Merge pull request #17 from davelopez/add_clean_workflow_command

Add clean workflow command

client/src/commands/cleanWorkflow.ts

@@ -0,0 +1,28 @@
+import { window } from "vscode";
+import { CleanWorkflowDocumentParams, CleanWorkflowDocumentRequest } from "../requestsDefinitions";
+import { CustomCommand, getCommandFullIdentifier } from "./common";
+
+/**
+ * Command to 'clean' the selected workflow document.
+ * It will apply edits to remove the non-workflow logic related parts.
+ */
+export class CleanWorkflowCommand extends CustomCommand {
+  public static id = getCommandFullIdentifier("cleanWorkflow");
+  readonly identifier: string = CleanWorkflowCommand.id;
+
+  async execute(args: any[]): Promise<void> {
+    if (!window.activeTextEditor) {
+      return;
+    }
+    const { document } = window.activeTextEditor;
+
+    const params: CleanWorkflowDocumentParams = { uri: this.client.code2ProtocolConverter.asUri(document.uri) };
+    const result = await this.client.sendRequest(CleanWorkflowDocumentRequest.type, params);
+    if (!result) {
+      throw new Error("Cannot clean the requested document. The server returned no result.");
+    }
+    if (result.error) {
+      throw new Error(result.error);
+    }
+  }
+}

client/src/commands/setup.ts

@@ -5,6 +5,7 @@ import { SelectForCleanCompareCommand } from "./selectForCleanCompare";
 import { PreviewCleanWorkflowCommand } from "./previewCleanWorkflow";
 import { CleanWorkflowProvider } from "../providers/cleanWorkflowProvider";
 import { GitProvider } from "../providers/git/common";
+import { CleanWorkflowCommand } from "./cleanWorkflow";
 
 /**
  * Registers all custom commands declared in package.json
@@ -13,6 +14,7 @@ import { GitProvider } from "../providers/git/common";
  */
 export function setupCommands(context: ExtensionContext, client: CommonLanguageClient, gitProvider: GitProvider) {
   context.subscriptions.push(new PreviewCleanWorkflowCommand(client).register());
+  context.subscriptions.push(new CleanWorkflowCommand(client).register());
   const selectForCompareProvider = new SelectForCleanCompareCommand(client);
   context.subscriptions.push(selectForCompareProvider.register());
   context.subscriptions.push(

client/src/requestsDefinitions.ts

@@ -3,9 +3,18 @@ import { RequestType } from "vscode-languageclient";
 // TODO: Move the contents of this file to a shared lib https://github.com/Microsoft/vscode/issues/15829
 
 export namespace LSRequestIdentifiers {
+  export const CLEAN_WORKFLOW_DOCUMENT = "galaxy-workflows-ls.cleanWorkflowDocument";
   export const CLEAN_WORKFLOW_CONTENTS = "galaxy-workflows-ls.cleanWorkflowContents";
 }
 
+export interface CleanWorkflowDocumentParams {
+  uri: string;
+}
+
+export interface CleanWorkflowDocumentResult {
+  error: string;
+}
+
 export interface CleanWorkflowContentsParams {
   contents: string;
 }
@@ -14,6 +23,12 @@ export interface CleanWorkflowContentsResult {
   contents: string;
 }
 
+export namespace CleanWorkflowDocumentRequest {
+  export const type = new RequestType<CleanWorkflowDocumentParams, CleanWorkflowDocumentResult, void>(
+    LSRequestIdentifiers.CLEAN_WORKFLOW_DOCUMENT
+  );
+}
+
 export namespace CleanWorkflowContentsRequest {
   export const type = new RequestType<CleanWorkflowContentsParams, CleanWorkflowContentsResult, void>(
     LSRequestIdentifiers.CLEAN_WORKFLOW_CONTENTS

