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[bugfix] check key ordering when isSorted = true #6267

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merged 4 commits into from
Jun 7, 2019
Merged

[bugfix] check key ordering when isSorted = true #6267

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7ad53cb
check key ordering when asserting that is sorted
Jun 5, 2019
16f0f6f
Fix MatrixEntriesTable lowering to deal with duplicate row keys.
tpoterba Jun 6, 2019
ec98f40
address Patrick's comments
tpoterba Jun 6, 2019
db9ec56
bump
tpoterba Jun 7, 2019
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6 changes: 6 additions & 0 deletions hail/python/benchmark/matrix_table_benchmarks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,12 @@ def matrix_table_entries_table():
mt = hl.read_matrix_table(resource('profile.mt'))
mt.entries()._force_count()


@benchmark
def matrix_table_entries_table_no_key():
mt = hl.read_matrix_table(resource('profile.mt')).key_rows_by().key_cols_by()
mt.entries()._force_count()

@benchmark
def matrix_table_rows_force_count():
ht = hl.read_matrix_table(resource('profile.mt')).rows().key_by()
Expand Down
18 changes: 16 additions & 2 deletions hail/src/main/scala/is/hail/expr/ir/IRBuilder.scala
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Expand Up @@ -216,8 +216,10 @@ object IRBuilder {

def castRename(t: Type): IRProxy = (env: E) => CastRename(ir(env), t)

def insertFields(fields: (Symbol, IRProxy)*): IRProxy = (env: E) =>
InsertFields(ir(env), fields.map { case (s, fir) => (s.name, fir(env)) })
def insertFields(fields: (Symbol, IRProxy)*): IRProxy = insertFieldsList(fields)

def insertFieldsList(fields: Seq[(Symbol, IRProxy)], ordering: Option[IndexedSeq[String]] = None): IRProxy = (env: E) =>
InsertFields(ir(env), fields.map { case (s, fir) => (s.name, fir(env))}, ordering)

def selectFields(fields: String*): IRProxy = (env: E) =>
SelectFields(ir(env), fields)
Expand All @@ -230,6 +232,18 @@ object IRBuilder {

def dropFields(fields: Symbol*): IRProxy = dropFieldList(fields.map(_.name))

def insertStruct(other: IRProxy, ordering: Option[IndexedSeq[String]] = None): IRProxy = (env: E) => {
val right = other(env)
val sym = genUID()
Let(
sym,
right,
InsertFields(
ir(env),
right.typ.asInstanceOf[TStruct].fieldNames.map(f => f -> GetField(Ref(sym, right.typ), f)),
ordering))
}

def len: IRProxy = (env: E) => ArrayLen(ir(env))

def isNA: IRProxy = (env: E) => IsNA(ir(env))
Expand Down
81 changes: 57 additions & 24 deletions hail/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -512,30 +512,63 @@ object LowerMatrixIR {
.mapRows('row.selectFields(child.typ.rowType.fieldNames ++ Array(entriesFieldName): _*))
.rename(Map(entriesFieldName -> entries), Map(colsFieldName -> cols))

case MatrixEntriesTable(child) =>
val oldColIdx = Symbol(genUID())
val lambdaIdx1 = Symbol(genUID())
val currentColIdx = Symbol(genUID())
lower(child, ab)
.mapGlobals('global.insertFields(oldColIdx ->
irRange(0, 'global (colsField).len)
.map(lambdaIdx1 ~> makeStruct('key -> 'global (colsField)(lambdaIdx1).selectFields(child.typ.colKey: _*), 'value -> lambdaIdx1))
.sort(ascending = true, onKey = true)
.map(lambdaIdx1 ~> lambdaIdx1('value))))
.mapRows('row.insertFields(currentColIdx -> 'global (oldColIdx)
.filter(lambdaIdx1 ~> !'row (entriesField)(lambdaIdx1).isNA)))
.explode(currentColIdx)
.mapRows(let(
__current_idx = 'row (currentColIdx),
__col_struct = 'global (colsField)('__current_idx),
__entry_struct = 'row (entriesField)('__current_idx)) {
val newFields = child.typ.colType.fieldNames.map(Symbol(_)).map(f => f -> '__col_struct (f)) ++
child.typ.entryType.fieldNames.map(Symbol(_)).map(f => f -> '__entry_struct (f))
'row
.dropFields(entriesField, currentColIdx)
.insertFields(newFields: _*)
}).mapGlobals('global.dropFields(colsField, oldColIdx))
.keyBy(child.typ.rowKey ++ child.typ.colKey, isSorted = !(child.typ.rowKey.isEmpty && child.typ.colKey.nonEmpty))
case x@MatrixEntriesTable(child) =>
val lc = lower(child, ab)

