From 5161b0ec48c61cda9cc9be118b47194376786af4 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sat, 4 Jan 2025 08:12:17 +0100
Subject: [PATCH 1/7] Rename build artifact archives to distinguish between
 Java and Typescript analysis.

---
 .github/workflows/java-code-analysis.yml       | 6 +++---
 .github/workflows/typescript-code-analysis.yml | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/java-code-analysis.yml b/.github/workflows/java-code-analysis.yml
index 96de3e8c8..2b810f4f6 100644
--- a/.github/workflows/java-code-analysis.yml
+++ b/.github/workflows/java-code-analysis.yml
@@ -142,7 +142,7 @@ jobs:
       if: failure()
       uses: actions/upload-artifact@v4
       with:
-        name: code-analysis-logs-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+        name: java-code-analysis-logs-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
         path: |
           ./temp/**/runtime/*
           ./temp/**/reports/*
@@ -153,7 +153,7 @@ jobs:
       if: success()
       uses: actions/upload-artifact@v4
       with:
-        name: code-report-results-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+        name: java-code-analysis-results-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
         path: ./results
         if-no-files-found: error
         retention-days: 5
@@ -164,7 +164,7 @@ jobs:
     #- name: Archive exported database
     #  uses: actions/upload-artifact@v3
     #  with:
-    #    name: code-report-database-export-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+    #    name: java-code-analysis-database-export-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
     #    path: ./temp/**/import
     #    if-no-files-found: error
     #    retention-days: 5
diff --git a/.github/workflows/typescript-code-analysis.yml b/.github/workflows/typescript-code-analysis.yml
index 1e38d989a..75a56ec4d 100644
--- a/.github/workflows/typescript-code-analysis.yml
+++ b/.github/workflows/typescript-code-analysis.yml
@@ -156,7 +156,7 @@ jobs:
       if: failure()
       uses: actions/upload-artifact@v4
       with:
-        name: code-analysis-logs-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+        name: typescript-code-analysis-logs-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
         path: |
           ./temp/**/runtime/*
           ./temp/**/reports/*
@@ -167,7 +167,7 @@ jobs:
       if: success()
       uses: actions/upload-artifact@v4
       with:
-        name: code-report-results-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+        name: typescript-code-analysis-results-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
         path: ./results
         if-no-files-found: error
         retention-days: 5
@@ -178,7 +178,7 @@ jobs:
     #- name: Archive exported database
     #  uses: actions/upload-artifact@v3
     #  with:
-    #    name: code-report-database-export-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
+    #    name: typescript-code-analysis-database-export-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
     #    path: ./temp/**/import
     #    if-no-files-found: error
     #    retention-days: 5

From 11d0bf37d5ae6073b46b573b00204e80138444b7 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sat, 4 Jan 2025 12:24:36 +0100
Subject: [PATCH 2/7] Reduce archived build artifacts to only contain the
 current reports

---
 .github/workflows/java-code-analysis.yml       | 2 +-
 .github/workflows/typescript-code-analysis.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/java-code-analysis.yml b/.github/workflows/java-code-analysis.yml
index 2b810f4f6..3d7853260 100644
--- a/.github/workflows/java-code-analysis.yml
+++ b/.github/workflows/java-code-analysis.yml
@@ -154,7 +154,7 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: java-code-analysis-results-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
-        path: ./results
+        path: ./temp/**/reports/*
         if-no-files-found: error
         retention-days: 5
 
diff --git a/.github/workflows/typescript-code-analysis.yml b/.github/workflows/typescript-code-analysis.yml
index 75a56ec4d..3b21b8a5f 100644
--- a/.github/workflows/typescript-code-analysis.yml
+++ b/.github/workflows/typescript-code-analysis.yml
@@ -168,7 +168,7 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: typescript-code-analysis-results-java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}
-        path: ./results
+        path: ./temp/**/reports/*
         if-no-files-found: error
         retention-days: 5
 

From f3829053375a9813375006b0be52bd9db1b14906 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 5 Jan 2025 08:25:58 +0100
Subject: [PATCH 3/7] Add Cypher query example to set parameters for
 topological sort algorithms.

---
 cypher/Topological_Sort/Set_Parameters.cypher | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 cypher/Topological_Sort/Set_Parameters.cypher

diff --git a/cypher/Topological_Sort/Set_Parameters.cypher b/cypher/Topological_Sort/Set_Parameters.cypher
new file mode 100644
index 000000000..8efaa345d
--- /dev/null
+++ b/cypher/Topological_Sort/Set_Parameters.cypher
@@ -0,0 +1,7 @@
+// Example on how to set the parameters for topological sort in this case for Java Artifacts and Node Similarity
+
+:params {
+    "dependencies_projection": "artifact-topology",     
+    "dependencies_projection_node": "Artifact",
+    "dependencies_projection_weight_property": "weight"
+}
\ No newline at end of file

From 806d6ed8d1a7b1fcc5f2e59da6819464e6da8a36 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Wed, 1 Jan 2025 21:07:19 +0100
Subject: [PATCH 4/7] Add scripts to visualize query results with GraphViz

---
 README.md                                     |   2 +
 .../convertQueryResultCsvToGraphVizDotFile.sh | 119 ++++++++++++++++++
 .../templates/default.template.gv             |  17 +++
 .../visualization/visualizeQueryResults.sh    |  67 ++++++++++
 4 files changed, 205 insertions(+)
 create mode 100755 scripts/visualization/convertQueryResultCsvToGraphVizDotFile.sh
 create mode 100644 scripts/visualization/templates/default.template.gv
 create mode 100755 scripts/visualization/visualizeQueryResults.sh

diff --git a/README.md b/README.md
index 68a6c7b0f..f771fa364 100644
--- a/README.md
+++ b/README.md
@@ -124,6 +124,8 @@ The [Code Structure Analysis Pipeline](./.github/workflows/java-code-analysis.ym
   - [openTSNE](https://github.com/pavlin-policar/openTSNE)
   - [wordcloud](https://github.com/amueller/word_cloud)
 - [Graph Visualization](./graph-visualization/README.md) uses [node.js](https://nodejs.org/de) and the dependencies listed in [package.json](./graph-visualization/package.json).
+- [HPCC-Systems (High Performance Computing Cluster) Web-Assembly (JavaScript)](https://github.com/hpcc-systems/hpcc-js-wasm) containing a wrapper for GraphViz to visualize graph structures.
+- [GraphViz](https://gitlab.com/graphviz/graphviz) for CLI Graph Visualization
 - [Check links in markdown documentation (GitHub workflow)](./.github/workflows/check-links-in-documentation.yml) uses [markdown-link-check](https://github.com/tcort/markdown-link-check).
 
