[
https://issues.apache.org/jira/browse/BEAM-3965?focusedWorklogId=87773&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-87773
]
ASF GitHub Bot logged work on BEAM-3965:
----------------------------------------
Author: ASF GitHub Bot
Created on: 04/Apr/18 21:41
Start Date: 04/Apr/18 21:41
Worklog Time Spent: 10m
Work Description: chamikaramj closed pull request #4979: [BEAM-3965] HDFS
Read fixes
URL: https://github.com/apache/beam/pull/4979
This is a PR merged from a forked repository.
As GitHub hides the original diff on merge, it is displayed below for
the sake of provenance:
As this is a foreign pull request (from a fork), the diff is supplied
below (as it won't show otherwise due to GitHub magic):
diff --git a/sdks/python/apache_beam/io/filesystem.py
b/sdks/python/apache_beam/io/filesystem.py
index 28a0c434dc5..3f7e9aba847 100644
--- a/sdks/python/apache_beam/io/filesystem.py
+++ b/sdks/python/apache_beam/io/filesystem.py
@@ -437,7 +437,8 @@ class FileSystem(BeamPlugin):
def __init__(self, pipeline_options):
"""
Args:
- pipeline_options: Instance of ``PipelineOptions``.
+ pipeline_options: Instance of ``PipelineOptions`` or dict of options and
+ values (like ``RuntimeValueProvider.runtime_options``).
"""
@staticmethod
diff --git a/sdks/python/apache_beam/io/filesystems.py
b/sdks/python/apache_beam/io/filesystems.py
index 17d8d37a061..5bc195bb0d9 100644
--- a/sdks/python/apache_beam/io/filesystems.py
+++ b/sdks/python/apache_beam/io/filesystems.py
@@ -24,6 +24,7 @@
from apache_beam.io.filesystem import BeamIOError
from apache_beam.io.filesystem import CompressionTypes
from apache_beam.io.filesystem import FileSystem
+from apache_beam.options.value_provider import RuntimeValueProvider
# All filesystem implements should be added here as
# best effort imports. We don't want to force loading
@@ -85,7 +86,11 @@ def get_filesystem(path):
if len(systems) == 0:
raise ValueError('Unable to get the Filesystem for path %s' % path)
elif len(systems) == 1:
- return systems[0](pipeline_options=FileSystems._pipeline_options)
+ # Pipeline options could come either from the Pipeline itself (using
+ # direct runner), or via RuntimeValueProvider (other runners).
+ options = (FileSystems._pipeline_options or
+ RuntimeValueProvider.runtime_options)
+ return systems[0](pipeline_options=options)
else:
raise ValueError('Found more than one filesystem for path %s' % path)
except ValueError:
diff --git a/sdks/python/apache_beam/io/hadoopfilesystem.py
b/sdks/python/apache_beam/io/hadoopfilesystem.py
index bff243aa555..7382c3c8ade 100644
--- a/sdks/python/apache_beam/io/hadoopfilesystem.py
+++ b/sdks/python/apache_beam/io/hadoopfilesystem.py
@@ -35,6 +35,7 @@
from apache_beam.io.filesystem import FileSystem
from apache_beam.io.filesystem import MatchResult
from apache_beam.options.pipeline_options import HadoopFileSystemOptions
+from apache_beam.options.pipeline_options import PipelineOptions
__all__ = ['HadoopFileSystem']
@@ -48,12 +49,11 @@
_FILE_CHECKSUM_BYTES = 'bytes'
_FILE_CHECKSUM_LENGTH = 'length'
