Improved Unparser

docs/datasets/eugen-bachelor-thesis.md

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+Project name       | Domain                  | Source code available (\*\*y\*\*es/\*\*n\*\*o)? | Is it a git repository (\*\*y\*\*es/\*\*n\*\*o)? | Repository URL                                               | Clone URL                                          | Estimated number of commits
+-------------------|-------------------------|-------------------------------------------------|--------------------------------------------------|--------------------------------------------------------------|----------------------------------------------------|---------------------------------
+berkeley-db-libdb  | database system         | y                                               | y                                                | https://github.com/berkeleydb/libdb                          | https://github.com/berkeleydb/libdb.git            | 7
+sylpheed           | e-mail client           | y                                               | y                                                | https://github.com/jan0sch/sylpheed                          | https://github.com/jan0sch/sylpheed.git            | 2,682
+vim                | text editor             | y                                               | y                                                | https://github.com/vim/vim                                   | https://github.com/vim/vim.git                     | 17,109

replication/thesis-es/Dockerfile

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+# syntax=docker/dockerfile:1
+
+FROM alpine:3.15
+# PACKAGE STAGE
+
+# Prepare the compile environment. JDK is automatically installed
+RUN apk add maven
+
+# Create and navigate to a working directory
+WORKDIR /home/user
+
+COPY local-maven-repo ./local-maven-repo
+
+# Copy the source code
+COPY src ./src
+# Copy the pom.xml if Maven is used
+COPY pom.xml .
+# Execute the maven package process
+RUN mvn package || exit
+
+FROM alpine:3.15
+
+# Create a user
+RUN adduser --disabled-password  --home /home/sherlock --gecos '' sherlock
+
+RUN apk add --no-cache --upgrade bash
+RUN apk add --update openjdk17
+
+# Change into the home directory
+WORKDIR /home/sherlock
+
+# Copy the compiled JAR file from the first stage into the second stage
+# Syntax: COPY --from=STAGE_ID SOURCE_PATH TARGET_PATH
+WORKDIR /home/sherlock/holmes
+COPY --from=0 /home/user/target/diffdetective-*-jar-with-dependencies.jar ./DiffDetective.jar
+WORKDIR /home/sherlock
+RUN mkdir results
+
+# Copy the setup
+COPY docs holmes/docs
+
+# Copy the docker resources
+COPY docker/* ./
+COPY replication/thesis-es/docker/* ./
+RUN mkdir DiffDetectiveMining
+
+#  Adjust permissions
+RUN chown sherlock:sherlock /home/sherlock -R
+RUN chmod +x execute.sh
+RUN chmod +x entrypoint.sh
+RUN chmod +x fix-perms.sh
+
+# Set the entrypoint
+ENTRYPOINT ["./entrypoint.sh", "./execute.sh"]
+
+# Set the user
+USER sherlock

replication/thesis-es/README.md

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+![Maven](https://github.com/VariantSync/DiffDetective/actions/workflows/maven.yml/badge.svg)
+[![Documentation](https://img.shields.io/badge/Documentation-Read-purple)][documentation]
+[![Install](https://img.shields.io/badge/Install-Instructions-blue)](INSTALL.md)
+[![GitHubPages](https://img.shields.io/badge/GitHub%20Pages-online-blue.svg?style=flat)][website]
+[![License](https://img.shields.io/badge/License-GNU%20LGPLv3-blue)](../../LICENSE.LGPL3)
+
+# Unparsing Experiment
+This is an experiment for the bachelor thesis by Eugen Shulimov which tests the unparser for variation trees and diffs.
+
+### Prerequisite
+All following commands assume that working directory of your terminal is the `thesis-es` directory. Please switch directories, if this is not the case:
+```shell
+cd DiffDetective/replication/thesis-es
+```
+
+### Build the Docker container
+Start the docker deamon.
+Clone this repository.
+Open a terminal and navigate to the root directory of this repository.
+To build the Docker container you can run the `build` script corresponding to your operating system.
+#### Windows:
+`.\build.bat`
+#### Linux/Mac (bash):
+`./build.sh`
+
+### Start the experiment
+To execute the experiment you can run the `execute`script corresponding to your operating system.
+
+#### Windows:
+`.\execute.bat
+#### Linux/Mac (bash):
+`./execute.sh
+
+> If you want to stop the execution, you can call the provided script for stopping the container in a separate terminal.
+> When restarted, the execution will continue processing by restarting at the last unfinished repository.
+> #### Windows:
+> `.\stop-execution.bat`
+> #### Linux/Mac (bash):
+> `./stop-execution.sh`
+
+You might see warnings or errors reported from SLF4J like `Failed to load class "org.slf4j.impl.StaticLoggerBinder"` which you can safely ignore.
+
+### View the results in the [results][resultsdir] directory
+All raw results are stored in the [results][resultsdir] directory.
+
+[documentation]: https://variantsync.github.io/DiffDetective/docs/javadoc/
+[website]: https://variantsync.github.io/DiffDetective/
+
+[resultsdir]: results

