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package overflowdb.formats.neo4jcsv
import com.github.tototoshi.csv._
import overflowdb.Graph
import overflowdb.formats.Importer
import java.nio.file.Path
import java.util
import scala.util.Using
/** Imports from neo4j csv files see
* https://neo4j.com/docs/operations-manual/current/tools/neo4j-admin/neo4j-admin-import/
*/
object Neo4jCsvImporter extends Importer {
val Neo4jAdminDoc = "https://neo4j.com/docs/operations-manual/current/tools/neo4j-admin/neo4j-admin-import"
override def runImport(graph: Graph, inputFiles: Seq[Path]): Unit = {
var importedNodeCount = 0
var importedEdgeCount = 0
groupInputFiles(inputFiles)
.sortBy(nodeFilesFirst)
.foreach { case HeaderAndDataFile(ParsedHeaderFile(fileType, columnDefs), dataFile) =>
Using.resource(CSVReader.open(dataFile.toFile)) { dataReader =>
dataReader.iterator.zipWithIndex.foreach { case (columnsRaw, idx) =>
assert(
columnsRaw.size == columnDefs.size,
s"datafile ${dataFile.toAbsolutePath} row must have the same column count as the headerfile (${columnDefs.size}) - instead found ${columnsRaw.size} for row=${columnsRaw
.mkString(",")}"
)
val lineNo = idx + 1
fileType match {
case FileType.Nodes =>
parseNodeRowData(columnsRaw, columnDefs, dataFile, lineNo) match {
case ParsedNodeRowData(id, label, properties) =>
val propertiesAsKeyValues =
properties.flatMap(parsedProperty => Seq(parsedProperty.name, parsedProperty.value))
graph.addNode(id, label, propertiesAsKeyValues: _*)
importedNodeCount += 1
}
case FileType.Relationships =>
parseEdgeRowData(columnsRaw, columnDefs, dataFile, lineNo) match {
case ParsedEdgeRowData(startId, endId, label, properties) =>
val startNode = graph.node(startId)
val endNode = graph.node(endId)
val propertiesMap = new util.HashMap[String, Object]
properties.foreach { case ParsedProperty(name, value) =>
propertiesMap.put(name, value.asInstanceOf[Object])
}
startNode.addEdge(label, endNode, propertiesMap)
importedEdgeCount += 1
}
}
}
}
}
logger.info(s"imported $importedNodeCount nodes")
}
private def groupInputFiles(inputFiles: Seq[Path]): Seq[HeaderAndDataFile] = {
val nonCsvFiles = inputFiles.filterNot(_.getFileName.toString.endsWith(".csv"))
assert(
nonCsvFiles.isEmpty,
s"input files must all have `.csv` extension, which is not the case for ${nonCsvFiles.mkString(",")}"
)
val (headerFiles, dataFiles) = inputFiles.partition(_.getFileName.toString.endsWith(s"$HeaderFileSuffix.csv"))
assert(
headerFiles.size == dataFiles.size,
s"number of header files (`xyz$HeaderFileSuffix.csv`) must equal the number of data files (`xyz.csv`)"
)
headerFiles.map { headerFile =>
val wantedBodyFilename = headerFile.getFileName.toString.replaceAll(HeaderFileSuffix, DataFileSuffix)
dataFiles.find(_.getFileName.toString == wantedBodyFilename) match {
case Some(dataFile) =>
HeaderAndDataFile(parseHeaderFile(headerFile), dataFile)
case None =>
val inputFilenames = inputFiles.map(_.getFileName).mkString(", ")
throw new AssertionError(
s"body filename `$wantedBodyFilename` wanted, but not found in given input files: $inputFilenames"
)
}
}
}
private def nodeFilesFirst(headerAndDataFile: HeaderAndDataFile): Int = {
headerAndDataFile.headerFile.fileType match {
case FileType.Nodes => 1 // we must import nodes first, because relationships refer to nodes
case FileType.Relationships => 2
}
}
private def parseHeaderFile(headerFile: Path): ParsedHeaderFile = {
val columnDefs = Using.resource(CSVReader.open(headerFile.toFile)) { headerReader =>
headerReader.all().headOption.getOrElse(throw new AssertionError(s"header file $headerFile is empty"))
}
val propertyDefs = Map.newBuilder[Int, ColumnDef]
var labelColumnFound = false
// will figure out if this is a node or relationship file during parsing
