diff --git a/client/jest.config.js b/client/jest.config.js index 9d817ae..ce536c3 100644 --- a/client/jest.config.js +++ b/client/jest.config.js @@ -1,15 +1,18 @@ // For a detailed explanation regarding each configuration property, visit: // https://jestjs.io/docs/en/configuration.html +/* eslint-disable @typescript-eslint/no-var-requires */ +const { compilerOptions } = require("./tsconfig.json"); + module.exports = { preset: "ts-jest", globals: { "ts-jest": { - tsconfig: "../tsconfig.json", + tsconfig: compilerOptions, }, }, // The glob patterns Jest uses to detect test files - testMatch: ["**/__tests__/*.+(ts|tsx|js)", "**/unit/*.test.ts"], + testMatch: ["**/__tests__/*.+(ts|tsx|js)", "**/*.test.ts"], // An array of file extensions your modules use moduleFileExtensions: ["ts", "tsx", "js"], diff --git a/client/tests/e2e/suite/extension.e2e.ts b/client/tests/e2e/suite/extension.e2e.ts deleted file mode 100644 index ddfcd14..0000000 --- a/client/tests/e2e/suite/extension.e2e.ts +++ /dev/null @@ -1,74 +0,0 @@ -// You can import and use all API from the 'vscode' module -// as well as import your extension to test it -import * as vscode from "vscode"; -import * as path from "path"; -import * as assert from "assert"; -import { beforeEach } from "mocha"; -import { - activateAndOpenInEditor, - getDocUri, - closeAllEditors, - openDocument, - sleep, - assertDiagnostics, - updateSettings, - resetSettings, -} from "./helpers"; - -suite("Extension Test Suite", () => { - teardown(closeAllEditors); - suite("Native (JSON) Workflows", () => { - suite("Commands Tests", () => { - test("Clean workflow command removes non-essential properties", async () => { - const dirtyDocUri = getDocUri(path.join("json", "clean", "wf_01_dirty.ga")); - const cleanDocUri = getDocUri(path.join("json", "clean", "wf_01_clean.ga")); - const { document } = await activateAndOpenInEditor(dirtyDocUri); - const dirtyDoc = document.getText(); - await vscode.commands.executeCommand("galaxy-workflows.cleanWorkflow"); - await sleep(1000); // Wait for command to apply changes - const actualCleanJson = document.getText(); - assert.notEqual(dirtyDoc, actualCleanJson); - const expectedCleanDocument = await openDocument(cleanDocUri); - const expectedCleanJson = expectedCleanDocument.getText(); - assert.strictEqual(actualCleanJson, expectedCleanJson); - }); - }); - - suite("Validation Tests", () => { - beforeEach(async () => { - await resetSettings(); - }); - test("Changing validation profile shows custom diagnostics", async () => { - const docUri = getDocUri(path.join("json", "validation", "test_wf_03.ga")); - await activateAndOpenInEditor(docUri); - await sleep(1000); // Wait for diagnostics - await assertDiagnostics(docUri, []); // Expect no issues - - // Change to stricter validation profile - await updateSettings("validation.profile", "iwc"); - await sleep(2000); // Wait for diagnostics - await assertDiagnostics(docUri, [ - { - message: 'Missing property "release".', - range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 1)), - severity: 0, - }, - { - message: "Missing label in workflow output.", - range: new vscode.Range(new vscode.Position(16, 16), new vscode.Position(19, 17)), - severity: 0, - }, - { - message: "Missing label in workflow output.", - range: new vscode.Range(new vscode.Position(20, 16), new vscode.Position(23, 17)), - severity: 0, - }, - ]); - - await resetSettings(); - await sleep(2000); // Wait for diagnostics - await assertDiagnostics(docUri, []); // Expect no issues - }); - }); - }); -}); diff --git a/client/tests/e2e/suite/extension.ga.e2e.ts b/client/tests/e2e/suite/extension.ga.e2e.ts new file mode 100644 index 0000000..8cab3cd --- /dev/null +++ b/client/tests/e2e/suite/extension.ga.e2e.ts @@ -0,0 +1,73 @@ +// You can import and use all API from the 'vscode' module +// as well as import your extension to test it +import * as vscode from "vscode"; +import * as path from "path"; +import * as assert from "assert"; +import { beforeEach } from "mocha"; +import { + activateAndOpenInEditor, + getDocUri, + closeAllEditors, + openDocument, + sleep, + assertDiagnostics, + updateSettings, + resetSettings, + waitForDiagnostics, +} from "./helpers"; + +suite("Native (JSON) Workflows", () => { + teardown(closeAllEditors); + suite("Commands Tests", () => { + test("Clean workflow command removes non-essential properties", async () => { + const dirtyDocUri = getDocUri(path.join("json", "clean", "wf_01_dirty.ga")); + const cleanDocUri = getDocUri(path.join("json", "clean", "wf_01_clean.ga")); + const { document } = await activateAndOpenInEditor(dirtyDocUri); + await sleep(500); // Wait for extension to fully activate... yes Windows CI I'm looking at you... + const dirtyDoc = document.getText(); + await vscode.commands.executeCommand("galaxy-workflows.cleanWorkflow"); + await sleep(500); // Wait for command to apply changes + const actualCleanJson = document.getText(); + assert.notEqual(dirtyDoc, actualCleanJson); + const expectedCleanDocument = await openDocument(cleanDocUri); + const expectedCleanJson = expectedCleanDocument.getText(); + assert.strictEqual(actualCleanJson, expectedCleanJson); + }); + }); + + suite("Validation Tests", () => { + beforeEach(async () => { + await resetSettings(); + }); + test("Changing validation profile shows custom diagnostics", async () => { + const docUri = getDocUri(path.join("json", "validation", "test_wf_03.ga")); + await activateAndOpenInEditor(docUri); + await assertDiagnostics(docUri, []); // Expect no issues + + // Change to stricter validation profile + await updateSettings("validation.profile", "iwc"); + await waitForDiagnostics(docUri); + await assertDiagnostics(docUri, [ + { + message: 'Missing property "release".', + range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 1)), + severity: vscode.DiagnosticSeverity.Error, + }, + { + message: "Missing label in workflow output.", + range: new vscode.Range(new vscode.Position(16, 16), new vscode.Position(19, 17)), + severity: vscode.DiagnosticSeverity.Error, + }, + { + message: "Missing label in workflow output.", + range: new vscode.Range(new vscode.Position(20, 16), new vscode.Position(23, 17)), + severity: vscode.DiagnosticSeverity.Error, + }, + ]); + + await resetSettings(); + await waitForDiagnostics(docUri); + await assertDiagnostics(docUri, []); // Expect no issues + }); + }); +}); diff --git a/client/tests/e2e/suite/extension.gxformat2.e2e.ts b/client/tests/e2e/suite/extension.gxformat2.e2e.ts new file mode 100644 index 0000000..09a7f08 --- /dev/null +++ b/client/tests/e2e/suite/extension.gxformat2.e2e.ts @@ -0,0 +1,45 @@ +// You can import and use all API from the 'vscode' module +// as well as import your extension to test it +import * as vscode from "vscode"; +import * as path from "path"; +import * as assert from "assert"; +import { beforeEach } from "mocha"; +import { + activateAndOpenInEditor, + getDocUri, + closeAllEditors, + assertDiagnostics, + resetSettings, + waitForDiagnostics, +} from "./helpers"; + +suite("Format2 (YAML) Workflows", () => { + teardown(closeAllEditors); + suite("Validation Tests", () => { + beforeEach(async () => { + await resetSettings(); + }); + test("Missing required fields return diagnostics", async () => { + const docUri = getDocUri(path.join("yaml", "validation", "test_wf_00.gxwf.yml")); + await activateAndOpenInEditor(docUri); + await waitForDiagnostics(docUri); + await assertDiagnostics(docUri, [ + { + message: "The 'steps' field is required.", + range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 21)), + severity: vscode.DiagnosticSeverity.Error, + }, + { + message: "The 'inputs' field is required.", + range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 21)), + severity: vscode.DiagnosticSeverity.Error, + }, + { + message: "The 'outputs' field is required.", + range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 21)), + severity: vscode.DiagnosticSeverity.Error, + }, + ]); + }); + }); +}); diff --git a/client/tests/e2e/suite/helpers.ts b/client/tests/e2e/suite/helpers.ts index 319b370..39d742a 100644 --- a/client/tests/e2e/suite/helpers.ts +++ b/client/tests/e2e/suite/helpers.ts @@ -41,7 +41,6 @@ export async function openDocument(docUri: vscode.Uri): Promise { await activate(); const documentEditor = await openDocumentInEditor(docUri); - await sleep(2000); // Wait for server activation return documentEditor; } @@ -49,6 +48,17 @@ export async function sleep(ms: number): Promise { return new Promise((resolve) => setTimeout(resolve, ms)); } +export async function waitForDiagnostics(docUri: vscode.Uri, timeoutInMilliseconds = 2000): Promise { + const waitMilliseconds = 100; + let waitTimeout = timeoutInMilliseconds; + let diagnostics = vscode.languages.getDiagnostics(docUri); + while (waitTimeout > 0 && !diagnostics.length) { + await sleep(waitMilliseconds); + waitTimeout -= waitMilliseconds; + diagnostics = vscode.languages.getDiagnostics(docUri); + } +} + export const getDocPath = (filePath: string): string => { return path.resolve(__dirname, path.join("..", "..", "..", "..", "test-data", filePath)); }; @@ -92,5 +102,6 @@ export async function updateSettings(setting: string, value: unknown): Promise { const configuration = vscode.workspace.getConfiguration("galaxyWorkflows"); await configuration.update("cleaning.cleanableProperties", undefined, true); - return configuration.update("validation.profile", undefined, true); + await configuration.update("validation.profile", undefined, true); + return sleep(500); // Wait for settings to be applied } diff --git a/jest.config.js b/jest.config.js index fe961f8..a13e749 100644 --- a/jest.config.js +++ b/jest.config.js @@ -1,16 +1,25 @@ // For a detailed explanation regarding each configuration property, visit: // https://jestjs.io/docs/en/configuration.html +/* eslint-disable @typescript-eslint/no-var-requires */ +const { pathsToModuleNameMapper } = require("ts-jest"); +const { compilerOptions } = require("./tsconfig.json"); + module.exports = { preset: "ts-jest", globals: { "ts-jest": { - tsconfig: "tsconfig.json", + tsconfig: compilerOptions, }, }, // The glob patterns Jest uses to detect test files - testMatch: ["**/__tests__/*.+(ts|tsx|js)", "**/unit/*.test.ts"], + testMatch: ["**/__tests__/*.+(ts|tsx|js)", "**/*.test.ts"], // An array of file extensions your modules use - moduleFileExtensions: ["ts", "tsx", "js"], + moduleFileExtensions: ["ts", "tsx", "js", "yaml"], + transform: { + // ... other transforms ... + "\\.yaml$": "jest-transform-yaml", + }, + moduleNameMapper: pathsToModuleNameMapper(compilerOptions.paths, { prefix: "/" }), }; diff --git a/package-lock.json b/package-lock.json index 9c8c5b8..2fcf64f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -22,18 +22,20 @@ "eslint": "^8.14.0", "eslint-config-prettier": "^8.5.0", "eslint-plugin-prettier": "^4.0.0", - "jest": "^28.0.3", + "jest": "^27.5.1", + "jest-transform-yaml": "^1.0.0", "merge-options": "^3.0.4", "mocha": "^9.2.2", "path-browserify": "^1.0.1", "prettier": "2.6.2", "process": "^0.11.10", "rimraf": "^3.0.2", - "ts-jest": "^28.0.1", + "ts-jest": "^27.1.5", "ts-loader": "^9.2.9", "typescript": "^4.6.3", "webpack": "^5.72.0", - "webpack-cli": "^4.9.2" + "webpack-cli": "^4.9.2", + "yaml-loader": "^0.8.0" }, "engines": { "vscode": "^1.66.0" @@ -222,9 +224,9 @@ } }, "node_modules/@babel/helper-plugin-utils": { - "version": "7.16.7", - "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.16.7.tgz", - "integrity": "sha512-Qg3Nk7ZxpgMrsox6HreY1ZNKdBq7K72tDSliA6dCl5f007jR4ne8iD5UzuNnCJH2xBf2BEEVGr+/OL6Gdp7RxA==", + "version": "7.18.9", + "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.18.9.tgz", + "integrity": 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"webidl-conversions": "^6.1.0" + } + }, "which": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz", @@ -12631,15 +13448,24 @@ "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", "dev": true }, - "write-file-atomic": { - "version": "4.0.1", - "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-4.0.1.tgz", - "integrity": "sha512-nSKUxgAbyioruk6hU87QzVbY279oYT6uiwgDoujth2ju4mJ+TZau7SQBhtbTmUyuNYTuXnSyRn66FV0+eCgcrQ==", + "ws": { + "version": "7.5.9", + "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.9.tgz", + "integrity": "sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q==", "dev": true, - "requires": { - "imurmurhash": "^0.1.4", - "signal-exit": "^3.0.7" - } + "requires": {} + }, + "xml-name-validator": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-3.0.0.tgz", + "integrity": 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"sha512-LjeKnTzVBKWiQBeE2L9ssl6WprqaUIxCSNs5tle8PaDydgu3wVFXTbMfsvF2MSErpy9TDVa092n4q6adYwJaWg==", + "dev": true, + "requires": { + "javascript-stringify": "^2.0.1", + "loader-utils": "^2.0.0", + "yaml": "^2.0.0" + } + }, "yargs": { "version": "16.2.0", "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz", diff --git a/package.json b/package.json index 577e1dc..89e81af 100644 --- a/package.json +++ b/package.json @@ -233,18 +233,20 @@ "eslint": "^8.14.0", "eslint-config-prettier": "^8.5.0", "eslint-plugin-prettier": "^4.0.0", - "jest": "^28.0.3", + "jest": "^27.5.1", + "jest-transform-yaml": "^1.0.0", "merge-options": "^3.0.4", "mocha": "^9.2.2", "path-browserify": "^1.0.1", "prettier": "2.6.2", "process": "^0.11.10", "rimraf": "^3.0.2", - "ts-jest": "^28.0.1", + "ts-jest": "^27.1.5", "ts-loader": "^9.2.9", "typescript": "^4.6.3", "webpack": "^5.72.0", - "webpack-cli": "^4.9.2" + "webpack-cli": "^4.9.2", + "yaml-loader": "^0.8.0" }, "__metadata": { "id": "2306ad21-fa2c-46f9-bba8-a22e32c7cb9a", diff --git a/server/gx-workflow-ls-format2/package.json b/server/gx-workflow-ls-format2/package.json index 9db4126..159abd9 100644 --- a/server/gx-workflow-ls-format2/package.json +++ b/server/gx-workflow-ls-format2/package.json @@ -7,11 +7,10 @@ "dependencies": { "@gxwf/server-common": "*", "@gxwf/yaml-language-service": "*", + "vscode-languageserver": "^7.0.0", "vscode-languageserver-textdocument": "^1.0.4", "vscode-languageserver-types": "^3.16.0", - "vscode-languageserver": "^7.0.0", "vscode-uri": "^3.0.3" }, - "devDependencies": {}, "scripts": {} } diff --git a/server/gx-workflow-ls-format2/src/languageService.ts b/server/gx-workflow-ls-format2/src/languageService.ts index 9c36b7c..bfffb2a 100644 --- a/server/gx-workflow-ls-format2/src/languageService.ts +++ b/server/gx-workflow-ls-format2/src/languageService.ts @@ -9,9 +9,14 @@ import { Hover, CompletionList, Diagnostic, + WorkflowValidator, } from "@gxwf/server-common/src/languageTypes"; import { LanguageService, getLanguageService } from "@gxwf/yaml-language-service/src/yamlLanguageService"; import { GxFormat2WorkflowDocument } from "./gxFormat2WorkflowDocument"; +import { GalaxyWorkflowFormat2SchemaLoader } from "./schema"; +import { GxFormat2CompletionService } from "./services/completionService"; +import { GxFormat2HoverService } from "./services/hoverService"; +import { GxFormat2SchemaValidationService, WorkflowValidationService } from "./services/validation"; /** * A wrapper around the YAML Language Service to support language features @@ -19,9 +24,20 @@ import { GxFormat2WorkflowDocument } from "./gxFormat2WorkflowDocument"; */ export class GxFormat2WorkflowLanguageService extends WorkflowLanguageService { private _yamlLanguageService: LanguageService; + private _schemaLoader: GalaxyWorkflowFormat2SchemaLoader; + private _hoverService: GxFormat2HoverService; + private _completionService: GxFormat2CompletionService; + private _validationServices: WorkflowValidator[]; constructor() { super(); + this._schemaLoader = new GalaxyWorkflowFormat2SchemaLoader(); this._yamlLanguageService = getLanguageService(); + this._hoverService = new GxFormat2HoverService(this._schemaLoader.nodeResolver); + this._completionService = new GxFormat2CompletionService(this._schemaLoader.nodeResolver); + this._validationServices = [ + new GxFormat2SchemaValidationService(this._schemaLoader.nodeResolver), + new WorkflowValidationService(), + ]; } public override parseWorkflowDocument(document: TextDocument): WorkflowDocument { @@ -33,19 +49,24 @@ export class GxFormat2WorkflowLanguageService extends WorkflowLanguageService { return this._yamlLanguageService.doFormat(document, options); } - public override async doHover(workflowDocument: WorkflowDocument, position: Position): Promise { - return null; + public override doHover(workflowDocument: WorkflowDocument, position: Position): Promise { + return