package.json

@@ -50,6 +50,13 @@
 				"icon": "$(eye)",
 				"category": "Galaxy Workflows"
 			},
+			{
+				"command": "galaxy-workflows.cleanWorkflow",
+				"title": "Clean workflow",
+				"enablement": "resourceLangId == galaxyworkflow",
+				"icon": "$(edit)",
+				"category": "Galaxy Workflows"
+			},
 			{
 				"command": "galaxy-workflows.selectForCleanCompare",
 				"title": "Select workflow for (clean) compare",
@@ -71,6 +78,10 @@
 					"command": "galaxy-workflows.previewCleanWorkflow",
 					"when": "activeEditor"
 				},
+				{
+					"command": "galaxy-workflows.cleanWorkflow",
+					"when": "activeEditor"
+				},
 				{
 					"command": "galaxy-workflows.selectForCleanCompare",
 					"when": "false"
@@ -103,6 +114,18 @@
 					"group": "3_compare@2",
 					"when": "config.git.enabled && !git.missing && galaxy-workflows.gitProviderInitialized"
 				}
+			],
+			"editor/context": [
+				{
+					"command": "galaxy-workflows.previewCleanWorkflow",
+					"group": "galaxyworkflow@1",
+					"when": "resourceLangId == galaxyworkflow"
+				},
+				{
+					"command": "galaxy-workflows.cleanWorkflow",
+					"group": "galaxyworkflow@2",
+					"when": "resourceLangId == galaxyworkflow"
+				}
 			]
 		}
 	},

server/src/commands/cleanWorkflow.ts

@@ -1,11 +1,30 @@
+import { ApplyWorkspaceEditParams, Range, TextDocumentEdit, TextEdit } from "vscode-languageserver";
 import { TextDocument } from "vscode-languageserver-textdocument";
 import { ASTNode, PropertyASTNode, WorkflowDocument } from "../languageTypes";
 import { GalaxyWorkflowLanguageServer } from "../server";
 import { CustomCommand } from "./common";
-import { CleanWorkflowContentsRequest, CleanWorkflowContentsResult } from "./requestsDefinitions";
+import {
+  CleanWorkflowContentsParams,
+  CleanWorkflowContentsRequest,
+  CleanWorkflowContentsResult,
+  CleanWorkflowDocumentParams,
+  CleanWorkflowDocumentRequest,
+  CleanWorkflowDocumentResult,
+} from "./requestsDefinitions";
 
+/**
+ * A set of property names that are unrelated to the workflow logic.
+ * Usually used by other tools like the workflow editor.
+ */
 const CLEANABLE_PROPERTY_NAMES = new Set(["position", "uuid", "errors", "version"]);
 
+/**
+ * Command for handling workflow `cleaning` requests.
+ * Supports both, direct contents (raw document text), and document uri requests
+ * for cleaning.
+ * When requesting with a document uri, the workflow document must be already registered in the server
+ * as a workflow document.
+ */
 export class CleanWorkflowCommand extends CustomCommand {
   public static register(server: GalaxyWorkflowLanguageServer): CleanWorkflowCommand {
     return new CleanWorkflowCommand(server);
@@ -16,30 +35,94 @@ export class CleanWorkflowCommand extends CustomCommand {
   }
 
