg title * feat: manual count unit (#69) * feat: use AppDatalist for count unit selection and add more options fix: expression table readAsText wasn't called correctly * fix: move onloadend out of onload * fix: restore preload functionality (#70) * fix: use the correct icon extension * fix: upload expression table does not read the file * fix: use VITE_ prefix for importing env variables * refactor: sort action handler * fix: remove leftover debug logs * refactor: prettify imports * chore: add *.local files to gitignore * fix: prefix env variables with VITE_ * fix: add mandatory groupOrder and sampleOrder to gxp_settings example * Typescript support (#72) * chore: add typescript + eslint support * fix: format and lint errors * refactor: ported a few components to typescript as an example - AppAnchor - AppButton - AppCheckbox * feat: Cypress testing (#73) * chore: port tests from jest to cypress fix: ensure all tests are passing * fix: missing updated yarn.lock file * chore: add create-cypress-tests helper * chore: support for component testing using vite-dev-server * refactor: separate integration (standard) tests from component (ct) tests * chore: ignore nyc coverage reports * docs: update README with testing commands and example files docs * tests: support path aliases in cypress tests (#74) * fix: update ci workflow to work with the new configuration - use yarn instead of npm (might require install?) - use the new build command * hotfix: when preloading, if no settings (or no group and sample order) are provided, use the default table colum order * chore: use plotly from npm (#75) * chore: use latest plotly from npm * fix: remove unused autosize and responsive plotly layout options * chore: eslint ignore index.html * fix: remaining linter warnings in config files * Chakra UI (#77) * chore: add chakra-ui and load the provider * chore: add react-icons package * refactor: port App to TypeScript - fix the dataframe loadFromObject config arg type to match the rows data structure - port fetch and parser utils to TypeScript - convert App to a function component * feat: new application layout - sidebar navigation has been replaced by a topbar (alternative sidebar also provided) - only top level routes are displayed in the topbar - delegate access to children subroutes and functionality * refactor: extract nav and link components from app-layout into their own components folders * feat: add prop to render accent conditionally * refactor: sidebar-nav styles - move the open transition to the stack - provide default styles but allow overriding props - add JSDoc to link props interface * feat: add the data-layout sidebar component * feat: add navigation cards to the data home page * fix: missing hover styles in nav-card * refactor: remove unused onMouse events * fix: icon is not a native anchor prop * fix: first-child is unsafe server-side error * feat: support partial path matching when setting the active link color * feat: support overriding FlexProps in topbar * feat: do not uppercase sidebar links * feat: add background color to the topbar * fix: data layout background color overrides app layout styles * feat: remove links prop from sidebar-nav - all children are loaded manually * feat: make sidebar-link accessible to kb navigation - add tabIndex prop - remove superfluous flex child * feat: add sidebar-file and -button to nav-sidebar * feat: remove unused data-layout * feat: make topbar-link accessible to kb navigation * feat: use list components for topbar-nav * feat: support kb navigation in nav-card * fix: nav-card content not growing in width * fix: focused sidebar items should expand the content * feat: matching hover and focus styles in sidebar -button and -file * feat: matching hover and focus styles in topbar-link * fix: sidebar-file should activate on kb input * chore: add type-fest package * refactor: rename data-page to data-home * feat: add data-files page - sidebar menu actions (no functionality yet) - formik integration with the upload gene expression table menu and form * feat: support kb navigation in sidebar-file * chore: disable tailwind and plotly css files * fix: consistent label styles in formik-file * feat: support isRequired indicator and aria props in formik inputs * feat: required separator and file fields in xtable-form * fix: do not attempt to show hint in formik-file (readonly) field * feat: integrate xtable submit with the stores * fix: add missing string util module * feat: add replicate cards to data-files page * fix: dataframe removeColumn should search for the literal column name * chore: remove unused DataLayout component and string utility module * chore: remove unused GroupCard component * feat: add bulkRemove fuctionality to data-files page * feat: add formik-modal component * feat: port info-form to chakra-ui * feat: add 'load gene info table' menu functionality to the data-files page * refactor: rename initialRef->initialFocusRef * feat: add db-form component * fix: duplicate input ids in formik-file * fix: import-gxp-database menu triggering is an input * feat: add import gxp database functionality * fix: use a unique name in the export-form * fix: escape the column delimiter before showing it on the form field * refactor: moved new data modules to a the pages folder * refactor: consistent names for data pages * refactor: consistent app-routes name * feat: improve data-files accessibility - move sidebar animation to sidebar-nav component - structure sidebar-nav as region->section-buttons - sidebar-button mouse click is only triggered by main mouse button - add aria-label to repl-card component - add tabIndex and focus visual cues to repl-card * fix: sidebar-nav hover area should be the full sidebar * feat: more props in sidebar-button - add textGap to control the text-to-icon spacing - inherit from FlexProps and pass props to the container * feat: tentative plots-home page and layout * fix: sidebar-nav actions should be sticky * feat: more accessible repl-card - add hover styles - remove tabIndex from non-interactive card - add aria-label to checkbox and button * refactor: slightly optimize for speed the bulk delete implementation * fix: center text icons in plots-home sidebar * feat: optional visually hidden label in formik fields * refactor: inherit ModalProps in formik-modal * chore: remove tailwindcss code and dependencies * feat: bars form and formik arrray (#78) * feat: support left-,right- input addons and elements in formik-field * feat: add groupProps API to formik-field * feat: add bars plot form * feat: expose form-control props in formik-field * feat: add formik-field component * feat: add legend and caption