Fixup for concatenated avro files

0001-Add-optional-offset-to-_read_header.patch

From 28938c5e63262d69f3c670e3cc7de9963318d239 Mon Sep 17 00:00:00 2001
From: Evan McClain <aeroevan@gmail.com>
Date: Mon, 7 Dec 2015 00:53:39 -0500
Subject: [PATCH] Add optional offset to _read_header.

---
 src/avro/datafile.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/avro/datafile.py b/src/avro/datafile.py
index e12a68f..208e965 100644
--- a/src/avro/datafile.py
+++ b/src/avro/datafile.py
@@ -98,7 +98,7 @@ class DataFileWriter(object):
     else:
       # open writer for reading to collect metadata
       dfr = DataFileReader(writer, io.DatumReader())
-      
+
       # TODO(hammer): collect arbitrary metadata
       # collect metadata
       self._sync_marker = dfr.sync_marker
@@ -179,7 +179,7 @@ class DataFileWriter(object):
 
       # Write block
       self.writer.write(compressed_data)
-      
+
       # Write CRC32 checksum for Snappy
       if self.get_meta(CODEC_KEY) == 'snappy':
         self.encoder.write_crc32(uncompressed_data)
@@ -188,7 +188,7 @@ class DataFileWriter(object):
       self.writer.write(self.sync_marker)
 
       # reset buffer
-      self.buffer_writer.truncate(0) 
+      self.buffer_writer.truncate(0)
       self.block_count = 0
 
   def append(self, datum):
@@ -223,14 +223,14 @@ class DataFileReader(object):
   """Read files written by DataFileWriter."""
   # TODO(hammer): allow user to specify expected schema?
   # TODO(hammer): allow user to specify the encoder
-  def __init__(self, reader, datum_reader):
+  def __init__(self, reader, datum_reader, offset=0):
     self._reader = reader
     self._raw_decoder = io.BinaryDecoder(reader)
     self._datum_decoder = None # Maybe reset at every block.
     self._datum_reader = datum_reader
-    
+
     # read the header: magic, meta, sync
-    self._read_header()
+    self._read_header(offset)
 
     # ensure codec is valid
     self.codec = self.get_meta('avro.codec')
@@ -290,9 +290,10 @@ class DataFileReader(object):
   def is_EOF(self):
     return self.reader.tell() == self.file_length
 
-  def _read_header(self):
+  def _read_header(self, offset):
     # seek to the beginning of the file to get magic block
-    self.reader.seek(0, 0) 
+    pos = self.reader.tell()
+    self.reader.seek(offset, 0)
 
     # read header into a dict
     header = self.datum_reader.read_data(
@@ -309,6 +310,8 @@ class DataFileReader(object):
 
     # set sync marker
     self._sync_marker = header['sync']
+    if pos > 0:
+        self.reader.seek(pos)
 
   def _read_block_header(self):
     self.block_count = self.raw_decoder.read_long()
@@ -359,7 +362,7 @@ class DataFileReader(object):
       else:
         self._read_block_header()
 
-    datum = self.datum_reader.read(self.datum_decoder) 
+    datum = self.datum_reader.read(self.datum_decoder)
     self.block_count -= 1
     return datum
 
-- 
2.6.3

repair.py

#!/usr/bin/env python
import os
import avro.schema
from avro.datafile import DataFileReader, DataFileWriter
from avro.io import DatumReader, DatumWriter


def fix_file(schemafile, infile, outfile):
    schema = avro.schema.parse(open(schemafile).read())

    writer = DataFileWriter(open(outfile, "wb"), DatumWriter(), schema,
                            codec='deflate')

    f = open(infile, "rb")
    while (f.tell() != os.fstat(f.fileno()).st_size):
        print("{0:6.2f}%".format(
            100.0 * float(f.tell()) / float(os.fstat(f.fileno()).st_size)))
        prev = f.tell()
        # HACK: had to modify DatFileReader's _read_header() to seek to the
        # given offset.
        reader = DataFileReader(f, DatumReader(), prev)
        try:
            for row in reader:
                writer.append(row)
                prev = f.tell()
            # once we have finished looping, we are done with the file.
            break
        except Exception:
            writer.close()
            writer = DataFileWriter(open(outfile, "ab+"), DatumWriter())
            # need to skip 16 byte sync
            f.seek(prev+16)
            continue
    reader.close()
    writer.close()

if __name__ == '__main__':
    import argparse
    parser = argparse.ArgumentParser(
        description="Fix avro file that has its schema defined multiple times.")
    parser.add_argument("-s", "--schema", help="JSON formatted Avro schema",
                        required=True)
    parser.add_argument("-i", "--input", help="Input Avro file to read",
                        required=True)
    parser.add_argument("-o", "--output", help="Output Avro file to write",
                        required=True)
    args = parser.parse_args()
    fix_file(args.schema, args.input, args.output)