Sync with upstream v1.7.7

.gitignore

@@ -4,6 +4,7 @@
 target/
 codepropertygraph/project/
 /codepropertygraph/src/main/resources/cpg.json
+/codepropertygraph/src/test/resources/cpg.odb.fg
 private-key.pem
 travis_wait_*
 **/*.pyc
@@ -14,7 +15,7 @@ project/.bloop
 .project
 *.class
 /.classpath
-/project/project/
+/project/project/target
 /project/target/
 /target
 /foo.c

build.sbt

@@ -1,14 +1,17 @@
 name := "codepropertygraph"
 
 // parsed by project/Versions.scala, updated by updateDependencies.sh
-val overflowdbVersion = "0.1.4"
-val overflowdbCodegenVersion = "2.110"
+val flatgraphVersion = "0.0.89"
 
 inThisBuild(
   List(
-    organization       := "io.shiftleft",
-    scalaVersion       := "3.4.2",
-    resolvers ++= Seq("Github Package Registry" at "https://maven.pkg.github.com/Privado-Inc/overflowdb", Resolver.mavenLocal, "Sonatype OSS" at "https://oss.sonatype.org/content/repositories/public"),
+    organization := "io.shiftleft",
+    scalaVersion := "3.4.2",
+    resolvers ++= Seq(
+      "Github Package Registry" at "https://maven.pkg.github.com/Privado-Inc/flatgraph",
+      Resolver.mavenLocal,
+      "Sonatype OSS" at "https://oss.sonatype.org/content/repositories/public"
+    ),
     packageDoc / publishArtifact := true,
     packageSrc / publishArtifact := true,
     scmInfo := Some(
@@ -42,7 +45,7 @@ ThisBuild / Test / javaOptions += s"-Duser.dir=${(ThisBuild / baseDirectory).val
 
 ThisBuild / libraryDependencies ++= Seq(
   "org.apache.logging.log4j" % "log4j-slf4j2-impl" % "2.19.0" % Optional,
-  "org.apache.logging.log4j" % "log4j-core"        % "2.19.0" % Optional,
+  "org.apache.logging.log4j" % "log4j-core"        % "2.19.0" % Optional
   // `Optional` means "not transitive", but still included in "stage/lib"
 )
 
@@ -56,7 +59,8 @@ lazy val codepropertygraph = Projects.codepropertygraph
 lazy val schema2json       = Projects.schema2json
 
 ThisBuild / scalacOptions ++= Seq(
-  "-release", "8",
+  "-release",
+  "8",
   "-deprecation",
   "-feature",
   // "-explain",
@@ -67,7 +71,8 @@ ThisBuild / scalacOptions ++= Seq(
 
 ThisBuild / javacOptions ++= Seq(
   "-g", // debug symbols
-  "--release", "8"
+  "--release",
+  "8"
 )
 
 Global / onChangedBuildSource := ReloadOnSourceChanges
@@ -84,4 +89,4 @@ credentials +=
     "maven.pkg.github.com",
     "Privado-Inc",
     sys.env.getOrElse("GITHUB_TOKEN", "N/A")
-  )
+  )

codepropertygraph/build.sbt

@@ -3,8 +3,9 @@ name := "codepropertygraph"
 dependsOn(Projects.protoBindings, Projects.domainClasses)
 
 libraryDependencies ++= Seq(
-  "io.shiftleft"          %% "overflowdb-traversal" % Versions.overflowdb,
-  "io.shiftleft"          %% "overflowdb-formats"   % Versions.overflowdb,
+  "io.joern"              %% "flatgraph-formats"     % Versions.flatgraph,
+  "io.joern"              %% "flatgraph-help"        % Versions.flatgraph,
+  "io.joern"              %% "flatgraph-odb-convert" % Versions.flatgraph,
   "com.github.scopt"      %% "scopt"                % "4.0.1",
   "com.github.pathikrit"  %% "better-files"         % "3.9.2",
   "org.slf4j"              % "slf4j-api"            % "2.0.6",

codepropertygraph/src/main/scala/io/shiftleft/SerializedCpg.scala

@@ -7,6 +7,7 @@ import java.net.{URI, URISyntaxException}
 import java.nio.file.{FileSystem, FileSystems, Files}
 import java.util
 
+@deprecated("New API functions do not use this class anymore")
 class SerializedCpg extends AutoCloseable {
 
   /** We allow creating a dummy serialized CPG that does not do anything.

codepropertygraph/src/main/scala/io/shiftleft/codepropertygraph/Cpg.scala

@@ -1,23 +1,23 @@
 package io.shiftleft.codepropertygraph
 
-import overflowdb.Graph
-import overflowdb.traversal.help.DocSearchPackages
+import flatgraph.Graph
+import flatgraph.help.DocSearchPackages
+import io.shiftleft.codepropertygraph.generated
 
 /** TODO this is now being generated as well - for now we'll just forward calls to `generated.Cpg` next step is to
   * remove this class and move remove the `generated` part from the generated package
   */
 object Cpg {
-  implicit val docSearchPackages: DocSearchPackages =
-    DocSearchPackages("io.shiftleft", "io.joern")
+  val defaultDocSearchPackage: DocSearchPackages = generated.Cpg.defaultDocSearchPackage
 