replication/thesis-es/build.bat

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+@echo off
+setlocal
+
+set "targetSubPath=thesis-es"
+
+rem Get the current directory
+for %%A in ("%CD%") do set "currentDir=%%~nxA"
+
+rem Check if the current directory ends with the target sub-path
+
+if "%currentDir:~-9%"=="%targetSubPath%" (
+    cd ..\..
+    docker build -t diff-detective-unparse -f replication\thesis-es\Dockerfile .
+    @pause
+) else (
+    echo error: the script must be run from inside the thesis-es directory, i.e., DiffDetective\replication\%targetSubPath%
+)
+endlocal
+

replication/thesis-es/build.sh

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+#!/usr/bin/env bash
+
+# We have to switch to the root directory of the project and build the Docker image from there,
+# because Docker only allows access to the files in the current file system subtree (i.e., no access to ancestors).
+# We have to do this to get access to 'src', 'docker', 'local-maven-repo', etc.
+# For resiliency against different working directories during execution of this
+# script we calculate the correct path using the special bash variable
+# BASH_SOURCE.
+cd "$(dirname "${BASH_SOURCE[0]}")/../.." || exit
+
+docker build -t diff-detective-unparse -f replication/thesis-es/Dockerfile .

replication/thesis-es/docker/DOCKER.md

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+# Docker Files
+
+This directory contains the files that are required to run the Docker container.
+
+## Execution
+The [`execute.sh`](execute.sh) script can be adjusted to run the program that should be executed by the Docker container.

replication/thesis-es/docker/execute.sh

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+#!/usr/bin/env bash
+
+cd /home/sherlock/holmes || exit
+
+echo "Running the experiment."
+java -cp DiffDetective.jar org.variantsync.diffdetective.experiments.thesis-es.Main
+
+echo "Collecting results."
+cp -r results/* ../results/
+echo "The results are located in the 'results' directory."
+

replication/thesis-es/execute.bat

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+@echo off
+setlocal
+
+set "targetSubPath=thesis-es"
+
+rem Get the current directory
+for %%A in ("%CD%") do set "currentDir=%%~nxA"
+
+rem Check if the current directory ends with the target sub-path
+if "%currentDir:~-9%"=="%targetSubPath%" (
+docker run --rm -v "%cd%\results":"/home/sherlock/results" diff-detective-unparse %*
+) else (
+    echo error: the script must be run from inside the thesis-es directory, i.e., DiffDetective\replication\%targetSubPath%
+)
+endlocal

replication/thesis-es/execute.sh

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+#!/usr/bin/env bash
+# Assure that the script is only called from the folder cotaining this script
+cd "$(dirname "${BASH_SOURCE[0]}")" || exit
+
+if [[ $# -gt 0 ]]; then
+echo "Executing $1"
+fi
+docker run --rm -v "$(pwd)/results":"/home/sherlock/results" diff-detective-unparse "$@"

replication/thesis-es/results/.gitignore

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+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

replication/thesis-es/stop-execution.bat

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+@echo "Stopping all running simulations. This will take a moment..."
+@FOR /f "tokens=*" %%i IN ('docker ps -a -q --filter "ancestor=diff-detective-unparse"') DO docker stop %%i
+@echo "...done."

replication/thesis-es/stop-execution.sh

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+#!/usr/bin/env bash
+echo "Stopping Docker container. This will take a moment..."
+docker stop "$(docker ps -a -q --filter "ancestor=diff-detective-unparse")"
+echo "...done."