   protected listenToRequests(): void {
-    this.connection.onRequest(CleanWorkflowContentsRequest.type, async (params) => {
-      const tempDocument = this.createTempWorkflowDocumentWithContents(params.contents);
-      const workflowDocument = this.languageService.parseWorkflowDocument(tempDocument);
+    this.connection.onRequest(CleanWorkflowContentsRequest.type, (params) =>
+      this.onCleanWorkflowContentsRequest(params)
+    );
+    this.connection.onRequest(CleanWorkflowDocumentRequest.type, (params) =>
+      this.onCleanWorkflowDocumentRequest(params)
+    );
+  }
+
+  /**
+   * Processes a `CleanWorkflowContentsRequest` by returning the `clean` contents
+   * of a workflow document given the raw text contents of the workflow document.
+   * @param params The request parameters containing the raw text contents of the workflow
+   * @returns The `clean` contents of the workflow document
+   */
+  private async onCleanWorkflowContentsRequest(
+    params: CleanWorkflowContentsParams
+  ): Promise<CleanWorkflowContentsResult | undefined> {
+    const tempDocument = this.createTempWorkflowDocumentWithContents(params.contents);
+    const workflowDocument = this.languageService.parseWorkflowDocument(tempDocument);
+    if (workflowDocument) {
+      return await this.cleanWorkflowContentsResult(workflowDocument);
+    }
+    return undefined;
+  }
+
+  /**
+   * Applies the necessary text edits to the workflow document identified by the given URI to
+   * remove all the properties in the workflow that are unrelated to the essential workflow logic.
+   * @param params The request parameters containing the URI of the workflow document.
+   * @returns An error message if something went wrong
+   */
+  private async onCleanWorkflowDocumentRequest(
+    params: CleanWorkflowDocumentParams
+  ): Promise<CleanWorkflowDocumentResult> {
+    try {
+      const workflowDocument = this.workflowDocuments.get(params.uri);
       if (workflowDocument) {
-        return await this.CleanWorkflowContentsResult(workflowDocument);
+        const edits = this.getTextEditsToCleanWorkflow(workflowDocument);
+        const editParams: ApplyWorkspaceEditParams = {
+          label: "Clean workflow",
+          edit: {
+            documentChanges: [
+              TextDocumentEdit.create(
+                {
+                  uri: params.uri,
+                  version: null,
+                },
+                edits
+              ),
+            ],
+          },
+        };
+        this.connection.workspace.applyEdit(editParams);
       }
-      return undefined;
+      return { error: "" };
+    } catch (error) {
+      return { error: String(error) };
+    }
+  }
+
+  private getTextEditsToCleanWorkflow(workflowDocument: WorkflowDocument): TextEdit[] {
+    const nodesToRemove = this.getNonEssentialNodes(workflowDocument, CLEANABLE_PROPERTY_NAMES);
+    const changes: TextEdit[] = [];
+    nodesToRemove.forEach((node) => {
+      const range = this.getReplaceRange(workflowDocument.textDocument, node);
+      changes.push(TextEdit.replace(range, ""));
     });
+    return changes;
   }
 
   private createTempWorkflowDocumentWithContents(contents: string) {
     return TextDocument.create("temp://temp-workflow", "galaxyworkflow", 0, contents);
   }
 
-  private async CleanWorkflowContentsResult(workflowDocument: WorkflowDocument): Promise<CleanWorkflowContentsResult> {
-    const nodesToRemove = this.getNonEssentialNodes(workflowDocument.jsonDocument.root);
+  private async cleanWorkflowContentsResult(workflowDocument: WorkflowDocument): Promise<CleanWorkflowContentsResult> {
+    const nodesToRemove = this.getNonEssentialNodes(workflowDocument, CLEANABLE_PROPERTY_NAMES);
     const contents = this.getCleanContents(workflowDocument.textDocument.getText(), nodesToRemove.reverse());
     const result: CleanWorkflowContentsResult = {
       contents: contents,
     };
     return result;
   }
 
