Creates PoC pipeline to estimate disk usage of vcf_to_bq on Dataflow.

hanjohn · hanjohn · commit 08b8772020e4 · 2018-08-17T01:47:16.000-07:00
The pipeline uses raw file size and raw+encoded sizes of a short snippet at beginning of VCF files to
estimate the encoded size for a commit. The major blocking bug is that when the snippets are being read from VCFs in an
encoded format, lines are being read more than once.
diff --git a/gcp_variant_transforms/beam_io/vcf_snippet_io.py b/gcp_variant_transforms/beam_io/vcf_snippet_io.py
@@ -0,0 +1,131 @@
+# Copyright 2017 Google Inc.  All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""A source for reading VCF file headers."""
+
+from __future__ import absolute_import
+
+import logging
+
+from apache_beam.io import filebasedsource
+from apache_beam.io import range_trackers  # pylint: disable=unused-import
+from apache_beam.io.filesystem import CompressionTypes
+from apache_beam.io.filesystems import FileSystems
+from apache_beam.io.iobase import Read
+from apache_beam.transforms import PTransform
+from typing import Iterable  # pylint: disable=unused-import
+
+from gcp_variant_transforms.beam_io import vcf_parser, vcfio
+
+
+class _VcfSnippetSource(filebasedsource.FileBasedSource):
+  """A source for reading a limited number of variants from a set of VCF files.
+
+  Lines that are malformed are skipped.
+
+  Parses VCF files (version 4) using PyVCF library.
+  """
+
+  DEFAULT_VCF_READ_BUFFER_SIZE = 65536  # 64kB
+
+  def __init__(self,
+               file_pattern,
+               snippet_size,
+               compression_type=CompressionTypes.AUTO,
+               validate=True):
+    # type: (str, int, str, bool) -> None
+    super(_VcfSnippetSource, self).__init__(file_pattern,
+                                          compression_type=compression_type,
+                                          validate=validate,
+                                          splittable=False)
+    self._compression_type = compression_type
+    self._snippet_size = snippet_size
+
+  def read_records(
+      self,
+      file_name,  # type: str
+      range_tracker  # type: range_trackers.UnsplittableRangeTracker
+      ):
+    # type: (...) -> Iterable[Tuple[str, str, vcfio.Variant]]
+    # Iterator to emit lines encoded as `Variant` objects.
+    record_iterator = vcf_parser.PyVcfParser(
+      file_name,
+      range_tracker,
+      self._pattern,
+      self._compression_type,
+      allow_malformed_records=True,
+      representative_header_lines=None,
+      buffer_size=self.DEFAULT_VCF_READ_BUFFER_SIZE,
+      skip_header_lines=0)
+
+    # Open distinct channel to read lines as raw bytestrings.
+    with FileSystems.open(file_name, self._compression_type) as raw_reader:
+      line = raw_reader.readline()
+      while line and line.startswith('#'):
+        # Skip headers, assume header size is negligible.
+        line = raw_reader.readline()
+
+      count = 0
+      for encoded_record in record_iterator:
+        raw_record = raw_reader.readline()
+
+        if count >= self._snippet_size:
+          break
+        if not isinstance(encoded_record, vcfio.Variant):
+          continue
+
+        count += 1
+        yield file_name, raw_record, encoded_record
+
+
+class ReadVcfSnippet(PTransform):
+  """A PTransform for reading a limited number of lines from a set of VCF files.
+
+  Output will be a PTable mapping from `file names -> Tuple[(line, Variant)]`
+  objects. The list contains the first `snippet_size` number of lines that are
+  not malformed, first as a raw string and then encoded as a `Variant` class.
+
+  Parses VCF files (version 4) using PyVCF library.
+  """
+
+  def __init__(
+      self,
+      file_pattern,  # type: str
+      snippet_size,  # type: int
+      compression_type=CompressionTypes.AUTO,  # type: str
+      validate=True,  # type: bool
+      **kwargs  # type: **str
+  ):
+    # type: (...) -> None
+    """Initialize the :class:`ReadVcfHeaders` transform.
+
+    Args:
+      file_pattern: The file path to read from either as a single file or a glob
+        pattern.
+      snippet_size: The number of lines that should be read from the file.
+      compression_type: Used to handle compressed input files.
+        Typical value is :attr:`CompressionTypes.AUTO
+        <apache_beam.io.filesystem.CompressionTypes.AUTO>`, in which case the
+        underlying file_path's extension will be used to detect the compression.
+      validate: Flag to verify that the files exist during the pipeline creation
+        time.
+    """
+    super(ReadVcfSnippet, self).__init__(**kwargs)
+    self._source = _VcfSnippetSource(
+      file_pattern, snippet_size, compression_type, validate=validate)
+
+  def expand(self, pvalue):
+    return pvalue.pipeline | Read(self._source)
+
+
diff --git a/gcp_variant_transforms/beam_io/vcf_snippet_io_test.py b/gcp_variant_transforms/beam_io/vcf_snippet_io_test.py
diff --git a/gcp_variant_transforms/libs/preprocess_reporter.py b/gcp_variant_transforms/libs/preprocess_reporter.py
@@ -26,6 +26,8 @@
 TODO(allieychen): Eventually, it also contains the resource estimation.
 
