From 1ea7c6956141d1fa69d9c9879f086aa9a4e17ac8 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 28 Aug 2024 16:25:40 +0100
Subject: [PATCH 01/28] wip: enable AI Fix

---
 .../ui/jcef/ThemeBasedStylingGenerator.kt     |  3 +-
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 60 +++++++++++++++----
 src/main/kotlin/snyk/common/lsp/Types.kt      |  3 +-
 .../stylesheets/snyk_code_suggestion.scss     | 13 ++++
 .../stylesheets/snyk_oss_suggestion.scss      |  2 +-
 ...uggestionDescriptionPanelFromLSCodeTest.kt |  2 +-
 ...SuggestionDescriptionPanelFromLSOSSTest.kt |  2 +-
 7 files changed, 66 insertions(+), 19 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
index 2089075fd..ec730d442 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
@@ -92,7 +92,8 @@ class ThemeBasedStylingGenerator {
                                 '--border-color': "$borderColor",
                                 '--editor-color': "$editorColor",
                                 '--label-color': "'$labelColor'",
-                                '--vulnerability-overview-pre-background-color': "${toCssHex(codeTagBgColor)}",
+                                '--container-background-color': "${toCssHex(codeTagBgColor)}",
+                                '--generated-ai-fix-button-background-color': "#3376CD", // TODO: From Figma. Find the correct JetBrains API to get this color
                             };
                             for (let [property, value] of Object.entries(properties)) {
                                 document.documentElement.style.setProperty(property, value);
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index 02bd0bf62..c3fd51bfc 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -60,7 +60,7 @@ class SuggestionDescriptionPanelFromLS(
                     openFileLoadHandlerGenerator.generate(it)
                 }
             }
-            val html = this.getStyledHTML()
+            val html = this.getCustomCssAndScript()
             val jbCefBrowserComponent =
                 JCEFUtils.getJBCefBrowserComponentIfSupported(html, loadHandlerGenerators)
             if (jbCefBrowserComponent == null) {
@@ -140,8 +140,9 @@ class SuggestionDescriptionPanelFromLS(
         return Pair(panel, lastRowToAddSpacer)
     }
 
-    fun getStyledHTML(): String {
+    fun getCustomCssAndScript(): String {
         var html = issue.details()
+        val ideScript = getCustomScript()
         var ideStyle = ""
         if (issue.additionalData.getProductType() == ProductType.CODE_SECURITY ||
             issue.additionalData.getProductType() == ProductType.CODE_QUALITY
@@ -150,19 +151,22 @@ class SuggestionDescriptionPanelFromLS(
         } else if (issue.additionalData.getProductType() == ProductType.OSS) {
             ideStyle = SnykStylesheets.SnykOSSSuggestion
         }
+
         html = html.replace("\${ideStyle}", "<style nonce=\${nonce}>$ideStyle</style>")
         html = html.replace("\${headerEnd}", "")
-        html =
-            html.replace(
-                "\${ideScript}",
-                "<script nonce=\${nonce}>" +
-                    "    // Ensure the document is fully loaded before executing script to manipulate DOM.\n" +
-                    "    document.addEventListener('DOMContentLoaded', () => {\n" +
-                    "        document.getElementById(\"ai-fix-wrapper\").classList.add(\"hidden\");\n" +
-                    "        document.getElementById(\"no-ai-fix-wrapper\").classList.remove(\"hidden\");\n" +
-                    "    })" +
-                    "</script>",
-            )
+//        html = html.replace("\${ideScript}", ideScript)
+        html = html.replace("\${ideScript}" ,"<script nonce=\${nonce}>$ideScript</script>")
+//        html =
+//            html.replace(
+//                "\${ideScript}",
+//                "<script nonce=\${nonce}>" +
+//                    "    // Ensure the document is fully loaded before executing script to manipulate DOM.\n" +
+//                    "    document.addEventListener('DOMContentLoaded', () => {\n" +
+//                    "        document.getElementById(\"ai-fix-wrapper\").classList.add(\"hidden\");\n" +
+//                    "        document.getElementById(\"no-ai-fix-wrapper\").classList.remove(\"hidden\");\n" +
+//                    "    })" +
+//                    "</script>",
+//            )
 
         val nonce = getNonce()
         html = html.replace("\${nonce}", nonce)
@@ -176,6 +180,36 @@ class SuggestionDescriptionPanelFromLS(
             .map { allowedChars.random() }
             .joinToString("")
     }
+
+    private fun getCustomScript(): String {
+        return """
+            (function () {
+              function toggleElement(element, toggle) {
+                if (!element) return;
+
+                if (toggle === 'show') {
+                  element.classList.remove('hidden');
+                } else if (toggle === 'hide') {
+                  element.classList.add('hidden');
+                } else {
+                  console.error('Unexpected toggle value', toggle);
+                }
+              }
+
+              const aiFixWrapperElem = document.getElementById('ai-fix-wrapper');
+              const generateAiFix = document.getElementById('generate-ai-fix');
+
+              // Basic toggle functionality
+              generateAiFix?.addEventListener('click', () => {
+                if (aiFixWrapperElem.classList.contains('hidden')) {
+                  toggleElement(aiFixWrapperElem, 'show');
+                } else {
+                  toggleElement(aiFixWrapperElem, 'hide');
+                }
+              });
+            })();
+        """.trimIndent()
+    }
 }
 
 fun defaultFontLabel(
diff --git a/src/main/kotlin/snyk/common/lsp/Types.kt b/src/main/kotlin/snyk/common/lsp/Types.kt
index 5d1b99310..3553a3305 100644
--- a/src/main/kotlin/snyk/common/lsp/Types.kt
+++ b/src/main/kotlin/snyk/common/lsp/Types.kt
@@ -276,8 +276,7 @@ data class ScanIssue(
     fun canLoadSuggestionPanelFromHTML(): Boolean {
         return when (this.additionalData.getProductType()) {
             ProductType.OSS -> true
-            ProductType.CODE_SECURITY, ProductType.CODE_QUALITY ->
-                pluginSettings().isGlobalIgnoresFeatureEnabled && this.additionalData.details != null
+            ProductType.CODE_SECURITY, ProductType.CODE_QUALITY -> this.additionalData.details != null
 
             else -> TODO()
         }
diff --git a/src/main/resources/stylesheets/snyk_code_suggestion.scss b/src/main/resources/stylesheets/snyk_code_suggestion.scss
index 8f9b6213e..a100fb5b0 100644
--- a/src/main/resources/stylesheets/snyk_code_suggestion.scss
+++ b/src/main/resources/stylesheets/snyk_code_suggestion.scss
@@ -108,3 +108,16 @@ a,
 .high-contrast:not(.high-contrast-light) .light-only {
   display: none;
 }
+
+.sn-fix-wrapper {
+  background-color: var(--container-background-color);  // same variable used in snyk_oss_suggestion.scss
+}
+
+button.generate-ai-fix {
+  background-color: var(--generated-ai-fix-button-background-color);
+  color: white;
+}
+
+button.generate-ai-fix:hover {
+  opacity: 0.9; /* Slightly reduces opacity on hover */
+}
diff --git a/src/main/resources/stylesheets/snyk_oss_suggestion.scss b/src/main/resources/stylesheets/snyk_oss_suggestion.scss
index 87f16d011..217c80c4a 100644
--- a/src/main/resources/stylesheets/snyk_oss_suggestion.scss
+++ b/src/main/resources/stylesheets/snyk_oss_suggestion.scss
@@ -64,6 +64,6 @@ a,
 }
 
 .vulnerability-overview pre {
-  background-color: var(--vulnerability-overview-pre-background-color); // VSCode does this styling by default
+  background-color: var(--container-background-color); // same variable as in snyk_code_suggestion.scss
   border: 1px solid transparent;
 }
diff --git a/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSCodeTest.kt b/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSCodeTest.kt
index a717a650b..6cd9d1062 100644
--- a/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSCodeTest.kt
+++ b/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSCodeTest.kt
@@ -162,7 +162,7 @@ class SuggestionDescriptionPanelFromLSCodeTest : BasePlatformTestCase() {
         every { issue.canLoadSuggestionPanelFromHTML() } returns true
         cut = SuggestionDescriptionPanelFromLS(snykFile, issue)
 
-        val actual = cut.getStyledHTML()
+        val actual = cut.getCustomCssAndScript()
         assertFalse(actual.contains("\${ideStyle}"))
         assertFalse(actual.contains("\${ideScript}"))
         assertFalse(actual.contains("\${nonce}"))
diff --git a/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSOSSTest.kt b/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSOSSTest.kt
index 418009594..7738adc1b 100644
--- a/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSOSSTest.kt
+++ b/src/test/kotlin/io/snyk/plugin/ui/toolwindow/SuggestionDescriptionPanelFromLSOSSTest.kt
@@ -138,7 +138,7 @@ class SuggestionDescriptionPanelFromLSOSSTest : BasePlatformTestCase() {
         every { issue.canLoadSuggestionPanelFromHTML() } returns true
         cut = SuggestionDescriptionPanelFromLS(snykFile, issue)
 
-        val actual = cut.getStyledHTML()
+        val actual = cut.getCustomCssAndScript()
 
         // we don't apply any custom style for oss
         assertFalse(actual.contains("\${ideStyle}"))

From 73b5081a86b9311d98ef6dae3b728f574fa3300f Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Tue, 3 Sep 2024 12:04:01 +0100
Subject: [PATCH 02/28] feat: wip - bridge button action with LS wrapper

---
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    | 49 +++++++++++++++++
 .../kotlin/io/snyk/plugin/ui/jcef/Utils.kt    |  2 +-
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 54 ++++++++-----------
 .../snyk/common/lsp/LanguageServerWrapper.kt  |  4 ++
 4 files changed, 77 insertions(+), 32 deletions(-)
 create mode 100644 src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
new file mode 100644
index 000000000..acc38e49c
--- /dev/null
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -0,0 +1,49 @@
+import com.intellij.openapi.project.Project
+import com.intellij.ui.jcef.JBCefBrowserBase
+import com.intellij.ui.jcef.JBCefJSQuery
+import org.cef.browser.CefBrowser
+import org.cef.browser.CefFrame
+import org.cef.handler.CefLoadHandlerAdapter
+import snyk.common.lsp.LanguageServerWrapper
+
+class GenerateAIFixHandler(private val project: Project) {
+
+    fun generateAIFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
+        val aiFixQuery = JBCefJSQuery.create(jbCefBrowser)
+        aiFixQuery.addHandler { value ->
+            val params = value.split(":")
+            val folderURI = params[0]
+            val fileURI = params[1]
+            val issueID = params[2]
+
+            println("Received folderURI: $folderURI, fileURI: $fileURI, issueID: $issueID")
+
+            LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
+            JBCefJSQuery.Response("success")
+        }
+
+        return object : CefLoadHandlerAdapter() {
+            override fun onLoadEnd(browser: CefBrowser, frame: CefFrame, httpStatusCode: Int) {
+                if (frame.isMain) {
+                    val script = """
+                    (function() {
+                        if (window.aiFixQuery) {
+                            return;
+                        }
+                        window.aiFixQuery = function(value) { ${aiFixQuery.inject("value")} };
+
+                        const aiFixButton = document.getElementById('generate-ai-fix');
+                        aiFixButton.addEventListener('click', () => {
+                            const folderURI = "someFolderURI"; // These should be dynamically set
+                            const fileURI = "someFileURI";
+                            const issueID = "someIssueID";
+                            window.aiFixQuery(folderURI + ":" + fileURI + ":" + issueID);
+                        });
+                    })();
+                    """
+                    browser.executeJavaScript(script, browser.url, 0)
+                }
+            }
+        }
+    }
+}
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt
index d5998e20d..00fda7413 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt
@@ -19,7 +19,7 @@ object JCEFUtils {
         val cefClient = JBCefApp.getInstance().createClient()
         cefClient.setProperty("JS_QUERY_POOL_SIZE", 1)
         val jbCefBrowser =
-            JBCefBrowserBuilder().setClient(cefClient).setEnableOpenDevToolsMenuItem(false)
+            JBCefBrowserBuilder().setClient(cefClient).setEnableOpenDevToolsMenuItem(true)
                 .setMouseWheelEventEnable(true).build()
         jbCefBrowser.setOpenLinksInExternalBrowser(true)
 
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index c3fd51bfc..398023c7e 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -1,5 +1,6 @@
 package io.snyk.plugin.ui.toolwindow.panels
 
+import GenerateAIFixHandler
 import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.openapi.vfs.VirtualFileManager
 import com.intellij.uiDesigner.core.GridLayoutManager
@@ -59,6 +60,12 @@ class SuggestionDescriptionPanelFromLS(
                 loadHandlerGenerators += {
                     openFileLoadHandlerGenerator.generate(it)
                 }
+
+                val generateAIFixHandler = GenerateAIFixHandler(snykFile.project)
+                loadHandlerGenerators += {
+                    generateAIFixHandler.generateAIFixCommand(it)
+                }
+
             }
             val html = this.getCustomCssAndScript()
             val jbCefBrowserComponent =
@@ -154,19 +161,7 @@ class SuggestionDescriptionPanelFromLS(
 
         html = html.replace("\${ideStyle}", "<style nonce=\${nonce}>$ideStyle</style>")
         html = html.replace("\${headerEnd}", "")
-//        html = html.replace("\${ideScript}", ideScript)
         html = html.replace("\${ideScript}" ,"<script nonce=\${nonce}>$ideScript</script>")
-//        html =
-//            html.replace(
-//                "\${ideScript}",
-//                "<script nonce=\${nonce}>" +
-//                    "    // Ensure the document is fully loaded before executing script to manipulate DOM.\n" +
-//                    "    document.addEventListener('DOMContentLoaded', () => {\n" +
-//                    "        document.getElementById(\"ai-fix-wrapper\").classList.add(\"hidden\");\n" +
-//                    "        document.getElementById(\"no-ai-fix-wrapper\").classList.remove(\"hidden\");\n" +
-//                    "    })" +
-//                    "</script>",
-//            )
 
         val nonce = getNonce()
         html = html.replace("\${nonce}", nonce)
@@ -184,29 +179,26 @@ class SuggestionDescriptionPanelFromLS(
     private fun getCustomScript(): String {
         return """
             (function () {
-              function toggleElement(element, toggle) {
-                if (!element) return;
-
-                if (toggle === 'show') {
-                  element.classList.remove('hidden');
-                } else if (toggle === 'hide') {
-                  element.classList.add('hidden');
-                } else {
-                  console.error('Unexpected toggle value', toggle);
+                function toggleElement(element, toggle) {
+                    if (!element) return;
+
+                    if (toggle === 'show') {
+                        element.classList.remove('hidden');
+                    } else if (toggle === 'hide') {
+                        element.classList.add('hidden');
+                    } else {
+                        console.error('Unexpected toggle value', toggle);
+                    }
                 }
-              }
 
-              const aiFixWrapperElem = document.getElementById('ai-fix-wrapper');
-              const generateAiFix = document.getElementById('generate-ai-fix');
+                const generateAiFixBtn = document.getElementById('generate-ai-fix');
 
-              // Basic toggle functionality
-              generateAiFix?.addEventListener('click', () => {
-                if (aiFixWrapperElem.classList.contains('hidden')) {
-                  toggleElement(aiFixWrapperElem, 'show');
-                } else {
-                  toggleElement(aiFixWrapperElem, 'hide');
+                function generateAIFix() {
+                    toggleElement(generateAiFixBtn, 'hide');
+                    toggleElement(document.getElementById('fix-loading-indicator'), 'show');
                 }
-              });
+
+                generateAiFixBtn?.addEventListener('click', generateAIFix);
             })();
         """.trimIndent()
     }
diff --git a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
index 9dbe962e7..850ff052f 100644
--- a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
+++ b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
@@ -494,6 +494,10 @@ class LanguageServerWrapper(
         return this.getFeatureFlagStatus("snykCodeConsistentIgnores")
     }
 
+    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String) {
+        println("[[sendCodeFixDiffsCommand]]")
+    }
+
     private fun ensureLanguageServerProtocolVersion(project: Project) {
         val protocolVersion = initializeResult?.serverInfo?.version
         pluginSettings().currentLSProtocolVersion = protocolVersion?.toIntOrNull()

From 5563b32679ee8ab9432129420de6ed74e2d35009 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Tue, 3 Sep 2024 14:34:04 +0100
Subject: [PATCH 03/28] feat: get Code Diff from LS

---
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    |  9 ++--
 .../snyk/common/lsp/LanguageServerWrapper.kt  | 17 ++++++-
 .../snyk/common/lsp/commands/Commands.kt      |  1 +
 .../test-fixtures/oss/annotator/go.sum        | 50 +++++++++++++++++++
 4 files changed, 71 insertions(+), 6 deletions(-)
 create mode 100644 src/test/resources/test-fixtures/oss/annotator/go.sum

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index acc38e49c..df5aadf67 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -33,11 +33,12 @@ class GenerateAIFixHandler(private val project: Project) {
                         window.aiFixQuery = function(value) { ${aiFixQuery.inject("value")} };
 
                         const aiFixButton = document.getElementById('generate-ai-fix');
+                        const issueId = aiFixButton.getAttribute('issue-id');
+                        const folderPath = aiFixButton.getAttribute('folder-path');
+                        const filePath = aiFixButton.getAttribute('file-path');
+
                         aiFixButton.addEventListener('click', () => {
-                            const folderURI = "someFolderURI"; // These should be dynamically set
-                            const fileURI = "someFileURI";
-                            const issueID = "someIssueID";
-                            window.aiFixQuery(folderURI + ":" + fileURI + ":" + issueID);
+                            window.aiFixQuery(folderPath + ":" + filePath + ":" + issueId);
                         });
                     })();
                     """
diff --git a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
index 850ff052f..3985c72c7 100644
--- a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
+++ b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
@@ -46,6 +46,7 @@ import org.eclipse.lsp4j.services.LanguageServer
 import org.jetbrains.concurrency.runAsync
 import snyk.common.EnvironmentHelper
 import snyk.common.getEndpointUrl
+import snyk.common.lsp.commands.COMMAND_CODE_FIX_DIFFS
 import snyk.common.lsp.commands.COMMAND_COPY_AUTH_LINK
 import snyk.common.lsp.commands.COMMAND_EXECUTE_CLI
 import snyk.common.lsp.commands.COMMAND_GET_ACTIVE_USER
@@ -494,8 +495,20 @@ class LanguageServerWrapper(
         return this.getFeatureFlagStatus("snykCodeConsistentIgnores")
     }
 
