From dd56d270f8e9758bc7a9e80297a56766a9c300ca Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Mon, 30 Oct 2023 09:50:44 +0100
Subject: [PATCH 1/9] Add operating system detection script functions

---
 scripts/operatingSystemFunctions.sh | 49 +++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 scripts/operatingSystemFunctions.sh

diff --git a/scripts/operatingSystemFunctions.sh b/scripts/operatingSystemFunctions.sh
new file mode 100644
index 000000000..6bdd98203
--- /dev/null
+++ b/scripts/operatingSystemFunctions.sh
@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+
+# Provides operating system dependent functions e.g. to detect Windows.
+
+# Requires executeQuery.sh
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -eo pipefail
+
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+
+# Return true if the script is running on Windows, otherwise false.
+# Example: if isWindows; then echo "Running on Windows"
+isWindows() {
+    [[ "$OSTYPE" == "cygwin" ]] || [[ "$OSTYPE" == "msys" ]] || [[ "$OSTYPE" == "win32" ]]
+}
+
+# Echoes/Returns the first argument if the script is running on Windows, otherwise the second argument.
+# Example: artifactPostfix=$(ifWindows "windows.zip" "unix.tar.gz")
+ifWindows() {
+    if isWindows; then
+        echo "$1"
+    else
+        echo "$2"
+    fi
+}
+
+# Prints out a message if Windows was detected for the current OSTYPE or not.
+# Example: printWindows
+printWindows() {
+    ifWindows "operatingSystemFunctions: Detected Windows for OSTYPE ${OSTYPE}" "operatingSystemFunctions: No Windows detected for OSTYPE ${OSTYPE}"
+}
+
+# Converts the POSIX path given as the first argument to Windows path format if the script is running on Windows.
+# Otherwise it just returns the path unchanged (for non-windows systems).
+# Example: path=$(convertPosixToWindowsPath "${path}")
+convertPosixToWindowsPathIfNecessary() {
+    if isWindows; then
+        echo "$1" | sed -e 's/^\///' -e 's/\//\\/g' -e 's/^./\0:/'
+    else
+        echo "$1"
+    fi
+}
+
+printWindows
\ No newline at end of file

From 5345a8d636928c6606eeab9d2218f72a2c70bdb8 Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Sat, 14 Oct 2023 11:01:27 +0200
Subject: [PATCH 2/9] Support Windows using git bash

---
 README.md                            |  3 +-
 scripts/downloadMavenArtifact.sh     |  2 +-
 scripts/executeQuery.sh              | 10 ++---
 scripts/executeQueryFunctions.sh     |  7 ++--
 scripts/setupJQAssistant.sh          |  2 +-
 scripts/setupNeo4j.sh                | 55 ++++++++++++++++++----------
 scripts/setupNeo4jInitialPassword.sh | 23 +++++++++---
 scripts/startNeo4j.sh                | 55 +++++++++++++++++++++-------
 scripts/stopNeo4j.sh                 | 45 ++++++++++++++++-------
 scripts/waitForNeo4jHttp.sh          | 10 ++---
 10 files changed, 143 insertions(+), 69 deletions(-)

diff --git a/README.md b/README.md
index 4b695fea5..024fe4da2 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,8 @@ Here are some reports that utilize Neo4j's [Graph Data Science Library](https://
 
 ## 🛠 Prerequisites
 
-- Java 17 is required (June 2023 Neo4j 5.x requirement)
+- Java 17 is [required for Neo4j](https://neo4j.com/docs/operations-manual/current/installation/requirements/#deployment-requirements-software) (5.x requirement)
+- [jq](https://github.com/jqlang/jq) the "lightweight and flexible command-line JSON processor" needs to be installed. Latest releases: https://github.com/jqlang/jq/releases/latest. Check using `jq --version`.
 - Python and a conda package manager are required for Jupyter Notebook reports
 - Chromium will automatically be downloaded if needed for Jupyter Notebook reports in PDF format
 
diff --git a/scripts/downloadMavenArtifact.sh b/scripts/downloadMavenArtifact.sh
index 238939568..b920e6923 100755
--- a/scripts/downloadMavenArtifact.sh
+++ b/scripts/downloadMavenArtifact.sh
@@ -70,7 +70,7 @@ DOWNLOAD_URL="${BASE_URL}/${GROUP_ID_FOR_API}/${artifactId}/${version}/${ARTIFAC
 
 # Download Maven Artifact into the "targetDirectory"
 if [ ! -f "./${targetDirectory}/${ARTIFACT_FILENAME}" ] ; then
-    source ${SCRIPTS_DIR}/download.sh --url "${DOWNLOAD_URL}"
+    source "${SCRIPTS_DIR}/download.sh" --url "${DOWNLOAD_URL}"
 
     # Create artifacts targetDirectory if it doen't exist
     mkdir -p "./${targetDirectory}"
diff --git a/scripts/executeQuery.sh b/scripts/executeQuery.sh
index 9fd2b61e0..e3210d8ae 100755
--- a/scripts/executeQuery.sh
+++ b/scripts/executeQuery.sh
@@ -97,14 +97,14 @@ cypher_query_for_api="{\"statements\":[{\"statement\":${cypher_query},\"paramete
 #echo "executeQuery: Cypher Query for API: ${cypher_query_for_api}"
 
 # Calls the Neo4j HTTP API using cURL ( https://curl.se )
-cyper_query_result=$(curl --silent -S --fail-with-body -H Accept:application/json -H Content-Type:application/json \
+cypher_query_result=$(curl --silent -S --fail-with-body -H Accept:application/json -H Content-Type:application/json \
      -u neo4j:"${NEO4J_INITIAL_PASSWORD}" \
      "http://localhost:${NEO4J_HTTP_PORT}/${NEO4J_HTTP_TRANSACTION_ENDPOINT}" \
      -d "${cypher_query_for_api}")
-#echo "executeQuery: Cypher Query Result: ${cyper_query_result}"
+#echo "executeQuery: Cypher Query Result: ${cypher_query_result}"
 
 # If there is a error message print it to syserr >&2 in red color
-error_message=$( echo "${cyper_query_result}" | jq -r '.errors[0] // empty' )
+error_message=$( echo "${cypher_query_result}" | jq -r '.errors[0] // empty' )
 if [[ -n "${error_message}" ]]; then 
   redColor='\033[0;31m'
   noColor='\033[0m' # No Color
@@ -114,9 +114,9 @@ fi
 
 # Output results in CSV format
 if [ "${no_source_reference}" = true ] ; then
-  echo -n "${cyper_query_result}" | jq -r '(.results[0])? | .columns,(.data[].row)? | map(if type == "array" then join(",") else . end) | flatten | @csv'
+  echo -n "${cypher_query_result}" | jq -r '(.results[0])? | .columns,(.data[].row)? | map(if type == "array" then join(",") else . end) | flatten | @csv'
 else
   cypher_query_file_relative_name=${cypher_query_file_name#/**/cypher/}
   sourceFileReferenceInfo="Source Cypher File: ${cypher_query_file_relative_name}"
-  echo -n "${cyper_query_result}" | jq -r --arg sourceReference "${sourceFileReferenceInfo}" '(.results[0])? | .columns + [$sourceReference], (.data[].row)? + [""]  | map(if type == "array" then join(",") else . end) | flatten | @csv'
+  echo -n "${cypher_query_result}" | jq -r --arg sourceReference "${sourceFileReferenceInfo}" '(.results[0])? | .columns + [$sourceReference], (.data[].row)? + [""]  | map(if type == "array" then join(",") else . end) | flatten | @csv'
 fi
\ No newline at end of file
diff --git a/scripts/executeQueryFunctions.sh b/scripts/executeQueryFunctions.sh
index a4ea6e057..ddd157bf4 100644
--- a/scripts/executeQueryFunctions.sh
+++ b/scripts/executeQueryFunctions.sh
@@ -48,8 +48,8 @@ execute_cypher_expect_results() {
 
 # Function to execute a cypher query from the given file (first and only argument) using Neo4j's HTTP API
 execute_cypher_http() { 
-    # (Neo4j HTTP API Script) Execute the Cyper query contained in the file and print the results as CSV
-    source $SCRIPTS_DIR/executeQuery.sh "${@}" # "${@}": Get all function arguments and forward them
+    # (Neo4j HTTP API Script) Execute the Cypher query contained in the file and print the results as CSV
+    source "$SCRIPTS_DIR/executeQuery.sh" "${@}" # "${@}": Get all function arguments and forward them
 }
 
 # Function to execute a cypher query from the given file (first and only argument) with a summarized (console) output using Neo4j's HTTP API
@@ -107,11 +107,10 @@ execute_cypher_shell() {
     query_parameters=$(cypher_shell_query_parameters "${@}")
     echo "executeQuery: query_parameters=${query_parameters}"
 
-    # (Neo4j Cyper Shell CLI) Execute the Cyper query contained in the file and print the results as CSV
+    # (Neo4j Cypher Shell CLI) Execute the Cypher query contained in the file and print the results as CSV
     cat $cypherFileName | NEO4J_HOME="${NEO4J_DIRECTORY}" ${NEO4J_BIN}/cypher-shell -u neo4j -p "${NEO4J_INITIAL_PASSWORD}" --format plain --param "${query_parameters}" || exit 1
 
     # Display the name of the Cypher file without its path at the bottom of the CSV (or console) separated by an empty line
-    # TODO Find a solution to move the source reference to the last column name
     echo ""
     echo "\"Source Cypher File:\",\"$(basename -- "${cypherFileName}")\""
 }
diff --git a/scripts/setupJQAssistant.sh b/scripts/setupJQAssistant.sh
index 931c4ba06..71801c574 100755
--- a/scripts/setupJQAssistant.sh
+++ b/scripts/setupJQAssistant.sh
@@ -52,7 +52,7 @@ JQASSISTANT_INSTALLATION_DIRECTORY="${TOOLS_DIRECTORY}/${JQASSISTANT_INSTALLATIO
 if [ ! -d "${JQASSISTANT_INSTALLATION_DIRECTORY}" ] ; then    
     jqassistant_cli_fulldownload_url=${JQASSISTANT_CLI_DOWNLOAD_URL}/${JQASSISTANT_CLI_ARTIFACT}/${JQASSISTANT_CLI_VERSION}/${JQASSISTANT_CLI_ARTIFACT}-${JQASSISTANT_CLI_VERSION}-${JQASSISTANT_CLI_DISTRIBUTION}
     jqassistant_cli_fulldownload_file="${JQASSISTANT_INSTALLATION_NAME}.zip"
-    source ${SCRIPTS_DIR}/download.sh --url "${jqassistant_cli_fulldownload_url}" --filename "${jqassistant_cli_fulldownload_file}"
+    source "${SCRIPTS_DIR}/download.sh" --url "${jqassistant_cli_fulldownload_url}" --filename "${jqassistant_cli_fulldownload_file}"
 
     # Unpack the ZIP file (-q option for less verbose output)
     unzip -q "${SHARED_DOWNLOADS_DIRECTORY}/${jqassistant_cli_fulldownload_file}" -d "${TOOLS_DIRECTORY}"
diff --git a/scripts/setupNeo4j.sh b/scripts/setupNeo4j.sh
index b455a0b23..ae25be238 100755
--- a/scripts/setupNeo4j.sh
+++ b/scripts/setupNeo4j.sh
@@ -4,7 +4,7 @@
 
 # Note: The environment variable NEO4J_INITIAL_PASSWORD needs to be set.
 
-# Requires download.sh,setupNeo4jInitialPassword.sh
+# Requires download.sh,setupNeo4jInitialPassword.sh,operatingSystemFunctions.sh
 
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -eo pipefail
@@ -68,14 +68,25 @@ if [ -z "${NEO4J_INITIAL_PASSWORD}" ]; then
     exit 1
 fi
 
