refactor cli

Bump the storybook group in /extensions/ql-vscode with 12 updates

.github/codeql/queries/ProgressBar.qll

@@ -1,36 +1,16 @@
 import javascript
 
-abstract class ProgressBar extends CallExpr {
-  ProgressBar() { any() }
-
-  abstract Function getCallback();
-
-  abstract ObjectExpr getOptions();
+class WithProgressCall extends CallExpr {
+  WithProgressCall() { this.getCalleeName() = "withProgress" }
 
   predicate usesToken() { exists(this.getTokenParameter()) }
 
-  Parameter getTokenParameter() { result = this.getCallback().getParameter(1) }
+  Parameter getTokenParameter() { result = this.getArgument(0).(Function).getParameter(1) }
 
-  Property getCancellableProperty() { result = this.getOptions().getPropertyByName("cancellable") }
+  Property getCancellableProperty() { result = this.getArgument(1).(ObjectExpr).getPropertyByName("cancellable") }
 
   predicate isCancellable() {
     this.getCancellableProperty().getInit().(BooleanLiteral).getBoolValue() =
       true
   }
 }
-
-class WithProgressCall extends ProgressBar {
-  WithProgressCall() { this.getCalleeName() = "withProgress" }
-
-  override Function getCallback() { result = this.getArgument(0) }
-
-  override ObjectExpr getOptions() { result = this.getArgument(1) }
-}
-
-class WithInheritedProgressCall extends ProgressBar {
-  WithInheritedProgressCall() { this.getCalleeName() = "withInheritedProgress" }
-
-  override Function getCallback() { result = this.getArgument(1) }
-
-  override ObjectExpr getOptions() { result = this.getArgument(2) }
-}

.github/codeql/queries/progress-not-cancellable.ql

@@ -12,7 +12,7 @@
 import javascript
 import ProgressBar
 
-from ProgressBar t
+from WithProgressCall t
 where not t.isCancellable() and t.usesToken()
 select t,
   "The $@ should not be used when the progress bar is not cancellable. Either stop using the $@ or mark the progress bar as cancellable.",

.github/codeql/queries/token-not-used.ql

@@ -13,6 +13,6 @@
 import javascript
 import ProgressBar
 
-from ProgressBar t
+from WithProgressCall t
 where t.isCancellable() and not t.usesToken()
 select t, "This progress bar is $@ but the token is not used. Either use the token or mark the progress bar as not cancellable.", t.getCancellableProperty(), "cancellable"

.github/dependabot.yml

@@ -17,6 +17,9 @@ updates:
       octokit:
         patterns:
           - "@octokit/*"
+        update-types:
+          - "minor"
+          - "patch"
       storybook:
         patterns:
           - "@storybook/*"
@@ -34,3 +37,10 @@ updates:
       day: "thursday" # Thursday is arbitrary
     labels:
       - "Update dependencies"
+  - package-ecosystem: docker
+    directory: "extensions/ql-vscode/test/e2e"
+    schedule:
+      interval: "weekly"
+      day: "thursday" # Thursday is arbitrary
+    labels:
+      - "Update dependencies"

.github/pull_request_template.md

@@ -5,8 +5,4 @@
 
 Replace this with a description of the changes your pull request makes.
 
-## Checklist
-
-- [ ] [CHANGELOG.md](https://github.com/github/vscode-codeql/blob/main/extensions/ql-vscode/CHANGELOG.md) has been updated to incorporate all user visible changes made by this pull request.
-- [ ] Issues have been created for any UI or other user-facing changes made by this pull request.
-- [ ] _[Maintainers only]_ If this pull request makes user-facing changes that require documentation changes, open a corresponding docs pull request in the [github/codeql](https://github.com/github/codeql/tree/main/docs/codeql/codeql-for-visual-studio-code) repo and add the `ready-for-doc-review` label there.
+Remember to update the [changelog](https://github.com/github/vscode-codeql/blob/main/extensions/ql-vscode/CHANGELOG.md) if there have been user-facing changes!

.github/workflows/main.yml

@@ -144,6 +144,19 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest]
     steps:
+      # Enable 8.3 filename creation. This is not required to run the extension but it is required for the unit tests to pass.
+      # This feature is currently enabled by default in Windows 11 for the C: drive and therefore we must maintain support for it.
+      # This setting needs to be enabled before files are created, i.e. before we checkout the repository.
+      - name: Enable 8.3 filenames
+        shell: pwsh
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: |
+          $shortNameEnableProcess = Start-Process -FilePath fsutil.exe -ArgumentList ('8dot3name', 'set', '0') -Wait -PassThru
+          $shortNameEnableExitCode = $shortNameEnableProcess.ExitCode
+          if ($shortNameEnableExitCode -ne 0) {
+              exit $shortNameEnableExitCode
+          }
+
       - name: Checkout
         uses: actions/checkout@v4
         with:

.github/workflows/release.yml

@@ -134,7 +134,7 @@ jobs:
 
       - name: Publish to Registry
         run: |
-          npx vsce publish -p $VSCE_TOKEN --packagePath *.vsix
+          npx @vscode/vsce publish -p $VSCE_TOKEN --packagePath *.vsix
 
   open-vsx-publish:
     name: Publish to Open VSX Registry

.vscode/settings.json

@@ -111,4 +111,10 @@
     "editor.defaultFormatter": "esbenp.prettier-vscode",
     "editor.formatOnSave": true,
   },
+  "github.copilot.advanced": {
+    
+
+  },
+  "codeQL.variantAnalysis.enableGhecDr": true,
+  "github-enterprise.uri": "http://server:8080/"
 }

CONTRIBUTING.md

@@ -28,6 +28,7 @@ Here are a few things you can do that will increase the likelihood of your pull
   - [Integration tests that do require the VS Code API are located here](extensions/ql-vscode/src/vscode-tests).
 - Keep your change as focused as possible. If there are multiple changes you would like to make that are not dependent upon each other, consider submitting them as separate pull requests.
 - Write a [good commit message](https://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html).
+- Update the [changelog](https://github.com/github/vscode-codeql/blob/main/extensions/ql-vscode/CHANGELOG.md) if you are making user-facing changes.
 
 ## Setting up a local build
 

docs/releasing.md

@@ -1,5 +1,6 @@
 # Releasing (write access required)
 
+1. Make sure the needed authentication keys are valid. Most likely the Azure DevOps PAT needs to be regenerated. See below.
 1. Determine the new version number. We default to increasing the patch version number, but make our own judgement about whether a change is big enough to warrant a minor version bump. Common reasons for a minor bump could include:
     - Making substantial new features available to all users. This can include lifting a feature flag.
     - Breakage in compatibility with recent versions of the CLI.
@@ -60,7 +61,7 @@
 
 ## Secrets and authentication for publishing
 
-Repository administrators, will need to manage the authentication keys for publishing to the VS Code marketplace and Open VSX. Each requires an authentication token. The VS Code marketplace token expires yearly.
+Repository administrators, will need to manage the authentication keys for publishing to the VS Code marketplace and Open VSX. Each requires an authentication token.
 
 To regenerate the Open VSX token:
 
@@ -69,4 +70,4 @@ To regenerate the Open VSX token:
 1. Go to the [Access Tokens](https://open-vsx.org/user-settings/tokens) page and generate a new token.
 1. Update the secret in the `publish-open-vsx` environment in the project settings.
 
-To regenerate the VSCode Marketplace token, please see our internal documentation. Note that Azure DevOps PATs expire every 90 days and must be regenerated.
+To regenerate the VSCode Marketplace token, please see our internal documentation. Note that Azure DevOps PATs expire every 7 days and must be regenerated.

docs/test-plan.md

@@ -179,7 +179,7 @@ Run one of the above MRVAs, but cancel it from within VS Code:
    import semmle.python.frameworks.data.internal.ApiGraphModelsExtensions
 
    from string path, string kind
-   where sinkModel("vscode-codeql", path, kind)
+   where sinkModel("vscode-codeql", path, kind, _)
    select path, kind
    ```
 
@@ -210,17 +210,7 @@ Run one of the above MRVAs, but cancel it from within VS Code:
 4. Open the ".model.yml" file corresponding to the library that was changed.
    - Check that the file contains entries for the methods that were modeled.
 
-#### Test Case 3: Model with AI
-
-Note that this test requires the feature flag: `codeQL.model.llmGeneration`
-
-A package that the AI normally gives models for is `javax.servlet-api` from the `jhy/jsoup` repository.
-
-1. Click "Model with AI".
-   - Check that rows change to "Thinking".
-   - Check that results come back and rows get filled out.
-
-#### Test Case 4: Model as dependency
+#### Test Case 3: Model as dependency
 
 Note that this test requires the feature flag: `codeQL.model.flowGeneration`
 

extensions/ql-vscode/.babelrc.json

@@ -1,16 +0,0 @@
-{
-  "sourceType": "unambiguous",
-  "presets": [
-    [
-      "@babel/preset-env",
-      {
-        "targets": {
-          "chrome": 100
-        }
-      }
-    ],
-    "@babel/preset-typescript",
-    "@babel/preset-react"
-  ],
-  "plugins": []
-}

extensions/ql-vscode/.eslintrc.js

@@ -48,7 +48,7 @@ const baseConfig = {
     "@typescript-eslint/no-throw-literal": "error",
     "@typescript-eslint/consistent-type-imports": "error",
     "import/consistent-type-specifier-style": ["error", "prefer-top-level"],
-    curly: ["error", "all"],
+    // curly: ["error", "all"],
     "escompat/no-regexp-lookbehind": "off",
     "etc/no-implicit-any-catch": "error",
     "filenames/match-regex": "off",

extensions/ql-vscode/.nvmrc

@@ -1 +1 @@
-v18.17.1
+v20.9.0

extensions/ql-vscode/.storybook/main.ts

@@ -1,7 +1,7 @@
-import type { StorybookConfig } from "@storybook/react-webpack5";
+import type { StorybookConfig } from "@storybook/react-vite";
 
 const config: StorybookConfig = {
-  stories: ["../src/**/*.stories.mdx", "../src/**/*.stories.@(js|jsx|ts|tsx)"],
+  stories: ["../src/**/*.mdx", "../src/**/*.stories.@(js|jsx|ts|tsx)"],
   addons: [
     "@storybook/addon-links",
     "@storybook/addon-essentials",
@@ -10,7 +10,7 @@ const config: StorybookConfig = {
     "./vscode-theme-addon/preset.ts",
   ],
   framework: {
-    name: "@storybook/react-webpack5",
+    name: "@storybook/react-vite",
     options: {},
   },
   docs: {

extensions/ql-vscode/.storybook/vscode-theme-addon/ThemeSelector.tsx

@@ -5,10 +5,10 @@ import { useCallback } from "react";
 import { useGlobals } from "@storybook/manager-api";
 import {
   IconButton,
-  Icons,
   TooltipLinkList,
   WithTooltip,
 } from "@storybook/components";
+import { DashboardIcon } from "@storybook/icons";
 
 import { themeNames, VSCodeTheme } from "./theme";
 
@@ -53,7 +53,7 @@ export const ThemeSelector: FunctionComponent = () => {
         title="Change the theme of the preview"
         active={vscodeTheme !== VSCodeTheme.Dark}
       >
-        <Icons icon="dashboard" />
+        <DashboardIcon />
       </IconButton>
     </WithTooltip>
   );

extensions/ql-vscode/.storybook/vscode-theme-addon/withTheme.ts

@@ -1,3 +1,5 @@
+/// <reference types="vite/client" />
+
 import { useEffect } from "react";
 import type {
   PartialStoryFn as StoryFunction,
@@ -6,31 +8,20 @@ import type {
 
 import { VSCodeTheme } from "./theme";
 
+import darkThemeStyle from "../../src/stories/vscode-theme-dark.css?url";
+import lightThemeStyle from "../../src/stories/vscode-theme-light.css?url";
+import lightHighContrastThemeStyle from "../../src/stories/vscode-theme-light-high-contrast.css?url";
+import darkHighContrastThemeStyle from "../../src/stories/vscode-theme-dark-high-contrast.css?url";
+import githubLightDefaultThemeStyle from "../../src/stories/vscode-theme-github-light-default.css?url";
+import githubDarkDefaultThemeStyle from "../../src/stories/vscode-theme-github-dark-default.css?url";
+
 const themeFiles: { [key in VSCodeTheme]: string } = {
-  [VSCodeTheme.Dark]:
-    // eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs,import/no-webpack-loader-syntax
-    require("!file-loader?modules!../../src/stories/vscode-theme-dark.css")
-      .default,
-  [VSCodeTheme.Light]:
-    // eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs,import/no-webpack-loader-syntax
-    require("!file-loader?modules!../../src/stories/vscode-theme-light.css")
-      .default,
-  [VSCodeTheme.LightHighContrast]:
-    // eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs,import/no-webpack-loader-syntax
-    require("!file-loader?modules!../../src/stories/vscode-theme-light-high-contrast.css")
-      .default,
-  [VSCodeTheme.DarkHighContrast]:
-    // eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs,import/no-webpack-loader-syntax
-    require("!file-loader?modules!../../src/stories/vscode-theme-dark-high-contrast.css")
-      .default,
-  [VSCodeTheme.GitHubLightDefault]:
-    // eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs,import/no-webpack-loader-syntax
-    require("!file-loader?modules!../../src/stories/vscode-theme-github-light-default.css")
-      .default,
-  [VSCodeTheme.GitHubDarkDefault]:
-    // eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs,import/no-webpack-loader-syntax
-    require("!file-loader?modules!../../src/stories/vscode-theme-github-dark-default.css")
-      .default,
+  [VSCodeTheme.Dark]: darkThemeStyle,
+  [VSCodeTheme.Light]: lightThemeStyle,
+  [VSCodeTheme.LightHighContrast]: lightHighContrastThemeStyle,
+  [VSCodeTheme.DarkHighContrast]: darkHighContrastThemeStyle,
+  [VSCodeTheme.GitHubLightDefault]: githubLightDefaultThemeStyle,
+  [VSCodeTheme.GitHubDarkDefault]: githubDarkDefaultThemeStyle,
 };
 
 export const withTheme = (StoryFn: StoryFunction, context: StoryContext) => {

extensions/ql-vscode/CHANGELOG.md

@@ -1,5 +1,23 @@
 # CodeQL for Visual Studio Code: Changelog
 
+## [UNRELEASED]
+
+## 1.13.1 - 29 May 2024
+
+- Fix a bug when re-importing test databases that erroneously showed old source code. [#3616](https://github.com/github/vscode-codeql/pull/3616)
+- Update the progress window with details on potentially long-running post-processing steps after running a query. [#3622](https://github.com/github/vscode-codeql/pull/3622)
+
+## 1.13.0 - 1 May 2024
+
+- Add Ruby support to the CodeQL Model Editor. [#3584](https://github.com/github/vscode-codeql/pull/3584)
+- Remove support for CodeQL CLI versions older than 2.14.6. [#3562](https://github.com/github/vscode-codeql/pull/3562)
+
+## 1.12.5 - 9 April 2024
+
+- Add new supported source and sink kinds in the CodeQL Model Editor [#3511](https://github.com/github/vscode-codeql/pull/3511)
+- Fix a bug where the test explorer wouldn't display certain tests. [#3527](https://github.com/github/vscode-codeql/pull/3527)
+- The "model dependency" operation in the model editor can now be cancelled. [#3517](https://github.com/github/vscode-codeql/pull/3517)
+
 ## 1.12.4 - 20 March 2024
 
 - Don't show notification after local query cancellation. [#3489](https://github.com/github/vscode-codeql/pull/3489)
@@ -486,7 +504,7 @@ No user facing changes.
 - Allow setting `codeQL.runningQueries.numberOfThreads` and `codeQL.runningTests.numberOfThreads` to 0, (which is interpreted as 'use one thread per core on the machine').
 - Clear the problems view of all CodeQL query results when a database is removed.
 - Add a `View DIL` command on query history items. This opens a text editor containing the Datalog Intermediary Language representation of the compiled query.
-- Remove feature flag for the AST Viewer. For more information on how to use the AST Viewer, [see the documentation](https://help.semmle.com/codeql/codeql-for-vscode/procedures/exploring-the-structure-of-your-source-code.html).
+- Remove feature flag for the AST Viewer. For more information on how to use the AST Viewer, [see the documentation](https://codeql.github.com/docs/codeql-for-visual-studio-code/exploring-the-structure-of-your-source-code/).
 - The `codeQL.runningTests.numberOfThreads` setting is now used correctly when running tests.
 - Alter structure of the _Test Explorer_ tree. It now follows the structure of the filesystem instead of the qlpacks.
 - Ensure output of CodeQL test runs includes compilation error messages and test failure messages.

extensions/ql-vscode/README.md

@@ -9,10 +9,12 @@ This project is an extension for Visual Studio Code that adds rich language supp
 
 To see what has changed in the last few versions of the extension, see the [Changelog](https://github.com/github/vscode-codeql/blob/main/extensions/ql-vscode/CHANGELOG.md).
 
+You can also read full documentation for the extension on the [GitHub documentation website](https://docs.github.com/code-security/codeql-for-vs-code/using-the-advanced-functionality-of-the-codeql-for-vs-code-extension).
+
 ## Quick start overview
 
 The information in this `README` file describes the quickest way to start using CodeQL.
-For information about other configurations, see the separate [CodeQL help](https://codeql.github.com/docs/codeql-for-visual-studio-code/).
+For information about other configurations, see "[Using the advanced functionality of the CodeQL for VS Code extension](https://docs.github.com/code-security/codeql-for-vs-code/using-the-advanced-functionality-of-the-codeql-for-vs-code-extension)" in the GitHub documentation.
 
 ### Quick start: Installing and configuring the extension
 
@@ -42,7 +44,7 @@ The CodeQL extension requires a minimum of Visual Studio Code 1.39. Older versio
 
 The extension uses the [CodeQL CLI](https://codeql.github.com/docs/codeql-cli/) to compile and run queries. The extension automatically manages access to the CLI for you by default (recommended). To check for updates to the CodeQL CLI, you can use the **CodeQL: Check for CLI Updates** command.
 
-If you want to override the default behavior and use a CodeQL CLI that's already on your machine, see [Configuring access to the CodeQL CLI](https://codeql.github.com/docs/codeql-for-visual-studio-code/setting-up-codeql-in-visual-studio-code/#configuring-access-to-the-codeql-cli).
+If you want to override the default behavior and use a CodeQL CLI that's already on your machine, see "[Configuring access to the CodeQL CLI](https://docs.github.com/code-security/codeql-for-vs-code/using-the-advanced-functionality-of-the-codeql-for-vs-code-extension/configuring-access-to-the-codeql-cli)" in the GitHub documentation.
 
 If you have any difficulty with CodeQL CLI access, see the **CodeQL Extension Log** in the **Output** view for any error messages.
 
@@ -52,7 +54,7 @@ When you're working with CodeQL, you need access to the standard CodeQL librarie
 Initially, we recommend that you clone and use the ready-to-use [starter workspace](https://github.com/github/vscode-codeql-starter/).
 This includes libraries and queries for the main supported languages, with folders set up ready for your custom queries. After cloning the workspace (use `git clone --recursive`), you can use it in the same way as any other VS Code workspace—with the added advantage that you can easily update the CodeQL libraries.
 
-For information about configuring an existing workspace for CodeQL, [see the documentation](https://codeql.github.com/docs/codeql-for-visual-studio-code/setting-up-codeql-in-visual-studio-code/#updating-an-existing-workspace-for-codeql).
+For information about configuring an existing workspace for CodeQL, see "[Setting up a CodeQL workspace](https://docs.github.com/code-security/codeql-for-vs-code/using-the-advanced-functionality-of-the-codeql-for-vs-code-extension/setting-up-a-codeql-workspace#option-2-updating-an-existing-workspace-for-codeql-advanced)" in the GitHub documentation.
 
 ## Upgrading CodeQL standard libraries
 
@@ -85,7 +87,7 @@ While you can use the [CodeQL CLI to create your own databases](https://codeql.g
 1. Select the language for the database you want to download (only required if the project has databases for multiple languages).
 1. Once the CodeQL database has been imported, it is displayed in the Databases view.
 
-For more information, see [Choosing a database](https://codeql.github.com/docs/codeql-for-visual-studio-code/analyzing-your-projects/#choosing-a-database) on codeql.github.com.
+For more information, see "[Managing CodeQL databases](https://docs.github.com/code-security/codeql-for-vs-code/getting-started-with-codeql-for-vs-code/managing-codeql-databases#choosing-a-database-to-analyze)" in the GitHub documentation.
 
 ### Running a query
 
@@ -106,12 +108,12 @@ If you wish to navigate the query results from your keyboard, you can bind short
 
 ## What next?
 
-For more information about the CodeQL extension, [see the documentation](https://codeql.github.com/docs/codeql-for-visual-studio-code/). Otherwise, you could:
+We recommend reading the [full documentation for the extension](https://docs.github.com/code-security/codeql-for-vs-code/) on the GitHub documentation website. You may also find the following resources useful:
 
 - [Create a database for a different codebase](https://codeql.github.com/docs/codeql-cli/creating-codeql-databases/).
-- [Try out variant analysis](https://help.semmle.com/QL/learn-ql/ql-training.html).
+- [Try out variant analysis](https://docs.github.com/code-security/codeql-for-vs-code/getting-started-with-codeql-for-vs-code/running-codeql-queries-at-scale-with-multi-repository-variant-analysis).
 - [Learn more about CodeQL](https://codeql.github.com/docs/).
-- [Read how security researchers use CodeQL to find CVEs](https://securitylab.github.com/research).
+- [Read how security researchers use CodeQL to find CVEs](https://github.blog/tag/github-security-lab/).
 