 **Big shout-out** 📣 to all the creators and contributors of these great libraries 👍. Projects like this wouldn't be possible without them. Feel free to [create an issue](https://github.com/JohT/code-graph-analysis-pipeline/issues/new/choose) if something is missing or wrong in the list.
diff --git a/scripts/visualization/convertQueryResultCsvToGraphVizDotFile.sh b/scripts/visualization/convertQueryResultCsvToGraphVizDotFile.sh
new file mode 100755
index 000000000..8955465f8
--- /dev/null
+++ b/scripts/visualization/convertQueryResultCsvToGraphVizDotFile.sh
@@ -0,0 +1,119 @@
+#!/usr/bin/env bash
+
+# Converts a Cypher query result in CSV format to a GraphViz DOT (https://graphviz.org/doc/info/lang.html) file for Visualization including layout templates.
+#
+# The template file is used to define the layout of the graph. 
+# It needs to contain the markers //Begin-Template and //End-Template to indicate the actual template content.
+# If no template is specified, "templates/default.template.gv" is used.
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -o errexit -o pipefail
+
+## Get this "scripts/visualization" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts for visualization
+echo "convertQueryResultCsvToGraphVizDotFile: VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR}"
+
+# Internal constants
+DEFAULT_TEMPLATE_FILE="templates/default.template.gv"
+
+# Function to display script usage
+usage() {
+  echo "Usage: $0 --filename path/to/query/result/file.csv [--name name-of-the-graph (default=name of the file)] [--template path/to/the/template/file (default=${DEFAULT_TEMPLATE_FILE})]"
+  exit 1
+}
+
+# Default values
+inputFilename=""
+graphName=""
+templateFile=""
+
+# Parse command line arguments
+while [ $# -gt 0 ]; do
+  key="$1"
+  case $key in
+    --filename)
+      inputFilename="$2"
+      shift
+      ;;
+    --name)
+      graphName="$2"
+      shift
+      ;;
+    --template)
+      templateFile="$2"
+      shift
+      ;;
+    *)
+      echo "convertQueryResultCsvToGraphVizDotFile: Error: Unknown option: ${key}"
+      usage
+      ;;
+  esac
+  shift
+done
+
+if [ -z "${inputFilename}" ]; then
+  echo "convertQueryResultCsvToGraphVizDotFile: Error: Missing required option: --filename"
+  echo "${USAGE}"
+  exit 1
+fi
+
+if [ ! -f "${inputFilename}" ]; then
+  echo "convertQueryResultCsvToGraphVizDotFile: Error: CSV file not found: ${inputFilename}"
+  echo "${USAGE}"
+  exit 1
+fi
+
+number_of_input_file_lines=$(wc -l < "${inputFilename}" | awk '{print $1}')
+if [ "${number_of_input_file_lines}" -le 1 ]; then
+  echo "convertQueryResultCsvToGraphVizDotFile: Info: Input file is empty. Skipping *.dot and *.svg file generation."
+  return 0
+fi
+
+if [ -z "${graphName}" ]; then
+  graphName=$(basename -- "${inputFilename}")
+  graphName="${graphName%.*}"
+  echo "convertQueryResultCsvToGraphVizDotFile: Info: Using default graph name: ${graphName}"
+fi
+
+# Replace all dashes in the graphName by underscores
+graphName=${graphName//-/_}
+
+if [ -z "${templateFile}" ]; then
+  templateFile="${VISUALIZATION_SCRIPTS_DIR}/${DEFAULT_TEMPLATE_FILE}"
+  echo "convertQueryResultCsvToGraphVizDotFile: Info: Using default template file: ${templateFile}"
+fi
+
+if [ ! -f "${templateFile}" ]; then
+  echo "convertQueryResultCsvToGraphVizDotFile: Error: Template file not found: ${templateFile}"
+  echo "${USAGE}"
+  exit 1
+fi
+
+templateFileName=$(basename -- "${templateFile}")
+inputFilePath=$(dirname "${inputFilename}")
+templateFileNameWithoutExtension="${templateFileName%.*}"
+outputFilename="${inputFilePath}/${graphName}.gv"
+
+{
+  # Add a comment to the beginning of the file to indicate that it was generated by this script
+  echo "// This GraphViz dot file was generated by the script convertQueryResultCsvToGraphVizDotFile.sh with ${templateFileNameWithoutExtension}"
+  echo ""
+  # Start the graph definition with the graph name
+  echo "strict digraph ${graphName} {"
+  # Extract the template content from the template file and remove the begin and end markers
+  sed -n '/\/\/Begin-Template/,/\/\/End-Template/{//!p;}' "${templateFile}"
+  # Remove the first (header) line of the CSV file, remove the enclosing double quotes and replace the escaped double quotes by double quotes
+  awk -F ',' 'NR>1 {print "\t" $1}' "${inputFilename}" \
+    | sed 's/^\t\"\"\"/\t"/' \
+    | sed 's/^\t\"\\\"\"/\t"/' \
+    | sed 's/\\\"\"/"/g' \
+    | sed 's/\"\"/"/g' \
+    | sed 's/\"$//'
+  # End the graph definition
+  echo "}"
+} > "${outputFilename}"
+
+
diff --git a/scripts/visualization/templates/default.template.gv b/scripts/visualization/templates/default.template.gv
new file mode 100644
index 000000000..84a53a086
--- /dev/null
+++ b/scripts/visualization/templates/default.template.gv
@@ -0,0 +1,17 @@
+// This is a GraphViz dot template file for the visualization of a graph in lightblue color scheme.
+// The main part of the template is marked by the comments "Begin-Template" and "End-Template".
+// It also contains a simple example graph.
+//
+strict digraph lightblue_template {
+    //Begin-Template
+    fontname = "Helvetica,Arial,sans-serif";
+    node [fontname = "Helvetica,Arial,sans-serif";];
+    edge [fontname = "Helvetica,Arial,sans-serif"; fontsize = 10;];
+    node [style = filled; fillcolor = "0.560 0.400 0.999";];
+    node [color = "0.560 0.900 0.700";];
+    edge [color = "0.560 0.900 0.700";];
+    //End-Template
+    "A" -> "B" [penwidth = 1.0; label = 1;];
+    "A" -> "C" [penwidth = 3.0; label = 4;];
+    "B" -> "V" [penwidth = 2.0; label = 2;];
+}
\ No newline at end of file
diff --git a/scripts/visualization/visualizeQueryResults.sh b/scripts/visualization/visualizeQueryResults.sh
new file mode 100755
index 000000000..bde45f820
--- /dev/null
+++ b/scripts/visualization/visualizeQueryResults.sh
@@ -0,0 +1,67 @@
+#!/usr/bin/env bash
+
+# Visualizes the Cypher query result (CSV format) using GraphViz and outputs it as SVG image.
+#
+# Requires convertQueryResultCsvToGraphVizDotFile.sh
+#
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -o errexit -o pipefail
+
+## Get this "scripts/visualization" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts for visualization
+echo "visualizeQueryResults: VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR}"
+
+# Read the first unnamed input argument containing the version of the project
+inputCsvFileName=""
+case "${1}" in
+  "--"*) ;; # Skipping named command line options to forward them later to the "analyze" command
+  *) 
+    inputCsvFileName="${1}" 
+    shift || true
+    ;;
+esac
+
+if [ -z "${inputCsvFileName}" ]; then
+  echo "visualizeQueryResults: Error: Please specify the CSV query result file as input parameter."
+  exit 1
+fi
+
+if [ ! -f "${inputCsvFileName}" ]; then
+  echo "visualizeQueryResults: Error: CSV file not found: ${inputCsvFileName}"
+  exit 1
+fi
+
+number_of_input_file_lines=$(wc -l < "${inputCsvFileName}" | awk '{print $1}')
+if [ "${number_of_input_file_lines}" -le 1 ]; then
+  echo "visualizeQueryResults: Info: Input file is empty. Skipping *.dot and *.svg file generation."
+  return 0
+fi
+
+echo "visualizeQueryResults: Info: CSV input file: ${inputCsvFileName}"
+
+graphName=$(basename -- "${inputCsvFileName}")
+graphName="${graphName%.*}" # Remove file extension
+graphName=${graphName//-/_} # Replace all dashes in the graphName by underscores
+inputCsvFilePath=$(dirname "${inputCsvFileName}")
+
+echo "visualizeQueryResults: Generating Visualization files ${inputCsvFilePath}/${graphName}.* ..."
+source "${VISUALIZATION_SCRIPTS_DIR}/convertQueryResultCsvToGraphVizDotFile.sh" "--filename" "${inputCsvFileName}" "${@}"
+
+if command -v "dot" &> /dev/null ; then
+    echo "visualizeQueryResults: Info: Using already installed GraphViz."
+    dot -T svg "${inputCsvFilePath}/${graphName}.gv" > "${inputCsvFilePath}/${graphName}.svg"
+    return 0
+fi
+
+if ! command -v "npx" &> /dev/null ; then
+    echo "visualizeQueryResults: Error: Command npx (to run npm locally) not found. It's needed for Graph visualization with GraphViz." >&2
+    exit 1
+fi
+
+# Run GraphViz command line interface (CLI) wrapped utilizing WASM (WebAssembly) 
+# to convert the DOT file to SVG operating system independently.
+echo "visualizeQueryResults: Info: Using npx to run GraphViz CLI (Web Assembly Wrapper) for SVG generation."
+npx --yes @hpcc-js/wasm-graphviz-cli@1.2.6 -T svg "${inputCsvFilePath}/${graphName}.gv" > "${inputCsvFilePath}/${graphName}.svg"
\ No newline at end of file