 Output example (assuming opening in spreedsheet):
+Estimated disk usage by Dataflow: 4846.0 GB. The total raw file sizes summed up
+to 1231.0 GB.
 Header Conflicts
 ID    Category    Conflicts            File Paths    Proposed Resolution
 NS    INFO        num=1 type=Float     file1         num=1 type=Float
@@ -43,6 +45,7 @@
 File Path   Variant Record              Error Message
 file 1      rs6 G A 29 PASS NS=3;       invalid literal for int() with base 10.
 """
+import math
 
 from typing import Dict, List, Optional, Union  # pylint: disable=unused-import
 
@@ -77,6 +80,7 @@ class _HeaderLine(object):
 def generate_report(
     header_definitions,  # type: merge_header_definitions.VcfHeaderDefinitions
     file_path,  # type: str
+    disk_usage_estimate,  # type: int
     resolved_headers=None,  # type: vcf_header_io.VcfHeader
     inferred_headers=None,  # type: vcf_header_io.VcfHeader
     malformed_records=None  # type: List[vcfio.MalformedVcfRecord]
@@ -97,6 +101,7 @@ def generate_report(
   """
   resolved_headers = resolved_headers or vcf_header_io.VcfHeader()
   with filesystems.FileSystems.create(file_path) as file_to_write:
+    _append_disk_usage_estimate_to_report(file_to_write, disk_usage_estimate)
     _append_conflicting_headers_to_report(file_to_write, header_definitions,
                                           resolved_headers)
     _append_inferred_headers_to_report(file_to_write, inferred_headers)
@@ -272,6 +277,15 @@ def _format_definition(num_value, type_value):
   ]
   return ' '.join(formatted_definition)
 
+def _append_disk_usage_estimate_to_report(file_to_write, disk_usage_estimate):
+  # type: (file, FileSizeInfo) -> None
+  if disk_usage_estimate is None:
+    return
+  file_to_write.write(
+    'Estimated disk usage by Dataflow: {} GB. The total raw file sizes summed '
+    'up to {} GB.\n'.format(
+        int(math.ceil(disk_usage_estimate.encoded / 1e9)),
+        int(math.ceil(disk_usage_estimate.raw / 1e9))))
 