 ## License
 
@@ -119,4 +121,4 @@ The CodeQL extension for Visual Studio Code is [licensed](LICENSE.md) under the
 
 ## Data and Telemetry
 
-If you specifically opt-in to permit GitHub to do so, GitHub will collect usage data and metrics for the purposes of helping the core developers to improve the CodeQL extension for VS Code. This data will not be shared with any parties outside of GitHub. IP addresses and installation IDs will be retained for a maximum of 30 days. Anonymous data will be retained for a maximum of 180 days. For more information about telemetry, [see the documentation](https://codeql.github.com/docs/codeql-for-visual-studio-code/about-telemetry-in-codeql-for-visual-studio-code).
+If you specifically opt-in to permit GitHub to do so, GitHub will collect usage data and metrics for the purposes of helping the core developers to improve the CodeQL extension for VS Code. This data will not be shared with any parties outside of GitHub. IP addresses and installation IDs will be retained for a maximum of 30 days. Anonymous data will be retained for a maximum of 180 days. For more information, see "[Telemetry in CodeQL for Visual Studio Code](https://docs.github.com/code-security/codeql-for-vs-code/using-the-advanced-functionality-of-the-codeql-for-vs-code-extension/telemetry-in-codeql-for-visual-studio-code)" in the GitHub documentation.

extensions/ql-vscode/package.json

@@ -4,7 +4,7 @@
   "description": "CodeQL for Visual Studio Code",
   "author": "GitHub",
   "private": true,
-  "version": "1.12.4",
+  "version": "1.13.2",
   "publisher": "GitHub",
   "license": "MIT",
   "icon": "media/VS-marketplace-CodeQL-icon.png",
@@ -14,7 +14,7 @@
   },
   "engines": {
     "vscode": "^1.82.0",
-    "node": "^18.17.1",
+    "node": "^20.9.0",
     "npm": ">=7.20.6"
   },
   "categories": [
@@ -339,13 +339,6 @@
         "title": "Variant analysis",
         "order": 5,
         "properties": {
-          "codeQL.variantAnalysis.controllerRepo": {
-            "type": "string",
-            "default": "",
-            "pattern": "^$|^(?:[a-zA-Z0-9]+-)*[a-zA-Z0-9]+/[a-zA-Z0-9-_]+$",
-            "patternErrorMessage": "Please enter a valid GitHub repository",
-            "markdownDescription": "[For internal use only] The name of the GitHub repository in which the GitHub Actions workflow is run when using the \"Run Variant Analysis\" command. The repository should be of the form `<owner>/<repo>`)."
-          },
           "codeQL.variantAnalysis.defaultResultsFilter": {
             "type": "string",
             "default": "all",
@@ -463,8 +456,25 @@
       },
       {
         "type": "object",
-        "title": "Log insights",
+        "title": "Model Editor",
         "order": 9,
+        "properties": {
+          "codeQL.model.packLocation": {
+            "type": "string",
+            "default": ".github/codeql/extensions/${name}-${language}",
+            "markdownDescription": "Location for newly created CodeQL model packs. The location can be either absolute or relative. If relative, it is relative to the workspace root.\n\nThe following variables are supported:\n* **${database}** - the name of the database\n* **${language}** - the name of the language\n* **${name}** - the name of the GitHub repository, or the name of the database if the database was not downloaded from GitHub\n* **${owner}** - the owner of the GitHub repository, or an empty string if the database was not downloaded from GitHub"
+          },
+          "codeQL.model.packName": {
+            "type": "string",
+            "default": "${owner}/${name}-${language}",
+            "markdownDescription": "Name of newly created CodeQL model packs. If the result is not a valid pack name, it will be converted to a valid pack name.\n\nThe following variables are supported:\n* **${database}** - the name of the database\n* **${language}** - the name of the language\n* **${name}** - the name of the GitHub repository, or the name of the database if the database was not downloaded from GitHub\n* **${owner}** - the owner of the GitHub repository, or an empty string if the database was not downloaded from GitHub"
+          }
+        }
+      },
+      {
+        "type": "object",
+        "title": "Log insights",
+        "order": 10,
         "properties": {
           "codeQL.logInsights.joinOrderWarningThreshold": {
             "type": "number",
@@ -478,7 +488,7 @@
       {
         "type": "object",
         "title": "Telemetry",
-        "order": 10,
+        "order": 11,
         "properties": {
           "codeQL.telemetry.enableTelemetry": {
             "type": "boolean",
@@ -1914,11 +1924,6 @@
       {
         "view": "codeQLEvalLogViewer",
         "contents": "Run the 'Show Evaluator Log (UI)' command on a CodeQL query run in the Query History view."
-      },
-      {
-        "view": "codeQLVariantAnalysisRepositories",
-        "contents": "Set up a controller repository to start using variant analysis. [Learn more](https://codeql.github.com/docs/codeql-for-visual-studio-code/running-codeql-queries-at-scale-with-mrva#controller-repository) about controller repositories. \n[Set up controller repository](command:codeQLVariantAnalysisRepositories.setupControllerRepository)",
-        "when": "!config.codeQL.variantAnalysis.controllerRepo"
       }
     ]
   },
@@ -1938,44 +1943,45 @@
     "format": "prettier --write **/*.{ts,tsx} && eslint . --ext .ts,.tsx --fix",
     "lint": "eslint . --ext .js,.ts,.tsx --max-warnings=0",
     "lint:markdown": "markdownlint-cli2 \"../../**/*.{md,mdx}\" \"!**/node_modules/**\" \"!**/.vscode-test/**\" \"!**/build/cli/v*/**\"",
-    "find-deadcode": "ts-node scripts/find-deadcode.ts",
+    "find-deadcode": "vite-node scripts/find-deadcode.ts",
     "format-staged": "lint-staged",
     "storybook": "storybook dev -p 6006",
     "build-storybook": "storybook build",
-    "lint:scenarios": "ts-node scripts/lint-scenarios.ts",
+    "lint:scenarios": "vite-node scripts/lint-scenarios.ts",
     "generate": "npm-run-all -p generate:*",
-    "generate:schemas": "ts-node scripts/generate-schemas.ts",
-    "generate:chromium-version": "ts-node scripts/generate-chromium-version.ts",
+    "generate:schemas": "vite-node scripts/generate-schemas.ts",
+    "generate:chromium-version": "vite-node scripts/generate-chromium-version.ts",
     "check-types": "find . -type f -name \"tsconfig.json\" -not -path \"./node_modules/*\" | sed -r 's|/[^/]+$||' | sort | uniq | xargs -I {} sh -c \"echo Checking types in {} && cd {} && npx tsc --noEmit\"",
     "postinstall": "patch-package",
     "prepare": "cd ../.. && husky install"
   },
   "dependencies": {
-    "@floating-ui/react": "^0.26.9",
+    "@floating-ui/react": "^0.26.12",
     "@octokit/plugin-retry": "^6.0.1",
+    "@octokit/plugin-throttling": "^8.0.0",
     "@octokit/rest": "^20.0.2",
     "@vscode/codicons": "^0.0.35",
     "@vscode/debugadapter": "^1.59.0",
-    "@vscode/debugprotocol": "^1.59.0",
+    "@vscode/debugprotocol": "^1.65.0",
     "@vscode/webview-ui-toolkit": "^1.0.1",
     "ajv": "^8.11.0",
     "child-process-promise": "^2.2.1",
     "chokidar": "^3.6.0",
-    "d3": "^7.6.1",
+    "d3": "^7.9.0",
     "d3-graphviz": "^5.0.2",
     "fs-extra": "^11.1.1",
     "js-yaml": "^4.1.0",
-    "msw": "^2.0.13",
-    "nanoid": "^5.0.6",
+    "msw": "^2.2.13",
+    "nanoid": "^5.0.7",
     "node-fetch": "^2.6.7",
     "p-queue": "^8.0.1",
-    "react": "^18.2.0",
-    "react-dom": "^18.2.0",
-    "semver": "^7.6.0",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1",
+    "semver": "^7.6.2",
     "source-map": "^0.7.4",
     "source-map-support": "^0.5.21",
     "stream-json": "^1.7.3",
-    "styled-components": "^6.1.8",
+    "styled-components": "^6.1.9",
     "tmp": "^0.2.1",
     "tmp-promise": "^3.0.2",
     "tree-kill": "^1.2.2",
@@ -1986,29 +1992,30 @@
     "zip-a-folder": "^3.1.6"
   },
   "devDependencies": {
-    "@babel/core": "^7.24.0",
+    "@babel/core": "^7.24.6",
     "@babel/plugin-transform-modules-commonjs": "^7.18.6",
-    "@babel/preset-env": "^7.24.0",
-    "@babel/preset-react": "^7.18.6",
+    "@babel/preset-env": "^7.24.4",
+    "@babel/preset-react": "^7.24.1",
     "@babel/preset-typescript": "^7.21.4",
     "@faker-js/faker": "^8.4.1",
-    "@github/markdownlint-github": "^0.6.0",
-    "@octokit/plugin-throttling": "^8.0.0",
+    "@github/markdownlint-github": "^0.6.2",
     "@playwright/test": "^1.40.1",
-    "@storybook/addon-a11y": "^7.6.15",
-    "@storybook/addon-actions": "^7.1.0",
-    "@storybook/addon-essentials": "^7.1.0",
-    "@storybook/addon-interactions": "^7.1.0",
-    "@storybook/addon-links": "^7.1.0",
-    "@storybook/components": "^7.6.17",
-    "@storybook/csf": "^0.1.1",
-    "@storybook/manager-api": "^7.6.7",
-    "@storybook/react": "^7.1.0",
-    "@storybook/react-webpack5": "^7.6.12",
-    "@storybook/theming": "^7.6.12",
-    "@testing-library/dom": "^9.3.4",
-    "@testing-library/jest-dom": "^6.4.2",
-    "@testing-library/react": "^14.2.1",
+    "@storybook/addon-a11y": "^8.1.10",
+    "@storybook/addon-actions": "^8.1.10",
+    "@storybook/addon-essentials": "^8.1.10",
+    "@storybook/addon-interactions": "^8.1.10",
+    "@storybook/addon-links": "^8.1.10",
+    "@storybook/blocks": "^8.0.2",
+    "@storybook/components": "^8.0.2",
+    "@storybook/csf": "^0.1.8",
+    "@storybook/icons": "^1.2.9",
+    "@storybook/manager-api": "^8.1.10",
+    "@storybook/react": "^8.1.10",
+    "@storybook/react-vite": "^8.1.10",
+    "@storybook/theming": "^8.1.10",
+    "@testing-library/dom": "^10.1.0",
+    "@testing-library/jest-dom": "^6.4.6",
+    "@testing-library/react": "^16.0.0",
     "@testing-library/user-event": "^14.5.2",
     "@types/child-process-promise": "^2.2.1",
     "@types/d3": "^7.4.0",
@@ -2020,12 +2027,12 @@
     "@types/jest": "^29.5.12",
     "@types/js-yaml": "^4.0.6",
     "@types/nanoid": "^3.0.0",
-    "@types/node": "18.17.*",
+    "@types/node": "20.9.*",
     "@types/node-fetch": "^2.5.2",
-    "@types/react": "^18.0.28",
-    "@types/react-dom": "^18.2.18",
+    "@types/react": "^18.3.1",
+    "@types/react-dom": "^18.3.0",
     "@types/sarif": "^2.1.2",
-    "@types/semver": "^7.2.0",
+    "@types/semver": "^7.5.8",
     "@types/stream-json": "^1.7.1",
     "@types/styled-components": "^5.1.11",
     "@types/tar-stream": "^3.1.3",
@@ -2033,54 +2040,52 @@
     "@types/tmp": "^0.2.6",
     "@types/vscode": "^1.82.0",
     "@types/yauzl": "^2.10.3",
-    "@typescript-eslint/eslint-plugin": "^7.2.0",
-    "@typescript-eslint/parser": "^6.21.0",
+    "@typescript-eslint/eslint-plugin": "^7.5.0",
+    "@typescript-eslint/parser": "^7.5.0",
     "@vscode/test-electron": "^2.3.9",
     "@vscode/vsce": "^2.24.0",
     "ansi-colors": "^4.1.1",
-    "applicationinsights": "^2.9.4",
+    "applicationinsights": "^2.9.5",
     "cosmiconfig": "^9.0.0",
     "cross-env": "^7.0.3",
-    "css-loader": "^6.10.0",
     "del": "^6.0.0",
     "eslint": "^8.56.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-import-resolver-typescript": "^3.6.1",
     "eslint-plugin-deprecation": "^2.0.0",
     "eslint-plugin-etc": "^2.0.2",
-    "eslint-plugin-github": "^4.4.1",
+    "eslint-plugin-github": "^4.10.2",
     "eslint-plugin-import": "^2.29.1",
-    "eslint-plugin-jest-dom": "^5.0.1",
+    "eslint-plugin-jest-dom": "^5.2.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-react": "^7.31.8",
+    "eslint-plugin-react": "^7.34.1",
     "eslint-plugin-react-hooks": "^4.6.0",
     "eslint-plugin-storybook": "^0.8.0",
-    "file-loader": "^6.2.0",
     "glob": "^10.0.0",
     "gulp": "^4.0.2",
     "gulp-esbuild": "^0.12.0",
     "gulp-replace": "^1.1.3",
     "gulp-typescript": "^5.0.1",
-    "husky": "^8.0.0",
+    "husky": "^9.1.7",
     "jest": "^29.0.3",
     "jest-environment-jsdom": "^29.0.3",
     "jest-runner-vscode": "^3.0.1",
-    "lint-staged": "^15.0.2",
-    "markdownlint-cli2": "^0.12.1",
-    "markdownlint-cli2-formatter-pretty": "^0.0.5",
-    "mini-css-extract-plugin": "^2.8.1",
+    "lint-staged": "^15.2.2",
+    "markdownlint-cli2": "^0.13.0",
+    "markdownlint-cli2-formatter-pretty": "^0.0.6",
     "npm-run-all": "^4.1.5",
     "patch-package": "^8.0.0",
     "prettier": "^3.2.5",
-    "storybook": "^7.6.15",
+    "storybook": "^8.1.10",
     "tar-stream": "^3.1.7",
     "through2": "^4.0.2",
-    "ts-jest": "^29.0.1",
-    "ts-json-schema-generator": "^1.1.2",
-    "ts-loader": "^9.4.2",
-    "ts-node": "^10.7.0",
-    "ts-unused-exports": "^10.0.0",
-    "typescript": "^5.0.2"
+    "ts-jest": "^29.1.4",
+    "ts-json-schema-generator": "^2.1.1",
+    "ts-node": "^10.9.2",
+    "ts-unused-exports": "^10.1.0",
+    "typescript": "^5.0.2",
+    "vite": "^5.2.11",
+    "vite-node": "^1.5.3"
   },
   "lint-staged": {
     "./**/*.{json,css,scss}": [

extensions/ql-vscode/src/common/authentication.ts

@@ -31,4 +31,9 @@ export interface Credentials {
    * @returns An OAuth access token, or undefined.
    */
   getExistingAccessToken(): Promise<string | undefined>;
+
+  /**
+   * Returns the ID of the authentication provider to use.
+   */
+  authProviderId: string;
 }

extensions/ql-vscode/src/common/commands.ts

@@ -273,6 +273,9 @@ export type VariantAnalysisCommands = {
   "codeQL.openVariantAnalysisLogs": (
     variantAnalysisId: number,
   ) => Promise<void>;
+  "codeQLModelAlerts.openVariantAnalysisLogs": (
+    variantAnalysisId: number,
+  ) => Promise<void>;
   "codeQL.openVariantAnalysisView": (
     variantAnalysisId: number,
   ) => Promise<void>;
@@ -287,7 +290,6 @@ export type DatabasePanelCommands = {
   "codeQLVariantAnalysisRepositories.openConfigFile": () => Promise<void>;
   "codeQLVariantAnalysisRepositories.addNewDatabase": () => Promise<void>;
   "codeQLVariantAnalysisRepositories.addNewList": () => Promise<void>;
-  "codeQLVariantAnalysisRepositories.setupControllerRepository": () => Promise<void>;
 
   "codeQLVariantAnalysisRepositories.setSelectedItem": TreeViewContextSingleSelectionCommandFunction<DbTreeViewItem>;
   "codeQLVariantAnalysisRepositories.setSelectedItemContextMenu": TreeViewContextSingleSelectionCommandFunction<DbTreeViewItem>;

extensions/ql-vscode/src/common/config-template.ts

@@ -0,0 +1,57 @@
+// Based on https://github.com/microsoft/vscode/blob/edfd5b8ba54d50f3f5c2ebee877af088803def88/src/vs/base/common/labels.ts#L316C1-L400
+
+/**
+ * Helper to insert values for specific template variables into the string. E.g. "this ${is} a ${template}" can be
+ * passed to this function together with an object that maps "is" and "template" to strings to have them replaced.
+ *
+ * @param template string to which template is applied
+ * @param values the values of the templates to use
+ */
+export function substituteConfigVariables(
+  template: string,
+  values: {
+    [key: string]: string | undefined | null;
+  },
+): string {
+  const segments: string[] = [];
+
+  let inVariable = false;
+  let currentValue = "";
+  for (const char of template) {
+    // Beginning of variable
+    if (char === "$" || (inVariable && char === "{")) {
+      if (currentValue) {
+        segments.push(currentValue);
+      }
+
+      currentValue = "";
+      inVariable = true;
+    }
+
+    // End of variable
+    else if (char === "}" && inVariable) {
+      const resolved = values[currentValue];
+
+      // Variable
+      if (resolved && resolved.length > 0) {
+        segments.push(resolved);
+      }
+      // If the variable, doesn't exist, we discard it (i.e. replace it by the empty string)
+
+      currentValue = "";
+      inVariable = false;
+    }
+
+    // Text or Variable Name
+    else {
+      currentValue += char;
+    }
+  }
+
+  // Tail
+  if (currentValue && !inVariable) {
+    segments.push(currentValue);
+  }
+
+  return segments.join("");
+}

extensions/ql-vscode/src/common/github-url-identifier-helper.ts

@@ -29,37 +29,45 @@ function validGitHubNwoOrOwner(
 
 /**
  * Extracts an NWO from a GitHub URL.
- * @param githubUrl The GitHub repository URL
+ * @param repositoryUrl The GitHub repository URL
+ * @param githubUrl The URL of the GitHub instance
  * @return The corresponding NWO, or undefined if the URL is not valid
  */
-export function getNwoFromGitHubUrl(githubUrl: string): string | undefined {
-  return getNwoOrOwnerFromGitHubUrl(githubUrl, "nwo");
+export function getNwoFromGitHubUrl(
+  repositoryUrl: string,
+  githubUrl: URL,
+): string | undefined {
+  return getNwoOrOwnerFromGitHubUrl(repositoryUrl, githubUrl, "nwo");
 }
 
 /**
  * Extracts an owner from a GitHub URL.
- * @param githubUrl The GitHub repository URL
+ * @param repositoryUrl The GitHub repository URL
+ * @param githubUrl The URL of the GitHub instance
  * @return The corresponding Owner, or undefined if the URL is not valid
  */
-export function getOwnerFromGitHubUrl(githubUrl: string): string | undefined {
-  return getNwoOrOwnerFromGitHubUrl(githubUrl, "owner");
+export function getOwnerFromGitHubUrl(
+  repositoryUrl: string,
+  githubUrl: URL,
+): string | undefined {
+  return getNwoOrOwnerFromGitHubUrl(repositoryUrl, githubUrl, "owner");
 }
 
 function getNwoOrOwnerFromGitHubUrl(
-  githubUrl: string,
+  repositoryUrl: string,
+  githubUrl: URL,
   kind: "owner" | "nwo",
 ): string | undefined {
+  const validHostnames = [githubUrl.hostname, `www.${githubUrl.hostname}`];
+
   try {
     let paths: string[];
-    const urlElements = githubUrl.split("/");
-    if (
-      urlElements[0] === "github.com" ||
-      urlElements[0] === "www.github.com"
-    ) {
-      paths = githubUrl.split("/").slice(1);
+    const urlElements = repositoryUrl.split("/");
+    if (validHostnames.includes(urlElements[0])) {
+      paths = repositoryUrl.split("/").slice(1);
     } else {
-      const uri = new URL(githubUrl);
-      if (uri.hostname !== "github.com" && uri.hostname !== "www.github.com") {
+      const uri = new URL(repositoryUrl);
+      if (!validHostnames.includes(uri.hostname)) {
         return;
       }
       paths = uri.pathname.split("/").filter((segment: string) => segment);

extensions/ql-vscode/src/common/interface-types.ts

@@ -10,7 +10,7 @@ import type {
 } from "../variant-analysis/shared/variant-analysis-filter-sort";
 import type { ErrorLike } from "../common/errors";
 import type { DataFlowPaths } from "../variant-analysis/shared/data-flow-paths";
-import type { Method } from "../model-editor/method";
+import type { Method, MethodSignature } from "../model-editor/method";
 import type { ModeledMethod } from "../model-editor/modeled-method";
 import type {
   MethodModelingPanelViewState,
@@ -605,6 +605,11 @@ interface OpenModelAlertsViewMessage {
   t: "openModelAlertsView";
 }
 
+interface RevealInModelAlertsViewMessage {
+  t: "revealInModelAlertsView";
+  modeledMethod: ModeledMethod;
+}
+
 interface ModelDependencyMessage {
   t: "modelDependency";
 }
@@ -677,11 +682,12 @@ export type FromModelEditorMessage =
   | SetMultipleModeledMethodsMessage
   | StartModelEvaluationMessage
   | StopModelEvaluationMessage
-  | OpenModelAlertsViewMessage;
+  | OpenModelAlertsViewMessage
+  | RevealInModelAlertsViewMessage;
 
 interface RevealInEditorMessage {
   t: "revealInModelEditor";
-  method: Method;
+  method: MethodSignature;
 }
 
 interface StartModelingMessage {
@@ -737,17 +743,29 @@ interface OpenModelPackMessage {
   path: string;
 }
 
+interface OpenActionsLogsMessage {
+  t: "openActionsLogs";
+  variantAnalysisId: number;
+}
+
 interface StopEvaluationRunMessage {
   t: "stopEvaluationRun";
 }
 
+interface RevealModelMessage {
+  t: "revealModel";
+  modeledMethod: ModeledMethod;
+}
+
 export type ToModelAlertsMessage =
   | SetModelAlertsViewStateMessage
   | SetVariantAnalysisMessage
   | SetRepoResultsMessage
-  | SetRepoStatesMessage;
+  | RevealModelMessage;
 
 export type FromModelAlertsMessage =
   | CommonFromViewMessages
   | OpenModelPackMessage
-  | StopEvaluationRunMessage;
+  | OpenActionsLogsMessage
+  | StopEvaluationRunMessage
+  | RevealInEditorMessage;

extensions/ql-vscode/src/common/logging/tee-logger.ts

@@ -1,7 +1,10 @@
-import { appendFile, ensureFile } from "fs-extra";
+import { ensureFile } from "fs-extra";
+import { open } from "node:fs/promises";
+import type { FileHandle } from "node:fs/promises";
 import { isAbsolute } from "path";
 import { getErrorMessage } from "../helpers-pure";
 import type { Logger, LogOptions } from "./logger";
+import type { Disposable } from "../disposable-object";
 
 /**
  * An implementation of {@link Logger} that sends the output both to another {@link Logger}
@@ -10,9 +13,10 @@ import type { Logger, LogOptions } from "./logger";
  * The first time a message is written, an additional banner is written to the underlying logger
  * pointing the user to the "side log" file.
  */
-export class TeeLogger implements Logger {
+export class TeeLogger implements Logger, Disposable {
   private emittedRedirectMessage = false;
   private error = false;
+  private fileHandle: FileHandle | undefined = undefined;
 
   public constructor(
     private readonly logger: Logger,
@@ -37,11 +41,15 @@ export class TeeLogger implements Logger {
 
     if (!this.error) {
       try {
-        const trailingNewline = options.trailingNewline ?? true;
-        await ensureFile(this.location);
+        if (!this.fileHandle) {
+          await ensureFile(this.location);
 
-        await appendFile(
-          this.location,
+          this.fileHandle = await open(this.location, "a");
+        }
+
+        const trailingNewline = options.trailingNewline ?? true;
+
+        await this.fileHandle.appendFile(
           message + (trailingNewline ? "\n" : ""),
           {
             encoding: "utf8",
@@ -50,6 +58,14 @@ export class TeeLogger implements Logger {
       } catch (e) {
         // Write an error message to the primary log, and stop trying to write to the side log.
         this.error = true;
+        try {
+          await this.fileHandle?.close();
+        } catch (e) {
+          void this.logger.log(
+            `Failed to close file handle: ${getErrorMessage(e)}`,
+          );
+        }
+        this.fileHandle = undefined;
         const errorMessage = getErrorMessage(e);
         await this.logger.log(
           `Error writing to additional log file: ${errorMessage}`,
@@ -65,4 +81,15 @@ export class TeeLogger implements Logger {
   show(preserveFocus?: boolean): void {
     this.logger.show(preserveFocus);
   }
+
+  dispose(): void {
+    try {
+      void this.fileHandle?.close();
+    } catch (e) {
+      void this.logger.log(
+        `Failed to close file handle: ${getErrorMessage(e)}`,
+      );
+    }
+    this.fileHandle = undefined;
+  }
 }

extensions/ql-vscode/src/common/vscode/archive-filesystem-provider.ts

@@ -26,6 +26,8 @@ import {
 // All path operations in this file must be on paths *within* the zip
 // archive.
 import { posix } from "path";
+import { DatabaseEventKind } from "../../databases/local-databases/database-events";
+import type { DatabaseManager } from "../../databases/local-databases/database-manager";
 
 const path = posix;
 
@@ -242,6 +244,10 @@ export class ArchiveFileSystemProvider implements FileSystemProvider {
 
   root = new Directory("");
 
+  flushCache(zipPath: string) {
+    this.archives.delete(zipPath);
+  }
+
   // metadata
 
   async stat(uri: Uri): Promise<FileStat> {
@@ -355,15 +361,35 @@ export class ArchiveFileSystemProvider implements FileSystemProvider {
  */
 export const zipArchiveScheme = "codeql-zip-archive";
 
-export function activate(ctx: ExtensionContext) {
+export function activate(ctx: ExtensionContext, dbm?: DatabaseManager) {
+  const afsp = new ArchiveFileSystemProvider();
+  if (dbm) {
+    ctx.subscriptions.push(
+      dbm.onDidChangeDatabaseItem(async ({ kind, item: db }) => {
+        if (kind === DatabaseEventKind.Remove) {
+          if (db?.sourceArchive) {
+            afsp.flushCache(db.sourceArchive.fsPath);
+          }
+        }
+      }),
+    );
+  }
+
   ctx.subscriptions.push(
-    workspace.registerFileSystemProvider(
-      zipArchiveScheme,
-      new ArchiveFileSystemProvider(),
-      {
-        isCaseSensitive: true,
-        isReadonly: true,
-      },
-    ),
+    // When a file system archive is removed from the workspace, we should
+    // also remove it from our cache.
+    workspace.onDidChangeWorkspaceFolders((event) => {
+      for (const removed of event.removed) {
+        const zipPath = removed.uri.fsPath;
+        afsp.flushCache(zipPath);
+      }
+    }),
+  );
+
+  ctx.subscriptions.push(
+    workspace.registerFileSystemProvider(zipArchiveScheme, afsp, {
+      isCaseSensitive: true,
+      isReadonly: true,
+    }),
   );
 }

extensions/ql-vscode/src/common/vscode/authentication.ts

@@ -2,8 +2,8 @@ import { authentication } from "vscode";
 import type { Octokit } from "@octokit/rest";
 import type { Credentials } from "../authentication";
 import { AppOctokit } from "../octokit";
-
-export const GITHUB_AUTH_PROVIDER_ID = "github";
+import { hasGhecDrUri } from "../../config";
+import { getOctokitBaseUrl } from "./octokit";
 