From acc65386cc11ecdb7ddc8ec4bfccc4bfd01000ab Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Wed, 1 Jan 2025 21:08:04 +0100
Subject: [PATCH 5/7] Visualize internal dependencies with GraphViz

---
 ..._Artifact_build_levels_for_graphviz.cypher | 31 ++++++++++
 ...pt_Module_build_levels_for_graphviz.cypher | 31 ++++++++++
 .../InternalDependenciesVisualization.sh      | 56 +++++++++++++++++++
 3 files changed, 118 insertions(+)
 create mode 100644 cypher/Internal_Dependencies/Java_Artifact_build_levels_for_graphviz.cypher
 create mode 100644 cypher/Internal_Dependencies/Typescript_Module_build_levels_for_graphviz.cypher
 create mode 100755 scripts/reports/InternalDependenciesVisualization.sh

diff --git a/cypher/Internal_Dependencies/Java_Artifact_build_levels_for_graphviz.cypher b/cypher/Internal_Dependencies/Java_Artifact_build_levels_for_graphviz.cypher
new file mode 100644
index 000000000..83c802b3b
--- /dev/null
+++ b/cypher/Internal_Dependencies/Java_Artifact_build_levels_for_graphviz.cypher
@@ -0,0 +1,31 @@
+// List of all Java Artifacts and their dependencies with build levels for GraphViz Visualization
+
+ MATCH (sourceForStatistics:Java:Artifact)-[dependencyForStatistics:DEPENDS_ON]->(targetForStatistics:Java:Artifact)
+ WHERE sourceForStatistics.maxDistanceFromSource IS NOT NULL
+   AND targetForStatistics.maxDistanceFromSource IS NOT NULL
+  WITH min(dependencyForStatistics.weight) AS minWeight
+      ,max(dependencyForStatistics.weight) AS maxWeight
+      ,max(targetForStatistics.maxDistanceFromSource) AS maxLevel
+ MATCH (source:Java:Artifact)-[dependency:DEPENDS_ON]->(target:Java:Artifact)
+ WHERE source.maxDistanceFromSource IS NOT NULL
+   AND target.maxDistanceFromSource IS NOT NULL
+  WITH *, toFloat(dependency.weight - minWeight) / toFloat(maxWeight - minWeight) AS normalizedWeight
+  WITH *, round((normalizedWeight * 5) + 1, 2) AS penWidth
+  WITH *, source.name + "\\n(level " + coalesce(source.maxDistanceFromSource + "/" + maxLevel, "?") + ")" AS fullSourceName
+  WITH *, target.name + "\\n(level " + coalesce(target.maxDistanceFromSource + "/" + maxLevel, "?") + ")" AS fullTargetName
+  WITH *, "\" -> \"" + fullTargetName 
+                   + "\" [label = "  + dependency.weight + ";"
+                   + " penwidth = "  + penWidth + ";"
+                   + " ];"    AS graphVizDotNotationEdge
+  WITH *, "\"" + fullSourceName + coalesce(graphVizDotNotationEdge, "\" [];") AS graphVizDotNotationLine
+ ORDER BY dependency.weight DESC, target.maxDistanceFromSource DESC
+RETURN graphVizDotNotationLine
+      //Debugging
+      //,source.name       AS sourceName
+      //,target.name       AS targetName
+      //,penWidth
+      //,normalizedWeight
+      //,dependency.weight AS weight
+      //,minWeight
+      //,maxWeight
+LIMIT 440
\ No newline at end of file
diff --git a/cypher/Internal_Dependencies/Typescript_Module_build_levels_for_graphviz.cypher b/cypher/Internal_Dependencies/Typescript_Module_build_levels_for_graphviz.cypher
new file mode 100644
index 000000000..667b7e883
--- /dev/null
+++ b/cypher/Internal_Dependencies/Typescript_Module_build_levels_for_graphviz.cypher
@@ -0,0 +1,31 @@
+// List of all Typescript modules and their dependencies with build levels for GraphViz Visualization
+
+ MATCH (sourceForStatistics:TS:Module)-[dependencyForStatistics:DEPENDS_ON]->(targetForStatistics:TS:Module)
+ WHERE sourceForStatistics.maxDistanceFromSource IS NOT NULL
+   AND targetForStatistics.maxDistanceFromSource IS NOT NULL
+  WITH min(dependencyForStatistics.weight) AS minWeight
+      ,max(dependencyForStatistics.weight) AS maxWeight
+      ,max(targetForStatistics.maxDistanceFromSource) AS maxLevel
+MATCH (source:TS:Module)-[dependency:DEPENDS_ON]->(target:TS:Module)
+ WHERE source.maxDistanceFromSource IS NOT NULL
+   AND target.maxDistanceFromSource IS NOT NULL
+  WITH *, toFloat(dependency.cardinality - minWeight) / toFloat(maxWeight - minWeight) AS normalizedWeight
+  WITH *, round((normalizedWeight * 5) + 1, 2) AS penWidth
+  WITH *, source.rootProjectName + "\\n" + source.name + "\\n(level " + coalesce(source.maxDistanceFromSource + "/" + maxLevel, "?") + ")" AS fullSourceName