this._hoverService.doHover(workflowDocument.textDocument, position, workflowDocument.nodeManager); } public override async doComplete( workflowDocument: WorkflowDocument, position: Position ): Promise { - return null; + return this._completionService.doComplete(workflowDocument.textDocument, position, workflowDocument.nodeManager); } protected override async doValidation(workflowDocument: WorkflowDocument): Promise { const format2WorkflowDocument = workflowDocument as GxFormat2WorkflowDocument; - return this._yamlLanguageService.doValidation(format2WorkflowDocument.yamlDocument); + const diagnostics = await this._yamlLanguageService.doValidation(format2WorkflowDocument.yamlDocument); + for (const validator of this._validationServices) { + const results = await validator.doValidation(workflowDocument); + diagnostics.push(...results); + } + return diagnostics; } } diff --git a/server/gx-workflow-ls-format2/src/schema/definitions.ts b/server/gx-workflow-ls-format2/src/schema/definitions.ts new file mode 100644 index 0000000..db02d71 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/schema/definitions.ts @@ -0,0 +1,353 @@ +export interface SchemaDocument { + $base: string; + $namespaces?: object; + $graph: SchemaEntryBase[]; +} + +export interface SchemaEntryBase { + name: string; + type: string | string[] | unknown; + documentRoot?: boolean; +} + +export interface DocumentedSchemaEntry extends SchemaEntryBase { + doc?: string; +} + +export interface IdMapper { + mapSubject?: string; + mapPredicate?: string; +} + +export interface SchemaField extends DocumentedSchemaEntry { + default?: unknown; + jsonldPredicate?: IdMapper; +} +export interface Specialization { + specializeFrom: string; + specializeTo: string; +} + +export interface SchemaRecord extends DocumentedSchemaEntry { + fields: SchemaField[]; + extends?: string[]; + specialize?: Specialization[]; +} + +export interface SchemaEnum extends DocumentedSchemaEntry { + symbols: string[]; + extends?: string; +} + +interface SchemaType { + type: string; +} + +interface SchemaEnumType extends SchemaType { + symbols: string[]; +} + +interface SchemaArrayType extends SchemaType { + items: string; +} + +export function isSchemaEntryBase(object: unknown): object is SchemaEntryBase { + return object instanceof Object && "type" in object; +} + +export function isSchemaRecord(object: unknown): object is SchemaRecord { + return object instanceof Object && "fields" in object; +} + +export function isSchemaEnumType(object: unknown): object is SchemaEnumType { + return object instanceof Object && "symbols" in object; +} + +export function isSchemaArrayType(object: unknown): object is SchemaArrayType { + return object instanceof Object && "items" in object; +} + +export function isArrayFieldType(object: unknown): object is ArrayFieldType { + return object instanceof Object && "itemType" in object; +} + +export function isBasicFieldType(object: unknown): object is BasicFieldType { + return object instanceof Object && "typeName" in object; +} + +export type SchemaEntry = SchemaEnum | SchemaRecord | SchemaField; + +interface FieldTypeBase { + isOptional: boolean; +} + +interface BasicFieldType extends FieldTypeBase { + typeName: string; +} + +interface ArrayFieldType extends BasicFieldType { + itemType: BasicFieldType | BasicFieldType[]; +} + +interface EnumFieldType extends BasicFieldType { + symbols: string[]; +} + +function fieldTypeFactory(typeEntry: unknown): BasicFieldType[] | undefined { + if (typeof typeEntry === "string") { + let baseType: string = typeEntry; + let isOptional = baseType.endsWith("?"); + if (isOptional) { + baseType = baseType.slice(0, baseType.length - 1); + } + isOptional = isOptional || baseType === "null"; + const isArray = baseType.endsWith("[]"); + if (isArray) { + baseType = baseType.slice(0, baseType.length - 2); + const arrayType: ArrayFieldType = { + isOptional, + itemType: buildBasicFieldType(isOptional, baseType), + typeName: "array", + }; + return [arrayType]; + } + return [buildBasicFieldType(isOptional, baseType)]; + } else if (typeof typeEntry === "object") { + if (isSchemaArrayType(typeEntry)) { + const itemType = fieldTypeFactory((typeEntry as SchemaArrayType).items); + if (itemType) { + const arrayType: ArrayFieldType = { + isOptional: false, + itemType: itemType, + typeName: "array", + }; + return [arrayType]; + } + } + if (isSchemaEnumType(typeEntry)) { + const enumType: EnumFieldType = { + isOptional: false, + symbols: (typeEntry as SchemaEnumType).symbols, + typeName: "enum", + }; + return [enumType]; + } + if (typeEntry instanceof Array) { + const types: BasicFieldType[] = []; + typeEntry.forEach((e) => { + const res = fieldTypeFactory(e); + if (res) { + types.push(...res); + } + }); + return types; + } + console.debug(`Object Field type UNKNOWN: ${JSON.stringify(typeEntry)} - ${typeof typeEntry}`); + return undefined; + } else { + console.debug(`Field type NOT PROCESSED: ${JSON.stringify(typeEntry)}`); + } + + function buildBasicFieldType(isOptional: boolean, baseType: string): BasicFieldType { + return { + isOptional, + typeName: baseType.replace("#", ""), + }; + } +} + +export interface SchemaNode { + name: string; + documentation: string | undefined; + canBeArray: boolean; + typeRef: string; + isRoot: boolean; +} + +export class FieldSchemaNode implements SchemaNode, IdMapper { + public static definitions: SchemaDefinitions; + + private _allowedTypes: BasicFieldType[] = []; + private readonly _schemaField: SchemaField; + + constructor(schemaField: SchemaField) { + this._schemaField = schemaField; + if (schemaField.type instanceof Array) { + schemaField.type.forEach((typeEntry) => { + const fieldType = fieldTypeFactory(typeEntry); + if (fieldType) { + fieldType.forEach((t) => this._allowedTypes.push(t)); + } + }); + } else { + const fieldType = fieldTypeFactory(schemaField.type); + if (fieldType) { + fieldType.forEach((t) => this._allowedTypes.push(t)); + } + } + } + + public get name(): string { + return this._schemaField.name; + } + + public get documentation(): string | undefined { + return this._schemaField.doc; + } + + public get isRoot(): boolean { + return false; + } + + public get isRequired(): boolean { + return !this.isOptional; + } + + public get isOptional(): boolean { + return this._allowedTypes.some((t) => t.isOptional); + } + + public get default(): unknown { + return this._schemaField.default; + } + + public get canBeAny(): boolean { + return this._allowedTypes.some((t) => t.typeName === "Any"); + } + + public get canBeArray(): boolean { + return this.canBeAny || this._allowedTypes.some((t) => isArrayFieldType(t)); + } + + public get canBeObject(): boolean { + return this.canBeAny || this._allowedTypes.some((t) => this.isObjectType(t.typeName)); + } + + public matchesType(typeName: string): boolean { + if (this.canBeAny) return true; + if (typeName === "null" && this.isOptional) return true; + for (const allowedType of this._allowedTypes) { + if (allowedType.typeName === typeName) { + return true; + } + if (isArrayFieldType(allowedType)) { + if (allowedType.itemType instanceof Array) { + const result = allowedType.itemType.find((t) => t.typeName === typeName); + if (result) return true; + } else { + if (allowedType.itemType.typeName === typeName) { + return true; + } + } + } + } + return false; + } + + public get typeRef(): string { + if (this.canBeAny) return "Any"; + if (this.canBeArray) { + return this.getArrayItemTypeName() || "undefined"; + } + const mainType = this._allowedTypes.find((t) => t.typeName !== "null"); + //TODO: this requires more logic... we cannot assume the first non-null type to be the main + return isBasicFieldType(mainType) ? mainType.typeName : "unknown"; + } + + public get mapSubject(): string | undefined { + return this._schemaField.jsonldPredicate?.mapSubject; + } + + public get mapPredicate(): string | undefined { + return this._schemaField.jsonldPredicate?.mapPredicate; + } + + public getArrayItemTypeName(): string | undefined { + const arrayType = this._allowedTypes.find((t) => isArrayFieldType(t)) as ArrayFieldType; + if (isBasicFieldType(arrayType?.itemType)) { + return arrayType?.itemType.typeName; + } + if (arrayType?.itemType instanceof Array) { + return arrayType.itemType.map((i) => i.typeName).at(0); // TODO REMOVE AT + } + console.debug("getArrayItemTypeName -> Type name not found"); + return undefined; + } + + private isPrimitiveType(typeName: string): boolean { + return FieldSchemaNode.definitions.primitiveTypes.has(typeName); + } + + private isObjectType(typeName: string): boolean { + return FieldSchemaNode.definitions.records.has(typeName); + } +} + +export class RecordSchemaNode implements SchemaNode { + public static definitions: SchemaDefinitions; + public static readonly NULL: SchemaNode = new RecordSchemaNode({ + name: "null", + type: "null", + fields: [], + documentRoot: true, + }); + + private readonly _schemaRecord: SchemaRecord; + private readonly _fields: Map; + + constructor(schemaRecord: SchemaRecord) { + this._schemaRecord = schemaRecord; + this._fields = new Map(); + schemaRecord.fields.forEach((field) => { + this._fields.set(field.name, new FieldSchemaNode(field)); + }); + } + + public get name(): string { + return this._schemaRecord.name; + } + + public get fields(): FieldSchemaNode[] { + return Array.from(this._fields.values()); + } + + public get documentation(): string | undefined { + return this._schemaRecord.doc; + } + public get isRoot(): boolean { + return !!this._schemaRecord.documentRoot; + } + + public get canBeArray(): boolean { + return false; + } + + public get typeRef(): string { + return this._schemaRecord.name; + } + + public get typeField(): FieldSchemaNode | undefined { + return this.getFieldByName("type"); + } + + public matchesTypeField(typeName: string): boolean { + return this.typeField?.matchesType(typeName) || false; + } + + public matchesMapping(typeName: string, idMapper?: IdMapper): boolean { + if (!idMapper || !idMapper.mapSubject) return false; + const mappedField = this.getFieldByName(idMapper.mapSubject); + return mappedField?.matchesType(typeName) || false; + } + + public getFieldByName(name: string): FieldSchemaNode | undefined { + return this.fields.find((t) => t.name === name); + } +} + +export interface SchemaDefinitions { + records: Map; + fields: Map; + specializations: Map; + primitiveTypes: Set; +} diff --git a/server/gx-workflow-ls-format2/src/schema/index.ts b/server/gx-workflow-ls-format2/src/schema/index.ts new file mode 100644 index 0000000..a4239af --- /dev/null +++ b/server/gx-workflow-ls-format2/src/schema/index.ts @@ -0,0 +1,5 @@ +import { GalaxyWorkflowFormat2SchemaLoader } from "./schemaLoader"; +import { RecordSchemaNode, FieldSchemaNode, SchemaNode } from "./definitions"; +import { SchemaNodeResolver } from "./schemaNodeResolver"; + +export { GalaxyWorkflowFormat2SchemaLoader, SchemaNodeResolver, SchemaNode, RecordSchemaNode, FieldSchemaNode }; diff --git a/server/gx-workflow-ls-format2/src/schema/schemaLoader.ts b/server/gx-workflow-ls-format2/src/schema/schemaLoader.ts new file mode 100644 index 0000000..0b3acaa --- /dev/null +++ b/server/gx-workflow-ls-format2/src/schema/schemaLoader.ts @@ -0,0 +1,302 @@ +import { + FieldSchemaNode, + isSchemaEntryBase, + isSchemaEnumType, + isSchemaRecord, + RecordSchemaNode, + SchemaDefinitions, + SchemaDocument, + SchemaEntry, + SchemaEntryBase, + SchemaEnum, + SchemaField, + SchemaRecord, +} from "./definitions"; +import { SchemaNodeResolver } from "./schemaNodeResolver"; +import { SCHEMA_DOCS_v19_09_MAP } from "./versions"; + +export class GalaxyWorkflowFormat2SchemaLoader { + private _documentEntryMap = new Map>(); + private _rawSchemaEntries = new Map(); + private _namespaces = new Map(); + private _unknownTypes: string[] = []; + private _extendedTypes: Set = new Set(); + private _root?: SchemaRecord; + public readonly definitions: SchemaDefinitions; + public readonly nodeResolver: SchemaNodeResolver; + + constructor(private readonly enableDebugTrace: boolean = false) { + this._rawSchemaEntries = this.loadSchemaEntriesMap_v19_09(); + this.definitions = this.loadSchemaDefinitions(this._rawSchemaEntries); + this.nodeResolver = this.createNodeResolver(); + RecordSchemaNode.definitions = this.definitions; + FieldSchemaNode.definitions = this.definitions; + + if (this.enableDebugTrace) { + if (this._unknownTypes) { + console.debug(`UNKNOWN Types: ${this._unknownTypes.length}`); + this._unknownTypes.forEach((t) => { + console.debug(` ${t}`); + }); + } + + if (this._extendedTypes) { + console.debug(`EXTENDED Types (Unresolved): ${this._extendedTypes.size}`); + this._extendedTypes.forEach((type) => { + if (!this._rawSchemaEntries.has(type)) { + console.debug(` ${type} ${this._rawSchemaEntries.has(type) ? "[found]" : ""}`); + } + }); + } + } + } + + private loadSchemaEntriesMap_v19_09(): Map { + const entries = new Map(); + for (const schemaDoc of SCHEMA_DOCS_v19_09_MAP.values()) { + const types = this.loadSchemaDocument(schemaDoc); + types.forEach((v, k) => { + entries.set(k, v); + }); + } + return entries; + } + + private loadSchemaDefinitions(schemaEntries: Map): SchemaDefinitions { + const definitions: SchemaDefinitions = { + records: new Map(), + fields: new Map(), + specializations: new Map(), + primitiveTypes: new Set(), + }; + + this.expandEntries(schemaEntries.values()); + schemaEntries.forEach((v, k) => { + if (isSchemaRecord(v)) { + definitions.records.set(k, new RecordSchemaNode(v)); + if (v.specialize) { + v.specialize.forEach((sp) => { + definitions.specializations.set(sp.specializeFrom, sp.specializeTo); + }); + } + v.fields.forEach((field) => { + if (definitions.fields.has(field.name)) { + if (this.enableDebugTrace) console.debug("****** DUPLICATED FIELD", field.name); + } + definitions.fields.set(field.name, new FieldSchemaNode(field)); + }); + } else if (isSchemaEnumType(v) && v.name === "GalaxyType") { + definitions.primitiveTypes = new Set(v.symbols); + } + }); + return definitions; + } + + private loadSchemaDocument(schemaDoc: SchemaDocument): Map { + if (this.enableDebugTrace) console.debug(`Loading schema doc: ${schemaDoc.$base}`); + this.registerDocumentNamespaces(schemaDoc); + const documentEntries = new Map(); + schemaDoc.$graph.forEach((entry: SchemaEntryBase) => { + let loadedEntry: SchemaEntry | undefined; + if (entry.type == "enum") { + loadedEntry = this.loadEnum(entry as SchemaEnum); + } else if (entry.type == "record") { + const recordEntry = this.loadRecord(entry as SchemaRecord); + if (entry.documentRoot) { + this._root = recordEntry; + } + loadedEntry = recordEntry; + } else { + this._unknownTypes.push(entry.type as string); + } + if (loadedEntry) { + documentEntries.set(entry.name, loadedEntry); + } + }); + this._documentEntryMap.set(schemaDoc.$base, documentEntries); + return documentEntries; + } + + private registerDocumentNamespaces(schemaDoc: SchemaDocument): void { + if (schemaDoc.$namespaces) { + Object.entries(schemaDoc.$namespaces).forEach(([k, v]) => { + this._namespaces.set(k, v); + }); + } + } + + private loadEnum(entry: SchemaEnum): SchemaEnum { + if (this.enableDebugTrace) console.debug(`Enum: ${entry.name} ${"abstract" in entry ? "[abstract]" : ""}`); + const enumEntry: SchemaEnum = { + name: entry.name, + type: entry.type, + doc: entry.doc, + symbols: entry.symbols, + extends: entry.extends, + }; + + return enumEntry; + } + + private loadRecord(entry: SchemaRecord): SchemaRecord { + if (this.enableDebugTrace) + console.debug( + `Record: ${entry.name} ${"abstract" in entry ? "[abstract]" : ""} ${"extends" in entry ? "[extends]" : ""}` + ); + const fields = this.readEntryFields(entry); + + const recordEntry: SchemaRecord = { + name: entry.name, + type: entry.type, + doc: entry.doc, + fields: fields, + extends: entry.extends ? (entry.extends instanceof Array ? [...entry.extends] : [entry.extends]) : [], + specialize: entry.specialize, + }; + + if (recordEntry.extends) { + if (recordEntry.extends instanceof Array) { + recordEntry.extends.forEach((type) => { + this._extendedTypes.add(type); + }); + } else { + this._extendedTypes.add(recordEntry.extends); + } + } + + if (recordEntry.specialize) { + recordEntry.specialize.forEach((sp) => { + sp.specializeFrom = this.resolveTypeName(sp.specializeFrom); + sp.specializeTo = this.resolveTypeName(sp.specializeTo); + }); + } + + return recordEntry; + } + + private readEntryFields(entry: SchemaRecord): SchemaField[] { + const fields: SchemaField[] = []; + if (entry.fields instanceof Array) { + entry.fields.forEach((field) => { + fields.push(this.loadField(field)); + }); + } else { + // Is an Object + if (entry.fields) { + Object.entries(entry.fields).forEach(([key, value]) => { + if (isSchemaEntryBase(value)) { + fields.push({ name: key, type: value.type }); + } + }); + } else { + if (this.enableDebugTrace) console.debug("------- NO FIELDS"); + } + } + // if (fields) { + // fields.forEach((field) => { + // console.debug(` ${field.name}: ${field.type}`); + // }); + // } + return fields; + } + + private loadField(field: SchemaField): SchemaField { + let fieldType = field.type; + + if (typeof fieldType === "string") { + fieldType = this.resolveTypeName(fieldType as string); + } else { + if (this.enableDebugTrace) + console.debug(` --Field type NOT string: ${JSON.stringify(fieldType)} -> ${typeof fieldType}`); + } + return { + name: field.name, + type: fieldType, + default: field.default, + doc: field.doc, + jsonldPredicate: field.jsonldPredicate, + documentRoot: field.documentRoot, + }; + } + + private resolveTypeName(rawTypeName: string): string { + const tokens = rawTypeName.split(":"); + if (tokens.length > 1) { + const namespace = tokens.at(0); + const type = tokens.at(1); + if (namespace && type) { + const docBase = this._namespaces.get(namespace); + if (docBase) { + const schemaTypes = this._documentEntryMap.get(docBase); + if (schemaTypes?.has(type)) { + rawTypeName = type; + } else { + if (this.enableDebugTrace) console.debug(`Type ${type} not found in namespace ${namespace}.