+# Include operation system function to for example detect Windows.
+source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
+
 # Download and extract Neo4j
 if [ ! -d "${NEO4J_INSTALLATION_DIRECTORY}" ] ; then
 
-    neo4jDownloadArchiveFileName="${NEO4J_INSTALLATION_NAME}-unix.tar.gz"
-    source ${SCRIPTS_DIR}/download.sh --url "https://dist.neo4j.org/${neo4jDownloadArchiveFileName}" || exit 1
+    neo4jInstallationSystemPostfix=$(ifWindows "windows.zip" "unix.tar.gz")
+    neo4jDownloadArchiveFileName="${NEO4J_INSTALLATION_NAME}-${neo4jInstallationSystemPostfix}"
+    echo "setupNeo4j: Using Neo4j distribution ${neo4jDownloadArchiveFileName}"
+
+    source "${SCRIPTS_DIR}/download.sh" --url "https://dist.neo4j.org/${neo4jDownloadArchiveFileName}" || exit 1
     
-    # Extract the tar file
-    tar -xf "${SHARED_DOWNLOADS_DIRECTORY}/${neo4jDownloadArchiveFileName}" --directory "${TOOLS_DIRECTORY}" || exit 1
+    if [[ ${neo4jInstallationSystemPostfix} == "unix.tar.gz" ]]; then
+        # Extract the unix tar file
+        tar -xf "${SHARED_DOWNLOADS_DIRECTORY}/${neo4jDownloadArchiveFileName}" --directory "${TOOLS_DIRECTORY}" || exit 1
+    else
+        # Unpack the windows ZIP file (-q option for less verbose output, ignore warnings (backslash) with || true)
+        unzip -q "${SHARED_DOWNLOADS_DIRECTORY}/${neo4jDownloadArchiveFileName}" -d "${TOOLS_DIRECTORY}" || true
+    fi
 
     # Fail if Neo4j hadn't been downloaded successfully
     if [ ! -d "${NEO4J_INSTALLATION_DIRECTORY}" ] ; then
@@ -87,16 +98,22 @@ if [ ! -d "${NEO4J_INSTALLATION_DIRECTORY}" ] ; then
     # instead of inside the neo4j directory
     echo "setupNeo4j: Configuring dynamic settings (data directories, ports, ...)"
 
+    neo4jDataPath=$(convertPosixToWindowsPathIfNecessary "${NEO4J_DATA_PATH}")
+    neo4jLogsPath=$(convertPosixToWindowsPathIfNecessary "${NEO4J_RUNTIME_PATH}/logs")
+    neo4jDumpsPath=$(convertPosixToWindowsPathIfNecessary "${NEO4J_RUNTIME_PATH}/dumps")
+    neo4jRunPath=$(convertPosixToWindowsPathIfNecessary "${NEO4J_RUNTIME_PATH}/run")
+    neo4jTransactionsPath=$(convertPosixToWindowsPathIfNecessary "${NEO4J_DATA_PATH}/transactions")
+
     if [[ "$NEO4J_MAJOR_VERSION_NUMBER" -ge 5 ]]; then
         echo "setupNeo4j: Neo4j v5 or higher detected"
         {
             echo ""
             echo "# Paths of data directories in the installation (v5)"
-            echo "server.directories.data=${NEO4J_DATA_PATH}"
-            echo "server.directories.logs=${NEO4J_RUNTIME_PATH}/logs"
-            echo "server.directories.dumps.root=${NEO4J_RUNTIME_PATH}/dumps"
-            echo "server.directories.run=${NEO4J_RUNTIME_PATH}/run"
-            echo "server.directories.transaction.logs.root=${NEO4J_DATA_PATH}/transactions"
+            echo "server.directories.data=${neo4jDataPath}"
+            echo "server.directories.logs=${neo4jLogsPath}"
+            echo "server.directories.dumps.root=${neo4jDumpsPath}"
+            echo "server.directories.run=${neo4jRunPath}"
+            echo "server.directories.transaction.logs.root=${neo4jTransactionsPath}"
             echo ""
             echo "# Ports Configuration (v5)"
             echo "server.bolt.listen_address=:${NEO4J_BOLT_PORT}"
@@ -111,11 +128,11 @@ if [ ! -d "${NEO4J_INSTALLATION_DIRECTORY}" ] ; then
         {
             echo ""
             echo "# Paths of data directories in the installation"
-            echo "dbms.directories.data=${NEO4J_DATA_PATH}"
-            echo "dbms.directories.logs=${NEO4J_RUNTIME_PATH}/logs"
-            echo "dbms.directories.dumps.root=${NEO4J_RUNTIME_PATH}/dumps"
-            echo "dbms.directories.run=${NEO4J_RUNTIME_PATH}/run"
-            echo "dbms.directories.transaction.logs.root=${NEO4J_DATA_PATH}/transactions"
+            echo "dbms.directories.data=${neo4jDataPath}"
+            echo "dbms.directories.logs=${neo4jLogsPath}"
+            echo "dbms.directories.dumps.root=${neo4jDumpsPath}"
+            echo "dbms.directories.run=${neo4jRunPath}"
+            echo "dbms.directories.transaction.logs.root=${neo4jTransactionsPath}"
             echo ""
             echo "# Ports Configuration"
             echo "dbms.connector.bolt.listen_address=:${NEO4J_BOLT_PORT}"
@@ -136,9 +153,9 @@ if [ ! -d "${NEO4J_INSTALLATION_DIRECTORY}" ] ; then
 
     # Set initial password for user "neo4j" otherwise the default password "neo4j" would need to be changed immediately (prompt).
     # This needs to be done after the configuration changes.
-    source ${SCRIPTS_DIR}/setupNeo4jInitialPassword.sh
+    source "${SCRIPTS_DIR}/setupNeo4jInitialPassword.sh"
 
-    echo "setupNeo4j: Installed sucessfully"
+    echo "setupNeo4j: Installed successfully"
 else
     echo "setupNeo4j: ${NEO4J_INSTALLATION_NAME} already installed"
 fi
@@ -146,7 +163,7 @@ fi
 # Download and Install the Neo4j Plugin "Awesome Procedures for Neo4j" (APOC)
 if [ ! -f "${NEO4J_PLUGINS}/${NEO4J_APOC_PLUGIN_ARTIFACT}" ] ; then
 
-    source ${SCRIPTS_DIR}/download.sh --url "https://github.com/${NEO4J_APOC_PLUGIN_GITHUB}/releases/download/${NEO4J_APOC_PLUGIN_VERSION}/${NEO4J_APOC_PLUGIN_ARTIFACT}" || exit 1
+    source "${SCRIPTS_DIR}/download.sh" --url "https://github.com/${NEO4J_APOC_PLUGIN_GITHUB}/releases/download/${NEO4J_APOC_PLUGIN_VERSION}/${NEO4J_APOC_PLUGIN_ARTIFACT}" || exit 1
 
     # Uninstall previously installed Neo4j Plugin "Awesome Procedures for Neo4j" (APOC)
     rm -f "${NEO4J_PLUGINS}/apoc*.jar"
@@ -192,7 +209,7 @@ fi
 
 if [ ! -f "${NEO4J_PLUGINS}/${neo4jGraphDataScienceReleaseArtifact}" ] ; then
     # Download the Neo4j Plugin "Graph Data Science" (GDS)
-    source ${SCRIPTS_DIR}/download.sh --url "${neo4jGraphDataScienceDownloadUrl}/${neo4jGraphDataScienceReleaseArtifact}" || exit 1
+    source "${SCRIPTS_DIR}/download.sh" --url "${neo4jGraphDataScienceDownloadUrl}/${neo4jGraphDataScienceReleaseArtifact}" || exit 1
 
     # Uninstall previously installed Neo4j Plugin "Graph Data Science" (GDS)
     rm -f "${NEO4J_PLUGINS}/*graph-data-science*.jar"
diff --git a/scripts/setupNeo4jInitialPassword.sh b/scripts/setupNeo4jInitialPassword.sh
index 7ffd4a208..bb62d6775 100755
--- a/scripts/setupNeo4jInitialPassword.sh
+++ b/scripts/setupNeo4jInitialPassword.sh
@@ -15,6 +15,13 @@ TOOLS_DIRECTORY=${TOOLS_DIRECTORY:-"tools"} # Get the tools directory (defaults
 NEO4J_INSTALLATION_NAME="neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
 NEO4J_INSTALLATION_DIRECTORY="${TOOLS_DIRECTORY}/${NEO4J_INSTALLATION_NAME}"
 
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+echo "startNeo4j: SCRIPTS_DIR=$SCRIPTS_DIR"
+
 # Check if environment variable is set
 if [ -z "${NEO4J_INITIAL_PASSWORD}" ]; then
     echo "Requires environment variable NEO4J_INITIAL_PASSWORD to be set first. Use 'export NEO4J_INITIAL_PASSWORD=<your-own-password>'."
@@ -32,18 +39,24 @@ echo "setupNeo4jInitialPassword: Using ${NEO4J_INSTALLATION_DIRECTORY} as NEO4J_
 
 # Extract the first component of the version number (=major version number)
 NEO4J_MAJOR_VERSION_NUMBER=$(echo "$NEO4J_VERSION" | cut -d'.' -f1)
+echo "setupNeo4jInitialPassword: Neo4j version ${NEO4J_MAJOR_VERSION_NUMBER} detected"
+
+# Include operation system function to for example detect Windows.
+source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
+
+scriptExtension=$(ifWindows ".bat" "")
 
 # Check if the first component is greater than or equal to 5
 if [[ "$NEO4J_MAJOR_VERSION_NUMBER" -ge 5 ]]; then
-    echo "setupNeo4jInitialPassword: Neo4j v5 or higher detected"
+    echo "setupNeo4jInitialPassword: Neo4j v5 or higher used"
     # Neo4j version < 5
     # Set the initial password using a temporary NEO4J_HOME environment variable pointing to the current setup
-    NEO4J_HOME="${NEO4J_INSTALLATION_DIRECTORY}" ${NEO4J_INSTALLATION_DIRECTORY}/bin/neo4j-admin dbms set-initial-password "${NEO4J_INITIAL_PASSWORD}"
+    NEO4J_HOME="${NEO4J_INSTALLATION_DIRECTORY}"; "${NEO4J_INSTALLATION_DIRECTORY}/bin/neo4j-admin${scriptExtension}" dbms set-initial-password "${NEO4J_INITIAL_PASSWORD}"
 else
-    echo "setupNeo4jInitialPassword: Neo4j v4 or lower detected"
+    echo "setupNeo4jInitialPassword: Neo4j v4 or lower used"
     # Neo4j version >= 5
     # Set the initial password using a temporary NEO4J_HOME environment variable pointing to the current setup
-    NEO4J_HOME="${NEO4J_INSTALLATION_DIRECTORY}" ${NEO4J_INSTALLATION_DIRECTORY}/bin/neo4j-admin set-initial-password "${NEO4J_INITIAL_PASSWORD}"
+    NEO4J_HOME="${NEO4J_INSTALLATION_DIRECTORY}"; "${NEO4J_INSTALLATION_DIRECTORY}/bin/neo4j-admin${scriptExtension}" set-initial-password "${NEO4J_INITIAL_PASSWORD}"
 fi
 
-echo "setupNeo4jInitialPassword: Initial password set sucessfully"
+echo "setupNeo4jInitialPassword: Initial password set successfully"
diff --git a/scripts/startNeo4j.sh b/scripts/startNeo4j.sh
index 08b97e6aa..9e6b2fe25 100755
--- a/scripts/startNeo4j.sh
+++ b/scripts/startNeo4j.sh
@@ -5,7 +5,7 @@
 # Note: Does nothing if the database is already running.
 # Note: It requires Neo4j to be installed in the TOOLS_DIRECTORY.
 
