diff --git a/apps/haddock3-download/integration-tests/dupheader.spec.ts b/apps/haddock3-download/integration-tests/dupheader.spec.ts index a4a703a..1c98eaa 100644 --- a/apps/haddock3-download/integration-tests/dupheader.spec.ts +++ b/apps/haddock3-download/integration-tests/dupheader.spec.ts @@ -14,7 +14,7 @@ test.describe('given an uploaded archive with a workflow.cfg file with a duplica molecules = [ 'some.pdb' ] - + [caprieval] [caprieval] @@ -23,30 +23,37 @@ test.describe('given an uploaded archive with a workflow.cfg file with a duplica // Upload workflow archive await page.locator('text="Upload" >> input[type="file"]') .setInputFiles({ name: 'workflow.zip', mimeType: 'application/zip', buffer: archive.toBuffer() }) + }) - // Click text=Text - await page.locator('text=Text').click() - + test('it should show uplaoded file', async ({ page }) => { + // Click Files tab + await page.locator('text=Files').click() + // validate file button is present await page.waitForSelector('button:has-text("some.pdb")') }) test('should have both headers and added index number', async ({ page }) => { + // Click Text tab + await page.locator('text=Text').click() + // debug + // await page.pause() + const highlightedCode = await page.locator('#highlightedcode pre') const lines = await highlightedCode.allTextContents() const content = lines.join('\n') const expected = dedent` - run_dir = 'run1' - molecules = [ - 'some.pdb', - ] - + molecules = [ + 'some.pdb', + ] - [caprieval] + run_dir = 'run1' + + [caprieval] - ['caprieval.2'] + ['caprieval.2'] - ` + ` expect(content).toEqual(expected) }) }) diff --git a/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts b/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts index b195994..59aa63a 100644 --- a/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts +++ b/apps/haddock3-download/integration-tests/syntaxhighlighter.spec.ts @@ -3,13 +3,19 @@ import { test, expect } from '@playwright/test' test('Verify that [object Object] bug does not show up (issue #74)', async ({ page }) => { await page.goto('http://localhost:3000') + // debugger + // await page.pause() + // Load the example await page.locator('text=docking-protein-ligand').click() - // Click 'text' and ensure the files appear - await page.locator('text=Text').click() + // validate that file is used + await page.locator('text=Files').click() await page.waitForSelector('button:has-text("data/target.pdb")') + // change to 'text' tab + await page.locator('text=Text').click() + // verify that the [object Object] text does not show up // see https://github.com/i-VRESSE/workflow-builder/issues/74 const highlightedCode = await page.locator('#highlightedcode pre') diff --git a/apps/haddock3-download/integration-tests/topoaamol.spec.ts b/apps/haddock3-download/integration-tests/topoaamol.spec.ts index 5b2a54c..470aa8e 100644 --- a/apps/haddock3-download/integration-tests/topoaamol.spec.ts +++ b/apps/haddock3-download/integration-tests/topoaamol.spec.ts @@ -5,32 +5,38 @@ import { readFile } from 'fs/promises' test.describe('given 1 molecule and a topoaa node', () => { test.beforeEach(async ({ page }) => { await page.goto('http://localhost:3000') + + // Disable autosave + // await page.locator('text=Autosave').click(); + // Click input[type="text"] await page.locator('input[type="text"]').click() // Fill input[type="text"] await page.locator('input[type="text"]').fill('x') // Upload e2a-hpr_1GGR.pdb const file1 = await readFile('./integration-tests/data/e2a-hpr_1GGR.pdb') + + // Click text=Input MoleculesThe input molecules that will be used for docking. >> button + await page.locator('text=Input MoleculesThe input molecules that will be used for docking. >> button').click() await page.locator('text=1* >> input[type="file"]') .setInputFiles({ name: 'e2a-hpr_1GGR.pdb', mimeType: 'chemical/x-pdb', buffer: file1 }) - // Click text=Save - await page.locator('button:has-text("Save")').click() - // Click text=Cancel - await page.locator('button:has-text("Cancel")').click() - // Click button:has-text("topoaa") + + // add topoaa step to workflow await page.locator('button:has-text("topoaa")').click() + // select topoaa step + await page.locator('button:has-text("1. topoaa")').click() // Click #expander4molecule svg await page.locator('#expander4molecule svg').click() // Click #expander4input_molecules svg await page.locator('#expander4input_molecules svg').click() // Click text=Save - await page.locator('button:has-text("Save")').click() - // Click text=Text - await page.locator('text=Text').click() + // await page.locator('button:has-text("Save")').click() }) test('should have "[topoaa.mol1]" header', async ({ page }) => { + // select Text tab + await page.locator('text=Text').click() await expectHighlightedCodeToContain(page, '[topoaa.mol1]') }) @@ -41,7 +47,7 @@ test.describe('given 1 molecule and a topoaa node', () => { // It is important to call waitForEvent before click to set up waiting. page.waitForEvent('download'), // Triggers the download. - page.locator('text=Download archive').click() + page.locator('text=Download').click() ]) // wait for download to complete path = await download.path() ?? '' @@ -64,10 +70,16 @@ test.describe('given 1 molecule and a topoaa node', () => { await page.locator('text="Upload" >> input[type="file"]') .setInputFiles({ name: 'workflow.zip', mimeType: 'application/zip', buffer: file1 }) + // ensure file is uploaded + await page.locator('text=Files').click() await page.waitForSelector('button:has-text("e2a-hpr_1GGR.pdb")') }) test('should have "[topoaa.mol1]" header', async ({ page }) => { + // debugger + // await page.pause() + // change to Text tab + await page.locator('text=Text').click() await expectHighlightedCodeToContain(page, '[topoaa.mol1]') }) }) diff --git a/apps/haddock3-download/src/App.css b/apps/haddock3-download/src/App.css index 272122c..540fc9f 100644 --- a/apps/haddock3-download/src/App.css +++ b/apps/haddock3-download/src/App.css @@ -10,7 +10,7 @@ grid-template-areas: "head head head" "catalog workflow node" "catalog workflow-actions node-actions"; - grid-template-columns: min-content minmax(12rem,1fr) minmax(20rem,2fr); + grid-template-columns: min-content minmax(19rem,1fr) minmax(20rem,2fr); grid-template-rows: auto 1fr auto; column-gap: 1rem; } @@ -91,6 +91,7 @@ div[role="button"], display: flex; gap: 1rem; padding: 1rem 0rem; + align-items: baseline; } /* Show panel section is clickable */ diff --git a/apps/haddock3-download/src/App.tsx b/apps/haddock3-download/src/App.tsx index 7b34644..86f8e61 100644 --- a/apps/haddock3-download/src/App.tsx +++ b/apps/haddock3-download/src/App.tsx @@ -9,40 +9,75 @@ import { WorkflowDownloadButton, WorkflowPanel, WorkflowUploadButton, - Wrapper + Wrapper, + useAutosaveValue, + useSetAutosave } from '@i-vresse/wb-core' import '@i-vresse/wb-form/dist/index.css' import './App.css' -function App (): JSX.Element { +function AutosaveManagement (): JSX.Element { + const autosave = useAutosaveValue() + const setAutosave = useSetAutosave() + return ( - -
- -
- - - - - - - - - - - - - - - +
+ { + setAutosave(!autosave) + }} + /> + +
+ ) +} + +function PageContent (): JSX.Element { + const autosave = useAutosaveValue() + + return ( +
+ +
+ + + + + + + + + - - - - -
+ + + + + + {/* show form actions if autosave is OFF */} + {!autosave ? : null} + +
+ ) +} + +function App (): JSX.Element { + return ( + + ) } diff --git a/apps/haddock3-galaxy/src/App.tsx b/apps/haddock3-galaxy/src/App.tsx index 824be30..446fe80 100644 --- a/apps/haddock3-galaxy/src/App.tsx +++ b/apps/haddock3-galaxy/src/App.tsx @@ -7,14 +7,13 @@ import { NodePanel, CatalogPicker, WorkflowClear, - WorkflowPanel, - WorkflowUploadButton + WorkflowPanel } from '@i-vresse/wb-core' import './App.css' import '@i-vresse/wb-form/dist/index.css' import { WorkflowSubmitButton } from './WorkflowSubmitButton' import originalCatalogIndexURL from '../public/catalog/index.json' -import { useCatalog, useSetCatalog, useWorkflow } from '@i-vresse/wb-core/dist/store' +import { useAutosaveValue, useCatalog, useSetAutosave, useSetCatalog, useWorkflow } from '@i-vresse/wb-core/dist/store' import { useEffect } from 'react' import { toast } from 'react-toastify' @@ -26,9 +25,37 @@ const catalogIndexURL = `data:application/json,${JSON.stringify( // reverse to load guru catalog by default (as it now is first entry) so example zip file is compliant )}` +function AutosaveManagement (): JSX.Element { + const autosave = useAutosaveValue() + const setAutosave = useSetAutosave() + + return ( +