 // We need 'repo' scope for triggering workflows, 'gist' scope for exporting results to Gist,
 // and 'read:packages' for reading private CodeQL packages.
@@ -16,30 +16,24 @@ const SCOPES = ["repo", "gist", "read:packages"];
  */
 export class VSCodeCredentials implements Credentials {
   /**
-   * A specific octokit to return, otherwise a new authenticated octokit will be created when needed.
-   */
-  private octokit: Octokit | undefined;
-
-  /**
-   * Creates or returns an instance of Octokit.
+   * Creates or returns an instance of Octokit. The returned instance should
+   * not be stored and reused, as it may become out-of-date with the current
+   * authentication session.
    *
    * @returns An instance of Octokit.
    */
   async getOctokit(): Promise<Octokit> {
-    if (this.octokit) {
-      return this.octokit;
-    }
-
     const accessToken = await this.getAccessToken();
 
     return new AppOctokit({
       auth: accessToken,
+      baseUrl: getOctokitBaseUrl(),
     });
   }
 
   async getAccessToken(): Promise<string> {
     const session = await authentication.getSession(
-      GITHUB_AUTH_PROVIDER_ID,
+      this.authProviderId,
       SCOPES,
       { createIfNone: true },
     );
@@ -49,11 +43,18 @@ export class VSCodeCredentials implements Credentials {
 
   async getExistingAccessToken(): Promise<string | undefined> {
     const session = await authentication.getSession(
-      GITHUB_AUTH_PROVIDER_ID,
+      this.authProviderId,
       SCOPES,
       { createIfNone: false },
     );
 
     return session?.accessToken;
   }
+
+  public get authProviderId(): string {
+    if (hasGhecDrUri()) {
+      return "github-enterprise";
+    }
+    return "github";
+  }
 }

extensions/ql-vscode/src/common/vscode/octokit.ts

@@ -0,0 +1,15 @@
+import { getGitHubInstanceApiUrl } from "../../config";
+
+/**
+ * Returns the Octokit base URL to use based on the GitHub instance URL.
+ *
+ * This is necessary because the Octokit base URL should not have a trailing
+ * slash, but this is included by default in a URL.
+ */
+export function getOctokitBaseUrl(): string {
+  let apiUrl = getGitHubInstanceApiUrl().toString();
+  if (apiUrl.endsWith("/")) {
+    apiUrl = apiUrl.slice(0, -1);
+  }
+  return apiUrl;
+}

extensions/ql-vscode/src/common/vscode/progress.ts

@@ -33,6 +33,14 @@ export interface ProgressUpdate {
   message: string;
 }
 
+export function progressUpdate(
+  step: number,
+  maxStep: number,
+  message: string,
+): ProgressUpdate {
+  return { step, maxStep, message };
+}
+
 export type ProgressCallback = (p: ProgressUpdate) => void;
 
 // Make certain properties within a type optional
@@ -48,7 +56,7 @@ type ProgressOptions = Optional<VSCodeProgressOptions, "location">;
  * denote some progress being achieved on this task.
  * @param token a cancellation token
  */
-export type ProgressTask<R> = (
+type ProgressTask<R> = (
   progress: ProgressCallback,
   token: CancellationToken,
 ) => Thenable<R>;

extensions/ql-vscode/src/config.ts

@@ -4,7 +4,7 @@ import type {
   ConfigurationScope,
   Event,
 } from "vscode";
-import { ConfigurationTarget, EventEmitter, workspace } from "vscode";
+import { ConfigurationTarget, EventEmitter, workspace, Uri } from "vscode";
 import type { DistributionManager } from "./codeql-cli/distribution";
 import { extLogger } from "./common/logging/vscode";
 import { ONE_DAY_IN_MS } from "./common/time";
@@ -13,6 +13,8 @@ import {
   FilterKey,
   SortKey,
 } from "./variant-analysis/shared/variant-analysis-filter-sort";
+import { substituteConfigVariables } from "./common/config-template";
+import { getErrorMessage } from "./common/helpers-pure";
 
 export const ALL_SETTINGS: Setting[] = [];
 
@@ -68,6 +70,97 @@ export const VSCODE_SAVE_BEFORE_START_SETTING = new Setting(
   VSCODE_DEBUG_SETTING,
 );
 
+const VSCODE_GITHUB_ENTERPRISE_SETTING = new Setting(
+  "github-enterprise",
+  undefined,
+);
+export const VSCODE_GITHUB_ENTERPRISE_URI_SETTING = new Setting(
+  "uri",
+  VSCODE_GITHUB_ENTERPRISE_SETTING,
+);
+
+/**
+ * Get the value of the `github-enterprise.uri` setting, parsed as a URI.
+ * If the value is not set or cannot be parsed, return `undefined`.
+ */
+export function getEnterpriseUri(): Uri | undefined {
+  const config = VSCODE_GITHUB_ENTERPRISE_URI_SETTING.getValue<string>();
+  if (config) {
+    try {
+      let uri = Uri.parse(config, true);
+      if (uri.scheme === "http") {
+        uri = uri.with({ scheme: "https" });
+      }
+      return uri;
+    } catch (e) {
+      void extLogger.log(
+        `Failed to parse the GitHub Enterprise URI: ${getErrorMessage(e)}`,
+      );
+    }
+  }
+  return undefined;
+}
+
+/**
+ * Is the GitHub Enterprise URI set?
+ */
+export function hasEnterpriseUri(): boolean {
+  return getEnterpriseUri() !== undefined;
+}
+
+/**
+ * Does the uri look like GHEC-DR?
+ */
+function isGhecDrUri(uri: Uri | undefined): boolean {
+  return (
+    uri !== undefined && !uri.authority.toLowerCase().endsWith("github.com")
+  );
+}
+
+/**
+ * Is the GitHub Enterprise URI set to something that looks like GHEC-DR?
+ */
+export function hasGhecDrUri(): boolean {
+  const uri = getEnterpriseUri();
+  return isGhecDrUri(uri);
+}
+
+/**
+ * The URI for GitHub.com.
+ */
+export const GITHUB_URL = new URL("https://github.com");
+export const GITHUB_API_URL = new URL("https://api.github.com");
+
+/**
+ * If the GitHub Enterprise URI is set to something that looks like GHEC-DR, return it.
+ */
+export function getGhecDrUri(): Uri | undefined {
+  const uri = getEnterpriseUri();
+  if (isGhecDrUri(uri)) {
+    return uri;
+  } else {
+    return undefined;
+  }
+}
+
+export function getGitHubInstanceUrl(): URL {
+  const ghecDrUri = getGhecDrUri();
+  if (ghecDrUri) {
+    return new URL(ghecDrUri.toString());
+  }
+  return GITHUB_URL;
+}
+
+export function getGitHubInstanceApiUrl(): URL {
+  const ghecDrUri = getGhecDrUri();
+  if (ghecDrUri) {
+    const url = new URL(ghecDrUri.toString());
+    url.hostname = `api.${url.hostname}`;
+    return url;
+  }
+  return GITHUB_API_URL;
+}
+
 const ROOT_SETTING = new Setting("codeQL");
 
 // Telemetry configuration
@@ -500,27 +593,13 @@ export const NO_CACHE_CONTEXTUAL_QUERIES = new Setting(
 // Settings for variant analysis
 const VARIANT_ANALYSIS_SETTING = new Setting("variantAnalysis", ROOT_SETTING);
 
-/**
- * The name of the "controller" repository that you want to use with the "Run Variant Analysis" command.
- * Note: This command is only available for internal users.
- *
- * This setting should be a GitHub repository of the form `<owner>/<repo>`.
- */
-const REMOTE_CONTROLLER_REPO = new Setting(
-  "controllerRepo",
-  VARIANT_ANALYSIS_SETTING,
-);
-
-export function getRemoteControllerRepo(): string | undefined {
-  return REMOTE_CONTROLLER_REPO.getValue<string>() || undefined;
-}
-
-export async function setRemoteControllerRepo(repo: string | undefined) {
-  await REMOTE_CONTROLLER_REPO.updateValue(repo, ConfigurationTarget.Global);
-}
-
 export interface VariantAnalysisConfig {
-  controllerRepo: string | undefined;
+  showSystemDefinedRepositoryLists: boolean;
+  /**
+   * This uses a URL instead of a URI because the URL class is available in
+   * unit tests and is fully browser-compatible.
+   */
+  githubUrl: URL;
   onDidChangeConfiguration?: Event<void>;
 }
 
@@ -530,13 +609,17 @@ export class VariantAnalysisConfigListener
 {
   protected handleDidChangeConfiguration(e: ConfigurationChangeEvent): void {
     this.handleDidChangeConfigurationForRelevantSettings(
-      [VARIANT_ANALYSIS_SETTING],
+      [VARIANT_ANALYSIS_SETTING, VSCODE_GITHUB_ENTERPRISE_URI_SETTING],
       e,
     );
   }
 
-  public get controllerRepo(): string | undefined {
-    return getRemoteControllerRepo();
+  public get showSystemDefinedRepositoryLists(): boolean {
+    return !hasEnterpriseUri();
+  }
+
+  public get githubUrl(): URL {
+    return getGitHubInstanceUrl();
   }
 }
 
@@ -724,7 +807,6 @@ export async function setAutogenerateQlPacks(choice: AutogenerateQLPacks) {
 const MODEL_SETTING = new Setting("model", ROOT_SETTING);
 const FLOW_GENERATION = new Setting("flowGeneration", MODEL_SETTING);
 const LLM_GENERATION = new Setting("llmGeneration", MODEL_SETTING);
-const SHOW_TYPE_MODELS = new Setting("showTypeModels", MODEL_SETTING);
 const LLM_GENERATION_BATCH_SIZE = new Setting(
   "llmGenerationBatchSize",
   MODEL_SETTING,
@@ -734,25 +816,34 @@ const LLM_GENERATION_DEV_ENDPOINT = new Setting(
   MODEL_SETTING,
 );
 const MODEL_EVALUATION = new Setting("evaluation", MODEL_SETTING);
-const EXTENSIONS_DIRECTORY = new Setting("extensionsDirectory", MODEL_SETTING);
+const MODEL_PACK_LOCATION = new Setting("packLocation", MODEL_SETTING);
+const MODEL_PACK_NAME = new Setting("packName", MODEL_SETTING);
 const ENABLE_PYTHON = new Setting("enablePython", MODEL_SETTING);
-const ENABLE_ACCESS_PATH_SUGGESTIONS = new Setting(
-  "enableAccessPathSuggestions",
-  MODEL_SETTING,
-);
+
+export type ModelConfigPackVariables = {
+  database: string;
+  owner: string;
+  name: string;
+  language: string;
+};
 
 export interface ModelConfig {
   flowGeneration: boolean;
   llmGeneration: boolean;
-  showTypeModels: boolean;
-  getExtensionsDirectory(languageId: string): string | undefined;
+  getPackLocation(
+    languageId: string,
+    variables: ModelConfigPackVariables,
+  ): string;
+  getPackName(languageId: string, variables: ModelConfigPackVariables): string;
   enablePython: boolean;
-  enableAccessPathSuggestions: boolean;
 }
 
 export class ModelConfigListener extends ConfigListener implements ModelConfig {
   protected handleDidChangeConfiguration(e: ConfigurationChangeEvent): void {
-    this.handleDidChangeConfigurationForRelevantSettings([MODEL_SETTING], e);
+    this.handleDidChangeConfigurationForRelevantSettings(
+      [MODEL_SETTING, VSCODE_GITHUB_ENTERPRISE_URI_SETTING],
+      e,
+    );
   }
 
   public get flowGeneration(): boolean {
@@ -760,11 +851,7 @@ export class ModelConfigListener extends ConfigListener implements ModelConfig {
   }
 
   public get llmGeneration(): boolean {
-    return !!LLM_GENERATION.getValue<boolean>();
-  }
-
-  public get showTypeModels(): boolean {
-    return !!SHOW_TYPE_MODELS.getValue<boolean>();
+    return !!LLM_GENERATION.getValue<boolean>() && !hasEnterpriseUri();
   }
 
   /**
@@ -787,19 +874,33 @@ export class ModelConfigListener extends ConfigListener implements ModelConfig {
     return !!MODEL_EVALUATION.getValue<boolean>();
   }
 
-  public getExtensionsDirectory(languageId: string): string | undefined {
-    return EXTENSIONS_DIRECTORY.getValue<string>({
-      languageId,
-    });
+  public getPackLocation(
+    languageId: string,
+    variables: ModelConfigPackVariables,
+  ): string {
+    return substituteConfigVariables(
+      MODEL_PACK_LOCATION.getValue<string>({
+        languageId,
+      }),
+      variables,
+    );
+  }
+
+  public getPackName(
+    languageId: string,
+    variables: ModelConfigPackVariables,
+  ): string {
+    return substituteConfigVariables(
+      MODEL_PACK_NAME.getValue<string>({
+        languageId,
+      }),
+      variables,
+    );
   }
 
   public get enablePython(): boolean {
     return !!ENABLE_PYTHON.getValue<boolean>();
   }
-
-  public get enableAccessPathSuggestions(): boolean {
-    return !!ENABLE_ACCESS_PATH_SUGGESTIONS.getValue<boolean>();
-  }
 }
 
 const GITHUB_DATABASE_SETTING = new Setting("githubDatabase", ROOT_SETTING);

extensions/ql-vscode/src/databases/code-search-api.ts

@@ -7,6 +7,7 @@ import { AppOctokit } from "../common/octokit";
 import type { ProgressCallback } from "../common/vscode/progress";
 import { UserCancellationException } from "../common/vscode/progress";
 import type { EndpointDefaults } from "@octokit/types";
+import { getOctokitBaseUrl } from "../common/vscode/octokit";
 
 export async function getCodeSearchRepositories(
   query: string,
@@ -54,6 +55,7 @@ async function provideOctokitWithThrottling(
 
   const octokit = new MyOctokit({
     auth,
+    baseUrl: getOctokitBaseUrl(),
     throttle: {
       onRateLimit: (retryAfter: number, options: EndpointDefaults): boolean => {
         void logger.log(

extensions/ql-vscode/src/databases/db-manager.ts

@@ -16,6 +16,7 @@ import {
 } from "./db-item-selection";
 import { createRemoteTree } from "./db-tree-creator";
 import type { DbConfigValidationError } from "./db-validation-errors";
+import type { VariantAnalysisConfig } from "../config";
 
 export class DbManager extends DisposableObject {
   public readonly onDbItemsChanged: AppEvent<void>;
@@ -25,6 +26,7 @@ export class DbManager extends DisposableObject {
   constructor(
     private readonly app: App,
     private readonly dbConfigStore: DbConfigStore,
+    private readonly variantAnalysisConfigListener: VariantAnalysisConfig,
   ) {
     super();
 
@@ -36,6 +38,10 @@ export class DbManager extends DisposableObject {
     this.dbConfigStore.onDidChangeConfig(() => {
       this.onDbItemsChangesEventEmitter.fire();
     });
+
+    this.variantAnalysisConfigListener.onDidChangeConfiguration?.(() => {
+      this.onDbItemsChangesEventEmitter.fire();
+    });
   }
 
   public getSelectedDbItem(): DbItem | undefined {
@@ -56,7 +62,11 @@ export class DbManager extends DisposableObject {
 
     const expandedItems = this.getExpandedItems();
 
-    const remoteTree = createRemoteTree(configResult.value, expandedItems);
+    const remoteTree = createRemoteTree(
+      configResult.value,
+      this.variantAnalysisConfigListener,
+      expandedItems,
+    );
     return ValueResult.ok(remoteTree.children);
   }
 

extensions/ql-vscode/src/databases/db-module.ts

@@ -7,6 +7,7 @@ import { DbManager } from "./db-manager";
 import { DbPanel } from "./ui/db-panel";
 import { DbSelectionDecorationProvider } from "./ui/db-selection-decoration-provider";
 import type { DatabasePanelCommands } from "../common/commands";
+import { VariantAnalysisConfigListener } from "../config";
 
 export class DbModule extends DisposableObject {
   public readonly dbManager: DbManager;
@@ -17,7 +18,13 @@ export class DbModule extends DisposableObject {
     super();
 
     this.dbConfigStore = new DbConfigStore(app);
-    this.dbManager = this.push(new DbManager(app, this.dbConfigStore));
+    this.dbManager = this.push(
+      new DbManager(
+        app,
+        this.dbConfigStore,
+        new VariantAnalysisConfigListener(),
+      ),
+    );
   }
 
   public static async initialize(app: App): Promise<DbModule> {

extensions/ql-vscode/src/databases/db-tree-creator.ts

@@ -1,3 +1,4 @@
+import type { VariantAnalysisConfig } from "../config";
 import type { DbConfig, RemoteRepositoryList } from "./config/db-config";
 import { SelectedDbItemKind } from "./config/db-config";
 import type {
@@ -13,13 +14,17 @@ import { ExpandedDbItemKind } from "./db-item-expansion";
 
 export function createRemoteTree(
   dbConfig: DbConfig,
+  variantAnalysisConfig: VariantAnalysisConfig,
   expandedItems: ExpandedDbItem[],
 ): RootRemoteDbItem {
-  const systemDefinedLists = [
-    createSystemDefinedList(10, dbConfig),
-    createSystemDefinedList(100, dbConfig),
-    createSystemDefinedList(1000, dbConfig),
-  ];
+  const systemDefinedLists =
+    variantAnalysisConfig.showSystemDefinedRepositoryLists
+      ? [
+          createSystemDefinedList(10, dbConfig),
+          createSystemDefinedList(100, dbConfig),
+          createSystemDefinedList(1000, dbConfig),
+        ]
+      : [];
 
   const userDefinedRepoLists =
     dbConfig.databases.variantAnalysis.repositoryLists.map((r) =>

extensions/ql-vscode/src/databases/github-databases/api.ts

@@ -3,6 +3,7 @@ import type { Octokit } from "@octokit/rest";
 import type { RestEndpointMethodTypes } from "@octokit/plugin-rest-endpoint-methods";
 import { showNeverAskAgainDialog } from "../../common/vscode/dialog";
 import type { GitHubDatabaseConfig } from "../../config";
+import { hasGhecDrUri } from "../../config";
 import type { Credentials } from "../../common/authentication";
 import { AppOctokit } from "../../common/octokit";
 import type { ProgressCallback } from "../../common/vscode/progress";
@@ -67,7 +68,10 @@ export async function listDatabases(
   credentials: Credentials,
   config: GitHubDatabaseConfig,
 ): Promise<ListDatabasesResult | undefined> {
-  const hasAccessToken = !!(await credentials.getExistingAccessToken());
+  // On GHEC-DR, unauthenticated requests will never work, so we should always ask
+  // for authentication.
+  const hasAccessToken =
+    !!(await credentials.getExistingAccessToken()) || hasGhecDrUri();
 
   let octokit = hasAccessToken
     ? await credentials.getOctokit()

extensions/ql-vscode/src/databases/github-databases/download.ts

@@ -2,10 +2,8 @@ import { window } from "vscode";
 import type { Octokit } from "@octokit/rest";
 import { showNeverAskAgainDialog } from "../../common/vscode/dialog";
 import { getLanguageDisplayName } from "../../common/query-language";
-import { downloadGitHubDatabaseFromUrl } from "../database-fetcher";
+import type { DatabaseFetcher } from "../database-fetcher";
 import { withProgress } from "../../common/vscode/progress";
-import type { DatabaseManager } from "../local-databases";
-import type { CodeQLCliServer } from "../../codeql-cli/cli";
 import type { AppCommandManager } from "../../common/commands";
 import type { GitHubDatabaseConfig } from "../../config";
 import type { CodeqlDatabase } from "./api";
@@ -58,9 +56,7 @@ export async function downloadDatabaseFromGitHub(
   owner: string,
   repo: string,
   databases: CodeqlDatabase[],
-  databaseManager: DatabaseManager,
-  storagePath: string,
-  cliServer: CodeQLCliServer,
+  databaseFetcher: DatabaseFetcher,
   commandManager: AppCommandManager,
 ): Promise<void> {
   const selectedDatabases = await promptForDatabases(databases);
@@ -72,7 +68,7 @@ export async function downloadDatabaseFromGitHub(
     selectedDatabases.map((database) =>
       withProgress(
         async (progress) => {
-          await downloadGitHubDatabaseFromUrl(
+          await databaseFetcher.downloadGitHubDatabaseFromUrl(
             database.url,
             database.id,
             database.created_at,
@@ -81,9 +77,6 @@ export async function downloadDatabaseFromGitHub(
             repo,
             octokit,
             progress,
-            databaseManager,
-            storagePath,
-            cliServer,
             true,
             false,
           );

extensions/ql-vscode/src/databases/github-databases/github-databases-module.ts

@@ -14,7 +14,6 @@ import {
 } from "./download";
 import type { GitHubDatabaseConfig } from "../../config";
 import type { DatabaseManager } from "../local-databases";
-import type { CodeQLCliServer } from "../../codeql-cli/cli";
 import type { CodeqlDatabase, ListDatabasesResult } from "./api";
 import { listDatabases } from "./api";
 import type { DatabaseUpdate } from "./updates";
@@ -24,6 +23,7 @@ import {
   isNewerDatabaseAvailable,
 } from "./updates";
 import type { Octokit } from "@octokit/rest";
+import type { DatabaseFetcher } from "../database-fetcher";
 
 export class GitHubDatabasesModule extends DisposableObject {
   /**
@@ -33,8 +33,7 @@ export class GitHubDatabasesModule extends DisposableObject {
   constructor(
     private readonly app: App,
     private readonly databaseManager: DatabaseManager,
-    private readonly databaseStoragePath: string,
-    private readonly cliServer: CodeQLCliServer,
+    private readonly databaseFetcher: DatabaseFetcher,
     private readonly config: GitHubDatabaseConfig,
   ) {
     super();
@@ -43,15 +42,13 @@ export class GitHubDatabasesModule extends DisposableObject {
   public static async initialize(
     app: App,
     databaseManager: DatabaseManager,
-    databaseStoragePath: string,
-    cliServer: CodeQLCliServer,
+    databaseFetcher: DatabaseFetcher,
     config: GitHubDatabaseConfig,
   ): Promise<GitHubDatabasesModule> {
     const githubDatabasesModule = new GitHubDatabasesModule(
       app,
       databaseManager,
-      databaseStoragePath,
-      cliServer,
+      databaseFetcher,
       config,
     );
     app.subscriptions.push(githubDatabasesModule);
@@ -185,9 +182,7 @@ export class GitHubDatabasesModule extends DisposableObject {
       owner,
       repo,
       databases,
-      this.databaseManager,
-      this.databaseStoragePath,
-      this.cliServer,
+      this.databaseFetcher,
       this.app.commands,
     );
   }
@@ -212,8 +207,7 @@ export class GitHubDatabasesModule extends DisposableObject {
       repo,
       databaseUpdates,
       this.databaseManager,
-      this.databaseStoragePath,
-      this.cliServer,
+      this.databaseFetcher,
       this.app.commands,
     );
   }

extensions/ql-vscode/src/databases/github-databases/updates.ts

@@ -1,11 +1,10 @@
 import type { CodeqlDatabase } from "./api";
 import type { DatabaseItem, DatabaseManager } from "../local-databases";
 import type { Octokit } from "@octokit/rest";
-import type { CodeQLCliServer } from "../../codeql-cli/cli";
 import type { AppCommandManager } from "../../common/commands";
 import { getLanguageDisplayName } from "../../common/query-language";
 import { showNeverAskAgainDialog } from "../../common/vscode/dialog";
-import { downloadGitHubDatabaseFromUrl } from "../database-fetcher";
+import type { DatabaseFetcher } from "../database-fetcher";
 import { withProgress } from "../../common/vscode/progress";
 import { window } from "vscode";
 import type { GitHubDatabaseConfig } from "../../config";
@@ -156,8 +155,7 @@ export async function downloadDatabaseUpdateFromGitHub(
   repo: string,
   updates: DatabaseUpdate[],
   databaseManager: DatabaseManager,
-  storagePath: string,
-  cliServer: CodeQLCliServer,
+  databaseFetcher: DatabaseFetcher,
   commandManager: AppCommandManager,
 ): Promise<void> {
   const selectedDatabases = await promptForDatabases(
@@ -179,21 +177,19 @@ export async function downloadDatabaseUpdateFromGitHub(
 
       return withProgress(
         async (progress) => {
-          const newDatabase = await downloadGitHubDatabaseFromUrl(
-            database.url,
-            database.id,
-            database.created_at,
-            database.commit_oid ?? null,
-            owner,
-            repo,
-            octokit,
-            progress,
-            databaseManager,
-            storagePath,
-            cliServer,
-            databaseManager.currentDatabaseItem === update.databaseItem,
-            update.databaseItem.hasSourceArchiveInExplorer(),
-          );
+          const newDatabase =
+            await databaseFetcher.downloadGitHubDatabaseFromUrl(
+              database.url,
+              database.id,
+              database.created_at,
+              database.commit_oid ?? null,
+              owner,
+              repo,
+              octokit,
+              progress,
+              databaseManager.currentDatabaseItem === update.databaseItem,
+              update.databaseItem.hasSourceArchiveInExplorer(),
+            );
           if (newDatabase === undefined) {
             return;
           }

extensions/ql-vscode/src/databases/local-databases-ui.ts

@@ -37,11 +37,7 @@ import {
   showAndLogExceptionWithTelemetry,
   showAndLogErrorMessage,
 } from "../common/logging";
-import {
-  importLocalDatabase,
-  promptImportGithubDatabase,
-  promptImportInternetDatabase,
-} from "./database-fetcher";
+import type { DatabaseFetcher } from "./database-fetcher";
 import { asError, asyncFilter, getErrorMessage } from "../common/helpers-pure";
 import type { QueryRunner } from "../query-server";
 import type { App } from "../common/app";
@@ -113,9 +109,8 @@ class DatabaseTreeDataProvider
     // Note that events from the database manager are instances of DatabaseChangedEvent
     // and events fired by the UI are instances of DatabaseItem
 