switches to bars-form refactor: improve bars-form semantic html * feat: improve bars-form modal styles - increase modal size to xl - move scrollbar to window * fix: remove legend and caption switch validation (dev leftover) * refactor: rename menu to Bars Plot (plural) for consistency * hotfix: replicate cards wrap does not retain full-width when only two or less cards exist * refactor: plot store (#79) * wip: plot store refactor * add missing plot-store types * refactor: Plot components (#80) * wip: plot-components * wip: plot-components * feat: add plot data utility functions * re-add plot-store functionality to compute plotly plot data * refactor: re-add functionality to the side-bar - add forms for plottypes - update generic PlotlyPlot component * refactor: port PlotCaption and GeneCard to typescript and chakra * chore: remove unused Plot component * chore: cleanup typescript warnings / logs * fix: legend name for singleGene bar/ind Lines * refactor: Individual lines navigation label name * feat: heatmap plot (#81) * feat: heatmap utility module - refactor functions to have a single responsibility - add a valuesToBins function to transform clustering results into visx consumable data - add and type the ml-distance package * chore: add documented regions to heatmap module * feat: add heatmap-plot component * feat: add heatmap plot store functionality * feat: add heatmap plot menus and form to plots-home * fix: add missing key to the loading spinner in plots-home * feat: support for resizing heatmap plots * fix: only one 'main' per page * fix: remove percentage-based resize limits * feat: show a loading indicator during internal plot computation * refactor: extract heatmap-plot container into a separate component * fix: hacking workaround to give time for observers to react to plot `isLoading` before blocking the UI * fix: non-matching bracket * feat: improvements to the heatmap-plot component - add custom interfaces for heatmap-plot bins - add bottom labels to the plot - increase container height * feat: add a `toBins` method to the dataframe class * fix: loadGxpSettings accepts a partial object * chore: use modular visx dependencies * feat: support selecting replicate subsets in heatmap visualizations * fix: in the heatmap, treat an empty replicates subset as if it were undefined * chore: minor code cleanup * chore: support path alias autocompletion in IDEs that read `tsconfig.json`. * refactor: use plot-container for plotly plots (#82) * feat: use plot-container for plotly plots refactor: plot-container to display plot-title as h1 fix: warning to cleanup ref in resizePlot useEffect * refactor: add flex direction column to PlotlyPlot * fix: heatmap padding not a property value in firefox * fix: prevent using stale reference for figureRef * fix: observe internalRef * fix: modebar styles * refactor: remove html title fix: re-add height 900 * fix: add overflow to Plot captions * refactor: reduce tick line height * refactor: reduce plot-container height * refactor: port dataframe and remaining utilities to typescript (#83) * refactor: port the dataframe class and all related utility modules to typescript * refactor: sort alphabetically * refactor: port data-store to typescript * refactor: rename internal arr2d variable to arrayOfColumns * Readd pca (#84) * feat: add PCA plot type * fix: PlotlyPlot adjust to full size of parent * refactor: add flexShrink to PlotlyPlot captions * fix: pca rename dataframe functions from develop merge * fix: setToColor utility. Object.fromEntries takes zipped Array * Gene browser tool (#85) * feat: tools routes and home page * feat: add formik-number input * feat: add gene-browser page, form, and card * chore: remove old unused gene-browser components * fix: consistent geneInfo structure in deprecated gene-card component * refactor: name useEffect function * feat: add gene-details table and modal * feat: add a spinner during page data loading * refactor: remove leftover demo caption * feat: Enter key in focused card opens the details table modal * feat: adjust modal size in larger screens * feat: increase table header font * chore: update legacy PlotCaption gene-card module path * feat: rename search accession -> search in accessions for clarity * feat: hack to show the loading spinner in heavy search computations * refactor: type the modalSize computed prop * Heatmap title tooltip (#86) * feat: add heatmap plot Title * feat: add tooltips to heatmap * chore: add comment to separate tooltip logic * fix: remove titleHeight from yScale. Add top offset instead * fix: remove additional title height from core plot bounds refactor: move all plotDims variables inside the useEffect computation refactor: tweak styles for the tooltip * refactor: rename clientWidth->plotBounds (clarity) Co-authored-by: David Velasco <davvelsan@gmail.com> * feat: add left axis to heatmap (#87) * feat: add left axis to heatmap (#87) * feat: accession autocomplete (#88) * feat: add left axis to heatmap (#87) * feat: add useMatchAccession hook * feat: add formik-accession input component * feat: add autocomplete formik-accession to bars and lines plots * feat: heatmap dendro (#89) * feat: createHeatmapPlot also returns a cluster tree * fix: correct heatmap plot props * wip: heatmap + dendrogram * feat: sort the clustered heatmap matrix - add a function to get leave names from a cluster object - add a function to sort a distance matrix to match the clustering results - createHeatmapPlot now returns the clustered matrix * fix: use standard tickLabelSize * fix: use correct row names * chore: remove unused imports * fix: tooltip placement did not account for the dendrogram plot offset * fix: sort the matrix rows to match the clustered tree * feat: invert the heatmap colors to match a distance value Co-authored-by: coeit <cbeiteneuer@gmail.com> * chore: remove leftover debug logs * feat: plots sidebar layout, icons, and delete functionality (#90) * feat: fixed plots sidebar with real icons * feat: add delete plots button * feat: rename menus to eliminate superfluous information * feat: Info routes (#92) * feat: add a new link-card component * feat: add info module route and page * fix: typo * feat: app layout and flow tweaks (#91) * feat: change the default data route to data-files * feat: disable plot actions when no meaningful action can be taken * feat: add warning alert to plots-home when no data has been loaded * fix: add missing disabled property to sidebar-button * fix: plots sidebar should not be on top of the plots form modal overlay * feat: disable remove data menu if no data is loaded * fix: remove plots should function if there are plots, even if