-    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String) {
-        println("[[sendCodeFixDiffsCommand]]")
+    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): Boolean {
+        if (!ensureLanguageServerInitialized()) return false
+
+        try {
+            val param = ExecuteCommandParams()
+            param.command = COMMAND_CODE_FIX_DIFFS
+            param.arguments = listOf(folderURI, fileURI, issueID)
+            val result = languageServer.workspaceService.executeCommand(param).get(30, TimeUnit.SECONDS)
+            println(result)
+            return result as? Boolean ?: false
+        } catch (err: Exception) {
+            println("[[sendCodeFixDiffsCommand]]: $err")
+            return false
+        }
     }
 
     private fun ensureLanguageServerProtocolVersion(project: Project) {
diff --git a/src/main/kotlin/snyk/common/lsp/commands/Commands.kt b/src/main/kotlin/snyk/common/lsp/commands/Commands.kt
index 4cd3032b8..854c789bd 100644
--- a/src/main/kotlin/snyk/common/lsp/commands/Commands.kt
+++ b/src/main/kotlin/snyk/common/lsp/commands/Commands.kt
@@ -9,3 +9,4 @@ internal const val COMMAND_LOGIN = "snyk.login"
 internal const val COMMAND_LOGOUT = "snyk.logout"
 internal const val COMMAND_GET_SETTINGS_SAST_ENABLED = "snyk.getSettingsSastEnabled"
 internal const val COMMAND_COPY_AUTH_LINK = "snyk.copyAuthLink"
+internal const val COMMAND_CODE_FIX_DIFFS = "snyk.code.fixDiffs"
diff --git a/src/test/resources/test-fixtures/oss/annotator/go.sum b/src/test/resources/test-fixtures/oss/annotator/go.sum
new file mode 100644
index 000000000..084f63e60
--- /dev/null
+++ b/src/test/resources/test-fixtures/oss/annotator/go.sum
@@ -0,0 +1,50 @@
+github.com/Unknwon/com v0.0.0-20190321035513-0fed4efef755/go.mod h1:voKvFVpXBJxdIPeqjoJuLK+UVcRlo/JLjeToGxPYu68=
+github.com/Unknwon/i18n v0.0.0-20171114194641-b64d33658966/go.mod h1:SFtfq0zFPsENI7DpE87QM2hcYu5QQ0fRdCgP+P1Hrqo=
+github.com/bradfitz/gomemcache v0.0.0-20190329173943-551aad21a668/go.mod h1:H0wQNHz2YrLsuXOZozoeDmnHXkNCRmMW0gwFWDfEZDA=
+github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/fatih/color v1.7.0/go.mod h1:Zm6kSWBoL9eyXnKyktHP6abPY2pDugNf5KwzbycvMj4=
+github.com/gin-contrib/sse v0.0.0-20190301062529-5545eab6dad3/go.mod h1:VJ0WA2NBN22VlZ2dKZQPAPnyWw5XTlK1KymzLKsr59s=
+github.com/gin-gonic/gin v1.4.0/go.mod h1:OW2EZn3DO8Ln9oIKOvM++LBO+5UPHJJDH72/q/3rZdM=
+github.com/go-macaron/cache v0.0.0-20151013081102-561735312776/go.mod h1:hHAsZm/oBZVcY+S7qdQL6Vbg5VrXF6RuKGuqsszt3Ok=
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+github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
+github.com/gopherjs/gopherjs v0.0.0-20181103185306-d547d1d9531e/go.mod h1:wJfORRmW1u3UXTncJ5qlYoELFm8eSnnEO6hX4iZ3EWY=
+github.com/json-iterator/go v1.1.6/go.mod h1:+SdeFBvtyEkXs7REEP0seUULqWtbJapLOCVDaaPEHmU=
+github.com/jtolds/gls v4.2.1+incompatible/go.mod h1:QJZ7F/aHp+rZTRtaJ1ow/lLfFfVYBRgL+9YlvaHOwJU=
+github.com/mattn/go-colorable v0.1.2/go.mod h1:U0ppj6V5qS13XJ6of8GYAs25YV2eR4EVcfRqFIhoBtE=
+github.com/mattn/go-isatty v0.0.7/go.mod h1:Iq45c/XA43vh69/j3iqttzPXn0bhXyGjM0Hdxcsrc5s=
+github.com/mattn/go-isatty v0.0.8/go.mod h1:Iq45c/XA43vh69/j3iqttzPXn0bhXyGjM0Hdxcsrc5s=
+github.com/mcuadros/go-version v0.0.0-20190308113854-92cdf37c5b75/go.mod h1:76rfSfYPWj01Z85hUf/ituArm797mNKcvINh1OlsZKo=
+github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
+github.com/modern-go/reflect2 v1.0.1/go.mod h1:bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=
+github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
+github.com/pstember/go-goof/hello v0.0.0-20190715094659-dd899fd4135f/go.mod h1:bsBXgfaZj2NmBzMOxU6GNMwExj6oxUkXV1mY3hJRk/4=
+github.com/saintfish/chardet v0.0.0-20120816061221-3af4cd4741ca/go.mod h1:uugorj2VCxiV1x+LzaIdVa9b4S4qGAcH6cbhh4qVxOU=
+github.com/smartystreets/assertions v0.0.0-20190116191733-b6c0e53d7304/go.mod h1:OnSkiWE9lh6wB0YB77sQom3nweQdgAjqCqsofrRNTgc=
+github.com/smartystreets/goconvey v0.0.0-20181108003508-044398e4856c/go.mod h1:XDJAKZRPZ1CvBcN2aX5YOUTYGHki24fSF0Iv48Ibg0s=
+github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
+github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc=
+golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
+golang.org/x/net v0.0.0-20190503192946-f4e77d36d62c/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
+golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
+golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20190222072716-a9d3bda3a223/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/text v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
+golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
+gopkg.in/bufio.v1 v1.0.0-20140618132640-567b2bfa514e/go.mod h1:xsQCaysVCudhrYTfzYWe577fCe7Ceci+6qjO2Rdc0Z4=
+gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/clog.v1 v1.2.0/go.mod h1:L6fgdpdhFgKX4eGuDvt+N6X2GwZE160NRrIHzvaF8ZM=
+gopkg.in/go-playground/assert.v1 v1.2.1/go.mod h1:9RXL0bg/zibRAgZUYszZSwO/z8Y/a8bDuhia5mkpMnE=
+gopkg.in/go-playground/validator.v8 v8.18.2/go.mod h1:RX2a/7Ha8BgOhfk7j780h4/u/RRjR0eouCJSH80/M2Y=
+gopkg.in/ini.v1 v1.44.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k=
+gopkg.in/macaron.v1 v1.3.2/go.mod h1:PrsiawTWAGZs6wFbT5hlr7SQ2Ns9h7cUVtcUu4lQOVo=
+gopkg.in/redis.v2 v2.3.2/go.mod h1:4wl9PJ/CqzeHk3LVq1hNLHH8krm3+AXEgut4jVc++LU=
+gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+rsc.io/quote v1.5.2/go.mod h1:LzX7hefJvL54yjefDEDHNONDjII0t9xZLPXsUe+TKr0=
+rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA=

From b1566535f696cda6e7fcb5bf89c9629ec16230a0 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 4 Sep 2024 09:38:02 +0100
Subject: [PATCH 04/28] debug: test Language Server response

---
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    | 13 ++++++-
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 24 ++++++++++++
 .../snyk/common/lsp/LanguageServerWrapper.kt  | 39 +++++++++++++++----
 3 files changed, 68 insertions(+), 8 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index df5aadf67..29dd80b69 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -1,3 +1,4 @@
+import com.google.gson.Gson
 import com.intellij.openapi.project.Project
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.ui.jcef.JBCefJSQuery
@@ -18,7 +19,16 @@ class GenerateAIFixHandler(private val project: Project) {
 
             println("Received folderURI: $folderURI, fileURI: $fileURI, issueID: $issueID")
 
-            LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
+            val responseDiff: List<LanguageServerWrapper.Fix> = LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
+            println("Received responseDiff: $responseDiff")
+            responseDiff.forEach { fix ->
+                println("Fix: $fix")
+            }
+
+            val script = """
+                window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
+           """
+            jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
             JBCefJSQuery.Response("success")
         }
 
@@ -38,6 +48,7 @@ class GenerateAIFixHandler(private val project: Project) {
                         const filePath = aiFixButton.getAttribute('file-path');
 
                         aiFixButton.addEventListener('click', () => {
+                            console.log('Clicked AI Fix button. Path: ' + folderPath + ':' + filePath + ':' + issueId)
                             window.aiFixQuery(folderPath + ":" + filePath + ":" + issueId);
                         });
                     })();
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index 398023c7e..38e75ffe7 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -192,13 +192,37 @@ class SuggestionDescriptionPanelFromLS(
                 }
 
                 const generateAiFixBtn = document.getElementById('generate-ai-fix');
+                const loadingIndicator = document.getElementById('fix-loading-indicator');
+                const fixesSection = document.getElementById('fixes-section');
+                const diffContainer = document.getElementById('diff');
 
                 function generateAIFix() {
                     toggleElement(generateAiFixBtn, 'hide');
                     toggleElement(document.getElementById('fix-loading-indicator'), 'show');
                 }
 
+                function showAIFixes(fixes) {
+                    toggleElement(loadingIndicator, 'hide');
+                    toggleElement(fixesSection, 'show');
+
+                    if (fixes.length > 0) {
+                        diffContainer.innerHTML = fixes.map(fix => `
+                            <div>
+                                <h3>Fix ID: ${'$'}{fix.fixId}</h3>
+                                <pre>${'$'}{fix.unifiedDiffsPerFile['/Users/cata/git/playground/project-with-vulns/lib/insecurity.ts']}</pre>
+                            </div>
+                        `).join('');
+                    } else {
+                        diffContainer.innerHTML = '<p>No fixes available.</p>';
+                    }
+                }
+
                 generateAiFixBtn?.addEventListener('click', generateAIFix);
+
+                // This function will be called once the response is received from the LS
+                window.receiveAIFixResponse = function(fixes) {
+                    showAIFixes(fixes);
+                };
             })();
         """.trimIndent()
     }
diff --git a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
index 3985c72c7..01ea831e5 100644
--- a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
+++ b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
@@ -1,6 +1,7 @@
 package snyk.common.lsp
 
 import com.google.gson.Gson
+import com.google.gson.reflect.TypeToken
 import com.intellij.openapi.Disposable
 import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.components.service
@@ -495,22 +496,46 @@ class LanguageServerWrapper(
         return this.getFeatureFlagStatus("snykCodeConsistentIgnores")
     }
 
-    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): Boolean {
-        if (!ensureLanguageServerInitialized()) return false
+    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): List<Fix>  {
+        println(">> sendCodeFixDiffsCommand: $folderURI, $fileURI, $issueID")
+        if (!ensureLanguageServerInitialized()) return emptyList()
 
         try {
             val param = ExecuteCommandParams()
             param.command = COMMAND_CODE_FIX_DIFFS
             param.arguments = listOf(folderURI, fileURI, issueID)
-            val result = languageServer.workspaceService.executeCommand(param).get(30, TimeUnit.SECONDS)
-            println(result)
-            return result as? Boolean ?: false
+            val result = languageServer.workspaceService.executeCommand(param).get(120, TimeUnit.SECONDS) as Map<*, *>
+//            result["unifiedDiffsPerFile"]
+            val diff = result["unifiedDiffsPerFile"]
+            println(diff)
+            // and parse to an JSON object
+//            println(result)
+//            return parseResponse(result.toString())
+            return result as List<Fix>
         } catch (err: Exception) {
-            println("[[sendCodeFixDiffsCommand]]: $err")
-            return false
+            logger.warn("Error in sendCodeFixDiffsCommand", err)
+            return emptyList()
         }
     }
 
+    data class Fix(
+        val fixId: String,
+        val unifiedDiffsPerFile: Map<String, String>
+    )
+
+    private fun parseResponse(response: String): List<Fix> {
+        val gson = Gson()
+        val processedResponse = preprocessResponse(response)
+        val type = object : TypeToken<List<Fix>>() {}.type
+        return gson.fromJson(processedResponse, type)
+    }
+
+    private fun preprocessResponse(response: String): String {
+        val processed = response.replace("=", ":")
+        println("Processed response: $processed")
+        return processed
+    }
+
     private fun ensureLanguageServerProtocolVersion(project: Project) {
         val protocolVersion = initializeResult?.serverInfo?.version
         pluginSettings().currentLSProtocolVersion = protocolVersion?.toIntOrNull()

From 575fa56941689630a56c9ea1eed8608aa8126f0b Mon Sep 17 00:00:00 2001
From: Bastian Doetsch <bastian.doetsch@snyk.io>
Date: Wed, 4 Sep 2024 11:00:14 +0200
Subject: [PATCH 05/28] fix: wip parsing of command

---
 .../snyk/common/lsp/LanguageServerWrapper.kt  | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
index 01ea831e5..b6f310107 100644
--- a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
+++ b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
@@ -1,6 +1,7 @@
 package snyk.common.lsp
 
 import com.google.gson.Gson
+import com.google.gson.annotations.SerializedName
 import com.google.gson.reflect.TypeToken
 import com.intellij.openapi.Disposable
 import com.intellij.openapi.application.ApplicationManager
@@ -496,6 +497,7 @@ class LanguageServerWrapper(
         return this.getFeatureFlagStatus("snykCodeConsistentIgnores")
     }
 
+    @Suppress("UNCHECKED_CAST")
     fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): List<Fix>  {
         println(">> sendCodeFixDiffsCommand: $folderURI, $fileURI, $issueID")
         if (!ensureLanguageServerInitialized()) return emptyList()
@@ -504,14 +506,14 @@ class LanguageServerWrapper(
             val param = ExecuteCommandParams()
             param.command = COMMAND_CODE_FIX_DIFFS
             param.arguments = listOf(folderURI, fileURI, issueID)
-            val result = languageServer.workspaceService.executeCommand(param).get(120, TimeUnit.SECONDS) as Map<*, *>
-//            result["unifiedDiffsPerFile"]
-            val diff = result["unifiedDiffsPerFile"]
-            println(diff)
-            // and parse to an JSON object
-//            println(result)
-//            return parseResponse(result.toString())
-            return result as List<Fix>
+            val result = languageServer.workspaceService.executeCommand(param).get(120, TimeUnit.SECONDS) as List<*>
+            val diffList : MutableList<Fix> = mutableListOf()
+            result.forEach {
+                val entry = it as Map<String, *>
+                val fix = Fix(entry["fixId"]!! as String, entry["unifiedDiffsPerFile"] as Map<String, String>)
+                diffList.add(fix)
+            }
+            return diffList
         } catch (err: Exception) {
             logger.warn("Error in sendCodeFixDiffsCommand", err)
             return emptyList()
@@ -519,8 +521,8 @@ class LanguageServerWrapper(
     }
 
     data class Fix(
-        val fixId: String,
-        val unifiedDiffsPerFile: Map<String, String>
+        @SerializedName("fixId") val fixId: String,
+        @SerializedName("unifiedDiffsPerFile") val unifiedDiffsPerFile: Map<String, String>
     )
 
     private fun parseResponse(response: String): List<Fix> {

From 7421d80207cf6eff4d758beb60c4eb9da5707978 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 4 Sep 2024 13:33:46 +0100
Subject: [PATCH 06/28] =?UTF-8?q?feat:=20display=20AI=20suggestions=20?=
 =?UTF-8?q?=E2=9A=A1=EF=B8=8F?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    |  17 +-
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 151 +++++++++++++-----
 .../snyk/common/lsp/LanguageServerWrapper.kt  |  37 ++---
 .../test-fixtures/oss/annotator/go.sum        |  50 ------
 4 files changed, 132 insertions(+), 123 deletions(-)
 delete mode 100644 src/test/resources/test-fixtures/oss/annotator/go.sum

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index 29dd80b69..0d18244b2 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -1,3 +1,5 @@
+package io.snyk.plugin.ui.jcef
+
 import com.google.gson.Gson
 import com.intellij.openapi.project.Project
 import com.intellij.ui.jcef.JBCefBrowserBase
@@ -16,18 +18,13 @@ class GenerateAIFixHandler(private val project: Project) {
             val folderURI = params[0]
             val fileURI = params[1]
             val issueID = params[2]
+            JBCefJSQuery.Response("success")
 
-            println("Received folderURI: $folderURI, fileURI: $fileURI, issueID: $issueID")
-
-            val responseDiff: List<LanguageServerWrapper.Fix> = LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
-            println("Received responseDiff: $responseDiff")
-            responseDiff.forEach { fix ->
-                println("Fix: $fix")
-            }
-
+            val responseDiff: List<LanguageServerWrapper.Fix> =
+                LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
             val script = """
-                window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
-           """
+                    window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
+                """.trimIndent()
             jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
             JBCefJSQuery.Response("success")
         }
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index 38e75ffe7..b50a2f320 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -1,6 +1,6 @@
 package io.snyk.plugin.ui.toolwindow.panels
 
-import GenerateAIFixHandler
+import io.snyk.plugin.ui.jcef.GenerateAIFixHandler
 import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.openapi.vfs.VirtualFileManager
 import com.intellij.uiDesigner.core.GridLayoutManager
@@ -31,9 +31,9 @@ class SuggestionDescriptionPanelFromLS(
     snykFile: SnykFile,
     private val issue: ScanIssue,
 ) : IssueDescriptionPanelBase(
-        title = issue.title(),
-        severity = issue.getSeverityAsEnum(),
-    ) {
+    title = issue.title(),
+    severity = issue.getSeverityAsEnum(),
+) {
     val project = snykFile.project
     private val unexpectedErrorMessage =
         "Snyk encountered an issue while rendering the vulnerability description. Please try again, or contact support if the problem persists. We apologize for any inconvenience caused."
@@ -161,7 +161,7 @@ class SuggestionDescriptionPanelFromLS(
 
         html = html.replace("\${ideStyle}", "<style nonce=\${nonce}>$ideStyle</style>")
         html = html.replace("\${headerEnd}", "")
-        html = html.replace("\${ideScript}" ,"<script nonce=\${nonce}>$ideScript</script>")
+        html = html.replace("\${ideScript}", "<script nonce=\${nonce}>$ideScript</script>")
 
         val nonce = getNonce()
         html = html.replace("\${nonce}", nonce)
@@ -179,50 +179,119 @@ class SuggestionDescriptionPanelFromLS(
     private fun getCustomScript(): String {
         return """
             (function () {
-                function toggleElement(element, toggle) {
-                    if (!element) return;
-
-                    if (toggle === 'show') {
-                        element.classList.remove('hidden');
-                    } else if (toggle === 'hide') {
-                        element.classList.add('hidden');
-                    } else {
-                        console.error('Unexpected toggle value', toggle);
-                    }
+              function toggleElement(element, toggle) {
+                if (!element) return;
+
+                if (toggle === "show") {
+                  element.classList.remove("hidden");
+                } else if (toggle === "hide") {
+                  element.classList.add("hidden");
+                } else {
+                  console.error("Unexpected toggle value", toggle);
                 }
+              }
 