-# Requires waitForNeo4jHttp.sh
+# Requires waitForNeo4jHttp.sh,operatingSystemFunctions.sh
 
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -eo pipefail
@@ -17,8 +17,9 @@ NEO4J_HTTP_PORT=${NEO4J_HTTP_PORT:-"7474"} # Neo4j's own "Bolt Protocol" port
 
 # Internal Constants
 NEO4J_DIR="${TOOLS_DIRECTORY}/neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
+NEO4J_DIR_WINDOWS="${TOOLS_DIRECTORY}\neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
 NEO4J_BIN="${NEO4J_DIR}/bin"
-WAIT_TIMES="1 2 4 8 16 32"
+NEO4J_BIN_WINDOWS="${NEO4J_DIR_WINDOWS}\bin"
 
 ## Get this "scripts" 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. 
@@ -41,30 +42,56 @@ else
     exit 1
 fi
 
+# Include operation system function to for example detect Windows.
+source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
+
+scriptExtension=$(ifWindows ".bat" "")
+echo "startNeo4j: Using scriptExtension ${scriptExtension} for Windows."
+
 # Check if Neo4j is stopped (not running) using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status 2>&1 || true)"
+neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
 neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
 if [ -n "${neo4jNotRunning}" ]; then
     echo "startNeo4j: Starting neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} in ${NEO4J_DIR}"
 
     # Check if there is already a process that listens to the Neo4j HTTP port
-    port_listener_process_id=$( lsof -t -i:"${NEO4J_HTTP_PORT}" -sTCP:LISTEN || true )
-    if [ -n "${port_listener_process_id}" ]; then
-        echo "startNeo4j: There is already a process that listens to port ${NEO4J_HTTP_PORT}"
-        ps -p "${port_listener_process_id}"
-        echo "startNeo4j: Use this command to stop it: kill -9 \$( lsof -t -i:${NEO4J_HTTP_PORT} -sTCP:LISTEN )"
-        exit 1
+    if isWindows; then
+        echo "startNeo4j: Skipping detection of processes listening to port ${NEO4J_HTTP_PORT} on Windows"
+    else
+        port_listener_process_id=$( lsof -t -i:"${NEO4J_HTTP_PORT}" -sTCP:LISTEN || true )
+        if [ -n "${port_listener_process_id}" ]; then
+            echo "startNeo4j: There is already a process that listens to port ${NEO4J_HTTP_PORT}"
+            ps -p "${port_listener_process_id}"
+            echo "startNeo4j: Use this command to stop it: kill -9 \$( lsof -t -i:${NEO4J_HTTP_PORT} -sTCP:LISTEN )"
+            exit 1
+        fi
     fi
 
     # Start Neo4j using a temporary NEO4J_HOME environment variable that points to the current installation
-    NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j start
-    
+    if isWindows; then
+        neo4jStartCommand="${NEO4J_BIN_WINDOWS}\neo4j.bat console --verbose"
+        # On Windows it is necessary to take the absolute full qualified path to Neo4j for the environment variable NEO4J_HOME.
+        # It also works without any environment variable but this would likely lead to ambiguity problems when there are multiple Neo4j instances installed.
+        # If the path is wrong content-wise this leads to a ClassNotFoundException.
+        # If the path is wrong syntactically there is an error while reading the plugins directory.
+        windowsCommandEnvironment="set NEO4J_HOME=%cd%\\${NEO4J_DIR_WINDOWS}&& echo NEO4J_HOME=!NEO4J_HOME!"
+        windowsCommand="${windowsCommandEnvironment}&&${neo4jStartCommand}"
+        
+        echo "startNeo4j: Starting Neo4j on Windows in a separate console window..."
+        echo "startNeo4j: The following Windows command is used: ${windowsCommand}"
+        echo "startNeo4j: IMPORTANT: Only close the console window when the scripts and your work is finished !"
+
+        cmd //c start cmd //v //k "${windowsCommand}"
+    else
+        NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j start --verbose
+    fi
+
     # Wait some time for the start of the database
     echo "${WAIT_TIMES}" | tr ' ' '\n' | while read waitTime; do
         echo "startNeo4j: Waiting for ${waitTime} second(s)"
         sleep ${waitTime}
 
-        neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status 2>&1 || true)"
+        neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
         neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
         if [ -z "${neo4jNotRunning}" ]; then
             echo "startNeo4j: Successfully started neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
@@ -76,11 +103,11 @@ else
 fi
 
 # Check if Neo4j is still not running using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status 2>&1 || true)"
+neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
 neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
 if [ -n "${neo4jNotRunning}" ]; then
     echo "startNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} still not running. Something went wrong. Details see 'NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status'."
     exit 1
 fi
 
-source ${SCRIPTS_DIR}/waitForNeo4jHttp.sh || exit 1
\ No newline at end of file
+source "${SCRIPTS_DIR}/waitForNeo4jHttp.sh" || exit 1
\ No newline at end of file
diff --git a/scripts/stopNeo4j.sh b/scripts/stopNeo4j.sh
index fe92bc8e6..a17bcc4a7 100755
--- a/scripts/stopNeo4j.sh
+++ b/scripts/stopNeo4j.sh
@@ -4,6 +4,8 @@
 
 # Note: Does nothing if the database is already stopped.
 
+# Requires waitForNeo4jHttp.sh,operatingSystemFunctions.sh
+
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -eo pipefail
 
@@ -24,36 +26,51 @@ fi
 
 # Check if Neo4j is installed
 if [ -d "${NEO4J_BIN}" ] ; then
-    echo "stopNeo4j: Using Neo4j binary directoy ${NEO4J_BIN}"
+    echo "stopNeo4j: Using Neo4j binary directory ${NEO4J_BIN}"
 else
     echo "stopNeo4j: Directory ${NEO4J_BIN} doesn't exist. Please run setupNeo4j.sh first."
     exit 1
 fi
 
+# Include operation system function to for example detect Windows.
+source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
+
 # Check if Neo4j is stopped (not running) using a temporary NEO4J_HOME environment variable that points to the current installation
-if NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status 2>&1 | grep -q "not running" ; then
+neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
+neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
+if [ -n "${neo4jNotRunning}" ]; then
     echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} aleady stopped"
     exit 0
 else
-    # Stop Neo4j using a temporary NEO4J_HOME environment variable that points to the current installation
-    NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j stop
+    if isWindows; then
+        echo "stopNeo4j: IMPORTANT on Windows: Please close the console window or stop the service manually where neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} is running."
+    else
+        # Stop Neo4j using a temporary NEO4J_HOME environment variable that points to the current installation
+        NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j stop
+    fi
 fi
 
 # Check if Neo4j is still not running using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status 2>&1 || true)"
+neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
 neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
 if [ -n "${neo4jNotRunning}" ]; then
     echo "stopNeo4j: Successfully stopped neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
 else
-    echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} still running. Something went wrong. Details see 'NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status'."
-    exit 1
+    if ! isWindows; then
+        echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} still running. Something went wrong. Details see 'NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j${scriptExtension} status'."
+        exit 1
+    fi
 fi
 
 # Check if there are still processes running that listen to the Neo4j HTTP port
-port_listener_process_id=$( lsof -t -i:"${NEO4J_HTTP_PORT}" -sTCP:LISTEN || true )
-if [ -n "${port_listener_process_id}" ]; then
-    echo "stopNeo4j: Terminating the following process that still listens to port ${NEO4J_HTTP_PORT}"
-    ps -p "${port_listener_process_id}"
-    # Terminate the process that is listening to the Neo4j HTTP port
-    kill -9 "${port_listener_process_id}"
-fi
+if isWindows; then
+    echo "stopNeo4j: Skipping detection of processes listening to port ${NEO4J_HTTP_PORT} on Windows"
+else
+    port_listener_process_id=$( lsof -t -i:"${NEO4J_HTTP_PORT}" -sTCP:LISTEN || true )
+    if [ -n "${port_listener_process_id}" ]; then
+        echo "stopNeo4j: Terminating the following process that still listens to port ${NEO4J_HTTP_PORT}"
+        ps -p "${port_listener_process_id}"
+        # Terminate the process that is listening to the Neo4j HTTP port
+        kill -9 "${port_listener_process_id}"
+    fi
+fi
\ No newline at end of file
diff --git a/scripts/waitForNeo4jHttp.sh b/scripts/waitForNeo4jHttp.sh
index cefbe6696..f987b5c69 100755
--- a/scripts/waitForNeo4jHttp.sh
+++ b/scripts/waitForNeo4jHttp.sh
@@ -21,7 +21,7 @@ echo "waitForNeo4jHttp: SCRIPTS_DIR=$SCRIPTS_DIR"
 CYPHER_DIR=${CYPHER_DIR:-"${SCRIPTS_DIR}/../cypher"}
 echo "waitForNeo4jHttp: CYPHER_DIR=$CYPHER_DIR"
 
-# Define functions to execute a cypher query from within the given file (first and only argument)
+# Define functions to execute a Cypher query from within the given file (first and only argument)
 source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
 
 # List of wait times in seconds per retry
@@ -34,19 +34,19 @@ echo "${WAIT_TIMES}" | tr ' ' '\n' | while read -r waitTime; do
     sleep "${waitTime}"
 
     # Queries node and relationship count as a basic validation
-    if ! cyper_elements_query_result=$(execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher");
+    if ! cypher_elements_query_result=$(execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher");
     then
         continue; # query failed -> try again
     fi
     
-    if [[ -n "${cyper_elements_query_result}" ]]; then 
+    if [[ -n "${cypher_elements_query_result}" ]]; then 
         echo "waitForNeo4jHttp: Successfully accessed Neo4j HTTP API."
-        echo "${cyper_elements_query_result}"
+        echo "${cypher_elements_query_result}"
         exit 0
     fi
 done
 
-if ! cyper_elements_query_result=$(execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher"); then
+if ! cypher_elements_query_result=$(execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher"); then
     # Error: Couldn't access HTTP after all wait iterations
     echo "waitForNeo4jHttp: Error: Failed to access Neo4j HTTP API."
     exit 1

From da2534bdefc472fd4a1ae6b01035bc8122756590 Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Sun, 22 Oct 2023 10:36:40 +0200
Subject: [PATCH 3/9] Introduce functions to check and wait for Neo4j

---
 scripts/executeQuery.sh              | 14 ++++--
 scripts/executeQueryFunctions.sh     |  7 ++-
 scripts/startNeo4j.sh                | 35 +++----------
 scripts/stopNeo4j.sh                 | 22 ++++++---
 scripts/waitForNeo4jHttp.sh          | 55 ---------------------
 scripts/waitForNeo4jHttpFunctions.sh | 73 ++++++++++++++++++++++++++++
 6 files changed, 108 insertions(+), 98 deletions(-)
 delete mode 100755 scripts/waitForNeo4jHttp.sh
 create mode 100644 scripts/waitForNeo4jHttpFunctions.sh

diff --git a/scripts/executeQuery.sh b/scripts/executeQuery.sh
index e3210d8ae..5759c0e46 100755
--- a/scripts/executeQuery.sh
+++ b/scripts/executeQuery.sh
@@ -97,17 +97,23 @@ cypher_query_for_api="{\"statements\":[{\"statement\":${cypher_query},\"paramete
 #echo "executeQuery: Cypher Query for API: ${cypher_query_for_api}"
 