there is no data * refactor: rename variables for clarity * fix: disabled buttons prevent sidebar collapse * fix: prevent toolbar-link text selection * feat: remove empty app home page and add a redirect to /data * feat: add an empty app-home page that for now redirects to /data * feat: warn the user if no data is loaded when in gene-browser tool * feat: plot actions (#93) * wip: download util * refactor: port download util to ts * feat: add default config to PlotlyPlot for downloading as svg * refactor: rename download util to svg util * feat: wip: add rudimentary downaload button to heatmap plot * feat: - rename plot key prop to id. - restore delete for PlotlyPlot * feat: add standard plot config to pca plot * fix: add missing key - id change * feat: add plot-container actions - download plot - delete plot * feat: only show plot actions in visx plots - workaround until the modebar is removed * feat: delete Plot for heatmap * fix: add missing id prop * fix: add missing id prop Co-authored-by: David Velasco <davvelsan@gmail.com> * feat: accession validation (#94) * feat: verify that the accession exists before submitting a plot * feat: do not validate accession inputs onBlur * hotfix: ensure form delimiters are correctly unescaped * chore: pre-deploy cleanup (#95) - remove old components - standard snake-case file names * chore: merge main into develop * chore: remove legacy layout components * chore: remove legacy modules * chore: remove unused icons Co-authored-by: coeit <36563701+coeit@users.noreply.github.com> Co-authored-by: coeit <cbeiteneuer@gmail.com>
davelsio
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Jul 7, 2021
* Feat import errors (#53) * chore: delete AppModal.jsx and rename AppModal2 to AppModal * feat: import Errors install react-toastify * feat: implement react-toastify toast notification on wrong file types * merge 'main' into 'development' * fix: linter errors * chore: update dependencies 2021-06-09 (#65) * fix: linter errors * chore: update babel * chore: update eslint * chore: update css packages - tailwindcss - postcss - autoprefixer - css-loader - mini-css-extract-plugin * chore: update @testing-library/jest-dom@5.13.0 * chore: update nanoid@3.1.23, react-toastify@7.0.4 * chore: update mobx@6.3.2, mobx-react@7.2.0 * chore: vite migration (#66) * chore: migrate from webpack to vitejs * chore: remove unused root index.jsx * fix: favicon is served from root * fix: serve icons from /public * chore: ignore public/ and index.html * fix: remove redundant svg title * feat: manual count unit (#69) * feat: use AppDatalist for count unit selection and add more options fix: expression table readAsText wasn't called correctly * fix: move onloadend out of onload * fix: restore preload functionality (#70) * fix: use the correct icon extension * fix: upload expression table does not read the file * fix: use VITE_ prefix for importing env variables * refactor: sort action handler * fix: remove leftover debug logs * refactor: prettify imports * chore: add *.local files to gitignore * fix: prefix env variables with VITE_ * fix: add mandatory groupOrder and sampleOrder to gxp_settings example * Typescript support (#72) * chore: add typescript + eslint support * fix: format and lint errors * refactor: ported a few components to typescript as an example - AppAnchor - AppButton - AppCheckbox * feat: Cypress testing (#73) * chore: port tests from jest to cypress fix: ensure all tests are passing * fix: missing updated yarn.lock file * chore: add create-cypress-tests helper * chore: support for component testing using vite-dev-server * refactor: separate integration (standard) tests from component (ct) tests * chore: ignore nyc coverage reports * docs: update README with testing commands and example files docs * tests: support path aliases in cypress tests (#74) * fix: update ci workflow to work with the new configuration - use yarn instead of npm (might require install?) - use the new build command * hotfix: when preloading, if no settings (or no group and sample order) are provided, use the default table colum order * chore: use plotly from npm (#75) * chore: use latest plotly from npm * fix: remove unused autosize and responsive plotly layout options * chore: eslint ignore index.html * fix: remaining linter warnings in config files * Chakra UI (#77) * chore: add chakra-ui and load the provider * chore: add react-icons package * refactor: port App to TypeScript - fix the dataframe loadFromObject config arg type to match the rows data structure - port fetch and parser utils to TypeScript - convert App to a function component * feat: new application layout - sidebar navigation has been replaced by a topbar (alternative sidebar also provided) - only top level routes are displayed in the topbar - delegate access to children subroutes and functionality * refactor: extract nav and link components from app-layout into their own components folders * feat: add prop to render accent conditionally * refactor: sidebar-nav styles - move the open transition to the stack - provide default styles but allow overriding props - add JSDoc to link props interface * feat: add the data-layout sidebar component * feat: add navigation cards to the data home page * fix: missing hover styles in nav-card * refactor: remove unused onMouse events * fix: icon is not a native anchor prop * fix: first-child is unsafe server-side error * feat: support partial path matching when setting the active link color * feat: support overriding FlexProps in topbar * feat: do not uppercase sidebar links * feat: add background color to the topbar * fix: data layout background color overrides app layout styles * feat: remove links prop from sidebar-nav - all children are loaded manually * feat: make sidebar-link accessible to kb navigation - add tabIndex prop - remove superfluous flex child * feat: add sidebar-file and -button to nav-sidebar * feat: remove unused data-layout * feat: make topbar-link accessible to kb navigation * feat: use list components for topbar-nav * feat: support kb navigation in nav-card * fix: nav-card content not growing in width * fix: focused sidebar items should expand the content * feat: matching hover and focus styles in sidebar -button and -file * feat: matching hover and focus styles in topbar-link * fix: sidebar-file should activate on kb input * chore: add type-fest package * refactor: rename data-page to data-home * feat: add data-files page - sidebar menu actions (no functionality yet) - formik integration with the upload gene expression table menu and form * feat: support kb navigation in sidebar-file * chore: disable tailwind and plotly css files * fix: consistent label styles in formik-file * feat: support isRequired indicator and aria props in formik inputs * feat: required separator and file fields in xtable-form * fix: do not attempt to show hint in formik-file (readonly) field * feat: integrate xtable submit with the stores * fix: add missing string util module * feat: add replicate cards to data-files page * fix: dataframe removeColumn should search for the literal column name * chore: remove unused DataLayout component and string utility module * chore: remove unused GroupCard component * feat: add bulkRemove fuctionality to data-files page * feat: add formik-modal component * feat: port info-form to chakra-ui * feat: add 'load gene info table' menu functionality to the data-files page * refactor: rename initialRef->initialFocusRef * feat: add db-form component * fix: duplicate input ids in formik-file * fix: import-gxp-database menu triggering is an input * feat: add import gxp database functionality * fix: use a unique name in the export-form * fix: escape the column delimiter before showing it on the form field * refactor: moved new data modules to a the pages folder * refactor: consistent names for data pages * refactor: consistent app-routes name * feat: improve data-files accessibility - move sidebar animation to sidebar-nav component - structure sidebar-nav as region->section-buttons - sidebar-button mouse click is only triggered by main mouse button - add aria-label to repl-card component - add tabIndex and focus visual cues to repl-card * fix: sidebar-nav hover area should be the full sidebar * feat: more props in sidebar-button - add textGap to control the text-to-icon spacing - inherit from FlexProps and pass props to the container * feat: tentative plots-home page and layout * fix: sidebar-nav actions should be sticky * feat: more accessible repl-card - add hover styles - remove tabIndex from non-interactive card - add aria-label to checkbox and button * refactor: slightly optimize for speed the bulk delete implementation * fix: center text icons in plots-home sidebar * feat: optional visually hidden label in formik fields * refactor: inherit ModalProps in formik-modal * chore: remove tailwindcss code and dependencies * feat: bars form and formik arrray (#78) * feat: support left-,right- input addons and elements in formik-field * feat: add groupProps API to formik-field * feat: add bars plot form * feat: expose form-control props in formik-field * feat: add formik-field component * feat: add legend and caption switches to bars-form refactor: improve bars-form semantic html * feat: improve bars-form modal styles - increase modal size to xl - move scrollbar to window * fix: remove legend and caption switch validation (dev leftover) * refactor: rename menu to Bars Plot (plural) for consistency * hotfix: replicate cards wrap does not retain full-width when only two or less cards exist * refactor: plot store (#79) * wip: plot store refactor * add missing plot-store types * refactor: Plot components (#80) * wip: plot-components * wip: plot-components * feat: add plot data utility functions * re-add plot-store functionality to compute plotly plot data * refactor: re-add functionality to the side-bar - add forms for plottypes - update generic PlotlyPlot component * refactor: port PlotCaption and GeneCard to typescript and chakra * chore: remove unused Plot component * chore: cleanup typescript warnings / logs * fix: legend name for singleGene bar/ind Lines * refactor: Individual lines navigation label name * feat: heatmap plot (#81) * feat: heatmap utility module - refactor functions to have a single responsibility - add a valuesToBins function to transform clustering results into visx consumable data - add and type the ml-distance package * chore: add documented regions to heatmap module * feat: add heatmap-plot component * feat: add heatmap plot store functionality * feat: add heatmap plot menus and form to plots-home * fix: add missing key to the loading spinner in plots-home * feat: support for resizing heatmap plots * fix: only one 'main' per page * fix: remove percentage-based resize limits * feat: show a loading indicator during internal plot computation * refactor: extract heatmap-plot container into a separate component * fix: hacking workaround to give time for observers to react to plot `isLoading` before blocking the UI * fix: non-matching bracket * feat: improvements to the heatmap-plot component - add custom interfaces for heatmap-plot bins - add bottom labels to the plot - increase container height * feat: add a `toBins` method to the dataframe class * fix: loadGxpSettings accepts a partial object * chore: use modular visx dependencies * feat: support selecting replicate subsets in heatmap visualizations * fix: in the heatmap, treat an empty replicates subset as if it were undefined * chore: minor code cleanup * chore: support path alias autocompletion in IDEs that read `tsconfig.json`. * refactor: use plot-container for plotly plots (#82) * feat: use plot-container for plotly plots refactor: plot-container to display plot-title as h1 fix: warning to cleanup ref in resizePlot useEffect * refactor: add flex direction column to PlotlyPlot * fix: heatmap padding not a property value in firefox * fix: prevent using stale reference for figureRef * fix: observe internalRef * fix: modebar styles * refactor: remove html title fix: re-add height 900 * fix: add overflow to Plot captions * refactor: reduce tick line height * refactor: reduce plot-container height * refactor: port dataframe and remaining utilities to typescript (#83) * refactor: port the dataframe class and all related utility modules to typescript * refactor: sort alphabetically * refactor: port data-store to typescript * refactor: rename internal arr2d variable to arrayOfColumns * Readd pca (#84) * feat: add PCA plot type * fix: PlotlyPlot adjust to full size of parent * refactor: add flexShrink to PlotlyPlot captions * fix: pca rename dataframe functions from develop merge * fix: setToColor utility. Object.fromEntries takes zipped Array * Gene browser tool (#85) * feat: tools routes and home page * feat: add formik-number input * feat: add gene-browser page, form, and card * chore: remove old unused gene-browser components * fix: consistent geneInfo structure in deprecated gene-card component * refactor: name useEffect function * feat: add gene-details table and modal * feat: add a spinner during page data loading * refactor: remove leftover demo caption * feat: Enter key in focused card opens the details table modal * feat: adjust modal size in larger screens * feat: increase table header font * chore: update legacy