-    // When event.item is undefined, then the entire tree is refreshed.
-    // When event.item is a db item, then only that item is refreshed.
-    this._onDidChangeTreeData.fire(event.item);
+    // When a full refresh has occurred, then all items are refreshed by passing undefined.
+    this._onDidChangeTreeData.fire(event.fullRefresh ? undefined : event.item);
   }
 
   private handleDidChangeCurrentDatabaseItem(
@@ -248,6 +243,7 @@ export class DatabaseUI extends DisposableObject {
   public constructor(
     private app: App,
     private databaseManager: DatabaseManager,
+    private readonly databaseFetcher: DatabaseFetcher,
     languageContext: LanguageContextStore,
     private readonly queryServer: QueryRunner,
     private readonly storagePath: string,
@@ -535,13 +531,7 @@ export class DatabaseUI extends DisposableObject {
   private async handleChooseDatabaseInternet(): Promise<void> {
     return withProgress(
       async (progress) => {
-        await promptImportInternetDatabase(
-          this.app.commands,
-          this.databaseManager,
-          this.storagePath,
-          progress,
-          this.queryServer.cliServer,
-        );
+        await this.databaseFetcher.promptImportInternetDatabase(progress);
       },
       {
         title: "Adding database from URL",
@@ -552,13 +542,7 @@ export class DatabaseUI extends DisposableObject {
   private async handleChooseDatabaseGithub(): Promise<void> {
     return withProgress(
       async (progress) => {
-        await promptImportGithubDatabase(
-          this.app,
-          this.databaseManager,
-          this.storagePath,
-          progress,
-          this.queryServer.cliServer,
-        );
+        await this.databaseFetcher.promptImportGithubDatabase(progress);
       },
       {
         title: "Adding database from GitHub",
@@ -660,14 +644,13 @@ export class DatabaseUI extends DisposableObject {
 
   private async handleClearCache(): Promise<void> {
     return withProgress(
-      async (_progress, token) => {
+      async () => {
         if (
           this.queryServer !== undefined &&
           this.databaseManager.currentDatabaseItem !== undefined
         ) {
           await this.queryServer.clearCacheInDatabase(
             this.databaseManager.currentDatabaseItem,
-            token,
           );
         }
       },
@@ -679,14 +662,13 @@ export class DatabaseUI extends DisposableObject {
 
   private async handleTrimCache(): Promise<void> {
     return withProgress(
-      async (_progress, token) => {
+      async () => {
         if (
           this.queryServer !== undefined &&
           this.databaseManager.currentDatabaseItem !== undefined
         ) {
           await this.queryServer.trimCacheInDatabase(
             this.databaseManager.currentDatabaseItem,
-            token,
           );
         }
       },
@@ -707,13 +689,9 @@ export class DatabaseUI extends DisposableObject {
         try {
           // Assume user has selected an archive if the file has a .zip extension
           if (uri.path.endsWith(".zip")) {
-            await importLocalDatabase(
-              this.app.commands,
+            await this.databaseFetcher.importLocalDatabase(
               uri.toString(true),
-              this.databaseManager,
-              this.storagePath,
               progress,
-              this.queryServer.cliServer,
             );
           } else {
             await this.databaseManager.openDatabase(uri, {
@@ -758,13 +736,9 @@ export class DatabaseUI extends DisposableObject {
             await this.databaseManager.removeDatabaseItem(existingItem);
           }
 
-          await importLocalDatabase(
-            this.app.commands,
+          await this.databaseFetcher.importLocalDatabase(
             uri.toString(true),
-            this.databaseManager,
-            this.storagePath,
             progress,
-            this.queryServer.cliServer,
           );
 
           if (existingItem !== undefined) {
@@ -1005,13 +979,9 @@ export class DatabaseUI extends DisposableObject {
       // we are selecting a database archive or a testproj.
       // Unzip archives (if an archive) and copy into a workspace-controlled area
       // before importing.
-      return await importLocalDatabase(
-        this.app.commands,
+      return await this.databaseFetcher.importLocalDatabase(
         uri.toString(true),
-        this.databaseManager,
-        this.storagePath,
         progress,
-        this.queryServer.cliServer,
       );
     }
   }

extensions/ql-vscode/src/databases/local-databases/database-contents.ts

@@ -1,4 +1,7 @@
+import { pathExists, remove } from "fs-extra";
+import { join } from "path";
 import type { Uri } from "vscode";
+import { zip } from "zip-a-folder";
 
 /**
  * The layout of the database.
@@ -28,3 +31,26 @@ export interface DatabaseContents {
 export interface DatabaseContentsWithDbScheme extends DatabaseContents {
   dbSchemeUri: Uri; // Always present
 }
+
+/**
+ * Databases created by the old odasa tool will not have a zipped
+ * source location. However, this extension works better if sources
+ * are zipped.
+ *
+ * This function ensures that the source location is zipped. If the
+ * `src` folder exists and the `src.zip` file does not, the `src`
+ * folder will be zipped and then deleted.
+ *
+ * @param databasePath The full path to the unzipped database
+ */
+export async function ensureZippedSourceLocation(
+  databasePath: string,
+): Promise<void> {
+  const srcFolderPath = join(databasePath, "src");
+  const srcZipPath = `${srcFolderPath}.zip`;
+
+  if ((await pathExists(srcFolderPath)) && !(await pathExists(srcZipPath))) {
+    await zip(srcFolderPath, srcZipPath);
+    await remove(srcFolderPath);
+  }
+}

extensions/ql-vscode/src/databases/local-databases/database-events.ts

@@ -16,4 +16,8 @@ export enum DatabaseEventKind {
 export interface DatabaseChangedEvent {
   kind: DatabaseEventKind;
   item: DatabaseItem | undefined;
+  // If true, event handlers should consider the database manager
+  // to have been fully refreshed. Any state managed by the
+  // event handler should be fully refreshed as well.
+  fullRefresh: boolean;
 }

extensions/ql-vscode/src/databases/local-databases/database-manager.ts

@@ -43,7 +43,7 @@ import { DatabaseResolver } from "./database-resolver";
 import { telemetryListener } from "../../common/vscode/telemetry";
 import type { LanguageContextStore } from "../../language-context-store";
 import type { DatabaseOrigin } from "./database-origin";
-import { ensureZippedSourceLocation } from "../database-fetcher";
+import { ensureZippedSourceLocation } from "./database-contents";
 
 /**
  * The name of the key in the workspaceState dictionary in which we
@@ -613,6 +613,7 @@ export class DatabaseManager extends DisposableObject {
       this._onDidChangeCurrentDatabaseItem.fire({
         item,
         kind: DatabaseEventKind.Change,
+        fullRefresh: false,
       });
     }
   }
@@ -662,8 +663,9 @@ export class DatabaseManager extends DisposableObject {
     }
     // note that we use undefined as the item in order to reset the entire tree
     this._onDidChangeDatabaseItem.fire({
-      item: undefined,
+      item,
       kind: DatabaseEventKind.Add,
+      fullRefresh: true,
     });
   }
 
@@ -671,9 +673,9 @@ export class DatabaseManager extends DisposableObject {
     item.name = newName;
     await this.updatePersistedDatabaseList();
     this._onDidChangeDatabaseItem.fire({
-      // pass undefined so that the entire tree is rebuilt in order to re-sort
-      item: undefined,
+      item,
       kind: DatabaseEventKind.Rename,
+      fullRefresh: true,
     });
   }
 
@@ -720,10 +722,10 @@ export class DatabaseManager extends DisposableObject {
       );
     }
 
-    // note that we use undefined as the item in order to reset the entire tree
     this._onDidChangeDatabaseItem.fire({
-      item: undefined,
+      item,
       kind: DatabaseEventKind.Remove,
+      fullRefresh: true,
     });
   }
 
@@ -776,6 +778,7 @@ export class DatabaseManager extends DisposableObject {
       this._onDidChangeDatabaseItem.fire({
         kind: DatabaseEventKind.Refresh,
         item: databaseItem,
+        fullRefresh: false,
       });
     }
   }

extensions/ql-vscode/src/databases/ui/db-panel.ts

@@ -18,13 +18,12 @@ import type { DbManager } from "../db-manager";
 import { DbTreeDataProvider } from "./db-tree-data-provider";
 import type { DbTreeViewItem } from "./db-tree-view-item";
 import { getGitHubUrl } from "./db-tree-view-item-action";
-import { getControllerRepo } from "../../variant-analysis/run-remote-query";
-import { getErrorMessage } from "../../common/helpers-pure";
 import type { DatabasePanelCommands } from "../../common/commands";
 import type { App } from "../../common/app";
 import { QueryLanguage } from "../../common/query-language";
 import { getCodeSearchRepositories } from "../code-search-api";
 import { showAndLogErrorMessage } from "../../common/logging";
+import { getGitHubInstanceUrl } from "../../config";
 
 export interface RemoteDatabaseQuickPickItem extends QuickPickItem {
   remoteDatabaseKind: string;
@@ -73,9 +72,6 @@ export class DbPanel extends DisposableObject {
         this.addNewRemoteDatabase.bind(this),
       "codeQLVariantAnalysisRepositories.addNewList":
         this.addNewList.bind(this),
-      "codeQLVariantAnalysisRepositories.setupControllerRepository":
-        this.setupControllerRepository.bind(this),
-
       "codeQLVariantAnalysisRepositories.setSelectedItem":
         this.setSelectedItem.bind(this),
       "codeQLVariantAnalysisRepositories.setSelectedItemContextMenu":
@@ -146,16 +142,19 @@ export class DbPanel extends DisposableObject {
   }
 
   private async addNewRemoteRepo(parentList?: string): Promise<void> {
+    const instanceUrl = getGitHubInstanceUrl();
+
     const repoName = await window.showInputBox({
       title: "Add a repository",
       prompt: "Insert a GitHub repository URL or name with owner",
-      placeHolder: "<owner>/<repo> or https://github.com/<owner>/<repo>",
+      placeHolder: `<owner>/<repo> or ${new URL("/", instanceUrl).toString()}<owner>/<repo>`,
     });
     if (!repoName) {
       return;
     }
 
-    const nwo = getNwoFromGitHubUrl(repoName) || repoName;
+    const nwo =
+      getNwoFromGitHubUrl(repoName, getGitHubInstanceUrl()) || repoName;
     if (!isValidGitHubNwo(nwo)) {
       void showAndLogErrorMessage(
         this.app.logger,
@@ -176,17 +175,20 @@ export class DbPanel extends DisposableObject {
   }
 
   private async addNewRemoteOwner(): Promise<void> {
+    const instanceUrl = getGitHubInstanceUrl();
+
     const ownerName = await window.showInputBox({
       title: "Add all repositories of a GitHub org or owner",
       prompt: "Insert a GitHub organization or owner name",
-      placeHolder: "<owner> or https://github.com/<owner>",
+      placeHolder: `<owner> or ${new URL("/", instanceUrl).toString()}<owner>`,
     });
 
     if (!ownerName) {
       return;
     }
 
-    const owner = getOwnerFromGitHubUrl(ownerName) || ownerName;
+    const owner =
+      getOwnerFromGitHubUrl(ownerName, getGitHubInstanceUrl()) || ownerName;
     if (!isValidGitHubOwner(owner)) {
       void showAndLogErrorMessage(
         this.app.logger,
@@ -411,7 +413,7 @@ export class DbPanel extends DisposableObject {
     if (treeViewItem.dbItem === undefined) {
       throw new Error("Unable to open on GitHub. Please select a valid item.");
     }
-    const githubUrl = getGitHubUrl(treeViewItem.dbItem);
+    const githubUrl = getGitHubUrl(treeViewItem.dbItem, getGitHubInstanceUrl());
     if (!githubUrl) {
       throw new Error(
         "Unable to open on GitHub. Please select a variant analysis repository or owner.",
@@ -420,22 +422,4 @@ export class DbPanel extends DisposableObject {
 
     await this.app.commands.execute("vscode.open", Uri.parse(githubUrl));
   }
-
-  private async setupControllerRepository(): Promise<void> {
-    try {
-      // This will also validate that the controller repository is valid
-      await getControllerRepo(this.app.credentials);
-    } catch (e: unknown) {
-      if (e instanceof UserCancellationException) {
-        return;
-      }
-
-      void showAndLogErrorMessage(
-        this.app.logger,
-        `An error occurred while setting up the controller repository: ${getErrorMessage(
-          e,
-        )}`,
-      );
-    }
-  }
 }

extensions/ql-vscode/src/databases/ui/db-tree-data-provider.ts

@@ -83,11 +83,6 @@ export class DbTreeDataProvider
   }
 
   private createTree(): DbTreeViewItem[] {
-    // Returning an empty tree here will show the welcome view
-    if (!this.variantAnalysisConfig.controllerRepo) {
-      return [];
-    }
-
     const dbItemsResult = this.dbManager.getDbItems();
 
     if (dbItemsResult.isFailure) {

extensions/ql-vscode/src/databases/ui/db-tree-view-item-action.ts

@@ -62,12 +62,15 @@ function canImportCodeSearch(dbItem: DbItem): boolean {
   return DbItemKind.RemoteUserDefinedList === dbItem.kind;
 }
 
-export function getGitHubUrl(dbItem: DbItem): string | undefined {
+export function getGitHubUrl(
+  dbItem: DbItem,
+  githubUrl: URL,
+): string | undefined {
   switch (dbItem.kind) {
     case DbItemKind.RemoteOwner:
-      return `https://github.com/${dbItem.ownerName}`;
+      return new URL(`/${dbItem.ownerName}`, githubUrl).toString();
     case DbItemKind.RemoteRepo:
-      return `https://github.com/${dbItem.repoFullName}`;
+      return new URL(`/${dbItem.repoFullName}`, githubUrl).toString();
     default:
       return undefined;
   }

extensions/ql-vscode/src/debugger/debugger-ui.ts

@@ -135,7 +135,7 @@ class QLDebugAdapterTracker
   ): Promise<void> {
     if (this.localQueryRun !== undefined) {
       const results: CoreQueryResults = body;
-      await this.localQueryRun.complete(results);
+      await this.localQueryRun.complete(results, (_) => {});
       this.localQueryRun = undefined;
     }
   }

extensions/ql-vscode/src/extension.ts

@@ -31,6 +31,7 @@ import {
   joinOrderWarningThreshold,
   QueryHistoryConfigListener,
   QueryServerConfigListener,
+  VariantAnalysisConfigListener,
 } from "./config";
 import {
   AstViewer,
@@ -109,7 +110,7 @@ import { VariantAnalysisManager } from "./variant-analysis/variant-analysis-mana
 import { createVariantAnalysisContentProvider } from "./variant-analysis/variant-analysis-content-provider";
 import { VSCodeMockGitHubApiServer } from "./common/mock-gh-api/vscode/vscode-mock-gh-api-server";
 import { VariantAnalysisResultsManager } from "./variant-analysis/variant-analysis-results-manager";
-import { ExtensionApp } from "./common/vscode/vscode-app";
+import { ExtensionApp } from "./common/vscode/extension-app";
 import { DbModule } from "./databases/db-module";
 import { redactableError } from "./common/errors";
 import { QLDebugAdapterDescriptorFactory } from "./debugger/debugger-factory";
@@ -133,6 +134,7 @@ import { OpenReferencedFileCodeLensProvider } from "./local-queries/open-referen
 import { LanguageContextStore } from "./language-context-store";
 import { LanguageSelectionPanel } from "./language-selection-panel/language-selection-panel";
 import { GitHubDatabasesModule } from "./databases/github-databases";
+import { DatabaseFetcher } from "./databases/database-fetcher";
 
 /**
  * extension.ts
@@ -183,11 +185,11 @@ function getCommands(
 
   const restartQueryServer = async () =>
     withProgress(
-      async (progress: ProgressCallback, token: CancellationToken) => {
+      async (progress: ProgressCallback) => {
         // Restart all of the spawned servers: cli, query, and language.
         cliServer.restartCliServer();
         await Promise.all([
-          queryRunner.restartQueryServer(progress, token),
+          queryRunner.restartQueryServer(progress),
           async () => {
             if (languageClient.isRunning()) {
               await languageClient.restart();
@@ -445,8 +447,9 @@ export async function activate(
       }
 
       if (
-        CliVersionConstraint.OLDEST_SUPPORTED_CLI_VERSION.compare(ver.version) <
-        0
+        CliVersionConstraint.OLDEST_SUPPORTED_CLI_VERSION.compare(
+          ver.version,
+        ) <= 0
       ) {
         return;
       }
@@ -714,12 +717,13 @@ async function installOrUpdateThenTryActivate(
   return undefined;
 }
 
-const PACK_GLOBS = [
+const CLEAR_PACK_CACHE_ON_EDIT_GLOBS = [
   "**/codeql-pack.yml",
   "**/qlpack.yml",
   "**/queries.xml",
   "**/codeql-pack.lock.yml",
   "**/qlpack.lock.yml",
+  "**/*.dbscheme",
   ".codeqlmanifest.json",
   "codeql-workspace.yml",
 ];
@@ -766,7 +770,7 @@ async function activateWithInstalledDistribution(
     ctx,
   );
 
-  for (const glob of PACK_GLOBS) {
+  for (const glob of CLEAR_PACK_CACHE_ON_EDIT_GLOBS) {
     const fsWatcher = workspace.createFileSystemWatcher(glob);
     ctx.subscriptions.push(fsWatcher);
 
@@ -799,12 +803,20 @@ async function activateWithInstalledDistribution(
   // Let this run async.
   void dbm.loadPersistedState();
 
+  const databaseFetcher = new DatabaseFetcher(
+    app,
+    dbm,
+    getContextStoragePath(ctx),
+    cliServer,
+  );
+
   ctx.subscriptions.push(dbm);
 
   void extLogger.log("Initializing database panel.");
   const databaseUI = new DatabaseUI(
     app,
     dbm,
+    databaseFetcher,
     languageContext,
     qs,
     getContextStoragePath(ctx),
@@ -855,8 +867,10 @@ async function activateWithInstalledDistribution(
     "variant-analyses",
   );
   await ensureDir(variantAnalysisStorageDir);
+  const variantAnalysisConfig = new VariantAnalysisConfigListener();
   const variantAnalysisResultsManager = new VariantAnalysisResultsManager(
     cliServer,
+    variantAnalysisConfig,
     extLogger,
   );
 
@@ -866,6 +880,7 @@ async function activateWithInstalledDistribution(
     variantAnalysisStorageDir,
     variantAnalysisResultsManager,
     dbModule.dbManager,
+    variantAnalysisConfig,
   );
   ctx.subscriptions.push(variantAnalysisManager);
   ctx.subscriptions.push(variantAnalysisResultsManager);
@@ -881,8 +896,7 @@ async function activateWithInstalledDistribution(
   await GitHubDatabasesModule.initialize(
     app,
     dbm,
-    getContextStoragePath(ctx),
-    cliServer,
+    databaseFetcher,
     githubDatabaseConfigListener,
   );
 
@@ -934,7 +948,7 @@ async function activateWithInstalledDistribution(
   ctx.subscriptions.push(compareView);
 
   void extLogger.log("Initializing source archive filesystem provider.");
-  archiveFilesystemProvider_activate(ctx);
+  archiveFilesystemProvider_activate(ctx, dbm);
 
   const qhelpTmpDir = dirSync({
     prefix: "qhelp_",
@@ -953,6 +967,7 @@ async function activateWithInstalledDistribution(
     qs,
     qhm,
     dbm,
+    databaseFetcher,
     cliServer,
     databaseUI,
     localQueryResultsView,
@@ -977,6 +992,7 @@ async function activateWithInstalledDistribution(
   const modelEditorModule = await ModelEditorModule.initialize(
     app,
     dbm,
+    databaseFetcher,
     variantAnalysisManager,
     cliServer,
     qs,
@@ -1068,14 +1084,12 @@ async function activateWithInstalledDistribution(
   });
 
   // Handle visibility changes in the CodeQL language client.
-  if (await cliServer.cliConstraints.supportsVisibilityNotifications()) {
-    Window.onDidChangeVisibleTextEditors((editors) => {
-      languageClient.notifyVisibilityChange(editors);
-    });
-    // Send an inital notification to the language server
-    // to set the initial state of the visible editors.
-    languageClient.notifyVisibilityChange(Window.visibleTextEditors);
-  }
+  Window.onDidChangeVisibleTextEditors((editors) => {
+    languageClient.notifyVisibilityChange(editors);
+  });
+  // Send an inital notification to the language server
+  // to set the initial state of the visible editors.
+  languageClient.notifyVisibilityChange(Window.visibleTextEditors);
 
   // Jump-to-definition and find-references
   void extLogger.log("Registering jump-to-definition handlers.");

extensions/ql-vscode/src/language-support/contextual/query-resolver.ts

@@ -92,11 +92,12 @@ export async function runContextualQuery(
   void extLogger.log(
     `Running contextual query ${query}; results will be stored in ${queryRun.outputDir.querySaveDir}`,
   );
-  const results = await queryRun.evaluate(
-    progress,
-    token,
-    new TeeLogger(qs.logger, queryRun.outputDir.logPath),
-  );
-  await cleanup?.();
-  return results;
+  const teeLogger = new TeeLogger(qs.logger, queryRun.outputDir.logPath);
+
+  try {
+    return await queryRun.evaluate(progress, token, teeLogger);
+  } finally {
+    await cleanup?.();
+    teeLogger.dispose();
+  }
 }

extensions/ql-vscode/src/local-queries/local-queries.ts

@@ -53,7 +53,8 @@ import { findLanguage } from "../codeql-cli/query-language";
 import type { QueryTreeViewItem } from "../queries-panel/query-tree-view-item";
 import { tryGetQueryLanguage } from "../common/query-language";
 import type { LanguageContextStore } from "../language-context-store";
-import type { ExtensionApp } from "../common/vscode/vscode-app";
+import type { ExtensionApp } from "../common/vscode/extension-app";
+import type { DatabaseFetcher } from "../databases/database-fetcher";
 
 export enum QuickEvalType {
   None,
@@ -69,6 +70,7 @@ export class LocalQueries extends DisposableObject {
     private readonly queryRunner: QueryRunner,
     private readonly queryHistoryManager: QueryHistoryManager,
     private readonly databaseManager: DatabaseManager,
+    private readonly databaseFetcher: DatabaseFetcher,
     private readonly cliServer: CodeQLCliServer,
     private readonly databaseUI: DatabaseUI,
     private readonly localQueryResultsView: ResultsView,
@@ -319,15 +321,13 @@ export class LocalQueries extends DisposableObject {
   private async createSkeletonQuery(): Promise<void> {
     await withProgress(
       async (progress: ProgressCallback) => {
-        const contextStoragePath =
-          this.app.workspaceStoragePath || this.app.globalStoragePath;
         const language = this.languageContextStore.selectedLanguage;
         const skeletonQueryWizard = new SkeletonQueryWizard(
           this.cliServer,
           progress,
           this.app,
           this.databaseManager,
-          contextStoragePath,
+          this.databaseFetcher,
           this.selectedQueryTreeViewItems,
           language,
         );
@@ -485,7 +485,7 @@ export class LocalQueries extends DisposableObject {
           localQueryRun.logger,
         );
 
-        await localQueryRun.complete(results);
+        await localQueryRun.complete(results, progress);
 
         return results;
       } catch (e) {

extensions/ql-vscode/src/local-queries/local-query-run.ts

@@ -25,6 +25,9 @@ import { redactableError } from "../common/errors";
 import type { LocalQueries } from "./local-queries";
 import { tryGetQueryMetadata } from "../codeql-cli/query-metadata";
 import { telemetryListener } from "../common/vscode/telemetry";
+import type { Disposable } from "../common/disposable-object";
+import type { ProgressCallback } from "../common/vscode/progress";
+import { progressUpdate } from "../common/vscode/progress";
 
 function formatResultMessage(result: CoreQueryResults): string {
   switch (result.resultType) {
@@ -61,7 +64,11 @@ export class LocalQueryRun {
     private readonly localQueries: LocalQueries,
     private readonly queryInfo: LocalQueryInfo,
     private readonly dbItem: DatabaseItem,
-    public readonly logger: Logger, // Public so that other clients, like the debug adapter, know where to send log output
+    /**
+     * The logger is only available while the query is running and will be disposed of when the
+     * query completes.
+     */
+    public readonly logger: Logger & Disposable, // Public so that other clients, like the debug adapter, know where to send log output
     private readonly queryHistoryManager: QueryHistoryManager,
     private readonly cliServer: CodeQLCliServer,
   ) {}
@@ -74,24 +81,34 @@ export class LocalQueryRun {
    * This function must be called when the evaluation completes, whether the evaluation was
    * successful or not.
    * */
-  public async complete(results: CoreQueryResults): Promise<void> {
+  public async complete(
+    results: CoreQueryResults,
+    progress: ProgressCallback,
+  ): Promise<void> {
     const evalLogPaths = await this.summarizeEvalLog(
       results.resultType,
       this.outputDir,
       this.logger,
+      progress,
     );
     if (evalLogPaths !== undefined) {
       this.queryInfo.setEvaluatorLogPaths(evalLogPaths);
     }
+    progress(progressUpdate(1, 4, "Getting completed query info"));
     const queryWithResults = await this.getCompletedQueryInfo(results);
+    progress(progressUpdate(2, 4, "Updating query history"));
     this.queryHistoryManager.completeQuery(this.queryInfo, queryWithResults);
+    progress(progressUpdate(3, 4, "Showing results"));
     await this.localQueries.showResultsForCompletedQuery(
       this.queryInfo as CompletedLocalQueryInfo,
       WebviewReveal.Forced,
     );
     // Note we must update the query history view after showing results as the
     // display and sorting might depend on the number of results
+    progress(progressUpdate(4, 4, "Updating query history"));
     await this.queryHistoryManager.refreshTreeView();
+
+    this.logger.dispose();
   }
 