+  WITH *, target.rootProjectName + "\\n" + target.name + "\\n(level " + coalesce(target.maxDistanceFromSource + "/" + maxLevel, "?") + ")" AS fullTargetName
+  WITH *, "\" -> \"" + fullTargetName 
+                   + "\" [label = "  + dependency.cardinality + ";"
+                   + " penwidth = "  + penWidth + ";"
+                   + " ];"    AS graphVizDotNotationEdge
+  WITH *, "\"" + fullSourceName + coalesce(graphVizDotNotationEdge, "\" [];") AS graphVizDotNotationLine
+ ORDER BY dependency.weight DESC, target.maxDistanceFromSource DESC
+RETURN graphVizDotNotationLine
+      //Debugging
+      //,source.name       AS sourceName
+      //,target.name       AS targetName
+      //,penWidth
+      //,normalizedWeight
+      //,dependency.cardinality AS weight
+      //,minWeight
+      //,maxWeight
+LIMIT 440
\ No newline at end of file
diff --git a/scripts/reports/InternalDependenciesVisualization.sh b/scripts/reports/InternalDependenciesVisualization.sh
new file mode 100755
index 000000000..a6a358d49
--- /dev/null
+++ b/scripts/reports/InternalDependenciesVisualization.sh
@@ -0,0 +1,56 @@
+#!/usr/bin/env bash
+
+# Executes selected "Internal_Dependencies" Cypher queries for GraphViz visualization.
+# Visualizes dependencies across artifacts and their build levels (topologically sorted).
+# It requires an already running Neo4j graph database with already scanned and analyzed artifacts.
+# The reports (csv, dot and svg files) will be written into the sub directory reports/internal-dependencies-visualization.
+
+# Requires executeQueryFunctions.sh, visualizeQueryResults.sh, cleanupAfterReportGeneration.sh
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -o errexit -o pipefail
+
+# Overrideable Constants (defaults also defined in sub scripts)
+REPORTS_DIRECTORY=${REPORTS_DIRECTORY:-"reports"}
+
+## Get this "scripts/reports" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+REPORTS_SCRIPT_DIR=${REPORTS_SCRIPT_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )}
+echo "InternalDependenciesVisualization: REPORTS_SCRIPT_DIR=${REPORTS_SCRIPT_DIR}"
+
+# Get the "scripts" directory by taking the path of this script and going one directory up.
+SCRIPTS_DIR=${SCRIPTS_DIR:-"${REPORTS_SCRIPT_DIR}/.."} # Repository directory containing the shell scripts
+echo "InternalDependenciesVisualization SCRIPTS_DIR=${SCRIPTS_DIR}"
+
+# Get the "scripts/visualization" directory.
+VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR:-"${SCRIPTS_DIR}/visualization"} # Repository directory containing the shell scripts for visualization
+echo "InternalDependenciesVisualization VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR}"
+
+# Get the "cypher" directory by taking the path of this script and going two directory up and then to "cypher".
+CYPHER_DIR=${CYPHER_DIR:-"${REPORTS_SCRIPT_DIR}/../../cypher"}
+echo "InternalDependenciesVisualization CYPHER_DIR=${CYPHER_DIR}"
+
+INTERNAL_DEPENDENCIES_CYPHER_DIR="${CYPHER_DIR}/Internal_Dependencies"
+
+# Define functions to execute cypher queries from within a given file
+source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
+
+# Create report directory
+REPORT_NAME="internal-dependencies-visualization"
+FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
+mkdir -p "${FULL_REPORT_DIRECTORY}"
+
+# Java Artifacts: Dependencies Visualization
+reportName="${FULL_REPORT_DIRECTORY}/JavaArtifactBuildLevels"
+execute_cypher "${INTERNAL_DEPENDENCIES_CYPHER_DIR}/Java_Artifact_build_levels_for_graphviz.cypher" > "${reportName}.csv"
+source "${VISUALIZATION_SCRIPTS_DIR}/visualizeQueryResults.sh" "${reportName}.csv"
+
+# TypeScript Modules: Dependencies Visualization
+reportName="${FULL_REPORT_DIRECTORY}/TypeScriptModuleBuildLevels"
+execute_cypher "${INTERNAL_DEPENDENCIES_CYPHER_DIR}/Typescript_Module_build_levels_for_graphviz.cypher" > "${reportName}.csv"
+source "${VISUALIZATION_SCRIPTS_DIR}/visualizeQueryResults.sh" "${reportName}.csv"
+
+# Clean-up after report generation. Empty reports will be deleted.
+source "${SCRIPTS_DIR}/cleanupAfterReportGeneration.sh" "${FULL_REPORT_DIRECTORY}"
\ No newline at end of file

