Add command to upgrade tests to comply with profile 24.2 validation

.vscode/launch.json

@@ -23,7 +23,7 @@
         },
         {
             "name": "Launch Server",
-            "type": "python",
+            "type": "debugpy",
             "console": "internalConsole",
             "request": "launch",
             "module": "galaxyls",

client/package.json

@@ -94,6 +94,13 @@
         "enablement": "galaxytools:isActive",
         "icon": "$(test-view-icon)"
       },
+      {
+        "command": "galaxytools.update.tests",
+        "title": "Update existing tests cases to comply with 24.2 profile validation",
+        "category": "Galaxy Tools",
+        "enablement": "galaxytools:isActive",
+        "icon": "$(test-view-icon)"
+      },
       {
         "command": "galaxytools.generate.command",
         "title": "Generate boilerplate command section for current tool",
@@ -156,6 +163,11 @@
         "key": "ctrl+alt+t",
         "mac": "cmd+alt+t"
       },
+      {
+        "command": "galaxytools.update.tests",
+        "key": "ctrl+alt+u",
+        "mac": "cmd+alt+u"
+      },
       {
         "command": "galaxytools.generate.command",
         "key": "ctrl+alt+c",

client/src/commands.ts

@@ -16,14 +16,15 @@ import {
 import { LanguageClient } from "vscode-languageclient/node";
 import { Constants } from "./constants";
 import { ICommand } from "./interfaces";
-import { GalaxyToolsExpadedDocumentContentProvider } from "./providers/contentProvider";
+import { GalaxyToolsExpandedDocumentContentProvider } from "./providers/contentProvider";
 import { AutoCloseTagResult, activateTagClosing } from "./tagClosing";
 import { changeUriScheme, cloneRange, getCommands } from "./utils";
 import { DirectoryTreeItem } from "./views/common";
 
 export namespace Commands {
     export const AUTO_CLOSE_TAGS: ICommand = getCommands("completion.autoCloseTags");
-    export const GENERATE_TEST: ICommand = getCommands("generate.tests");
+    export const GENERATE_TESTS: ICommand = getCommands("generate.tests");
+    export const UPDATE_TESTS: ICommand = getCommands("update.tests");
     export const GENERATE_COMMAND: ICommand = getCommands("generate.command");
     export const SORT_SINGLE_PARAM_ATTRS: ICommand = getCommands("sort.singleParamAttributes");
     export const SORT_DOCUMENT_PARAMS_ATTRS: ICommand = getCommands("sort.documentParamsAttributes");
@@ -43,6 +44,10 @@ interface GeneratedSnippetResult {
     replace_range: Range | null;
     error_message: string;
 }
+interface WorkspaceEditResult {
+    edits: ReplaceTextRangeResult[];
+    error_message: string;
+}
 
 interface ReplaceTextRangeResult {
     text: string;
@@ -63,6 +68,8 @@ export function setupCommands(client: LanguageClient, context: ExtensionContext)
 
     setupGenerateTestCases(client, context);
 
+    setupUpdateTestCases(client, context);
+
     setupGenerateCommandSection(client, context);
 
     setupSortSingleParamAttributes(client, context);
@@ -124,9 +131,16 @@ function setupGenerateCommandSection(client: LanguageClient, context: ExtensionC
 
 function setupGenerateTestCases(client: LanguageClient, context: ExtensionContext) {
     const generateTest = async () => {
-        requestInsertSnippet(client, Commands.GENERATE_TEST.external);
+        requestInsertSnippet(client, Commands.GENERATE_TESTS.external);
+    };
+    context.subscriptions.push(commands.registerCommand(Commands.GENERATE_TESTS.internal, generateTest));
+}
+
+function setupUpdateTestCases(client: LanguageClient, context: ExtensionContext) {
+    const updateTests = async () => {
+        requestWorkspaceEdits(client, Commands.UPDATE_TESTS.external);
     };
-    context.subscriptions.push(commands.registerCommand(Commands.GENERATE_TEST.internal, generateTest));
+    context.subscriptions.push(commands.registerCommand(Commands.UPDATE_TESTS.internal, updateTests));
 }
 
 function setupInsertParamReference(client: LanguageClient, context: ExtensionContext) {
@@ -229,6 +243,38 @@ async function requestInsertSnippet(client: LanguageClient, command: string) {
     }
 }
 