`); + } + } else { + if (this.enableDebugTrace) console.debug(`Namespace ${namespace} not found.`); + } + } + } + return rawTypeName; + } + + private resolveTypeToSchemaEntry(rawTypeName: string): SchemaEntry { + const typeName = this.resolveTypeName(rawTypeName); + if (this._rawSchemaEntries.has(typeName)) { + return this._rawSchemaEntries.get(typeName) as SchemaEntry; + } + throw new Error(`Unresolvable type ${rawTypeName}`); + } + + private createNodeResolver(): SchemaNodeResolver { + return new SchemaNodeResolver(this.definitions, this._root); + } + + /** Expands all entries with the types defined in the extended types.*/ + private expandEntries(schemaEntries: IterableIterator): void { + for (const entry of schemaEntries) { + if (isSchemaRecord(entry)) { + this.expandRecord(entry); + } else if (isSchemaEnumType(entry)) { + this.expandEnum(entry); + } + } + } + + private expandRecord(record: SchemaRecord): SchemaRecord { + if (!record.extends) { + return record; + } + const extensionFields = this.collectExtensionFields(record, []); + record.fields.push(...extensionFields); + record.extends = []; + return record; + } + + private expandEnum(entry: SchemaEnum): SchemaEnum { + if (!entry.extends) { + return entry; + } + const resolved = this.resolveTypeToSchemaEntry(entry.extends); + if (isSchemaEnumType(resolved)) { + resolved.symbols.forEach((s) => { + const symbol = s.indexOf(":") > 0 ? (s.split(":").at(1) as string) : s; + entry.symbols.push(symbol); + }); + } + entry.extends = undefined; + return entry; + } + + private collectExtensionFields(record: SchemaRecord, extensionFields: SchemaField[]): SchemaField[] { + record.extends?.forEach((typeToExtend) => { + const resolved = this.resolveTypeToSchemaEntry(typeToExtend); + if (isSchemaRecord(resolved)) { + extensionFields.push(...resolved.fields); + return this.collectExtensionFields(resolved, extensionFields); + } + }); + return extensionFields; + } +} diff --git a/server/gx-workflow-ls-format2/src/schema/schemaNodeResolver.ts b/server/gx-workflow-ls-format2/src/schema/schemaNodeResolver.ts new file mode 100644 index 0000000..17dc3c7 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/schema/schemaNodeResolver.ts @@ -0,0 +1,38 @@ +import { NodePath, Segment } from "@gxwf/server-common/src/ast/types"; +import { SchemaDefinitions, SchemaNode, RecordSchemaNode, SchemaRecord } from "./definitions"; + +export class SchemaNodeResolver { + public readonly rootNode: SchemaNode; + constructor(public readonly definitions: SchemaDefinitions, root?: SchemaRecord) { + this.rootNode = root ? new RecordSchemaNode(root) : RecordSchemaNode.NULL; + } + + public resolveSchemaContext(path: NodePath): SchemaNode | undefined { + const toWalk = path.slice(); + const lastSegment = toWalk.pop(); + const schemaNodeFound = this.getSchemaNodeForSegment(lastSegment); + while (toWalk.length && !schemaNodeFound) { + const parentSegment = toWalk.pop(); + const parentNode = this.getSchemaNodeForSegment(parentSegment); + if (parentNode) { + return this.getSchemaNodeForSegment(parentNode.typeRef); + } + } + return schemaNodeFound; + } + + public getSchemaNodeByTypeRef(typeRef: string): SchemaNode | undefined { + return this.getSchemaNodeForSegment(typeRef); + } + + private getSchemaNodeForSegment(pathSegment?: Segment): SchemaNode | undefined { + if (typeof pathSegment === "string") { + pathSegment = this.definitions.specializations.get(pathSegment) || pathSegment; + if (this.definitions.records.has(pathSegment)) { + return this.definitions.records.get(pathSegment); + } + return this.definitions.fields.get(pathSegment); + } + return undefined; + } +} diff --git a/server/gx-workflow-ls-format2/src/schema/versions.ts b/server/gx-workflow-ls-format2/src/schema/versions.ts new file mode 100644 index 0000000..ed737d6 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/schema/versions.ts @@ -0,0 +1,21 @@ +//TODO: remove this reference when https://github.com/sumwatshade/jest-transform-yaml/pull/20 is merged and upgrade to jest 28 +// eslint-disable-next-line @typescript-eslint/triple-slash-reference +/// + +import schema_v19_09_workflows from "@schemas/gxformat2/v19_09/workflows.yaml"; +import schema_common_metaschema_base from "@schemas/gxformat2/common/metaschema/metaschema_base.yaml"; +import schema_v19_09_process from "@schemas/gxformat2/v19_09/process.yaml"; +import schema_common from "@schemas/gxformat2/common/common.yaml"; +import { SchemaDocument } from "./definitions"; + +/** + * All gxformat2 version 19_09 schema documents. + * + * These documents are raw yaml documents loaded by webpack. + * */ +export const SCHEMA_DOCS_v19_09_MAP = new Map([ + [schema_common_metaschema_base.$base, schema_common_metaschema_base], + [schema_v19_09_process.$base, schema_v19_09_process], + [schema_common.$base, schema_common], + [schema_v19_09_workflows.$base, schema_v19_09_workflows], +]); diff --git a/server/gx-workflow-ls-format2/src/services/completionService.ts b/server/gx-workflow-ls-format2/src/services/completionService.ts new file mode 100644 index 0000000..bee39b7 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/services/completionService.ts @@ -0,0 +1,88 @@ +import { ASTNodeManager } from "@gxwf/server-common/src/ast/nodeManager"; +import { ASTNode } from "@gxwf/server-common/src/ast/types"; +import { + CompletionItem, + CompletionItemKind, + CompletionList, + Position, + TextDocument, +} from "@gxwf/server-common/src/languageTypes"; +import { TextBuffer } from "@gxwf/yaml-language-service/src/utils/textBuffer"; +import { RecordSchemaNode, SchemaNode, SchemaNodeResolver } from "../schema"; + +export class GxFormat2CompletionService { + constructor(protected readonly schemaNodeResolver: SchemaNodeResolver) {} + + public doComplete( + textDocument: TextDocument, + position: Position, + nodeManager: ASTNodeManager + ): Promise { + const result: CompletionList = { + items: [], + isIncomplete: false, + }; + // TODO: Refactor most of this to an Context class with all the information around the cursor + const textBuffer = new TextBuffer(textDocument); + const text = textBuffer.getText(); + const offset = textBuffer.getOffsetAt(position); + const node = nodeManager.getNodeFromOffset(offset); + if (!node) { + return Promise.resolve(result); + } + if (text.charAt(offset - 1) === ":") { + return Promise.resolve(result); + } + + const currentWord = textBuffer.getCurrentWord(offset); + + DEBUG_printNodeName(node); + + const existing = nodeManager.getDeclaredPropertyNames(node); + if (nodeManager.isRoot(node)) { + result.items = this.getProposedItems(this.schemaNodeResolver.rootNode, currentWord, existing); + return Promise.resolve(result); + } + const nodePath = nodeManager.getPathFromNode(node); + const schemaNode = this.schemaNodeResolver.resolveSchemaContext(nodePath); + if (schemaNode) { + result.items = this.getProposedItems(schemaNode, currentWord, existing); + } + return Promise.resolve(result); + } + + private getProposedItems(schemaNode: SchemaNode, currentWord: string, exclude: Set): CompletionItem[] { + const result: CompletionItem[] = []; + if (schemaNode instanceof RecordSchemaNode) { + schemaNode.fields + .filter((f) => f.name.startsWith(currentWord)) + .forEach((field) => { + if (exclude.has(field.name)) return; + const item: CompletionItem = { + label: field.name, + documentation: field.documentation, + sortText: `_${field.name}`, + kind: CompletionItemKind.Field, + insertText: `${field.name}: `, + }; + result.push(item); + }); + } + return result; + } +} + +function DEBUG_printNodeName(node: ASTNode): void { + let nodeName = "_root_"; + if (node?.type === "property") { + nodeName = node.keyNode.value; + console.debug("COMPLETION NODE PROPERTY", nodeName); + } else if (node?.type === "object") { + console.debug(`COMPLETION NODE OBJECT:`); + node.properties.forEach((p) => { + console.debug(` ${p.keyNode.value}`); + }); + } else { + console.debug("UNKNOWN"); + } +} diff --git a/server/gx-workflow-ls-format2/src/services/hoverService.ts b/server/gx-workflow-ls-format2/src/services/hoverService.ts new file mode 100644 index 0000000..11fd931 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/services/hoverService.ts @@ -0,0 +1,82 @@ +import { ASTNodeManager } from "@gxwf/server-common/src/ast/nodeManager"; +import { NodePath } from "@gxwf/server-common/src/ast/types"; +import { Hover, MarkupContent, MarkupKind, Position, Range, TextDocument } from "@gxwf/server-common/src/languageTypes"; +import { SchemaNode, SchemaNodeResolver } from "../schema"; + +export class GxFormat2HoverService { + constructor(protected readonly schemaNodeResolver: SchemaNodeResolver) {} + + //Based on https://github.com/microsoft/vscode-json-languageservice/blob/12275e448a91973777c94a2e5d92c961f281231a/src/services/jsonHover.ts#L23 + public async doHover( + textDocument: TextDocument, + position: Position, + nodeManager: ASTNodeManager + ): Promise { + const offset = textDocument.offsetAt(position); + let node = nodeManager.getNodeFromOffset(offset); + if ( + !node || + ((node.type === "object" || node.type === "array") && + offset > node.offset + 1 && + offset < node.offset + node.length - 1) + ) { + return Promise.resolve(null); + } + const hoverRangeNode = node; + + // use the property description when hovering over an object key + if (node.type === "string") { + const parent = node.parent; + if (parent && parent.type === "property" && parent.keyNode === node) { + node = parent.valueNode; + if (!node) { + return Promise.resolve(null); + } + } + } + + const hoverRange = Range.create( + textDocument.positionAt(hoverRangeNode.offset), + textDocument.positionAt(hoverRangeNode.offset + hoverRangeNode.length) + ); + + const location = nodeManager.getPathFromNode(hoverRangeNode); + const schemaNode = this.schemaNodeResolver.resolveSchemaContext(location); + const contents = this.getHoverMarkdownContentsForNode(schemaNode); + // DEBUG + //contents.push(...this.debugInfo(location, schemaNode)); + const hover = this.createHover(contents.join("\n\n"), hoverRange); + return Promise.resolve(hover); + } + + private getHoverMarkdownContentsForNode(schemaNode?: SchemaNode): string[] { + const contents = []; + if (schemaNode) { + contents.push(`**${schemaNode?.name}**`); + contents.push(schemaNode?.documentation || "Doc not found"); + } else { + contents.push("Schema node not found"); + } + return contents; + } + + private createHover(contents: string, hoverRange: Range): Hover { + const markupContent: MarkupContent = { + kind: MarkupKind.Markdown, + value: contents, + }; + const result: Hover = { + contents: markupContent, + range: hoverRange, + }; + return result; + } + + private debugInfo(location: NodePath, schemaNode?: SchemaNode): string[] { + return ["---", `## ${location}`, "---", `${this.toMarkdownFencedCodeBlock(schemaNode)}`]; + } + + private toMarkdownFencedCodeBlock(object: unknown): string { + return "```json\n" + `${JSON.stringify(object, null, 2)}` + "\n```"; + } +} diff --git a/server/gx-workflow-ls-format2/src/services/validation/index.ts b/server/gx-workflow-ls-format2/src/services/validation/index.ts new file mode 100644 index 0000000..904820f --- /dev/null +++ b/server/gx-workflow-ls-format2/src/services/validation/index.ts @@ -0,0 +1,4 @@ +import { GxFormat2SchemaValidationService } from "./schemaValidationService"; +import { WorkflowValidationService } from "./workflowValidationService"; + +export { GxFormat2SchemaValidationService, WorkflowValidationService }; diff --git a/server/gx-workflow-ls-format2/src/services/validation/schemaValidationService.ts b/server/gx-workflow-ls-format2/src/services/validation/schemaValidationService.ts new file mode 100644 index 0000000..4705302 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/services/validation/schemaValidationService.ts @@ -0,0 +1,105 @@ +import { ASTNodeManager } from "@gxwf/server-common/src/ast/nodeManager"; +import { ASTNode, ObjectASTNode } from "@gxwf/server-common/src/ast/types"; +import { + Diagnostic, + DiagnosticSeverity, + Range, + WorkflowDocument, + WorkflowValidator, +} from "@gxwf/server-common/src/languageTypes"; +import { SchemaNode, SchemaNodeResolver } from "../../schema"; +import { RecordSchemaNode, IdMapper } from "../../schema/definitions"; + +export class GxFormat2SchemaValidationService implements WorkflowValidator { + constructor(protected readonly schemaNodeResolver: SchemaNodeResolver) {} + + public doValidation(workflowDocument: WorkflowDocument): Promise { + const diagnostics: Diagnostic[] = []; + this.collectSchemaDiagnostics(workflowDocument, diagnostics); + return Promise.resolve(diagnostics); + } + + private collectSchemaDiagnostics(workflowDocument: WorkflowDocument, diagnostics: Diagnostic[]): void { + if (workflowDocument.nodeManager.root) { + this.collectDiagnostics( + workflowDocument.nodeManager, + workflowDocument.nodeManager.root, + this.schemaNodeResolver.rootNode, + diagnostics + ); + } + } + + private collectDiagnostics( + nodeManager: ASTNodeManager, + node: ASTNode, + schemaNode: SchemaNode, + diagnostics: Diagnostic[], + parenSchemaNode?: SchemaNode + ): void { + const range = this.getRange(nodeManager, node); + if (schemaNode instanceof RecordSchemaNode) { + switch (node.type) { + case "object": + this.validateObjectNode(nodeManager, node, schemaNode, range, diagnostics); + break; + + default: + this.validateNodeTypeDefinition(schemaNode, node, range, diagnostics, parenSchemaNode); + break; + } + } + } + + private validateObjectNode( + nodeManager: ASTNodeManager, + node: ObjectASTNode, + schemaNode: RecordSchemaNode, + range: Range, + diagnostics: Diagnostic[] + ): void { + schemaNode.fields.forEach((schemaFieldNode) => { + const propertyNode = node.properties.find((prop) => prop.keyNode.value === schemaFieldNode.name); + const nodeFound = propertyNode !== undefined; + if (schemaFieldNode.isRequired && !nodeFound) { + diagnostics.push( + Diagnostic.create(range, `The '${schemaFieldNode.name}' field is required.