From cd96939c919224a15784bd1c825d55641115e85f Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sat, 4 Jan 2025 22:16:13 +0100
Subject: [PATCH 6/7] Visualize longest paths with GraphViz

---
 ...est_paths_contributors_for_graphviz.cypher | 77 +++++++++++++++++
 ...inding_6_Longest_paths_for_graphviz.cypher | 35 ++++++++
 cypher/Path_Finding/Set_Parameters.cypher     |  2 +-
 scripts/reports/PathFindingVisualization.sh   | 84 +++++++++++++++++++
 4 files changed, 197 insertions(+), 1 deletion(-)
 create mode 100644 cypher/Path_Finding/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher
 create mode 100644 cypher/Path_Finding/Path_Finding_6_Longest_paths_for_graphviz.cypher
 create mode 100755 scripts/reports/PathFindingVisualization.sh

diff --git a/cypher/Path_Finding/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher b/cypher/Path_Finding/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher
new file mode 100644
index 000000000..81765164a
--- /dev/null
+++ b/cypher/Path_Finding/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher
@@ -0,0 +1,77 @@
+// Path Finding - Longest path - Stream - List all dependencies for nodes contributing to longest paths and highlight those paths in the Visualization with GraphViz.
+
+// Gather global statistics about dependency weights and levels for normalization and node details
+ MATCH (sourceNodeForStatistics)-[dependencyForStatistics:DEPENDS_ON]->(targetNodeForStatistics)
+ WHERE $dependencies_projection_node IN LABELS(sourceNodeForStatistics)
+   AND $dependencies_projection_node IN LABELS(targetNodeForStatistics)
+  WITH min(dependencyForStatistics[$dependencies_projection_weight_property]) AS minWeight
+      ,max(dependencyForStatistics[$dependencies_projection_weight_property]) AS maxWeight
+      ,max(targetNodeForStatistics.maxDistanceFromSource)                     AS maxLevel
+   WITH *, 1.0 / toFloat(maxWeight - minWeight)                               AS weightNormalizationFactor
+   WITH { minWeight: minWeight, maxLevel: maxLevel, weightNormalizationFactor: weightNormalizationFactor } AS statistics
+// -> Main call to execute "longest path" algorithm
+   CALL gds.dag.longestPath.stream($dependencies_projection + '-cleaned')
+  YIELD index, totalCost, path
+   WITH *
+// Sort longest paths by their length descending and - if equal - by their index ascending
+  ORDER BY totalCost DESC, index ASC
+// Only take the top 50 longest paths as a compromise between performance and visualization content
+  LIMIT 50
+// Collect all results of the longest path search as well as all nodes of the longest paths
+   WITH statistics
+       ,collect({index: index, distance: toInteger(totalCost), path: path}) AS longestPaths
+       ,collect(nodes(path)) AS allLongestPathNodes
+// Flatten and deduplicate the list of all nodes that contribute to at least one longest path
+ UNWIND allLongestPathNodes AS longestPathNodes
+ UNWIND longestPathNodes    AS longestPathNode
+   WITH statistics
+       ,longestPaths
+       ,collect(DISTINCT longestPathNode) AS allDistinctLongestPathNodes
+// Iterate over all longest paths
+ UNWIND longestPaths AS longestPath
+   WITH statistics
+       ,longestPaths, allDistinctLongestPathNodes
+       ,[ singleRelationship IN relationships(longestPath.path)     | [startNode(singleRelationship), endNode(singleRelationship)] ] AS allLongestPathStartAndEndNodeTuples
+       ,[ singleRelationship IN relationships(longestPaths[0].path) | [startNode(singleRelationship), endNode(singleRelationship)] ] AS longestPathStartAndEndNodeTuples
+       ,longestPath.index       AS index
+       ,longestPath.distance    AS distance
+// -> Main query of all dependencies of nodes contributing to the longest paths
+ MATCH (source)-[dependency:DEPENDS_ON]->(target)
+ WHERE $dependencies_projection_node IN labels(source)
+   AND $dependencies_projection_node IN labels(target)
+   // Dependent nodes need to be part of at least one longest paths
+   AND (source IN allDistinctLongestPathNodes AND target IN allDistinctLongestPathNodes)
+  WITH statistics.maxLevel                  AS maxLevel
+      ,statistics.minWeight                 AS minWeight
+      ,statistics.weightNormalizationFactor AS weightNormalizationFactor
+      ,count(index)                         AS numberOfLongestPathsPassing
+      ,max(distance)                        AS lengthOfLongestPathPassing
+      ,dependency
+      ,source
+      ,target
+      // If there is at least one longest path passing through the dependency then "contributesToALongestPath" is true
+      ,([source, target] IN allLongestPathStartAndEndNodeTuples)  AS contributesToALongestPath