 # Calls the Neo4j HTTP API using cURL ( https://curl.se )
-cypher_query_result=$(curl --silent -S --fail-with-body -H Accept:application/json -H Content-Type:application/json \
+if ! cypher_query_result=$(curl --silent -S --fail-with-body -H Accept:application/json -H Content-Type:application/json \
      -u neo4j:"${NEO4J_INITIAL_PASSWORD}" \
      "http://localhost:${NEO4J_HTTP_PORT}/${NEO4J_HTTP_TRANSACTION_ENDPOINT}" \
-     -d "${cypher_query_for_api}")
-#echo "executeQuery: Cypher Query Result: ${cypher_query_result}"
+     -d "${cypher_query_for_api}" 2>&1) ;
+then
+  redColor='\033[0;31m'
+  noColor='\033[0m'
+  echo -e "${redColor}${cypher_query_file_name}: ${cypher_query_result}${noColor}" >&2
+  exit 1
+fi
+#echo "executeQuery: Cypher Query OK Result: ${cypher_query_result}"
 
 # If there is a error message print it to syserr >&2 in red color
 error_message=$( echo "${cypher_query_result}" | jq -r '.errors[0] // empty' )
 if [[ -n "${error_message}" ]]; then 
   redColor='\033[0;31m'
-  noColor='\033[0m' # No Color
+  noColor='\033[0m'
   echo -e "${redColor}${cypher_query_file_name}: ${error_message}${noColor}" >&2
   exit 1
 fi
diff --git a/scripts/executeQueryFunctions.sh b/scripts/executeQueryFunctions.sh
index ddd157bf4..0e30ea4c5 100644
--- a/scripts/executeQueryFunctions.sh
+++ b/scripts/executeQueryFunctions.sh
@@ -13,7 +13,7 @@ set -eo pipefail
 # This way non-standard tools like readlink aren't needed.
 SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
 
-# Extact the value of one key out of a "key=value" array e.g. for query parameters. 
+# Extract the value of one key out of a "key=value" array e.g. for query parameters. 
 # The first argument is the name of the target key.
 # All following arguments are the "key=value" parameters.
 # Example: `extractQueryParameter "b" "a=1" "b=2" "c=3"` returns `2`
@@ -49,7 +49,7 @@ execute_cypher_expect_results() {
 # Function to execute a cypher query from the given file (first and only argument) using Neo4j's HTTP API
 execute_cypher_http() { 
     # (Neo4j HTTP API Script) Execute the Cypher query contained in the file and print the results as CSV
-    source "$SCRIPTS_DIR/executeQuery.sh" "${@}" # "${@}": Get all function arguments and forward them
+    source "${SCRIPTS_DIR}/executeQuery.sh" "${@}" # "${@}": Get all function arguments and forward them
 }
 
 # Function to execute a cypher query from the given file (first and only argument) with a summarized (console) output using Neo4j's HTTP API
@@ -63,8 +63,7 @@ execute_cypher_http_summarized() {
 execute_cypher_http_expect_results() { 
     # Get the Cypher file name from the first argument
     cypherFileName="${1}"
-
-    results=$( execute_cypher_http ${cypherFileName} | wc -l )
+    results=$( execute_cypher_http "${cypherFileName}" | wc -l )
     results=$((results - 1))
     if [[ "$results" -lt 1 ]]; then
         echo "$(basename -- "${cypherFileName}") (via http) Error: Expected at least one entry but was ${results}" >&2
diff --git a/scripts/startNeo4j.sh b/scripts/startNeo4j.sh
index 9e6b2fe25..a34acec84 100755
--- a/scripts/startNeo4j.sh
+++ b/scripts/startNeo4j.sh
@@ -45,13 +45,12 @@ fi
 # Include operation system function to for example detect Windows.
 source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
 
-scriptExtension=$(ifWindows ".bat" "")
-echo "startNeo4j: Using scriptExtension ${scriptExtension} for Windows."
+# Include functions to check or wait for the database to be ready
+source "${SCRIPTS_DIR}/waitForNeo4jHttpFunctions.sh"
 
 # Check if Neo4j is stopped (not running) using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
-neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
-if [ -n "${neo4jNotRunning}" ]; then
+isDatabaseReady=$(isDatabaseQueryable)
+if [[ ${isDatabaseReady} == "false" ]]; then
     echo "startNeo4j: Starting neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} in ${NEO4J_DIR}"
 
     # Check if there is already a process that listens to the Neo4j HTTP port
@@ -86,28 +85,8 @@ if [ -n "${neo4jNotRunning}" ]; then
         NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j start --verbose
     fi
 
-    # Wait some time for the start of the database
-    echo "${WAIT_TIMES}" | tr ' ' '\n' | while read waitTime; do
-        echo "startNeo4j: Waiting for ${waitTime} second(s)"
-        sleep ${waitTime}
-
-        neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
-        neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
-        if [ -z "${neo4jNotRunning}" ]; then
-            echo "startNeo4j: Successfully started neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
-            exit 0
-        fi
-    done
+   waitUntilDatabaseIsQueryable
+   
 else
     echo "startNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} already started"
-fi
-
-# Check if Neo4j is still not running using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
-neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
-if [ -n "${neo4jNotRunning}" ]; then
-    echo "startNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} still not running. Something went wrong. Details see 'NEO4J_HOME=${NEO4J_DIR} ${NEO4J_BIN}/neo4j status'."
-    exit 1
-fi
-
-source "${SCRIPTS_DIR}/waitForNeo4jHttp.sh" || exit 1
\ No newline at end of file
+fi
\ No newline at end of file
diff --git a/scripts/stopNeo4j.sh b/scripts/stopNeo4j.sh
index a17bcc4a7..f44e7b9cc 100755
--- a/scripts/stopNeo4j.sh
+++ b/scripts/stopNeo4j.sh
@@ -14,6 +14,13 @@ NEO4J_VERSION=${NEO4J_VERSION:-"5.12.0"}
 TOOLS_DIRECTORY=${TOOLS_DIRECTORY:-"tools"} # Get the tools directory (defaults to "tools")
 NEO4J_HTTP_PORT=${NEO4J_HTTP_PORT:-"7474"}
 
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+echo "stopNeo4j: SCRIPTS_DIR=$SCRIPTS_DIR"
+
 # Internal Constants
 NEO4J_DIR="${TOOLS_DIRECTORY}/neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
 NEO4J_BIN="${NEO4J_DIR}/bin"
@@ -35,11 +42,13 @@ fi
 # Include operation system function to for example detect Windows.
 source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
 
+# Include functions to check or wait for the database to be ready
+source "${SCRIPTS_DIR}/waitForNeo4jHttpFunctions.sh"
+
 # Check if Neo4j is stopped (not running) using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
-neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
-if [ -n "${neo4jNotRunning}" ]; then
-    echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} aleady stopped"
+isDatabaseReady=$(isDatabaseQueryable)
+if [[ ${isDatabaseReady} == "false" ]]; then
+    echo "stopNeo4j: neo4j-${NEO4J_EDITION}-${NEO4J_VERSION} already stopped"
     exit 0
 else
     if isWindows; then
@@ -51,9 +60,8 @@ else
 fi
 
 # Check if Neo4j is still not running using a temporary NEO4J_HOME environment variable that points to the current installation
-neo4jStatus="$( NEO4J_HOME=${NEO4J_DIR} | ${NEO4J_BIN}/neo4j${scriptExtension} status 2>&1 || true)"
-neo4jNotRunning=$(echo "$neo4jStatus" | grep "not running" || true)
-if [ -n "${neo4jNotRunning}" ]; then
+isDatabaseReady=$(isDatabaseQueryable)
+if [[ ${isDatabaseReady} == "false" ]]; then
     echo "stopNeo4j: Successfully stopped neo4j-${NEO4J_EDITION}-${NEO4J_VERSION}"
 else
     if ! isWindows; then
diff --git a/scripts/waitForNeo4jHttp.sh b/scripts/waitForNeo4jHttp.sh
deleted file mode 100755
index f987b5c69..000000000
--- a/scripts/waitForNeo4jHttp.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env bash
-
-# Waits until the HTTP Transactions API of Neo4j Graph Database is available.
-# It queries the number of nodes and relationships to assert the connection.
-
-# Requires executeQueryFunctions.sh
-
-# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
-set -eo pipefail
-
-NEO4J_HTTP_PORT=${NEO4J_HTTP_PORT:-"7474"}
-
-## Get this "scripts" directory if not already set
-# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
-# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
-# This way non-standard tools like readlink aren't needed.
-SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
-echo "waitForNeo4jHttp: SCRIPTS_DIR=$SCRIPTS_DIR"
-
-# Get the "cypher" directory by taking the path of this script and going one directory up and then to "cypher".
-CYPHER_DIR=${CYPHER_DIR:-"${SCRIPTS_DIR}/../cypher"}
-echo "waitForNeo4jHttp: CYPHER_DIR=$CYPHER_DIR"
-
-# Define functions to execute a Cypher query from within the given file (first and only argument)
-source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
-
-# List of wait times in seconds per retry
-WAIT_TIMES="1 1 2 4 8 16 32 64"
-
-# Wait until the HTTP endpoint is up and a cypher query can be executed
-
-echo "${WAIT_TIMES}" | tr ' ' '\n' | while read -r waitTime; do
-    echo "waitForNeo4jHttp: Waiting for ${waitTime} second(s)"
-    sleep "${waitTime}"
-
-    # Queries node and relationship count as a basic validation
-    if ! cypher_elements_query_result=$(execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher");
-    then
-        continue; # query failed -> try again
-    fi
-    
-    if [[ -n "${cypher_elements_query_result}" ]]; then 
-        echo "waitForNeo4jHttp: Successfully accessed Neo4j HTTP API."
-        echo "${cypher_elements_query_result}"
-        exit 0
-    fi
-done
-
-if ! cypher_elements_query_result=$(execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher"); then
-    # Error: Couldn't access HTTP after all wait iterations
-    echo "waitForNeo4jHttp: Error: Failed to access Neo4j HTTP API."
-    exit 1
-fi
-
-
diff --git a/scripts/waitForNeo4jHttpFunctions.sh b/scripts/waitForNeo4jHttpFunctions.sh
new file mode 100644
index 000000000..962b368c0
--- /dev/null
+++ b/scripts/waitForNeo4jHttpFunctions.sh
@@ -0,0 +1,73 @@
+#!/usr/bin/env bash
+
+# Waits until the HTTP Transactions API of Neo4j Graph Database is available.
+# It queries the number of nodes and relationships to assert the connection.
+
+# Requires executeQueryFunctions.sh
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -eo pipefail
+
+NEO4J_HTTP_PORT=${NEO4J_HTTP_PORT:-"7474"}
+
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+echo "waitForNeo4jHttp: SCRIPTS_DIR=$SCRIPTS_DIR"
+
+# Get the "cypher" directory by taking the path of this script and going one directory up and then to "cypher".
+CYPHER_DIR=${CYPHER_DIR:-"${SCRIPTS_DIR}/../cypher"}
+echo "waitForNeo4jHttp: CYPHER_DIR=${CYPHER_DIR}"
+
+# Define functions to execute a Cypher query from within the given file (first and only argument)
+source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
+
+queryDatabase() { 
+    execute_cypher "${CYPHER_DIR}/Count_nodes_and_relationships.cypher" "--no-source-reference-column"
+}
+
+isDatabaseQueryable() { 
+    local cypher_elements_query_result
+    if cypher_elements_query_result=$(queryDatabase);
+    then
+        echo "true"
+     else
+        echo "false"
+    fi
+}
+
+waitUntilDatabaseIsQueryable() { 
+    # List of wait times in seconds per retry
+    local WAIT_TIMES="16 1 1 2 4 8 16 32 64"
+    local retries=0
+    local isDatabaseReady="false"
+
+    # Wait until the HTTP endpoint is up and a cypher query can be executed
+    echo "${WAIT_TIMES}" | tr ' ' '\n' | while read -r waitTime; do
+        echo "waitForNeo4jHttp: Waiting for ${waitTime} second(s) before retry ${retries}"
+        sleep "${waitTime}"
+
+        # Queries node and relationship count as a basic validation
+        isDatabaseReady=$(isDatabaseQueryable)
+        if [[ ${isDatabaseReady} == "false" ]]; then
+            retries=$((retries+1))
+            continue; # query failed -> try again
+        fi
+        
+        local queryResult=$(queryDatabase || true)
+        if [[ -n "${queryResult}" ]]; then 
+            echo "waitForNeo4jHttp: Successfully accessed Neo4j HTTP API."
+            echo "${queryResult}"
+            exit 0
+        fi
+    done
+
+    isDatabaseReady=$(isDatabaseQueryable)
+    if [[ ${isDatabaseReady} == "false" ]]; then
+        # Error: Couldn't access HTTP after all wait iterations
+        echo "waitForNeo4jHttp: Error: Failed to access Neo4j HTTP API"
+        exit 1
+    fi
+}
\ No newline at end of file