`, DiagnosticSeverity.Error) + ); + } + if (nodeFound) { + const childSchemaNode = this.schemaNodeResolver.getSchemaNodeByTypeRef(schemaFieldNode.typeRef); + if (childSchemaNode && propertyNode.valueNode) { + if (schemaFieldNode.canBeArray) { + propertyNode.valueNode.children?.forEach((item) => { + if (item.type === "property" && item.valueNode) { + this.collectDiagnostics(nodeManager, item.valueNode, childSchemaNode, diagnostics, schemaFieldNode); + } + }); + } else { + this.collectDiagnostics(nodeManager, propertyNode.valueNode, childSchemaNode, diagnostics, schemaFieldNode); + } + } + } + }); + } + + private validateNodeTypeDefinition( + schemaNode: RecordSchemaNode, + node: ASTNode, + range: Range, + diagnostics: Diagnostic[], + parenSchemaNode?: SchemaNode + ): void { + if (!schemaNode.matchesTypeField(node.type) && !schemaNode.matchesMapping(node.type, parenSchemaNode as IdMapper)) { + diagnostics.push(Diagnostic.create(range, `${schemaNode.name} definition expected`, DiagnosticSeverity.Error)); + } + } + + private getRange(nodeManager: ASTNodeManager, node: ASTNode): Range { + if (node === nodeManager.root) { + const classNode = nodeManager.getNodeFromPath("class") ?? node; + return nodeManager.getNodeRange(classNode); + } + return nodeManager.getNodeRange(node); + } +} diff --git a/server/gx-workflow-ls-format2/src/services/validation/workflowValidationService.ts b/server/gx-workflow-ls-format2/src/services/validation/workflowValidationService.ts new file mode 100644 index 0000000..9e1f0e9 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/services/validation/workflowValidationService.ts @@ -0,0 +1,56 @@ +import { + Diagnostic, + DiagnosticSeverity, + WorkflowDocument, + WorkflowValidator, +} from "@gxwf/server-common/src/languageTypes"; + +export class WorkflowValidationService implements WorkflowValidator { + public doValidation(workflowDocument: WorkflowDocument): Promise { + const diagnostics: Diagnostic[] = [ + ...collectStepErrorDiagnostics(workflowDocument), + ...collectToolDiagnostics(workflowDocument), + ]; + return Promise.resolve(diagnostics); + } +} + +export function collectStepErrorDiagnostics(workflowDocument: WorkflowDocument): Diagnostic[] { + const diagnostics: Diagnostic[] = []; + const steps = workflowDocument.nodeManager.getStepNodes(true); + steps.forEach((step) => { + const errors = step.properties.find((p) => p.keyNode.value === "errors"); + if (errors) { + const range = workflowDocument.nodeManager.getNodeRange(errors); + diagnostics.push( + Diagnostic.create( + range, + `Tool step contains error indicated during Galaxy export - ${errors}`, + DiagnosticSeverity.Warning + ) + ); + } + }); + return diagnostics; +} + +export function collectToolDiagnostics(workflowDocument: WorkflowDocument): Diagnostic[] { + const diagnostics: Diagnostic[] = []; + const steps = workflowDocument.nodeManager.getStepNodes(true); + steps.forEach((step) => { + const tool_id = step.properties.find((p) => p.keyNode.value === "tool_id"); + if (tool_id) { + if (tool_id.valueNode?.value?.toString().includes("testtoolshed")) { + const range = workflowDocument.nodeManager.getNodeRange(tool_id); + diagnostics.push( + Diagnostic.create( + range, + `Step references a tool from the test tool shed, this should be replaced with a production tool`, + DiagnosticSeverity.Warning + ) + ); + } + } + }); + return diagnostics; +} diff --git a/server/gx-workflow-ls-format2/src/types.d.ts b/server/gx-workflow-ls-format2/src/types.d.ts new file mode 100644 index 0000000..6383136 --- /dev/null +++ b/server/gx-workflow-ls-format2/src/types.d.ts @@ -0,0 +1,4 @@ +declare module "*.yaml" { + const data: any; + export default data; +} diff --git a/server/gx-workflow-ls-format2/tests/integration/schema.test.ts b/server/gx-workflow-ls-format2/tests/integration/schema.test.ts new file mode 100644 index 0000000..f8dacda --- /dev/null +++ b/server/gx-workflow-ls-format2/tests/integration/schema.test.ts @@ -0,0 +1,197 @@ +import { NodePath } from "@gxwf/server-common/src/ast/types"; +import { GalaxyWorkflowFormat2SchemaLoader, RecordSchemaNode, SchemaNodeResolver } from "../../src/schema"; + +describe("Gxformat2 Schema Handling", () => { + describe("Schema Version 19_09", () => { + let schemaLoader: GalaxyWorkflowFormat2SchemaLoader; + beforeAll(() => { + schemaLoader = new GalaxyWorkflowFormat2SchemaLoader(); + }); + describe("GalaxyWorkflowFormat2SchemaLoader", () => { + it("should load all schema record definitions", () => { + expect(schemaLoader.definitions.records.size).toBe(25); + }); + }); + + describe("SchemaNodeResolver", () => { + let nodeResolver: SchemaNodeResolver; + beforeAll(() => { + nodeResolver = schemaLoader.nodeResolver; + }); + describe("resolveSchemaContext", () => { + it.each([ + [["class"], "class"], + [["inputs"], "inputs"], + [["inputs", 0], "WorkflowInputParameter"], + [["inputs", 0, "doc"], "doc"], + [["inputs", "input1"], "WorkflowInputParameter"], + [["inputs", "input1", "label"], "label"], + [["outputs"], "outputs"], + [["outputs", 1], "WorkflowOutputParameter"], + [["outputs", "output1"], "WorkflowOutputParameter"], + [["steps"], "steps"], + [["steps", 5], "WorkflowStep"], + [["steps", "random", "tool_id"], "tool_id"], + ])("returns expected schema node name from path", (nodePath: NodePath, expectedNodeName: string) => { + const schemaNode = nodeResolver.resolveSchemaContext(nodePath); + expect(schemaNode).toBeDefined(); + expect(schemaNode?.name).toBe(expectedNodeName); + }); + }); + }); + + describe("Definitions", () => { + function expectRecordHasOptionalStringField( + record: RecordSchemaNode, + fieldName: string, + canBeArray = false + ): void { + const field = record.getFieldByName(fieldName); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(canBeArray); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("string"); + } + describe("GalaxyWorkflow Record", () => { + it("should have the expected field definitions", () => { + const record = schemaLoader.definitions.records.get("GalaxyWorkflow") as RecordSchemaNode; + expect(record).toBeDefined(); + expect(record.name).toBe("GalaxyWorkflow"); + expect(record.documentation).toBeDefined(); + expect(record.fields.length).toBe(13); + let field = record.getFieldByName("class"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(false); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("string"); + field = record.getFieldByName("steps"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(false); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("WorkflowStep"); + field = record.getFieldByName("report"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(true); + expect(field?.typeRef).toBe("Report"); + field = record.getFieldByName("tags"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("string"); + field = record.getFieldByName("creator"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(true); + expect(field?.typeRef).toBe("Any"); + field = record.getFieldByName("license"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("string"); + field = record.getFieldByName("release"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("string"); + + // HasUUID + expectRecordHasOptionalStringField(record, "uuid"); + + expectRecordHasOptionalStringField(record, "id"); + expectRecordHasOptionalStringField(record, "label"); + expectRecordHasOptionalStringField(record, "doc", true); + }); + }); + + describe("WorkflowStep Record", () => { + it("should have the expected field definitions", () => { + const record = schemaLoader.definitions.records.get("WorkflowStep") as RecordSchemaNode; + expect(record).toBeDefined(); + expect(record.name).toBe("WorkflowStep"); + expect(record.documentation).toBeDefined(); + expect(record.fields.length).toBe(16); + let field = record.getFieldByName("in"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(false); + expect(field?.matchesType("null")).toBe(true); + expect(field?.matchesType("WorkflowStepInput")).toBe(true); + field = record.getFieldByName("out"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(false); + expect(field?.matchesType("null")).toBe(true); + expect(field?.matchesType("string")).toBe(true); + expect(field?.matchesType("WorkflowStepOutput")).toBe(true); + expect(field?.matchesType("Any")).toBe(false); + field = record.getFieldByName("state"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.typeRef).toBe("Any"); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(true); + expect(field?.matchesType("null")).toBe(true); + expect(field?.matchesType("string")).toBe(true); + expect(field?.matchesType("anything...")).toBe(true); + field = record.getFieldByName("type"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(false); + expect(field?.default).toBe("tool"); + field = record.getFieldByName("run"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(true); + expect(field?.typeRef).toBe("GalaxyWorkflow"); + field = record.getFieldByName("runtime_inputs"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(true); + expect(field?.canBeObject).toBe(false); + expect(field?.typeRef).toBe("string"); + + expectRecordHasOptionalStringField(record, "id"); + expectRecordHasOptionalStringField(record, "label"); + expectRecordHasOptionalStringField(record, "doc", true); + + // HasStepPosition + field = record.getFieldByName("position"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(true); + expect(field?.typeRef).toBe("StepPosition"); + + // ReferencesTool + expectRecordHasOptionalStringField(record, "tool_id"); + expectRecordHasOptionalStringField(record, "tool_version"); + field = record.getFieldByName("tool_shed_repository"); + expect(field).toBeDefined(); + expect(field?.isOptional).toBe(true); + expect(field?.canBeArray).toBe(false); + expect(field?.canBeObject).toBe(true); + expect(field?.typeRef).toBe("ToolShedRepository"); + + // HasStepErrors + expectRecordHasOptionalStringField(record, "errors"); + + // HasUUID + expectRecordHasOptionalStringField(record, "uuid"); + }); + }); + }); + }); +}); diff --git a/server/jest.config.js b/server/jest.config.js index 9d817ae..a13e749 100644 --- a/server/jest.config.js +++ b/server/jest.config.js @@ -1,16 +1,25 @@ // For a detailed explanation regarding each configuration property, visit: // https://jestjs.io/docs/en/configuration.html +/* eslint-disable @typescript-eslint/no-var-requires */ +const { pathsToModuleNameMapper } = require("ts-jest"); +const { compilerOptions } = require("./tsconfig.json"); + module.exports = { preset: "ts-jest", globals: { "ts-jest": { - tsconfig: "../tsconfig.json", + tsconfig: compilerOptions, }, }, // The glob patterns Jest uses to detect test files - testMatch: ["**/__tests__/*.+(ts|tsx|js)", "**/unit/*.test.ts"], + testMatch: ["**/__tests__/*.+(ts|tsx|js)", "**/*.test.ts"], // An array of file extensions your modules use - moduleFileExtensions: ["ts", "tsx", "js"], + moduleFileExtensions: ["ts", "tsx", "js", "yaml"], + transform: { + // ... other transforms ... + "\\.yaml$": "jest-transform-yaml", + }, + moduleNameMapper: pathsToModuleNameMapper(compilerOptions.paths, { prefix: "/" }), }; diff --git a/server/package-lock.json b/server/package-lock.json index 0be7312..61fd9f6 100644 --- a/server/package-lock.json +++ b/server/package-lock.json @@ -24,8 +24,7 @@ "vscode-languageserver-textdocument": "^1.0.4", "vscode-languageserver-types": "^3.16.0", "vscode-uri": "^3.0.3" - }, - "devDependencies": {} + } }, "gx-workflow-ls-native": { "version": "0.1.0", diff --git a/server/packages/server-common/src/ast/nodeManager.ts b/server/packages/server-common/src/ast/nodeManager.ts index ecd3726..2837796 100644 --- a/server/packages/server-common/src/ast/nodeManager.ts +++ b/server/packages/server-common/src/ast/nodeManager.ts @@ -1,6 +1,6 @@ import { Position, Range, TextDocument } from "../languageTypes"; -import { ParsedDocument, ASTNode, ObjectASTNode } from "./types"; -import { findNodeAtOffset, getPropertyNodeFromPath } from "./utils"; +import { ParsedDocument, ASTNode, ObjectASTNode, NodePath, Segment, PropertyASTNode } from "./types"; +import { getPropertyNodeFromPath } from "./utils"; export class ASTNodeManager { constructor(private readonly textDocument: TextDocument, private readonly parsedDocument: ParsedDocument) {} @@ -9,11 +9,8 @@ export class ASTNodeManager { return this.parsedDocument.root; } - public getNodeFromOffset(offset: number, includeRightBound = false): ASTNode | undefined { - if (this.root) { - return findNodeAtOffset(this.root, offset, includeRightBound); - } - return undefined; + public getNodeFromOffset(offset: number): ASTNode | undefined { + return this.parsedDocument.getNodeFromOffset(offset); } public getNodeAtPosition(position: Position): ASTNode | undefined { @@ -57,6 +54,10 @@ export class ASTNodeManager { return node === lastNode; } + public isRoot(node: ASTNode): boolean { + return node.parent === undefined; + } + public getPreviousSiblingNode(node: ASTNode): ASTNode | null { const parent = node.parent; if (!parent || !parent.children) { @@ -69,27 +70,92 @@ export class ASTNodeManager { return parent.children[previousNodeIndex]; } + public getChildren(node: ASTNode): ASTNode[] { + return node.children ?? []; + } + + public getDeclaredPropertyNames(node: ASTNode): Set { + const declaredNodes = this.getChildren(node); + const result = new Set(); + declaredNodes.forEach((node) => { + if (node.type === "property") { + const key = node.keyNode.value; + result.add(key); + } + }); + return result; + } + public getNodeFromPath(path: string): ASTNode | null { const root = this.root; if (!root) return null; return getPropertyNodeFromPath(root, path); } - public getStepNodes(): ObjectASTNode[] { + public getAllPropertyNodesByName(name: string): PropertyASTNode[] { + const result: PropertyASTNode[] = []; + const root = this.root; + if (!root) return result; + + this.visit((node) => { + if (node.type === "property" && node.keyNode.value === name && node.valueNode?.type === "object") { + result.push(node); + } + return true; + }); + return result; + } + + public getPathFromNode(node: ASTNode): NodePath { + const path: NodePath = []; + let current: ASTNode | undefined = node; + while (current) { + const segment = this.getNodeSegment(current); + if (segment) { + path.push(segment); + } + current = current.parent; + } + return path.reverse(); + } + + private getNodeSegment(node: ASTNode): Segment | undefined { + if (node.type === "property") { + const name = node.keyNode.value as string; + return name; + } + if (node.parent?.type === "array") { + const index = node.parent.children.indexOf(node); + if (index !== -1) { + return index; + } + } + } + + public getStepNodes(includeSubworkflows = false): ObjectASTNode[] { const root = this.root; if (!root) { return []; } const result: ObjectASTNode[] = []; - const stepsNode = this.getNodeFromPath("steps"); - if (stepsNode && stepsNode.type === "property" && stepsNode.valueNode && stepsNode.valueNode.type === "object") { - stepsNode.valueNode.properties.forEach((stepProperty) => { - const stepNode = stepProperty.valueNode; - if (stepNode && stepNode.type === "object") { - result.push(stepNode); - } - }); + let stepsPropertyNodes: PropertyASTNode[] = []; + if (includeSubworkflows) { + stepsPropertyNodes = this.getAllPropertyNodesByName("steps"); + } else { + const mainStepsProperty = this.getNodeFromPath("steps") as PropertyASTNode; + stepsPropertyNodes = mainStepsProperty ? [mainStepsProperty] : []; } + for (const stepsNode of stepsPropertyNodes) { + if (stepsNode && stepsNode.valueNode && stepsNode.valueNode.type === "object") { + stepsNode.valueNode.properties.forEach((stepProperty) => { + const stepNode = stepProperty.valueNode; + if (stepNode && stepNode.type === "object") { + result.push(stepNode); + } + }); + } + } + return result; } @@ -97,4 +163,20 @@ export class ASTNodeManager { const offset = this.textDocument.offsetAt(position); return Range.create(this.textDocument.positionAt(offset), this.textDocument.positionAt(offset + 1)); } + + public visit(visitor: (node: ASTNode) => boolean): void { + if (this.root) { + const doVisit = (node: ASTNode): boolean => { + let ctn = visitor(node); + const children = node.children; + if (Array.isArray(children)) { + for (let i = 0; i < children.length && ctn; i++) { + ctn = doVisit(children[i]); + } + } + return ctn; + }; + doVisit(this.root); + } + } } diff --git a/server/packages/server-common/src/ast/types.ts b/server/packages/server-common/src/ast/types.ts index 5af7b5a..cec2efd 100644 --- a/server/packages/server-common/src/ast/types.ts +++ b/server/packages/server-common/src/ast/types.ts @@ -24,4 +24,14 @@ export { export interface ParsedDocument { root?: ASTNode; + getNodeFromOffset(offset: number): ASTNode | undefined; } + +/** + * A NodePath segment. Either a string representing an object property name + * or a number (starting at 0) for array indices. + */ +export type Segment = string | number; + +/** Represents the full path to a node. */ +export type NodePath = Segment[]; diff --git a/server/packages/server-common/src/ast/utils.ts b/server/packages/server-common/src/ast/utils.ts index 220bc0d..790353a 100644 --- a/server/packages/server-common/src/ast/utils.ts +++ b/server/packages/server-common/src/ast/utils.ts @@ -39,29 +39,3 @@ export function getPropertyNodeFromPath(root: ASTNode, path: string): ASTNode | } return currentNode; } - -export function contains(node: ASTNode, offset: number, includeRightBound = false): boolean { - return ( - (offset >= node.offset && offset <= node.offset + node.length) || - (includeRightBound && offset === node.offset + node.length) - ); -} - -export function findNodeAtOffset(node: ASTNode, offset: number, includeRightBound: boolean): ASTNode | undefined { - if (includeRightBound === void 0) { - includeRightBound = false; - } - if (contains(node, offset, includeRightBound)) { - const children = node.children; - if (Array.isArray(children)) { - for (let i = 0; i < children.length && children[i].offset <= offset; i++) { - const item = findNodeAtOffset(children[i], offset, includeRightBound); - if (item) { - return item; - } - } - } - return node; - } - return undefined; -} diff --git a/server/packages/server-common/src/languageTypes.ts b/server/packages/server-common/src/languageTypes.ts index 744a648..09c8fe9 100644 --- a/server/packages/server-common/src/languageTypes.ts +++ b/server/packages/server-common/src/languageTypes.ts @@ -132,6 +132,14 @@ export interface ValidationProfile { get rules(): Set; } +/** + * Interface for validating workflows and collecting diagnostics. + */ +export interface WorkflowValidator { + /** Collects diagnostics for the given workflow document. */ + doValidation(workflowDocument: WorkflowDocument): Promise; +} + /** * Abstract service defining the base functionality that a workflow language must * implement to provide assistance for workflow documents editing. diff --git a/server/packages/server-common/src/providers/hover/hoverProvider.ts b/server/packages/server-common/src/providers/hover/hoverProvider.ts index e3aca38..094b924 100644 --- a/server/packages/server-common/src/providers/hover/hoverProvider.ts +++ b/server/packages/server-common/src/providers/hover/hoverProvider.ts @@ -28,7 +28,11 @@ export class HoverProvider extends Provider { return null; } const contentSections: string[] = [ - this.hoverHasEmptyContent(hover) ? `No documentation available` : `${hover.contents}`, + this.hoverHasEmptyContent(hover) + ? `No documentation available` + : MarkupContent.is(hover.contents) + ? hover.contents.value + : `${hover.contents}`, ]; this.contributors.forEach((contentContributor) => { const contributedContent = contentContributor.onHoverContent(workflowDocument, params.position); diff --git a/server/packages/yaml-language-service/src/parser/astTypes.ts b/server/packages/yaml-language-service/src/parser/astTypes.ts index 7d07f0f..534410c 100644 --- a/server/packages/yaml-language-service/src/parser/astTypes.ts +++ b/server/packages/yaml-language-service/src/parser/astTypes.ts @@ -39,9 +39,9 @@ export abstract class ASTNodeImpl { this.internalNode = internalNode; } - public getNodeFromOffsetEndInclusive(offset: number): ASTNode | null { + public getNodeFromOffsetEndInclusive(offset: number): ASTNode | undefined { const collector: BaseASTNode[] = []; - const findNode = (node: BaseASTNode): BaseASTNode | null => { + const findNode = (node: BaseASTNode): BaseASTNode | undefined => { if (offset >= node.offset && offset <= node.offset + node.length) { const children = node.children; if (children && children.length) { @@ -54,7 +54,7 @@ export abstract class ASTNodeImpl { return node; } } - return null; + return undefined; }; const foundNode = findNode(this); let currMinDist = Number.MAX_VALUE; @@ -66,7 +66,7 @@ export abstract class ASTNodeImpl { currMinDist = minDist; } } - return (currMinNode || foundNode) as ASTNode | null; + return (currMinNode || foundNode) as ASTNode | undefined; } public get children(): ASTNode[] { @@ -74,16 +74,7 @@ export abstract class ASTNodeImpl { } public toString(): string { - return ( - "type: " + - this.type + - " (" + - this.offset + - "/" + - this.length + - ")" + - (this.parent ? " parent: {" + this.parent.toString() + "}" : "") - ); + return this.internalNode.toString(); } } diff --git a/server/packages/yaml-language-service/src/parser/charCode.ts b/server/packages/yaml-language-service/src/parser/charCode.ts new file mode 100644 index 0000000..d7c8c33 --- /dev/null +++ b/server/packages/yaml-language-service/src/parser/charCode.ts @@ -0,0 +1,436 @@ +/*--------------------------------------------------------------------------------------------- + * Copyright (c) Microsoft Corporation. All rights reserved. + * Licensed under the MIT License. See License.txt in the project root for license information. + *--------------------------------------------------------------------------------------------*/ + +// copied from https://github.com/Microsoft/vscode/blob/015c3afe96966df50c15a7d66be2ab0ef1dc5f49/src/vs/base/common/charCode.ts + +// Names from https://blog.codinghorror.com/ascii-pronunciation-rules-for-programmers/ + +/** + * An inlined enum containing useful character codes (to be used with String.charCodeAt). + * Please leave the const keyword such that it gets inlined when compiled to JavaScript! + */ +export const enum CharCode { + Null = 0, + /** + * The `\b` character. + */ + Backspace = 8, + /** + * The `\t` character. + */ + Tab = 9, + /** + * The `\n` character. + */ + LineFeed = 10, + /** + * The `\r` character. + */ + CarriageReturn = 13, + Space = 32, + /** + * The `!` character. + */ + ExclamationMark = 33, + /** + * The `"` character. + */ + DoubleQuote = 34, + /** + * The `#` character. + */ + Hash = 35, + /** + * The `$` character. + */ + DollarSign = 36, + /** + * The `%` character. + */ + PercentSign = 37, + /** + * The `&` character. + */ + Ampersand = 38, + /** + * The `'` character. + */ + SingleQuote = 39, + /** + * The `(` character. + */ + OpenParen = 40, + /** + * The `)` character. + */ + CloseParen = 41, + /** + * The `*` character. + */ + Asterisk = 42, + /** + * The `+` character. + */ + Plus = 43, + /** + * The `,` character. + */ + Comma = 44, + /** + * The `-` character. + */ + Dash = 45, + /** + * The `.` character. + */ + Period = 46, + /** + * The `/` character. + */ + Slash = 47, + + Digit0 = 48, + Digit1 = 49, + Digit2 = 50, + Digit3 = 51, + Digit4 = 52, + Digit5 = 53, + Digit6 = 54, + Digit7 = 55, + Digit8 = 56, + Digit9 = 57, + + /** + * The `:` character. + */ + Colon = 58, + /** + * The `;` character. + */ + Semicolon = 59, + /** + * The `<` character. + */ + LessThan = 60, + /** + * The `=` character. + */ + Equals = 61, + /** + * The `>` character. + */ + GreaterThan = 62, + /** + * The `?` character. + */ + QuestionMark = 63, + /** + * The `@` character. + */ + AtSign = 64, + + A = 65, + B = 66, + C = 67, + D = 68, + E = 69, + F = 70, + G = 71, + H = 72, + I = 73, + J = 74, + K = 75, + L = 76, + M = 77, + N = 78, + O = 79, + P = 80, + Q = 81, + R = 82, + S = 83, + T = 84, + U = 85, + V = 86, + W = 87, + X = 88, + Y = 89, + Z = 90, + + /** + * The `[` character. + */ + OpenSquareBracket = 91, + /** + * The `\` character. + */ + Backslash = 92, + /** + * The `]` character. + */ + CloseSquareBracket = 93, + /** + * The `^` character. + */ + Caret = 94, + /** + * The `_` character. + */ + Underline = 95, + /** + * The ``(`)`` character. + */ + BackTick = 96, + + a = 97, + b = 98, + c = 99, + d = 100, + e = 101, + f = 102, + g = 103, + h = 104, + i = 105, + j = 106, + k = 107, + l = 108, + m = 109, + n = 110, + o = 111, + p = 112, + q = 113, + r = 114, + s = 115, + t = 116, + u = 117, + v = 118, + w = 119, + x = 120, + y = 121, + z = 122, + + /** + * The `{` character. + */ + OpenCurlyBrace = 123, + /** + * The `|` character. + */ + Pipe = 124, + /** + * The `}` character. + */ + CloseCurlyBrace = 125, + /** + * The `~` character. + */ + Tilde = 126, + + U_Combining_Grave_Accent = 0x0300, // U+0300 Combining Grave Accent + U_Combining_Acute_Accent = 0x0301, // U+0301 Combining Acute Accent + U_Combining_Circumflex_Accent = 0x0302, // U+0302 Combining Circumflex Accent + U_Combining_Tilde = 0x0303, // U+0303 Combining Tilde + U_Combining_Macron = 0x0304, // U+0304 Combining Macron + U_Combining_Overline = 0x0305, // U+0305 Combining Overline + U_Combining_Breve = 0x0306, // U+0306 Combining Breve + U_Combining_Dot_Above = 0x0307, // U+0307 Combining Dot Above + U_Combining_Diaeresis = 0x0308, // U+0308 Combining Diaeresis + U_Combining_Hook_Above = 0x0309, // U+0309 Combining Hook Above + U_Combining_Ring_Above = 0x030a, // U+030A Combining Ring Above + U_Combining_Double_Acute_Accent = 0x030b, // U+030B Combining Double Acute Accent + U_Combining_Caron = 0x030c, // U+030C Combining Caron + U_Combining_Vertical_Line_Above = 0x030d, // U+030D Combining Vertical Line Above + U_Combining_Double_Vertical_Line_Above = 0x030e, // U+030E Combining Double Vertical Line Above + U_Combining_Double_Grave_Accent = 0x030f, // U+030F Combining Double Grave Accent + U_Combining_Candrabindu = 0x0310, // U+0310 Combining Candrabindu + U_Combining_Inverted_Breve = 0x0311, // U+0311 Combining Inverted Breve + U_Combining_Turned_Comma_Above = 0x0312, // U+0312 Combining Turned Comma Above + U_Combining_Comma_Above = 0x0313, // U+0313 Combining Comma Above + U_Combining_Reversed_Comma_Above = 0x0314, // U+0314 Combining Reversed Comma Above + U_Combining_Comma_Above_Right = 0x0315, // U+0315 Combining Comma Above Right + U_Combining_Grave_Accent_Below = 0x0316, // U+0316 Combining Grave Accent Below + U_Combining_Acute_Accent_Below = 0x0317, // U+0317 Combining Acute Accent Below + U_Combining_Left_Tack_Below = 0x0318, // U+0318 Combining Left Tack Below + U_Combining_Right_Tack_Below = 0x0319, // U+0319 Combining Right Tack Below + U_Combining_Left_Angle_Above = 0x031a, // U+031A Combining Left Angle Above + U_Combining_Horn = 0x031b, // U+031B Combining Horn + U_Combining_Left_Half_Ring_Below = 0x031c, // U+031C Combining Left Half Ring Below + U_Combining_Up_Tack_Below = 0x031d, // U+031D Combining Up Tack Below + U_Combining_Down_Tack_Below = 0x031e, // U+031E Combining Down Tack Below + U_Combining_Plus_Sign_Below = 0x031f, // U+031F Combining Plus Sign Below + U_Combining_Minus_Sign_Below = 0x0320, // U+0320 Combining Minus Sign Below + U_Combining_Palatalized_Hook_Below = 0x0321, // U+0321 Combining Palatalized Hook Below + U_Combining_Retroflex_Hook_Below = 0x0322, // U+0322 Combining Retroflex Hook Below + U_Combining_Dot_Below = 0x0323, // U+0323 Combining Dot Below + U_Combining_Diaeresis_Below = 0x0324, // U+0324 Combining Diaeresis Below + U_Combining_Ring_Below = 0x0325, // U+0325 Combining Ring Below + U_Combining_Comma_Below = 0x0326, // U+0326 Combining Comma Below + U_Combining_Cedilla = 0x0327, // U+0327 Combining Cedilla + U_Combining_Ogonek = 0x0328, // U+0328 Combining Ogonek + U_Combining_Vertical_Line_Below = 0x0329, // U+0329 Combining Vertical Line Below + U_Combining_Bridge_Below = 0x032a, // U+032A Combining Bridge Below + U_Combining_Inverted_Double_Arch_Below = 0x032b, // U+032B Combining Inverted Double Arch Below + U_Combining_Caron_Below = 0x032c, // U+032C Combining Caron Below + U_Combining_Circumflex_Accent_Below = 0x032d, // U+032D Combining Circumflex Accent Below + U_Combining_Breve_Below = 0x032e, // U+032E Combining Breve Below + U_Combining_Inverted_Breve_Below = 0x032f, // U+032F Combining Inverted Breve Below + U_Combining_Tilde_Below = 0x0330, // U+0330 Combining Tilde Below + U_Combining_Macron_Below = 0x0331, // U+0331 Combining Macron Below + U_Combining_Low_Line = 0x0332, // U+0332 Combining Low Line + U_Combining_Double_Low_Line = 0x0333, // U+0333 Combining Double Low Line + U_Combining_Tilde_Overlay = 0x0334, // U+0334 Combining Tilde Overlay + U_Combining_Short_Stroke_Overlay = 0x0335, // U+0335 Combining Short Stroke Overlay + U_Combining_Long_Stroke_Overlay = 0x0336, // U+0336 Combining Long Stroke Overlay + U_Combining_Short_Solidus_Overlay = 0x0337, // U+0337 Combining Short Solidus Overlay + U_Combining_Long_Solidus_Overlay = 0x0338, // U+0338 Combining Long Solidus Overlay + U_Combining_Right_Half_Ring_Below = 0x0339, // U+0339 Combining Right Half Ring Below + U_Combining_Inverted_Bridge_Below = 0x033a, // U+033A Combining Inverted Bridge Below + U_Combining_Square_Below = 0x033b, // U+033B Combining Square Below + U_Combining_Seagull_Below = 0x033c, // U+033C Combining Seagull Below + U_Combining_X_Above = 0x033d, // U+033D Combining X Above + U_Combining_Vertical_Tilde = 0x033e, // U+033E Combining Vertical Tilde + U_Combining_Double_Overline = 0x033f, // U+033F Combining Double Overline + U_Combining_Grave_Tone_Mark = 0x0340, // U+0340 Combining Grave Tone Mark + U_Combining_Acute_Tone_Mark = 0x0341, // U+0341 Combining Acute Tone Mark + U_Combining_Greek_Perispomeni = 0x0342, // U+0342 Combining Greek Perispomeni + U_Combining_Greek_Koronis = 0x0343, // U+0343 Combining Greek Koronis + U_Combining_Greek_Dialytika_Tonos = 0x0344, // U+0344 Combining Greek Dialytika Tonos + U_Combining_Greek_Ypogegrammeni = 0x0345, // U+0345 Combining Greek Ypogegrammeni + U_Combining_Bridge_Above = 0x0346, // U+0346 Combining Bridge Above + U_Combining_Equals_Sign_Below = 0x0347, // U+0347 Combining Equals Sign Below + U_Combining_Double_Vertical_Line_Below = 0x0348, // U+0348 Combining Double Vertical Line Below + U_Combining_Left_Angle_Below = 0x0349, // U+0349 Combining Left Angle Below + U_Combining_Not_Tilde_Above = 0x034a, // U+034A Combining Not Tilde Above + U_Combining_Homothetic_Above = 0x034b, // U+034B Combining Homothetic Above + U_Combining_Almost_Equal_To_Above = 0x034c, // U+034C Combining Almost Equal To Above + U_Combining_Left_Right_Arrow_Below = 0x034d, // U+034D Combining Left Right Arrow Below + U_Combining_Upwards_Arrow_Below = 0x034e, // U+034E Combining Upwards Arrow Below + U_Combining_Grapheme_Joiner = 0x034f, // U+034F Combining Grapheme Joiner + U_Combining_Right_Arrowhead_Above = 0x0350, // U+0350 Combining Right Arrowhead Above + U_Combining_Left_Half_Ring_Above = 0x0351, // U+0351 Combining Left Half Ring Above + U_Combining_Fermata = 0x0352, // U+0352 Combining Fermata + U_Combining_X_Below = 0x0353, // U+0353 Combining X Below + U_Combining_Left_Arrowhead_Below = 0x0354, // U+0354 Combining Left Arrowhead Below + U_Combining_Right_Arrowhead_Below = 0x0355, // U+0355 Combining Right Arrowhead Below + U_Combining_Right_Arrowhead_And_Up_Arrowhead_Below = 0x0356, // U+0356 Combining Right Arrowhead And Up Arrowhead Below + U_Combining_Right_Half_Ring_Above = 0x0357, // U+0357 Combining Right Half Ring Above + U_Combining_Dot_Above_Right = 0x0358, // U+0358 Combining Dot Above Right + U_Combining_Asterisk_Below = 0x0359, // U+0359 Combining Asterisk Below + U_Combining_Double_Ring_Below = 0x035a, // U+035A Combining Double Ring Below + U_Combining_Zigzag_Above = 0x035b, // U+035B Combining Zigzag Above + U_Combining_Double_Breve_Below = 0x035c, // U+035C Combining Double Breve Below + U_Combining_Double_Breve = 0x035d, // U+035D Combining Double Breve + U_Combining_Double_Macron = 0x035e, // U+035E Combining Double Macron + U_Combining_Double_Macron_Below = 0x035f, // U+035F Combining Double Macron Below + U_Combining_Double_Tilde = 0x0360, // U+0360 Combining Double Tilde + U_Combining_Double_Inverted_Breve = 0x0361, // U+0361 Combining Double Inverted Breve + U_Combining_Double_Rightwards_Arrow_Below = 0x0362, // U+0362 Combining Double Rightwards Arrow Below + U_Combining_Latin_Small_Letter_A = 0x0363, // U+0363 Combining Latin Small Letter A + U_Combining_Latin_Small_Letter_E = 0x0364, // U+0364 Combining Latin Small Letter E + U_Combining_Latin_Small_Letter_I = 0x0365, // U+0365 Combining Latin Small Letter I + U_Combining_Latin_Small_Letter_O = 0x0366, // U+0366 Combining Latin Small Letter O + U_Combining_Latin_Small_Letter_U = 0x0367, // U+0367 Combining Latin Small Letter U + U_Combining_Latin_Small_Letter_C = 0x0368, // U+0368 Combining Latin Small Letter C + U_Combining_Latin_Small_Letter_D = 0x0369, // U+0369 Combining Latin Small Letter D + U_Combining_Latin_Small_Letter_H = 0x036a, // U+036A Combining Latin Small Letter H + U_Combining_Latin_Small_Letter_M = 0x036b, // U+036B Combining Latin Small Letter M + U_Combining_Latin_Small_Letter_R = 0x036c, // U+036C Combining Latin Small Letter R + U_Combining_Latin_Small_Letter_T = 0x036d, // U+036D Combining Latin Small Letter T + U_Combining_Latin_Small_Letter_V = 0x036e, // U+036E Combining Latin Small Letter V + U_Combining_Latin_Small_Letter_X = 0x036f, // U+036F Combining Latin Small Letter X + + /** + * Unicode Character 'LINE SEPARATOR' (U+2028) + * http://www.fileformat.info/info/unicode/char/2028/index.htm + */ + LINE_SEPARATOR = 0x2028, + /** + * Unicode Character 'PARAGRAPH SEPARATOR' (U+2029) + * http://www.fileformat.info/info/unicode/char/2029/index.htm + */ + PARAGRAPH_SEPARATOR = 0x2029, + /** + * Unicode Character 'NEXT LINE' (U+0085) + * http://www.fileformat.info/info/unicode/char/0085/index.htm + */ + NEXT_LINE = 0x0085, + + // http://www.fileformat.info/info/unicode/category/Sk/list.htm + U_CIRCUMFLEX = 0x005e, // U+005E CIRCUMFLEX + U_GRAVE_ACCENT = 0x0060, // U+0060 GRAVE ACCENT + U_DIAERESIS = 0x00a8, // U+00A8 DIAERESIS + U_MACRON = 0x00af, // U+00AF MACRON + U_ACUTE_ACCENT = 0x00b4, // U+00B4 ACUTE ACCENT + U_CEDILLA = 0x00b8, // U+00B8 CEDILLA + U_MODIFIER_LETTER_LEFT_ARROWHEAD = 0x02c2, // U+02C2 MODIFIER LETTER LEFT ARROWHEAD + U_MODIFIER_LETTER_RIGHT_ARROWHEAD = 0x02c3, // U+02C3 MODIFIER LETTER RIGHT ARROWHEAD + U_MODIFIER_LETTER_UP_ARROWHEAD = 0x02c4, // U+02C4 MODIFIER LETTER UP ARROWHEAD + U_MODIFIER_LETTER_DOWN_ARROWHEAD = 0x02c5, // U+02C5 MODIFIER LETTER DOWN ARROWHEAD + U_MODIFIER_LETTER_CENTRED_RIGHT_HALF_RING = 0x02d2, // U+02D2 MODIFIER LETTER CENTRED RIGHT HALF RING + U_MODIFIER_LETTER_CENTRED_LEFT_HALF_RING = 0x02d3, // U+02D3 MODIFIER LETTER CENTRED LEFT HALF RING + U_MODIFIER_LETTER_UP_TACK = 0x02d4, // U+02D4 MODIFIER LETTER UP TACK + U_MODIFIER_LETTER_DOWN_TACK = 0x02d5, // U+02D5 MODIFIER LETTER DOWN TACK + U_MODIFIER_LETTER_PLUS_SIGN = 0x02d6, // U+02D6 MODIFIER LETTER PLUS SIGN + U_MODIFIER_LETTER_MINUS_SIGN = 0x02d7, // U+02D7 MODIFIER LETTER MINUS SIGN + U_BREVE = 0x02d8, // U+02D8 BREVE + U_DOT_ABOVE = 0x02d9, // U+02D9 DOT ABOVE + U_RING_ABOVE = 0x02da, // U+02DA RING ABOVE + U_OGONEK = 0x02db, // U+02DB OGONEK + U_SMALL_TILDE = 0x02dc, // U+02DC SMALL TILDE + U_DOUBLE_ACUTE_ACCENT = 0x02dd, // U+02DD DOUBLE ACUTE ACCENT + U_MODIFIER_LETTER_RHOTIC_HOOK = 0x02de, // U+02DE MODIFIER LETTER RHOTIC HOOK + U_MODIFIER_LETTER_CROSS_ACCENT = 0x02df, // U+02DF MODIFIER LETTER CROSS ACCENT + U_MODIFIER_LETTER_EXTRA_HIGH_TONE_BAR = 0x02e5, // U+02E5 MODIFIER LETTER EXTRA-HIGH TONE BAR + U_MODIFIER_LETTER_HIGH_TONE_BAR = 0x02e6, // U+02E6 MODIFIER LETTER HIGH TONE BAR + U_MODIFIER_LETTER_MID_TONE_BAR = 0x02e7, // U+02E7 MODIFIER LETTER MID TONE BAR + U_MODIFIER_LETTER_LOW_TONE_BAR = 0x02e8, // U+02E8 MODIFIER LETTER LOW TONE BAR + U_MODIFIER_LETTER_EXTRA_LOW_TONE_BAR = 0x02e9, // U+02E9 MODIFIER LETTER EXTRA-LOW TONE BAR + U_MODIFIER_LETTER_YIN_DEPARTING_TONE_MARK = 0x02ea, // U+02EA MODIFIER LETTER YIN DEPARTING TONE MARK + U_MODIFIER_LETTER_YANG_DEPARTING_TONE_MARK = 0x02eb, // U+02EB MODIFIER LETTER YANG DEPARTING TONE MARK + U_MODIFIER_LETTER_UNASPIRATED = 0x02ed, // U+02ED MODIFIER LETTER UNASPIRATED + U_MODIFIER_LETTER_LOW_DOWN_ARROWHEAD = 0x02ef, // U+02EF MODIFIER LETTER LOW DOWN ARROWHEAD + U_MODIFIER_LETTER_LOW_UP_ARROWHEAD = 0x02f0, // U+02F0 MODIFIER LETTER LOW UP ARROWHEAD + U_MODIFIER_LETTER_LOW_LEFT_ARROWHEAD = 0x02f1, // U+02F1 MODIFIER LETTER LOW LEFT ARROWHEAD + U_MODIFIER_LETTER_LOW_RIGHT_ARROWHEAD = 0x02f2, // U+02F2 MODIFIER LETTER LOW RIGHT ARROWHEAD + U_MODIFIER_LETTER_LOW_RING = 0x02f3, // U+02F3 MODIFIER LETTER LOW RING + U_MODIFIER_LETTER_MIDDLE_GRAVE_ACCENT = 0x02f4, // U+02F4 MODIFIER LETTER MIDDLE GRAVE ACCENT + U_MODIFIER_LETTER_MIDDLE_DOUBLE_GRAVE_ACCENT = 0x02f5, // U+02F5 MODIFIER LETTER MIDDLE DOUBLE GRAVE ACCENT + U_MODIFIER_LETTER_MIDDLE_DOUBLE_ACUTE_ACCENT = 0x02f6, // U+02F6 MODIFIER LETTER MIDDLE DOUBLE ACUTE ACCENT + U_MODIFIER_LETTER_LOW_TILDE = 0x02f7, // U+02F7 MODIFIER LETTER LOW TILDE + U_MODIFIER_LETTER_RAISED_COLON = 0x02f8, // U+02F8 MODIFIER LETTER RAISED COLON + U_MODIFIER_LETTER_BEGIN_HIGH_TONE = 0x02f9, // U+02F9 MODIFIER LETTER BEGIN HIGH TONE + U_MODIFIER_LETTER_END_HIGH_TONE = 0x02fa, // U+02FA MODIFIER LETTER END HIGH TONE + U_MODIFIER_LETTER_BEGIN_LOW_TONE = 0x02fb, // U+02FB MODIFIER LETTER BEGIN LOW TONE + U_MODIFIER_LETTER_END_LOW_TONE = 0x02fc, // U+02FC MODIFIER LETTER END LOW TONE + U_MODIFIER_LETTER_SHELF = 0x02fd, // U+02FD MODIFIER LETTER SHELF + U_MODIFIER_LETTER_OPEN_SHELF = 0x02fe, // U+02FE MODIFIER LETTER OPEN SHELF + U_MODIFIER_LETTER_LOW_LEFT_ARROW = 0x02ff, // U+02FF MODIFIER LETTER LOW LEFT ARROW + U_GREEK_LOWER_NUMERAL_SIGN = 0x0375, // U+0375 GREEK LOWER NUMERAL SIGN + U_GREEK_TONOS = 0x0384, // U+0384 GREEK TONOS + U_GREEK_DIALYTIKA_TONOS = 0x0385, // U+0385 GREEK DIALYTIKA TONOS + U_GREEK_KORONIS = 0x1fbd, // U+1FBD GREEK KORONIS + U_GREEK_PSILI = 0x1fbf, // U+1FBF GREEK PSILI + U_GREEK_PERISPOMENI = 0x1fc0, // U+1FC0 GREEK PERISPOMENI + U_GREEK_DIALYTIKA_AND_PERISPOMENI = 0x1fc1, // U+1FC1 GREEK DIALYTIKA AND PERISPOMENI + U_GREEK_PSILI_AND_VARIA = 0x1fcd, // U+1FCD GREEK PSILI AND VARIA + U_GREEK_PSILI_AND_OXIA = 0x1fce, // U+1FCE GREEK PSILI AND OXIA + U_GREEK_PSILI_AND_PERISPOMENI = 0x1fcf, // U+1FCF GREEK PSILI AND PERISPOMENI + U_GREEK_DASIA_AND_VARIA = 0x1fdd, // U+1FDD GREEK DASIA AND VARIA + U_GREEK_DASIA_AND_OXIA = 0x1fde, // U+1FDE GREEK DASIA AND OXIA + U_GREEK_DASIA_AND_PERISPOMENI = 0x1fdf, // U+1FDF GREEK DASIA AND PERISPOMENI + U_GREEK_DIALYTIKA_AND_VARIA = 0x1fed, // U+1FED GREEK DIALYTIKA AND VARIA + U_GREEK_DIALYTIKA_AND_OXIA = 0x1fee, // U+1FEE GREEK DIALYTIKA AND OXIA + U_GREEK_VARIA = 0x1fef, // U+1FEF GREEK VARIA + U_GREEK_OXIA = 0x1ffd, // U+1FFD GREEK OXIA + U_GREEK_DASIA = 0x1ffe, // U+1FFE GREEK DASIA + + U_OVERLINE = 0x203e, // Unicode Character 'OVERLINE' + + /** + * UTF-8 BOM + * Unicode Character 'ZERO WIDTH NO-BREAK SPACE' (U+FEFF) + * http://www.fileformat.info/info/unicode/char/feff/index.htm + */ + UTF8_BOM = 65279, +} diff --git a/server/packages/yaml-language-service/src/parser/yamlDocument.ts b/server/packages/yaml-language-service/src/parser/yamlDocument.ts index faa8310..d587309 100644 --- a/server/packages/yaml-language-service/src/parser/yamlDocument.ts +++ b/server/packages/yaml-language-service/src/parser/yamlDocument.ts @@ -2,61 +2,19 @@ import { ParsedDocument } from "@gxwf/server-common/src/ast/types"; import { TextDocument } from "vscode-languageserver-textdocument"; import { Diagnostic, DiagnosticSeverity, Position } from "vscode-languageserver-types"; import { Document, Node, visit, YAMLError, YAMLWarning } from "yaml"; +import { guessIndentation } from "../utils/indentationGuesser"; import { TextBuffer } from "../utils/textBuffer"; -import { ASTNode } from "./astTypes"; +import { ASTNode, ObjectASTNodeImpl } from "./astTypes"; const FULL_LINE_ERROR = true; const YAML_SOURCE = "YAML"; +const YAML_COMMENT_SYMBOL = "#"; +const DEFAULT_INDENTATION = 2; export class LineComment { constructor(public readonly text: string) {} } -export class YAMLSubDocument { - private _lineComments: LineComment[] | undefined; - - constructor(public readonly root: ASTNode | undefined, private readonly parsedDocument: Document) {} - - get errors(): YAMLError[] { - return this.parsedDocument.errors; - } - - get warnings(): YAMLWarning[] { - return this.parsedDocument.warnings; - } - - get lineComments(): LineComment[] { - if (!this._lineComments) { - this._lineComments = this.collectLineComments(); - } - return this._lineComments; - } - - private collectLineComments(): LineComment[] { - const lineComments = []; - if (this.parsedDocument.commentBefore) { - const comments = this.parsedDocument.commentBefore.split("\n"); - comments.forEach((comment) => lineComments.push(new LineComment(`#${comment}`))); - } - visit(this.parsedDocument, (_key, docNode) => { - const node = docNode as Node; - if (node?.commentBefore) { - const comments = node?.commentBefore.split("\n"); - comments.forEach((comment) => lineComments.push(new LineComment(`#${comment}`))); - } - - if (node?.comment) { - lineComments.push(new LineComment(`#${node.comment}`)); - } - }); - - if (this.parsedDocument.comment) { - lineComments.push(new LineComment(`#${this.parsedDocument.comment}`)); - } - return lineComments; - } -} - /** * Represents a YAML document. * YAML documents can contain multiple sub-documents separated by "---". @@ -64,10 +22,12 @@ export class YAMLSubDocument { export class YAMLDocument implements ParsedDocument { private readonly _textBuffer: TextBuffer; private _diagnostics: Diagnostic[] | undefined; + private _indentation: number; constructor(public readonly subDocuments: YAMLSubDocument[], public readonly textDocument: TextDocument) { this._textBuffer = new TextBuffer(textDocument); this._diagnostics = undefined; + this._indentation = guessIndentation(this._textBuffer, DEFAULT_INDENTATION, true).tabSize; } public get root(): ASTNode | undefined { @@ -92,6 +52,47 @@ export class YAMLDocument implements ParsedDocument { return this.collectLineComments(); } + public isComment(offset: number): boolean { + const position = this._textBuffer.getPosition(offset); + const lineContent = this._textBuffer.getLineContent(position.line).trimStart(); + return lineContent.startsWith(YAML_COMMENT_SYMBOL); + } + + /** + * Gets the syntax node at this document offset. + * @param offset The offset in the text document + * @returns The syntax node that lies at the given offset + */ + public getNodeFromOffset(offset: number): ASTNode | undefined { + const rootNode = this.root as ObjectASTNodeImpl; + if (!rootNode) return undefined; + if (this.isComment(offset)) return undefined; + const position = this._textBuffer.getPosition(offset); + if (position.character === 0 && !this._textBuffer.hasTextAfterPosition(position)) return rootNode; + const indentation = this._textBuffer.getLineIndentationAtOffset(offset); + const lineContent = this._textBuffer.getLineContent(position.line); + const contentAfterCursor = lineContent.slice(position.character).replace(/\s/g, ""); + if (indentation === 0 && contentAfterCursor.length === 0) return rootNode; + let result = rootNode.getNodeFromOffsetEndInclusive(offset); + const parent = this.findParentNodeByIndentation(offset, indentation); + if (!result || (parent && result.offset < parent.offset && result.length > parent.length)) { + result = parent; + } + return result; + } + + private findParentNodeByIndentation(offset: number, indentation: number): ASTNode | undefined { + if (indentation === 0) return this.root; + const parentIndentation = Math.max(0, indentation - this._indentation); + const parentLine = this._textBuffer.findPreviousLineWithSameIndentation(offset, parentIndentation); + const parentOffset = this._textBuffer.getOffsetAt(Position.create(parentLine, parentIndentation)); + + const rootNode = this.root as ObjectASTNodeImpl; + if (!rootNode) return undefined; + const parentNode = rootNode.getNodeFromOffsetEndInclusive(parentOffset); + return parentNode; + } + /** Collects all syntax errors and warnings found on this document. */ private getSyntaxDiagnostics(): Diagnostic[] { const syntaxErrors = this.subDocuments.flatMap((subDoc) => @@ -128,3 +129,48 @@ export class YAMLDocument implements ParsedDocument { return lineComments; } } + +export class YAMLSubDocument { + private _lineComments: LineComment[] | undefined; + + constructor(public readonly root: ASTNode | undefined, private readonly parsedDocument: Document) {} + + get errors(): YAMLError[] { + return this.parsedDocument.errors; + } + + get warnings(): YAMLWarning[] { + return this.parsedDocument.warnings; + } + + get lineComments(): LineComment[] { + if (!this._lineComments) { + this._lineComments = this.collectLineComments(); + } + return this._lineComments; + } + + private collectLineComments(): LineComment[] { + const lineComments = []; + if (this.parsedDocument.commentBefore) { + const comments = this.parsedDocument.commentBefore.split("\n"); + comments.forEach((comment) => lineComments.push(new LineComment(`${YAML_COMMENT_SYMBOL}${comment}`))); + } + visit(this.parsedDocument, (_key, docNode) => { + const node = docNode as Node; + if (node?.commentBefore) { + const comments = node?.commentBefore.split("\n"); + comments.forEach((comment) => lineComments.push(new LineComment(`${YAML_COMMENT_SYMBOL}${comment}`))); + } + + if (node?.comment) { + lineComments.push(new LineComment(`${YAML_COMMENT_SYMBOL}${node.comment}`)); + } + }); + + if (this.parsedDocument.comment) { + lineComments.push(new LineComment(`${YAML_COMMENT_SYMBOL}${this.parsedDocument.comment}`)); + } + return lineComments; + } +} diff --git a/server/packages/yaml-language-service/src/utils/indentationGuesser.ts b/server/packages/yaml-language-service/src/utils/indentationGuesser.ts new file mode 100644 index 0000000..06d53ea --- /dev/null +++ b/server/packages/yaml-language-service/src/utils/indentationGuesser.ts @@ -0,0 +1,235 @@ +/*--------------------------------------------------------------------------------------------- + * Copyright (c) Microsoft Corporation. All rights reserved. + * Licensed under the MIT License. See License.txt in the project root for license information. + *--------------------------------------------------------------------------------------------*/ + +// Copied from: https://github.com/Microsoft/vscode/blob/main/src/vs/editor/common/model/indentationGuesser.ts + +import { CharCode } from "../parser/charCode"; +import { ITextBuffer } from "./textBuffer"; + +class SpacesDiffResult { + public spacesDiff = 0; + public looksLikeAlignment = false; +} + +/** + * Compute the diff in spaces between two line's indentation. + */ +function spacesDiff(a: string, aLength: number, b: string, bLength: number, result: SpacesDiffResult): void { + result.spacesDiff = 0; + result.looksLikeAlignment = false; + + // This can go both ways (e.g.): + // - a: "\t" + // - b: "\t " + // => This should count 1 tab and 4 spaces + + let i: number; + + for (i = 0; i < aLength && i < bLength; i++) { + const aCharCode = a.charCodeAt(i); + const bCharCode = b.charCodeAt(i); + + if (aCharCode !== bCharCode) { + break; + } + } + + let aSpacesCnt = 0, + aTabsCount = 0; + for (let j = i; j < aLength; j++) { + const aCharCode = a.charCodeAt(j); + if (aCharCode === CharCode.Space) { + aSpacesCnt++; + } else { + aTabsCount++; + } + } + + let bSpacesCnt = 0, + bTabsCount = 0; + for (let j = i; j < bLength; j++) { + const bCharCode = b.charCodeAt(j); + if (bCharCode === CharCode.Space) { + bSpacesCnt++; + } else { + bTabsCount++; + } + } + + if (aSpacesCnt > 0 && aTabsCount > 0) { + return; + } + if (bSpacesCnt > 0 && bTabsCount > 0) { + return; + } + + const tabsDiff = Math.abs(aTabsCount - bTabsCount); + const spacesDiff = Math.abs(aSpacesCnt - bSpacesCnt); + + if (tabsDiff === 0) { + // check if the indentation difference might be caused by alignment reasons + // sometime folks like to align their code, but this should not be used as a hint + result.spacesDiff = spacesDiff; + + if (spacesDiff > 0 && 0 <= bSpacesCnt - 1 && bSpacesCnt - 1 < a.length && bSpacesCnt < b.length) { + if (b.charCodeAt(bSpacesCnt) !== CharCode.Space && a.charCodeAt(bSpacesCnt - 1) === CharCode.Space) { + if (a.charCodeAt(a.length - 1) === CharCode.Comma) { + // This looks like an alignment desire: e.g. + // const a = b + c, + // d = b - c; + result.looksLikeAlignment = true; + } + } + } + return; + } + if (spacesDiff % tabsDiff === 0) { + result.spacesDiff = spacesDiff / tabsDiff; + return; + } +} + +/** + * Result for a guessIndentation + */ +export interface IGuessedIndentation { + /** + * If indentation is based on spaces (`insertSpaces` = true), then what is the number of spaces that make an indent? + */ + tabSize: number; + /** + * Is indentation based on spaces? + */ + insertSpaces: boolean; +} + +export function guessIndentation( + source: ITextBuffer, + defaultTabSize: number, + defaultInsertSpaces: boolean +): IGuessedIndentation { + // Look at most at the first 10k lines + const linesCount = Math.min(source.getLineCount(), 10000); + + let linesIndentedWithTabsCount = 0; // number of lines that contain at least one tab in indentation + let linesIndentedWithSpacesCount = 0; // number of lines that contain only spaces in indentation + + let previousLineText = ""; // content of latest line that contained non-whitespace chars + let previousLineIndentation = 0; // index at which latest line contained the first non-whitespace char + + const ALLOWED_TAB_SIZE_GUESSES = [2, 4, 6, 8, 3, 5, 7]; // prefer even guesses for `tabSize`, limit to [2, 8]. + const MAX_ALLOWED_TAB_SIZE_GUESS = 8; // max(ALLOWED_TAB_SIZE_GUESSES) = 8 + + const spacesDiffCount = [0, 0, 0, 0, 0, 0, 0, 0, 0]; // `tabSize` scores + const tmp = new SpacesDiffResult(); + + for (let lineNumber = 1; lineNumber <= linesCount; lineNumber++) { + const currentLineLength = source.getLineLength(lineNumber); + const currentLineText = source.getLineContent(lineNumber); + + // if the text buffer is chunk based, so long lines are cons-string, v8 will flattern the string when we check charCode. + // checking charCode on chunks directly is cheaper. + const useCurrentLineText = currentLineLength <= 65536; + + let currentLineHasContent = false; // does `currentLineText` contain non-whitespace chars + let currentLineIndentation = 0; // index at which `currentLineText` contains the first non-whitespace char + let currentLineSpacesCount = 0; // count of spaces found in `currentLineText` indentation + let currentLineTabsCount = 0; // count of tabs found in `currentLineText` indentation + for (let j = 0, lenJ = currentLineLength; j < lenJ; j++) { + const charCode = useCurrentLineText ? currentLineText.charCodeAt(j) : source.getLineCharCode(lineNumber, j); + + if (charCode === CharCode.Tab) { + currentLineTabsCount++; + } else if (charCode === CharCode.Space) { + currentLineSpacesCount++; + } else { + // Hit non whitespace character on this line + currentLineHasContent = true; + currentLineIndentation = j; + break; + } + } + + // Ignore empty or only whitespace lines + if (!currentLineHasContent) { + continue; + } + + if (currentLineTabsCount > 0) { + linesIndentedWithTabsCount++; + } else if (currentLineSpacesCount > 1) { + linesIndentedWithSpacesCount++; + } + + spacesDiff(previousLineText, previousLineIndentation, currentLineText, currentLineIndentation, tmp); + + if (tmp.looksLikeAlignment) { + // if defaultInsertSpaces === true && the spaces count == tabSize, we may want to count it as valid indentation + // + // - item1 + // - item2 + // + // otherwise skip this line entirely + // + // const a = 1, + // b = 2; + + if (!