+      ,([source, target] IN longestPathStartAndEndNodeTuples)     AS isPartOfLongestPath
+  WITH *, dependency[$dependencies_projection_weight_property]    AS weight
+  WITH *, toFloat(weight - minWeight) * weightNormalizationFactor AS normalizedWeight
+  WITH *, round((normalizedWeight * 5) + 1, 2)                    AS penWidth
+  WITH *, source.name + "\\n(level " + source.maxDistanceFromSource + "/" + maxLevel + ")"    AS startNodeTitle
+  WITH *, target.name   + "\\n(level " + target.maxDistanceFromSource + "/" + maxLevel + ")"  AS endNodeTitle
+               // The longest path will be highlighted in red.
+  WITH *, CASE WHEN isPartOfLongestPath       THEN "; color=\"red\"" 
+               // Dependencies contributing to the longest path will be highlighted in dark orange.
+               WHEN contributesToALongestPath THEN "; color=\"darkorange\"" 
+          ELSE "" END AS edgeColor
+// Prepare the GraphViz edge attributes for the visualization
+  WITH *, "[label=" + weight  + "; penwidth=" + penWidth + edgeColor + "; ];" AS graphVizEdgeAttributes
+// Assemble the final GraphViz DOT notation line for the edge representing the current dependency
+  WITH *, "\"" + startNodeTitle +  "\" -> \"" + endNodeTitle + "\" " + graphVizEdgeAttributes AS graphVizDotNotationLine
+RETURN DISTINCT graphVizDotNotationLine
+// Debugging
+//      ,source.name
+//      ,target.name
+//      ,numberOfLongestPathsPassing
+//      ,lengthOfLongestPathPassing
+//      ,contributesToALongestPath
+//      ,isPartOfLongestPath
+ LIMIT 440
\ No newline at end of file
diff --git a/cypher/Path_Finding/Path_Finding_6_Longest_paths_for_graphviz.cypher b/cypher/Path_Finding/Path_Finding_6_Longest_paths_for_graphviz.cypher
new file mode 100644
index 000000000..4f1152733
--- /dev/null
+++ b/cypher/Path_Finding/Path_Finding_6_Longest_paths_for_graphviz.cypher
@@ -0,0 +1,35 @@
+// Path Finding - Longest path - Stream - Find the top 100 dependencies contributing to the longest paths for Visualization with GraphViz
+
+ MATCH (sourceNodeForStatistics)-[dependencyForStatistics:DEPENDS_ON]->(targetNodeForStatistics)
+ WHERE $dependencies_projection_node IN LABELS(sourceNodeForStatistics)
+   AND $dependencies_projection_node IN LABELS(targetNodeForStatistics)
+  WITH min(dependencyForStatistics[$dependencies_projection_weight_property]) AS minWeight
+      ,max(dependencyForStatistics[$dependencies_projection_weight_property]) AS maxWeight
+      ,max(targetNodeForStatistics.maxDistanceFromSource)                     AS maxLevel
+   WITH *, 1.0 / toFloat(maxWeight - minWeight)  AS weightNormalizationFactor
+  CALL gds.dag.longestPath.stream($dependencies_projection + '-cleaned')
+ YIELD index, totalCost, path
+  WITH *, toInteger(totalCost) AS distance
+ ORDER BY distance DESC, index ASC
+ UNWIND relationships(path) AS pathRelationship
+  WITH *
+      ,startNode(pathRelationship) AS startNode
+      ,endNode(pathRelationship)   AS endNode
+ MATCH (startNode)-[dependency:DEPENDS_ON]->(endNode)
+  WITH *, dependency[$dependencies_projection_weight_property] AS weight
+  WITH *, toFloat(weight - minWeight) * weightNormalizationFactor AS normalizedWeight
+  WITH *, round((normalizedWeight * 5) + 1, 2) AS penWidth
+  WITH *, startNode.name + "\\n(level " + startNode.maxDistanceFromSource + "/" + maxLevel + ")" AS startNodeTitle
+  WITH *, endNode.name   + "\\n(level " + endNode.maxDistanceFromSource + "/" + maxLevel + ")"   AS endNodeTitle
+  WITH *, "[label=" + weight  + "; penwidth=" + penWidth + "; ];"    AS graphVizEdgeAttributes
+  WITH *, "\"" + startNodeTitle +  "\" -> \"" + endNodeTitle + "\" " + graphVizEdgeAttributes    AS graphVizDotNotationLine
+RETURN graphVizDotNotationLine
+// Debugging
+// RETURN startNode.name        AS startNodeName
+//       ,endNode.name          AS endNodeName
+//       ,dependency[$dependencies_projection_weight_property] AS dependencyWeight
+//       ,max(distance)         AS partOfLongestPathLength
+//       ,count(DISTINCT index) AS partOfLongestPathCounts
+//       ,startNode.maxDistanceFromSource AS startNodeLevel
+//       ,endNode.maxDistanceFromSource   AS endNodeLevel
+LIMIT 100
\ No newline at end of file
diff --git a/cypher/Path_Finding/Set_Parameters.cypher b/cypher/Path_Finding/Set_Parameters.cypher
index 6954fb494..55582f533 100644
--- a/cypher/Path_Finding/Set_Parameters.cypher
+++ b/cypher/Path_Finding/Set_Parameters.cypher
@@ -1,4 +1,4 @@
-// Example on how to set the parameters for centrality in this case for Packages and PageRank
+// Example on how to set the parameters for path finding in this case for Packages and PageRank
 