var fileType: Option[FileType.Value] = None
columnDefs.zipWithIndex.foreach { case (entry, idx) =>
val propertyDef = entry match {
case ColumnType.LabelMarker =>
if (labelColumnFound)
throw new NotImplementedError(
s"multiple ${ColumnType.Label} columns found in $headerFile, which is not supported by overflowdb"
)
labelColumnFound = true
fileType = Option(FileType.Nodes)
ColumnDef(None, ColumnType.Label)
case ColumnType.TypeMarker =>
fileType = Option(FileType.Relationships)
ColumnDef(None, ColumnType.Type)
case s if s.endsWith(ColumnType.Id.toString) =>
ColumnDef(None, ColumnType.Id)
case s if s.endsWith(ColumnType.StartId.toString) =>
ColumnDef(None, ColumnType.StartId)
case s if s.endsWith(ColumnType.EndId.toString) =>
ColumnDef(None, ColumnType.EndId)
case propertyDef if propertyDef.contains(":") =>
val name :: valueTpe0 :: Nil = propertyDef.split(':').toList
val isArray = propertyDef.endsWith(
ColumnType.ArrayMarker
) // from the docs: "To define an array type, append [] to the type"
val valueTpe =
if (isArray) valueTpe0.dropRight(2)
else valueTpe0
ColumnDef(Option(name), valueType = ColumnType.withName(valueTpe), isArray)
case propertyName =>
ColumnDef(
Option(propertyName),
valueType = ColumnType.String
) // if property is not annotated with `:someType`, default to String
}
propertyDefs.addOne((idx, propertyDef))
}
val propertyDefsRes = propertyDefs.result()
fileType match {
case Some(FileType.Nodes) =>
assert(
propertyDefsRes.values.exists(_.valueType == ColumnType.Id),
s"no :ID column found in headerFile $headerFile - see format definition in $Neo4jAdminDoc"
)
ParsedHeaderFile(FileType.Nodes, propertyDefsRes)
case Some(FileType.Relationships) =>
assert(
propertyDefsRes.values.exists(_.valueType == ColumnType.StartId),
s"no :START_ID column found in headerFile $headerFile - see format definition in $Neo4jAdminDoc"
)
assert(
propertyDefsRes.values.exists(_.valueType == ColumnType.EndId),
s"no :END_ID column found in headerFile $headerFile - see format definition in $Neo4jAdminDoc"
)
ParsedHeaderFile(FileType.Relationships, propertyDefsRes)
case _ =>
throw new AssertionError(
s"unable to determine file type - neither ${ColumnType.Label} (for nodes) nor ${ColumnType.Type} (for relationships) found"
)
}
}
private def parseNodeRowData(
columnsRaw: Seq[String],
columnDefs: Map[Int, ColumnDef],
inputFile: Path,
lineNo: Int
): ParsedNodeRowData = {
var id: Integer = null
var label: String = null
val properties = Seq.newBuilder[ParsedProperty]
columnsRaw.zipWithIndex.foreach { case (entry, idx) =>
val columnDef = columnDefs.getOrElse(
idx,
throw new AssertionError(s"column with index=$idx not found in column definitions derived from headerFile")
)
parseEntry(entry, columnDef, inputFile, lineNo) {
case ColumnDef(_, ColumnType.Id, _) =>
id = parseInt(entry, ColumnType.Id, lineNo)
case ColumnDef(_, ColumnType.Label, _) =>
label = entry
case ColumnDef(Some(name), valueType, false) =>
parseProperty(entry, name, valueType).foreach(properties.addOne)
case ColumnDef(Some(name), valueType, true) =>
parseArrayProperty(entry, name, valueType).foreach(properties.addOne)
}
}
assert(id != null, s"no ID column found in line $lineNo")
assert(label != null, s"no LABEL column found in line $lineNo")
val ret = ParsedNodeRowData(id, label, properties.result())
logger.debug("parsed line {}: {}", lineNo, ret)
ret
}
private def parseEdgeRowData(
columnsRaw: Seq[String],
columnDefs: Map[Int, ColumnDef],
inputFile: Path,
lineNo: Int
): ParsedEdgeRowData = {
var startId: Integer = null
var endId: Integer = null
var label: String = null
val properties = Seq.newBuilder[ParsedProperty]
columnsRaw.zipWithIndex.foreach { case (entry, idx) =>
val columnDef = columnDefs.getOrElse(
