Implement parse and compare hooks

.github/workflows/publish.yml

@@ -17,7 +17,7 @@ jobs:
         with:
           servers: '[{ "id": "ossrh", "username": "jplag", "password": "${{ secrets.OSSRH_TOKEN }}" }]'
       - name: Import GPG key
-        uses: crazy-max/ghaction-import-gpg@v5
+        uses: crazy-max/ghaction-import-gpg@v6
         with:
           gpg_private_key: ${{ secrets.PGP_SECRET }}
           passphrase: ${{ secrets.PGP_PW }}

.github/workflows/report-viewer-build-test.yml

@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Set version of Report Viewer
         shell: bash

.github/workflows/report-viewer-dev.yml

@@ -18,7 +18,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Set version of Report Viewer
         shell: bash

.github/workflows/report-viewer-e2e.yml

@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Install and Test 🧪
         working-directory: report-viewer

.github/workflows/report-viewer-lint.yml

@@ -4,7 +4,7 @@ name: Report Viewer ESLint Workflow # Checks linting of report viewer
 on:
   workflow_dispatch:
   push:
-    path:
+    paths:
       - ".github/workflows/report-viewer-lint.yml"
       - "report-viewer/**"
   pull_request:
@@ -35,7 +35,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Install and Lint 🎨
         working-directory: report-viewer

.github/workflows/report-viewer-prettier.yml

@@ -35,7 +35,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Install and Check 🎨
         working-directory: report-viewer

.github/workflows/report-viewer-unit.yml

@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Install and Test 🧪
         working-directory: report-viewer

.github/workflows/report-viewer.yml

@@ -15,7 +15,7 @@ jobs:
 
       - uses: actions/setup-node@v3
         with:
-          node-version: "16"
+          node-version: "18"
 
       - name: Set version of Report Viewer
         shell: bash

cli/src/main/java/de/jplag/cli/CLI.java

@@ -171,7 +171,8 @@ public JPlagOptions buildOptionsFromArguments(ParseResult parseResult) throws Cl
         JPlagOptions jPlagOptions = new JPlagOptions(loadLanguage(parseResult), this.options.minTokenMatch, submissionDirectories,
                 oldSubmissionDirectories, null, this.options.advanced.subdirectory, suffixes, this.options.advanced.exclusionFileName,
                 JPlagOptions.DEFAULT_SIMILARITY_METRIC, this.options.advanced.similarityThreshold, this.options.shownComparisons, clusteringOptions,
-                this.options.advanced.debug, mergingOptions);
+                this.options.advanced.debug, mergingOptions, JPlagOptions.DEFAULT_PRE_PARSE_HOOK, JPlagOptions.DEFAULT_PARSE_HOOK,
+                JPlagOptions.DEFAULT_PRE_COMPARE_HOOK, JPlagOptions.DEFAULT_COMPARE_HOOK);
 
         String baseCodePath = this.options.baseCode;
         File baseCodeDirectory = baseCodePath == null ? null : new File(baseCodePath);

cli/src/main/java/de/jplag/cli/CliOptions.java

@@ -53,7 +53,7 @@ public class CliOptions implements Runnable {
             "--result-directory"}, description = "Name of the directory in which the comparison results will be stored (default: result)%n")
     public String resultFolder = "results";
 
-    @ArgGroup(heading = "Advanced%n")
+    @ArgGroup(heading = "Advanced%n", exclusive = false)
     public Advanced advanced = new Advanced();
 
     @ArgGroup(validate = false, heading = "Clustering%n")

cli/src/test/java/de/jplag/cli/AdvancedGroupTest.java

@@ -0,0 +1,23 @@
+package de.jplag.cli;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.util.Arrays;
+
+import org.junit.jupiter.api.Test;
+
+class AdvancedGroupTest extends CommandLineInterfaceTest {
+    private static final String SUFFIXES = ".sc,.scala";
+
+    private static final double SIMILARITY_THRESHOLD = 0.5;
+
+    /**
+     * Verify that it is possible to set multiple options in the "advanced" options group.
+     */
+    @Test
+    void testNotExclusive() throws CliException {
+        buildOptionsFromCLI(defaultArguments().suffixes(SUFFIXES).similarityThreshold(SIMILARITY_THRESHOLD));
+        assertEquals(Arrays.stream(SUFFIXES.split(",")).toList(), options.fileSuffixes());
+        assertEquals(0.5, options.similarityThreshold());
+    }
+}

core/src/main/java/de/jplag/SubmissionSet.java

@@ -135,6 +135,8 @@ private void parseBaseCodeSubmission(Submission baseCode) throws BasecodeExcepti
      * Parse all given submissions.
      */
     private void parseSubmissions(List<Submission> submissions) {
+        this.options.preParseHook().accept(submissions);
+
         if (submissions.isEmpty()) {
             logger.warn("No submissions to parse!");
             return;
@@ -167,6 +169,8 @@ private void parseSubmissions(List<Submission> submissions) {
             } else {
                 logger.error("ERROR -> Submission {} removed", currentSubmissionName);
             }
+
+            this.options.parseHook().accept(submission);
         }
 
         int validSubmissions = submissions.size() - errors - tooShort;