 :params {
     "dependencies_projection": "package-path-finding",     
diff --git a/scripts/reports/PathFindingVisualization.sh b/scripts/reports/PathFindingVisualization.sh
new file mode 100755
index 000000000..6fe72e609
--- /dev/null
+++ b/scripts/reports/PathFindingVisualization.sh
@@ -0,0 +1,84 @@
+#!/usr/bin/env bash
+
+# Executes selected "Path_Finding" Cypher queries for GraphViz visualization.
+# Visualizes Java Artifact and TypeScript Module dependencies with their longest paths.
+# It requires an already running Neo4j graph database with already scanned and analyzed artifacts.
+# The reports (csv, dot and svg files) will be written into the sub directory reports/path-finding-visualization.
+
+# Requires executeQueryFunctions.sh, projectionFunctions.sh, visualizeQueryResults.sh, cleanupAfterReportGeneration.sh
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -o errexit -o pipefail
+
+# Overrideable Constants (defaults also defined in sub scripts)
+REPORTS_DIRECTORY=${REPORTS_DIRECTORY:-"reports"}
+
+## Get this "scripts/reports" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+REPORTS_SCRIPT_DIR=${REPORTS_SCRIPT_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )}
+echo "PathFindingVisualization: REPORTS_SCRIPT_DIR=${REPORTS_SCRIPT_DIR}"
+
+# Get the "scripts" directory by taking the path of this script and going one directory up.
+SCRIPTS_DIR=${SCRIPTS_DIR:-"${REPORTS_SCRIPT_DIR}/.."} # Repository directory containing the shell scripts
+echo "PathFindingVisualization SCRIPTS_DIR=${SCRIPTS_DIR}"
+
+# Get the "scripts/visualization" directory.
+VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR:-"${SCRIPTS_DIR}/visualization"} # Repository directory containing the shell scripts for visualization
+echo "PathFindingVisualization VISUALIZATION_SCRIPTS_DIR=${VISUALIZATION_SCRIPTS_DIR}"
+
+# Get the "cypher" directory by taking the path of this script and going two directory up and then to "cypher".
+CYPHER_DIR=${CYPHER_DIR:-"${REPORTS_SCRIPT_DIR}/../../cypher"}
+echo "PathFindingVisualization CYPHER_DIR=${CYPHER_DIR}"
+
+PATH_FINDINGS_CYPHER_DIR="${CYPHER_DIR}/Path_Finding"
+
+# Define functions to execute cypher queries from within a given file
+source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
+
+# Define functions to create and delete Graph Projections like "createDirectedDependencyProjection"
+source "${SCRIPTS_DIR}/projectionFunctions.sh"
+
+# Create report directory
+REPORT_NAME="path-finding-visualization"
+FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
+mkdir -p "${FULL_REPORT_DIRECTORY}"
+
+# Java Artifacts: Longest Paths Visualization
+ARTIFACT_PROJECTION="dependencies_projection=artifact-path-finding"
+ARTIFACT_NODE="dependencies_projection_node=Artifact"
+ARTIFACT_WEIGHT="dependencies_projection_weight_property=weight"
+
+if createDirectedDependencyProjection "${ARTIFACT_PROJECTION}" "${ARTIFACT_NODE}" "${ARTIFACT_WEIGHT}"; then
+    reportName="JavaArtifactLongestPathsIsolated"
+    echo "PathFindingVisualization: Creating visualization ${reportName}..."
+    execute_cypher "${PATH_FINDINGS_CYPHER_DIR}/Path_Finding_6_Longest_paths_for_graphviz.cypher" "${ARTIFACT_PROJECTION}" "${ARTIFACT_NODE}" "${ARTIFACT_WEIGHT}" > "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+    source "${VISUALIZATION_SCRIPTS_DIR}/visualizeQueryResults.sh" "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+    
+    reportName="JavaArtifactLongestPaths"
+    echo "PathFindingVisualization: Creating visualization ${reportName}..."
+    execute_cypher "${PATH_FINDINGS_CYPHER_DIR}/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher" "${ARTIFACT_PROJECTION}" "${ARTIFACT_NODE}" "${ARTIFACT_WEIGHT}" > "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+    source "${VISUALIZATION_SCRIPTS_DIR}/visualizeQueryResults.sh" "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+fi
+
+# TypeScript Modules: Longest Paths Visualization
+MODULE_LANGUAGE="dependencies_projection_language=Typescript"
+MODULE_PROJECTION="dependencies_projection=typescript-module-path-finding"
+MODULE_NODE="dependencies_projection_node=Module"
+MODULE_WEIGHT="dependencies_projection_weight_property=lowCouplingElement25PercentWeight"
+
+if createDirectedDependencyProjection "${MODULE_LANGUAGE}" "${MODULE_PROJECTION}" "${MODULE_NODE}" "${MODULE_WEIGHT}"; then
+    reportName="TypeScriptModuleLongestPathsIsolated"
+    echo "PathFindingVisualization: Creating visualization ${reportName}..."
+    execute_cypher "${PATH_FINDINGS_CYPHER_DIR}/Path_Finding_6_Longest_paths_for_graphviz.cypher" "${MODULE_PROJECTION}" "${MODULE_NODE}" "${MODULE_WEIGHT}" > "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+    source "${VISUALIZATION_SCRIPTS_DIR}/visualizeQueryResults.sh" "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+    
+    reportName="TypeScriptModuleLongestPaths"
+    echo "PathFindingVisualization: Creating visualization ${reportName}..."
+    execute_cypher "${PATH_FINDINGS_CYPHER_DIR}/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher" "${MODULE_PROJECTION}" "${MODULE_NODE}" "${MODULE_WEIGHT}" > "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+    source "${VISUALIZATION_SCRIPTS_DIR}/visualizeQueryResults.sh" "${FULL_REPORT_DIRECTORY}/${reportName}.csv"
+fi
+
+# Clean-up after report generation. Empty reports will be deleted.
+source "${SCRIPTS_DIR}/cleanupAfterReportGeneration.sh" "${FULL_REPORT_DIRECTORY}"
\ No newline at end of file