   /** Syntactic sugar for `new Cpg(graph)`. Usage: `Cpg(graph)` or simply `Cpg` if you have an `implicit Graph` in scope
     */
-  def apply(implicit graph: Graph) = new Cpg(graph)
+  def apply(implicit graph: Graph) = generated.Cpg(graph)
 
   /** Create an empty code property graph
     */
-  def emptyCpg: Cpg =
-    new Cpg(emptyGraph)
+  def emptyCpg: generated.Cpg =
+    generated.Cpg(emptyGraph)
 
   /** Instantiate cpg with storage. If the storage file already exists, it will load (a subset of) the data into memory.
     * Otherwise it will create an empty cpg. In either case, configuring storage means that OverflowDb will be stored to
@@ -26,13 +26,10 @@ object Cpg {
     * @param path
     *   to the storage file, e.g. /home/user1/overflowdb.bin
     */
-  def withStorage(path: String): Cpg =
-    new Cpg(generated.Cpg.withStorage(path).graph)
-
-  def withConfig(config: overflowdb.Config): Cpg =
-    Cpg(generated.Cpg.withConfig(config).graph)
+  def withStorage(path: String, deserializeOnClose: Boolean = true): generated.Cpg =
+    generated.Cpg.withStorage(java.nio.file.Paths.get(path), deserializeOnClose)
 
   def emptyGraph: Graph =
-    generated.Cpg.emptyGraph
+    generated.Cpg.empty.graph
 
 }

codepropertygraph/src/main/scala/io/shiftleft/codepropertygraph/cpgloading/CpgLoader.scala

@@ -1,91 +1,117 @@
 package io.shiftleft.codepropertygraph.cpgloading
 
-import better.files.File
 import io.shiftleft.codepropertygraph.generated.Cpg
-import io.shiftleft.codepropertygraph.generated.PropertyNames
 import org.slf4j.{Logger, LoggerFactory}
 
-import scala.util.Try
+import java.io.FileNotFoundException
+import java.nio.charset.StandardCharsets
+import java.nio.file.{Files, Path, Paths}
+import scala.util.Using
 
 object CpgLoader {
+  private val logger: Logger = LoggerFactory.getLogger(getClass)
 
-  private val logger: Logger = LoggerFactory.getLogger(classOf[CpgLoader])
+  /** Load a Code Property Graph from the given file */
+  def load(filename: String): Cpg =
+    load(Paths.get(filename))
 
-  /** Load a Code Property Graph
-    *
-    * @param filename
-    *   name of file that stores the code property graph
-    * @param config
-    *   loader configuration
+  /** Load a Code Property Graph from the given file - persist in given second file. I.e. the given input file will not
+    * be modified, all changes will be written to the given 'persistTo' file. *
     */
-  def load(filename: String, config: CpgLoaderConfig = CpgLoaderConfig()): Cpg =
-    new CpgLoader().load(filename, config)
+  def load(from: String, persistTo: String): Cpg =
+    load(Paths.get(from), Paths.get(persistTo))
 
-  /** Load Code Property Graph from an overflow DB file
-    *
-    * @param config
-    *   loader config
+  /** Load a Code Property Graph from the given file
     *
-    * This methods loads the CPG from an existing overflow DB file, specified in config.overflowDbConfig. In particular,
-    * this config specifies the filename. For example, to load the database at "foo.db", you can issue the following:
-    *
-    * val odbConfig = Config.withDefaults().withStorageLocation(config.spPath) val config =
-    * CpgLoaderConfig().withOverflowConfig(odbConfig) CpgLoader.loadFromOverflowDb(config)
+    * Notes:
+    *   - detects the format as either flatgraph, overflowdb or proto
+    *   - a flatgraph storage opened straight away
+    *   - OverflowDb and proto formats are first converted to flatgraph, which is written to the `persistTo` file
+    *   - OverflowDb and proto formats are first converted to flatgraph, and therefor we create a new flatgraph storage
+    *     path, which can be obtained via `cpg.graph.storagePathMaybe`
     */
-  def loadFromOverflowDb(config: CpgLoaderConfig = CpgLoaderConfig()): Cpg = {
-    new CpgLoader().loadFromOverflowDb(config)
+  def load(path: Path): Cpg = {
+    val absolutePath = path.toAbsolutePath
+    if (!Files.exists(absolutePath)) {
+      throw new FileNotFoundException(s"given input file $absolutePath does not exist")
+    } else if (isProtoFormat(absolutePath)) {
+      load(path, persistTo = absolutePath.resolveSibling(s"${path.getFileName}.fg"))
+    } else if (isOverflowDbFormat(absolutePath)) {
+      load(absolutePath, persistTo = path.resolveSibling(s"${path.getFileName}.fg"))
+    } else {
+      // assuming it's flatgraph format
+      Cpg.withStorage(absolutePath)
+    }
   }
 