PlotCaption gene-card module path * feat: rename search accession -> search in accessions for clarity * feat: hack to show the loading spinner in heavy search computations * refactor: type the modalSize computed prop * Heatmap title tooltip (#86) * feat: add heatmap plot Title * feat: add tooltips to heatmap * chore: add comment to separate tooltip logic * fix: remove titleHeight from yScale. Add top offset instead * fix: remove additional title height from core plot bounds refactor: move all plotDims variables inside the useEffect computation refactor: tweak styles for the tooltip * refactor: rename clientWidth->plotBounds (clarity) Co-authored-by: David Velasco <davvelsan@gmail.com> * feat: add left axis to heatmap (#87) * feat: add left axis to heatmap (#87) * feat: accession autocomplete (#88) * feat: add left axis to heatmap (#87) * feat: add useMatchAccession hook * feat: add formik-accession input component * feat: add autocomplete formik-accession to bars and lines plots * feat: heatmap dendro (#89) * feat: createHeatmapPlot also returns a cluster tree * fix: correct heatmap plot props * wip: heatmap + dendrogram * feat: sort the clustered heatmap matrix - add a function to get leave names from a cluster object - add a function to sort a distance matrix to match the clustering results - createHeatmapPlot now returns the clustered matrix * fix: use standard tickLabelSize * fix: use correct row names * chore: remove unused imports * fix: tooltip placement did not account for the dendrogram plot offset * fix: sort the matrix rows to match the clustered tree * feat: invert the heatmap colors to match a distance value Co-authored-by: coeit <cbeiteneuer@gmail.com> * chore: remove leftover debug logs * feat: plots sidebar layout, icons, and delete functionality (#90) * feat: fixed plots sidebar with real icons * feat: add delete plots button * feat: rename menus to eliminate superfluous information * feat: Info routes (#92) * feat: add a new link-card component * feat: add info module route and page * fix: typo * feat: app layout and flow tweaks (#91) * feat: change the default data route to data-files * feat: disable plot actions when no meaningful action can be taken * feat: add warning alert to plots-home when no data has been loaded * fix: add missing disabled property to sidebar-button * fix: plots sidebar should not be on top of the plots form modal overlay * feat: disable remove data menu if no data is loaded * fix: remove plots should function if there are plots, even if there is no data * refactor: rename variables for clarity * fix: disabled buttons prevent sidebar collapse * fix: prevent toolbar-link text selection * feat: remove empty app home page and add a redirect to /data * feat: add an empty app-home page that for now redirects to /data * feat: warn the user if no data is loaded when in gene-browser tool * feat: plot actions (#93) * wip: download util * refactor: port download util to ts * feat: add default config to PlotlyPlot for downloading as svg * refactor: rename download util to svg util * feat: wip: add rudimentary downaload button to heatmap plot * feat: - rename plot key prop to id. - restore delete for PlotlyPlot * feat: add standard plot config to pca plot * fix: add missing key - id change * feat: add plot-container actions - download plot - delete plot * feat: only show plot actions in visx plots - workaround until the modebar is removed * feat: delete Plot for heatmap * fix: add missing id prop * fix: add missing id prop Co-authored-by: David Velasco <davvelsan@gmail.com> * feat: accession validation (#94) * feat: verify that the accession exists before submitting a plot * feat: do not validate accession inputs onBlur * hotfix: ensure form delimiters are correctly unescaped * chore: pre-deploy cleanup (#95) - remove old components - standard snake-case file names * chore: merge main into develop * chore: remove legacy layout components * chore: remove legacy modules * chore: remove unused icons * fix: missing validateOnBlur for data forms (#98) * feat: color by for stacked lines form (#99) * wip: feat colorBy, formik radio component * feat: generic form-radio component * feat: stacked-lines use form-radio for colorBy * chore: remove debug logs * feat: add optional direction prop * refactor: RadioOptions extend RadioProps * feat: remove all modebar buttons but download and delete (#101) * feat: preload tweaks (#100) * feat: hide data manipulation menus when preloaded * fix: remove env var for not-implemented plot preloading * feat: disable repl-card delete and select buttons if preloaded * feat: remove resizer styles until a cross-browser solution is implemented * feat: add a new image plot type to the plots store * feat: display images in the plots page - new image-plot component to display images - new image-form component to load new images * fix: image alt should be required * fix: no need (probably) to async the addImagePlot action * fix: add a repl-card tabIndex if preloading (no button interactions) * feat: use plot-container for the image-plot - enable delete button - standardize plot styles * feat: delete image plot - reuse delete plot action - revoke url if plot type is image * fix: import the gxp database image as blob * fix: backwards compatibility with single-image databases - export the first image-plot within the generated zip * fix: preloaded should check for data property when disabling repl-card functionality * fix: missing delete replicate button * fix: tests failing (#102) * chore: remove AppAnchor test. AppAnchor no longer exists * chore: add chai-exclude package * fix: cypress tsconfig compiler options to use es2019 * fix: enrichment analyses test * fix: heatmap tests * chore: remove unused commented code * chore: delete deprecated tests folder * fix: test name * feat: app state (#103) * fix: fetchResource should not return undefined, but throw instead * refactor: app-layout inherits props from FlexProps * feat: add application state - when preloading, show a loading indicator and message - if preloading failed, override routes with an error message Co-authored-by: coeit <36563701+coeit@users.noreply.github.com> Co-authored-by: coeit <cbeiteneuer@gmail.com>
coeit
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this pull request
Aug 20, 2021