 def _append_to_report(file_to_write, error_type, header, contents):
   # type: (file, str, str, List[str]) -> None
diff --git a/gcp_variant_transforms/libs/resource_estimator.py b/gcp_variant_transforms/libs/resource_estimator.py
@@ -0,0 +1,179 @@
+# Copyright 2018 Google Inc.  All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Helper functions for estimating the resources that a vcf_to_bq will require.
+
+Currently, the resource estimator only estimates the disk usage that a Dataflow
+pipeline will take along with the `MergeVariants` step, since this can cause
+expensive pipeline failures late in the run.
+"""
+import logging
+
+import apache_beam as beam
+from apache_beam import coders
+from apache_beam.io.filesystem import CompressionTypes
+from apache_beam.io.filesystems import FileSystems
+
+from gcp_variant_transforms.beam_io import vcfio
+
+
+# TODO(hanjohn): Add unit tests.
+
+def _convert_variant_snippets_to_bytesize(variant):
+  # type: (vcfio.Variant -> int)
+  return coders.registry.get_coder(vcfio.Variant).estimate_size(variant)
+
+
+class SnippetSizeInfo(object):
+  def __init__(self,
+               raw_snippet_size,  # type: int
+               encoded_snippet_size,  # type: int
+               ):
+    # type: (...) -> (None)
+    self.raw = raw_snippet_size
+    self.encoded = encoded_snippet_size
+
+
+class FileSizeInfo(object):
+  def __init__(self, raw_file_size, encoded_file_size=None):
+    # type: (int, int) -> (None)
+    self.raw = raw_file_size
+    self.encoded = encoded_file_size
+
+  def calculateEncodedFileSize(self, snippet_size_info):
+    # type: (SnippetSizeInfo) -> (None)
+    """Estimate a VCF file's encoded size based on snippet analysis.
+
+    Given the raw_file_size and measurements of several VCF lines from the file,
+    estimate how much disk the file will take after expansion due to encoding
+    lines as `vcfio.Variant` objects. The encoded_snippet_size will be set as
+    `self.encoded`.
+
+    This is a simple ratio problem, solving for encoded_snippet_size which is
+    the only unknown:
+    encoded_snippet_size / raw_snippet_size = encoded_file_size / raw_file_size
+    """
+    if snippet_size_info.raw == 0:
+      logging.error("VCF file {} reported with 0 well-formed variant lines; "
+                    "its contribution to disk resource usage will be "
+                    "ignored.".format(self.name))
+      self.encoded = 0
+      self.raw = 0
+    else:
+      self.encoded = (self.raw * snippet_size_info.encoded /
+                      snippet_size_info.raw)
+
+
+def measure_variant_size(element):
+  # type: (Tuple[str, str, vcfio.Variant]) -> (Tuple[str, SnippetSizeInfo])
+  """Measure the lengths of the raw and encoded representations of a Variant.
+
+  Given a PTable mapping file_paths to the raw (bytestring) and vcfio.Variant-
+  encoded representations of a Variant line, have the output PTable instead map
+  from the file_paths to a Tuple with the (raw, encoded) representation sizes.
+
+  The file_path keys are not expected to be unique.
+  """
+  file_path, raw_variant, encoded_variant = element
+  encoded_variant_size = _convert_variant_snippets_to_bytesize(encoded_variant)
+  raw_variant_size = len(raw_variant)
+  return file_path, SnippetSizeInfo(raw_variant_size, encoded_variant_size)
+
+
+def estimate_file_encoded_size(element):
+  # type: (Tuple[str, Dict[str, Object]]) -> (Tuple[str, FileSizeInfo])
+  file_name, metrics = element
+  file_size_info = metrics['whole_file_raw_size'][0]  # type: FileSizeInfo
+  snippet_size_info = metrics['snippet_stats'][0]  # type: SnippetSizeInfo
+
+  # Assume that the ratio of encoded size to raw disk size is roughly the same
+  # throughout the file compared to the first several lines.
+  file_size_info.calculateEncodedFileSize(snippet_size_info)
+
+  logging.debug("File %s has raw file size %d, raw snippet size %d, encoded "
+                "size %d. Estimated encoded file size: %d",