-                const generateAiFixBtn = document.getElementById('generate-ai-fix');
-                const loadingIndicator = document.getElementById('fix-loading-indicator');
-                const fixesSection = document.getElementById('fixes-section');
-                const diffContainer = document.getElementById('diff');
+              let diffSelectedIndex = 0;
 
-                function generateAIFix() {
-                    toggleElement(generateAiFixBtn, 'hide');
-                    toggleElement(document.getElementById('fix-loading-indicator'), 'show');
-                }
+              const generateAiFixBtn = document.getElementById("generate-ai-fix");
+              const loadingIndicator = document.getElementById("fix-loading-indicator");
+              const fixWrapperElem = document.getElementById("fix-wrapper");
+              const fixSectionElem = document.getElementById("fixes-section");
+
+              const diffSelectedIndexElem = document.getElementById("diff-counter");
+
+              const diffTopElem = document.getElementById("diff-top");
+              const diffElem = document.getElementById("diff");
+              const noDiffsElem = document.getElementById("info-no-diffs");
+
+              const diffNumElem = document.getElementById("diff-number");
+              const diffNum2Elem = document.getElementById("diff-number2");
+
+              function generateAIFix() {
+                toggleElement(generateAiFixBtn, "hide");
+                toggleElement(loadingIndicator, "show");
+              }
+
+              function generateDiffHtml(patch) {
+                const codeLines = patch.split("\n");
+
+                // the first two lines are the file names
+                codeLines.shift();
+                codeLines.shift();
+
+                const diffHtml = document.createElement("div");
+                let blockDiv = null;
+
+                for (const line of codeLines) {
+                  if (line.startsWith("@@ ")) {
+                    blockDiv = document.createElement("div");
+                    blockDiv.className = "example";
+
+                    if (blockDiv) {
+                      diffHtml.appendChild(blockDiv);
+                    }
+                  } else {
+                    const lineDiv = document.createElement("div");
+                    lineDiv.className = "example-line";
 
-                function showAIFixes(fixes) {
-                    toggleElement(loadingIndicator, 'hide');
-                    toggleElement(fixesSection, 'show');
-
-                    if (fixes.length > 0) {
-                        diffContainer.innerHTML = fixes.map(fix => `
-                            <div>
-                                <h3>Fix ID: ${'$'}{fix.fixId}</h3>
-                                <pre>${'$'}{fix.unifiedDiffsPerFile['/Users/cata/git/playground/project-with-vulns/lib/insecurity.ts']}</pre>
-                            </div>
-                        `).join('');
-                    } else {
-                        diffContainer.innerHTML = '<p>No fixes available.</p>';
+                    if (line.startsWith("+")) {
+                      lineDiv.classList.add("added");
+                    } else if (line.startsWith("-")) {
+                      lineDiv.classList.add("removed");
                     }
+
+                    const lineCode = document.createElement("code");
+                    // if line is empty, we need to fallback to ' '
+                    // to make sure it displays in the diff
+                    lineCode.innerText = line.slice(1, line.length) || " ";
+
+                    lineDiv.appendChild(lineCode);
+                    blockDiv?.appendChild(lineDiv);
+                  }
                 }
 
-                generateAiFixBtn?.addEventListener('click', generateAIFix);
+                return diffHtml;
+              }
+
+              function getFilePathFromFix(fix) {
+                return Object.keys(fix.unifiedDiffsPerFile)[0];
+              }
+
+              function showCurrentDiff(fixes) {
+                toggleElement(diffTopElem, "show");
+                toggleElement(diffElem, "show");
+                toggleElement(noDiffsElem, "hide");
+
+                diffNumElem.innerText = fixes.length.toString();
+                diffNum2Elem.innerText = fixes.length.toString();
+
+                diffSelectedIndexElem.innerText = (diffSelectedIndex + 1).toString();
+
+                const diffSuggestion = fixes[diffSelectedIndex];
+                const filePath = getFilePathFromFix(diffSuggestion);
+                const patch = diffSuggestion.unifiedDiffsPerFile[filePath];
+
+                // clear all elements
+                while (diffElem.firstChild) {
+                  diffElem.removeChild(diffElem.firstChild);
+                }
+                diffElem.appendChild(generateDiffHtml(patch));
+              }
+
+              function showAIFixes(fixes) {
+                toggleElement(fixSectionElem, "show");
+                toggleElement(loadingIndicator, "hide");
+                toggleElement(fixWrapperElem, "hide");
+
+                showCurrentDiff(fixes);
+              }
+
+              generateAiFixBtn?.addEventListener("click", generateAIFix);
 
-                // This function will be called once the response is received from the LS
-                window.receiveAIFixResponse = function(fixes) {
-                    showAIFixes(fixes);
-                };
+              // This function will be called once the response is received from the LS
+              window.receiveAIFixResponse = function (fixes) {
+                showAIFixes(fixes);
+              };
             })();
         """.trimIndent()
     }
diff --git a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
index b6f310107..1bbb72f05 100644
--- a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
+++ b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
@@ -497,9 +497,13 @@ class LanguageServerWrapper(
         return this.getFeatureFlagStatus("snykCodeConsistentIgnores")
     }
 
+    data class Fix(
+        @SerializedName("fixId") val fixId: String,
+        @SerializedName("unifiedDiffsPerFile") val unifiedDiffsPerFile: Map<String, String>
+    )
+
     @Suppress("UNCHECKED_CAST")
-    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): List<Fix>  {
-        println(">> sendCodeFixDiffsCommand: $folderURI, $fileURI, $issueID")
+    fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): List<Fix> {
         if (!ensureLanguageServerInitialized()) return emptyList()
 
         try {
@@ -507,11 +511,17 @@ class LanguageServerWrapper(
             param.command = COMMAND_CODE_FIX_DIFFS
             param.arguments = listOf(folderURI, fileURI, issueID)
             val result = languageServer.workspaceService.executeCommand(param).get(120, TimeUnit.SECONDS) as List<*>
-            val diffList : MutableList<Fix> = mutableListOf()
+            val diffList: MutableList<Fix> = mutableListOf()
+
             result.forEach {
                 val entry = it as Map<String, *>
-                val fix = Fix(entry["fixId"]!! as String, entry["unifiedDiffsPerFile"] as Map<String, String>)
-                diffList.add(fix)
+                val fixId = entry["fixId"] as? String
+                val unifiedDiffsPerFile = entry["unifiedDiffsPerFile"] as? Map<String, String>
+
+                if (fixId != null && unifiedDiffsPerFile != null) {
+                    val fix = Fix(fixId, unifiedDiffsPerFile)
+                    diffList.add(fix)
+                }
             }
             return diffList
         } catch (err: Exception) {
@@ -520,23 +530,6 @@ class LanguageServerWrapper(
         }
     }
 
-    data class Fix(
-        @SerializedName("fixId") val fixId: String,
-        @SerializedName("unifiedDiffsPerFile") val unifiedDiffsPerFile: Map<String, String>
-    )
-
-    private fun parseResponse(response: String): List<Fix> {
-        val gson = Gson()
-        val processedResponse = preprocessResponse(response)
-        val type = object : TypeToken<List<Fix>>() {}.type
-        return gson.fromJson(processedResponse, type)
-    }
-
-    private fun preprocessResponse(response: String): String {
-        val processed = response.replace("=", ":")
-        println("Processed response: $processed")
-        return processed
-    }
 
     private fun ensureLanguageServerProtocolVersion(project: Project) {
         val protocolVersion = initializeResult?.serverInfo?.version
diff --git a/src/test/resources/test-fixtures/oss/annotator/go.sum b/src/test/resources/test-fixtures/oss/annotator/go.sum
deleted file mode 100644
index 084f63e60..000000000
--- a/src/test/resources/test-fixtures/oss/annotator/go.sum
+++ /dev/null
@@ -1,50 +0,0 @@
-github.com/Unknwon/com v0.0.0-20190321035513-0fed4efef755/go.mod h1:voKvFVpXBJxdIPeqjoJuLK+UVcRlo/JLjeToGxPYu68=
-github.com/Unknwon/i18n v0.0.0-20171114194641-b64d33658966/go.mod h1:SFtfq0zFPsENI7DpE87QM2hcYu5QQ0fRdCgP+P1Hrqo=
-github.com/bradfitz/gomemcache v0.0.0-20190329173943-551aad21a668/go.mod h1:H0wQNHz2YrLsuXOZozoeDmnHXkNCRmMW0gwFWDfEZDA=
-github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/fatih/color v1.7.0/go.mod h1:Zm6kSWBoL9eyXnKyktHP6abPY2pDugNf5KwzbycvMj4=
-github.com/gin-contrib/sse v0.0.0-20190301062529-5545eab6dad3/go.mod h1:VJ0WA2NBN22VlZ2dKZQPAPnyWw5XTlK1KymzLKsr59s=
-github.com/gin-gonic/gin v1.4.0/go.mod h1:OW2EZn3DO8Ln9oIKOvM++LBO+5UPHJJDH72/q/3rZdM=
-github.com/go-macaron/cache v0.0.0-20151013081102-561735312776/go.mod h1:hHAsZm/oBZVcY+S7qdQL6Vbg5VrXF6RuKGuqsszt3Ok=
-github.com/go-macaron/inject v0.0.0-20160627170012-d8a0b8677191/go.mod h1:VFI2o2q9kYsC4o7VP1HrEVosiZZTd+MVT3YZx4gqvJw=
-github.com/go-macaron/session v0.0.0-20190131233854-0a0a789bf193/go.mod h1:ScEJm9Gk+ez5JJTml5WlBIqavAfuE5nF8e4Gvyz/X+A=
-github.com/gogs/chardet v0.0.0-20150115103509-2404f7772561/go.mod h1:Pcatq5tYkCW2Q6yrR2VRHlbHpZ/R4/7qyL1TCF7vl14=
-github.com/gogs/go-libravatar v0.0.0-20161120025154-cd1abbd55d09/go.mod h1:Zas3BtO88pk1cwUfEYlvnl/CRwh0ybDxRWSwRjG8I3w=
-github.com/gogs/gogs v0.11.66/go.mod h1:qlbvdn16XTC6q7eR+thjW+OLdN+mi2PBZ8KqVT39T88=
-github.com/gogs/minwinsvc v0.0.0-20170301035411-95be6356811a/go.mod h1:TUIZ+29jodWQ8Gk6Pvtg4E09aMsc3C/VLZiVYfUhWQU=
-github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
-github.com/gopherjs/gopherjs v0.0.0-20181103185306-d547d1d9531e/go.mod h1:wJfORRmW1u3UXTncJ5qlYoELFm8eSnnEO6hX4iZ3EWY=
-github.com/json-iterator/go v1.1.6/go.mod h1:+SdeFBvtyEkXs7REEP0seUULqWtbJapLOCVDaaPEHmU=
-github.com/jtolds/gls v4.2.1+incompatible/go.mod h1:QJZ7F/aHp+rZTRtaJ1ow/lLfFfVYBRgL+9YlvaHOwJU=
-github.com/mattn/go-colorable v0.1.2/go.mod h1:U0ppj6V5qS13XJ6of8GYAs25YV2eR4EVcfRqFIhoBtE=
-github.com/mattn/go-isatty v0.0.7/go.mod h1:Iq45c/XA43vh69/j3iqttzPXn0bhXyGjM0Hdxcsrc5s=
-github.com/mattn/go-isatty v0.0.8/go.mod h1:Iq45c/XA43vh69/j3iqttzPXn0bhXyGjM0Hdxcsrc5s=
-github.com/mcuadros/go-version v0.0.0-20190308113854-92cdf37c5b75/go.mod h1:76rfSfYPWj01Z85hUf/ituArm797mNKcvINh1OlsZKo=
-github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
-github.com/modern-go/reflect2 v1.0.1/go.mod h1:bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=
-github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
-github.com/pstember/go-goof/hello v0.0.0-20190715094659-dd899fd4135f/go.mod h1:bsBXgfaZj2NmBzMOxU6GNMwExj6oxUkXV1mY3hJRk/4=
-github.com/saintfish/chardet v0.0.0-20120816061221-3af4cd4741ca/go.mod h1:uugorj2VCxiV1x+LzaIdVa9b4S4qGAcH6cbhh4qVxOU=
-github.com/smartystreets/assertions v0.0.0-20190116191733-b6c0e53d7304/go.mod h1:OnSkiWE9lh6wB0YB77sQom3nweQdgAjqCqsofrRNTgc=
-github.com/smartystreets/goconvey v0.0.0-20181108003508-044398e4856c/go.mod h1:XDJAKZRPZ1CvBcN2aX5YOUTYGHki24fSF0Iv48Ibg0s=
-github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
-github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
-github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc=
-golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
-golang.org/x/net v0.0.0-20190503192946-f4e77d36d62c/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
-golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
-golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
-golang.org/x/sys v0.0.0-20190222072716-a9d3bda3a223/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
-golang.org/x/text v0.0.0-20170915032832-14c0d48ead0c/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
-golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
-gopkg.in/bufio.v1 v1.0.0-20140618132640-567b2bfa514e/go.mod h1:xsQCaysVCudhrYTfzYWe577fCe7Ceci+6qjO2Rdc0Z4=
-gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/clog.v1 v1.2.0/go.mod h1:L6fgdpdhFgKX4eGuDvt+N6X2GwZE160NRrIHzvaF8ZM=
-gopkg.in/go-playground/assert.v1 v1.2.1/go.mod h1:9RXL0bg/zibRAgZUYszZSwO/z8Y/a8bDuhia5mkpMnE=
-gopkg.in/go-playground/validator.v8 v8.18.2/go.mod h1:RX2a/7Ha8BgOhfk7j780h4/u/RRjR0eouCJSH80/M2Y=
-gopkg.in/ini.v1 v1.44.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k=
-gopkg.in/macaron.v1 v1.3.2/go.mod h1:PrsiawTWAGZs6wFbT5hlr7SQ2Ns9h7cUVtcUu4lQOVo=
-gopkg.in/redis.v2 v2.3.2/go.mod h1:4wl9PJ/CqzeHk3LVq1hNLHH8krm3+AXEgut4jVc++LU=
-gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
-rsc.io/quote v1.5.2/go.mod h1:LzX7hefJvL54yjefDEDHNONDjII0t9xZLPXsUe+TKr0=
-rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA=

From ff1400b56cac820c5333618595c27ec424400210 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 4 Sep 2024 14:56:37 +0100
Subject: [PATCH 07/28] chore: update `Apply fix` button style

---
 .../stylesheets/snyk_code_suggestion.scss     | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/main/resources/stylesheets/snyk_code_suggestion.scss b/src/main/resources/stylesheets/snyk_code_suggestion.scss
index a100fb5b0..d0cad3c6a 100644
--- a/src/main/resources/stylesheets/snyk_code_suggestion.scss
+++ b/src/main/resources/stylesheets/snyk_code_suggestion.scss
@@ -109,15 +109,30 @@ a,
   display: none;
 }
 
+.example { // AI fix suggestion
+  background-color: var(--container-background-color);
+}
+
+.sn-ai-fixes {
+  padding-top: 20px;
+}
+
 .sn-fix-wrapper {
   background-color: var(--container-background-color);  // same variable used in snyk_oss_suggestion.scss
 }
 
-button.generate-ai-fix {
+button.generate-ai-fix, button.sn-apply-fix {
   background-color: var(--generated-ai-fix-button-background-color);
   color: white;
 }
 
-button.generate-ai-fix:hover {
+button.generate-ai-fix:hover, button.sn-apply-fix:hover {
   opacity: 0.9; /* Slightly reduces opacity on hover */
 }
+
+button.sn-apply-fix {
+  border-radius: 3px;
+  border: 1px solid var(--dark-button-border-default, #4C708C); // TODO: define the variable in the ThemeBasedStylingGenerator class to be theme-based
+  background: var(--dark-button-default, #365880); // TODO: define the variable in the ThemeBasedStylingGenerator class to be theme-based
+  padding: 4px 12px;
+}

From 8a4b2719948def63cf5d7ca019b14210081c2e0a Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 4 Sep 2024 15:31:36 +0100
Subject: [PATCH 08/28] chore: group similar JS logic

---
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 109 ++++++++----------
 1 file changed, 51 insertions(+), 58 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index b50a2f320..abff6ab41 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -179,116 +179,109 @@ class SuggestionDescriptionPanelFromLS(
     private fun getCustomScript(): String {
         return """
             (function () {
-              function toggleElement(element, toggle) {
+              // Utility function to show/hide an element based on a toggle value
+              function toggleElement(element, action) {
                 if (!element) return;
-
-                if (toggle === "show") {
-                  element.classList.remove("hidden");
-                } else if (toggle === "hide") {
-                  element.classList.add("hidden");
-                } else {
-                  console.error("Unexpected toggle value", toggle);
-                }
-              }
-
-              let diffSelectedIndex = 0;
-
-              const generateAiFixBtn = document.getElementById("generate-ai-fix");
-              const loadingIndicator = document.getElementById("fix-loading-indicator");
-              const fixWrapperElem = document.getElementById("fix-wrapper");
-              const fixSectionElem = document.getElementById("fixes-section");
-
-              const diffSelectedIndexElem = document.getElementById("diff-counter");
-
-              const diffTopElem = document.getElementById("diff-top");
-              const diffElem = document.getElementById("diff");
-              const noDiffsElem = document.getElementById("info-no-diffs");
-
-              const diffNumElem = document.getElementById("diff-number");
-              const diffNum2Elem = document.getElementById("diff-number2");
-
-              function generateAIFix() {
-                toggleElement(generateAiFixBtn, "hide");
-                toggleElement(loadingIndicator, "show");
+                element.classList.toggle("hidden", action === "hide");
               }
 