* Feat import errors (#53) * chore: delete AppModal.jsx and rename AppModal2 to AppModal * feat: import Errors install react-toastify * feat: implement react-toastify toast notification on wrong file types * merge 'main' into 'development' * fix: linter errors * chore: update dependencies 2021-06-09 (#65) * fix: linter errors * chore: update babel * chore: update eslint * chore: update css packages - tailwindcss - postcss - autoprefixer - css-loader - mini-css-extract-plugin * chore: update @testing-library/jest-dom@5.13.0 * chore: update nanoid@3.1.23, react-toastify@7.0.4 * chore: update mobx@6.3.2, mobx-react@7.2.0 * chore: vite migration (#66) * chore: migrate from webpack to vitejs * chore: remove unused root index.jsx * fix: favicon is served from root * fix: serve icons from /public * chore: ignore public/ and index.html * fix: remove redundant svg title * feat: manual count unit (#69) * feat: use AppDatalist for count unit selection and add more options fix: expression table readAsText wasn't called correctly * fix: move onloadend out of onload * fix: restore preload functionality (#70) * fix: use the correct icon extension * fix: upload expression table does not read the file * fix: use VITE_ prefix for importing env variables * refactor: sort action handler * fix: remove leftover debug logs * refactor: prettify imports * chore: add *.local files to gitignore * fix: prefix env variables with VITE_ * fix: add mandatory groupOrder and sampleOrder to gxp_settings example * Typescript support (#72) * chore: add typescript + eslint support * fix: format and lint errors * refactor: ported a few components to typescript as an example - AppAnchor - AppButton - AppCheckbox * feat: Cypress testing (#73) * chore: port tests from jest to cypress fix: ensure all tests are passing * fix: missing updated yarn.lock file * chore: add create-cypress-tests helper * chore: support for component testing using vite-dev-server * refactor: separate integration (standard) tests from component (ct) tests * chore: ignore nyc coverage reports * docs: update README with testing commands and example files docs * tests: support path aliases in cypress tests (#74) * fix: update ci workflow to work with the new configuration - use yarn instead of npm (might require install?) - use the new build command * hotfix: when preloading, if no settings (or no group and sample order) are provided, use the default table colum order * chore: use plotly from npm (#75) * chore: use latest plotly from npm * fix: remove unused autosize and responsive plotly layout options * chore: eslint ignore index.html * fix: remaining linter warnings in config files * Chakra UI (#77) * chore: add chakra-ui and load the provider * chore: add react-icons package * refactor: port App to TypeScript - fix the dataframe loadFromObject config arg type to match the rows data structure - port fetch and parser utils to TypeScript - convert App to a function component * feat: new application layout - sidebar navigation has been replaced by a topbar (alternative sidebar also provided) - only top level routes are displayed in the topbar - delegate access to children subroutes and functionality * refactor: extract nav and link components from app-layout into their own components folders * feat: add prop to render accent conditionally * refactor: sidebar-nav styles - move the open transition to the stack - provide default styles but allow overriding props - add JSDoc to link props interface * feat: add the data-layout sidebar component * feat: add navigation cards to the data home page * fix: missing hover styles in nav-card * refactor: remove unused onMouse events * fix: icon is not a native anchor prop * fix: first-child is unsafe server-side error * feat: support partial path matching when setting the active link color * feat: support overriding FlexProps in topbar * feat: do not uppercase sidebar links * feat: add background color to the topbar * fix: data layout background color overrides app layout styles * feat: remove links prop from sidebar-nav - all children are loaded manually * feat: make sidebar-link accessible to kb navigation - add tabIndex prop - remove superfluous flex child * feat: add sidebar-file and -button to nav-sidebar * feat: remove unused data-layout * feat: make topbar-link accessible to kb navigation * feat: use list components for topbar-nav * feat: support kb navigation in nav-card * fix: nav-card content not growing in width * fix: focused sidebar items should expand the content * feat: matching hover and focus styles in sidebar -button and -file * feat: matching hover and focus styles in topbar-link * fix: sidebar-file should activate on kb input * chore: add type-fest package * refactor: rename data-page to data-home * feat: add data-files page - sidebar menu actions (no functionality yet) - formik integration with the upload gene expression table menu and form * feat: support kb navigation in sidebar-file * chore: disable tailwind and plotly css files * fix: consistent label styles in formik-file * feat: support isRequired indicator and aria props in formik inputs * feat: required separator and file fields in xtable-form * fix: do not attempt to show hint in formik-file (readonly) field * feat: integrate xtable submit with the stores * fix: add missing string util module * feat: add replicate cards to data-files page * fix: dataframe removeColumn should search for the literal column name * chore: remove unused DataLayout component and string utility module * chore: remove unused GroupCard component * feat: add bulkRemove fuctionality to data-files page * feat: add formik-modal component * feat: port info-form to chakra-ui * feat: add 'load gene info table' menu functionality to the data-files page * refactor: rename initialRef->initialFocusRef * feat: add db-form component * fix: duplicate input ids in formik-file * fix: import-gxp-database menu triggering is an input * feat: add import gxp database functionality * fix: use a unique name in the export-form * fix: escape the column delimiter before showing it on the form field * refactor: moved new data modules to a the pages folder * refactor: consistent names for data pages * refactor: consistent app-routes name * feat: improve data-files accessibility - move sidebar animation to sidebar-nav component - structure sidebar-nav as region->section-buttons - sidebar-button mouse click is only triggered by main mouse button - add aria-label to repl-card component - add tabIndex and focus visual cues to repl-card * fix: sidebar-nav hover area should be the full sidebar * feat: more props in sidebar-button - add textGap to control the text-to-icon spacing - inherit from FlexProps and pass props to the container * feat: tentative plots-home page and layout * fix: sidebar-nav actions should be sticky * feat: more accessible repl-card - add hover styles - remove tabIndex from non-interactive card - add aria-label to checkbox and button * refactor: slightly optimize for speed the bulk delete implementation * fix: center text icons in plots-home sidebar * feat: optional visually hidden label in formik fields * refactor: inherit ModalProps in formik-modal * chore: remove tailwindcss code and dependencies * feat: bars form and formik arrray (#78) * feat: support left-,right- input addons and elements in formik-field * feat: add groupProps API to formik-field * feat: add bars plot form * feat: expose form-control props in formik-field * feat: add formik-field component * feat: add legend and caption switches to bars-form refactor: improve bars-form semantic html * feat: improve bars-form modal styles - increase modal size to xl - move scrollbar to window * fix: remove legend and caption switch validation (dev leftover) * refactor: rename menu to Bars Plot (plural) for consistency * hotfix: replicate cards wrap does not retain full-width when only two or less cards exist * refactor: plot store (#79) * wip: plot store refactor * add missing plot-store types * refactor: Plot components (#80) * wip: plot-components * wip: plot-components * feat: add plot data utility functions * re-add plot-store functionality to compute plotly plot data * refactor: re-add functionality to the side-bar - add forms for plottypes - update generic PlotlyPlot component * refactor: port PlotCaption and GeneCard to typescript and chakra * chore: remove unused Plot component * chore: cleanup typescript warnings / logs * fix: legend name for singleGene bar/ind Lines * refactor: Individual lines navigation label name * feat: heatmap plot (#81) * feat: heatmap utility module - refactor functions to have a single responsibility - add a valuesToBins function to transform clustering results into visx consumable data - add and type the ml-distance package * chore: add documented regions to heatmap module * feat: add heatmap-plot component * feat: add heatmap plot store functionality * feat: add heatmap plot menus and form to plots-home * fix: add missing key to the loading spinner in plots-home * feat: support for resizing heatmap plots * fix: only one 'main' per page * fix: remove percentage-based resize limits * feat: show a loading indicator during internal plot computation * refactor: extract heatmap-plot container into a separate component * fix: hacking workaround to give time for observers to react to plot `isLoading` before blocking the UI * fix: non-matching bracket * feat: improvements to the heatmap-plot component - add custom interfaces for heatmap-plot bins - add bottom labels to the plot - increase container height * feat: add a `toBins` method to the dataframe class * fix: loadGxpSettings accepts a partial object * chore: use modular visx dependencies * feat: support selecting replicate subsets in heatmap visualizations * fix: in the heatmap, treat an empty replicates subset as if it were undefined * chore: minor code cleanup * chore: support path alias autocompletion in IDEs that read `tsconfig.json`. * refactor: use plot-container for plotly plots (#82) * feat: use plot-container for plotly plots refactor: plot-container to display plot-title as h1 fix: warning to cleanup ref in resizePlot useEffect * refactor: add flex direction column to PlotlyPlot * fix: heatmap padding not a property value in firefox * fix: prevent using stale reference for figureRef * fix: observe internalRef * fix: modebar styles * refactor: remove html title fix: re-add height 900 * fix: add overflow to Plot captions * refactor: reduce tick line height * refactor: reduce plot-container height * refactor: port dataframe and remaining utilities to typescript (#83) * refactor: port the dataframe class and all related utility modules to typescript * refactor: sort alphabetically * refactor: port data-store to typescript * refactor: rename internal arr2d variable to arrayOfColumns * Readd pca (#84) * feat: add PCA plot type * fix: PlotlyPlot adjust to full size of parent * refactor: add flexShrink to PlotlyPlot captions * fix: pca rename dataframe functions from develop merge * fix: setToColor utility. Object.fromEntries takes zipped Array * Gene browser tool (#85) * feat: tools routes and home page * feat: add formik-number input * feat: add gene-browser page, form, and card * chore: remove old unused gene-browser components * fix: consistent geneInfo structure in deprecated gene-card component * refactor: name useEffect function * feat: add gene-details table and modal * feat: add a spinner during page data loading * refactor: remove leftover demo caption * feat: Enter key in focused card opens the details table modal * feat: adjust modal size in larger screens * feat: increase table header font * chore: update legacy PlotCaption gene-card module path * feat: rename search accession -> search in accessions for clarity * feat: hack to show the loading spinner in heavy search computations * refactor: type the modalSize computed prop * Heatmap title tooltip (#86) * feat: add heatmap plot Title * feat: add tooltips to heatmap * chore: add comment to separate tooltip logic * fix: remove titleHeight from yScale. Add top offset instead * fix: remove additional title height from core plot bounds refactor: move all plotDims variables inside the useEffect computation refactor: tweak styles for the tooltip * refactor: rename clientWidth->plotBounds (clarity) Co-authored-by: David Velasco <davvelsan@gmail.com> * feat: add left axis to heatmap (#87) * feat: add left axis to heatmap (#87) * feat: accession autocomplete (#88) * feat: add left axis to heatmap (#87) * feat: add useMatchAccession hook * feat: add formik-accession input component * feat: add autocomplete formik-accession to bars and lines plots * feat: heatmap dendro (#89) * feat: createHeatmapPlot also returns a cluster tree * fix: correct heatmap plot props * wip: heatmap + dendrogram * feat: sort the clustered heatmap matrix - add a function to get leave names from a cluster object - add a function to sort a distance matrix to match the clustering results - createHeatmapPlot now returns the clustered matrix * fix: use standard tickLabelSize * fix: use correct row names * chore: remove unused imports * fix: tooltip placement did not account for the dendrogram plot offset * fix: sort the matrix rows to match the clustered tree * feat: invert the heatmap colors to match a distance value Co-authored-by: coeit <cbeiteneuer@gmail.com> * chore: remove leftover debug logs * feat: plots sidebar layout, icons, and delete functionality (#90) * feat: fixed plots sidebar with real icons * feat: add delete plots button * feat: rename menus to eliminate superfluous information * feat: Info routes (#92) * feat: add a new link-card component * feat: add info module