From 1dbc616efd54d513b09044d752c61cba8c95cf26 Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Thu, 26 Oct 2023 14:44:44 +0200
Subject: [PATCH 4/9] Minor typo and other fixes

---
 scripts/prepareAnalysis.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/prepareAnalysis.sh b/scripts/prepareAnalysis.sh
index c3e725108..9188c2c70 100644
--- a/scripts/prepareAnalysis.sh
+++ b/scripts/prepareAnalysis.sh
@@ -22,7 +22,7 @@ fi
 
 # Get the "cypher" directory by taking the path of this script, going one directory up and then into "cypher".
 CYPHER_DIR=${CYPHER_DIR:-"${SCRIPTS_DIR}/../cypher"} # Repository directory containing the cypher queries
-echo "prepareAnalysis: CYPHER_DIR=$CYPHER_DIR"
+echo "prepareAnalysis: CYPHER_DIR=${CYPHER_DIR}"
 
 # Define functions to execute a cypher query from within the given file (first and only argument)
 source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
@@ -34,7 +34,7 @@ EXTERNAL_DEPENDENCIES_CYPHER_DIR="$CYPHER_DIR/External_Dependencies"
 ARTIFACT_DEPENDENCIES_CYPHER_DIR="$CYPHER_DIR/Artifact_Dependencies"
 TYPES_CYPHER_DIR="$CYPHER_DIR/Types"
 
-# Preparation - Create indizes
+# Preparation - Create indices
 execute_cypher "${CYPHER_DIR}/Create_index_for_full_qualified_type_name.cypher"
 
 # Preparation - Create DEPENDS_ON for every DEPENDS_ON_PACKAGE relationship

From ffa358732d6360535c459008a913dfa8e87b7719 Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Thu, 26 Oct 2023 15:17:54 +0200
Subject: [PATCH 5/9] Migrate to jq v1.7

- Fix jq error "is no valid in a csv row"
- Skip algorithm estimation result column "mapView" to overcome jq error
- Fix jq error "string and array cannot be added"
- jq flatten doesn't work on lists in lists on Windows/git bash jq-7
- Cypher plugin apoc provides a flatten function for that
---
 ..._Detection_3a_WeaklyConnectedComponents_Estimate.cypher | 2 +-
 ...ommunity_Detection_4a_Label_Propagation_Estimate.cypher | 2 +-
 ...unity_Detection_5a_K_Core_Decomposition_Estimate.cypher | 2 +-
 ..._Detection_6a_Approximate_Maximum_k_cut_Estimate.cypher | 2 +-
 .../External_package_usage_per_artifact_sorted_top.cypher  | 7 +++----
 ...de_Embeddings_1a_Fast_Random_Projection_Estimate.cypher | 4 ++--
 .../Node_Embeddings_2a_Hash_GNN_Estimate.cypher            | 4 ++--
 .../Node_Embeddings_3a_Node2Vec_Estimate.cypher            | 4 ++--
 cypher/Similarity/Similarity_1a_Estimate.cypher            | 4 ++--
 9 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/cypher/Community_Detection/Community_Detection_3a_WeaklyConnectedComponents_Estimate.cypher b/cypher/Community_Detection/Community_Detection_3a_WeaklyConnectedComponents_Estimate.cypher
index f860a8087..663364e3e 100644
--- a/cypher/Community_Detection/Community_Detection_3a_WeaklyConnectedComponents_Estimate.cypher
+++ b/cypher/Community_Detection/Community_Detection_3a_WeaklyConnectedComponents_Estimate.cypher
@@ -23,4 +23,4 @@ RETURN requiredMemory
       ,heapPercentageMin
       ,heapPercentageMax
       ,treeView
-      ,mapView
\ No newline at end of file
+      //,mapView //doesn't work on Windows with git bash jq version jq-1.7-dirty
\ No newline at end of file
diff --git a/cypher/Community_Detection/Community_Detection_4a_Label_Propagation_Estimate.cypher b/cypher/Community_Detection/Community_Detection_4a_Label_Propagation_Estimate.cypher
index d8a2925ac..f505397de 100644
--- a/cypher/Community_Detection/Community_Detection_4a_Label_Propagation_Estimate.cypher
+++ b/cypher/Community_Detection/Community_Detection_4a_Label_Propagation_Estimate.cypher
@@ -23,4 +23,4 @@ RETURN requiredMemory
       ,heapPercentageMin
       ,heapPercentageMax
       ,treeView
-      ,mapView
\ No newline at end of file
+      //,mapView //doesn't work on Windows with git bash jq version jq-1.7-dirty
\ No newline at end of file
diff --git a/cypher/Community_Detection/Community_Detection_5a_K_Core_Decomposition_Estimate.cypher b/cypher/Community_Detection/Community_Detection_5a_K_Core_Decomposition_Estimate.cypher
index ace1e4652..929d57040 100644
--- a/cypher/Community_Detection/Community_Detection_5a_K_Core_Decomposition_Estimate.cypher
+++ b/cypher/Community_Detection/Community_Detection_5a_K_Core_Decomposition_Estimate.cypher
@@ -21,4 +21,4 @@ RETURN requiredMemory
       ,heapPercentageMin
       ,heapPercentageMax
       ,treeView
-      ,mapView
\ No newline at end of file
+      //,mapView //doesn't work on Windows with git bash jq version jq-1.7-dirty
\ No newline at end of file
diff --git a/cypher/Community_Detection/Community_Detection_6a_Approximate_Maximum_k_cut_Estimate.cypher b/cypher/Community_Detection/Community_Detection_6a_Approximate_Maximum_k_cut_Estimate.cypher
index 9feb260ae..aab6da538 100644
--- a/cypher/Community_Detection/Community_Detection_6a_Approximate_Maximum_k_cut_Estimate.cypher
+++ b/cypher/Community_Detection/Community_Detection_6a_Approximate_Maximum_k_cut_Estimate.cypher
@@ -23,4 +23,4 @@ RETURN requiredMemory
       ,heapPercentageMin
       ,heapPercentageMax
       ,treeView
-      ,mapView
\ No newline at end of file
+      //,mapView //doesn't work on Windows with git bash jq version jq-1.7-dirty
\ No newline at end of file
diff --git a/cypher/External_Dependencies/External_package_usage_per_artifact_sorted_top.cypher b/cypher/External_Dependencies/External_package_usage_per_artifact_sorted_top.cypher
index 178b24e2c..5438c5be6 100644
--- a/cypher/External_Dependencies/External_package_usage_per_artifact_sorted_top.cypher
+++ b/cypher/External_Dependencies/External_package_usage_per_artifact_sorted_top.cypher
@@ -46,7 +46,6 @@ RETURN artifactName
       ,externalTypeRate
       ,numberOfExternalTypeCaller
       ,numberOfExternalTypeCalls
-      ,size(externalPackageNames) AS numberOfExternalPackages
-      ,externalPackageNames[0..4] AS top5ExternalPackages
-      ,externalTypeNames[0..1]    AS someExternalTypes
-LIMIT 40
\ No newline at end of file
+      ,size(externalPackageNames)                 AS numberOfExternalPackages
+      ,externalPackageNames[0..4]                 AS top5ExternalPackages
+      ,apoc.coll.flatten(externalTypeNames)[0..9] AS someExternalTypes
\ No newline at end of file
diff --git a/cypher/Node_Embeddings/Node_Embeddings_1a_Fast_Random_Projection_Estimate.cypher b/cypher/Node_Embeddings/Node_Embeddings_1a_Fast_Random_Projection_Estimate.cypher
index aae3e80be..366ae357c 100644
--- a/cypher/Node_Embeddings/Node_Embeddings_1a_Fast_Random_Projection_Estimate.cypher
+++ b/cypher/Node_Embeddings/Node_Embeddings_1a_Fast_Random_Projection_Estimate.cypher
@@ -6,5 +6,5 @@ CALL gds.fastRP.stream.estimate(
      ,relationshipWeightProperty: $dependencies_projection_weight_property
   }
 )
- YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
-RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
\ No newline at end of file
+ YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
+RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
\ No newline at end of file
diff --git a/cypher/Node_Embeddings/Node_Embeddings_2a_Hash_GNN_Estimate.cypher b/cypher/Node_Embeddings/Node_Embeddings_2a_Hash_GNN_Estimate.cypher
index 051362022..6dc7adc6b 100644
--- a/cypher/Node_Embeddings/Node_Embeddings_2a_Hash_GNN_Estimate.cypher
+++ b/cypher/Node_Embeddings/Node_Embeddings_2a_Hash_GNN_Estimate.cypher
@@ -11,5 +11,5 @@ CALL gds.beta.hashgnn.stream.estimate(
      ,outputDimension: toInteger($dependencies_projection_embedding_dimension)
   }
 )
- YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
-RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
\ No newline at end of file
+ YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
+RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
\ No newline at end of file
diff --git a/cypher/Node_Embeddings/Node_Embeddings_3a_Node2Vec_Estimate.cypher b/cypher/Node_Embeddings/Node_Embeddings_3a_Node2Vec_Estimate.cypher
index 01882b134..7583d039e 100644
--- a/cypher/Node_Embeddings/Node_Embeddings_3a_Node2Vec_Estimate.cypher
+++ b/cypher/Node_Embeddings/Node_Embeddings_3a_Node2Vec_Estimate.cypher
@@ -8,5 +8,5 @@ CALL gds.node2vec.write.estimate(
      ,writeProperty: $dependencies_projection_write_property
   }
 )
- YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
-RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
\ No newline at end of file
+ YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
+RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
\ No newline at end of file
diff --git a/cypher/Similarity/Similarity_1a_Estimate.cypher b/cypher/Similarity/Similarity_1a_Estimate.cypher
index 6e54ace9b..bbaa8f55a 100644
--- a/cypher/Similarity/Similarity_1a_Estimate.cypher
+++ b/cypher/Similarity/Similarity_1a_Estimate.cypher
@@ -8,5 +8,5 @@ CALL gds.nodeSimilarity.write.estimate(
     ,writeProperty: 'score'
     ,topK: 3
 })
- YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
-RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView, mapView
\ No newline at end of file
+ YIELD requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
+RETURN requiredMemory, nodeCount, relationshipCount, bytesMin, bytesMax, heapPercentageMin, heapPercentageMax, treeView
\ No newline at end of file

From 9fe313c4c73439a39e7f5985f5e390fa8e4533fd Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Thu, 26 Oct 2023 21:00:15 +0200
Subject: [PATCH 6/9] Support executing Jupyter Notebooks on Windows

