✨ Can Process DiffGraphs (#68)

* Vertex mapper can handle the case where ID isn't given

* Initial work on DiffGraph conversion

* Created initial diff graph processor

* Adjusted delete vertex for builders but ran into circular dependency

* Adjusted tests for new deleteVertex signature

* Added basic create and delete node

* Have tested DiffGraph operations

* Fixed ID bug in TigerGraphDriver.kt

* Documented new features and bumped version

* Added `updateVertexProperty` to IDriver and DiffGraphUtil.kt

CHANGELOG.md

@@ -7,12 +7,21 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 ## [Unreleased] - yyyy-mm-dd
 
 ### Added
-- `deleteEdge` to `IDriver`
 
 ### Changed
 
 ### Fixed
 
+## [0.1.8] - 2021-02-15
+
+### Added
+- `deleteEdge` to `IDriver`
+- `updateVertexProperty` to `IDriver`
+- `DiffGraphUtil::processDiffGraph` to accept `DiffGraph`s and apply changes to a given `IDriver`
+
+### Changed
+- Modified `deleteVertex` signature to take ID and optional label
+
 ## [0.1.7] - 2021-02-11
 
 ### Changed

cpgconv/build.gradle

@@ -14,7 +14,6 @@ dependencies {
 }
 
 group = "io.github.plume-oss"
-version = "0.0.3"
 
 sourceSets {
     main.java.srcDirs = []

plume/build.gradle

@@ -172,7 +172,7 @@ dockerCompose {
 def artifactDesc = "Plume is a code property graph analysis library with options to extract the CPG from" +
         " Java bytecode and store the result in various graph databases."
 def repoUrl = "https://github.com/plume-oss/plume.git"
-def artifactVersion = "0.1.7"
+def artifactVersion = "0.1.8"
 def website = "https://plume-oss.github.io/plume-docs/"
 
 group = "io.github.plume-oss"

plume/src/main/kotlin/io/github/plume/oss/Extractor.kt

@@ -464,7 +464,7 @@ class Extractor(val driver: IDriver) {
                     }
                 }
                 logger.debug("Deleting $fileV")
-                driver.deleteVertex(mapToVertex(fileV) as NewFileBuilder)
+                driver.deleteVertex(fileV.id(), fileV.label())
             } else {
                 logger.debug("Existing class was found and file hashes match, no need to rebuild.")
             }

plume/src/main/kotlin/io/github/plume/oss/domain/mappers/VertexMapper.kt

@@ -6,6 +6,7 @@ import overflowdb.Node
 import scala.Option
 import scala.collection.immutable.`$colon$colon`
 import scala.collection.immutable.`Nil$`
+import scala.jdk.CollectionConverters
 import java.util.*
 import kotlin.collections.HashMap
 
@@ -26,6 +27,17 @@ object VertexMapper {
         return mapToVertex(map)
     }
 
+    /**
+     * Converts a [NewNode] to its respective [NewNodeBuilder] object.
+     *
+     * @param v The [NewNode] to deserialize.
+     * @return a [NewNodeBuilder] represented by the information in the givennode.
+     */
+    fun mapToVertex(v: NewNode): NewNodeBuilder {
+        val map = CollectionConverters.MapHasAsJava(v.properties()).asJava() + mapOf<String, Any>("label" to v.label())
+        return mapToVertex(map)
+    }
+
     /**
      * Converts a [Map] containing vertex properties to its respective [NewNodeBuilder] object.
      *
@@ -34,30 +46,26 @@ object VertexMapper {
      */
     fun mapToVertex(mapToConvert: Map<String, Any>): NewNodeBuilder {
         val map = HashMap<String, Any>()
+        // Only ID should be left as Long
         mapToConvert.keys.forEach {
             when (val value = mapToConvert[it]) {
-                is Long -> map[it] = value.toInt()
+                is Long -> if (it != "id") map[it] = value.toInt() else map[it] = value as Any
                 else -> map[it] = value as Any
             }
         }
-        map.computeIfPresent("id") { _, v -> v.toString().toLong() }
         return when (map["label"] as String) {
             ArrayInitializer.Label() -> NewArrayInitializerBuilder()
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             Binding.Label() -> NewBindingBuilder()
                 .name(map["NAME"] as String)
                 .signature(map["SIGNATURE"] as String)
-                .id(map["id"] as Long)
             MetaData.Label() -> NewMetaDataBuilder()
                 .language(map["LANGUAGE"] as String)
                 .version(map["VERSION"] as String)
-                .id(map["id"] as Long)
             File.Label() -> NewFileBuilder()
                 .name(map["NAME"] as String)
                 .hash(Option.apply(map["HASH"] as String))
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             Method.Label() -> NewMethodBuilder()
                 .astParentFullName(map["AST_PARENT_FULL_NAME"] as String)
                 .astParentType(map["AST_PARENT_TYPE"] as String)
@@ -68,7 +76,6 @@ object VertexMapper {
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             MethodParameterIn.Label() -> NewMethodParameterInBuilder()
                 .code(map["CODE"] as String)
                 .name(map["NAME"] as String)
@@ -77,59 +84,49 @@ object VertexMapper {
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             MethodReturn.Label() -> NewMethodReturnBuilder()
                 .code(map["CODE"] as String)
                 .evaluationStrategy(map["EVALUATION_STRATEGY"] as String)
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             Modifier.Label() -> NewModifierBuilder()
                 .modifierType(map["MODIFIER_TYPE"] as String)
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             Type.Label() -> NewTypeBuilder()
                 .name(map["NAME"] as String)
                 .fullName(map["FULL_NAME"] as String)
                 .typeDeclFullName(map["TYPE_DECL_FULL_NAME"] as String)
-                .id(map["id"] as Long)
             TypeDecl.Label() -> NewTypeDeclBuilder()
                 .astParentFullName(map["AST_PARENT_FULL_NAME"] as String)
                 .astParentType(map["AST_PARENT_TYPE"] as String)
                 .name(map["NAME"] as String)
                 .fullName(map["FULL_NAME"] as String)
                 .order(map["ORDER"] as Int)
                 .isExternal(map["IS_EXTERNAL"] as Boolean)
-                .id(map["id"] as Long)
             TypeParameter.Label() -> NewTypeParameterBuilder()
                 .name(map["NAME"] as String)
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             TypeArgument.Label() -> NewTypeArgumentBuilder()
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             Member.Label() -> NewMemberBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .code(map["CODE"] as String)
                 .name(map["NAME"] as String)
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             NamespaceBlock.Label() -> NewNamespaceBlockBuilder()
                 .fullName(map["FULL_NAME"] as String)
                 .filename(map["FILENAME"] as String)
                 .name(map["NAME"] as String)
                 .order(map["ORDER"] as Int)
-                .id(map["id"] as Long)
             Literal.Label() -> NewLiteralBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             Call.Label() -> NewCallBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .code(map["CODE"] as String)
@@ -148,15 +145,13 @@ object VertexMapper {
                         else -> createScalaList("")
                     }
                 )
-                .id(map["id"] as Long)
             Local.Label() -> NewLocalBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .code(map["CODE"] as String)
                 .name(map["NAME"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
-                .id(map["id"] as Long)
             Identifier.Label() -> NewIdentifierBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .code(map["CODE"] as String)
@@ -165,30 +160,26 @@ object VertexMapper {
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             FieldIdentifier.Label() -> NewFieldIdentifierBuilder()
                 .canonicalName(map["CANONICAL_NAME"] as String)
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             Return.Label() -> NewReturnBuilder()
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             Block.Label() -> NewBlockBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             MethodRef.Label() -> NewMethodRefBuilder()
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
@@ -197,7 +188,6 @@ object VertexMapper {
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             TypeRef.Label() -> NewTypeRefBuilder()
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .dynamicTypeHintFullName(
@@ -212,31 +202,27 @@ object VertexMapper {
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             JumpTarget.Label() -> NewJumpTargetBuilder()
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
                 .name(map["NAME"] as String)
-                .id(map["id"] as Long)
             ControlStructure.Label() -> NewControlStructureBuilder()
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
-                .id(map["id"] as Long)
             else -> NewUnknownBuilder()
                 .code(map["CODE"] as String)
                 .order(map["ORDER"] as Int)
                 .argumentIndex(map["ARGUMENT_INDEX"] as Int)
                 .typeFullName(map["TYPE_FULL_NAME"] as String)
                 .lineNumber(Option.apply(map["LINE_NUMBER"] as Int))
                 .columnNumber(Option.apply(map["COLUMN_NUMBER"] as Int))
-                .id(map["id"] as Long)
-        }
+        }.apply { if (map.containsKey("id")) this.id(map["id"] as Long) }
     }
 
     /**

plume/src/main/kotlin/io/github/plume/oss/drivers/GremlinDriver.kt

@@ -10,10 +10,7 @@ import org.apache.logging.log4j.LogManager
 import org.apache.tinkerpop.gremlin.process.traversal.dsl.graph.GraphTraversal
 import org.apache.tinkerpop.gremlin.process.traversal.dsl.graph.GraphTraversalSource
 import org.apache.tinkerpop.gremlin.process.traversal.step.util.WithOptions
-import org.apache.tinkerpop.gremlin.structure.Edge
-import org.apache.tinkerpop.gremlin.structure.Graph
-import org.apache.tinkerpop.gremlin.structure.T
-import org.apache.tinkerpop.gremlin.structure.Vertex
+import org.apache.tinkerpop.gremlin.structure.*
 import org.apache.tinkerpop.gremlin.tinkergraph.structure.TinkerGraph
 import overflowdb.Config
 import scala.jdk.CollectionConverters
@@ -202,9 +199,9 @@ abstract class GremlinDriver : IDriver {
         return gremlinToPlume(neighbourSubgraph.traversal())
     }
 