From 0839c1f9cd4d56427c862c7b6c00a16c6589f658 Mon Sep 17 00:00:00 2001
From: JohT <7671054+JohT@users.noreply.github.com>
Date: Sun, 5 Jan 2025 10:05:29 +0100
Subject: [PATCH 7/7] Deprecate graph-visualization nodejs package in favor of
 GraphViz.

---
 .github/workflows/java-code-analysis.yml       | 9 ---------
 .github/workflows/typescript-code-analysis.yml | 9 ---------
 graph-visualization/DEPRECATED.md              | 5 +++++
 graph-visualization/README.md                  | 9 +++++++--
 scripts/reports/GraphVisualization.sh          | 5 ++++-
 5 files changed, 16 insertions(+), 21 deletions(-)
 create mode 100644 graph-visualization/DEPRECATED.md

diff --git a/.github/workflows/java-code-analysis.yml b/.github/workflows/java-code-analysis.yml
index 3d7853260..beb6e9f0c 100644
--- a/.github/workflows/java-code-analysis.yml
+++ b/.github/workflows/java-code-analysis.yml
@@ -69,15 +69,6 @@ jobs:
         distribution: 'adopt'
         java-version: ${{ matrix.java }}
 
-    - name: Setup Node.js for Graph Visualization
-      uses: actions/setup-node@v4
-      with:
-        node-version-file: 'graph-visualization/.nvmrc'
-
-    - name: Install Node packages for Graph Visualization
-      working-directory: graph-visualization
-      run: npm ci
-
     - name: Setup Cache for Conda package manager Miniforge
       uses: actions/cache@v4
       env:
diff --git a/.github/workflows/typescript-code-analysis.yml b/.github/workflows/typescript-code-analysis.yml
index 3b21b8a5f..348594a8d 100644
--- a/.github/workflows/typescript-code-analysis.yml
+++ b/.github/workflows/typescript-code-analysis.yml
@@ -69,15 +69,6 @@ jobs:
         distribution: 'adopt'
         java-version: ${{ matrix.java }}
 
-    - name: Setup Node.js for Graph Visualization
-      uses: actions/setup-node@v4
-      with:
-        node-version-file: 'graph-visualization/.nvmrc'
-
-    - name: Install Node packages for Graph Visualization
-      working-directory: graph-visualization
-      run: npm ci
-
     - name: Setup Cache for Conda package manager Miniforge
       uses: actions/cache@v4
       env:
diff --git a/graph-visualization/DEPRECATED.md b/graph-visualization/DEPRECATED.md
new file mode 100644
index 000000000..02f64d5f3
--- /dev/null
+++ b/graph-visualization/DEPRECATED.md
@@ -0,0 +1,5 @@
+# Render Graph Visualizations (Deprecated)
+
+:warning: **This package is deprecated and might get removed in future.** :warning:
+
+Visualizations are now done using [GraphViz](https://graphviz.org). Please use the new script [visualizeQueryResults.sh](./../scripts/visualization/visualizeQueryResults.sh) like it is done in [InternalDependenciesVisualization.sh](./../scripts/reports/InternalDependenciesVisualization.sh) to create Graph Visualizations.
diff --git a/graph-visualization/README.md b/graph-visualization/README.md
index 50e9a24fc..53953de24 100644
--- a/graph-visualization/README.md
+++ b/graph-visualization/README.md
@@ -1,6 +1,11 @@
-# Render Graph Visualizations
+# Render Graph Visualizations (Deprecated)
 
-This [node.js](https://nodejs.org/de) project provides the script [renderVisualizations.js](./renderVisualizations.js) to render all graph visualizations as image files.  
+:warning: **This package is deprecated and might get removed in future.** :warning:
+
+Visualizations are now done using [GraphViz](https://graphviz.org). Please use the new script [visualizeQueryResults.sh](./../scripts/visualization/visualizeQueryResults.sh) like it is done in [InternalDependenciesVisualization.sh](./../scripts/reports/InternalDependenciesVisualization.sh) to create Graph Visualizations.
+
+This [node.js](https://nodejs.org/de) project provides the script [renderVisualizations.js](./renderVisualizations.js) to render  graph visualizations as image files. It shows how to use [Puppeteer](https://pptr.dev) to render HTML5 Canvas elements as images,
+jimp to manipulate images and neovis to visualize Neo4j Graphs.
 
 ## Prerequisites
 
diff --git a/scripts/reports/GraphVisualization.sh b/scripts/reports/GraphVisualization.sh
index 99bde269c..6729a1a9f 100755
--- a/scripts/reports/GraphVisualization.sh
+++ b/scripts/reports/GraphVisualization.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# Creates the "graph-visualization" report (ipynb, md, pdf) based on the Jupyter Notebook "ArtifactDependencies.ipynb".
+# DEPRECATED: Creates the "graph-visualization" report using the (now deprecated) nodejs project "graph-visualization".
 # It contains the hierarchical artifact dependencies graph
 
 # Requires executeJupyterNotebook.sh
@@ -8,6 +8,9 @@
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -o errexit -o pipefail
 
+echo "GraphVisualization: Graph Visualization with the nodejs project 'graph-visualization' is deprecated and will be skipped."
+return 0
+
 # Overrideable Constants (defaults also defined in sub scripts)
 REPORTS_DIRECTORY=${REPORTS_DIRECTORY:-"reports"}