   /**
@@ -102,6 +119,7 @@ export class LocalQueryRun {
       QueryResultType.OTHER_ERROR,
       this.outputDir,
       this.logger,
+      (_) => {},
     );
     if (evalLogPaths !== undefined) {
       this.queryInfo.setEvaluatorLogPaths(evalLogPaths);
@@ -110,6 +128,8 @@ export class LocalQueryRun {
     err.message = `Error running query: ${err.message}`;
     this.queryInfo.failureReason = err.message;
     await this.queryHistoryManager.refreshTreeView();
+
+    this.logger.dispose();
   }
 
   /**
@@ -119,10 +139,12 @@ export class LocalQueryRun {
     resultType: QueryResultType,
     outputDir: QueryOutputDir,
     logger: BaseLogger,
+    progress: ProgressCallback,
   ): Promise<EvaluatorLogPaths | undefined> {
     const evalLogPaths = await generateEvalLogSummaries(
       this.cliServer,
       outputDir,
+      progress,
     );
     if (evalLogPaths !== undefined) {
       if (evalLogPaths.endSummary !== undefined) {

extensions/ql-vscode/src/local-queries/quick-query.ts

@@ -12,7 +12,7 @@ import { UserCancellationException } from "../common/vscode/progress";
 import { getErrorMessage } from "../common/helpers-pure";
 import { FALLBACK_QLPACK_FILENAME, getQlPackFilePath } from "../common/ql";
 import type { App } from "../common/app";
-import type { ExtensionApp } from "../common/vscode/vscode-app";
+import type { ExtensionApp } from "../common/vscode/extension-app";
 import type { QlPackFile } from "../packaging/qlpack-file";
 
 const QUICK_QUERIES_DIR_NAME = "quick-queries";

extensions/ql-vscode/src/local-queries/run-query.ts

@@ -47,21 +47,27 @@ export async function runQuery({
     undefined,
   );
 
-  const completedQuery = await queryRun.evaluate(
-    progress,
-    token,
-    new TeeLogger(queryRunner.logger, queryRun.outputDir.logPath),
+  const teeLogger = new TeeLogger(
+    queryRunner.logger,
+    queryRun.outputDir.logPath,
   );
 
-  if (completedQuery.resultType !== QueryResultType.SUCCESS) {
-    void showAndLogExceptionWithTelemetry(
-      extLogger,
-      telemetryListener,
-      redactableError`Failed to run ${basename(queryPath)} query: ${
-        completedQuery.message ?? "No message"
-      }`,
-    );
-    return;
+  try {
+    const completedQuery = await queryRun.evaluate(progress, token, teeLogger);
+
+    if (completedQuery.resultType !== QueryResultType.SUCCESS) {
+      void showAndLogExceptionWithTelemetry(
+        extLogger,
+        telemetryListener,
+        redactableError`Failed to run ${basename(queryPath)} query: ${
+          completedQuery.message ?? "No message"
+        }`,
+      );
+      return;
+    }
+
+    return completedQuery;
+  } finally {
+    teeLogger.dispose();
   }
-  return completedQuery;
 }

extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts

@@ -19,10 +19,7 @@ import {
   UserCancellationException,
   withProgress,
 } from "../common/vscode/progress";
-import {
-  askForGitHubRepo,
-  downloadGitHubDatabase,
-} from "../databases/database-fetcher";
+import type { DatabaseFetcher } from "../databases/database-fetcher";
 import {
   getQlPackLocation,
   isCodespacesTemplate,
@@ -62,7 +59,7 @@ export class SkeletonQueryWizard {
     private readonly progress: ProgressCallback,
     private readonly app: App,
     private readonly databaseManager: DatabaseManager,
-    private readonly databaseStoragePath: string | undefined,
+    private readonly databaseFetcher: DatabaseFetcher,
     private readonly selectedItems: readonly QueryTreeViewItem[],
     private language: QueryLanguage | undefined = undefined,
   ) {}
@@ -363,10 +360,6 @@ export class SkeletonQueryWizard {
   }
 
   private async downloadDatabase(progress: ProgressCallback) {
-    if (this.databaseStoragePath === undefined) {
-      throw new Error("Database storage path is undefined");
-    }
-
     if (this.language === undefined) {
       throw new Error("Language is undefined");
     }
@@ -378,20 +371,10 @@ export class SkeletonQueryWizard {
     });
 
     const githubRepoNwo = QUERY_LANGUAGE_TO_DATABASE_REPO[this.language];
-    const chosenRepo = await askForGitHubRepo(undefined, githubRepoNwo);
-
-    if (!chosenRepo) {
-      throw new UserCancellationException("No GitHub repository provided");
-    }
-
-    await downloadGitHubDatabase(
-      chosenRepo,
-      this.app,
-      this.databaseManager,
-      this.databaseStoragePath,
+    await this.databaseFetcher.promptImportGithubDatabase(
       progress,
-      this.cliServer,
       this.language,
+      githubRepoNwo,
     );
   }
 

extensions/ql-vscode/src/model-editor/extension-pack-metadata.schema.json

@@ -67,6 +67,9 @@
                 "$ref": "#/definitions/SuiteInstruction"
               }
             },
+            {
+              "$ref": "#/definitions/SuiteInstruction"
+            },
             {
               "type": "null"
             }
@@ -93,19 +96,33 @@
         "include": {
           "type": "object",
           "additionalProperties": {
-            "type": "array",
-            "items": {
-              "type": "string"
-            }
+            "anyOf": [
+              {
+                "type": "array",
+                "items": {
+                  "type": "string"
+                }
+              },
+              {
+                "type": "string"
+              }
+            ]
           }
         },
         "exclude": {
           "type": "object",
           "additionalProperties": {
-            "type": "array",
-            "items": {
-              "type": "string"
-            }
+            "anyOf": [
+              {
+                "type": "array",
+                "items": {
+                  "type": "string"
+                }
+              },
+              {
+                "type": "string"
+              }
+            ]
           }
         },
         "description": {

extensions/ql-vscode/src/model-editor/extension-pack-name.ts

@@ -15,11 +15,19 @@ export function formatPackName(packName: ExtensionPackName): string {
   return `${packName.scope}/${packName.name}`;
 }
 
-export function autoNameExtensionPack(
-  name: string,
-  language: string,
-): ExtensionPackName | undefined {
-  let packName = `${name}-${language}`;
+export function sanitizePackName(userPackName: string): ExtensionPackName {
+  let packName = userPackName;
+
+  packName = packName.trim();
+
+  while (packName.startsWith("/")) {
+    packName = packName.slice(1);
+  }
+
+  while (packName.endsWith("/")) {
+    packName = packName.slice(0, -1);
+  }
+
   if (!packName.includes("/")) {
     packName = `pack/${packName}`;
   }

extensions/ql-vscode/src/model-editor/extension-pack-picker.ts

@@ -2,7 +2,6 @@ import { join } from "path";
 import { outputFile, pathExists, readFile } from "fs-extra";
 import { dump as dumpYaml, load as loadYaml } from "js-yaml";
 import type { CancellationToken } from "vscode";
-import { Uri } from "vscode";
 import Ajv from "ajv";
 import type { CodeQLCliServer } from "../codeql-cli/cli";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
@@ -14,10 +13,17 @@ import { getErrorMessage } from "../common/helpers-pure";
 import type { ExtensionPack } from "./shared/extension-pack";
 import type { NotificationLogger } from "../common/logging";
 import { showAndLogErrorMessage } from "../common/logging";
-import type { ModelConfig } from "../config";
+import type { ModelConfig, ModelConfigPackVariables } from "../config";
 import type { ExtensionPackName } from "./extension-pack-name";
-import { autoNameExtensionPack, formatPackName } from "./extension-pack-name";
-import { autoPickExtensionsDirectory } from "./extensions-workspace-folder";
+import {
+  validatePackName,
+  sanitizePackName,
+  formatPackName,
+} from "./extension-pack-name";
+import {
+  ensurePackLocationIsInWorkspaceFolder,
+  packLocationToAbsolute,
+} from "./extensions-workspace-folder";
 
 import type { ExtensionPackMetadata } from "./extension-pack-metadata";
 import extensionPackMetadataSchemaJson from "./extension-pack-metadata.schema.json";
@@ -27,7 +33,7 @@ const extensionPackValidate = ajv.compile(extensionPackMetadataSchemaJson);
 
 export async function pickExtensionPack(
   cliServer: Pick<CodeQLCliServer, "resolveQlpacks">,
-  databaseItem: Pick<DatabaseItem, "name" | "language">,
+  databaseItem: Pick<DatabaseItem, "name" | "language" | "origin">,
   modelConfig: ModelConfig,
   logger: NotificationLogger,
   progress: ProgressCallback,
@@ -64,29 +70,34 @@ export async function pickExtensionPack(
     maxStep,
   });
 
-  // Get the `codeQL.model.extensionsDirectory` setting for the language
-  const userExtensionsDirectory = modelConfig.getExtensionsDirectory(
-    databaseItem.language,
+  // The default is .github/codeql/extensions/${name}-${language}
+  const packPath = await packLocationToAbsolute(
+    modelConfig.getPackLocation(
+      databaseItem.language,
+      getModelConfigPackVariables(databaseItem),
+    ),
+    logger,
   );
-
-  // If the setting is not set, automatically pick a suitable directory
-  const extensionsDirectory = userExtensionsDirectory
-    ? Uri.file(userExtensionsDirectory)
-    : await autoPickExtensionsDirectory(logger);
-
-  if (!extensionsDirectory) {
+  if (!packPath) {
     return undefined;
   }
 
-  // Generate the name of the extension pack
-  const packName = autoNameExtensionPack(
-    databaseItem.name,
+  await ensurePackLocationIsInWorkspaceFolder(packPath, modelConfig, logger);
+
+  const userPackName = modelConfig.getPackName(
     databaseItem.language,
+    getModelConfigPackVariables(databaseItem),
   );
-  if (!packName) {
+
+  // Generate the name of the extension pack
+  const packName = sanitizePackName(userPackName);
+
+  // Validate that the name isn't too long etc.
+  const packNameError = validatePackName(formatPackName(packName));
+  if (packNameError) {
     void showAndLogErrorMessage(
       logger,
-      `Could not automatically name extension pack for database ${databaseItem.name}`,
+      `Invalid model pack name '${formatPackName(packName)}' for database ${databaseItem.name}: ${packNameError}`,
     );
 
     return undefined;
@@ -139,14 +150,12 @@ export async function pickExtensionPack(
     return undefined;
   }
 
-  const packPath = join(extensionsDirectory.fsPath, packName.name);
-
   if (await pathExists(packPath)) {
     void showAndLogErrorMessage(
       logger,
       `Directory ${packPath} already exists for extension pack ${formatPackName(
         packName,
-      )}`,
+      )}, but wasn't returned by codeql resolve qlpacks --kind extension --no-recursive`,
     );
 
     return undefined;
@@ -155,6 +164,26 @@ export async function pickExtensionPack(
   return writeExtensionPack(packPath, packName, databaseItem.language);
 }
 
+function getModelConfigPackVariables(
+  databaseItem: Pick<DatabaseItem, "name" | "language" | "origin">,
+): ModelConfigPackVariables {
+  const database = databaseItem.name;
+  const language = databaseItem.language;
+  let name = databaseItem.name;
+  let owner = "";
+
+  if (databaseItem.origin?.type === "github") {
+    [owner, name] = databaseItem.origin.repository.split("/");
+  }
+
+  return {
+    database,
+    language,
+    name,
+    owner,
+  };
+}
+
 async function writeExtensionPack(
   packPath: string,
   packName: ExtensionPackName,

extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts

@@ -1,9 +1,12 @@
 import type { WorkspaceFolder } from "vscode";
 import { FileType, Uri, workspace } from "vscode";
 import { getOnDiskWorkspaceFoldersObjects } from "../common/vscode/workspace-folders";
-import { tmpdir } from "../common/files";
+import { containsPath, tmpdir } from "../common/files";
 import type { NotificationLogger } from "../common/logging";
 import { showAndLogErrorMessage } from "../common/logging";
+import { isAbsolute, normalize, resolve } from "path";
+import { nanoid } from "nanoid";
+import type { ModelConfig } from "../config";
 
 /**
  * Returns the ancestors of this path in order from furthest to closest (i.e. root of filesystem to parent directory)
@@ -22,26 +25,17 @@ function getAncestors(uri: Uri): Uri[] {
   return ancestors;
 }
 
-async function getRootWorkspaceDirectory(): Promise<Uri | undefined> {
-  // If there is a valid workspace file, just use its directory as the directory for the extensions
-  const workspaceFile = workspace.workspaceFile;
-  if (workspaceFile?.scheme === "file") {
-    return Uri.joinPath(workspaceFile, "..");
+function findCommonAncestor(uris: Uri[]): Uri | undefined {
+  if (uris.length === 0) {
+    return undefined;
   }
 
-  const allWorkspaceFolders = getOnDiskWorkspaceFoldersObjects();
-
-  // Get the system temp directory and convert it to a URI so it's normalized
-  const systemTmpdir = Uri.file(tmpdir());
-
-  const workspaceFolders = allWorkspaceFolders.filter((folder) => {
-    // Never use a workspace folder that is in the system temp directory
-    return !folder.uri.fsPath.startsWith(systemTmpdir.fsPath);
-  });
+  if (uris.length === 1) {
+    return uris[0];
+  }
 
   // Find the common root directory of all workspace folders by finding the longest common prefix
-  const commonRoot = workspaceFolders.reduce((commonRoot, folder) => {
-    const folderUri = folder.uri;
+  const commonRoot = uris.reduce((commonRoot, folderUri) => {
     const ancestors = getAncestors(folderUri);
 
     const minLength = Math.min(commonRoot.length, ancestors.length);
@@ -55,10 +49,10 @@ async function getRootWorkspaceDirectory(): Promise<Uri | undefined> {
     }
 
     return commonRoot.slice(0, commonLength);
-  }, getAncestors(workspaceFolders[0].uri));
+  }, getAncestors(uris[0]));
 
   if (commonRoot.length === 0) {
-    return await findGitFolder(workspaceFolders);
+    return undefined;
   }
 
   // The path closest to the workspace folders is the last element of the common root
@@ -67,6 +61,54 @@ async function getRootWorkspaceDirectory(): Promise<Uri | undefined> {
   // If we are at the root of the filesystem, we can't go up any further and there's something
   // wrong, so just return undefined
   if (commonRootUri.fsPath === Uri.joinPath(commonRootUri, "..").fsPath) {
+    return undefined;
+  }
+
+  return commonRootUri;
+}
+
+/**
+ * Finds the root directory of this workspace. It is determined
+ * heuristically based on the on-disk workspace folders.
+ *
+ * The heuristic is as follows:
+ * 1. If there is a workspace file (`<basename>.code-workspace`), use the directory containing that file
+ * 2. If there is only 1 workspace folder, use that folder
+ * 3. If there is a common root directory for all workspace folders, use that directory
+ *   - Workspace folders in the system temp directory are ignored
+ *   - If the common root directory is the root of the filesystem, then it's not used
+ * 4. If there is a .git directory in any workspace folder, use the directory containing that .git directory
+ *    for which the .git directory is closest to a workspace folder
+ * 5. If none of the above apply, return `undefined`
+ */
+export async function getRootWorkspaceDirectory(): Promise<Uri | undefined> {
+  // If there is a valid workspace file, just use its directory as the directory for the extensions
+  const workspaceFile = workspace.workspaceFile;
+  if (workspaceFile?.scheme === "file") {
+    return Uri.joinPath(workspaceFile, "..");
+  }
+
+  const allWorkspaceFolders = getOnDiskWorkspaceFoldersObjects();
+
+  if (allWorkspaceFolders.length === 1) {
+    return allWorkspaceFolders[0].uri;
+  }
+
+  // Get the system temp directory and convert it to a URI so it's normalized
+  const systemTmpdir = Uri.file(tmpdir());
+
+  const workspaceFolders = allWorkspaceFolders.filter((folder) => {
+    // Never use a workspace folder that is in the system temp directory
+    return !folder.uri.fsPath.startsWith(systemTmpdir.fsPath);
+  });
+
+  // The path closest to the workspace folders is the last element of the common root
+  const commonRootUri = findCommonAncestor(
+    workspaceFolders.map((folder) => folder.uri),
+  );
+
+  // If there is no common root URI, try to find a .git folder in the workspace folders
+  if (commonRootUri === undefined) {
     return await findGitFolder(workspaceFolders);
   }
 
@@ -126,90 +168,130 @@ async function findGitFolder(
   return closestFolder?.[1];
 }
 
-/**
- * Finds a suitable directory for extension packs to be created in. This will
- * always be a path ending in `.github/codeql/extensions`. The parent directory
- * will be determined heuristically based on the on-disk workspace folders.
- *
- * The heuristic is as follows (`.github/codeql/extensions` is added automatically unless
- * otherwise specified):
- * 1. If there is only 1 workspace folder, use that folder
- * 2. If there is a workspace folder for which the path ends in `.github/codeql/extensions`, use that folder
- *   - If there are multiple such folders, use the first one
- *   - Does not append `.github/codeql/extensions` to the path
- * 3. If there is a workspace file (`<basename>.code-workspace`), use the directory containing that file
- * 4. If there is a common root directory for all workspace folders, use that directory
- *   - Workspace folders in the system temp directory are ignored
- *   - If the common root directory is the root of the filesystem, then it's not used
- * 5. If there is a .git directory in any workspace folder, use the directory containing that .git directory
- *    for which the .git directory is closest to a workspace folder
- * 6. If none of the above apply, return `undefined`
- */
-export async function autoPickExtensionsDirectory(
+export async function packLocationToAbsolute(
+  packLocation: string,
   logger: NotificationLogger,
-): Promise<Uri | undefined> {
-  const workspaceFolders = getOnDiskWorkspaceFoldersObjects();
+): Promise<string | undefined> {
+  let userPackLocation = packLocation.trim();
 
-  // If there are no on-disk workspace folders, we can't do anything
-  if (workspaceFolders.length === 0) {
+  if (!isAbsolute(userPackLocation)) {
+    const rootDirectory = await getRootWorkspaceDirectory();
+    if (!rootDirectory) {
+      void logger.log("Unable to determine root workspace directory");
+
+      return undefined;
+    }
+
+    userPackLocation = resolve(rootDirectory.fsPath, userPackLocation);
+  }
+
+  userPackLocation = normalize(userPackLocation);
+
+  if (!isAbsolute(userPackLocation)) {
+    // This shouldn't happen, but just in case
     void showAndLogErrorMessage(
       logger,
-      `Could not find any on-disk workspace folders. Please ensure that you have opened a folder or workspace.`,
+      `Invalid pack location: ${userPackLocation}`,
     );
-    return undefined;
-  }
-
-  // If there's only 1 workspace folder, use the `.github/codeql/extensions` directory in that folder
-  if (workspaceFolders.length === 1) {
-    return Uri.joinPath(
-      workspaceFolders[0].uri,
-      ".github",
-      "codeql",
-      "extensions",
-    );
-  }
-
-  // Now try to find a workspace folder for which the path ends in `.github/codeql/extensions`
-  const workspaceFolderForExtensions = workspaceFolders.find((folder) =>
-    // Using path instead of fsPath because path always uses forward slashes
-    folder.uri.path.endsWith(".github/codeql/extensions"),
-  );
-  if (workspaceFolderForExtensions) {
-    return workspaceFolderForExtensions.uri;
-  }
-
-  // Get the root workspace directory, i.e. the common root directory of all workspace folders
-  const rootDirectory = await getRootWorkspaceDirectory();
-  if (!rootDirectory) {
-    void logger.log("Unable to determine root workspace directory");
 
     return undefined;
   }
 
-  // We'll create a new workspace folder for the extensions in the root workspace directory
-  // at `.github/codeql/extensions`
-  const extensionsUri = Uri.joinPath(
-    rootDirectory,
-    ".github",
-    "codeql",
-    "extensions",
+  // If we are at the root of the filesystem, then something is wrong since
+  // this should never be the location of a pack
+  if (userPackLocation === resolve(userPackLocation, "..")) {
+    void showAndLogErrorMessage(
+      logger,
+      `Invalid pack location: ${userPackLocation}`,
+    );
+
+    return undefined;
+  }
+
+  return userPackLocation;
+}
+
+/**
+ * This function will try to add the pack location as a workspace folder if it's not already in a
+ * workspace folder and the workspace is a multi-root workspace.
+ */
+export async function ensurePackLocationIsInWorkspaceFolder(
+  packLocation: string,
+  modelConfig: ModelConfig,
+  logger: NotificationLogger,
+): Promise<void> {
+  const workspaceFolders = getOnDiskWorkspaceFoldersObjects();
+
+  const existsInWorkspaceFolder = workspaceFolders.some((folder) =>
+    containsPath(folder.uri.fsPath, packLocation),
   );
 
+  if (existsInWorkspaceFolder) {
+    // If the pack location is already in a workspace folder, we don't need to do anything
+    return;
+  }
+
+  if (workspace.workspaceFile === undefined) {
+    // If we're not in a workspace, we can't add a workspace folder without reloading the window,
+    // so we'll not do anything
+    return;
+  }
+
+  // To find the "correct" directory to add as a workspace folder, we'll generate a few different
+  // pack locations and find the common ancestor of the directories. This is the directory that
+  // we'll add as a workspace folder.
+
+  // Generate a few different pack locations to get an accurate common ancestor
+  const otherPackLocations = await Promise.all(
+    Array.from({ length: 3 }).map(() =>
+      packLocationToAbsolute(
+        modelConfig.getPackLocation(nanoid(), {
+          database: nanoid(),
+          language: nanoid(),
+          name: nanoid(),
+          owner: nanoid(),
+        }),
+        logger,
+      ),
+    ),
+  );
+
+  const otherPackLocationUris = otherPackLocations
+    .filter((loc): loc is string => loc !== undefined)
+    .map((loc) => Uri.file(loc));
+
+  if (otherPackLocationUris.length === 0) {
+    void logger.log(
+      `Failed to generate different pack locations, not adding workspace folder.`,
+    );
+    return;
+  }
+
+  const commonRootUri = findCommonAncestor([
+    Uri.file(packLocation),
+    ...otherPackLocationUris,
+  ]);
+
+  if (commonRootUri === undefined) {
+    void logger.log(
+      `Failed to find common ancestor for ${packLocation} and ${otherPackLocationUris[0].fsPath}, not adding workspace folder.`,
+    );
+    return;
+  }
+
   if (
     !workspace.updateWorkspaceFolders(
       workspace.workspaceFolders?.length ?? 0,
       0,
       {
         name: "CodeQL Extension Packs",
-        uri: extensionsUri,
+        uri: commonRootUri,
       },
     )
   ) {
     void logger.log(
-      `Failed to add workspace folder for extensions at ${extensionsUri.fsPath}`,
+      `Failed to add workspace folder for extensions at ${commonRootUri.fsPath}`,
     );
-    return undefined;
+    return;
   }
-
-  return extensionsUri;
 }

extensions/ql-vscode/src/model-editor/languages/csharp/index.ts

@@ -0,0 +1,21 @@
+import type { ModelsAsDataLanguage } from "../models-as-data";
+import { staticLanguage } from "../static";
+
+export const csharp: ModelsAsDataLanguage = {
+  ...staticLanguage,
+  predicates: {
+    ...staticLanguage.predicates,
+    sink: {
+      ...staticLanguage.predicates.sink,
+    },
+    source: {
+      ...staticLanguage.predicates.source,
+      supportedKinds: [
+        ...staticLanguage.predicates.source.supportedKinds,
+        // https://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L122-L123
+        "file-write",
+        "windows-registry",
+      ],
+    },
+  },
+};

extensions/ql-vscode/src/model-editor/languages/java/index.ts

@@ -0,0 +1,42 @@
+import type { ModelsAsDataLanguage } from "../models-as-data";
+import { staticLanguage } from "../static";
+
+export const java: ModelsAsDataLanguage = {
+  ...staticLanguage,
+  predicates: {
+    ...staticLanguage.predicates,
+    sink: {
+      ...staticLanguage.predicates.sink,
+      supportedKinds: [
+        ...staticLanguage.predicates.sink.supportedKinds,
+        // https://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L32-L37
+        "bean-validation",
+        "fragment-injection",
+        "groovy-injection",
+        "hostname-verification",
+        "information-leak",
+        "intent-redirection",
+        "jexl-injection",
+        "jndi-injection",
+        "mvel-injection",
+        "notification",
+        "ognl-injection",
+        "pending-intents",
+        "response-splitting",
+        "trust-boundary-violation",
+        "template-injection",
+        "xpath-injection",
+        "xslt-injection",
+      ],
+    },
+    source: {
+      ...staticLanguage.predicates.source,
+      supportedKinds: [
+        ...staticLanguage.predicates.source.supportedKinds,
+        // https://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L120-L121
+        "android-external-storage-dir",
+        "contentprovider",
+      ],
+    },
+  },
+};

extensions/ql-vscode/src/model-editor/languages/languages.ts

@@ -3,13 +3,14 @@ import type {
   ModelsAsDataLanguage,
   ModelsAsDataLanguagePredicates,
 } from "./models-as-data";
+import { csharp } from "./csharp";
+import { java } from "./java";
 import { python } from "./python";
 import { ruby } from "./ruby";
-import { staticLanguage } from "./static";
 
 const languages: Partial<Record<QueryLanguage, ModelsAsDataLanguage>> = {
-  [QueryLanguage.CSharp]: staticLanguage,
-  [QueryLanguage.Java]: staticLanguage,
+  [QueryLanguage.CSharp]: csharp,
+  [QueryLanguage.Java]: java,
   [QueryLanguage.Python]: python,
   [QueryLanguage.Ruby]: ruby,
 };

extensions/ql-vscode/src/model-editor/languages/models-as-data.ts

@@ -20,7 +20,7 @@ import type { AccessPathSuggestionRow } from "../suggestions";
 // This is a subset of the model config that doesn't import the vscode module.
 // It only includes settings that are actually used.
 export type ModelConfig = {
-  showTypeModels: boolean;
+  flowGeneration: boolean;
 };
 