---
 COMMANDS.md                                   | 46 ++---------
 GETTING_STARTED.md                            | 73 +++++++++++++++++
 README.md                                     | 27 +++++--
 scripts/executeJupyterNotebook.sh             | 80 ++++++++++++-------
 .../reports/ArtifactDependenciesJupyter.sh    |  2 +-
 .../reports/ExternalDependenciesJupyter.sh    |  2 +-
 .../reports/InternalDependenciesJupyter.sh    |  2 +-
 scripts/reports/MethodMetricsJupyter.sh       |  2 +-
 scripts/reports/NodeEmbeddingsJupyter.sh      |  2 +-
 .../ObjectOrientedDesignMetricsJupyter.sh     |  2 +-
 scripts/reports/OverviewJupyter.sh            |  2 +-
 scripts/reports/VisibilityMetricsJupyter.sh   |  2 +-
 scripts/reports/WordcloudJupyter.sh           |  2 +-
 13 files changed, 161 insertions(+), 83 deletions(-)
 create mode 100644 GETTING_STARTED.md

diff --git a/COMMANDS.md b/COMMANDS.md
index 27aa1b54a..7f2ee91e0 100644
--- a/COMMANDS.md
+++ b/COMMANDS.md
@@ -2,47 +2,11 @@
 
 ## Start an analysis
 
-1. Create a directory for all analysis projects
-
-    ```shell
-    mkdir temp
-    cd temp
-    ```
-
-1. Create a working directory for your specific analysis
-  
-    ```shell
-    mkdir MyFirstAnalysis
-    cd MyFirstAnalysis
-    ```
-
-1. Choose an initial password for Neo4j
-
-    ```shell
-    export NEO4J_INITIAL_PASSWORD=theinitialpasswordthatihavechosenforneo4j
-    ```
-
-1. Create the `artifacts` directory for the code to be analyzed (without `cd` afterwards)
-
-    ```shell
-    mkdir artifacts
-    ```
-
-1. Move the artifacts you want to analyze into the `artifacts` directory
-
-1. Optionally run a predefined script to download artifacts
-
-    ```shell
-    ./../../scripts/downloader/downloadAxonFramework.sh <version>
-    ```
-
-1. Optionally use a script to download artifacts from Maven ([details](#download-maven-artifacts-to-analyze))
-
-1. Start the analysis
-
-    ```shell
-    ./../../scripts/analysis/analyze.sh
-    ```
+An analysis is started with the script [analyze.sh](./scripts/analysis/analyze.sh).
+To run all analysis steps simple execute the following command:
+```shell
+./../../scripts/analysis/analyze.sh
+```
 
 👉 See [scripts/examples/analyzeAxonFramework.sh](./scripts/examples/analyzeAxonFramework.sh) as an example script that combines all the above steps.  
 👉 See [Code Structure Analysis Pipeline](./.github/workflows/code-structure-analysis.yml) on how to do this within a GitHub Actions Workflow.
diff --git a/GETTING_STARTED.md b/GETTING_STARTED.md
new file mode 100644
index 000000000..4cb9fda65
--- /dev/null
+++ b/GETTING_STARTED.md
@@ -0,0 +1,73 @@
+# Code Graph Analysis Pipeline - Getting started guide
+
+This document describes the steps to get started as quickly as possible. 
+For more details on what you can do with this pipeline see [README](./README.md).
+For more details on how the commands work in detail see [COMMANDS](./COMMANDS.md).
+
+## 🛠 Prerequisites
+
+Please read through the [Prerequisites](./README.md#🛠-prerequisites) in the [README](./README.md) file for what is required to run the scripts.
+
+## Start an analysis
+
+1. Create a directory for all analysis projects
+
+    ```shell
+    mkdir temp
+    cd temp
+    ```
+
+1. Create a working directory for your specific analysis
+  
+    ```shell
+    mkdir MyFirstAnalysis
+    cd MyFirstAnalysis
+    ```
+
+1. Choose an initial password for Neo4j
+
+    ```shell
+    export NEO4J_INITIAL_PASSWORD=theinitialpasswordthatihavechosenforneo4j
+    ```
+
+1. Create the `artifacts` directory for the code to be analyzed (without `cd` afterwards)
+
+    ```shell
+    mkdir artifacts
+    ```
+
+1. Move the artifacts you want to analyze into the `artifacts` directory
+
+1. Optionally run a predefined script to download artifacts
+
+    ```shell
+    ./../../scripts/downloader/downloadAxonFramework.sh <version>
+    ```
+
+1. Optionally use a script to download artifacts from Maven ([details](#download-maven-artifacts-to-analyze))
+
+1. Start the analysis
+
+  - Without any additional dependencies:
+    ```shell
+    ./../../scripts/analysis/analyze.sh --report Csv
+    ```
+  - Jupyter notebook reports when Python and Conda are installed:
+    ```shell
+    ./../../scripts/analysis/analyze.sh --report Jupyter
+    ```
+  - Graph visualizations when Node.js and npm are installed:
+    ```shell
+    ./../../scripts/analysis/analyze.sh --report Jupyter
+    ```
+  - All reports with Python, Conda, Node.js and npm installed:
+    ```shell
+    ./../../scripts/analysis/analyze.sh
+    ```
+  - To explore the database yourself without any automatically generated reports and no additional requirements:
+    ```shell
+    ./../../scripts/analysis/analyze.sh
+    ```
+
+👉 See [scripts/examples/analyzeAxonFramework.sh](./scripts/examples/analyzeAxonFramework.sh) as an example script that combines all the above steps.  
+👉 See [Code Structure Analysis Pipeline](./.github/workflows/code-structure-analysis.yml) on how to do this within a GitHub Actions Workflow.
\ No newline at end of file
diff --git a/README.md b/README.md
index 024fe4da2..ef65c78a0 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@ Contained within this repository is a comprehensive and automated code graph ana
 
 ---
 
-## 🚀 Features
+## ✨ Features
 
 - Analyze static code structure as a graph
 - Fully automated [pipeline](./.github/workflows/code-structure-analysis.yml) from tool installation to report generation
@@ -37,14 +37,29 @@ Here are some reports that utilize Neo4j's [Graph Data Science Library](https://
 
 ## 🛠 Prerequisites
 
-- Java 17 is [required for Neo4j](https://neo4j.com/docs/operations-manual/current/installation/requirements/#deployment-requirements-software) (5.x requirement)
+- Java 17 is [required for Neo4j](https://neo4j.com/docs/operations-manual/current/installation/requirements/#deployment-requirements-software) (Neo4j 5.x requirement).
+- On Windows it is recommended to use the git bash provided by [git for windows](https://gitforwindows.org).
 - [jq](https://github.com/jqlang/jq) the "lightweight and flexible command-line JSON processor" needs to be installed. Latest releases: https://github.com/jqlang/jq/releases/latest. Check using `jq --version`.
-- Python and a conda package manager are required for Jupyter Notebook reports
-- Chromium will automatically be downloaded if needed for Jupyter Notebook reports in PDF format
+- Set environment variable `NEO4J_INITIAL_PASSWORD` to a password of your choice. For example:
+  ```shell
+  export NEO4J_INITIAL_PASSWORD=neo4j_password_of_my_choice
+  ```
+  To run Jupyter notebooks, create an `.env` file in the folder from where you open the notebook containing for example: `NEO4J_INITIAL_PASSWORD=neo4j_password_of_my_choice`
+
+### Further Prerequisites for Python Jupyter Notebooks
+
+- Python is required for Jupyter Notebook reports.
+- A conda package manager like [Miniconda](https://docs.conda.io/projects/miniconda/en/latest) or [Anaconda](https://www.anaconda.com/download)(Recommended for Windows) is required for Jupyter Notebook reports.
+- Chromium will automatically be downloaded if needed for Jupyter Notebook PDF reports generation.
+
+### Hints for Windows
+
+- Add this line to your `~/.bashrc` file if you are using Anaconda3: `/c/ProgramData/Anaconda3/etc/profile.d/conda.sh`. Try to find a similar script for other conda package managers or versions.
+- Run `conda init` in the git bash opened as administrator. Running it in normal mode usually leads to an error message.
 
-## Getting Started
+## 🚀 Getting Started
 
-See [Start an analysis](./COMMANDS.md#start-an-analysis) in the [Commands Reference](./COMMANDS.md) on how to start an analysis on your local machine.
+See [GETTING_STARTED.md](./GETTING_STARTED.md) on how to get started on your local machine.
 
 ## 🏗 Pipeline and Tools
 
diff --git a/scripts/executeJupyterNotebook.sh b/scripts/executeJupyterNotebook.sh
index 6b65bd357..ec9ac2e7a 100755
--- a/scripts/executeJupyterNotebook.sh
+++ b/scripts/executeJupyterNotebook.sh
@@ -15,17 +15,20 @@
 #       in the same directory as the given jupyter notebook ipynb file
 #       to create the environment.
 
-# Note: This script uses conda to activate the environment defined in CODEGRAPH_CONDA_ENVIRONMENT (defaults to "codegraph").
-#       It it isn't activated, it will save the currently activated environment, change to codegraph, and restore the original one at the end again.
-#       In cases of an error it might be, that the original conda environment isn't set back. Typically this shouldn't be the case though. 
-
-# Requires juypter nbconvert
+# Requires juypter nbconvert,operatingSystemFunctions.sh
 
 # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
 set -eo pipefail
 
 ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION=${ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION:-""} # Enable PDF generation for Jupyter Notebooks if set to any non empty value e.g. "true"
 
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+echo "executeJupyterNotebook: SCRIPTS_DIR=$SCRIPTS_DIR"
+
 # Check if environment variable is set
 if [ -z "${NEO4J_INITIAL_PASSWORD}" ]; then
     echo "executeJupyterNotebook: Requires environment variable NEO4J_INITIAL_PASSWORD to be set first. Use 'export NEO4J_INITIAL_PASSWORD=<your-own-password>'."
@@ -81,36 +84,59 @@ fi
 
 # Define conda environment to use for code structure analysis. Default "codegraph"
 CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT:-"codegraph"} # Name of the conda environment to use for code graph analysis
-echo "executeJupyterNotebook: CODEGRAPH_CONDA_ENVIRONMENT=$CODEGRAPH_CONDA_ENVIRONMENT"
+backupCondaEnvironment=$CONDA_DEFAULT_ENV
+echo "executeJupyterNotebook: CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT}"
+echo "executeJupyterNotebook: CONDA_PREFIX=${CONDA_PREFIX}"
+echo "executeJupyterNotebook: Current conda environment=${CONDA_DEFAULT_ENV}"
+
+# Include operation system function to for example detect Windows.
+source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
 
 # Determine the path to "conda"
 if [ -n "${CONDA}" ]; then
-    pathToConda="$CONDA/bin/" # the trailing slash character is required
+    if isWindows; then
+        pathToConda="${CONDA}\\Scripts\\" # the trailing backslash character is required
+    else
+        pathToConda="${CONDA}/bin/" # the trailing slash character is required
+    fi
 else
     pathToConda=""
 fi
+
 echo "executeJupyterNotebook: pathToConda=${pathToConda}"
 
-# Activate conda shell hook
-eval "$(${pathToConda}conda shell.bash hook)"
+scriptExtension=$(ifWindows ".bat" "")
+echo "executeJupyterNotebook: scriptExtension=${scriptExtension}"
 
-# Create (if missing) and activate Conda environment for code structure graph analysis
-backupCondaEnvironment=$CONDA_DEFAULT_ENV
-if [ ! "$backupCondaEnvironment" = "$CODEGRAPH_CONDA_ENVIRONMENT" ] ; then
-    backupCondaEnvironment=$CONDA_DEFAULT_ENV
+# Activate conda shell hook. Also resets CONDA_DEFAULT_ENV to base. 
+# Thats why CONDA_DEFAULT_ENV (base) is never equal to CODEGRAPH_CONDA_ENVIRONMENT (codegraph).
+eval "$(${pathToConda}conda${scriptExtension} shell.bash hook)"
+echo "executeJupyterNotebook: Current conda environment after shell hook=${CONDA_DEFAULT_ENV}"
 