+ { + setAutosave(!autosave) + }} + /> + +
+ ) +} + function App (): JSX.Element { // Examples URLS need to prepended baseUrl const catalog = useCatalog() + const autosave = useAutosaveValue() const setCatalog = useSetCatalog() const { loadWorkflowArchive } = useWorkflow() @@ -45,7 +72,6 @@ function App (): JSX.Element { })) if (touched) { setCatalog({ ...catalog, examples }) - // Load from dataset addDatasetToBuilder(loadWorkflowArchive).catch((e) => console.error(e)) } @@ -64,18 +90,15 @@ function App (): JSX.Element { - + + + - - - - - - - + {/* show form actions if autosave is OFF */} + {!autosave ? : null} ) diff --git a/apps/haddock3-submit/src/App.tsx b/apps/haddock3-submit/src/App.tsx index ea47e87..46dcd8d 100644 --- a/apps/haddock3-submit/src/App.tsx +++ b/apps/haddock3-submit/src/App.tsx @@ -7,40 +7,66 @@ import { NodePanel, CatalogPicker, WorkflowClear, - Wrapper, - WorkflowPanel + WorkflowPanel, + useAutosaveValue, + useSetAutosave } from '@i-vresse/wb-core' import './App.css' import '@i-vresse/wb-form/dist/index.css' import { WorkflowSubmitButton } from './WorkflowSubmitButton' +function AutosaveManagement (): JSX.Element { + const autosave = useAutosaveValue() + const setAutosave = useSetAutosave() + + return ( +
+ { + setAutosave(!autosave) + }} + /> + +
+ ) +} + function App (): JSX.Element { + const autosave = useAutosaveValue() return ( - -
- -
- - - - - - - - - - - - - +
+ +
+ + + + + + + + - - - - -
- + + + + + + {/* show form actions if autosave is OFF */} + {!autosave ? : null} + +
) } diff --git a/apps/haddock3-submit/src/main.tsx b/apps/haddock3-submit/src/main.tsx index 606a3cf..92b31ef 100644 --- a/apps/haddock3-submit/src/main.tsx +++ b/apps/haddock3-submit/src/main.tsx @@ -1,11 +1,14 @@ import React from 'react' import ReactDOM from 'react-dom' +import { Wrapper } from '@i-vresse/wb-core' import './index.css' import App from './App' ReactDOM.render( - + + + , document.getElementById('root') ) diff --git a/apps/kitchensink/src/App.tsx b/apps/kitchensink/src/App.tsx index aa7e2ce..2166a05 100644 --- a/apps/kitchensink/src/App.tsx +++ b/apps/kitchensink/src/App.tsx @@ -10,7 +10,7 @@ import { WorkflowPanel, WorkflowUploadButton } from '@i-vresse/wb-core' -import { useSetCatalog } from '@i-vresse/wb-core/dist/store' +import { useAutosaveValue, useSetAutosave, useSetCatalog } from '@i-vresse/wb-core/dist/store' import { prepareCatalog } from '@i-vresse/wb-core/dist/catalog' import 'bootstrap/dist/css/bootstrap.min.css' @@ -18,8 +18,37 @@ import '@i-vresse/wb-form/dist/index.css' import './App.css' import kitchensinkCatalog from './kitchensink.json' +function AutosaveManagement (): JSX.Element { + const autosave = useAutosaveValue() + const setAutosave = useSetAutosave() + + return ( +
+ { + setAutosave(!autosave) + }} + /> + +
+ ) +} + function App (): JSX.Element { const setCatalog = useSetCatalog() + const autosave = useAutosaveValue() + useEffect(() => { const catalog = prepareCatalog(kitchensinkCatalog) setCatalog(catalog) @@ -34,19 +63,24 @@ function App (): JSX.Element { + + + + {/* show form actions if autosave is OFF */} + {!autosave ? : null} - + {/* - + */} ) } diff --git a/packages/core/package.json b/packages/core/package.json index abcbb7d..3710eb8 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -55,7 +55,7 @@ "c8": "^7.11.0", "jsdom": "^20.0.0", "ts-dedent": "^2.2.0", - "ts-standard": "^11.0.0", + "ts-standard": "^12.0.2", "tsup": "^6.1.3", "typedoc": "^0.23.7", "vite": "^3.0.4", diff --git a/packages/core/src/CatalogCategory.tsx b/packages/core/src/CatalogCategory.tsx index dc726fb..b810c4b 100644 --- a/packages/core/src/CatalogCategory.tsx +++ b/packages/core/src/CatalogCategory.tsx @@ -9,17 +9,16 @@ export const CatalogCategory = ({ name, description, collapsed: initiallyCollaps const style = { // TODO On https://developer.mozilla.org/en-US/docs/Web/CSS/list-style-type // disclosure-open/closed are said to be experimental, find how much compatibility there is. - listStyleType: collapsed ? 'disclosure-closed' : 'disclosure-open' + listStyleType: collapsed ? 'disclosure-closed' : 'disclosure-open', + cursor: 'pointer' // utf failed in chrome // listStyleType: collapsed ? '⏷' : '⏵' } return (
  • { - if (e.target === e.currentTarget) { - // only toggle when list marker is clicked - return setCollapsed((c) => !c) - } + style={style} + onClick={(e) => { + setCollapsed((c) => !c) }} > {name} diff --git a/packages/core/src/CatalogNode.tsx b/packages/core/src/CatalogNode.tsx index 76506ac..70e0a34 100644 --- a/packages/core/src/CatalogNode.tsx +++ b/packages/core/src/CatalogNode.tsx @@ -22,7 +22,12 @@ export const CatalogNode = ({ id, label }: ICatalogNode): JSX.Element => { {...attributes} title={label} className='btn btn-light btn-sm btn-catalog-node' - onClick={() => addNodeToWorkflow(id)} + onClick={(e) => { + // prevent bubbling click even to parent which toggles the group + e.stopPropagation() + // add node to workflow + addNodeToWorkflow(id) + }} > {id}
    ): JSX.Element { + return ( + + + + + + ) +} diff --git a/packages/core/src/Example.tsx b/packages/core/src/Example.tsx index 8568a51..35db799 100644 --- a/packages/core/src/Example.tsx +++ b/packages/core/src/Example.tsx @@ -30,7 +30,7 @@ export const Example = ({ name, workflow }: IProps): JSX.Element => {
    • )} diff --git a/packages/core/src/FormActions.stories.tsx b/packages/core/src/FormActions.stories.tsx index f06f895..aa860e6 100644 --- a/packages/core/src/FormActions.stories.tsx +++ b/packages/core/src/FormActions.stories.tsx @@ -23,9 +23,9 @@ export const NothingSelected: ComponentStory = () => { export const GlobalParametersSelected: ComponentStory = () => { - const { toggleGlobalEdit } = useWorkflow() + const { setEditingGlobal } = useWorkflow() const submitFormRefSetter = useSetActiveSubmitButton() - useEffect(toggleGlobalEdit, []) + useEffect(() => setEditingGlobal(true), []) return ( <> - + ) } diff --git a/packages/core/src/VisualNode.tsx b/packages/core/src/VisualNode.tsx index a7c08d5..064e010 100644 --- a/packages/core/src/VisualNode.tsx +++ b/packages/core/src/VisualNode.tsx @@ -4,9 +4,14 @@ import { BsX } from 'react-icons/bs' import { CSS } from '@dnd-kit/utilities' import { useSortable } from '@dnd-kit/sortable' -import { useDraggingWorkflowNodeState, useSelectNodeIndex, useWorkflow } from './store' +import { + useDraggingWorkflowNodeState, useSelectNodeIndex, + useNodeHasErrorsValue, useWorkflow +} from './store' import { GripVertical } from './GripVertical' +import ErrorIcon from './ErrorIcon' + interface IProp { type: string index: number @@ -14,6 +19,7 @@ interface IProp { } export const VisualNode = ({ type, index, id }: IProp): JSX.Element => { + const nodeHasErrors = useNodeHasErrorsValue(id) const selectedNodeIndex = useSelectNodeIndex() const { selectNode, deleteNode } = useWorkflow() const draggingWorkflowNodeCode = useDraggingWorkflowNodeState()[0] @@ -36,20 +42,30 @@ export const VisualNode = ({ type, index, id }: IProp): JSX.Element => { const selectedStyle = selectedNodeIndex === index ? { fontWeight: 'bold' } : {} + function onNodeChange (): void { + // change node only if different + if (selectedNodeIndex !== index) { + selectNode(index) + } + } + // TODO after clicking node the active styling is not removed unless you activate another element return (
    ) +} +function AppendZone (): JSX.Element { const appendZoneStyle: CSSProperties = { padding: '1rem', textAlign: 'center' } - const appendZone = ( + return (
    Append node to workflow by clicking node in catalog or by dragging node from catalog to here.