 /**
@@ -32,12 +32,12 @@ export type ModelConfig = {
  */
 export function createModelConfig(modelConfig: ModelConfig): ModelConfig {
   return {
-    showTypeModels: modelConfig.showTypeModels,
+    flowGeneration: modelConfig.flowGeneration,
   };
 }
 
 export const defaultModelConfig: ModelConfig = {
-  showTypeModels: false,
+  flowGeneration: false,
 };
 
 type GenerateMethodDefinition<T> = (method: T) => DataTuple[];
@@ -105,15 +105,34 @@ type ParseResultsToYaml = (
   logger: BaseLogger,
 ) => ModelExtension[];
 
+export enum AutoModelGenerationType {
+  /**
+   * Auto model generation is disabled and will not be run.
+   */
+  Disabled = "disabled",
+  /**
+   * The models are generated to a separate file (suffixed with .model.generated.yml).
+   */
+  SeparateFile = "separateFile",
+  /**
+   * The models are added as a model in the model editor, but are not automatically saved.
+   * The user can view them and choose to save them.
+   */
+  Models = "models",
+}
+
 type ModelsAsDataLanguageAutoModelGeneration = {
   queryConstraints: (mode: Mode) => QueryConstraints;
   filterQueries?: (queryPath: string) => boolean;
+  /**
+   * This function is only used when type is `separateFile`.
+   */
   parseResultsToYaml: ParseResultsToYaml;
   /**
-   * By default, auto model generation is enabled for all modes. This function can be used to
-   * override that behavior.
+   * This function is only used when type is `models`.
    */
-  enabled?: (context: GenerationContext) => boolean;
+  parseResults: ParseGenerationResults;
+  type: (context: GenerationContext) => AutoModelGenerationType;
 };
 
 type ModelsAsDataLanguageAccessPathSuggestions = {

extensions/ql-vscode/src/model-editor/languages/python/access-paths.ts

@@ -112,7 +112,10 @@ export function pythonPath(
 export function pythonEndpointType(
   method: Omit<MethodDefinition, "endpointType">,
 ): EndpointType {
-  if (method.methodParameters.startsWith("(self,")) {
+  if (
+    method.methodParameters.startsWith("(self,") ||
+    method.methodParameters === "(self)"
+  ) {
     return EndpointType.Method;
   }
   return EndpointType.Function;

extensions/ql-vscode/src/model-editor/languages/python/index.ts

@@ -177,28 +177,49 @@ export const python: ModelsAsDataLanguage = {
     // Argument and Parameter are equivalent in Python, but we'll use Argument in the model editor
     const argumentsList = getArgumentsList(method.methodParameters).map(
       (argument, index): MethodArgument => {
-        if (argument.endsWith(":")) {
+        if (
+          method.endpointType === EndpointType.Method &&
+          argument === "self" &&
+          index === 0
+        ) {
           return {
-            path: `Argument[${argument}]`,
-            label: `Argument[${argument}]`,
+            path: "Argument[self]",
+            label: "Argument[self]: self",
           };
         }
 
+        // If this is a method, self does not count as an argument index, so we
+        // should start at 0 for the second argument
+        if (method.endpointType === EndpointType.Method) {
+          index -= 1;
+        }
+
+        // Keyword-only arguments end with `:` in the query
+        if (argument.endsWith(":")) {
+          return {
+            path: `Argument[${argument}]`,
+            label: `Argument[${argument}]: ${argument.substring(0, argument.length - 1)}`,
+          };
+        }
+
+        // Positional-only arguments end with `/` in the query
+        if (argument.endsWith("/")) {
+          return {
+            path: `Argument[${index}]`,
+            label: `Argument[${index}]: ${argument.substring(0, argument.length - 1)}`,
+          };
+        }
+
+        // All other arguments are both keyword and positional
         return {
-          path: `Argument[${index}]`,
-          label: `Argument[${index}]: ${argument}`,
+          path: `Argument[${index},${argument}:]`,
+          label: `Argument[${index},${argument}:]: ${argument}`,
         };
       },
     );
 
     return {
-      options: [
-        {
-          path: "Argument[self]",
-          label: "Argument[self]",
-        },
-        ...argumentsList,
-      ],
+      options: argumentsList,
       // If there are no arguments, we will default to "Argument[self]"
       defaultArgumentPath:
         argumentsList.length > 0 ? argumentsList[0].path : "Argument[self]",

extensions/ql-vscode/src/model-editor/languages/ruby/generate.ts

@@ -1,9 +1,6 @@
 import type { BaseLogger } from "../../../common/logging";
 import type { DecodedBqrs } from "../../../common/bqrs-cli-types";
-import type {
-  GenerationContext,
-  ModelsAsDataLanguage,
-} from "../models-as-data";
+import type { ModelsAsDataLanguage } from "../models-as-data";
 import type { ModeledMethod } from "../../modeled-method";
 import type { DataTuple } from "../../model-extension-file";
 
@@ -12,21 +9,10 @@ export function parseGenerateModelResults(
   bqrs: DecodedBqrs,
   modelsAsDataLanguage: ModelsAsDataLanguage,
   logger: BaseLogger,
-  { config }: GenerationContext,
 ): ModeledMethod[] {
   const modeledMethods: ModeledMethod[] = [];
 
   for (const resultSetName in bqrs) {
-    if (
-      resultSetName ===
-        modelsAsDataLanguage.predicates.type?.extensiblePredicate &&
-      !config.showTypeModels
-    ) {
-      // Don't load generated type results when type models are hidden. These are already
-      // automatically generated on start-up.
-      continue;
-    }
-
     const definition = Object.values(modelsAsDataLanguage.predicates).find(
       (definition) => definition.extensiblePredicate === resultSetName,
     );

extensions/ql-vscode/src/model-editor/languages/ruby/index.ts

@@ -1,4 +1,5 @@
 import type { ModelsAsDataLanguage } from "../models-as-data";
+import { AutoModelGenerationType } from "../models-as-data";
 import { sharedExtensiblePredicates, sharedKinds } from "../shared";
 import { Mode } from "../../shared/mode";
 import { parseGenerateModelResults } from "./generate";
@@ -169,7 +170,6 @@ export const ruby: ModelsAsDataLanguage = {
           methodParameters: "",
         };
       },
-      isHidden: ({ config }) => !config.showTypeModels,
     },
   },
   modelGeneration: {
@@ -209,9 +209,32 @@ export const ruby: ModelsAsDataLanguage = {
         },
       ];
     },
+    parseResults: (queryPath, bqrs, modelsAsDataLanguage, logger) => {
+      // Only parse type models when automatically generating models
+      const typePredicate = modelsAsDataLanguage.predicates.type;
+      if (!typePredicate) {
+        throw new Error("Type predicate not found");
+      }
+
+      const typeTuples = bqrs[typePredicate.extensiblePredicate];
+      if (!typeTuples) {
+        return [];
+      }
+
+      return parseGenerateModelResults(
+        queryPath,
+        {
+          [typePredicate.extensiblePredicate]: typeTuples,
+        },
+        modelsAsDataLanguage,
+        logger,
+      );
+    },
     // Only enabled for framework mode when type models are hidden
-    enabled: ({ mode, config }) =>
-      mode === Mode.Framework && !config.showTypeModels,
+    type: ({ mode }) =>
+      mode === Mode.Framework
+        ? AutoModelGenerationType.Models
+        : AutoModelGenerationType.Disabled,
   },
   accessPathSuggestions: {
     queryConstraints: (mode) => ({

extensions/ql-vscode/src/model-editor/languages/shared.ts

@@ -6,10 +6,13 @@ export const sharedExtensiblePredicates = {
 };
 
 export const sharedKinds = {
-  source: ["local", "remote"],
+  // https://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L118-L119
+  source: ["local", "remote", "file", "commandargs", "database", "environment"],
+  // Bhttps://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L28-L31
   sink: [
     "code-injection",
     "command-injection",
+    "environment-injection",
     "file-content-store",
     "html-injection",
     "js-injection",
@@ -20,6 +23,8 @@ export const sharedKinds = {
     "sql-injection",
     "url-redirection",
   ],
+  // https://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L142-L143
   summary: ["taint", "value"],
+  // https://github.com/github/codeql/blob/0c5ea975a4c4dc5c439b908c006e440cb9bdf926/shared/mad/codeql/mad/ModelValidation.qll#L155-L156
   neutral: ["summary", "source", "sink"],
 };

extensions/ql-vscode/src/model-editor/languages/static/index.ts

@@ -10,7 +10,7 @@ function readRowToMethod(row: DataTuple[]): string {
   return `${row[0]}.${row[1]}#${row[3]}${row[4]}`;
 }
 
-export const staticLanguage: ModelsAsDataLanguage = {
+export const staticLanguage = {
   createMethodSignature: ({
     packageName,
     typeName,
@@ -168,4 +168,4 @@ export const staticLanguage: ModelsAsDataLanguage = {
         argumentsList.length > 0 ? argumentsList[0].path : "Argument[this]",
     };
   },
-};
+} satisfies ModelsAsDataLanguage;

extensions/ql-vscode/src/model-editor/method-modeling/method-modeling-view-provider.ts

@@ -6,7 +6,7 @@ import { telemetryListener } from "../../common/vscode/telemetry";
 import { showAndLogExceptionWithTelemetry } from "../../common/logging/notifications";
 import type { App } from "../../common/app";
 import { redactableError } from "../../common/errors";
-import type { Method } from "../method";
+import type { Method, MethodSignature } from "../method";
 import type { ModelingStore } from "../modeling-store";
 import { AbstractWebviewViewProvider } from "../../common/vscode/abstract-webview-view-provider";
 import { assertNever } from "../../common/helpers-pure";
@@ -163,7 +163,7 @@ export class MethodModelingViewProvider extends AbstractWebviewViewProvider<
     }
   }
 
-  private async revealInModelEditor(method: Method): Promise<void> {
+  private async revealInModelEditor(method: MethodSignature): Promise<void> {
     if (!this.databaseItem) {
       return;
     }

extensions/ql-vscode/src/model-editor/model-alerts/alert-processor.ts

@@ -0,0 +1,100 @@
+import type { AnalysisAlert } from "../../variant-analysis/shared/analysis-result";
+import type { ModeledMethod } from "../modeled-method";
+import { EndpointType } from "../method";
+import type { ModelAlerts } from "./model-alerts";
+import type {
+  VariantAnalysis,
+  VariantAnalysisScannedRepositoryResult,
+} from "../../variant-analysis/shared/variant-analysis";
+
+/**
+ * Calculate which model has contributed to each alert.
+ * @param alerts The alerts to process.
+ * @param repoResults The analysis results for each repo.
+ * @returns The alerts grouped by modeled method.
+ */
+export function calculateModelAlerts(
+  variantAnalysis: VariantAnalysis,
+  repoResults: VariantAnalysisScannedRepositoryResult[],
+): ModelAlerts[] {
+  // For now we just return some mock data, but once we have provenance information
+  // we'll be able to calculate this properly based on the alerts that are passed in
+  // and potentially some other information.
+
+  const modelAlerts: ModelAlerts[] = [];
+
+  const repoMap = new Map<number, string>();
+  for (const scannedRepo of variantAnalysis.scannedRepos || []) {
+    repoMap.set(scannedRepo.repository.id, scannedRepo.repository.fullName);
+  }
+
+  for (const [i, repoResult] of repoResults.entries()) {
+    const results = repoResult.interpretedResults || [];
+    const repository = {
+      id: repoResult.repositoryId,
+      fullName: repoMap.get(repoResult.repositoryId) || "",
+    };
+
+    const alerts = results.map(() => {
+      return {
+        alert: createMockAlert(),
+        repository,
+      };
+    });
+
+    modelAlerts.push({
+      model: createModeledMethod(i.toString()),
+      alerts,
+    });
+  }
+
+  return modelAlerts;
+}
+
+function createModeledMethod(suffix: string): ModeledMethod {
+  return {
+    libraryVersion: "1.6.0",
+    signature: `org.sql2o.Connection#createQuery${suffix}(String)`,
+    endpointType: EndpointType.Method,
+    packageName: "org.sql2o",
+    typeName: "Connection",
+    methodName: `createQuery${suffix}`,
+    methodParameters: "(String)",
+    type: "sink",
+    input: "Argument[0]",
+    kind: "path-injection",
+    provenance: "manual",
+  };
+}
+
+function createMockAlert(): AnalysisAlert {
+  return {
+    message: {
+      tokens: [
+        {
+          t: "text",
+          text: "This is an empty block.",
+        },
+      ],
+    },
+    shortDescription: "This is an empty block.",
+    fileLink: {
+      fileLinkPrefix:
+        "https://github.com/expressjs/express/blob/33e8dc303af9277f8a7e4f46abfdcb5e72f6797b",
+      filePath: "test/app.options.js",
+    },
+    severity: "Warning",
+    codeSnippet: {
+      startLine: 10,
+      endLine: 14,
+      text: "    app.del('/', function(){});\n    app.get('/users', function(req, res){});\n    app.put('/users', function(req, res){});\n\n    request(app)\n",
+    },
+    highlightedRegion: {
+      startLine: 12,
+      startColumn: 41,
+      endLine: 12,
+      endColumn: 43,
+    },
+    codeFlows: [],
+  };
+}

extensions/ql-vscode/src/model-editor/model-alerts/model-alerts-view.ts

@@ -18,9 +18,10 @@ import type { ExtensionPack } from "../shared/extension-pack";
 import type {
   VariantAnalysis,
   VariantAnalysisScannedRepositoryResult,
-  VariantAnalysisScannedRepositoryState,
 } from "../../variant-analysis/shared/variant-analysis";
 import type { AppEvent, AppEventEmitter } from "../../common/events";
+import type { ModeledMethod } from "../modeled-method";
+import type { MethodSignature } from "../method";
 
 export class ModelAlertsView extends AbstractWebview<
   ToModelAlertsMessage,
@@ -49,12 +50,15 @@ export class ModelAlertsView extends AbstractWebview<
       this.onEvaluationRunStopClickedEventEmitter.event;
   }
 
-  public async showView() {
+  public async showView(
+    reposResults: VariantAnalysisScannedRepositoryResult[],
+  ) {
     const panel = await this.getPanel();
     panel.reveal(undefined, true);
 
     await this.waitForPanelLoaded();
     await this.setViewState();
+    await this.setReposResults(reposResults);
   }
 
   protected async getPanelConfig(): Promise<WebviewPanelConfig> {
@@ -91,9 +95,18 @@ export class ModelAlertsView extends AbstractWebview<
       case "openModelPack":
         await this.app.commands.execute("revealInExplorer", Uri.file(msg.path));
         break;
+      case "openActionsLogs":
+        await this.app.commands.execute(
+          "codeQLModelAlerts.openVariantAnalysisLogs",
+          msg.variantAnalysisId,
+        );
+        break;
       case "stopEvaluationRun":
         await this.stopEvaluationRun();
         break;
+      case "revealInModelEditor":
+        await this.revealInModelEditor(msg.method);
+        break;
       default:
         assertNever(msg);
     }
@@ -108,7 +121,7 @@ export class ModelAlertsView extends AbstractWebview<
     });
   }
 
-  public async updateVariantAnalysis(
+  public async setVariantAnalysis(
     variantAnalysis: VariantAnalysis,
   ): Promise<void> {
     if (!this.isShowingPanel) {
@@ -121,21 +134,8 @@ export class ModelAlertsView extends AbstractWebview<
     });
   }
 
-  public async updateRepoState(
-    repoState: VariantAnalysisScannedRepositoryState,
-  ): Promise<void> {
-    if (!this.isShowingPanel) {
-      return;
-    }
-
-    await this.postMessage({
-      t: "setRepoStates",
-      repoStates: [repoState],
-    });
-  }
-
-  public async updateRepoResults(
-    repositoryResult: VariantAnalysisScannedRepositoryResult,
+  public async setReposResults(
+    repoResults: VariantAnalysisScannedRepositoryResult[],
   ): Promise<void> {
     if (!this.isShowingPanel) {
       return;
@@ -143,7 +143,7 @@ export class ModelAlertsView extends AbstractWebview<
 
     await this.postMessage({
       t: "setRepoResults",
-      repoResults: [repositoryResult],
+      repoResults,
     });
   }
 
@@ -167,9 +167,39 @@ export class ModelAlertsView extends AbstractWebview<
         }
       }),
     );
+
+    this.push(
+      this.modelingEvents.onRevealInModelAlertsView(async (event) => {
+        if (event.dbUri === this.dbItem.databaseUri.toString()) {
+          await this.revealMethod(event.modeledMethod);
+        }
+      }),
+    );
   }
 
   private async stopEvaluationRun() {
     this.onEvaluationRunStopClickedEventEmitter.fire();
   }
+
+  private async revealInModelEditor(method: MethodSignature): Promise<void> {
+    if (!this.dbItem) {
+      return;
+    }
+
+    this.modelingEvents.fireRevealInModelEditorEvent(
+      this.dbItem.databaseUri.toString(),
+      method,
+    );
+  }
+
+  private async revealMethod(method: ModeledMethod): Promise<void> {
+    const panel = await this.getPanel();
+
+    panel?.reveal();
+
+    await this.postMessage({
+      t: "revealModel",
+      modeledMethod: method,
+    });
+  }
 }

extensions/ql-vscode/src/model-editor/model-alerts/model-alerts.ts

@@ -0,0 +1,13 @@
+import type { AnalysisAlert } from "../../variant-analysis/shared/analysis-result";
+import type { ModeledMethod } from "../modeled-method";
+
+export interface ModelAlerts {
+  model: ModeledMethod;
+  alerts: Array<{
+    alert: AnalysisAlert;
+    repository: {
+      id: number;
+      fullName: string;
+    };
+  }>;
+}

extensions/ql-vscode/src/model-editor/model-editor-module.ts

@@ -32,6 +32,7 @@ import { INITIAL_MODE } from "./shared/mode";
 import { isSupportedLanguage } from "./supported-languages";
 import { DefaultNotifier, checkConsistency } from "./consistency-check";
 import type { VariantAnalysisManager } from "../variant-analysis/variant-analysis-manager";
+import type { DatabaseFetcher } from "../databases/database-fetcher";
 
 export class ModelEditorModule extends DisposableObject {
   private readonly queryStorageDir: string;
@@ -42,6 +43,7 @@ export class ModelEditorModule extends DisposableObject {
   private constructor(
     private readonly app: App,
     private readonly databaseManager: DatabaseManager,
+    private readonly databaseFetcher: DatabaseFetcher,
     private readonly variantAnalysisManager: VariantAnalysisManager,
     private readonly cliServer: CodeQLCliServer,
     private readonly queryRunner: QueryRunner,
@@ -65,6 +67,7 @@ export class ModelEditorModule extends DisposableObject {
   public static async initialize(
     app: App,
     databaseManager: DatabaseManager,
+    databaseFetcher: DatabaseFetcher,
     variantAnalysisManager: VariantAnalysisManager,
     cliServer: CodeQLCliServer,
     queryRunner: QueryRunner,
@@ -73,6 +76,7 @@ export class ModelEditorModule extends DisposableObject {
     const modelEditorModule = new ModelEditorModule(
       app,
       databaseManager,
+      databaseFetcher,
       variantAnalysisManager,
       cliServer,
       queryRunner,
@@ -236,6 +240,7 @@ export class ModelEditorModule extends DisposableObject {
             this.modelingEvents,
             this.modelConfig,
             this.databaseManager,
+            this.databaseFetcher,
             this.variantAnalysisManager,
             this.cliServer,
             this.queryRunner,

extensions/ql-vscode/src/model-editor/model-editor-view.ts

@@ -29,14 +29,14 @@ import type {
 } from "../databases/local-databases";
 import type { CodeQLCliServer } from "../codeql-cli/cli";
 import { asError, assertNever, getErrorMessage } from "../common/helpers-pure";
-import { promptImportGithubDatabase } from "../databases/database-fetcher";
+import type { DatabaseFetcher } from "../databases/database-fetcher";
 import type { App } from "../common/app";
 import { redactableError } from "../common/errors";
 import {
   externalApiQueriesProgressMaxStep,
   runModelEditorQueries,
 } from "./model-editor-queries";
-import type { Method } from "./method";
+import type { MethodSignature } from "./method";
 import type { ModeledMethod } from "./modeled-method";
 import type { ExtensionPack } from "./shared/extension-pack";
 import type { ModelConfigListener } from "../config";
@@ -54,7 +54,11 @@ import { telemetryListener } from "../common/vscode/telemetry";
 import type { ModelingStore } from "./modeling-store";
 import type { ModelingEvents } from "./modeling-events";
 import type { ModelsAsDataLanguage } from "./languages";
-import { createModelConfig, getModelsAsDataLanguage } from "./languages";
+import {
+  AutoModelGenerationType,
+  createModelConfig,
+  getModelsAsDataLanguage,
+} from "./languages";
 import { runGenerateQueries } from "./generate";
 import { ResponseError } from "vscode-jsonrpc";
 import { LSPErrorCodes } from "vscode-languageclient";
@@ -86,6 +90,7 @@ export class ModelEditorView extends AbstractWebview<
     private readonly modelingEvents: ModelingEvents,
     private readonly modelConfig: ModelConfigListener,
     private readonly databaseManager: DatabaseManager,
+    private readonly databaseFetcher: DatabaseFetcher,
     private readonly variantAnalysisManager: VariantAnalysisManager,
     private readonly cliServer: CodeQLCliServer,
     private readonly queryRunner: QueryRunner,
@@ -273,7 +278,6 @@ export class ModelEditorView extends AbstractWebview<
                 modeledMethods,
                 mode,
                 this.cliServer,
-                this.modelConfig,
                 this.app.logger,
               );
 
@@ -347,17 +351,7 @@ export class ModelEditorView extends AbstractWebview<
           withProgress((progress) => this.loadMethods(progress), {
             cancellable: false,
           }),
-          // Only load access path suggestions if the feature is enabled
-          this.modelConfig.enableAccessPathSuggestions
-            ? withProgress(
-                (progress) => this.loadAccessPathSuggestions(progress),
-                {
-                  cancellable: false,
-                  location: ProgressLocation.Window,
-                  title: "Loading access path suggestions",
-                },
-              )
-            : undefined,
+          this.loadAccessPathSuggestions(),
         ]);
         void telemetryListener?.sendUIInteraction("model-editor-switch-modes");
 
@@ -384,6 +378,9 @@ export class ModelEditorView extends AbstractWebview<
       case "openModelAlertsView":
         await this.modelEvaluator.openModelAlertsView();
         break;
+      case "revealInModelAlertsView":
+        await this.modelEvaluator.revealInModelAlertsView(msg.modeledMethod);
+        break;
       case "telemetry":
         telemetryListener?.sendUIInteraction(msg.action);
         break;
@@ -412,14 +409,7 @@ export class ModelEditorView extends AbstractWebview<
         await this.generateModeledMethodsOnStartup();
       }),
       this.loadExistingModeledMethods(),
-      // Only load access path suggestions if the feature is enabled
-      this.modelConfig.enableAccessPathSuggestions
-        ? withProgress((progress) => this.loadAccessPathSuggestions(progress), {
-            cancellable: false,
-            location: ProgressLocation.Window,
-            title: "Loading access path suggestions",
-          })
-        : undefined,
+      this.loadAccessPathSuggestions(),
     ]);
   }
 
@@ -431,7 +421,7 @@ export class ModelEditorView extends AbstractWebview<
     this.panel?.reveal();
   }
 
-  public async revealMethod(method: Method): Promise<void> {
+  public async revealMethod(method: MethodSignature): Promise<void> {
     this.panel?.reveal();
 
     await this.postMessage({
@@ -496,7 +486,6 @@ export class ModelEditorView extends AbstractWebview<
         this.extensionPack,
         this.language,
         this.cliServer,
-        this.modelConfig,
         this.app.logger,
       );
       this.modelingStore.setModeledMethods(this.databaseItem, modeledMethods);
@@ -564,9 +553,7 @@ export class ModelEditorView extends AbstractWebview<
     }
   }
 
-  protected async loadAccessPathSuggestions(
-    progress: ProgressCallback,
-  ): Promise<void> {
+  protected async loadAccessPathSuggestions(): Promise<void> {
     const mode = this.modelingStore.getMode(this.databaseItem);
 
     const modelsAsDataLanguage = getModelsAsDataLanguage(this.language);
@@ -575,46 +562,55 @@ export class ModelEditorView extends AbstractWebview<
       return;
     }
 