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

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+package org.variantsync.diffdetective.experiments.thesis_es;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.function.BiConsumer;
+import java.util.function.BiFunction;
+import java.util.stream.Stream;
+import org.variantsync.diffdetective.AnalysisRunner;
+import org.variantsync.diffdetective.analysis.Analysis;
+import org.variantsync.diffdetective.datasets.DatasetDescription;
+import org.variantsync.diffdetective.datasets.DefaultDatasets;
+import org.variantsync.diffdetective.datasets.PatchDiffParseOptions;
+import org.variantsync.diffdetective.datasets.PatchDiffParseOptions.DiffStoragePolicy;
+import org.variantsync.diffdetective.datasets.Repository;
+import org.variantsync.diffdetective.diff.git.DiffFilter;
+import org.variantsync.diffdetective.variation.diff.parse.VariationDiffParseOptions;
+
+public class Main {
+
+    public static void main(String[] args) throws IOException {
+        startAnalysis();
+        evaluationAnalysis(Path.of("docs", "datasets", "eugen-bachelor-thesis.md"));
+
+    }
+
+    private static void startAnalysis() throws IOException {
+        final AnalysisRunner.Options analysisOptions = new AnalysisRunner.Options(
+                Paths.get("..", "DiffDetectiveReplicationDatasets"),
+                Paths.get("results", "thesis_es"),
+                Paths.get("docs", "datasets", "eugen-bachelor-thesis.md"),
+                repo -> new PatchDiffParseOptions(
+                        DiffStoragePolicy.REMEMBER_FULL_DIFF,
+                        VariationDiffParseOptions.Default),
+                repo -> new DiffFilter.Builder().allowMerge(true)
+                        .allowedFileExtensions("c", "cpp").build(),
+                true,
+                false);
+
+        AnalysisRunner.run(analysisOptions, extractionRunner());
+    }
+
+    protected static BiConsumer<Repository, Path> extractionRunner() {
+        return (repo, repoOutputDir) -> {
+
+            final BiFunction<Repository, Path, Analysis> AnalysisFactory = (r, out) -> new Analysis("Thesis Eugen Shulimov",
+                    List.of(new UnparseAnalysis()), r, out);
+
+            Analysis.forEachCommit(() -> AnalysisFactory.apply(repo, repoOutputDir));
+
+        };
+    }
+
+    /**
+     * Verarbeitet die Ergebnisse der Analyse um aus einzelnen
+     * Angaben eine gesamt Übersicht zu bekommen
+     *
+     * @param path Pfad zu der markdown datei, aus der die repositories für die
+     *             Analyse stammen
+     * @throws IOException
+     */
+    private static void evaluationAnalysis(Path path) throws IOException {
+        int count = 0;
+        int[] diffTest = { 0, 0, 0, 0, 0, 0, 0, 0 };
+        int[] diffSemEqTest = { 0, 0, 0, 0, };
+        int[] treeTest = { 0, 0, 0, 0, 0, 0, 0, 0 };
+        final List<DatasetDescription> datasets = DefaultDatasets.loadDatasets(path);
+
+        for (DatasetDescription description : datasets) {
+            Stream<Path> files = Files
+                    .list(Path.of("results", "thesis_es", description.name()))
+                    .filter(filename -> filename.getFileName().toString().endsWith(".thesis_es.csv"));
+            for (Path tempPath : files.toList()) {
+                String[] splitFileData = Files.readString(tempPath).split("\n");
+                for (int j = 1; j < splitFileData.length; j++) {
+                    String[] splitLineData = splitFileData[j].split(";");
+                    for (int i = 0; i < splitLineData.length; i++) {
+                        splitLineData[i] = parseNumberStringToIntWithLengthGreaterOne(splitLineData[i]);