+              // Generate HTML for the code diff from a patch
               function generateDiffHtml(patch) {
                 const codeLines = patch.split("\n");
-
-                // the first two lines are the file names
-                codeLines.shift();
-                codeLines.shift();
+                codeLines.splice(0, 2); // Skip the first two lines (file paths)
 
                 const diffHtml = document.createElement("div");
                 let blockDiv = null;
 
-                for (const line of codeLines) {
+                codeLines.forEach(line => {
                   if (line.startsWith("@@ ")) {
+                    // Start a new block for a diff hunk
                     blockDiv = document.createElement("div");
                     blockDiv.className = "example";
-
-                    if (blockDiv) {
-                      diffHtml.appendChild(blockDiv);
-                    }
+                    diffHtml.appendChild(blockDiv);
                   } else {
+                    // Generate a line div and apply the appropriate class based on addition/removal
                     const lineDiv = document.createElement("div");
                     lineDiv.className = "example-line";
-
                     if (line.startsWith("+")) {
                       lineDiv.classList.add("added");
                     } else if (line.startsWith("-")) {
                       lineDiv.classList.add("removed");
                     }
 
+                    // Create a <code> block for the line content
                     const lineCode = document.createElement("code");
-                    // if line is empty, we need to fallback to ' '
-                    // to make sure it displays in the diff
-                    lineCode.innerText = line.slice(1, line.length) || " ";
-
+                    lineCode.innerText = line.slice(1) || " "; // Ensure empty lines display properly
                     lineDiv.appendChild(lineCode);
-                    blockDiv?.appendChild(lineDiv);
+
+                    blockDiv?.appendChild(lineDiv); // Append the line to the current block
                   }
-                }
+                });
 
                 return diffHtml;
               }
 
+              // Extract the file path from the AI fix object
               function getFilePathFromFix(fix) {
                 return Object.keys(fix.unifiedDiffsPerFile)[0];
               }
 
+              // Show the diff for the currently selected AI fix
               function showCurrentDiff(fixes) {
                 toggleElement(diffTopElem, "show");
                 toggleElement(diffElem, "show");
                 toggleElement(noDiffsElem, "hide");
 
-                diffNumElem.innerText = fixes.length.toString();
-                diffNum2Elem.innerText = fixes.length.toString();
+                const totalFixes = fixes.length;
+                const currentFix = fixes[diffSelectedIndex];
+                const filePath = getFilePathFromFix(currentFix);
+                const patch = currentFix.unifiedDiffsPerFile[filePath];
 
+                // Update diff counters
+                diffNumElem.innerText = totalFixes.toString();
+                diffNum2Elem.innerText = totalFixes.toString();
                 diffSelectedIndexElem.innerText = (diffSelectedIndex + 1).toString();
 
-                const diffSuggestion = fixes[diffSelectedIndex];
-                const filePath = getFilePathFromFix(diffSuggestion);
-                const patch = diffSuggestion.unifiedDiffsPerFile[filePath];
-
-                // clear all elements
-                while (diffElem.firstChild) {
-                  diffElem.removeChild(diffElem.firstChild);
-                }
+                // Clear and update the diff container
+                diffElem.innerHTML = ''; // Clear previous diff
                 diffElem.appendChild(generateDiffHtml(patch));
               }
 
+              // Show the AI fixes received from the Language Server
               function showAIFixes(fixes) {
                 toggleElement(fixSectionElem, "show");
-                toggleElement(loadingIndicator, "hide");
+                toggleElement(fixLoadingIndicatorElem, "hide");
                 toggleElement(fixWrapperElem, "hide");
 
                 showCurrentDiff(fixes);
               }
 
+              // Handle AI fix generation button click
+              function generateAIFix() {
+                toggleElement(generateAiFixBtn, "hide");
+                toggleElement(fixLoadingIndicatorElem, "show");
+              }
+
+              // DOM element references
+              const generateAiFixBtn = document.getElementById("generate-ai-fix");
+              const fixLoadingIndicatorElem = document.getElementById("fix-loading-indicator");
+              const fixWrapperElem = document.getElementById("fix-wrapper");
+              const fixSectionElem = document.getElementById("fixes-section");
+
+              const diffSelectedIndexElem = document.getElementById("diff-counter");
+              const diffTopElem = document.getElementById("diff-top");
+              const diffElem = document.getElementById("diff");
+              const noDiffsElem = document.getElementById("info-no-diffs");
+
+              const diffNumElem = document.getElementById("diff-number");
+              const diffNum2Elem = document.getElementById("diff-number2");
+
+              let diffSelectedIndex = 0;
+
+              // Event listener for Generate AI fix button
               generateAiFixBtn?.addEventListener("click", generateAIFix);
 
-              // This function will be called once the response is received from the LS
+              // This function will be called once the response is received from the Language Server
               window.receiveAIFixResponse = function (fixes) {
                 showAIFixes(fixes);
               };

From e03954ce668e84c09f11389603481a3c4963077e Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 4 Sep 2024 15:56:45 +0100
Subject: [PATCH 09/28] fix: responsive UI during AI Fix call with LS async
 request

---
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    | 34 ++++++++++++++-----
 1 file changed, 25 insertions(+), 9 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index 0d18244b2..54891b78b 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -4,6 +4,10 @@ import com.google.gson.Gson
 import com.intellij.openapi.project.Project
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.ui.jcef.JBCefJSQuery
+import kotlinx.coroutines.CoroutineScope
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.launch
+import kotlinx.coroutines.withContext
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
@@ -13,20 +17,32 @@ class GenerateAIFixHandler(private val project: Project) {
 
     fun generateAIFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
         val aiFixQuery = JBCefJSQuery.create(jbCefBrowser)
+
         aiFixQuery.addHandler { value ->
             val params = value.split(":")
             val folderURI = params[0]
             val fileURI = params[1]
             val issueID = params[2]
-            JBCefJSQuery.Response("success")
-
-            val responseDiff: List<LanguageServerWrapper.Fix> =
-                LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
-            val script = """
-                    window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
-                """.trimIndent()
-            jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-            JBCefJSQuery.Response("success")
+
+            // Avoids blocking the UI thread
+            CoroutineScope(Dispatchers.IO).launch {
+                try {
+                    val responseDiff: List<LanguageServerWrapper.Fix> =
+                        LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
+
+                    val script = """
+                        window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
+                    """.trimIndent()
+
+                    withContext(Dispatchers.Main) {
+                        jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                        JBCefJSQuery.Response("success")
+                    }
+                } catch (e: Exception) {
+                    e.printStackTrace()
+                }
+            }
+            return@addHandler JBCefJSQuery.Response("success")
         }
 
         return object : CefLoadHandlerAdapter() {

From 6c0b5fcaa93c18d55ffe2db2987f990aba48d8c0 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Wed, 4 Sep 2024 16:53:37 +0100
Subject: [PATCH 10/28] feat: wip - apply fix

---
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 27 ++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index abff6ab41..e393bcc70 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -262,8 +262,30 @@ class SuggestionDescriptionPanelFromLS(
                 toggleElement(fixLoadingIndicatorElem, "show");
               }
 
+              function applyFix() {
+                console.log('Applying fix', fixes);
+                if (!fixes.length) return;
+
+                const currentFix = fixes[diffSelectedIndex];
+                const filePath = getFilePathFromFix(currentFix);
+                const patch = currentFix.unifiedDiffsPerFile[filePath];
+
+                // Following VSCode logic, the steps are:
+                // 1. Read the current file content.
+                // 2. Apply a patch to that content.
+                // 3. Edit the file in the workspace.
+                // 4. Highlight the added code.
+                // 5. Setup close or save events.
+                 console.log('Applying fix', patch);
+              }
+
               // DOM element references
               const generateAiFixBtn = document.getElementById("generate-ai-fix");
+              const applyFixBtn = document.getElementById('apply-fix')
+              const retryGenerateFixBtn = document.getElementById('retry-generate-fix')
+
+              console.log('applyFixBtn', applyFixBtn)
+
               const fixLoadingIndicatorElem = document.getElementById("fix-loading-indicator");
               const fixWrapperElem = document.getElementById("fix-wrapper");
               const fixSectionElem = document.getElementById("fixes-section");
@@ -277,12 +299,15 @@ class SuggestionDescriptionPanelFromLS(
               const diffNum2Elem = document.getElementById("diff-number2");
 
               let diffSelectedIndex = 0;
+              let fixes = [];
 
               // Event listener for Generate AI fix button
               generateAiFixBtn?.addEventListener("click", generateAIFix);
+              applyFixBtn?.addEventListener('click', applyFix);
 
               // This function will be called once the response is received from the Language Server
-              window.receiveAIFixResponse = function (fixes) {
+              window.receiveAIFixResponse = function (fixesResponse) {
+                fixes = [...fixesResponse];
                 showAIFixes(fixes);
               };
             })();

From 281670ab1d4f02867cb0b4b018bfa64b800ecfbf Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Thu, 5 Sep 2024 09:16:35 +0200
Subject: [PATCH 11/28] fix: added support for navigating between AI Fixes

---
 .../toolwindow/panels/JCEFDescriptionPanel.kt | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index e393bcc70..fc5b355b3 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -185,6 +185,20 @@ class SuggestionDescriptionPanelFromLS(
                 element.classList.toggle("hidden", action === "hide");
               }
 
+              function nextDiff() {
+                  console.log('nextDiff')
+                  if (!fixes || diffSelectedIndex >= fixes.length - 1) return;
+                  ++diffSelectedIndex;
+                  showCurrentDiff(fixes);
+              }
+
+              function previousDiff() {
+                  console.log('previousDiff')
+                  if (!fixes || diffSelectedIndex <= 0) return;
+                  --diffSelectedIndex;
+                  showCurrentDiff(fixes)
+              }
+
               // Generate HTML for the code diff from a patch
               function generateDiffHtml(patch) {
                 const codeLines = patch.split("\n");
@@ -290,6 +304,8 @@ class SuggestionDescriptionPanelFromLS(
               const fixWrapperElem = document.getElementById("fix-wrapper");
               const fixSectionElem = document.getElementById("fixes-section");
 
+              const nextDiffElem = document.getElementById('next-diff');
+              const previousDiffElem = document.getElementById('previous-diff');
               const diffSelectedIndexElem = document.getElementById("diff-counter");
               const diffTopElem = document.getElementById("diff-top");
               const diffElem = document.getElementById("diff");
@@ -305,6 +321,9 @@ class SuggestionDescriptionPanelFromLS(
               generateAiFixBtn?.addEventListener("click", generateAIFix);
               applyFixBtn?.addEventListener('click', applyFix);
 
+              nextDiffElem?.addEventListener("click", nextDiff);
+              previousDiffElem?.addEventListener("click", previousDiff);
+
               // This function will be called once the response is received from the Language Server
               window.receiveAIFixResponse = function (fixesResponse) {
                 fixes = [...fixesResponse];

From c987b116520e78d5594583cc25168252f6c70529 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Thu, 5 Sep 2024 14:47:10 +0200
Subject: [PATCH 12/28] feat: show section for error, if ai fix reqest fails to
 generate fixes

---
 .../ui/toolwindow/panels/JCEFDescriptionPanel.kt     | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index fc5b355b3..b1159639e 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -276,6 +276,13 @@ class SuggestionDescriptionPanelFromLS(
                 toggleElement(fixLoadingIndicatorElem, "show");
               }
 
+              function showGenerateAIFixError() {
+                toggleElement(fixLoadingIndicatorElem, "hide");
+                toggleElement(fixWrapperElem, "hide");
+                toggleElement(fixSectionElem, "hide");
+                toggleElement(fixErrorSectionElem, "show");
+              }
+
               function applyFix() {
                 console.log('Applying fix', fixes);
                 if (!fixes.length) return;
@@ -303,6 +310,7 @@ class SuggestionDescriptionPanelFromLS(
               const fixLoadingIndicatorElem = document.getElementById("fix-loading-indicator");
               const fixWrapperElem = document.getElementById("fix-wrapper");
               const fixSectionElem = document.getElementById("fixes-section");
+              const fixErrorSectionElem = document.getElementById("fixes-error-section");
 
               const nextDiffElem = document.getElementById('next-diff');
               const previousDiffElem = document.getElementById('previous-diff');
@@ -327,6 +335,10 @@ class SuggestionDescriptionPanelFromLS(
               // This function will be called once the response is received from the Language Server
               window.receiveAIFixResponse = function (fixesResponse) {
                 fixes = [...fixesResponse];
+                if (!fixes.length) {
+                  showGenerateAIFixError();
+                  return;
+                }
                 showAIFixes(fixes);
               };
             })();

From ddea6a74a9431fb87edb23b909dcca05e378698a Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Thu, 5 Sep 2024 15:00:22 +0200
Subject: [PATCH 13/28] fix: add the same spacing for error section as for show
 fixes section

---
 src/main/resources/stylesheets/snyk_code_suggestion.scss | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/resources/stylesheets/snyk_code_suggestion.scss b/src/main/resources/stylesheets/snyk_code_suggestion.scss
index d0cad3c6a..f941abe64 100644
--- a/src/main/resources/stylesheets/snyk_code_suggestion.scss
+++ b/src/main/resources/stylesheets/snyk_code_suggestion.scss
@@ -117,6 +117,10 @@ a,
   padding-top: 20px;
 }
 
+.sn-ai-fix-error {
+  padding-top: 20px;
+}
+
 .sn-fix-wrapper {
   background-color: var(--container-background-color);  // same variable used in snyk_oss_suggestion.scss
 }

From dbaacd1f0d5f755ce8d4b73479fca7fa1d24e485 Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Thu, 5 Sep 2024 16:22:30 +0100
Subject: [PATCH 14/28] chore: wip - apply fix

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 136 ++++++++++++++++++
 .../toolwindow/panels/JCEFDescriptionPanel.kt |  18 +++
 2 files changed, 154 insertions(+)
 create mode 100644 src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
new file mode 100644
index 000000000..f301e099c
--- /dev/null
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -0,0 +1,136 @@
+package io.snyk.plugin.ui.jcef
+
+import com.intellij.openapi.application.ApplicationManager
+import com.intellij.openapi.command.WriteCommandAction
+import com.intellij.openapi.fileEditor.FileDocumentManager
+import com.intellij.openapi.project.Project
+import com.intellij.openapi.vfs.LocalFileSystem
+import com.intellij.openapi.vfs.VirtualFile
+import com.intellij.ui.jcef.JBCefBrowserBase
+import com.intellij.ui.jcef.JBCefJSQuery
+import kotlinx.coroutines.CoroutineScope
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.launch
+import kotlinx.coroutines.withContext
+import org.cef.browser.CefBrowser
+import org.cef.browser.CefFrame
+import org.cef.handler.CefLoadHandlerAdapter
+
+class ApplyFixHandler(private val project: Project) {
+
+    fun generateApplyFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
+        val applyFixQuery = JBCefJSQuery.create(jbCefBrowser)
+
+        applyFixQuery.addHandler { value ->
+            val params = value.split(":")
+            val filePath = params[0]  // Path to the file that needs to be patched
+            val patch = params[1]      // The patch we received from LS
+
+            // Avoid blocking the UI thread
+            CoroutineScope(Dispatchers.IO).launch {
+                try {
+                    val success = applyPatchAndSave(project, filePath, patch)
+
+                    val script = """
+                        window.receiveApplyFixResponse($success);
+                    """.trimIndent()
+
+                    withContext(Dispatchers.Main) {
+                        jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                    }
+                } catch (e: Exception) {
+                    e.printStackTrace()
+                }
+            }
+            return@addHandler JBCefJSQuery.Response("success")
+        }
+
+        return object : CefLoadHandlerAdapter() {
+            override fun onLoadEnd(browser: CefBrowser, frame: CefFrame, httpStatusCode: Int) {
+                if (frame.isMain) {
+                    val script = """
+                    (function() {
+                        if (window.applyFixQuery) {
+                            return;
+                        }
+                        window.applyFixQuery = function(value) { ${applyFixQuery.inject("value")} };
+                    })();
+                    """.trimIndent()
+                    browser.executeJavaScript(script, browser.url, 0)
+                }
+            }
+        }
+    }
+
+    // Applies a patch to the file content and saves it
+    private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Boolean {
+        val virtualFile = findVirtualFile(filePath)
+
+        if (virtualFile == null) {
+            println("[applyPatchAndSave] Virtual file not found for path: $filePath")
+            return false
+        }
+
+        // Use runReadAction to read the file content
+        val fileContent = ApplicationManager.getApplication().runReadAction<String?> {
+            val document = FileDocumentManager.getInstance().getDocument(virtualFile)
+            document?.text
+        }
+
+        // If fileContent is null, log the error and return
+        if (fileContent == null) {
+            println("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
+            return false
+        }
+
+        // Apply the patch to the content outside any read or write actions
+        val patchedContent = applyPatch(fileContent, patch)
+
+        // If the patch fails to apply, log and return
+        if (patchedContent == null) {
+            println("[applyPatchAndSave] Failed to apply patch.")
+            return false
+        }
+
+        // Now apply the patch inside a WriteCommandAction
+        WriteCommandAction.runWriteCommandAction(project) {
+            val document = FileDocumentManager.getInstance().getDocument(virtualFile)
+            if (document != null) {
+                document.setText(patchedContent)
+                FileDocumentManager.getInstance().saveDocument(document)
+                println("[applyPatchAndSave] Patch applied successfully!")
+            }
+        }
+
+        return true
+    }
+
+    private fun applyPatch(fileContent: String, patch: String): String? {
+        println("[applyPatch] Applying patch: $patch")
+
+        // Simple patch application (find & replace logic)
+        val patchLines = patch.lines()
+        val patchedContent = StringBuilder(fileContent)
+
+        for (line in patchLines) {
+            if (line.startsWith("-")) {
+                // Remove the line that starts with '-'
+                val oldLine = line.substring(1).trim()
+                val startIndex = patchedContent.indexOf(oldLine)
+                if (startIndex != -1) {
+                    patchedContent.delete(startIndex, startIndex + oldLine.length)
+                }
+            } else if (line.startsWith("+")) {
+                // Add the line that starts with '+'
+                val newLine = line.substring(1).trim()
+                patchedContent.append("\n").append(newLine)
+            }
+        }
+
+        return patchedContent.toString()
+    }
+
+    private fun findVirtualFile(filePath: String): VirtualFile? {
+        return LocalFileSystem.getInstance().findFileByPath(filePath)
+    }
+}
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index b1159639e..8cc6b8827 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -10,6 +10,7 @@ import io.snyk.plugin.ui.DescriptionHeaderPanel
 import io.snyk.plugin.ui.SnykBalloonNotificationHelper
 import io.snyk.plugin.ui.baseGridConstraintsAnchorWest
 import io.snyk.plugin.ui.descriptionHeaderPanel
+import io.snyk.plugin.ui.jcef.ApplyFixHandler
 import io.snyk.plugin.ui.jcef.JCEFUtils
 import io.snyk.plugin.ui.jcef.LoadHandlerGenerator
 import io.snyk.plugin.ui.jcef.OpenFileLoadHandlerGenerator
@@ -66,6 +67,10 @@ class SuggestionDescriptionPanelFromLS(
                     generateAIFixHandler.generateAIFixCommand(it)
                 }
 