idx,
throw new AssertionError(s"column with index=$idx not found in column definitions derived from headerFile")
)
parseEntry(entry, columnDef, inputFile, lineNo) {
case ColumnDef(_, ColumnType.StartId, _) =>
startId = parseInt(entry, ColumnType.StartId, lineNo)
case ColumnDef(_, ColumnType.EndId, _) =>
endId = parseInt(entry, ColumnType.EndId, lineNo)
case ColumnDef(_, ColumnType.Type, _) =>
label = entry
case ColumnDef(Some(name), valueType, false) =>
parseProperty(entry, name, valueType).foreach(properties.addOne)
case ColumnDef(Some(name), valueType, true) =>
parseArrayProperty(entry, name, valueType).foreach(properties.addOne)
}
}
assert(startId != null, s"no START_ID column found in line $lineNo")
assert(endId != null, s"no END_ID column found in line $lineNo")
assert(label != null, s"no LABEL column found in line $lineNo")
val ret = ParsedEdgeRowData(startId, endId, label, properties.result())
logger.debug("parsed line {}: {}", lineNo, ret)
ret
}
private def parseEntry(rawValue: String, columnDef: ColumnDef, inputFile: Path, lineNo: Int)(
handleColumn: PartialFunction[ColumnDef, _]
): Unit = {
try {
handleColumn.applyOrElse(
columnDef,
{ (_: ColumnDef) =>
throw new MatchError(
s"unhandled case $columnDef for rawValue=$rawValue in ${inputFile.getFileName} line $lineNo"
)
}
)
} catch {
case err: Exception =>
throw new RuntimeException(
s"error while parsing input value '$rawValue' of valueType=${columnDef.valueType} in ${inputFile.getFileName} line $lineNo",
err
)
}
}
private def parseProperty(rawValue: String, name: String, valueType: ColumnType.Value): Option[ParsedProperty] = {
// an empty string in a csv is equivalent to `value not set`
Option(rawValue).filter(_.nonEmpty).map { value =>
ParsedProperty(name, parsePropertyValue(value, valueType))
}
}
private def parseArrayProperty(
rawValue: String,
name: String,
valueType: ColumnType.Value
): Option[ParsedProperty] = {
val values = rawValue.split(';') // from the docs: "By default, array values are separated by ;"
if (values.nonEmpty && values.head != "") { // csv parser always adds one empty string entry...
val parsedValues = values.map(parsePropertyValue(_, valueType))
Some(ParsedProperty(name, parsedValues))
} else {
None
}
}
private def parsePropertyValue(rawString: String, valueType: ColumnType.Value): Any = {
valueType match {
case ColumnType.Int => rawString.toInt
case ColumnType.Long => rawString.toLong
case ColumnType.Float => rawString.toFloat
case ColumnType.Double => rawString.toDouble
case ColumnType.Boolean => rawString.toBoolean
case ColumnType.Byte => rawString.toByte
case ColumnType.Short => rawString.toShort
case ColumnType.Char => rawString.head
case ColumnType.String => rawString
case ColumnType.Point => ???
case ColumnType.Date => ???
case ColumnType.LocalTime => ???
case ColumnType.Time => ???
case ColumnType.LocalDateTime => ???
case ColumnType.DateTime => ???
case ColumnType.Duration => ???
}
}
private def parseInt(entry: String, columnType: ColumnType.Value, lineNo: Int): Int = {
try entry.toInt
catch {
case err: Exception => throw new AssertionError(s"$columnType is not an Int ($lineNo): $entry: $err", err)
}
}
private case class HeaderAndDataFile(headerFile: ParsedHeaderFile, dataFile: Path)
private case class ParsedHeaderFile(fileType: FileType.Value, propertyByColumnIndex: Map[Int, ColumnDef])
private case class ColumnDef(name: Option[String], valueType: ColumnType.Value, isArray: Boolean = false)
private case class ParsedProperty(name: String, value: Any)
private case class ParsedNodeRowData(id: Int, label: String, properties: Seq[ParsedProperty])
private case class ParsedEdgeRowData(startId: Int, endId: Int, label: String, properties: Seq[ParsedProperty])
}