+                file_name, file_size_info.raw, snippet_size_info.raw,
+                snippet_size_info.encoded, file_size_info.encoded)
+  return file_name, file_size_info
+
+def get_file_sizes(input_pattern):
+  # type: (str) -> (List[FileSizeInfo])
+  match_results = FileSystems.match([input_pattern])
+  file_sizes = []
+  for match in match_results:
+    for file_metadata in match.metadata_list:
+      compression_type = CompressionTypes.detect_compression_type(
+          file_metadata.path)
+      if compression_type != CompressionTypes.UNCOMPRESSED:
+        logging.error("VCF file {} is compressed; disk requirement estimator "
+                      "will not be accurate.",
+                      file_metadata.path)
+
+      file_sizes.append((file_metadata.path,
+                         FileSizeInfo(file_metadata.size_in_bytes),))
+  return file_sizes
+
+
+class SnippetSizeInfoSumFn(beam.CombineFn):
+  """Combiner Function to sum up the size fields of SnippetSizeInfos.
+
+  Example: [SnippetSizeInfo(a, b), SnippetSizeInfo(c, d)] ->
+            SnippetSizeInfo(a+c, b+d)
+  """
+  def create_accumulator(self):
+    # type: (None) -> (Tuple[int, int])
+    return (0, 0)  # (raw, encoded) sums
+
+  def add_input(self, sums, input):
+    # type: (Tuple[int, int], SnippetSizeInfo) -> (Tuple[int, int])
+    return sums[0] + input.raw, sums[1] + input.encoded
+
+  def merge_accumulators(self, accumulators):
+    # type: (Iterable[Tuple[int, int]]) -> (Tuple[int, int])
+    first, second = zip(*accumulators)
+    return sum(first), sum(second)
+
+  def extract_output(self, sums):
+    # type: (Tuple[int, int]) -> (SnippetSizeInfo)
+    return SnippetSizeInfo(*sums)
+
+
+class FileSizeInfoSumFn(beam.CombineFn):
+  """Combiner Function to sum up the size fields of Tuple[str, FileSizeInfo]s.
+
+  Unlike SnippetSizeInfoSumFn, the input is a PTable mapping str to
+  FileSizeInfo, so the input is a tuple with the FileSizeInfos as the second
+  field. The output strips out the str key which represents the file path.
+
+  Example: [('/path/a', FileSizeInfo(a, b)), ('/path/b;, FileSizeInfo(c, d))] ->
+            FileSizeInfo(a+c, b+d)
+  """
+  def create_accumulator(self):
+    # type: (None) -> (Tuple[int, int])
+    return (0, 0)  # (raw, encoded) sums
+
+  def add_input(self, raw_encoded, input):
+    # type: (Tuple[int, int], Tuple[str, FileSizeInfo]) -> (Tuple[int, int])
+    raw, encoded = raw_encoded
+    _, file_size_info = input
+    return raw + file_size_info.raw, encoded + file_size_info.encoded
+
+  def merge_accumulators(self, accumulators):
+    # type: (Iterable[Tuple[int, int]]) -> (Tuple[int, int])
+    raw, encoded = zip(*accumulators)
+    return sum(raw), sum(encoded)
+
+  def extract_output(self, raw_encoded):
+    # type: (Tuple[int, int]) -> (FileSizeInfo)
+    raw, encoded = raw_encoded
+    return FileSizeInfo(raw, encoded)
diff --git a/gcp_variant_transforms/options/variant_transform_options.py b/gcp_variant_transforms/options/variant_transform_options.py
@@ -424,6 +424,13 @@ def add_arguments(self, parser):
         help=('The full path of the resolved headers. The file will not be'
               'generated if unspecified. Otherwise, please provide a local '
               'path if run locally, or a cloud path if run on Dataflow.'))
+    parser.add_argument(
+      '--estimate_disk_usage',
+      type='bool', default=False, nargs='?', const=True,
+      help=('By default, disk resource usage will not be estimated.'
+            'If true, the preprocessor will estimate the maximum disk usage '
+            'consumed at any step in the pipeline, which could lead to '
+            'out-of-disk errors at a shuffle step e.g. MergeVariants.'))
 
 class PartitionOptions(VariantTransformsOptions):
   """Options for partitioning Variant records."""
diff --git a/gcp_variant_transforms/vcf_to_bq_preprocess.py b/gcp_variant_transforms/vcf_to_bq_preprocess.py