+                    }
+                    count = count + 1;
+                    diffTest[0] = diffTest[0] + Integer.parseInt(splitLineData[8]);
+                    diffTest[1] = diffTest[1] + Integer.parseInt(splitLineData[9]);
+                    diffTest[2] = diffTest[2] + Integer.parseInt(splitLineData[10]);
+                    diffTest[3] = diffTest[3] + Integer.parseInt(splitLineData[11]);
+                    diffTest[4] = diffTest[4] + Integer.parseInt(splitLineData[12]);
+                    diffTest[5] = diffTest[5] + Integer.parseInt(splitLineData[13]);
+                    diffTest[6] = diffTest[6] + Integer.parseInt(splitLineData[14]);
+                    diffTest[7] = diffTest[7] + Integer.parseInt(splitLineData[15]);
+                    diffSemEqTest[0] = diffSemEqTest[0] + Integer.parseInt(splitLineData[16]);
+                    diffSemEqTest[1] = diffSemEqTest[1] + Integer.parseInt(splitLineData[17]);
+                    diffSemEqTest[2] = diffSemEqTest[2] + Integer.parseInt(splitLineData[18]);
+                    diffSemEqTest[3] = diffSemEqTest[3] + Integer.parseInt(splitLineData[19]);
+                    treeTest[0] = treeTest[0] + Integer.parseInt(splitLineData[20]);
+                    treeTest[1] = treeTest[1] + Integer.parseInt(splitLineData[21]);
+                    treeTest[2] = treeTest[2] + Integer.parseInt(splitLineData[22]);
+                    treeTest[3] = treeTest[3] + Integer.parseInt(splitLineData[23]);
+                    treeTest[4] = treeTest[4] + Integer.parseInt(splitLineData[24]);
+                    treeTest[5] = treeTest[5] + Integer.parseInt(splitLineData[25]);
+                    treeTest[6] = treeTest[6] + Integer.parseInt(splitLineData[26]);
+                    treeTest[7] = treeTest[7] + Integer.parseInt(splitLineData[27]);
+                    treeTest[0] = treeTest[0] + Integer.parseInt(splitLineData[28]);
+                    treeTest[1] = treeTest[1] + Integer.parseInt(splitLineData[29]);
+                    treeTest[2] = treeTest[2] + Integer.parseInt(splitLineData[30]);
+                    treeTest[3] = treeTest[3] + Integer.parseInt(splitLineData[31]);
+                    treeTest[4] = treeTest[4] + Integer.parseInt(splitLineData[32]);
+                    treeTest[5] = treeTest[5] + Integer.parseInt(splitLineData[33]);
+                    treeTest[6] = treeTest[6] + Integer.parseInt(splitLineData[34]);
+                    treeTest[7] = treeTest[7] + Integer.parseInt(splitLineData[35]);
+
+                }
+            }
+        }
+        List<String> result = new ArrayList<>();
+        result.add("Anzahl geprüfter Diffs : " + count + "\n");
+        result.add("Anzahl syntaktisch korrekter Diffs mit MultiLine0 und EmptyLine0 : " + diffTest[0] + "\n");
+        result.add("Anzahl syntaktisch korrekter Diffs ohne Whitespace mit MultiLine0 und EmptyLine0 : " + diffTest[4]
+                + "\n");
+        result.add("Anzahl semantisch korrekter Diffs mit MultiLine0 und EmptyLine0 : " + diffSemEqTest[0] + "\n");
+        result.add("Anzahl von Diffs mit MultiLine0 und EmptyLine0, welche keine Korrektheitskriterium erfühlt haben : "
+                + (count - diffSemEqTest[0]) + "\n");
+
+        result.add("Anzahl syntaktisch korrekter Diffs mit MultiLine1 und EmptyLine0 : " + diffTest[1] + "\n");
+        result.add("Anzahl syntaktisch korrekter Diffs ohne Whitespace mit MultiLine1 und EmptyLine0 : " + diffTest[5]
+                + "\n");
+        result.add("Anzahl semantisch korrekter Diffs mit MultiLine1 und EmptyLine0 : " + diffSemEqTest[1] + "\n");