if (child.typ.rowKey.nonEmpty && child.typ.colKey.nonEmpty) {
val oldColIdx = Symbol(genUID())
val lambdaIdx1 = Symbol(genUID())
val lambdaIdx2 = Symbol(genUID())
val lambdaIdx3 = Symbol(genUID())
val toExplode = Symbol(genUID())
val values = Symbol(genUID())
lc
.mapGlobals('global.insertFields(oldColIdx ->
irRange(0, 'global (colsField).len)
.map(lambdaIdx1 ~> makeStruct('key -> 'global (colsField)(lambdaIdx1).selectFields(child.typ.colKey: _*), 'value -> lambdaIdx1))
.sort(ascending = true, onKey = true)
.map(lambdaIdx1 ~> lambdaIdx1('value))))
.aggregateByKey(makeStruct(values -> applyAggOp(Collect(), seqOpArgs = FastIndexedSeq('row.selectFields(lc.typ.valueType.fieldNames: _*)))))
.mapRows('row.dropFields(values).insertFields(toExplode ->
'global (oldColIdx)
.flatMap(lambdaIdx1 ~> 'row (values)
.filter(lambdaIdx2 ~> !lambdaIdx2(entriesField)(lambdaIdx1).isNA)
.map(lambdaIdx3 ~> let(__col = 'global (colsField)(lambdaIdx1), __entry = lambdaIdx3(entriesField)(lambdaIdx1)) {
makeStruct(
child.typ.rowValueStruct.fieldNames.map(Symbol(_)).map(f => f -> lambdaIdx3(f)) ++
child.typ.colType.fieldNames.map(Symbol(_)).map(f => f -> '__col (f)) ++
child.typ.entryType.fieldNames.map(Symbol(_)).map(f => f -> '__entry (f)): _*
)
}))))

.explode(toExplode)
.mapRows('row.dropFields(toExplode).insertStruct('row (toExplode),
ordering = Some(x.typ.rowType.fieldNames.toFastIndexedSeq)))
.mapGlobals('global.dropFields(colsField, oldColIdx))
.keyBy(child.typ.rowKey ++ child.typ.colKey, isSorted = true)
} else {
val colIdx = Symbol(genUID())
val lambdaIdx = Symbol(genUID())
val result = lc
.mapRows('row.insertFields(colIdx -> irRange(0, 'global (colsField).len)
.filter(lambdaIdx ~> !'row (entriesField)(lambdaIdx).isNA)))
.explode(colIdx)
.mapRows(let(__col_struct = 'global (colsField)('row (colIdx)),
__entry_struct = 'row (entriesField)('row (colIdx))) {
val newFields = child.typ.colType.fieldNames.map(Symbol(_)).map(f => f -> '__col_struct (f)) ++
child.typ.entryType.fieldNames.map(Symbol(_)).map(f => f -> '__entry_struct (f))

'row.dropFields(entriesField, colIdx).insertFieldsList(newFields,
ordering = Some(x.typ.rowType.fieldNames.toFastIndexedSeq))
})
.mapGlobals('global.dropFields(colsField))
if (child.typ.colKey.isEmpty)
result
else {
assert(child.typ.rowKey.isEmpty)
result.keyBy(child.typ.colKey)
}
}

case MatrixToTableApply(child, function) =>
val loweredChild = lower(child, ab)
Expand Down
115 changes: 58 additions & 57 deletions hail/src/main/scala/is/hail/rvd/RVD.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ class RVD(
if (nPreservedFields == newKey.length)
this
else if (isSorted)
truncateKey(newKey.take(nPreservedFields)).extendKeyPreservesPartitioning(newKey)
truncateKey(newKey.take(nPreservedFields)).extendKeyPreservesPartitioning(newKey).checkKeyOrdering()
else
changeKey(newKey)
}
Expand All @@ -130,6 +130,61 @@ class RVD(
}
}