+                val applyFixHandler = ApplyFixHandler(snykFile.project)
+                loadHandlerGenerators += {
+                    applyFixHandler.generateApplyFixCommand(it)
+                }
             }
             val html = this.getCustomCssAndScript()
             val jbCefBrowserComponent =
@@ -291,6 +296,8 @@ class SuggestionDescriptionPanelFromLS(
                 const filePath = getFilePathFromFix(currentFix);
                 const patch = currentFix.unifiedDiffsPerFile[filePath];
 
+                window.applyFixQuery(filePath + ':' + patch);
+
                 // Following VSCode logic, the steps are:
                 // 1. Read the current file content.
                 // 2. Apply a patch to that content.
@@ -341,6 +348,17 @@ class SuggestionDescriptionPanelFromLS(
                 }
                 showAIFixes(fixes);
               };
+
+              window.receiveApplyFixResponse = function (success) {
+              console.log('[[receiveApplyFixResponse]]', success);
+                if (success) {
+                    applyFixBtn.disabled = true;
+                    console.log('Fix applied', success);
+                    document.getElementById('apply-fix').disabled = true;
+                } else {
+                    console.error('Failed to apply fix', success);
+                }
+              };
             })();
         """.trimIndent()
     }

From d0937bad788a7da5fa04252cabc1dd127499cd6c Mon Sep 17 00:00:00 2001
From: Catalina Oyaneder <catalina.oyaneder@snyk.io>
Date: Fri, 6 Sep 2024 10:01:28 +0100
Subject: [PATCH 15/28] chore: wip add test to handle patches

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 153 ++++++++++++----
 .../plugin/ui/jcef/ApplyFixHandlerTest.kt     | 163 ++++++++++++++++++
 2 files changed, 279 insertions(+), 37 deletions(-)
 create mode 100644 src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index f301e099c..80b883817 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -16,6 +16,26 @@ import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
 
+data class DiffPatch(
+    val originalFile: String,
+    val fixedFile: String,
+    val hunks: List<Hunk>
+)
+
+data class Hunk(
+    val startLineOriginal: Int,
+    val numLinesOriginal: Int,
+    val startLineFixed: Int,
+    val numLinesFixed: Int,
+    val changes: List<Change>
+)
+
+sealed class Change {
+    data class Addition(val line: String) : Change()
+    data class Deletion(val line: String) : Change()
+    data class Context(val line: String) : Change()  // Unchanged line for context
+}
+
 class ApplyFixHandler(private val project: Project) {
 
     fun generateApplyFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
@@ -26,6 +46,10 @@ class ApplyFixHandler(private val project: Project) {
             val filePath = params[0]  // Path to the file that needs to be patched
             val patch = params[1]      // The patch we received from LS
 
+            println("[applyFixHandler] Received request to apply fix on file: $filePath")
+            println("[applyFixHandler] Patch to apply: $patch")
+
+
             // Avoid blocking the UI thread
             CoroutineScope(Dispatchers.IO).launch {
                 try {
@@ -62,72 +86,127 @@ class ApplyFixHandler(private val project: Project) {
         }
     }
 
-    // Applies a patch to the file content and saves it
     private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Boolean {
-        val virtualFile = findVirtualFile(filePath)
-
-        if (virtualFile == null) {
+        val virtualFile = findVirtualFile(filePath) ?: run {
             println("[applyPatchAndSave] Virtual file not found for path: $filePath")
             return false
         }
 
-        // Use runReadAction to read the file content
+        println("[applyPatchAndSave] Found virtual file: $virtualFile")
+
         val fileContent = ApplicationManager.getApplication().runReadAction<String?> {
             val document = FileDocumentManager.getInstance().getDocument(virtualFile)
             document?.text
-        }
-
-        // If fileContent is null, log the error and return
-        if (fileContent == null) {
+        } ?: run {
             println("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
             return false
         }
 
-        // Apply the patch to the content outside any read or write actions
-        val patchedContent = applyPatch(fileContent, patch)
+        println("[applyPatchAndSave] Initial file content: $fileContent")
 
-        // If the patch fails to apply, log and return
-        if (patchedContent == null) {
-            println("[applyPatchAndSave] Failed to apply patch.")
-            return false
-        }
+        val diffPatch = parseDiff(patch)
+        val patchedContent = applyPatch(fileContent, diffPatch)
 
-        // Now apply the patch inside a WriteCommandAction
+        println("[applyPatchAndSave] Patched content that will be written: $patchedContent")
+
+        // Apply the patch inside a WriteCommandAction
         WriteCommandAction.runWriteCommandAction(project) {
             val document = FileDocumentManager.getInstance().getDocument(virtualFile)
-            if (document != null) {
-                document.setText(patchedContent)
-                FileDocumentManager.getInstance().saveDocument(document)
+            document?.let {
+                it.setText(patchedContent)
+
+                println("[applyPatchAndSave] Content after applying patch: ${it.text}")
+
+                FileDocumentManager.getInstance().saveDocument(it)
                 println("[applyPatchAndSave] Patch applied successfully!")
+            } ?: run {
+                println("[applyPatchAndSave] Failed to find document for saving patched content.")
             }
         }
 
         return true
     }
 
-    private fun applyPatch(fileContent: String, patch: String): String? {
-        println("[applyPatch] Applying patch: $patch")
+    fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
+        val lines = fileContent.lines().toMutableList()
 
-        // Simple patch application (find & replace logic)
-        val patchLines = patch.lines()
-        val patchedContent = StringBuilder(fileContent)
+        for (hunk in diffPatch.hunks) {
+            var originalLineIndex = hunk.startLineOriginal - 1  // Convert to 0-based index
 
-        for (line in patchLines) {
-            if (line.startsWith("-")) {
-                // Remove the line that starts with '-'
-                val oldLine = line.substring(1).trim()
-                val startIndex = patchedContent.indexOf(oldLine)
-                if (startIndex != -1) {
-                    patchedContent.delete(startIndex, startIndex + oldLine.length)
+            for (change in hunk.changes) {
+                when (change) {
+                    is Change.Addition -> {
+                        lines.add(originalLineIndex, change.line)
+                        originalLineIndex++
+                    }
+                    is Change.Deletion -> {
+                        if (originalLineIndex < lines.size && lines[originalLineIndex].trim() == change.line) {
+                            lines.removeAt(originalLineIndex)
+                        }
+                    }
+                    is Change.Context -> {
+                        originalLineIndex++  // Move past unchanged context lines
+                    }
                 }
-            } else if (line.startsWith("+")) {
-                // Add the line that starts with '+'
-                val newLine = line.substring(1).trim()
-                patchedContent.append("\n").append(newLine)
             }
         }
+        return lines.joinToString("\n")
+    }
+
+    fun parseDiff(diff: String): DiffPatch {
+        val lines = diff.lines()
+        val originalFile = lines.first { it.startsWith("---") }.substringAfter("--- ")
+        val fixedFile = lines.first { it.startsWith("+++") }.substringAfter("+++ ")
+
+        val hunks = mutableListOf<Hunk>()
+        var currentHunk: Hunk? = null
+        val changes = mutableListOf<Change>()
+
+        for (line in lines) {
+            when {
+                line.startsWith("@@") -> {
+                    // Parse hunk header (e.g., @@ -4,9 +4,14 @@)
+                    val hunkHeader = line.substringAfter("@@ ").substringBefore(" @@").split(" ")
+                    val original = hunkHeader[0].substring(1).split(",")
+                    val fixed = hunkHeader[1].substring(1).split(",")
+
+                    val startLineOriginal = original[0].toInt()
+                    val numLinesOriginal = original.getOrNull(1)?.toInt() ?: 1
+                    val startLineFixed = fixed[0].toInt()
+                    val numLinesFixed = fixed.getOrNull(1)?.toInt() ?: 1
+
+                    if (currentHunk != null) {
+                        hunks.add(currentHunk.copy(changes = changes.toList()))
+                        changes.clear()
+                    }
+                    currentHunk = Hunk(
+                        startLineOriginal = startLineOriginal,
+                        numLinesOriginal = numLinesOriginal,
+                        startLineFixed = startLineFixed,
+                        numLinesFixed = numLinesFixed,
+                        changes = emptyList()
+                    )
+                }
+                line.startsWith("---") || line.startsWith("+++") -> {
+                    // Skip file metadata lines (--- and +++)
+                    continue
+                }
+                line.startsWith("-") -> changes.add(Change.Deletion(line.substring(1).trim()))
+                line.startsWith("+") -> changes.add(Change.Addition(line.substring(1).trim()))
+                else -> changes.add(Change.Context(line.trim()))
+            }
+        }
+
+        // Add the last hunk
+        if (currentHunk != null) {
+            hunks.add(currentHunk.copy(changes = changes.toList()))
+        }
 
-        return patchedContent.toString()
+        return DiffPatch(
+            originalFile = originalFile,
+            fixedFile = fixedFile,
+            hunks = hunks
+        )
     }
 
     private fun findVirtualFile(filePath: String): VirtualFile? {
diff --git a/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt b/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
new file mode 100644
index 000000000..76725efc1
--- /dev/null
+++ b/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
@@ -0,0 +1,163 @@
+package io.snyk.plugin.ui.jcef
+
+import org.junit.Test
+import junit.framework.TestCase.assertEquals
+
+class DiffPatchTest {
+    private  val originalFileContent = """
+        /*
+         * Copyright (c) 2014-2023 Bjoern Kimminich & the OWASP Juice Shop contributors.
+         * SPDX-License-Identifier: MIT
+         */
+
+        import path = require('path')
+        import { type Request, type Response } from 'express'
+
+        import challengeUtils = require('../lib/challengeUtils')
+        const challenges = require('../data/datacache').challenges
+
+        module.exports = function servePremiumContent () {
+          return (req: Request, res: Response) => {
+            challengeUtils.solveIf(challenges.premiumPaywallChallenge, () => { return true })
+            res.sendFile(path.resolve('frontend/dist/frontend/assets/private/JuiceShop_Wallpaper_1920x1080_VR.jpg'))
+          }
+        }
+    """.trimIndent()
+
+    private val responseDiff = """
+        --- /Users/cata/git/playground/project-with-vulns
+        +++ /Users/cata/git/playground/project-with-vulns-fixed
+        @@ -4,9 +4,14 @@
+         */
+
+         import path = require('path')
+        +import rateLimit = require('express-rate-limit')
+         import { type Request, type Response } from 'express'
+
+         import challengeUtils = require('../lib/challengeUtils')
+        +const apiLimiter = rateLimit({
+        +  windowMs: 15 * 60 * 1000, // 15 minutes
+        +  max: 100, // limit each IP to 100 requests per windowMs
+        +})
+         const challenges = require('../data/datacache').challenges
+
+         module.exports = function servePremiumContent () {
+    """.trimIndent()
+
+    @Test
+    fun `test applying patch`() {
+        val diffPatch = parseDiff(responseDiff)
+        val patchedContent = applyPatch(originalFileContent, diffPatch)
+
+        val expectedPatchedContent = """
+            /*
+             * Copyright (c) 2014-2023 Bjoern Kimminich & the OWASP Juice Shop contributors.
+             * SPDX-License-Identifier: MIT
+             */
+
+            import path = require('path')
+            import rateLimit = require('express-rate-limit')
+            import { type Request, type Response } from 'express'
+
+            import challengeUtils = require('../lib/challengeUtils')
+            const apiLimiter = rateLimit({
+            windowMs: 15 * 60 * 1000, // 15 minutes
+            max: 100, // limit each IP to 100 requests per windowMs
+            })
+            const challenges = require('../data/datacache').challenges
+
+            module.exports = function servePremiumContent () {
+              return (req: Request, res: Response) => {
+                challengeUtils.solveIf(challenges.premiumPaywallChallenge, () => { return true })
+                res.sendFile(path.resolve('frontend/dist/frontend/assets/private/JuiceShop_Wallpaper_1920x1080_VR.jpg'))
+              }
+            }
+        """.trimIndent()
+
+        assertEquals(expectedPatchedContent, patchedContent)
+    }
+
+    private fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
+        val lines = fileContent.lines().toMutableList()
+
+        for (hunk in diffPatch.hunks) {
+            var originalLineIndex = hunk.startLineOriginal - 1  // Convert to 0-based index
+
+            for (change in hunk.changes) {
+                when (change) {
+                    is Change.Addition -> {
+                        lines.add(originalLineIndex, change.line)
+                        originalLineIndex++
+                    }
+                    is Change.Deletion -> {
+                        if (originalLineIndex < lines.size && lines[originalLineIndex].trim() == change.line) {
+                            lines.removeAt(originalLineIndex)
+                        }
+                    }
+                    is Change.Context -> {
+                        originalLineIndex++  // Move past unchanged context lines
+                    }
+                }
+            }
+        }
+        return lines.joinToString("\n")
+    }
+
+    private fun parseDiff(diff: String): DiffPatch {
+        val lines = diff.lines()
+        val originalFile = lines.first { it.startsWith("---") }.substringAfter("--- ")
+        val fixedFile = lines.first { it.startsWith("+++") }.substringAfter("+++ ")
+
+        val hunks = mutableListOf<Hunk>()
+        var currentHunk: Hunk? = null
+        val changes = mutableListOf<Change>()
+
+        for (line in lines) {
+            when {
+                line.startsWith("@@") -> {
+                    // Parse hunk header (e.g., @@ -4,9 +4,14 @@)
+                    val hunkHeader = line.substringAfter("@@ ").substringBefore(" @@").split(" ")
+                    val original = hunkHeader[0].substring(1).split(",")
+                    val fixed = hunkHeader[1].substring(1).split(",")
+
+                    val startLineOriginal = original[0].toInt()
+                    val numLinesOriginal = original.getOrNull(1)?.toInt() ?: 1
+                    val startLineFixed = fixed[0].toInt()
+                    val numLinesFixed = fixed.getOrNull(1)?.toInt() ?: 1
+
+                    if (currentHunk != null) {
+                        hunks.add(currentHunk.copy(changes = changes.toList()))
+                        changes.clear()
+                    }
+                    currentHunk = Hunk(
+                        startLineOriginal = startLineOriginal,
+                        numLinesOriginal = numLinesOriginal,
+                        startLineFixed = startLineFixed,
+                        numLinesFixed = numLinesFixed,
+                        changes = emptyList()
+                    )
+                }
+
+                line.startsWith("---") || line.startsWith("+++") -> {
+                    // Skip file metadata lines (--- and +++)
+                    continue
+                }
+
+                line.startsWith("-") -> changes.add(Change.Deletion(line.substring(1).trim()))
+                line.startsWith("+") -> changes.add(Change.Addition(line.substring(1).trim()))
+                else -> changes.add(Change.Context(line.trim()))
+            }
+        }
+
+        // Add the last hunk
+        if (currentHunk != null) {
+            hunks.add(currentHunk.copy(changes = changes.toList()))
+        }
+
+        return DiffPatch(
+            originalFile = originalFile,
+            fixedFile = fixedFile,
+            hunks = hunks
+        )
+    }
+}

From 8a387b6e49afd7b51f28cafbef89db2dbb10c5d6 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Fri, 6 Sep 2024 15:32:45 +0200
Subject: [PATCH 16/28] fix: fix flow for regenerating ai fixes after error

---
 .../io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt  |  6 +++++-
 .../ui/toolwindow/panels/JCEFDescriptionPanel.kt    | 13 +++++++++----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index 54891b78b..3ffe79644 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -56,12 +56,16 @@ class GenerateAIFixHandler(private val project: Project) {
                         window.aiFixQuery = function(value) { ${aiFixQuery.inject("value")} };
 
                         const aiFixButton = document.getElementById('generate-ai-fix');
+                        const retryFixButton = document.getElementById('retry-generate-fix');
                         const issueId = aiFixButton.getAttribute('issue-id');
                         const folderPath = aiFixButton.getAttribute('folder-path');
                         const filePath = aiFixButton.getAttribute('file-path');
 
                         aiFixButton.addEventListener('click', () => {
-                            console.log('Clicked AI Fix button. Path: ' + folderPath + ':' + filePath + ':' + issueId)
+                            window.aiFixQuery(folderPath + ":" + filePath + ":" + issueId);
+                        });
+
+                        retryFixButton.addEventListener('click', () => {
                             window.aiFixQuery(folderPath + ":" + filePath + ":" + issueId);
                         });
                     })();
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index 8cc6b8827..b82b05035 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -191,14 +191,12 @@ class SuggestionDescriptionPanelFromLS(
               }
 
               function nextDiff() {
-                  console.log('nextDiff')
                   if (!fixes || diffSelectedIndex >= fixes.length - 1) return;
                   ++diffSelectedIndex;
                   showCurrentDiff(fixes);
               }
 
               function previousDiff() {
-                  console.log('previousDiff')
                   if (!fixes || diffSelectedIndex <= 0) return;
                   --diffSelectedIndex;
                   showCurrentDiff(fixes)
@@ -281,6 +279,14 @@ class SuggestionDescriptionPanelFromLS(
                 toggleElement(fixLoadingIndicatorElem, "show");
               }
 
+              // Handle AI fix re-generation button click
+              function reGenerateAIFix() {
+                toggleElement(fixErrorSectionElem, "hide");
+                toggleElement(fixWrapperElem, "show");
+
+                generateAIFix()
+              }
+
               function showGenerateAIFixError() {
                 toggleElement(fixLoadingIndicatorElem, "hide");
                 toggleElement(fixWrapperElem, "hide");
@@ -312,8 +318,6 @@ class SuggestionDescriptionPanelFromLS(
               const applyFixBtn = document.getElementById('apply-fix')
               const retryGenerateFixBtn = document.getElementById('retry-generate-fix')
 