route and page * fix: typo * feat: app layout and flow tweaks (#91) * feat: change the default data route to data-files * feat: disable plot actions when no meaningful action can be taken * feat: add warning alert to plots-home when no data has been loaded * fix: add missing disabled property to sidebar-button * fix: plots sidebar should not be on top of the plots form modal overlay * feat: disable remove data menu if no data is loaded * fix: remove plots should function if there are plots, even if there is no data * refactor: rename variables for clarity * fix: disabled buttons prevent sidebar collapse * fix: prevent toolbar-link text selection * feat: remove empty app home page and add a redirect to /data * feat: add an empty app-home page that for now redirects to /data * feat: warn the user if no data is loaded when in gene-browser tool * feat: plot actions (#93) * wip: download util * refactor: port download util to ts * feat: add default config to PlotlyPlot for downloading as svg * refactor: rename download util to svg util * feat: wip: add rudimentary downaload button to heatmap plot * feat: - rename plot key prop to id. - restore delete for PlotlyPlot * feat: add standard plot config to pca plot * fix: add missing key - id change * feat: add plot-container actions - download plot - delete plot * feat: only show plot actions in visx plots - workaround until the modebar is removed * feat: delete Plot for heatmap * fix: add missing id prop * fix: add missing id prop Co-authored-by: David Velasco <davvelsan@gmail.com> * feat: accession validation (#94) * feat: verify that the accession exists before submitting a plot * feat: do not validate accession inputs onBlur * hotfix: ensure form delimiters are correctly unescaped * chore: pre-deploy cleanup (#95) - remove old components - standard snake-case file names * chore: merge main into develop * chore: remove legacy layout components * chore: remove legacy modules * chore: remove unused icons * fix: missing validateOnBlur for data forms (#98) * feat: color by for stacked lines form (#99) * wip: feat colorBy, formik radio component * feat: generic form-radio component * feat: stacked-lines use form-radio for colorBy * chore: remove debug logs * feat: add optional direction prop * refactor: RadioOptions extend RadioProps * feat: remove all modebar buttons but download and delete (#101) * feat: preload tweaks (#100) * feat: hide data manipulation menus when preloaded * fix: remove env var for not-implemented plot preloading * feat: disable repl-card delete and select buttons if preloaded * feat: remove resizer styles until a cross-browser solution is implemented * feat: add a new image plot type to the plots store * feat: display images in the plots page - new image-plot component to display images - new image-form component to load new images * fix: image alt should be required * fix: no need (probably) to async the addImagePlot action * fix: add a repl-card tabIndex if preloading (no button interactions) * feat: use plot-container for the image-plot - enable delete button - standardize plot styles * feat: delete image plot - reuse delete plot action - revoke url if plot type is image * fix: import the gxp database image as blob * fix: backwards compatibility with single-image databases - export the first image-plot within the generated zip * fix: preloaded should check for data property when disabling repl-card functionality * fix: missing delete replicate button * fix: tests failing (#102) * chore: remove AppAnchor test. AppAnchor no longer exists * chore: add chai-exclude package * fix: cypress tsconfig compiler options to use es2019 * fix: enrichment analyses test * fix: heatmap tests * chore: remove unused commented code * chore: delete deprecated tests folder * fix: test name * feat: app state (#103) * fix: fetchResource should not return undefined, but throw instead * refactor: app-layout inherits props from FlexProps * feat: add application state - when preloading, show a loading indicator and message - if preloading failed, override routes with an error message * fix: heatmap label alignment * feat: webworkers for heatmap and pca (#106) * refactor: move webworker utilites * refactor: heatmap + pca use webworker * feat: heatmap webworker * feat: pca webworker * chore: remove debug logs refactor: separate webworker functions to separate modules * chore: mark unsued functions in dataframe as deprecated * fix: add a minimal size for tickLabel * hotfix: remove debug log * feat: add example data/info table to public folder (#108) feat: add Alert to load example data if no data available refactor: delete all also clears info table * feat: Enrichment analyses (#109) * feat: formik-select component * feat: wip: enrichment analysis tools components * feat: enrichment types * feat: enrichment store * refactor: info_table example * refactor: enrichment analysis helper to typescript * fix: formik select name * chore: remove unused imports / debug logs * feat: add hypergeometric pdf compiled to .wasm from the GSL * chore: remove fisher-exact-test library * chore: eslintignore utils/gsl * feat: workerize and implement enrichment analysis * feat: add info alert to enrichment tool feat: add delete button to analyses feat: add Spinner on load * remove table caption * feat: enrichment import/export * refactor: test_for_enrichment return all values + contingency_table * feat: break extremify matrix if change is 0. * fix: enrichment types * wip: fix: enrichment test. WASM not working * chore: update example data * chore: remove dev comments * refactor: rename DataRow -> DataRows * feat: Heatmap transpose matrix + filter for genes (#110) * refactor: formik-radio optional disable * feat: match-replicate hook * feat: formik replicate component * feat: heatmap add optional gene filter and transpose option * refactor: plot-sidebar rename heatmap -> cluster heatmap * fix: add default empty arry for row-filter * feat: pca transpose matrix + filter genes/replicates (#111) * feat: add generic geColors method * feat: add replicates / accession filter feat: transpose matrix * feat: Export plots (#112) * feat: add optional export enrichment / plots to export form * chore: rename raw_data -> rawData * feat: export/import plots * fix: export enrichment - only create metaSrc when checked * fix: round enrichment pValues to 4 digits Co-authored-by: David Velasco <davvelsan@gmail.com>
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Closes #50
Description
This PR implements a Error snackbar via react-toastify for Data import. For now only wrong file types are thrown, since no validations on the files themselves is implemented yet.