-    try {
-      const suggestions = await runSuggestionsQuery(mode, {
-        parseResults: (results) =>
-          accessPathSuggestions.parseResults(
-            results,
-            modelsAsDataLanguage,
+    await withProgress(
+      async (progress) => {
+        try {
+          const suggestions = await runSuggestionsQuery(mode, {
+            parseResults: (results) =>
+              accessPathSuggestions.parseResults(
+                results,
+                modelsAsDataLanguage,
+                this.app.logger,
+              ),
+            queryConstraints: accessPathSuggestions.queryConstraints(mode),
+            cliServer: this.cliServer,
+            queryRunner: this.queryRunner,
+            queryStorageDir: this.queryStorageDir,
+            databaseItem: this.databaseItem,
+            progress,
+            token: this.cancellationTokenSource.token,
+            logger: this.app.logger,
+          });
+
+          if (!suggestions) {
+            return;
+          }
+
+          const options: AccessPathSuggestionOptions = {
+            input: parseAccessPathSuggestionRowsToOptions(suggestions.input),
+            output: parseAccessPathSuggestionRowsToOptions(suggestions.output),
+          };
+
+          await this.postMessage({
+            t: "setAccessPathSuggestions",
+            accessPathSuggestions: options,
+          });
+        } catch (e: unknown) {
+          void showAndLogExceptionWithTelemetry(
             this.app.logger,
-          ),
-        queryConstraints: accessPathSuggestions.queryConstraints(mode),
-        cliServer: this.cliServer,
-        queryRunner: this.queryRunner,
-        queryStorageDir: this.queryStorageDir,
-        databaseItem: this.databaseItem,
-        progress,
-        token: this.cancellationTokenSource.token,
-        logger: this.app.logger,
-      });
-
-      if (!suggestions) {
-        return;
-      }
-
-      const options: AccessPathSuggestionOptions = {
-        input: parseAccessPathSuggestionRowsToOptions(suggestions.input),
-        output: parseAccessPathSuggestionRowsToOptions(suggestions.output),
-      };
-
-      await this.postMessage({
-        t: "setAccessPathSuggestions",
-        accessPathSuggestions: options,
-      });
-    } catch (e: unknown) {
-      void showAndLogExceptionWithTelemetry(
-        this.app.logger,
-        this.app.telemetry,
-        redactableError(
-          asError(e),
-        )`Failed to fetch access path suggestions: ${getErrorMessage(e)}`,
-      );
-    }
+            this.app.telemetry,
+            redactableError(
+              asError(e),
+            )`Failed to fetch access path suggestions: ${getErrorMessage(e)}`,
+          );
+        }
+      },
+      {
+        cancellable: false,
+        location: ProgressLocation.Window,
+        title: "Loading access path suggestions",
+      },
+    );
   }
 
   protected async generateModeledMethods(): Promise<void> {
@@ -706,10 +702,12 @@ export class ModelEditorView extends AbstractWebview<
       return;
     }
 
-    if (
-      autoModelGeneration.enabled &&
-      !autoModelGeneration.enabled({ mode, config: this.modelConfig })
-    ) {
+    const autoModelType = autoModelGeneration.type({
+      mode,
+      config: this.modelConfig,
+    });
+
+    if (autoModelType === AutoModelGenerationType.Disabled) {
       return;
     }
 
@@ -730,14 +728,37 @@ export class ModelEditorView extends AbstractWebview<
             queryConstraints: autoModelGeneration.queryConstraints(mode),
             filterQueries: autoModelGeneration.filterQueries,
             onResults: (queryPath, results) => {
-              const extensions = autoModelGeneration.parseResultsToYaml(
-                queryPath,
-                results,
-                modelsAsDataLanguage,
-                this.app.logger,
-              );
+              switch (autoModelType) {
+                case AutoModelGenerationType.SeparateFile: {
+                  const extensions = autoModelGeneration.parseResultsToYaml(
+                    queryPath,
+                    results,
+                    modelsAsDataLanguage,
+                    this.app.logger,
+                  );
 
-              extensionFile.extensions.push(...extensions);
+                  extensionFile.extensions.push(...extensions);
+                  break;
+                }
+                case AutoModelGenerationType.Models: {
+                  const modeledMethods = autoModelGeneration.parseResults(
+                    queryPath,
+                    results,
+                    modelsAsDataLanguage,
+                    this.app.logger,
+                    {
+                      mode,
+                      config: this.modelConfig,
+                    },
+                  );
+
+                  this.addModeledMethodsFromArray(modeledMethods);
+                  break;
+                }
+                default: {
+                  assertNever(autoModelType);
+                }
+              }
             },
             cliServer: this.cliServer,
             queryRunner: this.queryRunner,
@@ -757,22 +778,24 @@ export class ModelEditorView extends AbstractWebview<
           return;
         }
 
-        progress({
-          step: 4000,
-          maxStep: 4000,
-          message: "Saving generated models",
-        });
+        if (autoModelType === AutoModelGenerationType.SeparateFile) {
+          progress({
+            step: 4000,
+            maxStep: 4000,
+            message: "Saving generated models",
+          });
 
-        const fileContents = `# This file was automatically generated from ${this.databaseItem.name}. Manual changes will not persist.\n\n${modelExtensionFileToYaml(extensionFile)}`;
-        const filePath = join(
-          this.extensionPack.path,
-          "models",
-          `${this.language}${GENERATED_MODELS_SUFFIX}`,
-        );
+          const fileContents = `# This file was automatically generated from ${this.databaseItem.name}. Manual changes will not persist.\n\n${modelExtensionFileToYaml(extensionFile)}`;
+          const filePath = join(
+            this.extensionPack.path,
+            "models",
+            `${this.language}${GENERATED_MODELS_SUFFIX}`,
+          );
 
-        await outputFile(filePath, fileContents);
+          await outputFile(filePath, fileContents);
 
-        void this.app.logger.log(`Saved generated model file to ${filePath}`);
+          void this.app.logger.log(`Saved generated model file to ${filePath}`);
+        }
       },
       {
         cancellable: false,
@@ -810,57 +833,61 @@ export class ModelEditorView extends AbstractWebview<
   }
 
   private async modelDependency(): Promise<void> {
-    return withProgress(async (progress, token) => {
-      const addedDatabase =
-        await this.promptChooseNewOrExistingDatabase(progress);
-      if (!addedDatabase || token.isCancellationRequested) {
-        return;
-      }
+    return withProgress(
+      async (progress, token) => {
+        const addedDatabase =
+          await this.promptChooseNewOrExistingDatabase(progress);
+        if (!addedDatabase || token.isCancellationRequested) {
+          return;
+        }
 
-      const addedDbUri = addedDatabase.databaseUri.toString();
-      if (this.modelingStore.isDbOpen(addedDbUri)) {
-        this.modelingEvents.fireFocusModelEditorEvent(addedDbUri);
-        return;
-      }
+        const addedDbUri = addedDatabase.databaseUri.toString();
+        if (this.modelingStore.isDbOpen(addedDbUri)) {
+          this.modelingEvents.fireFocusModelEditorEvent(addedDbUri);
+          return;
+        }
 
-      const modelFile = await pickExtensionPack(
-        this.cliServer,
-        addedDatabase,
-        this.modelConfig,
-        this.app.logger,
-        progress,
-        token,
-        3,
-      );
-      if (!modelFile) {
-        return;
-      }
+        const modelFile = await pickExtensionPack(
+          this.cliServer,
+          addedDatabase,
+          this.modelConfig,
+          this.app.logger,
+          progress,
+          token,
+          3,
+        );
+        if (!modelFile) {
+          return;
+        }
 
-      // Check again just before opening the editor to ensure no model editor has been opened between
-      // our first check and now.
-      if (this.modelingStore.isDbOpen(addedDbUri)) {
-        this.modelingEvents.fireFocusModelEditorEvent(addedDbUri);
-        return;
-      }
+        // Check again just before opening the editor to ensure no model editor has been opened between
+        // our first check and now.
+        if (this.modelingStore.isDbOpen(addedDbUri)) {
+          this.modelingEvents.fireFocusModelEditorEvent(addedDbUri);
+          return;
+        }
 
-      const view = new ModelEditorView(
-        this.app,
-        this.modelingStore,
-        this.modelingEvents,
-        this.modelConfig,
-        this.databaseManager,
-        this.variantAnalysisManager,
-        this.cliServer,
-        this.queryRunner,
-        this.queryStorageDir,
-        this.queryDir,
-        addedDatabase,
-        modelFile,
-        this.language,
-        Mode.Framework,
-      );
-      await view.openView();
-    });
+        const view = new ModelEditorView(
+          this.app,
+          this.modelingStore,
+          this.modelingEvents,
+          this.modelConfig,
+          this.databaseManager,
+          this.databaseFetcher,
+          this.variantAnalysisManager,
+          this.cliServer,
+          this.queryRunner,
+          this.queryStorageDir,
+          this.queryDir,
+          addedDatabase,
+          modelFile,
+          this.language,
+          Mode.Framework,
+        );
+        await view.openView();
+      },
+      { cancellable: true },
+    );
   }
 
   private async promptChooseNewOrExistingDatabase(
@@ -917,13 +944,10 @@ export class ModelEditorView extends AbstractWebview<
     // the user to import the library database. We need to have the database
     // imported to the query server, so we need to register it to our workspace.
     const makeSelected = false;
-    const addedDatabase = await promptImportGithubDatabase(
-      this.app,
-      this.databaseManager,
-      this.app.workspaceStoragePath ?? this.app.globalStoragePath,
+    const addedDatabase = await this.databaseFetcher.promptImportGithubDatabase(
       progress,
-      this.cliServer,
       this.databaseItem.language,
+      undefined,
       makeSelected,
       false,
     );

extensions/ql-vscode/src/model-editor/model-evaluator.ts

@@ -13,6 +13,7 @@ import {
   UserCancellationException,
   withProgress,
 } from "../common/vscode/progress";
+import { VariantAnalysisScannedRepositoryDownloadStatus } from "../variant-analysis/shared/variant-analysis";
 import type { VariantAnalysis } from "../variant-analysis/shared/variant-analysis";
 import type { CancellationToken } from "vscode";
 import { CancellationTokenSource } from "vscode";
@@ -20,6 +21,7 @@ import type { QlPackDetails } from "../variant-analysis/ql-pack-details";
 import type { App } from "../common/app";
 import { ModelAlertsView } from "./model-alerts/model-alerts-view";
 import type { ExtensionPack } from "./shared/extension-pack";
+import type { ModeledMethod } from "./modeled-method";
 
 export class ModelEvaluator extends DisposableObject {
   // Cancellation token source to allow cancelling of the current run
@@ -126,7 +128,6 @@ export class ModelEvaluator extends DisposableObject {
         this.dbItem,
         this.extensionPack,
       );
-      await this.modelAlertsView.showView();
 
       this.modelAlertsView.onEvaluationRunStopClicked(async () => {
         await this.stopEvaluation();
@@ -148,10 +149,26 @@ export class ModelEvaluator extends DisposableObject {
         throw new Error("No variant analysis available");
       }
 
-      await this.modelAlertsView.updateVariantAnalysis(variantAnalysis);
+      const reposResults =
+        this.variantAnalysisManager.getLoadedResultsForVariantAnalysis(
+          variantAnalysis.id,
+        );
+      await this.modelAlertsView.showView(reposResults);
+
+      await this.modelAlertsView.setVariantAnalysis(variantAnalysis);
     }
   }
 
+  public async revealInModelAlertsView(modeledMethod: ModeledMethod) {
+    if (!this.modelingStore.isModelAlertsViewOpen(this.dbItem)) {
+      await this.openModelAlertsView();
+    }
+    this.modelingEvents.fireRevealInModelAlertsViewEvent(
+      this.dbItem.databaseUri.toString(),
+      modeledMethod,
+    );
+  }
+
   private registerToModelingEvents() {
     this.push(
       this.modelingEvents.onModelEvaluationRunChanged(async (event) => {
@@ -254,7 +271,7 @@ export class ModelEvaluator extends DisposableObject {
             });
 
             // Update model alerts view
-            await this.modelAlertsView?.updateVariantAnalysis(variantAnalysis);
+            await this.modelAlertsView?.setVariantAnalysis(variantAnalysis);
           }
         },
       ),
@@ -262,8 +279,15 @@ export class ModelEvaluator extends DisposableObject {
 
     this.push(
       this.variantAnalysisManager.onRepoStatesUpdated(async (e) => {
-        if (e.variantAnalysisId === variantAnalysisId) {
-          await this.modelAlertsView?.updateRepoState(e.repoState);
+        if (
+          e.variantAnalysisId === variantAnalysisId &&
+          e.repoState.downloadStatus ===
+            VariantAnalysisScannedRepositoryDownloadStatus.Succeeded
+        ) {
+          await this.readAnalysisResults(
+            variantAnalysisId,
+            e.repoState.repositoryId,
+          );
         }
       }),
     );
@@ -271,9 +295,44 @@ export class ModelEvaluator extends DisposableObject {
     this.push(
       this.variantAnalysisManager.onRepoResultsLoaded(async (e) => {
         if (e.variantAnalysisId === variantAnalysisId) {
-          await this.modelAlertsView?.updateRepoResults(e);
+          await this.modelAlertsView?.setReposResults([e]);
         }
       }),
     );
   }
+
+  private async readAnalysisResults(
+    variantAnalysisId: number,
+    repositoryId: number,
+  ) {
+    const variantAnalysis =
+      this.variantAnalysisManager.tryGetVariantAnalysis(variantAnalysisId);
+    if (!variantAnalysis) {
+      void this.app.logger.log(
+        `Could not find variant analysis with id ${variantAnalysisId}`,
+      );
+      throw new Error(
+        "There was an error when trying to retrieve variant analysis information",
+      );
+    }
+
+    const repository = variantAnalysis.scannedRepos?.find(
+      (r) => r.repository.id === repositoryId,
+    );
+    if (!repository) {
+      void this.app.logger.log(
+        `Could not find repository with id ${repositoryId} in scanned repos`,
+      );
+      throw new Error(
+        "There was an error when trying to retrieve repository information",
+      );
+    }
+
+    // Trigger loading the results for the repository. This will trigger a
+    // onRepoResultsLoaded event that we'll process.
+    await this.variantAnalysisManager.loadResults(
+      variantAnalysisId,
+      repository.repository.fullName,
+    );
+  }
 }

extensions/ql-vscode/src/model-editor/modeled-method-fs.ts

@@ -12,7 +12,6 @@ import { load as loadYaml } from "js-yaml";
 import type { CodeQLCliServer } from "../codeql-cli/cli";
 import { pathsEqual } from "../common/files";
 import type { QueryLanguage } from "../common/query-language";
-import type { ModelConfig } from "./languages";
 
 export const GENERATED_MODELS_SUFFIX = ".model.generated.yml";
 
@@ -23,14 +22,12 @@ export async function saveModeledMethods(
   modeledMethods: Readonly<Record<string, readonly ModeledMethod[]>>,
   mode: Mode,
   cliServer: CodeQLCliServer,
-  modelConfig: ModelConfig,
   logger: NotificationLogger,
 ): Promise<void> {
   const existingModeledMethods = await loadModeledMethodFiles(
     extensionPack,
     language,
     cliServer,
-    modelConfig,
     logger,
   );
 
@@ -53,14 +50,9 @@ async function loadModeledMethodFiles(
   extensionPack: ExtensionPack,
   language: QueryLanguage,
   cliServer: CodeQLCliServer,
-  modelConfig: ModelConfig,
   logger: NotificationLogger,
 ): Promise<Record<string, Record<string, ModeledMethod[]>>> {
-  const modelFiles = await listModelFiles(
-    extensionPack.path,
-    cliServer,
-    modelConfig,
-  );
+  const modelFiles = await listModelFiles(extensionPack.path, cliServer);
 
   const modeledMethodsByFile: Record<
     string,
@@ -92,7 +84,6 @@ export async function loadModeledMethods(
   extensionPack: ExtensionPack,
   language: QueryLanguage,
   cliServer: CodeQLCliServer,
-  modelConfig: ModelConfig,
   logger: NotificationLogger,
 ): Promise<Record<string, ModeledMethod[]>> {
   const existingModeledMethods: Record<string, ModeledMethod[]> = {};
@@ -101,7 +92,6 @@ export async function loadModeledMethods(
     extensionPack,
     language,
     cliServer,
-    modelConfig,
     logger,
   );
   for (const modeledMethods of Object.values(modeledMethodsByFile)) {
@@ -120,7 +110,6 @@ export async function loadModeledMethods(
 export async function listModelFiles(
   extensionPackPath: string,
   cliServer: CodeQLCliServer,
-  modelConfig: ModelConfig,
 ): Promise<Set<string>> {
   const result = await cliServer.resolveExtensions(
     extensionPackPath,
@@ -131,11 +120,8 @@ export async function listModelFiles(
   for (const [path, extensions] of Object.entries(result.data)) {
     if (pathsEqual(path, extensionPackPath)) {
       for (const extension of extensions) {
-        // We only load generated models when type models are shown
-        if (
-          !modelConfig.showTypeModels &&
-          extension.file.endsWith(GENERATED_MODELS_SUFFIX)
-        ) {
+        // We never load generated models
+        if (extension.file.endsWith(GENERATED_MODELS_SUFFIX)) {
           continue;
         }
 

extensions/ql-vscode/src/model-editor/modeled-method.ts

@@ -1,3 +1,4 @@
+import { assertNever } from "../common/helpers-pure";
 import type { MethodSignature } from "./method";
 import type { ModelingStatus } from "./shared/modeling-status";
 
@@ -169,3 +170,86 @@ export function calculateNewProvenance(
       return "manual";
   }
 }
+
+export function createModeledMethodKey(modeledMethod: ModeledMethod): string {
+  const canonicalModeledMethod = canonicalizeModeledMethod(modeledMethod);
+  return JSON.stringify(
+    canonicalModeledMethod,
+    // This ensures the keys are always in the same order
+    Object.keys(canonicalModeledMethod).sort(),
+  );
+}
+
+/**
+ * This method will reset any properties which are not used for the specific type of modeled method.
+ *
+ * It will also set the `provenance` to `manual` since multiple modelings of the same method with a
+ * different provenance are not actually different.
+ *
+ * The returned canonical modeled method should only be used for comparisons. It should not be used
+ * for display purposes, saving the model, or any other purpose which requires the original modeled
+ * method to be preserved.
+ *
+ * @param modeledMethod The modeled method to canonicalize
+ */
+function canonicalizeModeledMethod(
+  modeledMethod: ModeledMethod,
+): ModeledMethod {
+  const methodSignature: MethodSignature = {
+    endpointType: modeledMethod.endpointType,
+    signature: modeledMethod.signature,
+    packageName: modeledMethod.packageName,
+    typeName: modeledMethod.typeName,
+    methodName: modeledMethod.methodName,
+    methodParameters: modeledMethod.methodParameters,
+  };
+
+  switch (modeledMethod.type) {
+    case "none":
+      return {
+        ...methodSignature,
+        type: "none",
+      };
+    case "source":
+      return {
+        ...methodSignature,
+        type: "source",
+        output: modeledMethod.output,
+        kind: modeledMethod.kind,
+        provenance: "manual",
+      };
+    case "sink":
+      return {
+        ...methodSignature,
+        type: "sink",
+        input: modeledMethod.input,
+        kind: modeledMethod.kind,
+        provenance: "manual",
+      };
+    case "summary":
+      return {
+        ...methodSignature,
+        type: "summary",
+        input: modeledMethod.input,
+        output: modeledMethod.output,
+        kind: modeledMethod.kind,
+        provenance: "manual",
+      };
+    case "neutral":
+      return {
+        ...methodSignature,
+        type: "neutral",
+        kind: modeledMethod.kind,
+        provenance: "manual",
+      };
+    case "type":
+      return {
+        ...methodSignature,
+        type: "type",
+        relatedTypeName: modeledMethod.relatedTypeName,
+        path: modeledMethod.path,
+      };
+    default:
+      assertNever(modeledMethod);
+  }
+}

extensions/ql-vscode/src/model-editor/modeling-events.ts

@@ -2,7 +2,7 @@ import type { App } from "../common/app";
 import { DisposableObject } from "../common/disposable-object";
 import type { AppEvent, AppEventEmitter } from "../common/events";
 import type { DatabaseItem } from "../databases/local-databases";
-import type { Method, Usage } from "./method";
+import type { Method, MethodSignature, Usage } from "./method";
 import type { ModelEvaluationRun } from "./model-evaluation-run";
 import type { ModeledMethod } from "./modeled-method";
 import type { Mode } from "./shared/mode";
@@ -58,7 +58,7 @@ interface ModelEvaluationRunChangedEvent {
 
 interface RevealInModelEditorEvent {
   dbUri: string;
-  method: Method;
+  method: MethodSignature;
 }
 
 interface FocusModelEditorEvent {
@@ -69,6 +69,11 @@ interface FocusModelAlertsViewEvent {
   dbUri: string;
 }
 
+interface RevealInModelAlertsViewEvent {
+  dbUri: string;
+  modeledMethod: ModeledMethod;
+}
+
 export class ModelingEvents extends DisposableObject {
   public readonly onActiveDbChanged: AppEvent<void>;
   public readonly onDbOpened: AppEvent<DatabaseItem>;
@@ -84,6 +89,7 @@ export class ModelingEvents extends DisposableObject {
   public readonly onRevealInModelEditor: AppEvent<RevealInModelEditorEvent>;
   public readonly onFocusModelEditor: AppEvent<FocusModelEditorEvent>;
   public readonly onFocusModelAlertsView: AppEvent<FocusModelAlertsViewEvent>;
+  public readonly onRevealInModelAlertsView: AppEvent<RevealInModelAlertsViewEvent>;
 
   private readonly onActiveDbChangedEventEmitter: AppEventEmitter<void>;
   private readonly onDbOpenedEventEmitter: AppEventEmitter<DatabaseItem>;
@@ -99,6 +105,7 @@ export class ModelingEvents extends DisposableObject {
   private readonly onRevealInModelEditorEventEmitter: AppEventEmitter<RevealInModelEditorEvent>;
   private readonly onFocusModelEditorEventEmitter: AppEventEmitter<FocusModelEditorEvent>;
   private readonly onFocusModelAlertsViewEventEmitter: AppEventEmitter<FocusModelAlertsViewEvent>;
+  private readonly onRevealInModelAlertsViewEventEmitter: AppEventEmitter<RevealInModelAlertsViewEvent>;
 
   constructor(app: App) {
     super();
@@ -176,6 +183,12 @@ export class ModelingEvents extends DisposableObject {
       app.createEventEmitter<FocusModelAlertsViewEvent>(),
     );
     this.onFocusModelAlertsView = this.onFocusModelAlertsViewEventEmitter.event;
+
+    this.onRevealInModelAlertsViewEventEmitter = this.push(
+      app.createEventEmitter<RevealInModelAlertsViewEvent>(),
+    );
+    this.onRevealInModelAlertsView =
+      this.onRevealInModelAlertsViewEventEmitter.event;
   }
 
   public fireActiveDbChangedEvent() {
@@ -285,7 +298,7 @@ export class ModelingEvents extends DisposableObject {
     });
   }
 
-  public fireRevealInModelEditorEvent(dbUri: string, method: Method) {
+  public fireRevealInModelEditorEvent(dbUri: string, method: MethodSignature) {
     this.onRevealInModelEditorEventEmitter.fire({
       dbUri,
       method,
@@ -301,4 +314,11 @@ export class ModelingEvents extends DisposableObject {
   public fireFocusModelAlertsViewEvent(dbUri: string) {
     this.onFocusModelAlertsViewEventEmitter.fire({ dbUri });
   }
+
+  public fireRevealInModelAlertsViewEvent(
+    dbUri: string,
+    modeledMethod: ModeledMethod,
+  ) {
+    this.onRevealInModelAlertsViewEventEmitter.fire({ dbUri, modeledMethod });
+  }
 }

extensions/ql-vscode/src/model-editor/shared/model-alerts-filter-sort.ts

@@ -0,0 +1,75 @@
+import type { ModelAlerts } from "../model-alerts/model-alerts";
+
+export enum SortKey {
+  Alphabetically = "alphabetically",
+  NumberOfResults = "numberOfResults",
+}
+
+export type ModelAlertsFilterSortState = {
+  modelSearchValue: string;
+  repositorySearchValue: string;
+  sortKey: SortKey;
+};
+
+export const defaultFilterSortState: ModelAlertsFilterSortState = {
+  modelSearchValue: "",
+  repositorySearchValue: "",
+  sortKey: SortKey.NumberOfResults,
+};
+
+export function filterAndSort(
+  modelAlerts: ModelAlerts[],
+  filterSortState: ModelAlertsFilterSortState,
+): ModelAlerts[] {
+  if (!modelAlerts || modelAlerts.length === 0) {
+    return [];
+  }
+
+  return modelAlerts
+    .filter((item) => matchesFilter(item, filterSortState))
+    .sort((a, b) => {
+      switch (filterSortState.sortKey) {
+        case SortKey.Alphabetically:
+          return a.model.signature.localeCompare(b.model.signature);
+        case SortKey.NumberOfResults:
+          return (b.alerts.length || 0) - (a.alerts.length || 0);
+        default:
+          return 0;
+      }
+    });
+}
+
+function matchesFilter(
+  item: ModelAlerts,
+  filterSortState: ModelAlertsFilterSortState | undefined,
+): boolean {
+  if (!filterSortState) {
+    return true;
+  }
+
+  return (
+    matchesRepository(item, filterSortState.repositorySearchValue) &&
+    matchesModel(item, filterSortState.modelSearchValue)
+  );
+}
+
+function matchesRepository(
+  item: ModelAlerts,
+  repositorySearchValue: string,
+): boolean {
+  // We may want to only return alerts that have a repository match
+  // but for now just return true if the model has any alerts
+  // with a matching repo.
+
+  return item.alerts.some((alert) =>
+    alert.repository.fullName
+      .toLowerCase()
+      .includes(repositorySearchValue.toLowerCase()),
+  );
+}
+
+function matchesModel(item: ModelAlerts, modelSearchValue: string): boolean {
+  return item.model.signature
+    .toLowerCase()
+    .includes(modelSearchValue.toLowerCase());
+}

extensions/ql-vscode/src/model-editor/shared/validation.ts

@@ -1,6 +1,5 @@
+import { createModeledMethodKey } from "../modeled-method";
 import type { ModeledMethod, NeutralModeledMethod } from "../modeled-method";
-import type { MethodSignature } from "../method";
-import { assertNever } from "../../common/helpers-pure";
 
 export type ModeledMethodValidationError = {
   title: string;
@@ -9,80 +8,6 @@ export type ModeledMethodValidationError = {
   index: number;
 };
 