(defaultInsertSpaces && defaultTabSize === tmp.spacesDiff)) { + continue; + } + } + + const currentSpacesDiff = tmp.spacesDiff; + if (currentSpacesDiff <= MAX_ALLOWED_TAB_SIZE_GUESS) { + spacesDiffCount[currentSpacesDiff]++; + } + + previousLineText = currentLineText; + previousLineIndentation = currentLineIndentation; + } + + let insertSpaces = defaultInsertSpaces; + if (linesIndentedWithTabsCount !== linesIndentedWithSpacesCount) { + insertSpaces = linesIndentedWithTabsCount < linesIndentedWithSpacesCount; + } + + let tabSize = defaultTabSize; + + // Guess tabSize only if inserting spaces... + if (insertSpaces) { + let tabSizeScore = insertSpaces ? 0 : 0.1 * linesCount; + + // console.log("score threshold: " + tabSizeScore); + + ALLOWED_TAB_SIZE_GUESSES.forEach((possibleTabSize) => { + const possibleTabSizeScore = spacesDiffCount[possibleTabSize]; + if (possibleTabSizeScore > tabSizeScore) { + tabSizeScore = possibleTabSizeScore; + tabSize = possibleTabSize; + } + }); + + // Let a tabSize of 2 win even if it is not the maximum + // (only in case 4 was guessed) + if ( + tabSize === 4 && + spacesDiffCount[4] > 0 && + spacesDiffCount[2] > 0 && + spacesDiffCount[2] >= spacesDiffCount[4] / 2 + ) { + tabSize = 2; + } + } + + // console.log('--------------------------'); + // console.log('linesIndentedWithTabsCount: ' + linesIndentedWithTabsCount + ', linesIndentedWithSpacesCount: ' + linesIndentedWithSpacesCount); + // console.log('spacesDiffCount: ' + spacesDiffCount); + // console.log('tabSize: ' + tabSize + ', tabSizeScore: ' + tabSizeScore); + + return { + insertSpaces: insertSpaces, + tabSize: tabSize, + }; +} diff --git a/server/packages/yaml-language-service/src/utils/textBuffer.ts b/server/packages/yaml-language-service/src/utils/textBuffer.ts index 5d68240..5b0f9d5 100644 --- a/server/packages/yaml-language-service/src/utils/textBuffer.ts +++ b/server/packages/yaml-language-service/src/utils/textBuffer.ts @@ -5,19 +5,27 @@ import { TextDocument } from "vscode-languageserver-textdocument"; import { Position, Range } from "vscode-languageserver-types"; +import { CharCode } from "../parser/charCode"; interface FullTextDocument { getLineOffsets(): number[]; } +export interface ITextBuffer { + getLineCount(): number; + getLineLength(lineNumber: number): number; + getLineCharCode(lineNumber: number, index: number): number; + getLineContent(lineNumber: number): string; +} + export class TextBuffer { constructor(private doc: TextDocument) {} - getLineCount(): number { + public getLineCount(): number { return this.doc.lineCount; } - getLineLength(lineNumber: number): number { + public getLineLength(lineNumber: number): number { const lineOffsets = (this.doc as unknown as FullTextDocument).getLineOffsets(); if (lineNumber >= lineOffsets.length) { return this.doc.getText().length; @@ -30,7 +38,7 @@ export class TextBuffer { return nextLineOffset - lineOffsets[lineNumber]; } - getLineContent(lineNumber: number): string { + public getLineContent(lineNumber: number): string { const lineOffsets = (this.doc as unknown as FullTextDocument).getLineOffsets(); if (lineNumber >= lineOffsets.length) { return this.doc.getText(); @@ -42,15 +50,73 @@ export class TextBuffer { return this.doc.getText().substring(lineOffsets[lineNumber], nextLineOffset); } - getLineCharCode(lineNumber: number, index: number): number { + public getLineCharCode(lineNumber: number, index: number): number { return this.doc.getText(Range.create(lineNumber - 1, index - 1, lineNumber - 1, index)).charCodeAt(0); } - getText(range?: Range): string { + public getText(range?: Range): string { return this.doc.getText(range); } - getPosition(offest: number): Position { - return this.doc.positionAt(offest); + public getPosition(offset: number): Position { + return this.doc.positionAt(offset); + } + + public getOffsetAt(position: Position): number { + return this.doc.offsetAt(position); + } + + public getCurrentWord(offset: number): string { + let i = offset - 1; + const text = this.getText(); + while (i >= 0 && ' \t\n\r\v":{[,]}'.indexOf(text.charAt(i)) === -1) { + i--; + } + return text.substring(i + 1, offset); + } + + public hasTextAfterPosition(position: Position): boolean { + const lineContent = this.getLineContent(position.line); + return lineContent.charAt(position.character + 1).trim() !== ""; + } + + public getLineIndentationAtOffset(offset: number): number { + const position = this.getPosition(offset); + const lineContent = this.getLineContent(position.line); + const indentation = this.getIndentation(lineContent, position.character); + return indentation; + } + + public findPreviousLineWithSameIndentation(offset: number, indentation: number): number { + const position = this.getPosition(offset); + const indentationSpaces = " ".repeat(indentation); + let currentLine = position.line - 1; + let found = false; + + while (currentLine > 0 && !found) { + const lineContent = this.getLineContent(currentLine); + if (lineContent.startsWith(indentationSpaces) && lineContent.charCodeAt(indentation + 1) !== CharCode.Space) { + found = true; + } else { + currentLine--; + } + } + return currentLine; + } + + private getIndentation(lineContent: string, lineOffset: number): number { + if (lineContent.length < lineOffset) { + return 0; + } + + for (let i = 0; i < lineOffset; i++) { + const char = lineContent.charCodeAt(i); + if (char !== CharCode.Space && char !== CharCode.Tab) { + return i; + } + } + + // assuming that current position is indentation + return lineOffset; } } diff --git a/server/packages/yaml-language-service/tests/unit/yamlParser.test.ts b/server/packages/yaml-language-service/tests/unit/yamlParser.test.ts index aa2d068..87d2776 100644 --- a/server/packages/yaml-language-service/tests/unit/yamlParser.test.ts +++ b/server/packages/yaml-language-service/tests/unit/yamlParser.test.ts @@ -158,3 +158,55 @@ namespace: defaul`; ).toBeDefined(); }); }); + +describe("YamlDocument", () => { + it("should identify comments", () => { + const parsedDocument = parse("# a comment\ntest: test\n# a second comment"); + let isComment = parsedDocument.isComment(11); + expect(isComment).toBe(true); + isComment = parsedDocument.isComment(12); + expect(isComment).toBe(false); + isComment = parsedDocument.isComment(22); + expect(isComment).toBe(false); + isComment = parsedDocument.isComment(23); + expect(isComment).toBe(true); + }); + describe("getNodeFromOffset", () => { + const SAMPLE_DOC = ` +test: value +test02: + prop03: + test04: val + +`; + it.each([ + [0, "_root_"], // _root_ is not a property, is an object + [1, "test"], + [12, "_root_"], + [13, "test02"], + [20, "_root_"], + [22, "test02"], + [23, "prop03"], + [30, "prop03"], + [31, "_root_"], + [35, "test04"], + [46, "test04"], + [47, "_root_"], + [49, "test02"], + [51, "prop03"], + [53, "test04"], + ])("should return for offset %p the expected node name %p", (offset: number, expectedNodeName: string) => { + const parsedDocument = parse(SAMPLE_DOC); + const node = parsedDocument.getNodeFromOffset(offset); + expect(node).toBeDefined(); + if (expectedNodeName === "_root_") { + expect(node?.parent).toBeUndefined(); + } else { + expect(node?.parent).toBeDefined(); + } + if (node?.type === "property") { + expect(node.keyNode.value).toBe(expectedNodeName); + } + }); + }); +}); diff --git a/server/tsconfig.json b/server/tsconfig.json index aa03c3f..5200861 100644 --- a/server/tsconfig.json +++ b/server/tsconfig.json @@ -8,7 +8,10 @@ "esModuleInterop": true, "sourceMap": true, "strict": true, - "composite": true + "composite": true, + "paths": { + "@schemas/*": ["../workflow-languages/schemas/*"] + } }, "files": [], "include": [], diff --git a/shared.webpack.config.js b/shared.webpack.config.js index 3ccd869..8bff832 100644 --- a/shared.webpack.config.js +++ b/shared.webpack.config.js @@ -24,6 +24,9 @@ module.exports = function withDefaults(/**@type WebpackConfig*/ extConfig) { fallback: { path: require.resolve("path-browserify"), }, + alias: { + "@schemas": path.resolve(__dirname, "./workflow-languages/schemas/"), + }, }, module: { rules: [ @@ -36,11 +39,18 @@ module.exports = function withDefaults(/**@type WebpackConfig*/ extConfig) { options: { compilerOptions: { sourceMap: true, + paths: { + "@schemas": [path.resolve(__dirname, "./workflow-languages/schemas/")], + }, }, }, }, ], }, + { + test: /\.ya?ml$/, + use: "yaml-loader", + }, ], }, externals: { diff --git a/test-data/yaml/validation/test_wf_00.gxwf.yml b/test-data/yaml/validation/test_wf_00.gxwf.yml index b5e534f..3c5d77a 100644 --- a/test-data/yaml/validation/test_wf_00.gxwf.yml +++ b/test-data/yaml/validation/test_wf_00.gxwf.yml @@ -1,5 +1,2 @@ class: GalaxyWorkflow -label: Test Workflow Without Steps -inputs: {} -outputs: {} -steps: {} +label: Test workflow with missing required fields diff --git a/test-data/yaml/validation/test_wf_03.gxwf.yml b/test-data/yaml/validation/test_wf_03.gxwf.yml new file mode 100644 index 0000000..ba0c552 --- /dev/null +++ b/test-data/yaml/validation/test_wf_03.gxwf.yml @@ -0,0 +1,19 @@ +class: GalaxyWorkflow +inputs: + - label: input1 +steps: + - tool_id: cat1 + label: first_cat + state: + input1: + $link: input1 + - label: embed1 + run: + "@import": embed_test_1_tool.gxtool.yml + - tool_id: cat1 + state: + input1: + $link: first_cat/out_file1 + queries: + - input2: + $link: embed1/output1 diff --git a/test-data/yaml/validation/test_wf_04.gxwf.yml b/test-data/yaml/validation/test_wf_04.gxwf.yml new file mode 100644 index 0000000..6bd8696 --- /dev/null +++ b/test-data/yaml/validation/test_wf_04.gxwf.yml @@ -0,0 +1,35 @@ +class: GalaxyWorkflow +inputs: + outer_input: data +outputs: + outer_output: + outputSource: second_cat/out_file1 +steps: + first_cat: + tool_id: cat1 + in: + input1: outer_input + nested_workflow: + run: + class: GalaxyWorkflow + inputs: + - id: inner_input + outputs: + - outputSource: 1/out_file1 + steps: + random: + tool_id: random_lines1 + state: + num_lines: 1 + input: + $link: inner_input + seed_source: + seed_source_selector: set_seed + seed: asdf + in: + inner_input: first_cat/out_file1 + second_cat: + tool_id: cat1 + in: + input1: nested_workflow/1:out_file1 + queries_0|input2: nested_workflow/1:out_file1 diff --git a/test-data/yaml/validation/test_wf_05.gxwf.yml b/test-data/yaml/validation/test_wf_05.gxwf.yml new file mode 100644 index 0000000..973b6b6 --- /dev/null +++ b/test-data/yaml/validation/test_wf_05.gxwf.yml @@ -0,0 +1,25 @@ +class: GalaxyWorkflow +steps: + - type: input + label: input1 + - tool_id: cat1 + label: first_cat + state: + input1: + $link: 0 + - label: embed1 + run: + class: GalaxyTool + command: echo 'hello world 2' > $output1 + outputs: + output1: + format: txt + - tool_id: cat1 + state: + input1: + $link: first_cat/out_file1 + queries: + - input2: + $link: embed1/output1 +test_data: + input1: hello world diff --git a/tsconfig.json b/tsconfig.json index 209a682..b373707 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -8,7 +8,10 @@ "esModuleInterop": true, "sourceMap": true, "strict": true, - "composite": true + "composite": true, + "paths": { + "@schemas/*": ["./workflow-languages/schemas/*"] + } }, "files": [], "include": [], diff --git a/workflow-languages/schemas/gxformat2/common/common.yaml b/workflow-languages/schemas/gxformat2/common/common.yaml new file mode 100644 index 0000000..808dd0f --- /dev/null +++ b/workflow-languages/schemas/gxformat2/common/common.yaml @@ -0,0 +1,93 @@ +saladVersion: v1.1 +$base: "https://galaxyproject.org/gxformat2/gxformat2common#" + +$graph: + - name: HasUUID + type: record + abstract: true + fields: + - name: uuid + type: string? + doc: | + UUID uniquely representing this element. + + - name: HasStepErrors + type: record + abstract: true + fields: + - name: errors + type: string? + doc: | + During Galaxy export there may be some problem validating the tool state, tool used, etc.. + that will be indicated by this field. The Galaxy user should be warned of these problems before + the workflow can be used in Galaxy. + + This field should not be used in human written Galaxy workflow files. + + A typical problem is the referenced tool is not installed, this can be fixed by installed the tool + and re-saving the workflow and then re-exporting it. + + - name: HasStepPosition + type: record + abstract: true + fields: + - name: position + type: StepPosition? + + - name: StepPosition + type: record + doc: This field specifies the location of the step's node when rendered in the workflow editor. + fields: + - name: top + type: + - float + - int + default: 0.0 + doc: | + Relative vertical position of the step's node when rendered in the workflow editor. + - name: left + type: + - float + - int + default: 0.0 + doc: | + Relative horizontal position of the step's node when rendered in the workflow editor. + + - name: ReferencesTool + type: record + abstract: true + fields: + - name: tool_id + type: string? + doc: | + The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0'). + - name: tool_shed_repository + type: ToolShedRepository? + doc: | + The Galaxy Tool Shed repository that should be installed in order to use this tool. + - name: tool_version + type: string? + doc: | + The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version + and this field is optional. + + - name: ToolShedRepository + type: record + fields: + - name: changeset_revision + type: string + doc: | + The revision of the tool shed repository this tool can be found in. + - name: name + type: string + jsonldPredicate: "@id" # will this bite me? + doc: | + The name of the tool shed repository this tool can be found in. + - name: owner + type: string + doc: | + The owner of the tool shed repository this tool can be found in. + - name: tool_shed + type: string + doc: | + The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu. diff --git a/workflow-languages/schemas/gxformat2/common/metaschema/metaschema_base.yaml b/workflow-languages/schemas/gxformat2/common/metaschema/metaschema_base.yaml new file mode 100644 index 0000000..cc4fab4 --- /dev/null +++ b/workflow-languages/schemas/gxformat2/common/metaschema/metaschema_base.yaml @@ -0,0 +1,169 @@ +$base: "https://w3id.org/cwl/salad#" + +$namespaces: + sld: "https://w3id.org/cwl/salad#" + dct: "http://purl.org/dc/terms/" + rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + rdfs: "http://www.w3.org/2000/01/rdf-schema#" + xsd: "http://www.w3.org/2001/XMLSchema#" + +$graph: + - name: "Schema" + type: documentation + doc: | + # Schema + + - name: Documented + type: record + abstract: true + docParent: "#Schema" + fields: + - name: doc + type: + - string? + - string[]? + doc: "A documentation string for this object, or an array of strings which should be concatenated." + jsonldPredicate: "rdfs:comment" + + - name: PrimitiveType + type: enum + symbols: + - "sld:null" + - "xsd:boolean" + - "xsd:int" + - "xsd:long" + - "xsd:float" + - "xsd:double" + - "xsd:string" + doc: + - | + Salad data types are based on Avro schema declarations. Refer to the + [Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for + detailed information. + - "null: no value" + - "boolean: a binary value" + - "int: 