-              console.log('applyFixBtn', applyFixBtn)
-
               const fixLoadingIndicatorElem = document.getElementById("fix-loading-indicator");
               const fixWrapperElem = document.getElementById("fix-wrapper");
               const fixSectionElem = document.getElementById("fixes-section");
@@ -335,6 +339,7 @@ class SuggestionDescriptionPanelFromLS(
               // Event listener for Generate AI fix button
               generateAiFixBtn?.addEventListener("click", generateAIFix);
               applyFixBtn?.addEventListener('click', applyFix);
+              retryGenerateFixBtn?.addEventListener('click', reGenerateAIFix);
 
               nextDiffElem?.addEventListener("click", nextDiff);
               previousDiffElem?.addEventListener("click", previousDiff);

From e0fc1d22133e1825ceeea24aef1c169d04adb067 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Wed, 11 Sep 2024 15:03:52 +0200
Subject: [PATCH 17/28] tidy: replace hardcoded colors with JBUI theme colors

---
 .../io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt | 9 +++++++--
 src/main/resources/stylesheets/snyk_code_suggestion.scss | 4 ++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
index ec730d442..a253ad914 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
@@ -3,8 +3,10 @@ package io.snyk.plugin.ui.jcef
 import com.intellij.openapi.editor.colors.ColorKey
 import com.intellij.openapi.editor.colors.EditorColors
 import com.intellij.openapi.editor.colors.EditorColorsManager
+import com.intellij.ui.JBColor
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.util.ui.JBUI
+import com.intellij.util.ui.PlatformColors
 import com.intellij.util.ui.UIUtil
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
@@ -63,8 +65,8 @@ class ThemeBasedStylingGenerator {
                     val textColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
                     val linkColor = toCssHex(JBUI.CurrentTheme.Link.Foreground.ENABLED)
                     val dataFlowColor = toCssHex(baseColor)
+                    val editorColor = toCssHex(baseColor)
                     val borderColor = toCssHex(JBUI.CurrentTheme.CustomFrameDecorations.separatorForeground())
-                    val editorColor = toCssHex(UIUtil.getTextFieldBackground())
                     val labelColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
 
                     val globalScheme = EditorColorsManager.getInstance().globalScheme
@@ -93,7 +95,10 @@ class ThemeBasedStylingGenerator {
                                 '--editor-color': "$editorColor",
                                 '--label-color': "'$labelColor'",
                                 '--container-background-color': "${toCssHex(codeTagBgColor)}",
-                                '--generated-ai-fix-button-background-color': "#3376CD", // TODO: From Figma. Find the correct JetBrains API to get this color
+                                '--generated-ai-fix-button-background-color': "$linkColor",
+                                '--dark-button-border-default': "$borderColor",
+                                '--dark-button-default': "$linkColor",
+
                             };
                             for (let [property, value] of Object.entries(properties)) {
                                 document.documentElement.style.setProperty(property, value);
diff --git a/src/main/resources/stylesheets/snyk_code_suggestion.scss b/src/main/resources/stylesheets/snyk_code_suggestion.scss
index f941abe64..ba2c6c3ef 100644
--- a/src/main/resources/stylesheets/snyk_code_suggestion.scss
+++ b/src/main/resources/stylesheets/snyk_code_suggestion.scss
@@ -136,7 +136,7 @@ button.generate-ai-fix:hover, button.sn-apply-fix:hover {
 
 button.sn-apply-fix {
   border-radius: 3px;
-  border: 1px solid var(--dark-button-border-default, #4C708C); // TODO: define the variable in the ThemeBasedStylingGenerator class to be theme-based
-  background: var(--dark-button-default, #365880); // TODO: define the variable in the ThemeBasedStylingGenerator class to be theme-based
+  border: 1px solid var(--dark-button-border-default);
+  background: var(--dark-button-default);
   padding: 4px 12px;
 }

From adaca2aaab87f089bff6835da041bfffa5df4ee7 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Thu, 12 Sep 2024 10:03:33 +0200
Subject: [PATCH 18/28] tidy: remove println's and disable devtools

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 21 +++++--------------
 .../kotlin/io/snyk/plugin/ui/jcef/Utils.kt    |  2 +-
 2 files changed, 6 insertions(+), 17 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 80b883817..3aaf88b5d 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -15,6 +15,7 @@ import kotlinx.coroutines.withContext
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
+import com.intellij.openapi.diagnostic.Logger
 
 data class DiffPatch(
     val originalFile: String,
@@ -37,6 +38,7 @@ sealed class Change {
 }
 
 class ApplyFixHandler(private val project: Project) {
+    private val logger = Logger.getInstance(this::class.java)
 
     fun generateApplyFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
         val applyFixQuery = JBCefJSQuery.create(jbCefBrowser)
@@ -46,10 +48,6 @@ class ApplyFixHandler(private val project: Project) {
             val filePath = params[0]  // Path to the file that needs to be patched
             val patch = params[1]      // The patch we received from LS
 
-            println("[applyFixHandler] Received request to apply fix on file: $filePath")
-            println("[applyFixHandler] Patch to apply: $patch")
-
-
             // Avoid blocking the UI thread
             CoroutineScope(Dispatchers.IO).launch {
                 try {
@@ -88,39 +86,30 @@ class ApplyFixHandler(private val project: Project) {
 
     private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Boolean {
         val virtualFile = findVirtualFile(filePath) ?: run {
-            println("[applyPatchAndSave] Virtual file not found for path: $filePath")
+            logger.debug("[applyPatchAndSave] Virtual file not found for path: $filePath")
             return false
         }
 
-        println("[applyPatchAndSave] Found virtual file: $virtualFile")
-
         val fileContent = ApplicationManager.getApplication().runReadAction<String?> {
             val document = FileDocumentManager.getInstance().getDocument(virtualFile)
             document?.text
         } ?: run {
-            println("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
+            logger.debug("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
             return false
         }
 
-        println("[applyPatchAndSave] Initial file content: $fileContent")
-
         val diffPatch = parseDiff(patch)
         val patchedContent = applyPatch(fileContent, diffPatch)
 
-        println("[applyPatchAndSave] Patched content that will be written: $patchedContent")
-
         // Apply the patch inside a WriteCommandAction
         WriteCommandAction.runWriteCommandAction(project) {
             val document = FileDocumentManager.getInstance().getDocument(virtualFile)
             document?.let {
                 it.setText(patchedContent)
 
-                println("[applyPatchAndSave] Content after applying patch: ${it.text}")
-
                 FileDocumentManager.getInstance().saveDocument(it)
-                println("[applyPatchAndSave] Patch applied successfully!")
             } ?: run {
-                println("[applyPatchAndSave] Failed to find document for saving patched content.")
+                logger.debug("[applyPatchAndSave] Failed to find document for saving patched content.\"")
             }
         }
 
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt
index 00fda7413..d5998e20d 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/Utils.kt
@@ -19,7 +19,7 @@ object JCEFUtils {
         val cefClient = JBCefApp.getInstance().createClient()
         cefClient.setProperty("JS_QUERY_POOL_SIZE", 1)
         val jbCefBrowser =
-            JBCefBrowserBuilder().setClient(cefClient).setEnableOpenDevToolsMenuItem(true)
+            JBCefBrowserBuilder().setClient(cefClient).setEnableOpenDevToolsMenuItem(false)
                 .setMouseWheelEventEnable(true).build()
         jbCefBrowser.setOpenLinksInExternalBrowser(true)
 

From 097875a73bf89b990433531fa5686d027467caeb Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Fri, 13 Sep 2024 16:39:36 +0200
Subject: [PATCH 19/28] chore: updating logging and error handling, changing
 threading to runAsync

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 72 +++++++++++--------
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    | 17 ++---
 .../ui/jcef/ThemeBasedStylingGenerator.kt     |  5 +-
 3 files changed, 54 insertions(+), 40 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 3aaf88b5d..f32a9250d 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -2,20 +2,17 @@ package io.snyk.plugin.ui.jcef
 
 import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.command.WriteCommandAction
+import com.intellij.openapi.diagnostic.Logger
 import com.intellij.openapi.fileEditor.FileDocumentManager
 import com.intellij.openapi.project.Project
-import com.intellij.openapi.vfs.LocalFileSystem
-import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.ui.jcef.JBCefJSQuery
-import kotlinx.coroutines.CoroutineScope
-import kotlinx.coroutines.Dispatchers
-import kotlinx.coroutines.launch
-import kotlinx.coroutines.withContext
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
-import com.intellij.openapi.diagnostic.Logger
+import org.jetbrains.concurrency.runAsync
+import io.snyk.plugin.toVirtualFile
+
 
 data class DiffPatch(
     val originalFile: String,
@@ -38,30 +35,36 @@ sealed class Change {
 }
 
 class ApplyFixHandler(private val project: Project) {
+
+    private val enableDebug = Logger.getInstance("Snyk Language Server").isDebugEnabled
+    private val enableTrace = Logger.getInstance("Snyk Language Server").isTraceEnabled
     private val logger = Logger.getInstance(this::class.java)
 
+
     fun generateApplyFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
         val applyFixQuery = JBCefJSQuery.create(jbCefBrowser)
 
+        //temporary logs
+        logger.info("[generateApplyFixCommand] calling applyPatchAndSave")
+
         applyFixQuery.addHandler { value ->
             val params = value.split(":")
             val filePath = params[0]  // Path to the file that needs to be patched
             val patch = params[1]      // The patch we received from LS
 
             // Avoid blocking the UI thread
-            CoroutineScope(Dispatchers.IO).launch {
+            runAsync {
                 try {
                     val success = applyPatchAndSave(project, filePath, patch)
 
+
                     val script = """
                         window.receiveApplyFixResponse($success);
                     """.trimIndent()
 
-                    withContext(Dispatchers.Main) {
-                        jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-                    }
+                    jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
                 } catch (e: Exception) {
-                    e.printStackTrace()
+                    log("Error applying fix: ${e.message}")
                 }
             }
             return@addHandler JBCefJSQuery.Response("success")
@@ -85,35 +88,40 @@ class ApplyFixHandler(private val project: Project) {
     }
 
     private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Boolean {
-        val virtualFile = findVirtualFile(filePath) ?: run {
-            logger.debug("[applyPatchAndSave] Virtual file not found for path: $filePath")
-            return false
-        }
+        val virtualFile = filePath.toVirtualFile()
 
         val fileContent = ApplicationManager.getApplication().runReadAction<String?> {
             val document = FileDocumentManager.getInstance().getDocument(virtualFile)
             document?.text
         } ?: run {
-            logger.debug("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
+            log("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
             return false
         }
 
         val diffPatch = parseDiff(patch)
         val patchedContent = applyPatch(fileContent, diffPatch)
+        var result = false
 
         // Apply the patch inside a WriteCommandAction
-        WriteCommandAction.runWriteCommandAction(project) {
-            val document = FileDocumentManager.getInstance().getDocument(virtualFile)
-            document?.let {
-                it.setText(patchedContent)
-
-                FileDocumentManager.getInstance().saveDocument(it)
-            } ?: run {
-                logger.debug("[applyPatchAndSave] Failed to find document for saving patched content.\"")
+        result = try {
+            WriteCommandAction.runWriteCommandAction(project) {
+                val document = FileDocumentManager.getInstance().getDocument(virtualFile)
+                if (document != null) {
+                    document.setText(patchedContent)
+
+                    //temporary logs
+                    logger.info("[applyPatchAndSave] Content after applying patch:${document.text}")
+                } else {
+                    log("[applyPatchAndSave] Failed to find document for saving patched content.")
+                }
             }
+            true // Success
+        } catch (e: Exception) {
+            log("[applyPatchAndSave] Error applying patch: ${e.message}")
+            false // Failure
         }
 
-        return true
+        return result
     }
 
     fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
@@ -128,11 +136,13 @@ class ApplyFixHandler(private val project: Project) {
                         lines.add(originalLineIndex, change.line)
                         originalLineIndex++
                     }
+
                     is Change.Deletion -> {
                         if (originalLineIndex < lines.size && lines[originalLineIndex].trim() == change.line) {
                             lines.removeAt(originalLineIndex)
                         }
                     }
+
                     is Change.Context -> {
                         originalLineIndex++  // Move past unchanged context lines
                     }
@@ -176,10 +186,12 @@ class ApplyFixHandler(private val project: Project) {
                         changes = emptyList()
                     )
                 }
+
                 line.startsWith("---") || line.startsWith("+++") -> {
                     // Skip file metadata lines (--- and +++)
                     continue
                 }
+
                 line.startsWith("-") -> changes.add(Change.Deletion(line.substring(1).trim()))
                 line.startsWith("+") -> changes.add(Change.Addition(line.substring(1).trim()))
                 else -> changes.add(Change.Context(line.trim()))
@@ -198,7 +210,11 @@ class ApplyFixHandler(private val project: Project) {
         )
     }
 
-    private fun findVirtualFile(filePath: String): VirtualFile? {
-        return LocalFileSystem.getInstance().findFileByPath(filePath)
+    private fun log(logMessage: String) {
+        when {
+            enableDebug -> logger.debug(logMessage)
+            enableTrace -> logger.trace(logMessage)
+            else -> logger.error(logMessage)
+        }
     }
 }
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index 3ffe79644..a21a14818 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -4,13 +4,10 @@ import com.google.gson.Gson
 import com.intellij.openapi.project.Project
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.ui.jcef.JBCefJSQuery
-import kotlinx.coroutines.CoroutineScope
-import kotlinx.coroutines.Dispatchers
-import kotlinx.coroutines.launch
-import kotlinx.coroutines.withContext
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
+import org.jetbrains.concurrency.runAsync
 import snyk.common.lsp.LanguageServerWrapper
 
 class GenerateAIFixHandler(private val project: Project) {
@@ -24,20 +21,20 @@ class GenerateAIFixHandler(private val project: Project) {
             val fileURI = params[1]
             val issueID = params[2]
 
-            // Avoids blocking the UI thread
-            CoroutineScope(Dispatchers.IO).launch {
+
+            runAsync {
                 try {
                     val responseDiff: List<LanguageServerWrapper.Fix> =
                         LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
 
+                    //What happens when sendCodeFixDiffsCommand fails or is empty?
+
                     val script = """
                         window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
                     """.trimIndent()
 
-                    withContext(Dispatchers.Main) {
-                        jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-                        JBCefJSQuery.Response("success")
-                    }
+                    jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                    JBCefJSQuery.Response("success")
                 } catch (e: Exception) {
                     e.printStackTrace()
                 }
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
index a253ad914..661941ace 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
@@ -62,10 +62,11 @@ class ThemeBasedStylingGenerator {
                     val baseColor = UIUtil.getTextFieldBackground()
                     val (addedColor, removedColor) = getCodeDiffColors(baseColor, isHighContrast)
 
-                    val textColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
-                    val linkColor = toCssHex(JBUI.CurrentTheme.Link.Foreground.ENABLED)
                     val dataFlowColor = toCssHex(baseColor)
                     val editorColor = toCssHex(baseColor)
+
+                    val textColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
+                    val linkColor = toCssHex(JBUI.CurrentTheme.Link.Foreground.ENABLED)
                     val borderColor = toCssHex(JBUI.CurrentTheme.CustomFrameDecorations.separatorForeground())
                     val labelColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
 

From 16ae0a163f60de7f26c40110448e9bbbfb6d9e7b Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 15:18:57 +0200
Subject: [PATCH 20/28] fix: solved a problem with applying patch

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt       | 13 ++++++++-----
 .../ui/toolwindow/panels/JCEFDescriptionPanel.kt    |  3 ++-
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index f32a9250d..0122601ab 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -48,7 +48,7 @@ class ApplyFixHandler(private val project: Project) {
         logger.info("[generateApplyFixCommand] calling applyPatchAndSave")
 
         applyFixQuery.addHandler { value ->
-            val params = value.split(":")
+            val params = value.split("|@", limit = 2)
             val filePath = params[0]  // Path to the file that needs to be patched
             val patch = params[1]      // The patch we received from LS
 
@@ -63,6 +63,7 @@ class ApplyFixHandler(private val project: Project) {
                     """.trimIndent()
 
                     jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                    JBCefJSQuery.Response("success")
                 } catch (e: Exception) {
                     log("Error applying fix: ${e.message}")
                 }
@@ -100,22 +101,24 @@ class ApplyFixHandler(private val project: Project) {
 
         val diffPatch = parseDiff(patch)
         val patchedContent = applyPatch(fileContent, diffPatch)
-        var result = false
 
         // Apply the patch inside a WriteCommandAction
-        result = try {
+        val result = try {
+            var appliedPatchSuccessfully = true
             WriteCommandAction.runWriteCommandAction(project) {
                 val document = FileDocumentManager.getInstance().getDocument(virtualFile)
-                if (document != null) {
+                if (document != null && fileContent != patchedContent) {
                     document.setText(patchedContent)
 
                     //temporary logs
                     logger.info("[applyPatchAndSave] Content after applying patch:${document.text}")
+                    appliedPatchSuccessfully = true
                 } else {
                     log("[applyPatchAndSave] Failed to find document for saving patched content.")
+                    appliedPatchSuccessfully = false
                 }
             }
-            true // Success
+            appliedPatchSuccessfully
         } catch (e: Exception) {
             log("[applyPatchAndSave] Error applying patch: ${e.message}")
             false // Failure
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index b82b05035..667d77f48 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -302,7 +302,8 @@ class SuggestionDescriptionPanelFromLS(
                 const filePath = getFilePathFromFix(currentFix);
                 const patch = currentFix.unifiedDiffsPerFile[filePath];
 
-                window.applyFixQuery(filePath + ':' + patch);
+
+                window.applyFixQuery(filePath + '|@' + patch);
 
                 // Following VSCode logic, the steps are:
                 // 1. Read the current file content.