-  /** Create any indexes necessary for quick access.
-    *
-    * @param cpg
-    *   the CPG to create indexes in
-    */
-  def createIndexes(cpg: Cpg): Unit =
-    new CpgLoader().createIndexes(cpg)
-
-  /** Determine whether the CPG is a legacy (proto) CPG
+  /** Load a Code Property Graph from the given file, but persist it in the given second file. I.e. the given input file
+    * will not be modified, all changes will be written to the given 'persistTo' file.
     *
-    * @param filename
-    *   name of the file to probe
+    * Notes:
+    *   - if the given 'persistTo' file already exists, it will be overridden
+    *   - detects the format as either flatgraph, overflowdb or proto
+    *   - a flatgraph storage is copied to the `persistTo` file and then opened straight away
+    *   - OverflowDb and proto formats are first converted to flatgraph, which is written to the `persistTo` file
     */
-  def isLegacyCpg(filename: String): Boolean =
-    isLegacyCpg(File(filename))
-
-  /** Determine whether the CPG is a legacy (proto) CPG
-    *
-    * @param file
-    *   file to probe
-    */
-  def isLegacyCpg(file: File): Boolean = {
-    val bytes = file.bytes
-    Try {
-      bytes.next() == 'P' && bytes.next() == 'K'
-    }.getOrElse(false)
+  def load(from: Path, persistTo: Path): Cpg = {
+    val absolutePath = from.toAbsolutePath
+    if (persistTo != from)
+      Files.deleteIfExists(persistTo)
+
+    if (!Files.exists(absolutePath)) {
+      throw new FileNotFoundException(s"given input file $absolutePath does not exist")
+    } else if (isProtoFormat(absolutePath)) {
+      logger.debug(s"Converting $from from proto cpg into new flatgraph storage: $persistTo")
+      ProtoCpgLoader.loadFromProtoZip(absolutePath.toString, Option(persistTo))
+    } else if (isOverflowDbFormat(absolutePath)) {
+      loadFromOverflowDb(absolutePath, persistTo)
+    } else if (isFlatgraphFormat(absolutePath)) {
+      Files.copy(absolutePath, persistTo)
+      Cpg.withStorage(persistTo)
+    } else {
+      throw new AssertionError(
+        s"unknown file format - we probed the first bytes but it didn't look like one of our known formats (proto.zip, flatgraph, overflowdb)"
+      )
+    }
   }
 
-}
+  /** Determine whether the CPG is a legacy (proto) CPG */
+  def isProtoFormat(path: Path): Boolean =
+    probeFirstBytes(path, "PK")
 
-private class CpgLoader {
+  /** Determine whether the CPG is a proto CPG */
+  def isProtoFormat(filename: String): Boolean =
+    isProtoFormat(Paths.get(filename))
 
-  import CpgLoader.logger
+  def isOverflowDbFormat(path: Path): Boolean =
+    probeFirstBytes(path, "H:2")
 
-  def load(filename: String, config: CpgLoaderConfig = CpgLoaderConfig.withoutOverflow): Cpg = {
-    logger.debug("Loading " + filename)
+  def isFlatgraphFormat(path: Path): Boolean =
+    probeFirstBytes(path, "FLT GRPH") // flatgraph.storage.MagicBytesString
 
-    val cpg =
-      ProtoCpgLoader.loadFromProtoZip(filename, config.overflowDbConfig)
-    if (config.createIndexes) { createIndexes(cpg) }
-    cpg
+  /** Load Code Property Graph from an overflow DB file, by first converting it into a flatgraph binary */
+  def loadFromOverflowDb(path: Path, persistTo: Path): Cpg = {
+    logger.info(s"Converting $path from overflowdb to new flatgraph storage: $persistTo")
+    flatgraph.convert.Convert.convertOdbToFlatgraph(overflowDbFile = path, outputFile = persistTo)
+    Cpg.withStorage(persistTo)
   }
 
-  def loadFromOverflowDb(config: CpgLoaderConfig = CpgLoaderConfig()): Cpg = {
-    val cpg = Cpg.withConfig(config.overflowDbConfig)
-    if (config.createIndexes) { createIndexes(cpg) }
-    cpg
+  /** Determine whether the CPG is a legacy (proto) CPG */
+  @deprecated("use `isProtoCpg` instead")
+  def isLegacyCpg(filename: String): Boolean =
+    isProtoFormat(Paths.get(filename))
+
+  /** Determine whether the CPG is a legacy (proto) CPG */
+  @deprecated("use `isProtoCpg` instead")
+  def isLegacyCpg(path: Path): Boolean =
+    isProtoFormat(path)
+
+  private def probeFirstBytes(path: Path, probeFor: String): Boolean = {
+    Using(Files.newInputStream(path)) { is =>
+      val buffer = new Array[Byte](probeFor.size)
+      is.read(buffer)
+      new String(buffer, StandardCharsets.UTF_8) == probeFor
+    }.getOrElse(false)
   }
 
-  def createIndexes(cpg: Cpg): Unit =
-    cpg.graph.indexManager.createNodePropertyIndex(PropertyNames.FULL_NAME)
-
 }