-    override fun deleteVertex(v: NewNodeBuilder) {
-        if (!exists(v)) return
-        findVertexTraversal(v).drop().iterate()
+    override fun deleteVertex(id: Long, label: String?) {
+        if (!g.V(id).hasNext()) return
+        g.V(id).drop().iterate()
     }
 
     override fun deleteEdge(src: NewNodeBuilder, tgt: NewNodeBuilder, edge: String) {
@@ -226,6 +223,11 @@ abstract class GremlinDriver : IDriver {
         }
     }
 
+    override fun updateVertexProperty(id: Long, label: String?, key: String, value: Any) {
+        if (!g.V(id).hasNext()) return
+        g.V(id).property(key, value).iterate()
+    }
+
     /**
      * Converts a [GraphTraversalSource] instance to a [overflowdb.Graph] instance.
      *

plume/src/main/kotlin/io/github/plume/oss/drivers/IDriver.kt

@@ -91,9 +91,10 @@ interface IDriver : AutoCloseable {
     /**
      * Given a vertex, will remove it from the graph if present.
      *
-     * @param v The vertex to remove.
+     * @param id The id to remove.
+     * @param label The label, if known.
      */
-    fun deleteVertex(v: NewNodeBuilder)
+    fun deleteVertex(id: Long, label: String? = null)
 
     /**
      * Given the full signature of a method, removes the method and its body from the graph.
@@ -112,4 +113,14 @@ interface IDriver : AutoCloseable {
      */
     fun deleteEdge(src: NewNodeBuilder, tgt: NewNodeBuilder, edge: String)
 
+    /**
+     * Updates a vertex's property if the node exists.
+     *
+     * @param id The ID of the vertex to update.
+     * @param label The label of the node, if known.
+     * @param key The key of the property to update.
+     * @param value The updated value.
+     */
+    fun updateVertexProperty(id: Long, label: String?, key: String, value: Any)
+
 }

plume/src/main/kotlin/io/github/plume/oss/drivers/Neo4jDriver.kt

@@ -153,14 +153,15 @@ class Neo4jDriver : IDriver {
         }
     }
 
-    override fun exists(v: NewNodeBuilder): Boolean {
-        val node = v.build()
+    override fun exists(v: NewNodeBuilder): Boolean = checkVertexExist(v.id(), v.build().label())
+
+    private fun checkVertexExist(id: Long, label: String? = null): Boolean {
         driver.session().use { session ->
             return session.writeTransaction { tx ->
                 val result = tx.run(
                     """
-                    MATCH (n:${node.label()})
-                    WHERE id(n) = ${v.id()}
+                    MATCH (n${if (label != null) ":$label" else ""})
+                    WHERE id(n) = $id
                     RETURN n
                     """.trimIndent()
                 )
@@ -374,14 +375,14 @@ class Neo4jDriver : IDriver {
             }
     }
 
-    override fun deleteVertex(v: NewNodeBuilder) {
-        if (!exists(v)) return
+    override fun deleteVertex(id: Long, label: String?) {
+        if (!checkVertexExist(id, label)) return
         driver.session().use { session ->
             session.writeTransaction { tx ->
                 tx.run(
                     """
-                    MATCH (n)
-                    WHERE ID(n) = ${v.id()}
+                    MATCH (n${if (label != null) ":$label" else ""})
+                    WHERE ID(n) = $id
                     DETACH DELETE n
                     """.trimIndent()
                 )
@@ -421,6 +422,21 @@ class Neo4jDriver : IDriver {
         }
     }
 
+    override fun updateVertexProperty(id: Long, label: String?, key: String, value: Any) {
+        if (!checkVertexExist(id, label)) return
+        driver.session().use { session ->
+            session.writeTransaction { tx ->
+                tx.run(
+                    """
+                    MATCH (n${if (label != null) ":$label" else ""})
+                    WHERE ID(n) = $id
+                    SET n.$key = ${if (value is String) "\"$value\"" else value}
+                    """.trimIndent()
+                )
+            }
+        }
+    }
+
     private fun newOverflowGraph(): Graph = Graph.open(
         Config.withDefaults(),
         NodeFactories.allAsJava(),