-    if { ${pathToConda}conda env list | grep "$CODEGRAPH_CONDA_ENVIRONMENT "; } >/dev/null 2>&1; then
-        echo "executeJupyterNotebook: Conda environment $CODEGRAPH_CONDA_ENVIRONMENT already created"
-    else
-        if [ ! -f "${jupyter_notebook_file_path}/environment.yml" ] ; then
-            echo "executeJupyterNotebook: Couldn't find environment file ${jupyter_notebook_file_path}/environment.yml."
-            exit 2
-        fi
-        echo "executeJupyterNotebook: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
-        ${pathToConda}conda env create --file ${jupyter_notebook_file_path}/environment.yml --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
+# Create (if missing) and activate Conda environment for code structure graph analysis
+if { "${pathToConda}conda" env list | grep "$CODEGRAPH_CONDA_ENVIRONMENT "; } >/dev/null 2>&1; then
+    echo "executeJupyterNotebook: Conda environment $CODEGRAPH_CONDA_ENVIRONMENT already created"
+else
+    if [ ! -f "${jupyter_notebook_file_path}/environment.yml" ] ; then
+        echo "executeJupyterNotebook: Couldn't find environment file ${jupyter_notebook_file_path}/environment.yml."
+        exit 2
     fi
-    ${pathToConda}conda activate "${CODEGRAPH_CONDA_ENVIRONMENT}" 
-    echo "executeJupyterNotebook: Activated Conda environment: $CODEGRAPH_CONDA_ENVIRONMENT "
+    echo "executeJupyterNotebook: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
+    "${pathToConda}conda" env create --file "${jupyter_notebook_file_path}/environment.yml" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
+fi
+
+echo "executeJupyterNotebook: Activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
+if isWindows; then
+    "${pathToConda}conda" activate ${CODEGRAPH_CONDA_ENVIRONMENT}
+else
+    conda activate "${CODEGRAPH_CONDA_ENVIRONMENT}"
+fi
+
+if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
+    echo "executeJupyterNotebook: Activated Conda environment: ${CONDA_DEFAULT_ENV}"
+else
+    echo "executeJupyterNotebook: Error: Failed to activate Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}. ${CONDA_DEFAULT_ENV} still active."
+    exit 1
 fi
 
 # Execute the Jupyter Notebook and write it to the output file name
@@ -135,7 +161,7 @@ if [ -n "${ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION}" ]; then
 fi
 
 # Restore Conda environment
-if [ ! "$backupCondaEnvironment" = "$CODEGRAPH_CONDA_ENVIRONMENT" ] ; then
-    ${pathToConda}conda activate "${backupCondaEnvironment}"
-    echo "executeJupyterNotebook: Restored Conda Environment: ${backupCondaEnvironment}"
+if [ ! "${backupCondaEnvironment}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
+    "${pathToConda}conda" activate "${backupCondaEnvironment}"
+    echo "executeJupyterNotebook: Restored Conda Environment to ${backupCondaEnvironment}: ${CONDA_DEFAULT_ENV}"
 fi
\ No newline at end of file
diff --git a/scripts/reports/ArtifactDependenciesJupyter.sh b/scripts/reports/ArtifactDependenciesJupyter.sh
index 6ac1f3ea1..414eecec0 100755
--- a/scripts/reports/ArtifactDependenciesJupyter.sh
+++ b/scripts/reports/ArtifactDependenciesJupyter.sh
@@ -36,4 +36,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the Jupyter Notebook "ArtifactDependencies.ipynb" within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/ArtifactDependencies.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/ArtifactDependencies.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/ExternalDependenciesJupyter.sh b/scripts/reports/ExternalDependenciesJupyter.sh
index fea028d51..102e8f613 100755
--- a/scripts/reports/ExternalDependenciesJupyter.sh
+++ b/scripts/reports/ExternalDependenciesJupyter.sh
@@ -34,4 +34,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the following Jupyter Notebook within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/ExternalDependencies.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/ExternalDependencies.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/InternalDependenciesJupyter.sh b/scripts/reports/InternalDependenciesJupyter.sh
index c5fadb757..3e817c28f 100755
--- a/scripts/reports/InternalDependenciesJupyter.sh
+++ b/scripts/reports/InternalDependenciesJupyter.sh
@@ -33,4 +33,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the Jupyter Notebook "InternalDependencies.ipynb" within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/InternalDependencies.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/InternalDependencies.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/MethodMetricsJupyter.sh b/scripts/reports/MethodMetricsJupyter.sh
index ff21a844e..59f37e057 100755
--- a/scripts/reports/MethodMetricsJupyter.sh
+++ b/scripts/reports/MethodMetricsJupyter.sh
@@ -33,4 +33,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the following Jupyter Notebook within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/MethodMetrics.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/MethodMetrics.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/NodeEmbeddingsJupyter.sh b/scripts/reports/NodeEmbeddingsJupyter.sh
index 4ff212796..fd03873ed 100755
--- a/scripts/reports/NodeEmbeddingsJupyter.sh
+++ b/scripts/reports/NodeEmbeddingsJupyter.sh
@@ -34,4 +34,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the Jupyter Notebook "InternalDependencies.ipynb" within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/NodeEmbeddings.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/NodeEmbeddings.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/ObjectOrientedDesignMetricsJupyter.sh b/scripts/reports/ObjectOrientedDesignMetricsJupyter.sh
index 63e9ca4b7..dad4805e5 100755
--- a/scripts/reports/ObjectOrientedDesignMetricsJupyter.sh
+++ b/scripts/reports/ObjectOrientedDesignMetricsJupyter.sh
@@ -33,4 +33,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the Jupyter Notebook "ObjectOrientedDesignMetrics.ipynb" within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/ObjectOrientedDesignMetrics.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/ObjectOrientedDesignMetrics.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/OverviewJupyter.sh b/scripts/reports/OverviewJupyter.sh
index 7489d8401..2741299c2 100755
--- a/scripts/reports/OverviewJupyter.sh
+++ b/scripts/reports/OverviewJupyter.sh
@@ -33,4 +33,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the following Jupyter Notebook within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/Overview.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/Overview.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/VisibilityMetricsJupyter.sh b/scripts/reports/VisibilityMetricsJupyter.sh
index 93a28cd77..28c5efd20 100755
--- a/scripts/reports/VisibilityMetricsJupyter.sh
+++ b/scripts/reports/VisibilityMetricsJupyter.sh
@@ -32,4 +32,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the Jupyter Notebook "VisibilityMetrics.ipynb" within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/VisibilityMetrics.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/VisibilityMetrics.ipynb")
\ No newline at end of file
diff --git a/scripts/reports/WordcloudJupyter.sh b/scripts/reports/WordcloudJupyter.sh
index a63e5877e..817dcc34c 100755
--- a/scripts/reports/WordcloudJupyter.sh
+++ b/scripts/reports/WordcloudJupyter.sh
@@ -34,4 +34,4 @@ FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
 mkdir -p "${FULL_REPORT_DIRECTORY}"
 
 # Execute and convert the following Jupyter Notebook within the given reports directory
-(cd "${FULL_REPORT_DIRECTORY}" && exec ${SCRIPTS_DIR}/executeJupyterNotebook.sh ${JUPYTER_NOTEBOOK_DIRECTORY}/Wordcloud.ipynb)
\ No newline at end of file
+(cd "${FULL_REPORT_DIRECTORY}" && exec "${SCRIPTS_DIR}/executeJupyterNotebook.sh" "${JUPYTER_NOTEBOOK_DIRECTORY}/Wordcloud.ipynb")
\ No newline at end of file

From 211399bf02f59f2e749fb368918dd4e79476903c Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Sun, 29 Oct 2023 17:01:52 +0100
Subject: [PATCH 7/9] Support graph visualizations on Windows