+async function requestWorkspaceEdits(client: LanguageClient, command: string) {
+    const activeEditor = window.activeTextEditor;
+    if (!activeEditor) return;
+    const isSaved = await ensureDocumentIsSaved(activeEditor);
+    if (!isSaved) return;
+    const document = activeEditor.document;
+    const param = client.code2ProtocolConverter.asTextDocumentIdentifier(document);
+    const response = (await commands.executeCommand(command, param)) as WorkspaceEditResult;
+
+    if (!response || response.error_message) {
+        if (response.error_message) {
+            window.showErrorMessage(response.error_message);
+        }
+        return;
+    }
+    try {
+        await activeEditor.edit((builder) => {
+            for (let index = 0; index < response.edits.length; index++) {
+                const element = response.edits[index];
+                const range = cloneRange(element.replace_range);
+                builder.replace(range, element.text);
+            }
+        });
+        // Format the document after the edits
+        await commands.executeCommand("editor.action.formatDocument");
+
+    }
+    catch (err: any) {
+        window.showErrorMessage(err);
+    }
+}
+
 async function pickParamReferenceToInsert(client: LanguageClient, command: string, pickerTitle: string = "Select a parameter reference to insert") {
     const activeEditor = window.activeTextEditor;
     if (!activeEditor) return;
@@ -311,7 +357,7 @@ async function previewExpandedDocument() {
         return;
     }
     const expandedDocumentUri = convertToExpandedDocumentUri(document.uri);
-    GalaxyToolsExpadedDocumentContentProvider.getInstance().update(expandedDocumentUri);
+    GalaxyToolsExpandedDocumentContentProvider.getInstance().update(expandedDocumentUri);
     const doc = await workspace.openTextDocument(expandedDocumentUri);
     await window.showTextDocument(doc, { preview: false, viewColumn: ViewColumn.Beside });
 }

client/src/providers/contentProvider.ts

@@ -3,16 +3,16 @@ import { Commands, GeneratedExpandedDocument } from "../commands";
 import { Constants } from "../constants";
 import { changeUriScheme } from "../utils";
 
-export class GalaxyToolsExpadedDocumentContentProvider implements TextDocumentContentProvider {
-    private static instance: GalaxyToolsExpadedDocumentContentProvider;
+export class GalaxyToolsExpandedDocumentContentProvider implements TextDocumentContentProvider {
+    private static instance: GalaxyToolsExpandedDocumentContentProvider;
 
     private onDidChangeEmitter = new EventEmitter<Uri>();
 
     private constructor() {}
 
-    public static getInstance(): GalaxyToolsExpadedDocumentContentProvider {
+    public static getInstance(): GalaxyToolsExpandedDocumentContentProvider {
         if (!this.instance) {
-            this.instance = new GalaxyToolsExpadedDocumentContentProvider();
+            this.instance = new GalaxyToolsExpandedDocumentContentProvider();
         }
         return this.instance;
     }

client/src/providers/setup.ts

@@ -2,7 +2,7 @@ import { ExtensionContext, languages, workspace } from "vscode";
 import { LanguageClient } from "vscode-languageclient/node";
 import { Constants } from "../constants";
 import { GalaxyToolsCodeActionProvider } from "./codeActions";
-import { GalaxyToolsExpadedDocumentContentProvider } from "./contentProvider";
+import { GalaxyToolsExpandedDocumentContentProvider } from "./contentProvider";
 
 export function setupProviders(client: LanguageClient, context: ExtensionContext) {
     const codeActionProvider = new GalaxyToolsCodeActionProvider();
@@ -12,7 +12,7 @@ export function setupProviders(client: LanguageClient, context: ExtensionContext
         })
     );
 
-    const expandedDocumentProvider = GalaxyToolsExpadedDocumentContentProvider.getInstance();
+    const expandedDocumentProvider = GalaxyToolsExpandedDocumentContentProvider.getInstance();
     context.subscriptions.push(
         workspace.registerTextDocumentContentProvider(Constants.EXPAND_DOCUMENT_SCHEMA, expandedDocumentProvider)
     );

server/galaxyls/constants.py

@@ -9,6 +9,7 @@
 class Commands:
     AUTO_CLOSE_TAGS = "gls.completion.autoCloseTags"
     GENERATE_TESTS = "gls.generate.tests"
+    UPDATE_TESTS_PROFILE = "gls.update.tests"
     GENERATE_COMMAND = "gls.generate.command"
     SORT_SINGLE_PARAM_ATTRS = "gls.sort.singleParamAttributes"
     SORT_DOCUMENT_PARAMS_ATTRS = "gls.sort.documentParamsAttributes"

server/galaxyls/server.py

@@ -59,6 +59,7 @@
     ParamReferencesResult,
     ReplaceTextRangeResult,
     TestSuiteInfoResult,
+    WorkspaceEditResult,
 )
 from galaxyls.utils import convert_to
 from galaxyls.version import GLS_VERSION
@@ -230,6 +231,18 @@ async def cmd_generate_test(
     return None
 