32-bit signed integer" + - "long: 64-bit signed integer" + - "float: single precision (32-bit) IEEE 754 floating-point number" + - "double: double precision (64-bit) IEEE 754 floating-point number" + - "string: Unicode character sequence" + + - name: Any + type: enum + symbols: ["#Any"] + docAfter: "#PrimitiveType" + doc: | + The **Any** type validates for any non-null value. + + - name: RecordField + type: record + extends: Documented + doc: A field of a record. + fields: + - name: name + type: string + jsonldPredicate: "@id" + doc: | + The name of the field + + - name: type + type: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + - type: array + items: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + jsonldPredicate: + _id: sld:type + _type: "@vocab" + typeDSL: true + refScope: 2 + doc: | + The field type + + - name: RecordSchema + type: record + fields: + type: + doc: "Must be `record`" + type: + type: enum + symbols: + - "sld:record" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 + fields: + type: RecordField[]? + jsonldPredicate: + _id: sld:fields + mapSubject: name + mapPredicate: type + doc: "Defines the fields of the record." + + - name: EnumSchema + type: record + doc: | + Define an enumerated type. + fields: + type: + doc: "Must be `enum`" + type: + type: enum + symbols: + - "sld:enum" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 + symbols: + type: string[] + jsonldPredicate: + _id: "sld:symbols" + _type: "@id" + identity: true + doc: "Defines the set of valid symbols." + + - name: ArraySchema + type: record + fields: + type: + doc: "Must be `array`" + type: + type: enum + symbols: + - "sld:array" + jsonldPredicate: + _id: "sld:type" + _type: "@vocab" + typeDSL: true + refScope: 2 + items: + type: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + - type: array + items: + - PrimitiveType + - RecordSchema + - EnumSchema + - ArraySchema + - string + jsonldPredicate: + _id: "sld:items" + _type: "@vocab" + refScope: 2 + doc: "Defines the type of the array elements." diff --git a/workflow-languages/schemas/gxformat2/v19_09/process.yaml b/workflow-languages/schemas/gxformat2/v19_09/process.yaml new file mode 100644 index 0000000..ffa5073 --- /dev/null +++ b/workflow-languages/schemas/gxformat2/v19_09/process.yaml @@ -0,0 +1,101 @@ +# Subset of CWL's process, can't use process as is because of types not implemented. +saladVersion: v1.1 +$base: "https://w3id.org/cwl/cwl#" + +$namespaces: + cwl: "https://w3id.org/cwl/cwl#" + sld: "https://w3id.org/cwl/salad#" + rdfs: "http://www.w3.org/2000/01/rdf-schema#" + +$graph: + - name: Labeled + type: record + abstract: true + fields: + - name: label + type: + - "null" + - string + jsonldPredicate: "rdfs:label" + doc: "A short, human-readable label of this object." + + - name: Identified + type: record + abstract: true + fields: + - name: id + type: string? + jsonldPredicate: "@id" + doc: "The unique identifier for this object." + + - name: Parameter + type: record + extends: [Labeled, sld:Documented, Identified] # Replaced FieldBase with Labeled. + abstract: true + doc: | + Define an input or output parameter to a process. + + - name: InputParameter + type: record + abstract: true + extends: [Parameter] # , InputFormat, LoadContents] + fields: + - name: default + type: Any? + jsonldPredicate: + _id: sld:default + noLinkCheck: true + doc: | + The default value to use for this parameter if the parameter is missing + from the input object, or if the value of the parameter in the input + object is `null`. Default values are applied before evaluating expressions + (e.g. dependent `valueFrom` fields). + + - name: OutputParameter + type: record + extends: [Parameter] + abstract: true + + - type: record + name: Process + extends: [Identified, Labeled, sld:Documented] + abstract: true + doc: | + + The base executable type in CWL is the `Process` object defined by the + document. Note that the `Process` object is abstract and cannot be + directly executed. + + fields: + - name: inputs + type: + type: array + items: InputParameter + jsonldPredicate: + _id: "cwl:inputs" + mapSubject: id + mapPredicate: type + doc: | + Defines the input parameters of the process. The process is ready to + run when all required input parameters are associated with concrete + values. Input parameters include a schema for each parameter which is + used to validate the input object. It may also be used to build a user + interface for constructing the input object. + + When accepting an input object, all input parameters must have a value. + If an input parameter is missing from the input object, it must be + assigned a value of `null` (or the value of `default` for that + parameter, if provided) for the purposes of validation and evaluation + of expressions. + + - name: outputs + type: + type: array + items: OutputParameter + jsonldPredicate: + _id: "cwl:outputs" + mapSubject: id + mapPredicate: type + doc: | + Defines the parameters representing the output of the process. May be + used to generate and/or validate the output object. diff --git a/workflow-languages/schemas/gxformat2/v19_09/workflows.yaml b/workflow-languages/schemas/gxformat2/v19_09/workflows.yaml new file mode 100644 index 0000000..7f50924 --- /dev/null +++ b/workflow-languages/schemas/gxformat2/v19_09/workflows.yaml @@ -0,0 +1,390 @@ +saladVersion: v1.1 +$base: "https://galaxyproject.org/gxformat2/v19_09#" + +$namespaces: + gxformat2: "https://galaxyproject.org/gxformat2/v19_09#" + gxformat2common: "https://galaxyproject.org/gxformat2/gxformat2common#" + cwl: "https://w3id.org/cwl/cwl#" + sld: "https://w3id.org/cwl/salad#" + rdfs: "http://www.w3.org/2000/01/rdf-schema#" + +$graph: + - name: "WorkflowDoc" + type: documentation + doc: + - | + # Galaxy Workflow Format 2 Description + + The traditional Galaxy workflow description (.ga) is not meant to be concise and is neither readily human readable or human writable. + Format 2 addresses all three of these limitations while also converging (where it makes sense without sacrificing these other goals) + with the workflow description with that used by the Common Workflow Language. + + This standard is in active development and a moving target in many ways, but we will try to keep what is ingestible by Galaxy + backward-compatible going forward. + + - $import: "../common/metaschema/metaschema_base.yml" + - $import: "./Process.yml" # trimmed down version of cwl's Process.yml + - $import: "../common/common.yml" + + - name: GalaxyType + type: enum + extends: sld:PrimitiveType + symbols: + - integer + - text + - File + - data + - collection + doc: + - "Extends primitive types with the native Galaxy concepts such datasets and collections." + - "integer: an alias for int type - matches syntax used by Galaxy tools" + - "text: an alias for string type - matches syntax used by Galaxy tools" + - "File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future" + - "data: a Galaxy dataset" + - "collection: a Galaxy dataset collection" + + - name: WorkflowStepType + type: enum + symbols: + - tool + - subworkflow + - pause + doc: + - | + Module types used by Galaxy steps. Galaxy's native format allows additional types such as data_input, data_input_collection, and parameter_type + but these should be represented as ``inputs`` in Format2. + - "tool: Run a tool." + - "subworkflow: Run a subworkflow." + - "pause: Pause computation on this branch of workflow until user allows it to continue." + + - name: WorkflowInputParameter + type: record + extends: + - cwl:InputParameter + - gxformat2common:HasStepPosition + docParent: "#GalaxyWorkflow" + fields: + - name: type + type: + - GalaxyType + - string + - "null" + default: data + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + doc: | + Specify valid types of data that may be assigned to this parameter. + - name: optional + type: + - boolean + - "null" + default: false + doc: | + If set to true, `WorkflowInputParameter` is not required to submit the workflow. + - name: format + doc: | + Specify datatype extension for valid input datasets. + type: + - "null" + - type: array + items: string + - name: collection_type + doc: | + Collection type (defaults to `list` if `type` is `collection`). Nested + collection types are separated with colons, e.g. `list:list:paired`. + type: + - "null" + - string + + - name: WorkflowOutputParameter + type: record + extends: cwl:OutputParameter + docParent: "#GalaxyWorkflow" + doc: | + Describe an output parameter of a workflow. The parameter must be + connected to one parameter defined in the workflow that + will provide the value of the output parameter. It is legal to + connect a WorkflowInputParameter to a WorkflowOutputParameter. + fields: + - name: outputSource + doc: | + Specifies workflow parameter that supply the value of to + the output parameter. + # Steps don't reference outputs in gxformat2 (yet anyway). + # Can we just link the step if before the / + #jsonldPredicate: + # "_id": "gxformat2:outputSource" + # "_type": "@id" + # refScope: 0 + type: + - string? + - name: type + type: GalaxyType? + default: data + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + doc: | + Specify valid types of data that may be assigned to this parameter. + + - name: WorkflowStep + type: record + extends: + - cwl:Identified + - cwl:Labeled + - sld:Documented + - gxformat2common:HasStepPosition + - gxformat2common:ReferencesTool + - gxformat2common:HasStepErrors + - gxformat2common:HasUUID + docParent: "#GalaxyWorkflow" + doc: | + This represents a non-input step a Galaxy Workflow. + + # A note about `state` and `tool_state` fields. + + Only one or the other should be specified. These are two ways to represent the "state" + of a tool at this workflow step. Both are essentially maps from parameter names to + parameter values. + + `tool_state` is much more low-level and expects a flat dictionary with each value a JSON + dump. Nested tool structures such as conditionals and repeats should have all their values + in the JSON dumped string. In general `tool_state` may be present in workflows exported from + Galaxy but shouldn't be written by humans. + + `state` can contained a typed map. Repeat values can be represented as YAML arrays. An alternative + to representing `state` this way is defining inputs with default values. + fields: + - name: in + type: WorkflowStepInput[]? + jsonldPredicate: + _id: "gxformat2:in" + mapSubject: id + mapPredicate: source + doc: | + Defines the input parameters of the workflow step. The process is ready to + run when all required input parameters are associated with concrete + values. Input parameters include a schema for each parameter which is + used to validate the input object. It may also be used build a user + interface for constructing the input object. + - name: out + type: + - type: array + items: [string, WorkflowStepOutput] + - "null" + jsonldPredicate: + _id: "gxformat2:out" + mapSubject: id + mapPredicate: source + doc: | + Defines the parameters representing the output of the process. May be + used to generate and/or validate the output object. + + This can also be called 'outputs' for legacy reasons - but the resulting + workflow document is not a valid instance of this schema. + - name: state + type: Any? + doc: | + Structured tool state. + jsonldPredicate: + _id: "gxformat2:state" + noLinkCheck: true + - name: tool_state + type: Any? + jsonldPredicate: + _id: "gxformat2:tool_state" + noLinkCheck: true + doc: | + Unstructured tool state. + - name: type + type: WorkflowStepType? + jsonldPredicate: + "_id": "sld:type" + "_type": "@vocab" + refScope: 2 + typeDSL: True + default: tool + doc: | + Workflow step module's type (defaults to 'tool'). + - name: run + type: + - "null" + - GalaxyWorkflow + jsonldPredicate: + _id: "cwl:run" + _type: "@id" + subscope: run + doc: | + Specifies a subworkflow to run. + - name: runtime_inputs + type: + - "null" + - type: array + items: string + #- name: when + # type: + # - "null" + # - string # TODO: cwl defines an enum for this, not sure how that works + # jsonldPredicate: + # _id: "gxformat2:when" + # noLinkCheck: true + # doc: | + # If defined, only run the step when the expression evaluates to + # `true`. If `false` the step is skipped. A skipped step + # produces a `null` on each output. + + # Expression should be an ecma5.1 expression. + + - name: Sink + type: record + abstract: true + fields: + - name: source + doc: | + Specifies one or more workflow parameters that will provide input to + the underlying step parameter. + jsonldPredicate: + "_id": "cwl:source" + "_type": "@id" + refScope: 2 + type: + - string? + - string[]? + + - type: record + name: WorkflowStepInput + extends: [cwl:Identified, Sink, cwl:Labeled] + docParent: "#WorkflowStep" + doc: | + TODO: + + fields: + - name: default + type: ["null", Any] + doc: | + The default value for this parameter to use if either there is no + `source` field, or the value produced by the `source` is `null`. The + default must be applied prior to scattering or evaluating `valueFrom`. + jsonldPredicate: + _id: "sld:default" + noLinkCheck: true + + - type: record + name: Report + doc: | + Definition of an invocation report for this workflow. Currently the only + field is 'markdown'. + fields: + - name: markdown + type: string + doc: | + Galaxy flavored Markdown to define an invocation report. + + - type: record + name: WorkflowStepOutput + docParent: "#WorkflowStep" + extends: cwl:Identified + doc: | + Associate an output parameter of the underlying process with a workflow + parameter. The workflow parameter (given in the `id` field) be may be used + as a `source` to connect with input parameters of other workflow steps, or + with an output parameter of the process. + + A unique identifier for this workflow output parameter. This is + the identifier to use in the `source` field of `WorkflowStepInput` + to connect the output value to downstream parameters. + fields: + rename: + type: string? + hide: + type: boolean? + delete_intermediate_datasets: + type: boolean? + change_datatype: + type: string? + set_columns: + type: + - "null" + - type: array + items: string + add_tags: + type: + - "null" + - type: array + items: string + remove_tags: + type: + - "null" + - type: array + items: string + + - name: GalaxyWorkflow + type: record + extends: + - cwl:Process + - gxformat2common:HasUUID + specialize: + - specializeFrom: cwl:InputParameter + specializeTo: WorkflowInputParameter + - specializeFrom: cwl:OutputParameter + specializeTo: WorkflowOutputParameter + documentRoot: true + doc: | + A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable + on a Galaxy server that includes the contained tool definitions. + + The workflows API or the user interface of Galaxy instances that are of version 19.09 or newer should be able to + import a document defining this record. + + ## A note about `label` field. + + This is the name of the workflow in the Galaxy user interface. This is the mechanism that + users will primarily identify the workflow using. Legacy support - this may also be called 'name' and Galaxy will + consume the workflow document fine and treat this attribute correctly - however in order to validate against this + workflow definition schema the attribute should be called `label`. + fields: + # I can't find a way to override the documentation of label, even though I contextual. + # - name: label + # type: + # - "null" + # - string + # jsonldPredicate: "rdfs:label" + # doc: {$include: ../common/workflow_label_description.txt} + # # Legacy support - this may also be called 'name' and Galaxy will consume the workflow fine and treat this + # # attribute correctly - however in order to validate against this schema the attribute should be called label. + - name: "class" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + type: string + - name: steps + doc: { $include: ../common/steps_description.txt } + type: + - type: array + items: "#WorkflowStep" + jsonldPredicate: + mapSubject: id + - name: report + doc: Workflow invocation report template. + type: Report? + - name: tags + type: + - type: array + items: string + - "null" + doc: | + Tags for the workflow. + - name: creator + type: Any? + doc: Can be a schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entity + - name: license + type: string? + doc: Must be a valid license listed at https://spdx.org/licenses/ + - name: release + type: string? + doc: If listed should correspond to the release of the workflow in its source reposiory.