def checkKeyOrdering(): RVD = {
val partitionerBc = partitioner.broadcast(crdd.sparkContext)
val localType = typ
val localKPType = typ.kType

new RVD(
typ,
partitioner,
crdd.cmapPartitionsWithIndex { case (i, ctx, it) =>
val prevK = WritableRegionValue(localType.kType, ctx.freshRegion)
val kUR = new UnsafeRow(localKPType)

new Iterator[RegionValue] {
var first = true

def hasNext: Boolean = it.hasNext

def next(): RegionValue = {
val rv = it.next()

if (first)
first = false
else {
if (localType.kRowOrd.gt(prevK.value, rv)) {
kUR.set(prevK.value)
val prevKeyString = kUR.toString()

prevK.setSelect(localType.rowType, localType.kFieldIdx, rv)
kUR.set(prevK.value)
val currKeyString = kUR.toString()
fatal(
s"""RVD error! Keys found out of order:
| Current key: $currKeyString
| Previous key: $prevKeyString
|This error can occur after a split_multi if the dataset
|contains both multiallelic variants and duplicated loci.
""".stripMargin)
}
}

prevK.setSelect(localType.rowType, localType.kFieldIdx, rv)
kUR.set(prevK.value)

if (!partitionerBc.value.rangeBounds(i).contains(localType.kType.virtualType.ordering, kUR))
fatal(
s"""RVD error! Unexpected key in partition $i
| Range bounds for partition $i: ${ partitionerBc.value.rangeBounds(i) }
| Range of partition IDs for key: [${ partitionerBc.value.lowerBound(kUR) }, ${ partitionerBc.value.upperBound(kUR) })
| Invalid key: ${ kUR.toString() }""".stripMargin)
rv
}
}
})
}

def truncateKey(n: Int): RVD = {
require(n <= typ.key.length)
truncateKey(typ.key.take(n))
Expand Down Expand Up @@ -1275,62 +1330,8 @@ object RVD {
): RVD = {
if (!HailContext.get.checkRVDKeys)
return new RVD(typ, partitioner, crdd)

val sc = crdd.sparkContext

val partitionerBc = partitioner.broadcast(sc)
val localType = typ
val localKPType = typ.kType

new RVD(
typ,
partitioner,
crdd.cmapPartitionsWithIndex { case (i, ctx, it) =>
val prevK = WritableRegionValue(localType.kType, ctx.freshRegion)
val kUR = new UnsafeRow(localKPType)

new Iterator[RegionValue] {
var first = true

def hasNext: Boolean = it.hasNext

def next(): RegionValue = {
val rv = it.next()

if (first)
first = false
else {
if (localType.kRowOrd.gt(prevK.value, rv)) {
kUR.set(prevK.value)
val prevKeyString = kUR.toString()

prevK.setSelect(localType.rowType, localType.kFieldIdx, rv)
kUR.set(prevK.value)
val currKeyString = kUR.toString()
fatal(
s"""RVD error! Keys found out of order:
| Current key: $currKeyString
| Previous key: $prevKeyString
|This error can occur after a split_multi if the dataset
|contains both multiallelic variants and duplicated loci.
""".stripMargin)
}
}

prevK.setSelect(localType.rowType, localType.kFieldIdx, rv)
kUR.set(prevK.value)

if (!partitionerBc.value.rangeBounds(i).contains(localType.kType.virtualType.ordering, kUR))
fatal(
s"""RVD error! Unexpected key in partition $i
| Range bounds for partition $i: ${ partitionerBc.value.rangeBounds(i) }
| Range of partition IDs for key: [${ partitionerBc.value.lowerBound(kUR) }, ${ partitionerBc.value.upperBound(kUR) })
| Invalid key: ${ kUR.toString() }""".stripMargin)

rv
}
}
})
else
return new RVD(typ, partitioner, crdd).checkKeyOrdering()
}

def union(rvds: Seq[RVD], joinKey: Int): RVD = rvds match {
Expand Down