    ) +} - let listStyle: CSSProperties = { lineHeight: '2.5em', height: '100%' } - if (draggingWorkflowNodeCode !== null || draggingCatalogNode !== null || nodes.length === 0) { - listStyle = { - ...listStyle, - borderStyle: 'dashed', - borderWidth: 1 - } +function NodeList ({ showBorder = false }: { showBorder: boolean }): JSX.Element { + const { nodes } = useWorkflow() + + const listStyle: CSSProperties = { + lineHeight: '2.5em', + height: '100%' + } + // add dashed border + if (showBorder) { + listStyle.borderStyle = 'dashed' + listStyle.borderWidth = 1 } - const nodeList = ( + + return (
    {nodes.map((node, i) => ( ))} - {nodes.length === 0 ? appendZone : <>} + {nodes.length === 0 ? : null}
    ) +} +export const VisualPanel = (): JSX.Element => { + const { nodes } = useWorkflow() + const draggingCatalogNode = useDraggingCatalogNodeState()[0] + const draggingWorkflowNodeCode = useDraggingWorkflowNodeState()[0] + const draggingWorkflowNode = nodes.find( + (n) => n.id === draggingWorkflowNodeCode + ) const sortableItems = nodes.map((n) => n.id) if (draggingCatalogNode !== null) { sortableItems.push(draggingCatalogNode.toString()) } const { setNodeRef } = useDroppable({ id: 'catalog-dropzone' }) + return (
    + - {nodeList} + {/* {nodeList} */} + {draggingCatalogNode !== null diff --git a/packages/core/src/WorkflowDownloadButton.tsx b/packages/core/src/WorkflowDownloadButton.tsx index b82072e..b982d18 100644 --- a/packages/core/src/WorkflowDownloadButton.tsx +++ b/packages/core/src/WorkflowDownloadButton.tsx @@ -1,9 +1,10 @@ import React from 'react' import { toast } from 'react-toastify' -import { useWorkflow } from './store' +import { useWorkflow, useWorkflowHasErrors } from './store' export const WorkflowDownloadButton = (): JSX.Element => { const { save } = useWorkflow() + const hasErrors = useWorkflowHasErrors() async function downloadWorkflow (): Promise { await toast.promise( @@ -22,6 +23,6 @@ export const WorkflowDownloadButton = (): JSX.Element => { } return ( - + ) } diff --git a/packages/core/src/WorkflowPanel.tsx b/packages/core/src/WorkflowPanel.tsx index a830a6e..8c63ce0 100644 --- a/packages/core/src/WorkflowPanel.tsx +++ b/packages/core/src/WorkflowPanel.tsx @@ -1,22 +1,32 @@ import React, { PropsWithChildren, useState } from 'react' import { TextPanel } from './TextPanel' import { VisualPanel } from './VisualPanel' -import { useWorkflow } from './store' +import { FilesList } from './FilesList' -type ITab = 'text' | 'visual' +type ITab = 'text' | 'visual' | 'files' + +/** + * Return selected tab content + * @param tab ITab + * @returns JSX.Element + */ +function SelectedTab ({ tab }: { tab: ITab }): JSX.Element { + switch (tab) { + case 'text': + return + case 'files': + return + // visual panel is default + default: + return + } +} /** * Panel which renders the workflow. - * - * Used selected the node of which edit its parameters. */ export const WorkflowPanel = ({ children }: PropsWithChildren<{}>): JSX.Element => { const [tab, setTab] = useState('visual') - const { toggleGlobalEdit } = useWorkflow() - - const selectedPanel = tab === 'visual' ? : - const visualTabStyle = tab === 'visual' ? 'nav-link active' : 'nav-link' - const textTabStyle = tab === 'text' ? 'nav-link active' : 'nav-link' return (
    ): JSX.Element > Workflow
    - {children}
    -
      +
        +
      • + +
      • - +
      • - +
      - {selectedPanel} +
    ) } diff --git a/packages/core/src/WorkflowUploadButton.tsx b/packages/core/src/WorkflowUploadButton.tsx index 439f6bf..2be9ba5 100644 --- a/packages/core/src/WorkflowUploadButton.tsx +++ b/packages/core/src/WorkflowUploadButton.tsx @@ -1,6 +1,6 @@ import React, { useRef } from 'react' import { UpdateOptions, toast } from 'react-toastify' -import { useWorkflow } from './store' +import { useClearErrors, useWorkflow } from './store' import { ValidationError, flattenValidationErrors } from './validate' function ErrorsList ({ error }: { error: ValidationError }): JSX.Element { @@ -19,6 +19,7 @@ function ErrorsList ({ error }: { error: ValidationError }): JSX.Element { export const WorkflowUploadButton = (): JSX.Element => { const uploadRef = useRef(null) const { loadWorkflowArchive } = useWorkflow() + const { clearErrors } = useClearErrors() async function uploadWorkflow ( event: React.ChangeEvent @@ -29,6 +30,8 @@ export const WorkflowUploadButton = (): JSX.Element => { const file = event.target.files[0] const url = URL.createObjectURL(file) const toastId = toast.loading('Loading workfow ...') + // clear all form errors before loading different configuration + clearErrors() try { await loadWorkflowArchive(url) toast.update(toastId, { @@ -63,22 +66,32 @@ export const WorkflowUploadButton = (): JSX.Element => { } } finally { URL.revokeObjectURL(url) + if (uploadRef.current != null) { + // remove value in order to trigger on change event + // when uploading same file for the second time + uploadRef.current.value = '' + } } } return ( ) diff --git a/packages/core/src/index.tsx b/packages/core/src/index.tsx index 6c498c9..24af497 100644 --- a/packages/core/src/index.tsx +++ b/packages/core/src/index.tsx @@ -9,3 +9,4 @@ export { WorkflowUploadButton } from './WorkflowUploadButton' export { WorkflowClear } from './WorkflowClear' export { FormActions } from './FormActions' export { CatalogPicker } from './CatalogPicker' +export { useSetAutosave, useAutosaveValue, useWorkflowHasErrors } from './store' diff --git a/packages/core/src/molecule/addMoleculeValidation.test.ts b/packages/core/src/molecule/addMoleculeValidation.test.ts index fe2ed41..10ef3ba 100644 --- a/packages/core/src/molecule/addMoleculeValidation.test.ts +++ b/packages/core/src/molecule/addMoleculeValidation.test.ts @@ -1,6 +1,7 @@ import { UiSchema } from '@rjsf/core' import { JSONSchema7 } from 'json-schema' -import { beforeEach, describe, expect, it } from 'vitest' +import { beforeEach, describe, expect, it, beforeAll } from 'vitest' +import { init } from '@i-vresse/pdbtbx-ts' import { JSONSchema7WithMaxItemsFrom } from '../resolveMaxItemsFrom' import { IFiles, IParameters } from '../types' @@ -11,6 +12,10 @@ import { } from './addMoleculeValidation' import { MoleculeInfo } from './parse' +beforeAll(async () => { + await init() +}) + describe('parseMolecules()', () => { describe('given bad global schema or parameters', () => { const unchangedCases: Array< @@ -53,8 +58,8 @@ describe('parseMolecules()', () => { ] it.each(unchangedCases)( 'given %s should find zero files', - async (_description, globalSchema, globalParameters, files) => { - const actual = await parseMolecules( + (_description, globalSchema, globalParameters, files) => { + const actual = parseMolecules( globalParameters, globalSchema, files @@ -70,7 +75,7 @@ describe('addMoleculeValidation()', () => { let moleculeInfos: MoleculeInfo[] let moleculesPropName: string | undefined - beforeEach(async () => { + beforeEach(() => { const globalParameters = { molecules: ['a.pdb'] } @@ -94,14 +99,14 @@ describe('addMoleculeValidation()', () => { const files = { 'a.pdb': file }; - [moleculeInfos, moleculesPropName] = await parseMolecules( + [moleculeInfos, moleculesPropName] = parseMolecules( globalParameters, globalSchema, files ) }) - it('should return schema unchanged', async () => { + it('should return schema unchanged', () => { const itemsSchema: JSONSchema7 = { type: 'string' } @@ -115,7 +120,7 @@ describe('addMoleculeValidation()', () => { prop1: propSchema } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName @@ -124,7 +129,7 @@ describe('addMoleculeValidation()', () => { }) describe('in array of array of object with prop with format:chain', () => { - it('should set enum to [A]', async () => { + it('should set enum to [A]', () => { const propSchema: JSONSchema7WithMaxItemsFrom = { type: 'array', maxItemsFrom: 'molecules', @@ -147,7 +152,7 @@ describe('addMoleculeValidation()', () => { prop1: propSchema } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName @@ -182,7 +187,7 @@ describe('addMoleculeValidation()', () => { }) describe('in array of array of object with prop with format:residue', () => { - it('should set enum to [-3]', async () => { + it('should set enum to [-3]', () => { const propSchema: JSONSchema7WithMaxItemsFrom = { type: 'array', maxItemsFrom: 'molecules', @@ -205,7 +210,7 @@ describe('addMoleculeValidation()', () => { prop1: propSchema } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName @@ -241,7 +246,7 @@ describe('addMoleculeValidation()', () => { // Test for topoaa mol prop describe('in array of object of array of scalar with format:residue', () => { - it('should set enum to [-3]', async () => { + it('should set enum to [-3]', () => { const propSchema: JSONSchema7WithMaxItemsFrom = { type: 'array', maxItemsFrom: 'molecules', @@ -270,7 +275,7 @@ describe('addMoleculeValidation()', () => { } } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName @@ -311,7 +316,7 @@ describe('addMoleculeValidation()', () => { }) describe('in grouped object of array of array of object with prop with format:residue', () => { - it('should set enum to [-3]', async () => { + it('should set enum to [-3]', () => { const propSchema: JSONSchema7WithMaxItemsFrom = { type: 'array', maxItemsFrom: 'molecules', @@ -339,7 +344,7 @@ describe('addMoleculeValidation()', () => { } } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName @@ -464,7 +469,7 @@ describe('addMoleculeValidation()', () => { }) describe('given array of array of object with props with format:chain, format:residue and no format', () => { - it('should make items an array and set enums', async () => { + it('should make items an array and set enums', () => { const propSchema: JSONSchema7WithMaxItemsFrom = { type: 'array', maxItemsFrom: 'molecules', @@ -494,7 +499,7 @@ describe('addMoleculeValidation()', () => { prop1: propSchema } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName @@ -562,9 +567,10 @@ describe('addMoleculeValidation()', () => { let moleculeInfos: MoleculeInfo[] let moleculesPropName: string | undefined - beforeEach(async () => { + beforeEach(() => { const globalParameters = { - molecules: ['a.pdb'] + // ensure unique name due to local cache + molecules: ['xyz.pdb'] } const globalSchema: JSONSchema7 = { type: 'object', @@ -583,9 +589,10 @@ describe('addMoleculeValidation()', () => { 'data:text/plain;name=a.pdb;base64,' + Buffer.from(body).toString('base64') const files = { - 'a.pdb': file + // ensure unique name due to local cache + 'xyz.pdb': file }; - [moleculeInfos, moleculesPropName] = await parseMolecules( + [moleculeInfos, moleculesPropName] = parseMolecules( globalParameters, globalSchema, files @@ -596,7 +603,7 @@ describe('addMoleculeValidation()', () => { it.each([ ['residue', 'number'], ['chain', 'string'] - ] as const)('should make items an array and not set enums for %s format', async (moleculeformat, moleculeType) => { + ] as const)('should make items an array and not set enums for %s format', (moleculeformat, moleculeType) => { const propSchema: JSONSchema7WithMaxItemsFrom = { type: 'array', maxItemsFrom: 'molecules', @@ -619,7 +626,7 @@ describe('addMoleculeValidation()', () => { prop1: propSchema } } - const actual = await addMoleculeValidation( + const actual = addMoleculeValidation( schema, moleculeInfos, moleculesPropName diff --git a/packages/core/src/molecule/addMoleculeValidation.ts b/packages/core/src/molecule/addMoleculeValidation.ts index 69bde66..78b107f 100644 --- a/packages/core/src/molecule/addMoleculeValidation.ts +++ b/packages/core/src/molecule/addMoleculeValidation.ts @@ -6,12 +6,17 @@ import { IFiles, IParameters } from '../types' import { MoleculeInfo, parsePDB } from './parse' import { UiSchema, utils } from '@rjsf/core' -// TODO can be quite expensive to parse big molecules, should try to use memoization -export async function parseMolecules ( +// save in memory parsed molecule info +interface parsedMoleculeInfoProps { + [key: string]: Omit +} +const parsedMoleculeInfo: parsedMoleculeInfoProps = {} + +export function parseMolecules ( globalParameters: IParameters, globalSchema: JSONSchema7, files: IFiles -): Promise<[MoleculeInfo[], string | undefined]> { +): [MoleculeInfo[], string | undefined] { if (globalSchema.properties === undefined) { return [[], undefined] } @@ -33,20 +38,38 @@ export async function parseMolecules ( if (!Array.isArray(moleculeFilePaths)) { return [[], undefined] } + // find file of molecule path // TODO check whether files are actually PDB files using uiSchema.molecules..items.ui:options.accept: .pdb - const moleculeFiles = moleculeFilePaths.map((p) => files[p]) + const moleculeFiles = moleculeFilePaths + // ignore undefined entries (invalid entries) + .filter(file => file !== undefined) + .map((p) => files[p]) + // parse file - const moleculeInfos = await Promise.all( - moleculeFiles.map(async (f, i) => { - const body = dataURL2content(f) - const info = await parsePDB(body) + const moleculeInfos = moleculeFiles.map((f, i) => { + // debugger + // check if already parsed + const path = moleculeFilePaths[i] + if (Object.hasOwn(parsedMoleculeInfo, path)) { + // console.log("from memory...",path) return { - ...info, - path: moleculeFilePaths[i] + ...parsedMoleculeInfo[path], + path } - }) - ) + } + // else parse the info + const body = dataURL2content(f) + const info = parsePDB(body) + // save info in memory + parsedMoleculeInfo[path] = { ...info } + // return new info from memory + return { + ...parsedMoleculeInfo[path], + path + } + }) + return [moleculeInfos, moleculesPropName] } @@ -63,9 +86,8 @@ function walkSchemaForMoleculeFormats ( const entries = Object.entries(newSchema.properties).map(([k, v]) => { const s = v as JSONSchema7WithMaxItemsFrom const isArrayWithItems = s.type === 'array' && 'items' in s - const isObjectWithUserNames = + const isObjectWitAdditionalProps = s.type === 'object' && - s.additionalProperties && typeof s.additionalProperties === 'object' && !