Merge branch 'main' into feature/arcotl-models

# Conflicts: # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/InputDiagramData.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/Box.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/Classification.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/Connector.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/Diagram.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/DiagramRecognitionState.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/TextBox.java # framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/util/DataRepositoryHelper.java # framework/models/pom.xml # pipeline/pipeline-core/src/main/java/edu/kit/kastel/mcse/ardoco/core/execution/PipelineUtils.java # pipeline/pipeline-core/src/test/resources/teastore-paper.png # pipeline/pom.xml # pom.xml # stages/pom.xml
ArDoCo · May 22, 2023 · 2afcb75 · 2afcb75
2 parents 34ebb88 + 72cda7a
commit 2afcb75
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diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,6 @@
+[*.{kt,kts}]
+insert_final_newline = true
+ij_kotlin_allow_trailing_comma = false
+ij_kotlin_allow_trailing_comma_on_call_site = false
+ij_kotlin_name_count_to_use_star_import = 999
+ij_kotlin_name_count_to_use_star_import_for_members = 999
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -2,6 +2,9 @@ name: Documentation
 
 on:
   push:
+    branches: 
+      - main
+    tags: "v**"
     paths:
       - 'docs/**'
       - '.github/workflows/docs.yml'
@@ -11,30 +14,23 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Fix Deployment for GH Pages
-        run: mkdir -p docs/_build/dirhtml/ && touch docs/_build/dirhtml/.nojekyll
-      - uses: joshlong/java-version-export-github-action@v28
-        id: jve
-      - name: Set up JDK
-        uses: actions/setup-java@v3
+      - uses: actions/[email protected]
         with:
-          distribution: 'temurin'
-          java-version: ${{ steps.jve.outputs.java_major_version }}
-          cache: 'maven'
-      - uses: actions/setup-python@v4
+          token: ${{ secrets.SDQ_TOKEN }}
+      - uses: actions/[email protected]
         with:
-          python-version: '3.9'
-
-      - run: pip install -r requirements.txt && sudo apt update && sudo apt install graphviz -y
-        working-directory: docs
-      - run: make html dirhtml
-        working-directory: docs
-
+          repository: ${{ github.repository }}.wiki
+          path: wiki
+          token: ${{ secrets.SDQ_TOKEN }}
+
+      - name: Remove contents in Wiki
+        working-directory: wiki
+        run: ls -A1 | grep -v '.git' | xargs rm -r
+
+      - name: Copy Wiki from Docs folder
+        run: cp -r ./docs/. ./wiki
+
       - name: Deploy 🚀
-        if: github.ref == 'refs/heads/main'
-        uses: JamesIves/[email protected]
+        uses: stefanzweifel/git-auto-commit-action@v4
         with:
-          branch: gh-pages
-          folder: docs/_build/dirhtml/
-          clean: true
+          repository: wiki
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+wiki
 .flattened-pom.xml
 
 tests/src/test/resources/testout/*

diff --git a/.mvn/jvm.config b/.mvn/jvm.config
@@ -1 +1 @@
- -XX:-TieredCompilation -XX:TieredStopAtLevel=1 --add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED  --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED
+ -XX:-TieredCompilation -XX:TieredStopAtLevel=1 --add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED  --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ Future user interfaces like a Graphical User Interface (GUI) or a web interface
 
 ## Documentation
 
-For more information about the setup or the architecture have a look on the [docs](https://ardoco.github.io/Core).
+For more information about the setup or the architecture have a look on the [Wiki](https://github.com/ArDoCo/Core/wiki).
 The docs are at some points deprecated, the general overview and setup should still hold.
 You can find the generated JavaDocs at [ArDoCo.github.io/Core-Docs](https://ArDoCo.github.io/Core-Docs/).
 