+        result.add("Anzahl von Diffs mit MultiLine1 und EmptyLine0, welche keine Korrektheitskriterium erfühlt haben : "
+                + (count - diffSemEqTest[1]) + "\n");
+
+        result.add("Anzahl syntaktisch korrekter Diffs mit MultiLine0 und EmptyLine1 : " + diffTest[2] + "\n");
+        result.add("Anzahl syntaktisch korrekter Diffs ohne Whitespace mit MultiLine0 und EmptyLine1 : " + diffTest[6]
+                + "\n");
+        result.add("Anzahl semantisch korrekter Diffs mit MultiLine0 und EmptyLine1 : " + diffSemEqTest[2] + "\n");
+        result.add("Anzahl von Diffs mit MultiLine0 und EmptyLine1, welche keine Korrektheitskriterium erfühlt haben : "
+                + (count - diffSemEqTest[2]) + "\n");
+
+        result.add("Anzahl syntaktisch korrekter Diffs mit MultiLine1 und EmptyLine1 : " + diffTest[3] + "\n");
+        result.add("Anzahl syntaktisch korrekter Diffs ohne Whitespace mit MultiLine1 und EmptyLine1 : " + diffTest[7]
+                + "\n");
+        result.add("Anzahl semantisch korrekter Diffs mit MultiLine1 und EmptyLine1 : " + diffSemEqTest[3] + "\n");
+        result.add("Anzahl von Diffs mit MultiLine1 und EmptyLine1, welche keine Korrektheitskriterium erfühlt haben : "
+                + (count - diffSemEqTest[3]) + "\n");
+
+        result.add("-------------------------------------------------------------------------------------------");
+        result.add("Anzahl geprüfter Trees : " + count * 2 + "\n");
+        result.add("Anzahl syntaktisch korrekter Trees mit MultiLine0 und EmptyLine0 : " + treeTest[0] + "\n");
+        result.add("Anzahl syntaktisch korrekter Trees ohne Whitespace mit MultiLine0 und EmptyLine0 : " + treeTest[4]
+                + "\n");
+        result.add("Anzahl von Trees mit MultiLine0 und EmptyLine0, welche keine Korrektheitskriterium erfühlt haben : "
+                + (2 * count - treeTest[4]) + "\n");
+
+        result.add("Anzahl syntaktisch korrekter Trees mit MultiLine1 und EmptyLine0 : " + treeTest[1] + "\n");
+        result.add("Anzahl syntaktisch korrekter Trees ohne Whitespace mit MultiLine1 und EmptyLine0 : " + treeTest[5]
+                + "\n");
+        result.add("Anzahl von Trees mit MultiLine1 und EmptyLine0, welche keine Korrektheitskriterium erfühlt haben : "
+                + (2 * count - treeTest[5]) + "\n");
+
+        result.add("Anzahl syntaktisch korrekter Trees mit MultiLine0 und EmptyLine1 : " + treeTest[2] + "\n");
+        result.add("Anzahl syntaktisch korrekter Trees ohne Whitespace mit MultiLine0 und EmptyLine1 : " + treeTest[6]
+                + "\n");
+        result.add("Anzahl von Trees mit MultiLine0 und EmptyLine1, welche keine Korrektheitskriterium erfühlt haben : "
+                + (2 * count - treeTest[6]) + "\n");
+
+        result.add("Anzahl syntaktisch korrekter Trees mit MultiLine1 und EmptyLine1 : " + treeTest[3] + "\n");
+        result.add("Anzahl syntaktisch korrekter Trees ohne Whitespace mit MultiLine1 und EmptyLine1 : " + treeTest[7]
+                + "\n");
+        result.add("Anzahl von Trees mit MultiLine1 und EmptyLine1, welche keine Korrektheitskriterium erfühlt haben : "
+                + (2 * count - treeTest[7]) + "\n");
+
+        Files.write(Path.of("results", "thesis_es", "resultOfAnalysis.txt"), result);
+
+    }
+
+    private static String parseNumberStringToIntWithLengthGreaterOne(String string) {
+        string = string.trim();
+        for (char c : string.toCharArray()) {
+            if (Character.isDigit(c)) {
+                return Character.toString(c);
+            }
+        }
+        return "";
+    }
+}