('properties' in s) if (isArrayWithItems && s.maxItemsFrom === moleculesPropName) { @@ -212,7 +234,7 @@ function walkSchemaForMoleculeFormats ( } } } else if ( - isObjectWithUserNames === true && + isObjectWitAdditionalProps && s.maxPropertiesFrom === moleculesPropName ) { // TODO implement diff --git a/packages/core/src/molecule/parse.test.ts b/packages/core/src/molecule/parse.test.ts index e197838..2a41818 100644 --- a/packages/core/src/molecule/parse.test.ts +++ b/packages/core/src/molecule/parse.test.ts @@ -1,7 +1,12 @@ -import { describe, expect, it } from 'vitest' +import { describe, expect, it, beforeAll } from 'vitest' +import { init } from '@i-vresse/pdbtbx-ts' import dedent from 'ts-dedent' import { parsePDB, MoleculeInfo } from './parse' +beforeAll(async () => { + await init() +}) + describe('parsePDB', () => { const cases: Array<[string, string, Omit]> = [ [ diff --git a/packages/core/src/molecule/parse.ts b/packages/core/src/molecule/parse.ts index 4b84998..170ca95 100644 --- a/packages/core/src/molecule/parse.ts +++ b/packages/core/src/molecule/parse.ts @@ -15,9 +15,15 @@ export interface MoleculeInfo { residueSequenceNumbers: number[] } -export async function parsePDB (content: string): Promise> { - // TODO do init only once - await init() +// use init only once +// NOTE! when init is in parseDB function is causes undesired page reloads +// when using autosave function. It results in the layout shift and lost +// of focus on the input element user is editing. +init() + .then(() => console.log('pdbtx...initialized')) + .catch(e => console.error(e.message)) + +export function parsePDB (content: string): Omit { try { const info = open_pdb(content) if (info.warnings.length > 0) { diff --git a/packages/core/src/store.test.tsx b/packages/core/src/store.test.tsx index 690ab65..b51a2be 100644 --- a/packages/core/src/store.test.tsx +++ b/packages/core/src/store.test.tsx @@ -1,4 +1,4 @@ -import { afterEach, describe, expect, it } from 'vitest' +import { afterEach, describe, expect, it, vi } from 'vitest' import { renderHook, act, cleanup } from '@testing-library/react-hooks' import { useGlobalFormData, @@ -17,6 +17,16 @@ import { prepareCatalog } from './catalog' afterEach(cleanup) +async function flushPromisesAndTimers (): Promise { + return await act( + async () => + await new Promise((resolve) => { + setTimeout(resolve, 100) + vi.runAllTimers() + }) + ) +} + describe('useSelectNodeIndex()', () => { it('should have -1 as initial value', () => { const { result } = renderHook(useSelectNodeIndex, { @@ -28,17 +38,10 @@ describe('useSelectNodeIndex()', () => { }) describe('useText()', () => { - describe('given empty catalog, no nodes and no global parameters', () => { - it('should return empty string', () => { - const { result } = renderHook(useText, { - wrapper: RecoilRoot - }) - expect(result.current).toEqual('') - }) - }) - describe('given catalog and a global parameter', () => { - it('should return global parameter as TOML formatted string', () => { + it('should return global parameter as TOML formatted string', async () => { + vi.useFakeTimers() + const { result } = renderHook( () => { // Custom hook to return hook under test and other hooks to fill global state @@ -57,6 +60,8 @@ describe('useText()', () => { } ) + await flushPromisesAndTimers() + act(() => { // Fill global state const catalog = { @@ -82,6 +87,8 @@ describe('useText()', () => { }) }) + await flushPromisesAndTimers() + const expected = ` parameterX = 'some value' ` @@ -92,10 +99,11 @@ parameterX = 'some value' describe('useSelectedCatalogNode()', () => { describe('given catalog and workflow with single node', () => { - it('should return catalog of selected node', () => { + it('should return catalog of selected node', async () => { + vi.useFakeTimers() + const { result } = renderHook( () => { - // TODO be able to use hooks with have async code const catalogNode = useSelectedCatalogNode() const setCatalog = useSetCatalog() const { addNodeToWorkflow, selectNode } = useWorkflow() @@ -153,6 +161,8 @@ describe('useSelectedCatalogNode()', () => { c.selectNode(0) }) + await flushPromisesAndTimers() + const expected = { type: 'object', properties: { diff --git a/packages/core/src/store.ts b/packages/core/src/store.ts index 753bb69..be8a150 100644 --- a/packages/core/src/store.ts +++ b/packages/core/src/store.ts @@ -24,13 +24,14 @@ import { IWorkflowNode, IFiles, IParameters, - ICatalogNode + ICatalogNode, + NodeErrorsType } from './types' import { catalog2tomlSchemas, workflow2tomltext } from './toml' import { dropUnusedFiles, loadWorkflowArchive, - emptyParams, + emptyGlobalParams, clearFiles } from './workflow' import { @@ -209,9 +210,16 @@ function parameters2formData ( const globalFormDataState = selector({ key: 'globalFormData', get: ({ get }) => { - const parameters = get(globalParametersState) const files = get(filesState) const catalog = get(catalogState) + let parameters = get(globalParametersState) + + if (Object.keys(parameters)?.length === 0 && + Object.keys(catalog?.global?.schema)?.length > 0) { + // get initial values only if global schema is loaded + // and parameters is empty object?s + parameters = emptyGlobalParams(catalog.global.schema) + } const formData = parameters2formData( parameters, files, @@ -227,8 +235,10 @@ const globalFormDataState = selector({ const newFiles = { ...files } const catalog = get(catalogState) let parameters: IParameters + // debugger if (formData instanceof DefaultValue) { - parameters = {} + // get default/inital state + parameters = emptyGlobalParams(catalog.global.schema) } else { parameters = formData2parameters( formData, @@ -259,6 +269,9 @@ const selectedNodeState = selector({ get: ({ get }) => { const index = get(selectedNodeIndexState) const nodes = get(workflowNodesState) + // console.group('selectedNodeState') + // console.log('index...', index) + // console.groupEnd() if (index in nodes) { return nodes[index] } @@ -323,8 +336,17 @@ const selectedNodeFormDataState = selector({ if (catalogNode === undefined) { return } + let formErrors = [] + if (Object.hasOwn(formData, 'formErrors')) { + // NOTE! 2024-04-11 + // extract form errors info from ajv validator + formErrors = (formData as any)?.formErrors + // remove hasErrors from formData because it is not part of "real" data + delete (formData as any).formErrors + } const files = get(filesState) const newFiles = { ...files } + // debugger let parameters: IParameters if (formData instanceof DefaultValue) { parameters = {} @@ -337,13 +359,26 @@ const selectedNodeFormDataState = selector({ ) } const nodes = get(workflowNodesState) + const errors = get(nodeErrors) const selectedNodeIndex = get(selectedNodeIndexState) - const newNode = { ...nodes[selectedNodeIndex], parameters } + const newNode = { + ...nodes[selectedNodeIndex], + parameters + } const newNodes = replaceItemAtIndex(nodes, selectedNodeIndex, newNode) const global = get(globalParametersState) const newUsedFiles = dropUnusedFiles(global, newNodes, newFiles) set(workflowNodesState, newNodes) set(filesState, newUsedFiles) + // save errors status of each node + const newErrors = { + ...errors, + [newNode.id]: { + hasErrors: formErrors?.length > 0, + errors: formErrors + } + } + set(nodeErrors, newErrors) } }) @@ -359,16 +394,19 @@ export function useSelectedNodeFormData (): [ const moleculeInfosState = selector<[MoleculeInfo[], string | undefined]>({ key: 'moleculeInfos', - get: async ({ get }) => { + // NOTE 2024-05-15! making get async causes page reload + get: ({ get }) => { const catalog = get(catalogState) const globalSchema = catalog.global.schema const globalParameters = get(globalParametersState) const files = get(filesState) - return await parseMolecules( + const moleculeInfo = parseMolecules( globalParameters, globalSchema, files ) + // debugger + return moleculeInfo } }) @@ -377,26 +415,44 @@ const selectedNodeFormSchemaState = selector({ get: ({ get }) => { const catalogNode = get(selectedCatalogNodeState) const globalParameters = get(globalParametersState) - if ( - catalogNode === undefined || - catalogNode.formSchema === undefined - ) { - return undefined - } - const schemaWithMaxItems = resolveMaxItemsFrom( - catalogNode.formSchema, - globalParameters - ) - const [moleculeInfos, moleculesPropName] = get(moleculeInfosState) - const schemaWithMolInfo = addMoleculeValidation( - schemaWithMaxItems, - moleculeInfos, - moleculesPropName - ) + const info = get(moleculeInfosState) + const schemaWithMolInfo = enrichSchemaWithMolInfo(catalogNode, globalParameters, info) return schemaWithMolInfo } }) +function