-  private getNonEssentialNodes(root: ASTNode | undefined): PropertyASTNode[] {
+  private getNonEssentialNodes(
+    workflowDocument: WorkflowDocument,
+    cleanablePropertyNames: Set<string>
+  ): PropertyASTNode[] {
+    const root = workflowDocument.jsonDocument.root;
     if (!root) {
       return [];
     }
@@ -57,7 +140,7 @@ export class CleanWorkflowCommand extends CustomCommand {
       } else if (node.type === "object") {
         node.properties.forEach((property: PropertyASTNode) => {
           const key = property.keyNode.value;
-          if (CLEANABLE_PROPERTY_NAMES.has(key)) {
+          if (cleanablePropertyNames.has(key)) {
             result.push(property);
           }
           if (property.valueNode) {
@@ -79,17 +162,35 @@ export class CleanWorkflowCommand extends CustomCommand {
     const removeChunks: string[] = [];
     let result = documentText;
     nodesToRemove.forEach((node) => {
-      let startPos = node.offset;
-      let endPos = node.offset + node.length;
-      startPos = documentText.lastIndexOf("\n", startPos);
-      if (documentText.charAt(endPos) === ",") {
-        endPos++;
-      }
-      removeChunks.push(documentText.substring(startPos, endPos));
+      const rangeOffsets = this.getFullNodeRangeOffsets(documentText, node);
+      removeChunks.push(documentText.substring(rangeOffsets.start, rangeOffsets.end));
     });
     removeChunks.forEach((chunk) => {
       result = result.replace(chunk, "");
     });
     return result;
   }
+
+  /**
+   * Gets the range offsets (`start` and `end`) for a given syntax node including
+   * the blank spaces/indentation before and after the node and possible ending comma.
+   * @param documentText The full workflow document text
+   * @param node The syntax node
+   * @returns The `start` and `end` offsets for the given syntax node
+   */
+  private getFullNodeRangeOffsets(documentText: string, node: ASTNode) {
+    let startPos = node.offset;
+    let endPos = node.offset + node.length;
+    startPos = documentText.lastIndexOf("\n", startPos);
+    if (documentText.charAt(endPos) === ",") {
+      endPos++;
+    }
+    return { start: startPos, end: endPos };
+  }
+
+  private getReplaceRange(document: TextDocument, node: ASTNode): Range {
+    const documentText = document.getText();
+    const rangeOffsets = this.getFullNodeRangeOffsets(documentText, node);
+    return Range.create(document.positionAt(rangeOffsets.start), document.positionAt(rangeOffsets.end));
+  }
 }

server/src/commands/requestsDefinitions.ts

@@ -3,9 +3,18 @@ import { RequestType } from "vscode-languageserver";
 // TODO: Move the contents of this file to a shared lib https://github.com/Microsoft/vscode/issues/15829
 
 export namespace LSRequestIdentifiers {
+  export const CLEAN_WORKFLOW_DOCUMENT = "galaxy-workflows-ls.cleanWorkflowDocument";
   export const CLEAN_WORKFLOW_CONTENTS = "galaxy-workflows-ls.cleanWorkflowContents";
 }
 
+export interface CleanWorkflowDocumentParams {
+  uri: string;
+}
+
+export interface CleanWorkflowDocumentResult {
+  error: string;
+}
+
 export interface CleanWorkflowContentsParams {
   contents: string;
 }
@@ -14,6 +23,12 @@ export interface CleanWorkflowContentsResult {
   contents: string;
 }
 
+export namespace CleanWorkflowDocumentRequest {
+  export const type = new RequestType<CleanWorkflowDocumentParams, CleanWorkflowDocumentResult, void>(
+    LSRequestIdentifiers.CLEAN_WORKFLOW_DOCUMENT
+  );
+}
+
 export namespace CleanWorkflowContentsRequest {
   export const type = new RequestType<CleanWorkflowContentsParams, CleanWorkflowContentsResult, void>(
     LSRequestIdentifiers.CLEAN_WORKFLOW_CONTENTS

server/src/models/workflowDocuments.ts

@@ -16,17 +16,17 @@ export class WorkflowDocuments {
   }
 
   public addOrReplaceWorkflowDocument(document: WorkflowDocument) {
-    console.log("registered workflow file: ", document.documentUri);
     this._documentsCache.set(document.documentUri, document);
+    //console.debug("workflow files registered: ", this._documentsCache.size);
   }
 
   public removeWorkflowDocument(documentUri: string) {
-    console.log("unregistered workflow file: ", documentUri);
     this._documentsCache.delete(documentUri);
+    //console.debug("workflow files registered: ", this._documentsCache.size);
   }
 
   public dispose() {
     this._documentsCache.clear();
-    console.log("workflow document cache cleared");
+    //console.debug("workflow document cache cleared");
   }
 }