vscode-plugin fix for refreshing list of issues after applying patche…

…s. (#106)

* Applied new 'grouped' json config layout to vscode-plugin.

#59

* Update issues TreeView to show the number of subelements.

* vscode-plugin issues bugfix (1.0.11)

#60
#73
#78
#79
#80

* Bugfix for #90.

-Selection and cursor are now set to the warning's position whenever an issue is opened up in the editor.

* vscode-plugin bugfix for #73.

-The config.properties file are now generated into the folder set up as the "Executable Path".

* Update version of vscode-plugin.

* Vscode-Plugin update 1.0.13.

- #94: Fixed bug where declining a warning patch candidate would result the removal of the entire warning from the analysis output window.
- #73: Changed format of generated config.property file.

* Update patch.ts to fix refreshing the list of the detected vulnerabilities issue.

- Referenced issue: #105

* Update plugin version.

* Remove unnecessary settings from plugin config.

Reducing the users' responsibility #109

* Update README.md

* Update plugin README.md

* Started reworking analysis call to only run on current cu.

* Minor fixes for windows with using OpenStaticAnalyzer.

* Minor fix for multiple analysis failure in plugin.

* Update plugin with new analyzer executable as parameter

-Reworked treeview generation with merging multiple json input as one json.

* Update saving previous state after patching in case of redo.

* Update status bar to support analysis on currently opened file.

* Starting multiple simultaneous analysis are no longer possible when status bar command is pressed repeatedly.

* Create custom output channel for the extensions logging.

* Remove old issue config updates.

* Minor fixes with patch view mode.

* Update treeview builder.

* Analysis output treeView build bugfix.

-Incorrect number of issues would show up in the treeview after analysis.

* Simplified configuration handling.

- use of -config flag is no longer needed in executableParameters, the plugin now uses it automatically.
- Only one config file are used for both the executable and the plugin.

* Update analyzer logic with new config handling and treeview refresh.

* Fixed Testview command already exists unhandled errors issue.

* Revert "Fixed Testview command already exists unhandled errors issue."

This reverts commit f3756e8.

* (Re) Fixed Testview command already exists unhandled errors issue.

* After manual save of a file, a file analysis now starts to refresh the results.

* Fixed unhandled 'webview is disposed' error.

* Analysis no longer runs on unsupported documents.

* Fix bug where code actions no longer appeared at other files but the file that was lastly analyzed.

* Analysis will no longer be started after declining a patch.

* Fixed some treeview refreshing issues after editing and analyzing a file.

* Add new try-catch scopes for previously unhandled errors.

* update treeView refresh after applying or declining patches.

* fixed bug at issue tree where after a patch was applied the issue tree had many duplicate issues pointing to the same location.

* Sorting patches by score.

* sorter wrapper

* add sorter

---------

Co-authored-by: Ákos <[email protected]>
Co-authored-by: Péter Mészáros <[email protected]>

pom.xml

@@ -153,7 +153,7 @@
                         <manifest>
                             <addClasspath>true</addClasspath>
                             <classpathPrefix>${project.build.finalName}.lib/</classpathPrefix>
-                            <mainClass>eu.assuremoss.VulnRepairDriver</mainClass>
+                            <mainClass>eu.assuremoss.VulnerabilityRepairDriver</mainClass>
                         </manifest>
                     </archive>
                 </configuration>

sorter/JSONHandler.py

@@ -0,0 +1,137 @@
+import json
+from numpy import dtype
+
+
+# Data classes to encode the json into objects
+class Patch:
+    def __init__(self, path, score, explanation):
+        self.path, self.score, self.explanation = path, score, explanation
+
+
+class TextRange:
+    def __init__(self, endLine, endColumn, startColumn, startLine):
+        self.endLine, self.endColumn = endLine, endColumn
+        self.startColumn, self.startLine = startColumn, startLine
+
+
+class PatchesArray:
+    def __init__(self, patches, textRange):
+        self.patches = [
+            Patch(patch["path"], patch["score"], patch["explanation"])
+            for patch in patches
+        ]
+        self.textRange = TextRange(
+            textRange["endLine"],
+            textRange["endColumn"],
+            textRange["startColumn"],
+            textRange["startLine"],
+        )
+
+
+class JSONEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, dtype):
+            return obj.val()
+        try:
+            return vars(obj)
+        except Exception as e:
+            return str(obj)
+
+
+class Issue:
+    def __init__(self, name, patchList):
+        self.name = name
+
+        if isinstance(patchList, list):
+            self.patchesArray = [
+                PatchesArray(patchesArray["patches"], patchesArray["textRange"])
+                for patchesArray in patchList
+            ]
+        elif isinstance(patchList, dict):
+            self.patchesArray = [
+                PatchesArray(patchList["patches"], patchList["textRange"])
+            ]
+        else:
+            raise TypeError("patchList should be list or dict")
+
+
+class JSONHandler:
+    def __init__(self):
+        self.issues = []
+        self.initialScores = []
+
+    def parseJSON(self, issuesPath):
+        """Parses the json file which contains the issues into objects
+
+        Parameters
+        ----------
+        issuesPath : str
+            The path to the json file
+
+        Returns
+        -------
+        list[str]
+            A list containing all the paths to the patches extracted from the json file
+        """
+        with open(issuesPath, "rt") as file:
+            parsedjsondict = json.load(file)
+        self.issues = [Issue(key, parsedjsondict[key]) for key in parsedjsondict.keys()]
+
+        patchPaths = []
+        for issue in self.issues:
+            for patchesArray in issue.patchesArray:
+                for patch in patchesArray.patches:
+                    patchPaths.append(patch)
+                    self.initialScores.append(patch.score)
+        return patchPaths
+
+    def extractPatchesArrays(self) -> list[PatchesArray]:
+        """Gets the patches arrays (textrange and a list of candidate patches) from the previously read json file
+
+        Returns
+        -------
+        list[PatchesArray]
+            A list of all the patchesArrays in the json file
+        """
+        patchesArrays = []
+        for issue in self.issues:
+            patchesArrays.extend(issue.patchesArray)
+        return patchesArrays
+
+    def updateJSON(self, issuesPath, scores):
+        """Updates the scores for the patches in the json file
+
+        Parameters
+        ----------
+        issuesPath :
+            The path to the json file
+        scores : list[float]
+            A list of the scores, the scores should be in the same order as
+            previously read from the json file (e. g. with parseJSON method)
+        """
+        i = 0
+        for issue in self.issues:
+            for patchlocation in issue.patchesArray:
+                for patch in patchlocation.patches:
+                    patch.score = scores[i]
+                    i += 1
+
+        completejson = dict()
+        for issue in self.issues:
+            completejson[issue.name] = issue.patchesArray
+        with open(issuesPath, "w") as file:
+            json.dump(completejson, file, indent=2, cls=JSONEncoder)
+
+    def extract_patches(self):
+        """Gets the patches from the previously read json file
+
+        Returns
+        -------
+        list(Patch)
+            A list of all the patches
+        """
+        patches = []
+        for issue in self.issues:
+            for patchlocation in issue.patchesArray:
+                patches.extend(patchlocation.patches)
+        return patches