enrichSchemaWithMolInfo (catalogNode: ICatalogNode | undefined, globalParameters: IParameters, info: [MoleculeInfo[], string | undefined]): JSONSchema7 | undefined { + if ( + catalogNode === undefined || + catalogNode.formSchema === undefined + ) { + return undefined + } + const schemaWithMaxItems = resolveMaxItemsFrom( + catalogNode.formSchema, + globalParameters + ) + const [moleculeInfos, moleculesPropName] = info + const schemaWithMolInfo = addMoleculeValidation( + schemaWithMaxItems, + moleculeInfos, + moleculesPropName + ) + return schemaWithMolInfo +} + +function emptyNodeParams (catalog: ICatalog, globalParameters: IParameters, info: [MoleculeInfo[], string | undefined], nodeType: string): IParameters { + const catalogNode = catalog.nodes.find((n) => n.id === nodeType) + if (catalogNode === undefined) { + return {} + } + const schemaWithMolInfo = enrichSchemaWithMolInfo(catalogNode, globalParameters, info) + if (schemaWithMolInfo === undefined) { + return emptyGlobalParams(catalogNode.schema) + } + return emptyGlobalParams(schemaWithMolInfo) +} + /** * Hook to get JSON schema for currently selected node that can be used in a rjsf form. */ @@ -437,7 +493,8 @@ export interface UseWorkflow { */ editingGlobal: boolean global: IParameters - toggleGlobalEdit: () => void + setEditingGlobal: (editing: boolean) => void + selectGlobalEdit: () => void /** * @param nodeType A {@link types!ICatalogNode.id | catalog node id} */ @@ -497,13 +554,17 @@ export function useWorkflow (): UseWorkflow { ) const [files, setFiles] = useRecoilState(filesState) const catalog = useCatalog() + // clear errors method + const { clearErrors } = useClearErrors() + const moleculeInfos = useRecoilValue(moleculeInfosState) return { nodes, editingGlobal, global, - toggleGlobalEdit () { - setEditingGlobal(!editingGlobal) + setEditingGlobal, + selectGlobalEdit () { + setEditingGlobal(true) setSelectedNodeIndex(-1) }, addNodeToWorkflowAt (nodeType: string, targetId: string) { @@ -515,24 +576,26 @@ export function useWorkflow (): UseWorkflow { ] return moveItem(newNodes, newNodes.length - 1, targetIndex) }) - if (selectedNodeIndex === -1 && !editingGlobal) { - setSelectedNodeIndex(targetIndex) - } + // debugger + setSelectedNodeIndex(targetIndex) }, addNodeToWorkflow (nodeType: string) { + const parameters = emptyNodeParams(catalog, global, moleculeInfos, nodeType) setNodes((oldNodes) => [ ...oldNodes, - { type: nodeType, parameters: {}, id: nanoid() } + { type: nodeType, parameters, id: nanoid() } ]) - if (selectedNodeIndex === -1 && !editingGlobal) { - setSelectedNodeIndex(nodes.length) - } + setSelectedNodeIndex(nodes.length) }, selectNode: (nodeIndex: number) => { + // console.group('selectNode') + // console.log('nodeIndex...', nodeIndex) + // console.groupEnd() + + setSelectedNodeIndex(nodeIndex) if (editingGlobal) { setEditingGlobal(false) } - setSelectedNodeIndex(nodeIndex) }, deleteNode (nodeIndex: number) { if (selectedNodeIndex !== -1) { @@ -550,11 +613,16 @@ export function useWorkflow (): UseWorkflow { clearNodeSelection: () => setSelectedNodeIndex(-1), clear () { const blankNodes = removeAllItems(nodes) - const blankGlobals = emptyParams() + const blankGlobals = emptyGlobalParams(catalog.global.schema) const blankFiles = clearFiles() setNodes(blankNodes) setGlobal(blankGlobals) setFiles(blankFiles) + // preselect global + setEditingGlobal(true) + setSelectedNodeIndex(-1) + // clear errors + clearErrors() }, async loadWorkflowArchive (archiveURL: string) { const r = await loadWorkflowArchive(archiveURL, catalog) @@ -591,3 +659,102 @@ export function useText (): string { const catalog = useCatalog() return workflow2tomltext(nodes, global, catalog2tomlSchemas(catalog)) } + +/** + * Autosave state and hooks + */ +const autosave = atom({ + key: 'autosave', + default: true +}) + +export function useAutosave (): [boolean, SetterOrUpdater] { + return useRecoilState(autosave) +} + +export function useSetAutosave (): SetterOrUpdater { + return useSetRecoilState(autosave) +} + +export function useAutosaveValue (): boolean { + return useRecoilValue(autosave) +} + +const nodeErrors = atom<{ + [key: string]: NodeErrorsType +}>({ + key: 'nodeErrors', + default: {} +}) + +export function useNodeHasErrors (): [{ + [key: string]: NodeErrorsType +}, SetterOrUpdater<{ + [key: string]: NodeErrorsType +}>] { + return useRecoilState(nodeErrors) +} + +export function useSetNodeErrors (): (key: string, value: NodeErrorsType) => void { + const [errorNodes, setErrorNodes] = useNodeHasErrors() + // return function to update single node state + return function setNodeHasErrors (key: string, value: NodeErrorsType) { + // debugger + if (errorNodes[key] !== value) { + const newValid = { + ...errorNodes, + [key]: value + } + setErrorNodes(newValid) + } + } +} + +export function useNodeHasErrorsValue (key: string): boolean { + const nodes = useRecoilValue(nodeErrors) + + // console.group("useNodeHasErrorsValue") + // console.log("key...", key) + // console.log("nodes...", nodes) + // console.groupEnd() + + // debugger + if (Object.hasOwn(nodes, key)) { + return nodes[key].hasErrors + } else { + return false + } +} + +export function useClearErrors (): { + clearErrors: () => void +} { + const setErrors = useSetRecoilState(nodeErrors) + // set to empty object + function clearErrors (): void { + setErrors({}) + } + return { + clearErrors + } +} + +export function useWorkflowHasErrors (): boolean { + const errors = useRecoilValue(nodeErrors) + const keys = Object.keys(errors) + + // at least one node has error + const errorKey = keys.find(key => { + return errors[key]?.hasErrors + }) + // if errorKey is found it has string type + const hasErrors = typeof errorKey === 'string' + + // console.group('useWorkflowHasErrors') + // console.log('errors...', errors) + // console.log('errorKey...', errorKey) + // console.log('hasErrors...', hasErrors) + // console.groupEnd() + + return hasErrors +} diff --git a/packages/core/src/toml.ts b/packages/core/src/toml.ts index 491981a..b6e36b2 100644 --- a/packages/core/src/toml.ts +++ b/packages/core/src/toml.ts @@ -80,13 +80,19 @@ function parameters2toml (parameters: IParameters, tomlSchema: TomlObjectSchema) const d2 = parameters2toml(d, nestedTomlSchema as TomlObjectSchema) return Section(d2) }) + } else if (isArray) { + // debugger + // clear array of undefined entries + tomledParameters[k] = v.filter(item => item !== undefined) } else if (isObject(v) && isSectioned) { tomledParameters[k] = Section(v as any) } else if (isObject(v) && isIndexed) { Object.entries(v).forEach(([k2, v2]) => { - tomledParameters[`${k}_${k2}`] = v2 + const v3 = Array.isArray(v2) ? v2.filter(item => item !== undefined) : v2 + tomledParameters[`${k}_${k2}`] = v3 }) - } else { + } else if (v !