---
 README.md                                   |  9 ++++++++-
 graph-visualization/renderVisualizations.js |  8 ++++++--
 scripts/reports/GraphVisualization.sh       | 10 ++++++++--
 3 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index ef65c78a0..041b53ed8 100644
--- a/README.md
+++ b/README.md
@@ -46,12 +46,19 @@ Here are some reports that utilize Neo4j's [Graph Data Science Library](https://
   ```
   To run Jupyter notebooks, create an `.env` file in the folder from where you open the notebook containing for example: `NEO4J_INITIAL_PASSWORD=neo4j_password_of_my_choice`
 
-### Further Prerequisites for Python Jupyter Notebooks
+### Further Prerequisites for Python and Jupyter Notebooks
 
 - Python is required for Jupyter Notebook reports.
 - A conda package manager like [Miniconda](https://docs.conda.io/projects/miniconda/en/latest) or [Anaconda](https://www.anaconda.com/download)(Recommended for Windows) is required for Jupyter Notebook reports.
 - Chromium will automatically be downloaded if needed for Jupyter Notebook PDF reports generation.
 
+### Further Prerequisites for Graph Visualization
+
+These tools are needed to run the graph visualization scripts of directory [graph-visualization](./graph-visualization):
+
+- [Node.js](https://nodejs.org/en)
+- [npm](https://www.npmjs.com)
+
 ### Hints for Windows
 
 - Add this line to your `~/.bashrc` file if you are using Anaconda3: `/c/ProgramData/Anaconda3/etc/profile.d/conda.sh`. Try to find a similar script for other conda package managers or versions.
diff --git a/graph-visualization/renderVisualizations.js b/graph-visualization/renderVisualizations.js
index c069609bd..1c3850890 100644
--- a/graph-visualization/renderVisualizations.js
+++ b/graph-visualization/renderVisualizations.js
@@ -9,6 +9,7 @@ import jimp from "jimp";
 const indexOfScriptFilePathArgument = 1;
 const __filename = process.argv[indexOfScriptFilePathArgument];
 const __dirname = dirname(__filename);
+console.log(`renderVisualizations.js: dirname=${__dirname}`);
 
 /**
  * Crops the image in the buffer so that there is no empty frame around it.
@@ -88,14 +89,17 @@ let browser;
  * and takes a screenshot of the canvas elements using {@link takeCanvasScreenshots}.
  */
 (async () => {
+  console.log('renderVisualizations.js: Starting headless browser...');
   browser = await puppeteer.launch({ headless: "new" }); // { headless: false } for testing
 
   // Get all *.html files in this (script) directory and its subdirectories
-  const htmlFiles = globSync(`${__dirname}/**/*.html`, { ignore: `${__dirname}/node_modules/**` });
+  // The separate filter is needed to ignore the "node_modules" directory. 
+  // Glob's build-in filter doesn't seem to work on Windows.
+  const htmlFiles = globSync(`${__dirname}/**/*.html`, { absolute: true }).filter(file => !file.includes('node_modules'));
   for (const htmlFile of htmlFiles) {
     await takeCanvasScreenshots(browser, htmlFile);
   }
-  console.log(`Successfully rendered ${htmlFiles.length} html file(s)`);
+  console.log(`renderVisualizations.js: Successfully rendered ${htmlFiles.length} html file(s)`);
 })()
   .catch((err) => console.error(err))
   .finally(() => browser?.close());
diff --git a/scripts/reports/GraphVisualization.sh b/scripts/reports/GraphVisualization.sh
index 0ece0c08d..dbc0b12d8 100755
--- a/scripts/reports/GraphVisualization.sh
+++ b/scripts/reports/GraphVisualization.sh
@@ -24,7 +24,13 @@ echo "GraphVisualization: SCRIPTS_DIR=${SCRIPTS_DIR}"
 
 # Get the "graph-visualization" directory by taking the path of this script and going two directory up and then to "visualization".
 GRAPH_VISUALIZATION_DIRECTORY=${GRAPH_VISUALIZATION_DIRECTORY:-"${SCRIPTS_DIR}/../graph-visualization"} # Repository directory containing the Jupyter Notebooks
-echo "GraphVisualization: GRAPH_VISUALIZATION_DIRECTORY=$GRAPH_VISUALIZATION_DIRECTORY"
+echo "GraphVisualization: GRAPH_VISUALIZATION_DIRECTORY=${GRAPH_VISUALIZATION_DIRECTORY}"
+
+# Execute "npm ci" to get all required node modules from npm package manager
+if [ ! -d "${GRAPH_VISUALIZATION_DIRECTORY}/node_modules" ] ; then
+    echo "GraphVisualization: Resolving node_modules..."
+    (cd "${GRAPH_VISUALIZATION_DIRECTORY}" && exec npm ci)
+fi
 
 # Execute the node.js script to render the graph visualizations as image files
-(cd "${REPORTS_DIRECTORY}" && exec node ${GRAPH_VISUALIZATION_DIRECTORY}/renderVisualizations.js)
\ No newline at end of file
+(cd "${REPORTS_DIRECTORY}" && exec node "${GRAPH_VISUALIZATION_DIRECTORY}/renderVisualizations.js")
\ No newline at end of file

From 5860d84dbc64f57a2532b281e3315e16ef237a95 Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Mon, 30 Oct 2023 18:14:13 +0100
Subject: [PATCH 8/9] Add info about conda environment in pipeline

---
 .github/workflows/code-structure-analysis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/code-structure-analysis.yml b/.github/workflows/code-structure-analysis.yml
index 06cd7ee16..c9c77d670 100644
--- a/.github/workflows/code-structure-analysis.yml
+++ b/.github/workflows/code-structure-analysis.yml
@@ -97,6 +97,10 @@ jobs:
         auto-activate-base: false
         use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
+    - name: Conda environment info
+      shell: bash -el {0}
+      run: conda info
+
     - name: Setup temp directory if missing
       run: mkdir -p ./temp
 

From 831fb8df1014fc2f241fe5482bd6f96c81201f4e Mon Sep 17 00:00:00 2001
From: JohT <johnnyt@gmx.at>
Date: Tue, 31 Oct 2023 08:34:05 +0100
Subject: [PATCH 9/9] Move conda environment activation to own script

---
 scripts/activateCondaEnvironment.sh | 85 +++++++++++++++++++++++++++++
 scripts/executeJupyterNotebook.sh   | 64 +---------------------
 2 files changed, 87 insertions(+), 62 deletions(-)
 create mode 100755 scripts/activateCondaEnvironment.sh

diff --git a/scripts/activateCondaEnvironment.sh b/scripts/activateCondaEnvironment.sh
new file mode 100755
index 000000000..5eaf662f7
--- /dev/null
+++ b/scripts/activateCondaEnvironment.sh
@@ -0,0 +1,85 @@
+#!/usr/bin/env bash
+
+# Activates the Conda (Python package manager) environment "codegraph" with all packages needed to execute the Jupyter Notebooks.
+
+# Note: This script uses the conda environment defined in CODEGRAPH_CONDA_ENVIRONMENT (defaults to "codegraph").
+#       If the environment hadn't been created yet it will use "environment.yml" 
+#       in the same directory as the given jupyter notebook ipynb file
+#       to create the environment.
+
+# Requires operatingSystemFunctions.sh
+
+# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
+set -eo pipefail
+
+## Get this "scripts" directory if not already set
+# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. 
+# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
+# This way non-standard tools like readlink aren't needed.
+SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts
+echo "activateCondaEnvironment: SCRIPTS_DIR=$SCRIPTS_DIR"
+
+# Get the "jupyter" directory by taking the path of this script and going two directory up and then to "jupyter".
+JUPYTER_NOTEBOOK_DIRECTORY=${JUPYTER_NOTEBOOK_DIRECTORY:-"${SCRIPTS_DIR}/../jupyter"} # Repository directory containing the Jupyter Notebooks
+echo "activateCondaEnvironment: JUPYTER_NOTEBOOK_DIRECTORY=$JUPYTER_NOTEBOOK_DIRECTORY"
+
+# Define conda environment to use for code structure analysis. Default "codegraph"
+CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT:-"codegraph"} # Name of the conda environment to use for code graph analysis
+echo "activateCondaEnvironment: CONDA_PREFIX=${CONDA_PREFIX}"
+echo "activateCondaEnvironment: Current conda environment=${CONDA_DEFAULT_ENV}"
+echo "activateCondaEnvironment: Target conda environment=${CODEGRAPH_CONDA_ENVIRONMENT}"
+
+if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
+    echo "activateCondaEnvironment: Skipping activation. Target conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} is already activated."
+    exit 0
+fi
+
+# Include operation system function to for example detect Windows.
+source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
+
+# Determine the path to "conda"
+if [ -n "${CONDA}" ]; then
+    if isWindows; then
+        pathToConda="${CONDA}\\Scripts\\" # the trailing backslash character is required
+    else
+        pathToConda="${CONDA}/bin/" # the trailing slash character is required
+    fi
+else
+    pathToConda=""
+fi
+echo "activateCondaEnvironment: pathToConda=${pathToConda}"
+
+scriptExtension=$(ifWindows ".bat" "")
+echo "activateCondaEnvironment: scriptExtension=${scriptExtension}"
+
+# Activate conda shell hook. Also resets CONDA_DEFAULT_ENV to base. 
+# Thats why CONDA_DEFAULT_ENV (base) is never equal to CODEGRAPH_CONDA_ENVIRONMENT (codegraph).
+eval "$(${pathToConda}conda${scriptExtension} shell.bash hook)"
+echo "activateCondaEnvironment: Current conda environment after shell hook=${CONDA_DEFAULT_ENV}"
+
+# Create (if missing) and activate Conda environment for code structure graph analysis
+if { "${pathToConda}conda" env list | grep "$CODEGRAPH_CONDA_ENVIRONMENT "; } >/dev/null 2>&1; then
+    echo "activateCondaEnvironment: Conda environment $CODEGRAPH_CONDA_ENVIRONMENT already created"
+else
+    if [ ! -f "${JUPYTER_NOTEBOOK_DIRECTORY}/environment.yml" ] ; then
+        echo "activateCondaEnvironment: Couldn't find environment file ${jupyter_notebook_file_path}/environment.yml."
+        exit 2
+    fi
+    echo "activateCondaEnvironment: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
+    "${pathToConda}conda" env create --file "${jupyter_notebook_file_path}/environment.yml" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
+fi
+
+echo "activateCondaEnvironment: Activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
+"${pathToConda}conda" activate ${CODEGRAPH_CONDA_ENVIRONMENT}
+
+if [ "${CONDA_DEFAULT_ENV}" != "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
+    echo "activateCondaEnvironment: Retry activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT} with plain 'conda' command"
+    conda activate ${CODEGRAPH_CONDA_ENVIRONMENT}
+fi
+
+if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
+    echo "activateCondaEnvironment: Activated Conda environment: ${CONDA_DEFAULT_ENV}"
+else
+    echo "activateCondaEnvironment: Error: Failed to activate Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}. ${CONDA_DEFAULT_ENV} still active."
+    exit 1
+fi
\ No newline at end of file
diff --git a/scripts/executeJupyterNotebook.sh b/scripts/executeJupyterNotebook.sh
index ec9ac2e7a..44b335af5 100755
--- a/scripts/executeJupyterNotebook.sh
+++ b/scripts/executeJupyterNotebook.sh
@@ -82,62 +82,8 @@ if [ ! -f "${jupyter_notebook_file_path}/.env" ] ; then
     echo "NEO4J_INITIAL_PASSWORD=${NEO4J_INITIAL_PASSWORD}" > "${jupyter_notebook_file_path}/.env"
 fi
 
-# Define conda environment to use for code structure analysis. Default "codegraph"
-CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT:-"codegraph"} # Name of the conda environment to use for code graph analysis
-backupCondaEnvironment=$CONDA_DEFAULT_ENV
-echo "executeJupyterNotebook: CODEGRAPH_CONDA_ENVIRONMENT=${CODEGRAPH_CONDA_ENVIRONMENT}"
-echo "executeJupyterNotebook: CONDA_PREFIX=${CONDA_PREFIX}"
-echo "executeJupyterNotebook: Current conda environment=${CONDA_DEFAULT_ENV}"
-
-# Include operation system function to for example detect Windows.
-source "${SCRIPTS_DIR}/operatingSystemFunctions.sh"
-
-# Determine the path to "conda"
-if [ -n "${CONDA}" ]; then
-    if isWindows; then
-        pathToConda="${CONDA}\\Scripts\\" # the trailing backslash character is required
-    else
-        pathToConda="${CONDA}/bin/" # the trailing slash character is required
-    fi
-else
-    pathToConda=""
-fi
-
-echo "executeJupyterNotebook: pathToConda=${pathToConda}"
-
-scriptExtension=$(ifWindows ".bat" "")
-echo "executeJupyterNotebook: scriptExtension=${scriptExtension}"
-
-# Activate conda shell hook. Also resets CONDA_DEFAULT_ENV to base. 
-# Thats why CONDA_DEFAULT_ENV (base) is never equal to CODEGRAPH_CONDA_ENVIRONMENT (codegraph).
-eval "$(${pathToConda}conda${scriptExtension} shell.bash hook)"
-echo "executeJupyterNotebook: Current conda environment after shell hook=${CONDA_DEFAULT_ENV}"
-
-# Create (if missing) and activate Conda environment for code structure graph analysis
-if { "${pathToConda}conda" env list | grep "$CODEGRAPH_CONDA_ENVIRONMENT "; } >/dev/null 2>&1; then
-    echo "executeJupyterNotebook: Conda environment $CODEGRAPH_CONDA_ENVIRONMENT already created"
-else
-    if [ ! -f "${jupyter_notebook_file_path}/environment.yml" ] ; then
-        echo "executeJupyterNotebook: Couldn't find environment file ${jupyter_notebook_file_path}/environment.yml."
-        exit 2
-    fi
-    echo "executeJupyterNotebook: Creating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
-    "${pathToConda}conda" env create --file "${jupyter_notebook_file_path}/environment.yml" --name "${CODEGRAPH_CONDA_ENVIRONMENT}"
-fi
-
-echo "executeJupyterNotebook: Activating Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}"
-if isWindows; then
-    "${pathToConda}conda" activate ${CODEGRAPH_CONDA_ENVIRONMENT}
-else
-    conda activate "${CODEGRAPH_CONDA_ENVIRONMENT}"
-fi
-
-if [ "${CONDA_DEFAULT_ENV}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
-    echo "executeJupyterNotebook: Activated Conda environment: ${CONDA_DEFAULT_ENV}"
-else
-    echo "executeJupyterNotebook: Error: Failed to activate Conda environment ${CODEGRAPH_CONDA_ENVIRONMENT}. ${CONDA_DEFAULT_ENV} still active."
-    exit 1
-fi
+# Create and activate (if necessary) Conda environment as defined in environment variable CODEGRAPH_CONDA_ENVIRONMENT (default "codegraph")
+source "${SCRIPTS_DIR}/activateCondaEnvironment.sh"
 
 # Execute the Jupyter Notebook and write it to the output file name
 jupyter nbconvert --to notebook \
@@ -158,10 +104,4 @@ mv -f "${jupyter_notebook_markdown_file}.nostyle" "${jupyter_notebook_markdown_f
 # Convert the Jupyter Notebook to PDF
 if [ -n "${ENABLE_JUPYTER_NOTEBOOK_PDF_GENERATION}" ]; then
     jupyter nbconvert --to webpdf --no-input --allow-chromium-download --disable-chromium-sandbox "$jupyter_notebook_output_file"
-fi
-
-# Restore Conda environment
-if [ ! "${backupCondaEnvironment}" = "${CODEGRAPH_CONDA_ENVIRONMENT}" ] ; then
-    "${pathToConda}conda" activate "${backupCondaEnvironment}"
-    echo "executeJupyterNotebook: Restored Conda Environment to ${backupCondaEnvironment}: ${CONDA_DEFAULT_ENV}"
 fi
\ No newline at end of file