@@ -43,7 +43,7 @@ To test the Core, you could use case studies and benchmarks provided in ..
 	<dependency>
 		<groupId>io.github.ardoco.core</groupId>
 		<artifactId>pipeline</artifactId> <!-- or any other subproject -->
-		<version>0.7.0-SNAPSHOT</version>
+		<version>VERSION</version>
 	</dependency>
 </dependencies>
 ```

diff --git a/docs/.gitignore b/docs/.gitignore
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
diff --git a/docs/Home.md b/docs/Home.md
@@ -0,0 +1,49 @@
+ArDoCo (Architecture Documentation Consistency) is a framework to connect architecture documentation and models while
+identifying missing or deviating elements (inconsistencies). An element can be any representable item of the model, like
+a component or a relation. To do so, ArDoCo first creates trace links and then makes use of them and other information
+to identify inconsistencies.
+
+You can find [ArDoCo on GitHub](https://github.com/ArDoCo).
+
+Before contributing, please read the [Quickstart Guide](quickstart).
+
+JavaDocs can be found [here](https://ardoco.github.io/Core-Docs/).
+
+## System Requirements
+
+The `complete` profile includes all the requirements that the special profiles also need. This profile is activated by
+default.
+
+All profiles require JDK 17.
+
+The dependencies of the other profiles at a glance:
+
+* tlr: -
+* inconsistency: -
+* lissa (LInking Sketches and Software Architecture): Docker (local
+  or [remote](https://github.com/ArDoCo/Core/blob/lissa/stages/diagram-recognition/src/main/kotlin/edu/kit/kastel/mcse/ardoco/lissa/diagramrecognition/informants/DockerInformant.kt#L20-L23))
+
+## Case Studies & Benchmarks
+
+You can test ArDoCo using our case studies and benchmarks provided in ...
+
+* [Case Studies](https://github.com/ArDoCo/SWATTR)
+* [Benchmarks](https://github.com/ArDoCo/Benchmark)
+
+## Publications
+
+Trace Link Recovery for Software Architecture Documentation Keim, J.; Schulz, S.; Fuchß, D.; Kocher, C.; Speit, J.;
+Koziolek, A. 2021. Software Architecture: 15th European Conference, ECSA 2021, Virtual Event, Sweden, September 13-17,
+2021, Proceedings. Ed.: S. Biffl, 101–116, Springer
+Verlag. [doi:10.1007/978-3-030-86044-8_7](https://doi.org/10.1007/978-3-030-86044-8_7)
+
+The initial version of ArDoCo is based on the master
+thesis [Linking Software Architecture Documentation and Models](https://publikationen.bibliothek.kit.edu/1000126194).
+
+## Contact
+
+This project is currently developed by researchers of the Karlsruhe Institute of Technology.
+
+You find us on our
+websites: [Jan Keim](https://mcse.kastel.kit.edu/staff_Keim_Jan.php), [Sophie Corallo](https://mcse.kastel.kit.edu/staff_sophie_corallo.php),
+and [Dominik Fuchß](https://mcse.kastel.kit.edu/staff_dominik_fuchss.php)
diff --git a/docs/LiSSA.md b/docs/LiSSA.md
@@ -0,0 +1,26 @@
+The LiSSA approach aims to connect sketches and informal diagrams (such as class diagrams, component diagrams, ...) with
+formal models like component models.
+
+## Linking Sketches and Software Architecture (LiSSA)
+The following diagram shows the pipeline that is planned for the LiSSA approach.
+
+```mermaid
+stateDiagram-v2
+    DiagramDetection
+    TextPreprocessing
+    ArchitectureModel
+    TextExtraction
+    EntityRecognition
+    RecommendationGeneration
+    ConnectionGeneration
+    InconsistencyDetection
+    
+    DiagramDetection --> RecommendationGeneration
+    TextPreprocessing --> TextExtraction
+    ArchitectureModel --> RecommendationGeneration
+    TextExtraction --> EntityRecognition
+    DiagramDetection --> EntityRecognition
+    EntityRecognition --> RecommendationGeneration
+    RecommendationGeneration --> ConnectionGeneration
+    ConnectionGeneration --> InconsistencyDetection
+```
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/Profiles.md b/docs/Profiles.md
@@ -0,0 +1,32 @@
+ArDoCo uses maven profiles to provide subsets of its functionality and speed up development time.
+
+## Current Profiles
+
+* **complete** (activated by default)
+* **deployment** (profile for deployment to maven central)
+* **tlr** (profile for traceability link recovery)
+* **inconsistency** (profile for inconsistency detection)
+
+## Adding new profiles
+
+In order to add a new profile, you have to extend the profile section in the main pom.xml (as well as in all submodules
+that contain submodules; i.e., stages, tests)
+
+```xml
+
+<profile>
+    <!-- Name of the new Profile -->
+    <id>new-profile-id</id>
+    <activation>
+        <activeByDefault>false</activeByDefault>
+    </activation>
+    <modules>
+        <module>framework</module>
+        <module>pipeline</module>
+        <module>stages</module>
+        <module>tests</module>
+    </modules>
+</profile>
+```
+
+
diff --git a/docs/Quickstart.md b/docs/Quickstart.md
@@ -0,0 +1,134 @@
+The ArDoCo-Core is a maven project and can be embedded by using its specs (from
+the [pom](https://github.com/ArDoCo/Core/blob/main/pom.xml)).
+
+You can run and configure the execution with the CLI.
+
+Please acknowledge the [code of conduct](https://github.com/ArDoCo/Core/blob/main/CODE_OF_CONDUCT.md).
+
+## Forking the project & submitting pull requests
+
+This project uses Sonarcloud to check code quality. There are Github Actions that automatically verify the build and
+generate a Sonarcloud-report. Additionally, pull requests are automatically checked. If the build fails or the Quality
+Gate is not passed, it is marked in the Pull Request and you need to fix the PR until it passes. Otherwise, the PR won’t
+get merged.
+
+If you fork the project, make sure to create a Sonarcloud token to make sure everything works for you and the Sonarcloud
