fix: the parse bug but not really

I could prevent the bug by setting ignoreEmptyLines to false upon parsing. I still do not know what the bug actually is and documented where I found it in the code for now.

Author: pmbittner

src/main/java/org/variantsync/diffdetective/experiments/views/Main.java

@@ -3,31 +3,50 @@
 import org.variantsync.diffdetective.AnalysisRunner;
 import org.variantsync.diffdetective.analysis.Analysis;
 import org.variantsync.diffdetective.analysis.FilterAnalysis;
-import org.variantsync.diffdetective.analysis.PreprocessingAnalysis;
 import org.variantsync.diffdetective.analysis.StatisticsAnalysis;
 import org.variantsync.diffdetective.datasets.PatchDiffParseOptions;
 import org.variantsync.diffdetective.datasets.Repository;
 import org.variantsync.diffdetective.variation.diff.filter.DiffTreeFilter;
 import org.variantsync.diffdetective.variation.diff.parse.DiffTreeParseOptions;
-import org.variantsync.diffdetective.variation.diff.transform.CutNonEditedSubtrees;
+import org.variantsync.diffdetective.variation.tree.view.query.ArtifactQuery;
 
 import java.io.IOException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.List;
 
 public class Main {
+    /*
+     * There is a bug in DiffView::naive when ignoreEmptyLines is set to true under
+     * some very rare circumstances that I do not know so far. The bug occurred for
+     * repo: emacs
+     * commit: 2254b6c09cff8f3a83684fd159289d0e305b0e7d
+     * patch: "src/alloc.c"
+     * view_naive
+     * with the following query.
+     * What is weird that the parsing only failed when running the analyses but not when extracting the diff to a unit
+     * test and parsing it there.
+     * Maybe it has something to do with linebreak or whitespace characters?
+     */
+    private static final ArtifactQuery bugQuery = new ArtifactQuery("  /* Check both of the above conditions, for symbols.  */");
+    public static DiffTreeParseOptions DIFFTREE_PARSE_OPTIONS =
+            new DiffTreeParseOptions(
+                    true,
+                    false
+            );
+
     public static Analysis AnalysisFactory(Repository repo, Path repoOutputDir) {
         return new Analysis(
                 "Views Analysis",
-                List.of(
-                        new PreprocessingAnalysis(new CutNonEditedSubtrees(true)),
+                new ArrayList<>(List.of(
+//                        new PreprocessingAnalysis(new CutNonEditedSubtrees(true)),
                         new FilterAnalysis( // filters unwanted trees
                                 DiffTreeFilter.notEmpty()
                         ),
                         new ViewAnalysis(),
                         new StatisticsAnalysis()
-                ),
+                )),
                 repo,
                 repoOutputDir
         );
@@ -36,23 +55,22 @@ public static Analysis AnalysisFactory(Repository repo, Path repoOutputDir) {
     public static void main(String[] args) throws IOException {
         final AnalysisRunner.Options defaultOptions = AnalysisRunner.Options.DEFAULT(args);
         final AnalysisRunner.Options analysisOptions = new AnalysisRunner.Options(
-                defaultOptions.repositoriesDirectory(),
+                Paths.get("..", "DiffDetectiveReplicationDatasets"),
                 Paths.get("results", "views", "current"),
                 defaultOptions.datasetsFile(),
                 repo -> new PatchDiffParseOptions(
                         PatchDiffParseOptions.DiffStoragePolicy.DO_NOT_REMEMBER,
-                        new DiffTreeParseOptions(
-                                true,
-                                false
-                        )
+                        DIFFTREE_PARSE_OPTIONS
                 ),
                 defaultOptions.getFilterForRepo(),
                 true,
                 false
         );
 
-        AnalysisRunner.run(analysisOptions, (repository, path) ->
-                Analysis.forEachCommit(() -> AnalysisFactory(repository, path))
-        );
+        AnalysisRunner.run(analysisOptions, (repository, path) -> {
+            //1b424533675341a2090b79a6ffc420ac6b179ce7
+//            Analysis.forSinglePatch("2254b6c09cff8f3a83684fd159289d0e305b0e7d", "src/alloc.c", AnalysisFactory(repository, path));
+            Analysis.forEachCommit(() -> AnalysisFactory(repository, path));
+        });
     }
 }

src/main/java/org/variantsync/diffdetective/variation/diff/view/DiffView.java

@@ -4,11 +4,11 @@
 import org.tinylog.Logger;
 import org.variantsync.diffdetective.diff.git.GitDiffer;
 import org.variantsync.diffdetective.diff.result.DiffParseException;
+import org.variantsync.diffdetective.experiments.views.Main;
 import org.variantsync.diffdetective.util.Assert;
 import org.variantsync.diffdetective.util.CollectionUtils;
 import org.variantsync.diffdetective.variation.diff.*;
 import org.variantsync.diffdetective.variation.diff.bad.BadVDiff;
-import org.variantsync.diffdetective.variation.diff.parse.DiffTreeParseOptions;
 import org.variantsync.diffdetective.variation.diff.parse.DiffTreeParser;
 import org.variantsync.diffdetective.variation.tree.VariationTree;
 import org.variantsync.diffdetective.variation.tree.VariationTreeNode;
@@ -19,7 +19,6 @@
 import java.nio.charset.StandardCharsets;
 import java.util.*;
 import java.util.function.BiPredicate;
-import java.util.function.Consumer;
 import java.util.regex.Pattern;
 
 public class DiffView {
@@ -106,31 +105,18 @@ Using our own formatter without diff headers (paired with a maximum context (?))
 //        Logger.info("Full Diff\n" + textDiff);
         final DiffTree view;
         try {
-            view = DiffTreeParser.createDiffTree(textDiff,
-                    new DiffTreeParseOptions(
-                            true,
-                            true
-                    ));
+            view = DiffTreeParser.createDiffTree(textDiff, Main.DIFFTREE_PARSE_OPTIONS);
         } catch (DiffParseException e) {
             Logger.error("""
-                            Could not parse diff obtained with query {}:
-                            Text before:
-                            {}
-                            
-                            Text after:
-                            {}
-                            
+                            Could not parse diff obtained with query {} at {}:
                             Diff:
-                            {}
                             """,
-                    q,
-                    projectionViewText[0],
-                    projectionViewText[1],
-                    textDiff);
+                    d.getSource(), q);
+            System.out.println(textDiff);
             throw e;
         }
         view.setSource(new ViewSource(d, q));
-//        Logger.info("success");
+
         return view;
     }
 

src/test/resources/badvdiff/emacsbug1.diff

@@ -29,10 +29,9 @@
    do {						\
      if (!c_symbol_p (ptr))			\
        {						\
-     CHECK_ALLOCATED ();			\
-     CHECK_LIVE (live_symbol_p);		\
+    CHECK_ALLOCATED ();			\
+    CHECK_LIVE (live_symbol_p);		\
        }						\
    } while (0)					\
 
- #endif
- 
+ #endif