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Introduce anomaly detection pipeline with tuned clustering
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‎domains/anomaly-detection/AnomalyDetection.ipynb

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‎domains/anomaly-detection/anomalyDetectionPipeline.sh

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#!/usr/bin/env bash
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# Pipeline that coordinates anomaly detection using the Graph Data Science Library of Neo4j.
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# It requires an already running Neo4j graph database with already scanned and analyzed artifacts.
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# The results will be written into the sub directory reports/anomaly-detection.
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# Note that "scripts/prepareAnalysis.sh" is required to run prior to this script.
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# Requires executeQueryFunctions.sh, projectionFunctions.sh, cleanupAfterReportGeneration.sh
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# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands)
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set -o errexit -o pipefail
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# Overrideable Constants (defaults also defined in sub scripts)
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REPORTS_DIRECTORY=${REPORTS_DIRECTORY:-"reports"}
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## Get this "scripts/reports" directory if not already set
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# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution.
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# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
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# This way non-standard tools like readlink aren't needed.
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ANOMALY_DETECTION_SCRIPT_DIR=${ANOMALY_DETECTION_SCRIPT_DIR:-$(CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P)}
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echo "anomalyDetectionPipeline: ANOMALY_DETECTION_SCRIPT_DIR=${ANOMALY_DETECTION_SCRIPT_DIR}"
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# Get the "scripts" directory by taking the path of this script and going one directory up.
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SCRIPTS_DIR=${SCRIPTS_DIR:-"${ANOMALY_DETECTION_SCRIPT_DIR}/../../scripts"} # Repository directory containing the shell scripts
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# Get the "cypher" query directory for gathering features.
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ANOMALY_DETECTION_FEATURE_CYPHER_DIR=${ANOMALY_DETECTION_FEATURE_CYPHER_DIR:-"${ANOMALY_DETECTION_SCRIPT_DIR}/features"}
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ANOMALY_DETECTION_QUERY_CYPHER_DIR=${ANOMALY_DETECTION_QUERY_CYPHER_DIR:-"${ANOMALY_DETECTION_SCRIPT_DIR}/queries"}
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# Function to display script usage
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usage() {
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echo -e "${COLOR_ERROR}" >&2
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echo "Usage: $0 [--verbose]" >&2
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echo -e "${COLOR_DEFAULT}" >&2
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exit 1
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}
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# Default values
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verboseMode="" # either "" or "--verbose"
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# Parse command line arguments
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while [[ $# -gt 0 ]]; do
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key="$1"
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value="${2}"
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case ${key} in
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--verbose)
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verboseMode="--verbose"
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;;
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*)
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echo -e "${COLOR_ERROR}anomalyDetectionPipeline: Error: Unknown option: ${key}${COLOR_DEFAULT}" >&2
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usage
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;;
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esac
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shift || true # ignore error when there are no more arguments
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done
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# Define functions to execute a cypher query from within a given file (first and only argument) like "execute_cypher"
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source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
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# Define functions to create and delete Graph Projections like "createUndirectedDependencyProjection"
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source "${SCRIPTS_DIR}/projectionFunctions.sh"
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# Query or recalculate features.
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#
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# Required Parameters:
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# - projection_name=...
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# Name prefix for the in-memory projection name. Example: "package-anomaly-detection"
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# - projection_node_label=...
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# Label of the nodes that will be used for the projection. Example: "Package"
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# - projection_weight_property=...
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# Name of the node property that contains the dependency weight. Example: "weight"
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anomaly_detection_features() {
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# Determine the Betweenness centrality (with the directed graph projection) if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-Betweenness-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-Betweenness-Write.cypher" "${@}"
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# Determine the local clustering coefficient if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-LocalClusteringCoefficient-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-LocalClusteringCoefficient-Write.cypher" "${@}"
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# Determine the page rank if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-PageRank-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-PageRank-Write.cypher" "${@}"
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# Determine the article rank if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-ArticleRank-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-PageRank-Write.cypher" "${@}"
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}
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# Run queries to find anomalies in the graph.
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#
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# Required Parameters:
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# - projection_node_label=...
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# Label of the nodes that will be used for the projection. Example: "Package"
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anomaly_detection_queries() {
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local nodeLabel
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nodeLabel=$( extractQueryParameter "projection_node_label" "${@}" )
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# Determine the article rank if not already done
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execute_cypher "${ANOMALY_DETECTION_QUERY_CYPHER_DIR}/AnomalyDetectionPageToArticleRankDifference.cypher" "${@}" > "${FULL_REPORT_DIRECTORY}/${nodeLabel}AnomalyDetection_ArticleVsPageRankDifference.csv"
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}
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# Run the anomaly detection pipeline.
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#
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# Required Parameters:
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# - projection_name=...
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# Name prefix for the in-memory projection name. Example: "package-anomaly-detection"
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# - projection_node_label=...
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# Label of the nodes that will be used for the projection. Example: "Package"
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# - projection_weight_property=...
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# Name of the node property that contains the dependency weight. Example: "weight"
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anomaly_detection_pipeline() {
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time anomaly_detection_features "${@}"
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time anomaly_detection_queries "${@}"
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# Get tuned Leiden communities as a reference to tune clustering
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time "${ANOMALY_DETECTION_SCRIPT_DIR}/tunedLeidenCommunityDetection.py" "${@}" ${verboseMode}
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# Tuned Fast Random Projection and tuned HDBSCAN clustering
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time "${ANOMALY_DETECTION_SCRIPT_DIR}/tunedNodeEmbeddingClustering.py" "${@}" ${verboseMode}
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# Reduce the dimensionality of the node embeddings down to 2D for visualization using UMAP
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time "${ANOMALY_DETECTION_SCRIPT_DIR}/umap2dNodeEmbeddings.py" "${@}" ${verboseMode}
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# Query Results: Output all collected features into a CSV file.
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local nodeLabel
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nodeLabel=$( extractQueryParameter "projection_node_label" "${@}" )
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execute_cypher "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeatures.cypher" "${@}" > "${FULL_REPORT_DIRECTORY}/${nodeLabel}AnomalyDetectionFeatures.csv"
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}
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# Create report directory
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REPORT_NAME="anomaly-detection"
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FULL_REPORT_DIRECTORY="${REPORTS_DIRECTORY}/${REPORT_NAME}"
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mkdir -p "${FULL_REPORT_DIRECTORY}"
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# Query Parameter key pairs for projection and algorithm side
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PROJECTION_NAME="dependencies_projection"
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ALGORITHM_PROJECTION="projection_name"
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PROJECTION_NODE="dependencies_projection_node"
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ALGORITHM_NODE="projection_node_label"
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PROJECTION_WEIGHT="dependencies_projection_weight_property"
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ALGORITHM_WEIGHT="projection_weight_property"
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# Code independent algorithm parameters
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COMMUNITY_PROPERTY="community_property=communityLeidenIdTuned"
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# Query (or recalculate) features.
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#
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# Required Parameters:
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# - projection_name=...
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# Name prefix for the in-memory projection name. Example: "package-anomaly-detection"
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# - projection_node_label=...
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# Label of the nodes that will be used for the projection. Example: "Package"
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# - projection_weight_property=...
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# Name of the node property that contains the dependency weight. Example: "weight"
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anomaly_detection_features() {
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# Query Feature: Determine the Betweenness centrality (with the directed graph projection) if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-Betweenness-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-Betweenness-Write.cypher" "${@}"
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# Query Feature: Determine the local clustering coefficient if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-LocalClusteringCoefficient-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-LocalClusteringCoefficient-Write.cypher" "${@}"
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# Query Feature: Determine the page rank if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-PageRank-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-PageRank-Write.cypher" "${@}"
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# Query Feature: Determine the article rank if not already done
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execute_cypher_queries_until_results "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-ArticleRank-Exists.cypher" \
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"${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeature-ArticleRank-Write.cypher" "${@}"
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}
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# Run the anomaly detection pipeline.
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#
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# Required Parameters:
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# - projection_name=...
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# Name prefix for the in-memory projection name. Example: "package-anomaly-detection"
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# - projection_node_label=...
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# Label of the nodes that will be used for the projection. Example: "Package"
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# - projection_weight_property=...
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# Name of the node property that contains the dependency weight. Example: "weight"
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anomaly_detection_pipeline() {
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time anomaly_detection_features "${@}"
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# Run Python: Get tuned Leiden communities as a reference to tune clustering
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time "${ANOMALY_DETECTION_SCRIPT_DIR}/tunedLeidenCommunityDetection.py" "${@}" ${verboseMode}
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# Run Python: Tuned Fast Random Projection and tuned HDBSCAN clustering
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time "${ANOMALY_DETECTION_SCRIPT_DIR}/tunedNodeEmbeddingClustering.py" "${@}" ${verboseMode}
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# Query Results: Output all collected features into a CSV file.
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local nodeLabel
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nodeLabel=$( extractQueryParameter "projection_node_label" "${@}" )
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execute_cypher "${ANOMALY_DETECTION_FEATURE_CYPHER_DIR}/AnomalyDetectionFeatures.cypher" "${@}" > "${FULL_REPORT_DIRECTORY}/${nodeLabel}AnomalyDetection.csv"
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}
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# -- Java Artifact Node Embeddings -------------------------------
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if createUndirectedDependencyProjection "${PROJECTION_NAME}=artifact-anomaly-detection" "${PROJECTION_NODE}=Artifact" "${PROJECTION_WEIGHT}=weight"; then
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createDirectedDependencyProjection "${PROJECTION_NAME}=artifact-anomaly-detection-directed" "${PROJECTION_NODE}=Artifact" "${PROJECTION_WEIGHT}=weight"
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anomaly_detection_pipeline "${ALGORITHM_PROJECTION}=artifact-anomaly-detection" "${ALGORITHM_NODE}=Artifact" "${ALGORITHM_WEIGHT}=weight" "${COMMUNITY_PROPERTY}"
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fi
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# -- Java Package Node Embeddings --------------------------------
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if createUndirectedDependencyProjection "${PROJECTION_NAME}=package-anomaly-detection" "${PROJECTION_NODE}=Package" "${PROJECTION_WEIGHT}=weight25PercentInterfaces"; then
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createDirectedDependencyProjection "${PROJECTION_NAME}=package-anomaly-detection-directed" "${PROJECTION_NODE}=Package" "${PROJECTION_WEIGHT}=weight25PercentInterfaces"
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anomaly_detection_pipeline "${ALGORITHM_PROJECTION}=package-anomaly-detection" "${ALGORITHM_NODE}=Package" "${ALGORITHM_WEIGHT}=weight25PercentInterfaces" "${COMMUNITY_PROPERTY}"
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fi
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# -- Java Type Node Embeddings -----------------------------------
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if createUndirectedJavaTypeDependencyProjection "${PROJECTION_NAME}=type-anomaly-detection"; then
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createDirectedJavaTypeDependencyProjection "${PROJECTION_NAME}=type-anomaly-detection-directed"
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anomaly_detection_pipeline "${ALGORITHM_PROJECTION}=type-anomaly-detection" "${ALGORITHM_NODE}=Type" "${ALGORITHM_WEIGHT}=weight" "${COMMUNITY_PROPERTY}" "${EMBEDDING_PROPERTY}"
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fi
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# -- Typescript Module Node Embeddings ---------------------------
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if createUndirectedDependencyProjection "${PROJECTION_NAME}=typescript-module-embedding" "${PROJECTION_NODE}=Module" "${PROJECTION_WEIGHT}=lowCouplingElement25PercentWeight"; then
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createDirectedDependencyProjection "${PROJECTION_NAME}=typescript-module-embedding-directed" "${PROJECTION_NODE}=Module" "${PROJECTION_WEIGHT}=lowCouplingElement25PercentWeight"
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anomaly_detection_pipeline "${ALGORITHM_PROJECTION}=typescript-module-embedding" "${ALGORITHM_NODE}=Module" "${ALGORITHM_WEIGHT}=lowCouplingElement25PercentWeight" "${COMMUNITY_PROPERTY}" "${EMBEDDING_PROPERTY}"
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fi
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# ---------------------------------------------------------------
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# Clean-up after report generation. Empty reports will be deleted.
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source "${SCRIPTS_DIR}/cleanupAfterReportGeneration.sh" "${FULL_REPORT_DIRECTORY}"
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echo "anomalyDetectionPipeline: $(date +'%Y-%m-%dT%H:%M:%S%z') Successfully finished."

‎domains/anomaly-detection/features/AnomalyDetectionFeature-ArticleRank-Exists.cypher

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// Return the first node with a centralityArticleRank if it exists
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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AND codeUnit.centralityArticleRank IS NOT NULL
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RETURN codeUnit.name AS shortCodeUnitName
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,elementId(codeUnit) AS nodeElementId
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,codeUnit.centralityArticleRank AS articleRank
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LIMIT 1

‎domains/anomaly-detection/features/AnomalyDetectionFeature-ArticleRank-Write.cypher

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// Calculates and writes the Article Rank centrality score for anomaly detection
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CALL gds.articleRank.write(
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$projection_name + '-directed-cleaned', {
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maxIterations: 50
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,relationshipWeightProperty: $projection_weight_property
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,writeProperty: 'centralityArticleRank'
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})
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YIELD nodePropertiesWritten, ranIterations, didConverge, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis
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RETURN nodePropertiesWritten, ranIterations, didConverge, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis

‎domains/anomaly-detection/features/AnomalyDetectionFeature-Betweenness-Exists.cypher

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// Return the first node with a centralityBetweenness if it exists
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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AND codeUnit.centralityBetweenness IS NOT NULL
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RETURN codeUnit.name AS shortCodeUnitName
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,elementId(codeUnit) AS nodeElementId
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,codeUnit.centralityBetweenness AS pageRank
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LIMIT 1

‎domains/anomaly-detection/features/AnomalyDetectionFeature-Betweenness-Write.cypher

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// Calculates and writes the Betweeness centrality score for anomaly detection
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CALL gds.betweenness.write(
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$projection_name + '-directed-cleaned', {
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relationshipWeightProperty: $projection_weight_property
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,writeProperty: 'centralityBetweenness'
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})
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YIELD nodePropertiesWritten, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis
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RETURN nodePropertiesWritten, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis

‎domains/anomaly-detection/features/AnomalyDetectionFeature-LocalClusteringCoefficient-Exists.cypher

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// Return the first node with a clusteringCoefficient if it exists
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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AND codeUnit.communityLocalClusteringCoefficient IS NOT NULL
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RETURN codeUnit.name AS shortCodeUnitName
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,elementId(codeUnit) AS nodeElementId
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,codeUnit.communityLocalClusteringCoefficient AS clusteringCoefficient
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LIMIT 1

‎domains/anomaly-detection/features/AnomalyDetectionFeature-LocalClusteringCoefficient-Write.cypher

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// Calculates and writes the local clustering coefficient for anomaly detection
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CALL gds.localClusteringCoefficient.write(
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$projection_name + '-cleaned', {
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writeProperty: 'communityLocalClusteringCoefficient'
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})
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YIELD averageClusteringCoefficient, nodeCount, nodePropertiesWritten, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis
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RETURN averageClusteringCoefficient, nodeCount, nodePropertiesWritten, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis

‎domains/anomaly-detection/features/AnomalyDetectionFeature-PageRank-Exists.cypher

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// Return the first node with a centralityPageRank if it exists
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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AND codeUnit.centralityPageRank IS NOT NULL
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RETURN codeUnit.name AS shortCodeUnitName
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,elementId(codeUnit) AS nodeElementId
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,codeUnit.centralityPageRank AS pageRank
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LIMIT 1

‎domains/anomaly-detection/features/AnomalyDetectionFeature-PageRank-Write.cypher

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// Calculates and writes the Article Rank centrality score for anomaly detection
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CALL gds.pageRank.write(
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$projection_name + '-directed-cleaned', {
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maxIterations: 50
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,relationshipWeightProperty: $projection_weight_property
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,writeProperty: 'centralityPageRank'
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})
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YIELD nodePropertiesWritten, ranIterations, didConverge, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis
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RETURN nodePropertiesWritten, ranIterations, didConverge, preProcessingMillis, computeMillis, postProcessingMillis, writeMillis

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