-/**
- * This method will reset any properties which are not used for the specific type of modeled method.
- *
- * It will also set the `provenance` to `manual` since multiple modelings of the same method with a
- * different provenance are not actually different.
- *
- * The returned canonical modeled method should only be used for comparisons. It should not be used
- * for display purposes, saving the model, or any other purpose which requires the original modeled
- * method to be preserved.
- *
- * @param modeledMethod The modeled method to canonicalize
- */
-function canonicalizeModeledMethod(
-  modeledMethod: ModeledMethod,
-): ModeledMethod {
-  const methodSignature: MethodSignature = {
-    endpointType: modeledMethod.endpointType,
-    signature: modeledMethod.signature,
-    packageName: modeledMethod.packageName,
-    typeName: modeledMethod.typeName,
-    methodName: modeledMethod.methodName,
-    methodParameters: modeledMethod.methodParameters,
-  };
-
-  switch (modeledMethod.type) {
-    case "none":
-      return {
-        ...methodSignature,
-        type: "none",
-      };
-    case "source":
-      return {
-        ...methodSignature,
-        type: "source",
-        output: modeledMethod.output,
-        kind: modeledMethod.kind,
-        provenance: "manual",
-      };
-    case "sink":
-      return {
-        ...methodSignature,
-        type: "sink",
-        input: modeledMethod.input,
-        kind: modeledMethod.kind,
-        provenance: "manual",
-      };
-    case "summary":
-      return {
-        ...methodSignature,
-        type: "summary",
-        input: modeledMethod.input,
-        output: modeledMethod.output,
-        kind: modeledMethod.kind,
-        provenance: "manual",
-      };
-    case "neutral":
-      return {
-        ...methodSignature,
-        type: "neutral",
-        kind: modeledMethod.kind,
-        provenance: "manual",
-      };
-    case "type":
-      return {
-        ...methodSignature,
-        type: "type",
-        relatedTypeName: modeledMethod.relatedTypeName,
-        path: modeledMethod.path,
-      };
-    default:
-      assertNever(modeledMethod);
-  }
-}
-
 export function validateModeledMethods(
   modeledMethods: ModeledMethod[],
 ): ModeledMethodValidationError[] {
@@ -97,12 +22,7 @@ export function validateModeledMethods(
   // an error for any duplicates.
   const seenModeledMethods = new Set<string>();
   for (const modeledMethod of consideredModeledMethods) {
-    const canonicalModeledMethod = canonicalizeModeledMethod(modeledMethod);
-    const key = JSON.stringify(
-      canonicalModeledMethod,
-      // This ensures the keys are always in the same order
-      Object.keys(canonicalModeledMethod).sort(),
-    );
+    const key = createModeledMethodKey(modeledMethod);
 
     if (seenModeledMethods.has(key)) {
       result.push({

extensions/ql-vscode/src/model-editor/supported-languages.ts

@@ -1,6 +1,5 @@
 import { QueryLanguage } from "../common/query-language";
 import type { ModelConfig } from "../config";
-import { isCanary } from "../config";
 
 /**
  * Languages that are always supported by the model editor. These languages
@@ -9,6 +8,7 @@ import { isCanary } from "../config";
 export const SUPPORTED_LANGUAGES: QueryLanguage[] = [
   QueryLanguage.Java,
   QueryLanguage.CSharp,
+  QueryLanguage.Ruby,
 ];
 
 export function isSupportedLanguage(
@@ -19,11 +19,6 @@ export function isSupportedLanguage(
     return true;
   }
 
-  if (language === QueryLanguage.Ruby) {
-    // Ruby is only enabled when in canary mode
-    return isCanary();
-  }
-
   if (language === QueryLanguage.Python) {
     // Python is only enabled when the config setting is set
     return modelConfig.enablePython;

extensions/ql-vscode/src/packaging/qlpack-file.schema.json

@@ -51,6 +51,9 @@
                 "$ref": "#/definitions/SuiteInstruction"
               }
             },
+            {
+              "$ref": "#/definitions/SuiteInstruction"
+            },
             {
               "type": "null"
             }
@@ -93,19 +96,33 @@
         "include": {
           "type": "object",
           "additionalProperties": {
-            "type": "array",
-            "items": {
-              "type": "string"
-            }
+            "anyOf": [
+              {
+                "type": "array",
+                "items": {
+                  "type": "string"
+                }
+              },
+              {
+                "type": "string"
+              }
+            ]
           }
         },
         "exclude": {
           "type": "object",
           "additionalProperties": {
-            "type": "array",
-            "items": {
-              "type": "string"
-            }
+            "anyOf": [
+              {
+                "type": "array",
+                "items": {
+                  "type": "string"
+                }
+              },
+              {
+                "type": "string"
+              }
+            ]
           }
         },
         "description": {

extensions/ql-vscode/src/packaging/qlpack-file.ts

@@ -10,7 +10,7 @@ export interface QlPackFile {
   extensionTargets?: Record<string, string> | null;
   dbscheme?: string | null;
   library?: boolean | null;
-  defaultSuite?: SuiteInstruction[] | null;
+  defaultSuite?: SuiteInstruction[] | SuiteInstruction | null;
   defaultSuiteFile?: string | null;
   dataExtensions?: string[] | string | null;
 }

extensions/ql-vscode/src/packaging/suite-instruction.ts

@@ -5,8 +5,8 @@ export interface SuiteInstruction {
   qlpack?: string;
   query?: string;
   queries?: string;
-  include?: Record<string, string[]>;
-  exclude?: Record<string, string[]>;
+  include?: Record<string, string[] | string>;
+  exclude?: Record<string, string[] | string>;
   description?: string;
   import?: string;
   from?: string;

extensions/ql-vscode/src/query-history/query-history-info.ts

@@ -7,6 +7,7 @@ import {
   getActionsWorkflowRunUrl as getVariantAnalysisActionsWorkflowRunUrl,
 } from "../variant-analysis/shared/variant-analysis";
 import type { QueryLanguage } from "../common/query-language";
+import { getGitHubInstanceUrl } from "../config";
 
 export type QueryHistoryInfo = LocalQueryInfo | VariantAnalysisHistoryItem;
 
@@ -79,5 +80,8 @@ export function buildRepoLabel(item: VariantAnalysisHistoryItem): string {
 export function getActionsWorkflowRunUrl(
   item: VariantAnalysisHistoryItem,
 ): string {
-  return getVariantAnalysisActionsWorkflowRunUrl(item.variantAnalysis);
+  return getVariantAnalysisActionsWorkflowRunUrl(
+    item.variantAnalysis,
+    getGitHubInstanceUrl(),
+  );
 }

extensions/ql-vscode/src/query-history/store/query-history-variant-analysis-domain-mapper.ts

@@ -48,11 +48,6 @@ function mapVariantAnalysisDtoToDto(
 ): VariantAnalysisDto {
   return {
     id: variantAnalysis.id,
-    controllerRepo: {
-      id: variantAnalysis.controllerRepo.id,
-      fullName: variantAnalysis.controllerRepo.fullName,
-      private: variantAnalysis.controllerRepo.private,
-    },
     query: {
       name: variantAnalysis.query.name,
       filePath: variantAnalysis.query.filePath,

extensions/ql-vscode/src/query-history/store/query-history-variant-analysis-dto-mapper.ts

@@ -48,12 +48,12 @@ function mapVariantAnalysisToDomainModel(
 ): VariantAnalysis {
   return {
     id: variantAnalysis.id,
-    controllerRepo: {
-      id: variantAnalysis.controllerRepo.id,
-      fullName: variantAnalysis.controllerRepo.fullName,
-      private: variantAnalysis.controllerRepo.private,
-    },
     language: mapQueryLanguageToDomainModel(variantAnalysis.query.language),
+    controllerRepo: {
+      id: 0,
+      fullName: "",
+      private: false,
+    },
     query: {
       name: variantAnalysis.query.name,
       filePath: variantAnalysis.query.filePath,

extensions/ql-vscode/src/query-history/store/query-history-variant-analysis-dto.ts

@@ -15,11 +15,6 @@ export interface QueryHistoryVariantAnalysisDto {
 
 export interface VariantAnalysisDto {
   id: number;
-  controllerRepo: {
-    id: number;
-    fullName: string;
-    private: boolean;
-  };
   query: {
     name: string;
     filePath: string;

extensions/ql-vscode/src/query-server/query-runner.ts

@@ -91,26 +91,15 @@ export class QueryRunner {
     return this.qs.logger;
   }
 
-  async restartQueryServer(
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<void> {
-    await this.qs.restartQueryServer(progress, token);
+  async restartQueryServer(progress: ProgressCallback): Promise<void> {
+    await this.qs.restartQueryServer(progress);
   }
 
-  onStart(
-    callBack: (
-      progress: ProgressCallback,
-      token: CancellationToken,
-    ) => Promise<void>,
-  ) {
+  onStart(callBack: (progress: ProgressCallback) => Promise<void>) {
     this.qs.onDidStartQueryServer(callBack);
   }
 
-  async clearCacheInDatabase(
-    dbItem: DatabaseItem,
-    token: CancellationToken,
-  ): Promise<void> {
+  async clearCacheInDatabase(dbItem: DatabaseItem): Promise<void> {
     if (dbItem.contents === undefined) {
       throw new Error("Can't clear the cache in an invalid database.");
     }
@@ -120,13 +109,10 @@ export class QueryRunner {
       dryRun: false,
       db,
     };
-    await this.qs.sendRequest(clearCache, params, token);
+    await this.qs.sendRequest(clearCache, params);
   }
 
-  async trimCacheInDatabase(
-    dbItem: DatabaseItem,
-    token: CancellationToken,
-  ): Promise<void> {
+  async trimCacheInDatabase(dbItem: DatabaseItem): Promise<void> {
     if (dbItem.contents === undefined) {
       throw new Error("Can't trim the cache in an invalid database.");
     }
@@ -135,7 +121,7 @@ export class QueryRunner {
     const params: TrimCacheParams = {
       db,
     };
-    await this.qs.sendRequest(trimCache, params, token);
+    await this.qs.sendRequest(trimCache, params);
   }
 
   public async compileAndRunQueryAgainstDatabaseCore(

extensions/ql-vscode/src/query-server/query-server-client.ts

@@ -14,7 +14,7 @@ import type { ProgressReporter } from "../common/logging/vscode";
 import { extLogger } from "../common/logging/vscode";
 import type { ProgressMessage, WithProgressId } from "./messages";
 import { progress } from "./messages";
-import type { ProgressCallback, ProgressTask } from "../common/vscode/progress";
+import type { ProgressCallback } from "../common/vscode/progress";
 import { withProgress } from "../common/vscode/progress";
 import { ServerProcess } from "./server-process";
 import type { App } from "../common/app";
@@ -51,12 +51,16 @@ export class QueryServerClient extends DisposableObject {
 
   withProgressReporting: WithProgressReporting;
 
-  private readonly queryServerStartListeners = [] as Array<ProgressTask<void>>;
+  private readonly queryServerStartListeners = [] as Array<
+    (progress: ProgressCallback) => void
+  >;
 
   // Can't use standard vscode EventEmitter here since they do not cause the calling
   // function to fail if one of the event handlers fail. This is something that
   // we need here.
-  readonly onDidStartQueryServer = (e: ProgressTask<void>) => {
+  readonly onDidStartQueryServer = (
+    e: (progress: ProgressCallback) => void,
+  ) => {
     this.queryServerStartListeners.push(e);
   };
 
@@ -105,14 +109,11 @@ export class QueryServerClient extends DisposableObject {
    * This resets the unexpected termination count. As hopefully it is an indication that the user has fixed the
    * issue.
    */
-  async restartQueryServer(
-    progress: ProgressCallback,
-    token: CancellationToken,
-  ): Promise<void> {
+  async restartQueryServer(progress: ProgressCallback): Promise<void> {
     // Reset the unexpected termination count when we restart the query server manually
     // or due to config change
     this.unexpectedTerminationCount = 0;
-    await this.restartQueryServerInternal(progress, token);
+    await this.restartQueryServerInternal(progress);
   }
 
   /**
@@ -121,8 +122,7 @@ export class QueryServerClient extends DisposableObject {
   private restartQueryServerOnFailure() {
     if (this.unexpectedTerminationCount < MAX_UNEXPECTED_TERMINATIONS) {
       void withProgress(
-        async (progress, token) =>
-          this.restartQueryServerInternal(progress, token),
+        async (progress) => this.restartQueryServerInternal(progress),
         {
           title: "Restarting CodeQL query server due to unexpected termination",
         },
@@ -144,7 +144,6 @@ export class QueryServerClient extends DisposableObject {
    */
   private async restartQueryServerInternal(
     progress: ProgressCallback,
-    token: CancellationToken,
   ): Promise<void> {
     this.stopQueryServer();
     await this.startQueryServer();
@@ -152,7 +151,7 @@ export class QueryServerClient extends DisposableObject {
     // Ensure we await all responses from event handlers so that
     // errors can be properly reported to the user.
     await Promise.all(
-      this.queryServerStartListeners.map((handler) => handler(progress, token)),
+      this.queryServerStartListeners.map((handler) => handler(progress)),
     );
   }
 
@@ -241,8 +240,32 @@ export class QueryServerClient extends DisposableObject {
     this.nextCallback = 0;
     this.nextProgress = 0;
     this.progressCallbacks = {};
-    child.on("close", () => {
-      this.restartQueryServerOnFailure();
+
+    // 'exit' may or may not fire after 'error' event, so we want to guard against restarting the
+    // query server twice if both events fire.
+    let wasExitOrErrorHandled = false;
+    child.on("error", (err: Error) => {
+      if (!wasExitOrErrorHandled) {
+        void this.logger.log(`Query server terminated with error: ${err}.`);
+        this.restartQueryServerOnFailure();
+        wasExitOrErrorHandled = true;
+      }
+    });
+    child.on("exit", (code: number, signal: string) => {
+      if (!wasExitOrErrorHandled) {
+        if (code !== null) {
+          void this.logger.log(
+            `Query server terminated with exit code: ${code}.`,
+          );
+        }
+        if (signal !== null) {
+          void this.logger.log(
+            `Query server terminated due to receipt of signal: ${signal}.`,
+          );
+        }
+        this.restartQueryServerOnFailure();
+        wasExitOrErrorHandled = true;
+      }
     });
   }
 

extensions/ql-vscode/src/run-queries-shared.ts

@@ -31,6 +31,8 @@ import { generateSummarySymbolsFile } from "./log-insights/summary-parser";
 import { getErrorMessage } from "./common/helpers-pure";
 import { createHash } from "crypto";
 import { QueryOutputDir } from "./local-queries/query-output-dir";
+import { progressUpdate } from "./common/vscode/progress";
+import type { ProgressCallback } from "./common/vscode/progress";
 
 /**
  * run-queries.ts
@@ -519,6 +521,7 @@ export async function createInitialQueryInfo(
 export async function generateEvalLogSummaries(
   cliServer: CodeQLCliServer,
   outputDir: QueryOutputDir,
+  progress: ProgressCallback,
 ): Promise<EvaluatorLogPaths | undefined> {
   const log = outputDir.evalLogPath;
   if (!(await pathExists(log))) {
@@ -527,6 +530,7 @@ export async function generateEvalLogSummaries(
   }
   let humanReadableSummary: string | undefined = undefined;
   let endSummary: string | undefined = undefined;
+  progress(progressUpdate(1, 3, "Generating evaluator log summary"));
   if (await generateHumanReadableLogSummary(cliServer, outputDir)) {
     humanReadableSummary = outputDir.evalLogSummaryPath;
     endSummary = outputDir.evalLogEndSummaryPath;
@@ -535,10 +539,12 @@ export async function generateEvalLogSummaries(
   let summarySymbols: string | undefined = undefined;
   if (isCanary()) {
     // Generate JSON summary for viewer.
+    progress(progressUpdate(2, 3, "Generating JSON log summary"));
     jsonSummary = outputDir.jsonEvalLogSummaryPath;
     await cliServer.generateJsonLogSummary(log, jsonSummary);
 
     if (humanReadableSummary !== undefined) {
+      progress(progressUpdate(3, 3, "Generating summary symbols file"));
       summarySymbols = outputDir.evalLogSummarySymbolsPath;
       await generateSummarySymbolsFile(humanReadableSummary, summarySymbols);
     }

extensions/ql-vscode/src/stories/Overview.mdx

@@ -1,4 +1,4 @@
-import { Canvas, Meta, Story } from '@storybook/addon-docs';
+import { Canvas, Meta, Story } from '@storybook/blocks';
 
 import { VSCodeButton } from '@vscode/webview-ui-toolkit/react';
 
@@ -39,23 +39,29 @@ updated manually if new variables are added to VSCode. It can also be updated if
 these variables, follow these steps:
 
 1. Make sure you have selected the correct theme. If you want to use a variable which is currently not available and will be committed, please
-select the **Dark+** theme. You can use **Preferences: Color Theme** in the *Command Palette* to select the theme.
+   select the **Dark+** theme. You can use **Preferences: Color Theme** in the *Command Palette* to select the theme.
+
 2. Open a WebView in VSCode (for example the results of a query)
+
 3. Open the *Command Palette* (Ctrl/Cmd+Shift+P)
+
 4. Select **Developer: Open WebView Developer Tools**
+
 5. Now, you will need to find the `<html>` element in the lowest-level `<iframe>`. See the image below:
 
    <img src={iframeImage} alt="The iframe element showing in the VS Code webview developer tools element inspector" />
 
 6. Once you have selected the `<html>` element as in the image above, click on **Show All Properties (... more)** (see image below). This will
-expand all CSS variables.
+   expand all CSS variables.
 
    <img src={stylesImage} alt="The styles tab of the VS Code webview developer tools element inspector" />
 
 7. Copy all variables to the `src/stories/vscode-theme-dark.css` file.
+
 8. Now, select the `<body>` element which is a direct child of the `<html>` element.
+
 9. This time, you do not need to copy the variables. Instead, copy the styles on the `<body>` element to the `src/stories/vscode-theme-dark.css` file.
-See the image below for which styles need to be copied.
+   See the image below for which styles need to be copied.
 
 <img src={bodyImage} alt="The styles on the body element showing in the VS Code webview developer tools element inspector" />
 

extensions/ql-vscode/src/stories/common/SearchBox.stories.tsx

@@ -0,0 +1,29 @@
+import { useState } from "react";
+
+import type { Meta } from "@storybook/react";
+
+import { SearchBox as SearchBoxComponent } from "../../view/common/SearchBox";
+
+export default {
+  title: "Search Box",
+  component: SearchBoxComponent,
+  argTypes: {
+    value: {
+      control: {
+        disable: true,
+      },
+    },
+  },
+} as Meta<typeof SearchBoxComponent>;
+
+export const SearchBox = () => {
+  const [value, setValue] = useState("");
+
+  return (
+    <SearchBoxComponent
+      value={value}
+      placeholder="Filter by x/y/z..."
+      onChange={setValue}
+    />
+  );
+};

extensions/ql-vscode/src/stories/model-alerts/ModelAlerts.stories.tsx

@@ -2,6 +2,9 @@ import type { Meta, StoryFn } from "@storybook/react";
 
 import { ModelAlerts as ModelAlertsComponent } from "../../view/model-alerts/ModelAlerts";
 import { createMockVariantAnalysis } from "../../../test/factories/variant-analysis/shared/variant-analysis";
+import { VariantAnalysisRepoStatus } from "../../variant-analysis/shared/variant-analysis";
+import type { VariantAnalysisScannedRepositoryResult } from "../../variant-analysis/shared/variant-analysis";
+import { createMockAnalysisAlert } from "../../../test/factories/variant-analysis/shared/analysis-alert";
 
 export default {
   title: "Model Alerts/Model Alerts",
@@ -12,19 +15,94 @@ const Template: StoryFn<typeof ModelAlertsComponent> = (args) => (
   <ModelAlertsComponent {...args} />
 );
 
+const variantAnalysis = createMockVariantAnalysis({
+  modelPacks: [
+    {
+      name: "Model pack 1",
+      path: "/path/to/model-pack-1",
+    },
+    {
+      name: "Model pack 2",
+      path: "/path/to/model-pack-2",
+    },
+  ],
+  scannedRepos: [
+    {
+      repository: {
+        id: 1,
+        fullName: "org/repo1",
+        private: false,
+        stargazersCount: 100,
+        updatedAt: new Date().toISOString(),
+      },
+      analysisStatus: VariantAnalysisRepoStatus.InProgress,
+      resultCount: 0,
+      artifactSizeInBytes: 0,
+    },
+    {
+      repository: {
+        id: 2,
+        fullName: "org/repo2",
+        private: false,
+        stargazersCount: 100,
+        updatedAt: new Date().toISOString(),
+      },
+      analysisStatus: VariantAnalysisRepoStatus.Succeeded,
+      resultCount: 0,
+      artifactSizeInBytes: 0,
+    },
+    {
+      repository: {
+        id: 3,
+        fullName: "org/repo3",
+        private: false,
+        stargazersCount: 100,
+        updatedAt: new Date().toISOString(),
+      },
+      analysisStatus: VariantAnalysisRepoStatus.Succeeded,
+      resultCount: 1,
+      artifactSizeInBytes: 0,
+    },
+    {
+      repository: {
+        id: 4,
+        fullName: "org/repo4",
+        private: false,
+        stargazersCount: 100,
+        updatedAt: new Date().toISOString(),
+      },
+      analysisStatus: VariantAnalysisRepoStatus.Succeeded,
+      resultCount: 3,
+      artifactSizeInBytes: 0,
+    },
+  ],
+});
+
+const repoResults: VariantAnalysisScannedRepositoryResult[] = [
+  {
+    variantAnalysisId: variantAnalysis.id,
+    repositoryId: 2,
+    interpretedResults: [createMockAnalysisAlert(), createMockAnalysisAlert()],
+  },
+  {
+    variantAnalysisId: variantAnalysis.id,
+    repositoryId: 3,
+    interpretedResults: [
+      createMockAnalysisAlert(),
+      createMockAnalysisAlert(),
+      createMockAnalysisAlert(),
+    ],
+  },
+  {
+    variantAnalysisId: variantAnalysis.id,
+    repositoryId: 4,
+    interpretedResults: [createMockAnalysisAlert()],
+  },
+];
+
 export const ModelAlerts = Template.bind({});
 ModelAlerts.args = {
   initialViewState: { title: "codeql/sql2o-models" },
-  variantAnalysis: createMockVariantAnalysis({
-    modelPacks: [
-      {
-        name: "Model pack 1",
-        path: "/path/to/model-pack-1",
-      },
-      {
-        name: "Model pack 2",
-        path: "/path/to/model-pack-2",
-      },
-    ],
-  }),
+  variantAnalysis,
+  repoResults,
 };

extensions/ql-vscode/src/stories/model-alerts/ModelAlertsHeader.stories.tsx

@@ -13,6 +13,12 @@ export default {
         disable: true,
       },
     },
+    onViewLogsClick: {
+      action: "view-logs-clicked",
+      table: {
+        disable: true,
+      },
+    },
     stopRunClick: {
       action: "stop-run-clicked",
       table: {

extensions/ql-vscode/src/stories/model-alerts/ModelAlertsResults.stories.tsx

@@ -0,0 +1,30 @@
+import type { Meta, StoryFn } from "@storybook/react";
+
+import { ModelAlertsResults as ModelAlertsResultsComponent } from "../../view/model-alerts/ModelAlertsResults";
+import { createSinkModeledMethod } from "../../../test/factories/model-editor/modeled-method-factories";
+import { createMockAnalysisAlert } from "../../../test/factories/variant-analysis/shared/analysis-alert";
+
+export default {
+  title: "Model Alerts/Model Alerts Results",
+  component: ModelAlertsResultsComponent,
+} as Meta<typeof ModelAlertsResultsComponent>;
+
+const Template: StoryFn<typeof ModelAlertsResultsComponent> = (args) => (
+  <ModelAlertsResultsComponent {...args} />
+);
+
+export const ModelAlertsResults = Template.bind({});
+ModelAlertsResults.args = {
+  modelAlerts: {
+    model: createSinkModeledMethod(),
+    alerts: [
+      {
+        repository: {
+          id: 1,
+          fullName: "expressjs/express",
+        },
+        alert: createMockAnalysisAlert(),
+      },
+    ],
+  },
+};