From 4387f5d9f56b32b175b7de35c856a4dcb8c8cbff Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 15:31:23 +0200
Subject: [PATCH 21/28] chore: replace colors with colors from JBUI

---
 .../ui/jcef/ThemeBasedStylingGenerator.kt     | 21 +++++++++----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
index 661941ace..f50caa3f9 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ThemeBasedStylingGenerator.kt
@@ -3,10 +3,9 @@ package io.snyk.plugin.ui.jcef
 import com.intellij.openapi.editor.colors.ColorKey
 import com.intellij.openapi.editor.colors.EditorColors
 import com.intellij.openapi.editor.colors.EditorColorsManager
-import com.intellij.ui.JBColor
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.util.ui.JBUI
-import com.intellij.util.ui.PlatformColors
+import com.intellij.ui.JBColor
 import com.intellij.util.ui.UIUtil
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
@@ -59,21 +58,21 @@ class ThemeBasedStylingGenerator {
                 httpStatusCode: Int,
             ) {
                 if (frame.isMain) {
-                    val baseColor = UIUtil.getTextFieldBackground()
-                    val (addedColor, removedColor) = getCodeDiffColors(baseColor, isHighContrast)
-
+                    val baseColor = UIUtil.getTextFieldBackground() //TODO Replace with JBUI.CurrentTheme colors
+                    val (addedColor, removedColor) = getCodeDiffColors(baseColor, isHighContrast) //TODO Replace with JBUI.CurrentTheme colors
                     val dataFlowColor = toCssHex(baseColor)
                     val editorColor = toCssHex(baseColor)
 
-                    val textColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
+                    val textColor = toCssHex(JBUI.CurrentTheme.Tree.FOREGROUND)
                     val linkColor = toCssHex(JBUI.CurrentTheme.Link.Foreground.ENABLED)
+                    val buttonColor = toCssHex(JBUI.CurrentTheme.Button.defaultButtonColorStart())
                     val borderColor = toCssHex(JBUI.CurrentTheme.CustomFrameDecorations.separatorForeground())
                     val labelColor = toCssHex(JBUI.CurrentTheme.Label.foreground())
 
                     val globalScheme = EditorColorsManager.getInstance().globalScheme
-                    val tearLineColor = globalScheme.getColor(ColorKey.find("TEARLINE_COLOR")) // The closest color to target_rgb = (198, 198, 200)
-                    val tabItemHoverColor = globalScheme.getColor(ColorKey.find("INDENT_GUIDE")) // The closest color to target_rgb = RGB (235, 236, 240)
-                    val codeTagBgColor = globalScheme.getColor(EditorColors.GUTTER_BACKGROUND)  ?: globalScheme.defaultBackground
+                    val tearLineColor = globalScheme.getColor(ColorKey.find("TEARLINE_COLOR")) //TODO Replace with JBUI.CurrentTheme colors
+                    val tabItemHoverColor = globalScheme.getColor(ColorKey.find("INDENT_GUIDE")) //TODO Replace with JBUI.CurrentTheme colors
+                    val codeTagBgColor = globalScheme.getColor(EditorColors.GUTTER_BACKGROUND)  ?: globalScheme.defaultBackground //TODO Replace with JBUI.CurrentTheme colors
 
                     val themeScript = """
                         (function(){
@@ -96,9 +95,9 @@ class ThemeBasedStylingGenerator {
                                 '--editor-color': "$editorColor",
                                 '--label-color': "'$labelColor'",
                                 '--container-background-color': "${toCssHex(codeTagBgColor)}",
-                                '--generated-ai-fix-button-background-color': "$linkColor",
+                                '--generated-ai-fix-button-background-color': "$buttonColor",
                                 '--dark-button-border-default': "$borderColor",
-                                '--dark-button-default': "$linkColor",
+                                '--dark-button-default': "$buttonColor",
 
                             };
                             for (let [property, value] of Object.entries(properties)) {

From cc02eb7649b52ce0940edadc17f4af3173a321cf Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 15:56:59 +0200
Subject: [PATCH 22/28] tidy: cleanup code, remove temporary logging

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt    | 16 ++++------------
 .../snyk/plugin/ui/jcef/GenerateAIFixHandler.kt  | 16 +++++-----------
 2 files changed, 9 insertions(+), 23 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 0122601ab..5221cb361 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -44,9 +44,6 @@ class ApplyFixHandler(private val project: Project) {
     fun generateApplyFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
         val applyFixQuery = JBCefJSQuery.create(jbCefBrowser)
 
-        //temporary logs
-        logger.info("[generateApplyFixCommand] calling applyPatchAndSave")
-
         applyFixQuery.addHandler { value ->
             val params = value.split("|@", limit = 2)
             val filePath = params[0]  // Path to the file that needs to be patched
@@ -54,19 +51,14 @@ class ApplyFixHandler(private val project: Project) {
 
             // Avoid blocking the UI thread
             runAsync {
-                try {
-                    val success = applyPatchAndSave(project, filePath, patch)
-
+                val success = applyPatchAndSave(project, filePath, patch)
 
-                    val script = """
+                val script = """
                         window.receiveApplyFixResponse($success);
                     """.trimIndent()
 
-                    jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-                    JBCefJSQuery.Response("success")
-                } catch (e: Exception) {
-                    log("Error applying fix: ${e.message}")
-                }
+                jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                JBCefJSQuery.Response("success")
             }
             return@addHandler JBCefJSQuery.Response("success")
         }
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index a21a14818..93e08c3af 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -23,21 +23,15 @@ class GenerateAIFixHandler(private val project: Project) {
 
 
             runAsync {
-                try {
-                    val responseDiff: List<LanguageServerWrapper.Fix> =
-                        LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
+                val responseDiff: List<LanguageServerWrapper.Fix> =
+                    LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
 
-                    //What happens when sendCodeFixDiffsCommand fails or is empty?
-
-                    val script = """
+                val script = """
                         window.receiveAIFixResponse(${Gson().toJson(responseDiff)});
                     """.trimIndent()
 
-                    jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-                    JBCefJSQuery.Response("success")
-                } catch (e: Exception) {
-                    e.printStackTrace()
-                }
+                jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                JBCefJSQuery.Response("success")
             }
             return@addHandler JBCefJSQuery.Response("success")
         }

From a174e45aed8d3aba5569bd5c96254ab112050152 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 16:15:48 +0200
Subject: [PATCH 23/28] fix: update unit test and remove duplicate code

---
 .../plugin/ui/jcef/ApplyFixHandlerTest.kt     | 94 ++-----------------
 1 file changed, 6 insertions(+), 88 deletions(-)

diff --git a/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt b/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
index 76725efc1..0177528e9 100644
--- a/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
+++ b/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
@@ -1,9 +1,9 @@
 package io.snyk.plugin.ui.jcef
 
 import org.junit.Test
-import junit.framework.TestCase.assertEquals
+import com.intellij.testFramework.fixtures.BasePlatformTestCase
 
-class DiffPatchTest {
+class DiffPatchTest : BasePlatformTestCase(){
     private  val originalFileContent = """
         /*
          * Copyright (c) 2014-2023 Bjoern Kimminich & the OWASP Juice Shop contributors.
@@ -46,8 +46,10 @@ class DiffPatchTest {
 
     @Test
     fun `test applying patch`() {
-        val diffPatch = parseDiff(responseDiff)
-        val patchedContent = applyPatch(originalFileContent, diffPatch)
+        val applyFixHandler = ApplyFixHandler(project)
+
+        val diffPatch = applyFixHandler.parseDiff(responseDiff)
+        val patchedContent = applyFixHandler.applyPatch(originalFileContent, diffPatch)
 
         val expectedPatchedContent = """
             /*
@@ -76,88 +78,4 @@ class DiffPatchTest {
 
         assertEquals(expectedPatchedContent, patchedContent)
     }
-
-    private fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
-        val lines = fileContent.lines().toMutableList()
-
-        for (hunk in diffPatch.hunks) {
-            var originalLineIndex = hunk.startLineOriginal - 1  // Convert to 0-based index
-
-            for (change in hunk.changes) {
-                when (change) {
-                    is Change.Addition -> {
-                        lines.add(originalLineIndex, change.line)
-                        originalLineIndex++
-                    }
-                    is Change.Deletion -> {
-                        if (originalLineIndex < lines.size && lines[originalLineIndex].trim() == change.line) {
-                            lines.removeAt(originalLineIndex)
-                        }
-                    }
-                    is Change.Context -> {
-                        originalLineIndex++  // Move past unchanged context lines
-                    }
-                }
-            }
-        }
-        return lines.joinToString("\n")
-    }
-
-    private fun parseDiff(diff: String): DiffPatch {
-        val lines = diff.lines()
-        val originalFile = lines.first { it.startsWith("---") }.substringAfter("--- ")
-        val fixedFile = lines.first { it.startsWith("+++") }.substringAfter("+++ ")
-
-        val hunks = mutableListOf<Hunk>()
-        var currentHunk: Hunk? = null
-        val changes = mutableListOf<Change>()
-
-        for (line in lines) {
-            when {
-                line.startsWith("@@") -> {
-                    // Parse hunk header (e.g., @@ -4,9 +4,14 @@)
-                    val hunkHeader = line.substringAfter("@@ ").substringBefore(" @@").split(" ")
-                    val original = hunkHeader[0].substring(1).split(",")
-                    val fixed = hunkHeader[1].substring(1).split(",")
-
-                    val startLineOriginal = original[0].toInt()
-                    val numLinesOriginal = original.getOrNull(1)?.toInt() ?: 1
-                    val startLineFixed = fixed[0].toInt()
-                    val numLinesFixed = fixed.getOrNull(1)?.toInt() ?: 1
-
-                    if (currentHunk != null) {
-                        hunks.add(currentHunk.copy(changes = changes.toList()))
-                        changes.clear()
-                    }
-                    currentHunk = Hunk(
-                        startLineOriginal = startLineOriginal,
-                        numLinesOriginal = numLinesOriginal,
-                        startLineFixed = startLineFixed,
-                        numLinesFixed = numLinesFixed,
-                        changes = emptyList()
-                    )
-                }
-
-                line.startsWith("---") || line.startsWith("+++") -> {
-                    // Skip file metadata lines (--- and +++)
-                    continue
-                }
-
-                line.startsWith("-") -> changes.add(Change.Deletion(line.substring(1).trim()))
-                line.startsWith("+") -> changes.add(Change.Addition(line.substring(1).trim()))
-                else -> changes.add(Change.Context(line.trim()))
-            }
-        }
-
-        // Add the last hunk
-        if (currentHunk != null) {
-            hunks.add(currentHunk.copy(changes = changes.toList()))
-        }
-
-        return DiffPatch(
-            originalFile = originalFile,
-            fixedFile = fixedFile,
-            hunks = hunks
-        )
-    }
 }

From ee0b923c1ab160ec616141bdd4567f1a3e63c4b5 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 17:02:38 +0200
Subject: [PATCH 24/28] fix: improve error handling and added balloon notifier
 for failing to apply patch

---
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 78 ++++++++++---------
 1 file changed, 43 insertions(+), 35 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 5221cb361..a1fa8beaa 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -12,6 +12,8 @@ import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
 import org.jetbrains.concurrency.runAsync
 import io.snyk.plugin.toVirtualFile
+import io.snyk.plugin.ui.SnykBalloonNotificationHelper
+import java.io.IOException
 
 
 data class DiffPatch(
@@ -51,14 +53,32 @@ class ApplyFixHandler(private val project: Project) {
 
             // Avoid blocking the UI thread
             runAsync {
-                val success = applyPatchAndSave(project, filePath, patch)
-
-                val script = """
-                        window.receiveApplyFixResponse($success);
-                    """.trimIndent()
+                //var success = true
+                val result = try {
+                    applyPatchAndSave(project, filePath, patch)
+                } catch (e: IOException) { // Catch specific file-related exceptions
+                    log("Error applying patch to file: $filePath. e:$e")
+                    Result.failure(e)
+                } catch (e: Exception) {
+                    log("Unexpected error applying patch. e:$e")
+                    Result.failure(e)
+                }
 
-                jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-                JBCefJSQuery.Response("success")
+                ApplicationManager.getApplication().invokeLater {
+                    if (result.isSuccess) {
+                        val script = """
+                            window.receiveApplyFixResponse(true);
+                        """.trimIndent()
+                        jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                    } else {
+                        val errorMessage = "Error applying fix: ${result.exceptionOrNull()?.message}"
+                        SnykBalloonNotificationHelper.showError(errorMessage, project)
+                        val errorScript = """
+                            window.receiveApplyFixResponse(false, "$errorMessage");
+                        """.trimIndent()
+                        jbCefBrowser.cefBrowser.executeJavaScript(errorScript, jbCefBrowser.cefBrowser.url, 0)
+                    }
+                }
             }
             return@addHandler JBCefJSQuery.Response("success")
         }
@@ -80,45 +100,33 @@ class ApplyFixHandler(private val project: Project) {
         }
     }
 
-    private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Boolean {
+    private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Result<Unit> {
         val virtualFile = filePath.toVirtualFile()
 
-        val fileContent = ApplicationManager.getApplication().runReadAction<String?> {
-            val document = FileDocumentManager.getInstance().getDocument(virtualFile)
-            document?.text
-        } ?: run {
-            log("[applyPatchAndSave] Document not found or is null for virtual file: $filePath")
-            return false
-        }
-
-        val diffPatch = parseDiff(patch)
-        val patchedContent = applyPatch(fileContent, diffPatch)
-
-        // Apply the patch inside a WriteCommandAction
-        val result = try {
-            var appliedPatchSuccessfully = true
+        return try {
             WriteCommandAction.runWriteCommandAction(project) {
                 val document = FileDocumentManager.getInstance().getDocument(virtualFile)
-                if (document != null && fileContent != patchedContent) {
-                    document.setText(patchedContent)
-
-                    //temporary logs
-                    logger.info("[applyPatchAndSave] Content after applying patch:${document.text}")
-                    appliedPatchSuccessfully = true
+                if (document != null) {
+                    val originalContent = document.text
+                    val patchedContent = applyPatch(originalContent, parseDiff(patch))
+                    if (originalContent != patchedContent) {
+                        document.setText(patchedContent)
+                    } else {
+                        log("[applyPatchAndSave] Patch did not modify content: $filePath")
+                    }
                 } else {
-                    log("[applyPatchAndSave] Failed to find document for saving patched content.")
-                    appliedPatchSuccessfully = false
+                    log("[applyPatchAndSave] Failed to find document for: $filePath")
+                    return@runWriteCommandAction
                 }
             }
-            appliedPatchSuccessfully
+            Result.success(Unit)
         } catch (e: Exception) {
-            log("[applyPatchAndSave] Error applying patch: ${e.message}")
-            false // Failure
+            log("[applyPatchAndSave] Error applying patch to: $filePath. e: $e")
+            Result.failure(e)
         }
-
-        return result
     }
 
+
     fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
         val lines = fileContent.lines().toMutableList()
 

From 280a979a17131eee669ef50ff2f99486fdba2149 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 17:41:07 +0200
Subject: [PATCH 25/28] tidy: refactor functions to a new patcher

---
 src/main/kotlin/io/snyk/plugin/DiffPatcher.kt | 94 +++++++++++++++++++
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 92 +-----------------
 ...lyFixHandlerTest.kt => DiffPatcherTest.kt} | 12 +--
 3 files changed, 104 insertions(+), 94 deletions(-)
 create mode 100644 src/main/kotlin/io/snyk/plugin/DiffPatcher.kt
 rename src/test/kotlin/io/snyk/plugin/{ui/jcef/ApplyFixHandlerTest.kt => DiffPatcherTest.kt} (88%)

diff --git a/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt b/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt
new file mode 100644
index 000000000..5d4e28006
--- /dev/null
+++ b/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt
@@ -0,0 +1,94 @@
+package io.snyk.plugin
+
+import io.snyk.plugin.ui.jcef.Change
+import io.snyk.plugin.ui.jcef.DiffPatch
+import io.snyk.plugin.ui.jcef.Hunk
+
+class DiffPatcher {
+
+    fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
+        val lines = fileContent.lines().toMutableList()
+
+        for (hunk in diffPatch.hunks) {
+            var originalLineIndex = hunk.startLineOriginal - 1  // Convert to 0-based index
+
+            for (change in hunk.changes) {
+                when (change) {
+                    is Change.Addition -> {
+                        lines.add(originalLineIndex, change.line)
+                        originalLineIndex++
+                    }
+
+                    is Change.Deletion -> {
+                        if (originalLineIndex < lines.size && lines[originalLineIndex].trim() == change.line) {
+                            lines.removeAt(originalLineIndex)
+                        }
+                    }
+
+                    is Change.Context -> {
+                        originalLineIndex++  // Move past unchanged context lines
+                    }
+                }
+            }
+        }
+        return lines.joinToString("\n")
+    }
+
+    fun parseDiff(diff: String): DiffPatch {
+        val lines = diff.lines()
+        val originalFile = lines.first { it.startsWith("---") }.substringAfter("--- ")
+        val fixedFile = lines.first { it.startsWith("+++") }.substringAfter("+++ ")
+
+        val hunks = mutableListOf<Hunk>()
+        var currentHunk: Hunk? = null
+        val changes = mutableListOf<Change>()
+
+        for (line in lines) {
+            when {
+                line.startsWith("@@") -> {
+                    // Parse hunk header (e.g., @@ -4,9 +4,14 @@)
+                    val hunkHeader = line.substringAfter("@@ ").substringBefore(" @@").split(" ")
+                    val original = hunkHeader[0].substring(1).split(",")
+                    val fixed = hunkHeader[1].substring(1).split(",")
+
+                    val startLineOriginal = original[0].toInt()
+                    val numLinesOriginal = original.getOrNull(1)?.toInt() ?: 1
+                    val startLineFixed = fixed[0].toInt()
+                    val numLinesFixed = fixed.getOrNull(1)?.toInt() ?: 1
+
+                    if (currentHunk != null) {
+                        hunks.add(currentHunk.copy(changes = changes.toList()))
+                        changes.clear()
+                    }
+                    currentHunk = Hunk(
+                        startLineOriginal = startLineOriginal,
+                        numLinesOriginal = numLinesOriginal,
+                        startLineFixed = startLineFixed,
+                        numLinesFixed = numLinesFixed,
+                        changes = emptyList()
+                    )
+                }
+
+                line.startsWith("---") || line.startsWith("+++") -> {
+                    // Skip file metadata lines (--- and +++)
+                    continue
+                }
+
+                line.startsWith("-") -> changes.add(Change.Deletion(line.substring(1).trim()))
+                line.startsWith("+") -> changes.add(Change.Addition(line.substring(1).trim()))
+                else -> changes.add(Change.Context(line.trim()))
+            }
+        }
+
+        // Add the last hunk
+        if (currentHunk != null) {
+            hunks.add(currentHunk.copy(changes = changes.toList()))
+        }
+
+        return DiffPatch(
+            originalFile = originalFile,
+            fixedFile = fixedFile,
+            hunks = hunks
+        )
+    }
+}
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index a1fa8beaa..717de21df 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -7,11 +7,12 @@ import com.intellij.openapi.fileEditor.FileDocumentManager
 import com.intellij.openapi.project.Project
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.ui.jcef.JBCefJSQuery
+import io.snyk.plugin.DiffPatcher
+import io.snyk.plugin.toVirtualFile
 import org.cef.browser.CefBrowser
 import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
 import org.jetbrains.concurrency.runAsync
-import io.snyk.plugin.toVirtualFile
 import io.snyk.plugin.ui.SnykBalloonNotificationHelper
 import java.io.IOException
 