== undefined) { + // avoid params with undefined value tomledParameters[k] = v } }) diff --git a/packages/core/src/types.ts b/packages/core/src/types.ts index 978be7f..367dad1 100644 --- a/packages/core/src/types.ts +++ b/packages/core/src/types.ts @@ -1,5 +1,5 @@ import { JSONSchema7 } from 'json-schema' -import { UiSchema } from '@rjsf/core' +import { UiSchema, AjvError } from '@rjsf/core' /** * Array of tuples. @@ -88,3 +88,8 @@ export interface IWorkflowSchema { global: IGlobal nodes: ICatalogNode[] } + +export interface NodeErrorsType { + hasErrors: boolean + errors: AjvError[] +} diff --git a/packages/core/src/validate.test.ts b/packages/core/src/validate.test.ts index 1db5170..235a221 100644 --- a/packages/core/src/validate.test.ts +++ b/packages/core/src/validate.test.ts @@ -312,7 +312,8 @@ describe('validateWorkflow()', () => { properties: { chain: { type: 'string', - format: 'chain' + format: 'chain', + enum: ['A'] } } } @@ -381,6 +382,7 @@ describe('validateWorkflow()', () => { } ] } + const errors = await validateWorkflow(workflow, schemas, files) const expected = [{ @@ -388,9 +390,7 @@ describe('validateWorkflow()', () => { keyword: 'enum', message: 'must be equal to one of the allowed values', params: { - allowedValues: [ - 'A' - ] + allowedValues: ['A'] }, schemaPath: '#/properties/seg/items/0/items/properties/chain/enum', workflowPath: 'nodes[0]' diff --git a/packages/core/src/validate.ts b/packages/core/src/validate.ts index 296c9ae..18fcb26 100644 --- a/packages/core/src/validate.ts +++ b/packages/core/src/validate.ts @@ -81,7 +81,7 @@ async function validateNodeFactory ( ): Promise< (value: IWorkflowNode, index: number, array: IWorkflowNode[]) => Errors > { - const [moleculeInfos, moleculesPropName] = await parseMolecules( + const [moleculeInfos, moleculesPropName] = parseMolecules( globalParameters, globalSchema, files diff --git a/packages/core/src/workflow.ts b/packages/core/src/workflow.ts index 97768bf..09fc2c5 100644 --- a/packages/core/src/workflow.ts +++ b/packages/core/src/workflow.ts @@ -1,3 +1,4 @@ +import { JSONSchema7 } from 'json-schema' import { readArchive } from './archive' import { parseWorkflow } from './toml' import { ICatalog, IFiles, IParameters, IWorkflow, IWorkflowNode } from './types' @@ -46,8 +47,22 @@ export function dropUnusedFiles (global: IParameters, nodes: IWorkflowNode[], fi return newFiles } -export function emptyParams (): IParameters { - return {} +export function emptyGlobalParams (schema: JSONSchema7): IParameters { + const parameters: IParameters = {} + for (const key in schema.properties) { + const propSchema = schema.properties[key] + if (typeof propSchema !== 'boolean' && propSchema.type === 'array') { + if (propSchema.maxItems !== undefined && propSchema.format !== 'moleculefilepaths' && ( + typeof propSchema.items === 'object' || + (Array.isArray(propSchema.items) && propSchema.items[0].type === 'object') + )) { + parameters[key] = new Array(propSchema.maxItems).fill({}) + } else { + parameters[key] = [] + } + } + } + return parameters } export function clearFiles (): IFiles { diff --git a/packages/form/package.json b/packages/form/package.json index f8b8eca..c167907 100644 --- a/packages/form/package.json +++ b/packages/form/package.json @@ -57,7 +57,7 @@ "babel-loader": "^8.2.5", "jsdom": "^20.0.0", "postcss": "^8.4.14", - "ts-standard": "^11.0.0", + "ts-standard": "^12.0.2", "tsup": "^6.1.3", "typedoc": "^0.23.7", "vitest": "^0.20.2" diff --git a/packages/form/src/ArrayFieldTemplate.tsx b/packages/form/src/ArrayFieldTemplate.tsx index 6052b20..647a07a 100644 --- a/packages/form/src/ArrayFieldTemplate.tsx +++ b/packages/form/src/ArrayFieldTemplate.tsx @@ -279,11 +279,10 @@ const DefaultNormalArrayFieldTemplate = (props: ArrayFieldTemplateProps) => { props.items.map((p) => DefaultArrayItem({ ...p, indexable, indexLookup }))} {props.canAdd && ( - + - {' '} ( ( const CaretDownSquare = (): JSX.Element => ( ( ) +// Error icon shown in error (comes from bootstrap.css) +const ErrorIcon = (): JSX.Element => { + return ( + + + + + + ) +} + const CollapsedIcon = CaretDownSquare const ExpandedIcon = CaretUpSquare @@ -46,40 +64,48 @@ export const CollapsibleField = (props: FieldProps): JSX.Element => { : true const [collapsed, setCollapsed] = useState(initialCollapsed) const title = extractTitle(props, uiOptions) - const expanderId = props.id ?? `expander4${props.name.replaceAll(' ', '_')}` // TODO find rjsf func to get more stable id + const expanderId = props.id ?? `expander4${props.name.replaceAll(' ', '_')}` // TODO find rjsf func to get more stable - // To render button + name use styling from https://github.com/rjsf-team/react-jsonschema-form/blob/master/packages/bootstrap-4/src/TitleField/TitleField.tsx - // Card styling from bootstrap 4.6 https://getbootstrap.com/docs/4.6/components/card/ - if (collapsed) { - return ( -
    -
    -
    setCollapsed(false)} - id={expanderId} - > - - {title} -
    -
    -
    - ) - } + // console.group('CollapsibleField') + // console.log('errorSchema...', props.errorSchema) + // console.groupEnd() + + // check for errors in the field. On error we show title in red and warning icon + const hasError = Object.keys(props.errorSchema).length > 0 - // TitleField inside the ObjectField is not rendered when there is no title or name - const oprops = dropTitle(props) return (
    -
    -
    setCollapsed(true)} id={expanderId}> - - {title} +
    { + setCollapsed(!collapsed) + }} + > + {/* icon */} + {collapsed ? : } + {/* title */} +
    + {title}
    + {/* error icon */} + {hasError ? : null}
    -
    - -
    + {/* show content when not collapsed */} + {/* TitleField inside the ObjectField is not rendered when there is no title or name */} + {!collapsed ?
    : null}
    ) } diff --git a/yarn.lock b/yarn.lock index 04d6bc0..f310720 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1909,6 +1909,24 @@ __metadata: languageName: node linkType: hard +"@eslint-community/eslint-utils@npm:^4.2.0": + version: 4.4.0 + resolution: "@eslint-community/eslint-utils@npm:4.4.0" + dependencies: + eslint-visitor-keys: ^3.3.0 + peerDependencies: + eslint: ^6.0.0 || ^7.0.0 || >=8.0.0 + checksum: cdfe3ae42b4f572cbfb46d20edafe6f36fc5fb52bf2d90875c58aefe226892b9677fef60820e2832caf864a326fe4fc225714c46e8389ccca04d5f9288aabd22 + languageName: node + linkType: hard + +"@eslint-community/regexpp@npm:^4.4.0, @eslint-community/regexpp@npm:^4.6.1": + version: 4.10.0 + resolution: "@eslint-community/regexpp@npm:4.10.0" + checksum: 2a6e345429ea8382aaaf3a61f865cae16ed44d31ca917910033c02dc00d505d939f10b81e079fa14d43b51499c640138e153b7e40743c4c094d9df97d4e56f7b + languageName: node + linkType: hard + "@eslint/eslintrc@npm:^0.4.3": version: 0.4.3 resolution: "@eslint/eslintrc@npm:0.4.3" @@ -1943,6 +1961,30 @@ __metadata: languageName: node linkType: hard +"@eslint/eslintrc@npm:^2.1.4": + version: 2.1.4 + resolution: "@eslint/eslintrc@npm:2.1.4" + dependencies: + ajv: ^6.12.4 + debug: ^4.3.2 + espree: ^9.6.0 + globals: ^13.19.0 + ignore: ^5.2.0 + import-fresh: ^3.2.1 + js-yaml: ^4.1.0 + minimatch: ^3.1.2 + strip-json-comments: ^3.1.1 + checksum: 10957c7592b20ca0089262d8c2a8accbad14b4f6507e35416c32ee6b4dbf9cad67dfb77096bbd405405e9ada2b107f3797fe94362e1c55e0b09d6e90dd149127 + languageName: node + linkType: hard + +"@eslint/js@npm:8.57.0": + version: 8.57.0 + resolution: "@eslint/js@npm:8.57.0" + checksum: 315dc65b0e9893e2bff139bddace7ea601ad77ed47b4550e73da8c9c2d2766c7a575c3cddf17ef85b8fd6a36ff34f91729d0dcca56e73ca887c10df91a41b0bb + languageName: node + linkType: hard + "@gar/promisify@npm:^1.0.1, @gar/promisify@npm:^1.1.3": version: 1.1.3 resolution: "@gar/promisify@npm:1.1.3" @@ -1950,6 +1992,17 @@ __metadata: languageName: node linkType: hard +"@humanwhocodes/config-array@npm:^0.11.14": + version: 0.11.14 + resolution: "@humanwhocodes/config-array@npm:0.11.14" + dependencies: + "@humanwhocodes/object-schema": ^2.0.2 + debug: ^4.3.1 + minimatch: ^3.0.5 + checksum: 861ccce9eaea5de19546653bccf75bf09fe878bc39c3aab00aeee2d2a0e654516adad38dd1098aab5e3af0145bbcbf3f309bdf4d964f8dab9dcd5834ae4c02f2 + languageName: node + linkType: hard + "@humanwhocodes/config-array@npm:^0.5.0": version: 0.5.0 resolution: "@humanwhocodes/config-array@npm:0.5.0" @@ -1972,6 +2025,13 @@ __metadata: languageName: node linkType: hard +"@humanwhocodes/module-importer@npm:^1.0.1": + version: 1.0.1 + resolution: "@humanwhocodes/module-importer@npm:1.0.1" + checksum: 0fd22007db8034a2cdf2c764b140d37d9020bbfce8a49d3ec5c05290e77d4b0263b1b972b752df8c89e5eaa94073408f2b7d977aed131faf6cf396ebb5d7fb61 + languageName: node + linkType: hard + "@humanwhocodes/object-schema@npm:^1.2.0, @humanwhocodes/object-schema@npm:^1.2.1": version: 1.2.1 resolution: "@humanwhocodes/object-schema@npm:1.2.1" @@ -1979,6 +2039,13 @@ __metadata: languageName: node linkType: hard +"@humanwhocodes/object-schema@npm:^2.0.2": + version: 2.0.3 + resolution: "@humanwhocodes/object-schema@npm:2.0.3" + checksum: d3b78f6c5831888c6ecc899df0d03bcc25d46f3ad26a11d7ea52944dc36a35ef543fad965322174238d677a43d5c694434f6607532cff7077062513ad7022631 + languageName: node + linkType: hard + "@i-vresse/haddock3-config-builder-download@workspace:apps/haddock3-download": version: 0.0.0-use.local resolution: "@i-vresse/haddock3-config-builder-download@workspace:apps/haddock3-download" @@ -2091,7 +2158,7 @@ __metadata: react-toastify: ^8.1.0 recoil: ^0.5.2 ts-dedent: ^2.2.0 - ts-standard: ^11.0.0 + ts-standard: ^12.0.2 tsup: ^6.1.3 typedoc: ^0.23.7 vite: ^3.0.4 @@ -2127,7 +2194,7 @@ __metadata: postcss: ^8.4.14 react-bootstrap: ^1 react-icons: ^3.10.0 - ts-standard: ^11.0.0 + ts-standard: ^12.0.2 tsup: ^6.1.3 typedoc: ^0.23.7 vitest: ^0.20.2 @@ -2386,7 +2453,7 @@ __metadata: languageName: node linkType: hard -"@nodelib/fs.walk@npm:^1.2.3": +"@nodelib/fs.walk@npm:^1.2.3, @nodelib/fs.walk@npm:^1.2.8": version: 1.2.8 resolution: "@nodelib/fs.walk@npm:1.2.8" dependencies: @@ -4013,6 +4080,13 @@ __metadata: languageName: node linkType: hard +"@types/json-schema@npm:^7.0.9": + version: 7.0.15 + resolution: "@types/json-schema@npm:7.0.15" + checksum: 97ed0cb44d4070aecea772b7b2e2ed971e10c81ec87dd4ecc160322ffa55ff330dace1793489540e3e318d90942064bb697cc0f8989391797792d919737b3b98 + languageName: node + linkType: hard + "@types/json5@npm:^0.0.29": version: 0.0.29 resolution: "@types/json5@npm:0.0.29" @@ -4179,6 +4253,13 @@ __metadata: languageName: node linkType: hard +"@types/semver@npm:^7.3.12": + version: 7.5.8 + resolution: "@types/semver@npm:7.5.8" + checksum: ea6f5276f5b84c55921785a3a27a3cd37afee0111dfe2bcb3e03c31819c197c782598f17f0b150a69d453c9584cd14c4c4d7b9a55d2c5e6cacd4d66fdb3b3663 + languageName: node + linkType: hard + "@types/source-list-map@npm:*": 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version: 2.1.0 resolution: "eslint-utils@npm:2.1.0" @@ -8062,6 +8770,13 @@ __metadata: languageName: node linkType: hard +"eslint-visitor-keys@npm:^3.4.1, eslint-visitor-keys@npm:^3.4.3": + version: 3.4.3 + resolution: "eslint-visitor-keys@npm:3.4.3" + checksum: 36e9ef87fca698b6fd7ca5ca35d7b2b6eeaaf106572e2f7fd31c12d3bfdaccdb587bba6d3621067e5aece31c8c3a348b93922ab8f7b2cbc6aaab5e1d89040c60 + languageName: node + linkType: hard + "eslint@npm:8.4.1": version: 8.4.1 resolution: "eslint@npm:8.4.1" @@ -8160,6 +8875,54 @@ __metadata: languageName: node linkType: hard +"eslint@npm:^8.0.1": + version: 8.57.0 + resolution: "eslint@npm:8.57.0" + dependencies: + "@eslint-community/eslint-utils": ^4.2.0 + "@eslint-community/regexpp": ^4.6.1 + "@eslint/eslintrc": ^2.1.4 + "@eslint/js": 8.57.0 + "@humanwhocodes/config-array": ^0.11.14 + "@humanwhocodes/module-importer": ^1.0.1 + "@nodelib/fs.walk": ^1.2.8 + "@ungap/structured-clone": ^1.2.0 + ajv: ^6.12.4 + chalk: ^4.0.0 + cross-spawn: ^7.0.2 + 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dependencies: + locate-path: ^7.1.0 + path-exists: ^5.0.0 + checksum: 9a21b7f9244a420e54c6df95b4f6fc3941efd3c3e5476f8274eb452f6a85706e7a6a90de71353ee4f091fcb4593271a6f92810a324ec542650398f928783c280 + languageName: node + linkType: hard + "flat-cache@npm:^3.0.4": version: 3.0.4 resolution: "flat-cache@npm:3.0.4" @@ -8949,6 +9742,13 @@ __metadata: languageName: node linkType: hard +"function-bind@npm:^1.1.2": + version: 1.1.2 + resolution: "function-bind@npm:1.1.2" + checksum: 2b0ff4ce708d99715ad14a6d1f894e2a83242e4a52ccfcefaee5e40050562e5f6dafc1adbb4ce2d4ab47279a45dc736ab91ea5042d843c3c092820dfe032efb1 + languageName: node + linkType: hard + "function.prototype.name@npm:^1.1.0, function.prototype.name@npm:^1.1.5": version: 1.1.5 resolution: "function.prototype.name@npm:1.1.5" @@ -8961,6 +9761,18 @@ __metadata: languageName: node linkType: hard +"function.prototype.name@npm:^1.1.6": + version: 1.1.6 + resolution: "function.prototype.name@npm:1.1.6" + dependencies: + call-bind: ^1.0.2 + 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^1.3.0 + function-bind: ^1.1.2 + has-proto: ^1.0.1 + has-symbols: ^1.0.3 + hasown: ^2.0.0 + checksum: 414e3cdf2c203d1b9d7d33111df746a4512a1aa622770b361dadddf8ed0b5aeb26c560f49ca077e24bfafb0acb55ca908d1f709216ccba33ffc548ec8a79a951 + languageName: node + linkType: hard + "get-package-type@npm:^0.1.0": version: 0.1.0 resolution: "get-package-type@npm:0.1.0" @@ -9087,6 +9912,17 @@ __metadata: languageName: node linkType: hard +"get-symbol-description@npm:^1.0.2": + version: 1.0.2 + resolution: "get-symbol-description@npm:1.0.2" + dependencies: + call-bind: ^1.0.5 + es-errors: ^1.3.0 + get-intrinsic: ^1.2.4 + checksum: e1cb53bc211f9dbe9691a4f97a46837a553c4e7caadd0488dc24ac694db8a390b93edd412b48dcdd0b4bbb4c595de1709effc75fc87c0839deedc6968f5bd973 + languageName: node + linkType: hard + "get-value@npm:^2.0.3, get-value@npm:^2.0.6": version: 2.0.6 resolution: "get-value@npm:2.0.6" @@ -9120,7 +9956,7 @@ __metadata: languageName: node linkType: hard -"glob-parent@npm:^6.0.1": +"glob-parent@npm:^6.0.1, glob-parent@npm:^6.0.2": version: 6.0.2 resolution: "glob-parent@npm:6.0.2" dependencies: @@ -9232,6 +10068,15 @@ __metadata: languageName: node linkType: hard +"globals@npm:^13.19.0": + version: 13.24.0 + resolution: "globals@npm:13.24.0" + dependencies: + type-fest: ^0.20.2 + checksum: 56066ef058f6867c04ff203b8a44c15b038346a62efbc3060052a1016be9f56f4cf0b2cd45b74b22b81e521a889fc7786c73691b0549c2f3a6e825b3d394f43c + languageName: node + linkType: hard + "globalthis@npm:^1.0.0": version: 1.0.3 resolution: "globalthis@npm:1.0.3" @@ -9241,7 +10086,17 @@ __metadata: languageName: node linkType: hard -"globby@npm:^11.0.2, globby@npm:^11.0.3": +"globalthis@npm:^1.0.3": + version: 1.0.4 + resolution: "globalthis@npm:1.0.4" + dependencies: + define-properties: ^1.2.1 + gopd: ^1.0.1 + checksum: 39ad667ad9f01476474633a1834a70842041f70a55571e8dcef5fb957980a92da5022db5430fca8aecc5d47704ae30618c0bc877a579c70710c904e9ef06108a + languageName: node + linkType: hard + +"globby@npm:^11.0.2, globby@npm:^11.0.3, globby@npm:^11.1.0": version: 11.1.0 resolution: "globby@npm:11.1.0" dependencies: @@ -9271,6 +10126,15 @@ __metadata: languageName: node linkType: hard +"gopd@npm:^1.0.1": + version: 1.0.1 + resolution: "gopd@npm:1.0.1" + dependencies: + get-intrinsic: ^1.1.3 + checksum: a5ccfb8806e0917a94e0b3de2af2ea4979c1da920bc381667c260e00e7cafdbe844e2cb9c5bcfef4e5412e8bf73bab837285bc35c7ba73aaaf0134d4583393a6 + languageName: node + linkType: hard + "graceful-fs@npm:^4.1.11, graceful-fs@npm:^4.1.15, graceful-fs@npm:^4.1.2, graceful-fs@npm:^4.1.6, graceful-fs@npm:^4.2.0, graceful-fs@npm:^4.2.4, graceful-fs@npm:^4.2.6, graceful-fs@npm:^4.2.9": version: 4.2.10 resolution: "graceful-fs@npm:4.2.10" @@ -9278,6 +10142,13 @@ __metadata: languageName: node linkType: hard +"graphemer@npm:^1.4.0": + version: 1.4.0 + resolution: "graphemer@npm:1.4.0" + checksum: 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