 
+@language_server.command(Commands.UPDATE_TESTS_PROFILE)
+async def cmd_update_test_profile(
+    server: GalaxyToolsLanguageServer, parameters: CommandParameters
+) -> Optional[WorkspaceEditResult]:
+    """Updates the test cases to be compatible with the 24.2 profile validation."""
+    params = convert_to(parameters[0], TextDocumentIdentifier)
+    document = _get_valid_document(server, params.uri)
+    if document:
+        return server.service.update_tests_profile(document)
+    return None
+
+
 @language_server.command(Commands.GENERATE_COMMAND)
 async def cmd_generate_command(
     server: GalaxyToolsLanguageServer, parameters: CommandParameters

server/galaxyls/services/language.py

@@ -34,7 +34,7 @@
 )
 from galaxyls.services.tools.document import GalaxyToolXmlDocument
 from galaxyls.services.tools.generators.command import GalaxyToolCommandSnippetGenerator
-from galaxyls.services.tools.generators.tests import GalaxyToolTestSnippetGenerator
+from galaxyls.services.tools.generators.tests import GalaxyToolTestSnippetGenerator, GalaxyToolTestUpdater
 from galaxyls.services.tools.iuc import IUCToolParamAttributeSorter
 from galaxyls.services.tools.linting import GalaxyToolLinter
 from galaxyls.services.tools.macros import MacroDefinitionsProvider
@@ -48,6 +48,7 @@
 from ..types import (
     GeneratedSnippetResult,
     ReplaceTextRangeResult,
+    WorkspaceEditResult,
 )
 from .completion import (
     AutoCloseTagResult,
@@ -141,6 +142,13 @@ def generate_tests(self, document: Document) -> Optional[GeneratedSnippetResult]
         generator = GalaxyToolTestSnippetGenerator(tool)
         return generator.generate_snippet()
 
+    def update_tests_profile(self, document: Document) -> Optional[WorkspaceEditResult]:
+        """Generates a workspace edit to update the test cases if they are not
+        compatible with the 24.2 profile validation."""
+        tool = GalaxyToolXmlDocument(document)
+        generator = GalaxyToolTestUpdater(tool)
+        return generator.generate_workspace_edit()
+
     def generate_command(self, document: Document) -> Optional[GeneratedSnippetResult]:
         """Generates a boilerplate Cheetah code snippet based on the current inputs and outputs
         of this tool wrapper."""

server/galaxyls/services/tools/document.py

@@ -155,9 +155,9 @@ def get_inputs(self) -> List[XmlElement]:
         Returns:
             List[XmlElement]: The outputs defined in the document.
         """
-        outputs = self.find_element(INPUTS)
-        if outputs:
-            return outputs.elements
+        inputs = self.find_element(INPUTS)
+        if inputs:
+            return inputs.elements
         return []
 
     def get_outputs(self) -> List[XmlElement]:

server/galaxyls/services/tools/generators/__init__.py

@@ -0,0 +1,5 @@
+class DisplayableException(Exception):
+    """Exception class for displaying error messages in the UI."""
+
+    def __init__(self, message: str) -> None:
+        super().__init__(message)

server/galaxyls/services/tools/generators/snippets.py

@@ -20,7 +20,34 @@
     UNDERSCORE,
 )
 from galaxyls.services.tools.document import GalaxyToolXmlDocument
-from galaxyls.types import GeneratedSnippetResult
+from galaxyls.services.tools.generators import DisplayableException
+from galaxyls.types import GeneratedSnippetResult, ReplaceTextRangeResult, WorkspaceEditResult
+
+
+class WorkspaceEditsGenerator(ABC):
+    """This class is used to generate workspace edits using the information of the tool document."""
+
+    def __init__(self, tool_document: GalaxyToolXmlDocument, tabSize: int = 4) -> None:
+        self.tool_document = tool_document
+        self.expanded_document = tool_document.get_expanded_tool_document()
+        self.tabstop_count: int = 0
+        self.indent_spaces: str = " " * tabSize
+        super().__init__()
+
+    def generate_workspace_edit(self) -> WorkspaceEditResult:
+        """Generates a workspace edit using this generator."""
+        try:
+            edits = self._build_workspace_edits()
+            return WorkspaceEditResult(edits)
+        except DisplayableException as e:
+            return WorkspaceEditResult.as_error(str(e))
+
+    @abstractmethod
+    def _build_workspace_edits(self) -> List[ReplaceTextRangeResult]:
+        """This abstract function should return a list of ReplaceTextRangeResult
+        with the generated workspace edits.
+        """
+        pass
 
 
 class SnippetGenerator(ABC):