+check does not fail. You need to enable Sonarcloud for you and add a Sonarcloud token to the repository of the fork as
+secret.
+
+Follow the following steps to do so:
+
+* Log into SonarCloud and click on your profile and then go to My Account and then Security. Alternatively go directly
+  to account/security.
+* Generate your access token for SonarCloud and copy it. The access token will be provided to the build pipeline as a
+  secret environment variable.
+* Go to your repository settings in GitHub, then to Secrets
+* Add a new secret with name SONAR_TOKEN and the value of the just generated access token.
+
+### Formatter
+
+Please use the provided [formatter](https://github.com/ArDoCo/Core/blob/main/formatter.xml) when contributing.
+
+Additionally, make use of the spotless-plugin for maven to format your code. You can run it via mvn spotless:
+apply ([more info](https://github.com/diffplug/spotless/tree/main/plugin-maven)).
+
+### Documentation
+
+⚠️ WIP
+
+## Command Line Interface (CLI)
+
+[ArDoCo CLI](https://github.com/ArDoCo/CLI) contains a CLI that supports the execution of ArDoCo.
+
+It is necessary to specify an input model as well as a textual documentation. Usually, our model is an architectural
+model. However, the model can also contain a (Java) code model that you can insert using
+the [CodeModelExtractors](https://github.com/ArDoCo/Core/tree/main/framework/java-model-extractor).
+
+All results (trace links, inconsistencies, etc. between the input model and documentation) are written to the specified
+output location.
+
+The [CLI](https://github.com/ArDoCo/CLI/blob/main/src/main/java/edu/kit/kastel/mcse/ardoco/core/pipeline/ArDoCoCLI.java)
+is part of the [CLI project](https://github.com/ArDoCo/CLI) of ArDoCo.
+
+## Standard Configuration
+
+⚠️ WIP
+
+## Save Actions (Eclipse)
+
+Go to your Eclipse Workspace folder and open the
+file `.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs`.
+There, exchange all the `sp_cleanup.` properties to the following:
+
+```
+sp_cleanup.add_default_serial_version_id=true
+sp_cleanup.add_generated_serial_version_id=false
+sp_cleanup.add_missing_annotations=true
+sp_cleanup.add_missing_deprecated_annotations=true
+sp_cleanup.add_missing_methods=false
+sp_cleanup.add_missing_nls_tags=false
+sp_cleanup.add_missing_override_annotations=true
+sp_cleanup.add_missing_override_annotations_interface_methods=true
+sp_cleanup.add_serial_version_id=false
+sp_cleanup.always_use_blocks=true
+sp_cleanup.always_use_parentheses_in_expressions=true
+sp_cleanup.always_use_this_for_non_static_field_access=false
+sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=true
+sp_cleanup.convert_to_enhanced_for_loop=true
+sp_cleanup.convert_to_enhanced_for_loop_if_loop_var_used=false
+sp_cleanup.correct_indentation=true
+sp_cleanup.format_source_code=true
+sp_cleanup.format_source_code_changes_only=false
+sp_cleanup.insert_inferred_type_arguments=false
+sp_cleanup.lazy_logical_operator=false
+sp_cleanup.make_local_variable_final=true
+sp_cleanup.make_parameters_final=false
+sp_cleanup.make_private_fields_final=true
+sp_cleanup.make_type_abstract_if_missing_method=false
+sp_cleanup.make_variable_declarations_final=false
+sp_cleanup.merge_conditional_blocks=false
+sp_cleanup.never_use_blocks=false
+sp_cleanup.never_use_parentheses_in_expressions=false
+sp_cleanup.number_suffix=true
+sp_cleanup.on_save_use_additional_actions=true
+sp_cleanup.organize_imports=true
+sp_cleanup.push_down_negation=false
+sp_cleanup.qualify_static_field_accesses_with_declaring_class=false
+sp_cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true
+sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true
+sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
+sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
+sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_modifiers=true
+sp_cleanup.remove_redundant_semicolons=true
+sp_cleanup.remove_redundant_type_arguments=true
+sp_cleanup.remove_trailing_whitespaces=true
+sp_cleanup.remove_trailing_whitespaces_all=true
+sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
+sp_cleanup.remove_unnecessary_array_creation=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unused_imports=true
+sp_cleanup.remove_unused_local_variables=false
+sp_cleanup.remove_unused_private_fields=true
+sp_cleanup.remove_unused_private_members=false
+sp_cleanup.remove_unused_private_methods=true
+sp_cleanup.remove_unused_private_types=true
+sp_cleanup.simplify_lambda_expression_and_method_ref=false
+sp_cleanup.sort_members=false
+sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
+sp_cleanup.use_autoboxing=true
+sp_cleanup.use_blocks=true
+sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_directly_map_method=false
+sp_cleanup.use_lambda=true
+sp_cleanup.use_parentheses_in_expressions=false
+sp_cleanup.use_this_for_non_static_field_access=true
+sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
+sp_cleanup.use_this_for_non_static_method_access=true
+sp_cleanup.use_this_for_non_static_method_access_only_if_necessary=true
+sp_cleanup.use_unboxing=true
+sp_cleanup.use_var=false
+```
diff --git a/docs/_static/ArDoCo-dark.svg b/docs/_static/ArDoCo-dark.svg
diff --git a/docs/_static/ArDoCo-light.svg b/docs/_static/ArDoCo-light.svg
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		-XX:-TieredCompilation -XX:TieredStopAtLevel=1 --add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED
		-XX:-TieredCompilation -XX:TieredStopAtLevel=1 --add-exports jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED --add-exports jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED