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Add anomaly detection Markdown summary report
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‎domains/anomaly-detection/anomalyDetectionCsv.sh‎

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@@ -70,6 +70,8 @@ anomaly_detection_features() {
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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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# - projection_language=...
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# Name of the associated programming language. Default: "Java". Example: "Typescript"
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anomaly_detection_queries() {
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local nodeLabel
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nodeLabel=$( extractQueryParameter "projection_node_label" "${@}" )
@@ -99,6 +101,8 @@ anomaly_detection_queries() {
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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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# - projection_language=...
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# Name of the associated programming language. Examples: "Java", "Typescript"
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anomaly_detection_labels() {
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local nodeLabel
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nodeLabel=$( extractQueryParameter "projection_node_label" "${@}" )
@@ -129,6 +133,8 @@ anomaly_detection_labels() {
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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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# - projection_language=...
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# Name of the associated programming language. Examples: "Java", "Typescript"
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anomaly_detection_csv_reports() {
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time anomaly_detection_features "${@}"
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time anomaly_detection_queries "${@}"

‎domains/anomaly-detection/summary/AnomaliesDeepDiveArchetypes.cypher‎

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// Anomaly Detection Summary: Summarizes all labelled archetypes by their anomaly score including examples. Requires all other labels/*.cypher queries to run first. Variables: projection_language, projection_node_label
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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UNWIND keys(codeUnit) AS codeUnitProperty
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WITH *
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WHERE codeUnitProperty STARTS WITH 'anomaly'
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AND codeUnitProperty ENDS WITH 'Rank'
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WITH *
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,coalesce(codeUnit.fqn, codeUnit.globalFqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
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,split(split(codeUnitProperty, 'anomaly')[1], 'Rank')[0] AS archetype
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,codeUnit[codeUnitProperty] AS archetypeRank
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,codeUnit.anomalyScore AS anomalyScore
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WITH *, collect(archetype)[0] AS archetype
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ORDER BY codeUnit.anomalyScore DESC, archetypeRank ASC, codeUnitName ASC, archetype ASC
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WITH archetype
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,anomalyScore
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,CASE WHEN codeUnit.anomalyScore <= 0 THEN 'Typical'
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WHEN codeUnit.anomalyTopFeature1 IS NULL THEN 'Undetermined'
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ELSE 'Anomalous' END AS modelStatus
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,codeUnitName
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RETURN archetype AS `Archetype`
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,count(DISTINCT codeUnitName) AS `Count`
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,round(max(anomalyScore), 4, 'HALF_UP') AS `Max. Score`
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,modelStatus AS `Model Status`
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,apoc.text.join(collect(DISTINCT codeUnitName)[0..3], ', ') AS `Examples`
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ORDER BY modelStatus, archetype, `Max. Score` DESC

‎domains/anomaly-detection/summary/AnomaliesDeepDiveOverview.cypher‎

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// Anomaly Detection DeepDive: Overview of analyzed code units and the number of anomalies detected. Requires all other labels/*.cypher queries to run first. Variables: projection_language, projection_node_label
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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AND (codeUnit.incomingDependencies IS NOT NULL
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OR codeUnit.outgoingDependencies IS NOT NULL)
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WITH sum(codeUnit.anomalyLabel) AS anomalyCount
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,sum(sign(codeUnit.anomalyAuthorityRank)) AS authorityCount
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,sum(sign(codeUnit.anomalyBottleneckRank)) AS bottleNeckCount
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,sum(sign(codeUnit.anomalyBridgeRank)) AS bridgeCount
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,sum(sign(codeUnit.anomalyHubRank)) AS hubCount
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,sum(sign(codeUnit.anomalyOutlierRank)) AS outlierCount
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//,collect(codeUnit.name)[0..4] AS exampleNames
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RETURN anomalyCount AS `Anomalies`
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,authorityCount AS `Authorities`
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,bottleNeckCount AS `Bottlenecks`
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,bridgeCount AS `Bridges`
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,hubCount AS `Hubs`
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,outlierCount AS `Outliers`
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//,exampleNames

‎domains/anomaly-detection/summary/AnomaliesInTotal.cypher‎

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// Anomaly Detection Summary: Overview of all analyzed code units in total. Requires all other labels/*.cypher queries to run first. Variables: projection_language, projection_node_label
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MATCH (codeUnit)
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WHERE (codeUnit.incomingDependencies IS NOT NULL
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OR codeUnit.outgoingDependencies IS NOT NULL)
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WITH count(DISTINCT codeUnit) AS codeUnitCount
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,sum(codeUnit.anomalyLabel) AS anomalyCount
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,sum(sign(codeUnit.anomalyAuthorityRank)) AS authorityCount
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,sum(sign(codeUnit.anomalyBottleneckRank)) AS bottleNeckCount
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,sum(sign(codeUnit.anomalyBridgeRank)) AS bridgeCount
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,sum(sign(codeUnit.anomalyHubRank)) AS hubCount
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,sum(sign(codeUnit.anomalyOutlierRank)) AS outlierCount
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//,collect(codeUnit.name)[0..4] AS exampleNames
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RETURN codeUnitCount AS `Analyzed Units`
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,anomalyCount AS `Anomalies`
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,authorityCount AS `Authorities`
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,bottleNeckCount AS `Bottlenecks`
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,bridgeCount AS `Bridges`
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,hubCount AS `Hubs`
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,outlierCount AS `Outliers`
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//,exampleNames
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ORDER BY anomalyCount DESC, codeUnitCount DESC

‎domains/anomaly-detection/summary/AnomaliesPerAbstractionLayer.cypher‎

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// Anomaly Detection Summary: Overview of analyzed code units and the number of anomalies detected. Requires all other labels/*.cypher queries to run first. Variables: projection_language, projection_node_label
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MATCH (codeUnit)
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WHERE (codeUnit.incomingDependencies IS NOT NULL
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OR codeUnit.outgoingDependencies IS NOT NULL)
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UNWIND labels(codeUnit) AS codeUnitLabel
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WITH *
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WHERE NOT codeUnitLabel STARTS WITH 'Mark4'
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AND NOT codeUnitLabel IN ['File', 'Directory', 'ByteCode', 'GenericDeclaration']
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WITH collect(codeUnitLabel) AS codeUnitLabels
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,codeUnit
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WITH apoc.text.join(codeUnitLabels, ',') AS codeUnitLabels
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,count(DISTINCT codeUnit) AS codeUnitCount
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,sum(codeUnit.anomalyLabel) AS anomalyCount
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,sum(sign(codeUnit.anomalyAuthorityRank)) AS authorityCount
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,sum(sign(codeUnit.anomalyBottleneckRank)) AS bottleNeckCount
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,sum(sign(codeUnit.anomalyBridgeRank)) AS bridgeCount
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,sum(sign(codeUnit.anomalyHubRank)) AS hubCount
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,sum(sign(codeUnit.anomalyOutlierRank)) AS outlierCount
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//,collect(codeUnit.name)[0..4] AS exampleNames
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RETURN codeUnitLabels AS `Abstraction Level`
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,codeUnitCount AS `Units`
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,anomalyCount AS `Anomalies`
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,authorityCount AS `Authorities`
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,bottleNeckCount AS `Bottlenecks`
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,bridgeCount AS `Bridges`
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,hubCount AS `Hubs`
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,outlierCount AS `Outliers`
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//,exampleNames
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ORDER BY anomalyCount DESC, codeUnitCount DESC

‎domains/anomaly-detection/summary/AnomalyDeepDiveTopAnomalies.cypher‎

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// Anomaly Detection Summary: Lists top anomalies (at most 20), the top 3 features that contributed to the decision and the archetype(s) classification (if available) they are assigned to. Requires all other labels/*.cypher queries to run first. Variables: projection_language, projection_node_label
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MATCH (codeUnit)
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WHERE $projection_node_label IN labels(codeUnit)
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AND codeUnit.anomalyScore > 0
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ORDER BY codeUnit.anomalyScore DESC
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UNWIND keys(codeUnit) AS codeUnitProperty
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WITH codeUnit
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,CASE WHEN codeUnitProperty STARTS WITH 'anomaly'
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AND codeUnitProperty ENDS WITH 'Rank'
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THEN split(split(codeUnitProperty, 'anomaly')[1], 'Rank')[0]
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END AS archetype
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,CASE WHEN codeUnitProperty STARTS WITH 'anomaly'
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AND codeUnitProperty ENDS WITH 'Rank'
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THEN codeUnit[codeUnitProperty]
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END AS archetypeRank
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ORDER BY codeUnit.anomalyScore DESC, archetypeRank ASC
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WITH codeUnit
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,coalesce(codeUnit.fqn, codeUnit.globalFqn, codeUnit.fileName, codeUnit.signature, codeUnit.name) AS codeUnitName
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,apoc.text.join(collect(DISTINCT archetype), ', ') AS archetypes
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OPTIONAL MATCH (artifact:Java:Artifact)-[:CONTAINS]->(codeUnit)
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WITH *, artifact.name AS artifactName
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OPTIONAL MATCH (projectRoot:Directory)<-[:HAS_ROOT]-(proj:TS:Project)-[:CONTAINS]->(codeUnit)
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WITH *, last(split(projectRoot.absoluteFileName, '/')) AS projectName
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OPTIONAL MATCH (codeDirectory:File:Directory)-[:CONTAINS]->(codeUnit)
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WITH *, split(replace(codeDirectory.fileName, './', ''), '/')[-2] AS directoryName
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WITH *, coalesce(artifactName, projectName, directoryName, "") AS projectName
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RETURN codeUnitName AS `Name`
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,projectName AS `Contained in`
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,round(codeUnit.anomalyScore, 4, 'HALF_UP') AS `Anomaly Score`
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,collect(archetypes)[0] AS `Archetypes`
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,nullif(codeUnit.anomalyTopFeature1, "") AS `Top Feature 1`
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,nullif(round(codeUnit.anomalyTopFeatureSHAPValue1, 4, 'HALF_UP'), 0.0) AS `Top Feature 1 SHAP`
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,nullif(codeUnit.anomalyTopFeature2, "") AS `Top Feature 2`
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,nullif(round(codeUnit.anomalyTopFeatureSHAPValue2, 4, 'HALF_UP'), 0.0) AS `Top Feature 2 SHAP`
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,nullif(codeUnit.anomalyTopFeature3, "") AS `Top Feature 3`
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,nullif(round(codeUnit.anomalyTopFeatureSHAPValue3, 4, 'HALF_UP'), 0.0) AS `Top Feature 3 SHAP`
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,CASE WHEN codeUnit.anomalyScore <= 0 THEN 'Typical'
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WHEN codeUnit.anomalyTopFeature1 IS NULL THEN 'Undetermined'
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ELSE 'Anomalous' END AS `Model Status`
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LIMIT 20

‎domains/anomaly-detection/summary/anomalyDetectionSummary.sh‎

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#!/usr/bin/env bash
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# Creates a Markdown report that contains all results of all the anomaly detection methods.
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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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# Note that either "anomalyDetectionCsv.sh" or "anomalyDetectionPython.sh" is required to run prior to this script.
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# Requires executeQueryFunctions.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=${REPORTS_DIRECTORY:-"reports"}
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MARKDOWN_INCLUDES_DIRECTORY=${MARKDOWN_INCLUDES_DIRECTORY:-"includes"}
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## Get this "domains/anomaly-detection/summary" directory if not already set
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# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution.
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# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes.
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# This way non-standard tools like readlink aren't needed.
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ANOMALY_DETECTION_SUMMARY_DIR=${ANOMALY_DETECTION_SUMMARY_DIR:-$(CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P)}
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#echo "anomalyDetectionSummary: ANOMALY_DETECTION_SUMMARY_DIR=${ANOMALY_DETECTION_SUMMARY_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_SUMMARY_DIR}/../../../scripts"} # Repository directory containing the shell scripts
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MARKDOWN_INCLUDES_DIRECTORY="includes"
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MARKDOWN_SCRIPTS_DIR=${MARKDOWN_SCRIPTS_DIR:-"${SCRIPTS_DIR}/markdown"}
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#echo "anomalyDetectionSummary: MARKDOWN_SCRIPTS_DIR=${MARKDOWN_SCRIPTS_DIR}" >&2
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# Define functions to execute a cypher query from within a given file (first and only argument) like "execute_cypher" and "execute_cypher_summarized"
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source "${SCRIPTS_DIR}/executeQueryFunctions.sh"
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# Appends a Markdown table to an existing file and
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# removes redundant header + separator rows.
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#
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# Usage:
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# cat newTable.md | append_table myMarkdownFile.md
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#
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# append_table myMarkdownFile.md <<'EOF'
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# | Name | Score | Archetype |
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# | --- | --- | --- |
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# | Bar | 0.9 | Something |
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# EOF
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#
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# Behavior:
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# - Keeps the first header row and its following separator row.
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# - Removes all subsequent duplicate header + separator pairs.
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# - Leaves all data rows untouched.
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append_to_markdown_table() {
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local file="$1"
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# Append stdin to the target file
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cat >> "${file}"
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# Clean up duplicate headers (header row + --- row)
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awk '!seen[$0]++ || NR <= 2' "${file}" > "${file}.tmp" && mv "${file}.tmp" "${file}"
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}
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# Run the anomaly detection main report generation.
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anomaly_detection_report_first_section() {
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local report_markdown_includes_directory="${FULL_REPORT_DIRECTORY}/${MARKDOWN_INCLUDES_DIRECTORY}"
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mkdir -p "${report_markdown_includes_directory}"
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execute_cypher "${ANOMALY_DETECTION_SUMMARY_DIR}/AnomaliesPerAbstractionLayer.cypher" --output-markdown-table > "${report_markdown_includes_directory}/AnomaliesPerAbstractionLayer.md"
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execute_cypher "${ANOMALY_DETECTION_SUMMARY_DIR}/AnomaliesInTotal.cypher" --output-markdown-table > "${report_markdown_includes_directory}/AnomaliesInTotal.md"
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}
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# Aggregates all results in a Markdown report.
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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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# - projection_language=...
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# Name of the associated programming language. Examples: "Java", "Typescript"
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anomaly_detection_deep_dive_report() {
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local nodeLabel
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nodeLabel=$( extractQueryParameter "projection_node_label" "${@}" )
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local language
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language=$( extractQueryParameter "projection_language" "${@}" )
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local report_number
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report_number=$( extractQueryParameter "report_number" "${@}" )
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echo "anomalyDetectionSummary: $(date +'%Y-%m-%dT%H:%M:%S%z') Creating ${language} ${nodeLabel} anomaly summary Markdown report..."
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detail_report_directory_name="${language}_${nodeLabel}"
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detail_report_directory="${FULL_REPORT_DIRECTORY}/${detail_report_directory_name}"
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detail_report_include_directory="${detail_report_directory}/${MARKDOWN_INCLUDES_DIRECTORY}"
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mkdir -p "${detail_report_include_directory}"
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# Collect dynamic Markdown includes
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execute_cypher "${ANOMALY_DETECTION_SUMMARY_DIR}/AnomaliesDeepDiveOverview.cypher" "${@}" --output-markdown-table > "${detail_report_include_directory}/DeepDiveOverview.md"
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execute_cypher "${ANOMALY_DETECTION_SUMMARY_DIR}/AnomaliesDeepDiveArchetypes.cypher" "${@}" --output-markdown-table > "${detail_report_include_directory}/DeepDiveArchetypes.md"
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execute_cypher "${ANOMALY_DETECTION_SUMMARY_DIR}/AnomalyDeepDiveTopAnomalies.cypher" "${@}" --output-markdown-table > "${detail_report_include_directory}/DeepDiveTopAnomalies.md"
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# Remove empty Markdown includes
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source "${SCRIPTS_DIR}/cleanupAfterReportGeneration.sh" "${detail_report_include_directory}"
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# Collect static Markdown includes (after cleanup to not remove one-liner)
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echo "### 2.${report_number} ${language} ${nodeLabel}" > "${detail_report_include_directory}/DeepDiveSectionTitle.md"
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echo "" > "${detail_report_include_directory}/empty.md"
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cp -f "${ANOMALY_DETECTION_SUMMARY_DIR}/report_no_data_info.template.md" "${detail_report_include_directory}/report_no_data_info.template.md"
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cp -f "${detail_report_directory}/Top_anomaly_features.md" "${detail_report_include_directory}" || true
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if [ -f "${detail_report_directory}/Anomaly_feature_importance_explained.svg" ] ; then
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cp -f "${ANOMALY_DETECTION_SUMMARY_DIR}/report_deep_dive_anomalies_explained.template.md" "${detail_report_include_directory}/report_deep_dive_anomalies_explained.md"
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fi
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# Use Markdown template to assemble the final deep dive section of the Markdown report and replace variables
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cp -f "${ANOMALY_DETECTION_SUMMARY_DIR}/report_deep_dive.template.md" "${detail_report_directory}/report_deep_dive.template.md"
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cat "${detail_report_directory}/report_deep_dive.template.md" | "${MARKDOWN_SCRIPTS_DIR}/embedMarkdownIncludes.sh" "${detail_report_include_directory}" > "${detail_report_directory}/report_deep_dive_with_vars.md"
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sed "s/{{deep_dive_directory}}/${detail_report_directory_name}/g" "${detail_report_directory}/report_deep_dive_with_vars.md" > "${detail_report_directory}/report_deep_dive_${report_number}.md"
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rm -rf "${detail_report_directory}/report_deep_dive_with_vars.md"
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rm -rf "${detail_report_directory}/report_deep_dive.template.md"
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rm -rf "${detail_report_include_directory}"
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# Clean-up after report generation. Empty reports will be deleted.
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source "${SCRIPTS_DIR}/cleanupAfterReportGeneration.sh" "${detail_report_directory}"
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}
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# Run the anomaly detection report generation.
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#
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# Required Parameters:
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# - projection_node_label=...
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# Label of the nodes that will be used for the projection. Example: "Package"
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# - projection_language=...
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# Name of the associated programming language. Examples: "Java", "Typescript"
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anomaly_detection_report() {
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time anomaly_detection_deep_dive_report "${@}"
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}
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# Finalize the anomaly detection report by taking the main template, applying includes and appending all deep dive reports
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anomaly_detection_finalize_report() {
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echo "anomalyDetectionSummary: $(date +'%Y-%m-%dT%H:%M:%S%z') Finalizing ${language} ${nodeLabel} anomaly detection Markdown report..."
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report_include_directory="${FULL_REPORT_DIRECTORY}/${MARKDOWN_INCLUDES_DIRECTORY}"
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mkdir -p "${report_include_directory}"
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# Concatenate all deep dive reports as Markdown include
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rm -rf "${report_include_directory}/AnomalyDetectionDeepDive.md"
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for markdown_file in $(find . -type f -name 'report_deep_dive_*.md' | sort); do
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cat "${markdown_file}" >> "${report_include_directory}/AnomalyDetectionDeepDive.md"
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echo "" >> "${report_include_directory}/AnomalyDetectionDeepDive.md"
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rm -rf "${markdown_file}"
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done
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# Remove empty Markdown includes
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source "${SCRIPTS_DIR}/cleanupAfterReportGeneration.sh" "${report_include_directory}"
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cp -f "${ANOMALY_DETECTION_SUMMARY_DIR}/report.template.md" "${FULL_REPORT_DIRECTORY}/report.template.md"
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cat "${FULL_REPORT_DIRECTORY}/report.template.md" | "${MARKDOWN_SCRIPTS_DIR}/embedMarkdownIncludes.sh" "${report_include_directory}" > "${FULL_REPORT_DIRECTORY}/anomaly_detection_report.md"
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rm -rf "${FULL_REPORT_DIRECTORY}/report.template.md"
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rm -rf "${report_include_directory}"
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}
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# Create report directory
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REPORT_NAME="anomaly-detection"
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FULL_REPORT_DIRECTORY="${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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ALGORITHM_NODE="projection_node_label"
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ALGORITHM_LANGUAGE="projection_language"
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REPORT_NUMBER="report_number"
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# -- Overview Report for all code type -------------------------------
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anomaly_detection_report_first_section
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# -- Detail Reports for each code type -------------------------------
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anomaly_detection_report "${REPORT_NUMBER}=1" "${ALGORITHM_NODE}=Artifact" "${ALGORITHM_LANGUAGE}=Java"
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anomaly_detection_report "${REPORT_NUMBER}=2" "${ALGORITHM_NODE}=Package" "${ALGORITHM_LANGUAGE}=Java"
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anomaly_detection_report "${REPORT_NUMBER}=3" "${ALGORITHM_NODE}=Type" "${ALGORITHM_LANGUAGE}=Java"
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anomaly_detection_report "${REPORT_NUMBER}=4" "${ALGORITHM_NODE}=Module" "${ALGORITHM_LANGUAGE}=Typescript"
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# ---------------------------------------------------------------
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anomaly_detection_finalize_report
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echo "anomalyDetectionSummary: $(date +'%Y-%m-%dT%H:%M:%S%z') Successfully finished."

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