@@ -102,13 +103,14 @@ class ApplyFixHandler(private val project: Project) {
 
     private fun applyPatchAndSave(project: Project, filePath: String, patch: String): Result<Unit> {
         val virtualFile = filePath.toVirtualFile()
+        val patcher = DiffPatcher()
 
         return try {
             WriteCommandAction.runWriteCommandAction(project) {
                 val document = FileDocumentManager.getInstance().getDocument(virtualFile)
                 if (document != null) {
                     val originalContent = document.text
-                    val patchedContent = applyPatch(originalContent, parseDiff(patch))
+                    val patchedContent = patcher.applyPatch(originalContent, patcher.parseDiff(patch))
                     if (originalContent != patchedContent) {
                         document.setText(patchedContent)
                     } else {
@@ -127,92 +129,6 @@ class ApplyFixHandler(private val project: Project) {
     }
 
 
-    fun applyPatch(fileContent: String, diffPatch: DiffPatch): String {
-        val lines = fileContent.lines().toMutableList()
-
-        for (hunk in diffPatch.hunks) {
-            var originalLineIndex = hunk.startLineOriginal - 1  // Convert to 0-based index
-
-            for (change in hunk.changes) {
-                when (change) {
-                    is Change.Addition -> {
-                        lines.add(originalLineIndex, change.line)
-                        originalLineIndex++
-                    }
-
-                    is Change.Deletion -> {
-                        if (originalLineIndex < lines.size && lines[originalLineIndex].trim() == change.line) {
-                            lines.removeAt(originalLineIndex)
-                        }
-                    }
-
-                    is Change.Context -> {
-                        originalLineIndex++  // Move past unchanged context lines
-                    }
-                }
-            }
-        }
-        return lines.joinToString("\n")
-    }
-
-    fun parseDiff(diff: String): DiffPatch {
-        val lines = diff.lines()
-        val originalFile = lines.first { it.startsWith("---") }.substringAfter("--- ")
-        val fixedFile = lines.first { it.startsWith("+++") }.substringAfter("+++ ")
-
-        val hunks = mutableListOf<Hunk>()
-        var currentHunk: Hunk? = null
-        val changes = mutableListOf<Change>()
-
-        for (line in lines) {
-            when {
-                line.startsWith("@@") -> {
-                    // Parse hunk header (e.g., @@ -4,9 +4,14 @@)
-                    val hunkHeader = line.substringAfter("@@ ").substringBefore(" @@").split(" ")
-                    val original = hunkHeader[0].substring(1).split(",")
-                    val fixed = hunkHeader[1].substring(1).split(",")
-
-                    val startLineOriginal = original[0].toInt()
-                    val numLinesOriginal = original.getOrNull(1)?.toInt() ?: 1
-                    val startLineFixed = fixed[0].toInt()
-                    val numLinesFixed = fixed.getOrNull(1)?.toInt() ?: 1
-
-                    if (currentHunk != null) {
-                        hunks.add(currentHunk.copy(changes = changes.toList()))
-                        changes.clear()
-                    }
-                    currentHunk = Hunk(
-                        startLineOriginal = startLineOriginal,
-                        numLinesOriginal = numLinesOriginal,
-                        startLineFixed = startLineFixed,
-                        numLinesFixed = numLinesFixed,
-                        changes = emptyList()
-                    )
-                }
-
-                line.startsWith("---") || line.startsWith("+++") -> {
-                    // Skip file metadata lines (--- and +++)
-                    continue
-                }
-
-                line.startsWith("-") -> changes.add(Change.Deletion(line.substring(1).trim()))
-                line.startsWith("+") -> changes.add(Change.Addition(line.substring(1).trim()))
-                else -> changes.add(Change.Context(line.trim()))
-            }
-        }
-
-        // Add the last hunk
-        if (currentHunk != null) {
-            hunks.add(currentHunk.copy(changes = changes.toList()))
-        }
-
-        return DiffPatch(
-            originalFile = originalFile,
-            fixedFile = fixedFile,
-            hunks = hunks
-        )
-    }
-
     private fun log(logMessage: String) {
         when {
             enableDebug -> logger.debug(logMessage)
diff --git a/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt b/src/test/kotlin/io/snyk/plugin/DiffPatcherTest.kt
similarity index 88%
rename from src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
rename to src/test/kotlin/io/snyk/plugin/DiffPatcherTest.kt
index 0177528e9..01bc6782d 100644
--- a/src/test/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandlerTest.kt
+++ b/src/test/kotlin/io/snyk/plugin/DiffPatcherTest.kt
@@ -1,9 +1,9 @@
-package io.snyk.plugin.ui.jcef
+package io.snyk.plugin
 
 import org.junit.Test
-import com.intellij.testFramework.fixtures.BasePlatformTestCase
+import org.junit.Assert.assertEquals
 
-class DiffPatchTest : BasePlatformTestCase(){
+class DiffPatcherTest (){
     private  val originalFileContent = """
         /*
          * Copyright (c) 2014-2023 Bjoern Kimminich & the OWASP Juice Shop contributors.
@@ -46,10 +46,10 @@ class DiffPatchTest : BasePlatformTestCase(){
 
     @Test
     fun `test applying patch`() {
-        val applyFixHandler = ApplyFixHandler(project)
+        val diffPatcher = DiffPatcher()
 
-        val diffPatch = applyFixHandler.parseDiff(responseDiff)
-        val patchedContent = applyFixHandler.applyPatch(originalFileContent, diffPatch)
+        val diffPatch = diffPatcher.parseDiff(responseDiff)
+        val patchedContent = diffPatcher.applyPatch(originalFileContent, diffPatch)
 
         val expectedPatchedContent = """
             /*

From f155b48fec3f46090efbb261082477bf3712606a Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Mon, 16 Sep 2024 17:58:10 +0200
Subject: [PATCH 26/28] tidy: remove unused parameters

---
 src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt      | 1 -
 src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt | 3 +--
 .../snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt   | 2 +-
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 717de21df..952835236 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -128,7 +128,6 @@ class ApplyFixHandler(private val project: Project) {
         }
     }
 
-
     private fun log(logMessage: String) {
         when {
             enableDebug -> logger.debug(logMessage)
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index 93e08c3af..9435e50e9 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -1,7 +1,6 @@
 package io.snyk.plugin.ui.jcef
 
 import com.google.gson.Gson
-import com.intellij.openapi.project.Project
 import com.intellij.ui.jcef.JBCefBrowserBase
 import com.intellij.ui.jcef.JBCefJSQuery
 import org.cef.browser.CefBrowser
@@ -10,7 +9,7 @@ import org.cef.handler.CefLoadHandlerAdapter
 import org.jetbrains.concurrency.runAsync
 import snyk.common.lsp.LanguageServerWrapper
 
-class GenerateAIFixHandler(private val project: Project) {
+class GenerateAIFixHandler() {
 
     fun generateAIFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
         val aiFixQuery = JBCefJSQuery.create(jbCefBrowser)
diff --git a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
index 667d77f48..95c1751d0 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/toolwindow/panels/JCEFDescriptionPanel.kt
@@ -62,7 +62,7 @@ class SuggestionDescriptionPanelFromLS(
                     openFileLoadHandlerGenerator.generate(it)
                 }
 
-                val generateAIFixHandler = GenerateAIFixHandler(snykFile.project)
+                val generateAIFixHandler = GenerateAIFixHandler()
                 loadHandlerGenerators += {
                     generateAIFixHandler.generateAIFixCommand(it)
                 }

From 69e7c1ea33a4a61bd3c51d7ce83f8b1547725aac Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Thu, 19 Sep 2024 11:46:47 +0200
Subject: [PATCH 27/28] fix: updating logging and refactor types

---
 src/main/kotlin/io/snyk/plugin/DiffPatcher.kt | 22 ++++-
 .../io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 94 ++++++-------------
 .../plugin/ui/jcef/GenerateAIFixHandler.kt    |  4 +-
 .../snyk/common/lsp/LanguageServerWrapper.kt  |  7 --
 src/main/kotlin/snyk/common/lsp/Types.kt      |  5 +
 5 files changed, 58 insertions(+), 74 deletions(-)

diff --git a/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt b/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt
index 5d4e28006..4eb2aee14 100644
--- a/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt
+++ b/src/main/kotlin/io/snyk/plugin/DiffPatcher.kt
@@ -1,8 +1,24 @@
 package io.snyk.plugin
 
-import io.snyk.plugin.ui.jcef.Change
-import io.snyk.plugin.ui.jcef.DiffPatch
-import io.snyk.plugin.ui.jcef.Hunk
+data class DiffPatch(
+    val originalFile: String,
+    val fixedFile: String,
+    val hunks: List<Hunk>
+)
+
+data class Hunk(
+    val startLineOriginal: Int,
+    val numLinesOriginal: Int,
+    val startLineFixed: Int,
+    val numLinesFixed: Int,
+    val changes: List<Change>
+)
+
+sealed class Change {
+    data class Addition(val line: String) : Change()
+    data class Deletion(val line: String) : Change()
+    data class Context(val line: String) : Change()  // Unchanged line for context
+}
 
 class DiffPatcher {
 
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 952835236..53bc85659 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -1,7 +1,7 @@
 package io.snyk.plugin.ui.jcef
 
-import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.command.WriteCommandAction
+import com.intellij.openapi.diagnostic.LogLevel
 import com.intellij.openapi.diagnostic.Logger
 import com.intellij.openapi.fileEditor.FileDocumentManager
 import com.intellij.openapi.project.Project
@@ -14,34 +14,17 @@ import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
 import org.jetbrains.concurrency.runAsync
 import io.snyk.plugin.ui.SnykBalloonNotificationHelper
+import snyk.common.lsp.LanguageServerWrapper
 import java.io.IOException
 
-
-data class DiffPatch(
-    val originalFile: String,
-    val fixedFile: String,
-    val hunks: List<Hunk>
-)
-
-data class Hunk(
-    val startLineOriginal: Int,
-    val numLinesOriginal: Int,
-    val startLineFixed: Int,
-    val numLinesFixed: Int,
-    val changes: List<Change>
-)
-
-sealed class Change {
-    data class Addition(val line: String) : Change()
-    data class Deletion(val line: String) : Change()
-    data class Context(val line: String) : Change()  // Unchanged line for context
-}
-
 class ApplyFixHandler(private val project: Project) {
 
-    private val enableDebug = Logger.getInstance("Snyk Language Server").isDebugEnabled
-    private val enableTrace = Logger.getInstance("Snyk Language Server").isTraceEnabled
-    private val logger = Logger.getInstance(this::class.java)
+    val logger = Logger.getInstance(this::class.java).apply {
+        // tie log level to language server log level
+        val languageServerWrapper = LanguageServerWrapper.getInstance()
+        if (languageServerWrapper.logger.isDebugEnabled) this.setLevel(LogLevel.DEBUG)
+        if (languageServerWrapper.logger.isTraceEnabled) this.setLevel(LogLevel.TRACE)
+    }
 
 
     fun generateApplyFixCommand(jbCefBrowser: JBCefBrowserBase): CefLoadHandlerAdapter {
@@ -54,32 +37,30 @@ class ApplyFixHandler(private val project: Project) {
 
             // Avoid blocking the UI thread
             runAsync {
-                //var success = true
                 val result = try {
                     applyPatchAndSave(project, filePath, patch)
                 } catch (e: IOException) { // Catch specific file-related exceptions
-                    log("Error applying patch to file: $filePath. e:$e")
+                    logger.error("Error applying patch to file: $filePath. e:$e")
                     Result.failure(e)
                 } catch (e: Exception) {
-                    log("Unexpected error applying patch. e:$e")
+                    logger.error("Unexpected error applying patch. e:$e")
                     Result.failure(e)
                 }
 
-                ApplicationManager.getApplication().invokeLater {
-                    if (result.isSuccess) {
-                        val script = """
+                if (result.isSuccess) {
+                    val script = """
                             window.receiveApplyFixResponse(true);
                         """.trimIndent()
-                        jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
-                    } else {
-                        val errorMessage = "Error applying fix: ${result.exceptionOrNull()?.message}"
-                        SnykBalloonNotificationHelper.showError(errorMessage, project)
-                        val errorScript = """
+                    jbCefBrowser.cefBrowser.executeJavaScript(script, jbCefBrowser.cefBrowser.url, 0)
+                } else {
+                    val errorMessage = "Error applying fix: ${result.exceptionOrNull()?.message}"
+                    SnykBalloonNotificationHelper.showError(errorMessage, project)
+                    val errorScript = """
                             window.receiveApplyFixResponse(false, "$errorMessage");
                         """.trimIndent()
-                        jbCefBrowser.cefBrowser.executeJavaScript(errorScript, jbCefBrowser.cefBrowser.url, 0)
-                    }
+                    jbCefBrowser.cefBrowser.executeJavaScript(errorScript, jbCefBrowser.cefBrowser.url, 0)
                 }
+
             }
             return@addHandler JBCefJSQuery.Response("success")
         }
@@ -105,34 +86,21 @@ class ApplyFixHandler(private val project: Project) {
         val virtualFile = filePath.toVirtualFile()
         val patcher = DiffPatcher()
 
-        return try {
-            WriteCommandAction.runWriteCommandAction(project) {
-                val document = FileDocumentManager.getInstance().getDocument(virtualFile)
-                if (document != null) {
-                    val originalContent = document.text
-                    val patchedContent = patcher.applyPatch(originalContent, patcher.parseDiff(patch))
-                    if (originalContent != patchedContent) {
-                        document.setText(patchedContent)
-                    } else {
-                        log("[applyPatchAndSave] Patch did not modify content: $filePath")
-                    }
+        WriteCommandAction.runWriteCommandAction(project) {
+            val document = FileDocumentManager.getInstance().getDocument(virtualFile)
+            if (document != null) {
+                val originalContent = document.text
+                val patchedContent = patcher.applyPatch(originalContent, patcher.parseDiff(patch))
+                if (originalContent != patchedContent) {
+                    document.setText(patchedContent)
                 } else {
-                    log("[applyPatchAndSave] Failed to find document for: $filePath")
-                    return@runWriteCommandAction
+                    logger.warn("[applyPatchAndSave] Patch did not modify content: $filePath")
                 }
+            } else {
+                logger.error("[applyPatchAndSave] Failed to find document for: $filePath")
+                return@runWriteCommandAction
             }
-            Result.success(Unit)
-        } catch (e: Exception) {
-            log("[applyPatchAndSave] Error applying patch to: $filePath. e: $e")
-            Result.failure(e)
-        }
-    }
-
-    private fun log(logMessage: String) {
-        when {
-            enableDebug -> logger.debug(logMessage)
-            enableTrace -> logger.trace(logMessage)
-            else -> logger.error(logMessage)
         }
+        return Result.success(Unit)
     }
 }
diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
index 9435e50e9..d430c2ae7 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/GenerateAIFixHandler.kt
@@ -8,6 +8,8 @@ import org.cef.browser.CefFrame
 import org.cef.handler.CefLoadHandlerAdapter
 import org.jetbrains.concurrency.runAsync
 import snyk.common.lsp.LanguageServerWrapper
+import snyk.common.lsp.Fix
+
 
 class GenerateAIFixHandler() {
 
@@ -22,7 +24,7 @@ class GenerateAIFixHandler() {
 
 
             runAsync {
-                val responseDiff: List<LanguageServerWrapper.Fix> =
+                val responseDiff: List<Fix> =
                     LanguageServerWrapper.getInstance().sendCodeFixDiffsCommand(folderURI, fileURI, issueID)
 
                 val script = """
diff --git a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
index 1bbb72f05..13dbfdffc 100644
--- a/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
+++ b/src/main/kotlin/snyk/common/lsp/LanguageServerWrapper.kt
@@ -1,8 +1,6 @@
 package snyk.common.lsp
 
 import com.google.gson.Gson
-import com.google.gson.annotations.SerializedName
-import com.google.gson.reflect.TypeToken
 import com.intellij.openapi.Disposable
 import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.components.service
@@ -497,11 +495,6 @@ class LanguageServerWrapper(
         return this.getFeatureFlagStatus("snykCodeConsistentIgnores")
     }
 
-    data class Fix(
-        @SerializedName("fixId") val fixId: String,
-        @SerializedName("unifiedDiffsPerFile") val unifiedDiffsPerFile: Map<String, String>
-    )
-
     @Suppress("UNCHECKED_CAST")
     fun sendCodeFixDiffsCommand(folderURI: String, fileURI: String, issueID: String): List<Fix> {
         if (!ensureLanguageServerInitialized()) return emptyList()
diff --git a/src/main/kotlin/snyk/common/lsp/Types.kt b/src/main/kotlin/snyk/common/lsp/Types.kt
index 3553a3305..fe88f5c35 100644
--- a/src/main/kotlin/snyk/common/lsp/Types.kt
+++ b/src/main/kotlin/snyk/common/lsp/Types.kt
@@ -337,6 +337,11 @@ data class ExampleCommitFix(
     @SerializedName("lines") val lines: List<CommitChangeLine>,
 )
 
+data class Fix(
+    @SerializedName("fixId") val fixId: String,
+    @SerializedName("unifiedDiffsPerFile") val unifiedDiffsPerFile: Map<String, String>
+)
+
 data class CommitChangeLine(
     @SerializedName("line") val line: String,
     @SerializedName("lineNumber") val lineNumber: Int,

From 2d00d294353da6e4ddbd178550cc4618bd55abc1 Mon Sep 17 00:00:00 2001
From: Knut Funkel <knut.funkel@snyk.io>
Date: Fri, 20 Sep 2024 11:02:54 +0200
Subject: [PATCH 28/28] fix: add balloon notifier for file not found

---
 src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
index 53bc85659..c397ecd1f 100644
--- a/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
+++ b/src/main/kotlin/io/snyk/plugin/ui/jcef/ApplyFixHandler.kt
@@ -98,6 +98,8 @@ class ApplyFixHandler(private val project: Project) {
                 }
             } else {
                 logger.error("[applyPatchAndSave] Failed to find document for: $filePath")
+                val errorMessage = "Failed to find document for: $filePath"
+                SnykBalloonNotificationHelper.showError(errorMessage, project)
                 return@runWriteCommandAction
             }
         }