# WebHDFS FileStatus property constants.
-_FILE_STATUS_NAME = 'name'
+_FILE_STATUS_LENGTH = 'length'
_FILE_STATUS_PATH_SUFFIX = 'pathSuffix'
_FILE_STATUS_TYPE = 'type'
_FILE_STATUS_TYPE_DIRECTORY = 'DIRECTORY'
_FILE_STATUS_TYPE_FILE = 'FILE'
-_FILE_STATUS_SIZE = 'size'
class HdfsDownloader(filesystemio.Downloader):
@@ -61,7 +61,7 @@ class HdfsDownloader(filesystemio.Downloader):
def __init__(self, hdfs_client, path):
self._hdfs_client = hdfs_client
self._path = path
- self._size = self._hdfs_client.status(path)[_FILE_STATUS_SIZE]
+ self._size = self._hdfs_client.status(path)[_FILE_STATUS_LENGTH]
@property
def size(self):
@@ -106,20 +106,26 @@ def __init__(self, pipeline_options):
"""
super(HadoopFileSystem, self).__init__(pipeline_options)
logging.getLogger('hdfs.client').setLevel(logging.WARN)
-
if pipeline_options is None:
raise ValueError('pipeline_options is not set')
- hdfs_options = pipeline_options.view_as(HadoopFileSystemOptions)
- if hdfs_options.hdfs_host is None:
+ if isinstance(pipeline_options, PipelineOptions):
+ hdfs_options = pipeline_options.view_as(HadoopFileSystemOptions)
+ hdfs_host = hdfs_options.hdfs_host
+ hdfs_port = hdfs_options.hdfs_port
+ hdfs_user = hdfs_options.hdfs_user
+ else:
+ hdfs_host = pipeline_options.get('hdfs_host')
+ hdfs_port = pipeline_options.get('hdfs_port')
+ hdfs_user = pipeline_options.get('hdfs_user')
+
+ if hdfs_host is None:
raise ValueError('hdfs_host is not set')
- if hdfs_options.hdfs_port is None:
+ if hdfs_port is None:
raise ValueError('hdfs_port is not set')
- if hdfs_options.hdfs_user is None:
+ if hdfs_user is None:
raise ValueError('hdfs_user is not set')
self._hdfs_client = hdfs.InsecureClient(
- 'http://%s:%s' % (
- hdfs_options.hdfs_host, str(hdfs_options.hdfs_port)),
- user=hdfs_options.hdfs_user)
+ 'http://%s:%s' % (hdfs_host, str(hdfs_port)), user=hdfs_user)
@classmethod
def scheme(cls):
@@ -188,13 +194,15 @@ def _match(path_pattern, limit):
"""Find all matching paths to the pattern provided."""
fs = self._hdfs_client.status(path_pattern, strict=False)
if fs and fs[_FILE_STATUS_TYPE] == _FILE_STATUS_TYPE_FILE:
- file_statuses = [(fs[_FILE_STATUS_PATH_SUFFIX], fs)][:limit]
+ file_statuses = [(path_pattern, fs)][:limit]
else:
- file_statuses = self._hdfs_client.list(path_pattern,
- status=True)[:limit]
- metadata_list = [FileMetadata(file_status[1][_FILE_STATUS_NAME],
- file_status[1][_FILE_STATUS_SIZE])
- for file_status in file_statuses]
+ file_statuses = [(self._join(path_pattern, fs[0]), fs[1])
+ for fs in self._hdfs_client.list(path_pattern,
+ status=True)[:limit]]
+ metadata_list = [
+ FileMetadata(_HDFS_PREFIX + file_status[0],
+ file_status[1][_FILE_STATUS_LENGTH])
+ for file_status in file_statuses]
return MatchResult(path_pattern, metadata_list)
exceptions = {}
diff --git a/sdks/python/apache_beam/io/hadoopfilesystem_test.py
b/sdks/python/apache_beam/io/hadoopfilesystem_test.py
index f6616b38dc4..6302831ebca 100644
--- a/sdks/python/apache_beam/io/hadoopfilesystem_test.py
+++ b/sdks/python/apache_beam/io/hadoopfilesystem_test.py
@@ -67,9 +67,8 @@ def size(self):
def get_file_status(self):
"""Returns a partial WebHDFS FileStatus object."""
return {
- hdfs._FILE_STATUS_NAME: self.stat['path'],
hdfs._FILE_STATUS_PATH_SUFFIX: posixpath.basename(self.stat['path']),
- hdfs._FILE_STATUS_SIZE: self.size,
+ hdfs._FILE_STATUS_LENGTH: self.size,
hdfs._FILE_STATUS_TYPE: self.stat['type'],
}
@@ -237,11 +236,6 @@ def test_url_split(self):
def test_mkdirs(self):
url = self.fs.join(self.tmpdir, 't1/t2')
self.fs.mkdirs(url)
- match_results = self.fs.match([url])
- self.assertEqual(1, len(match_results))
- self.assertEqual(1, len(match_results[0].metadata_list))
- metadata = match_results[0].metadata_list[0]
- self.assertEqual(metadata.path, self.fs._parse_url(url))
self.assertTrue(self.fs.exists(url))
def test_mkdirs_failed(self):
@@ -252,17 +246,17 @@ def test_mkdirs_failed(self):
self.fs.mkdirs(url)
def test_match_file(self):
- files = [self.fs.join(self.tmpdir, filename)
- for filename in ['old_file1', 'old_file2']]
- expected_files = [self.fs._parse_url(file) for file in files]
- result = self.fs.match(files)
+ expected_files = [self.fs.join(self.tmpdir, filename)
+ for filename in ['old_file1', 'old_file2']]
+ match_patterns = expected_files
+ result = self.fs.match(match_patterns)
returned_files = [f.path
for match_result in result
for f in match_result.metadata_list]
self.assertItemsEqual(expected_files, returned_files)
def test_match_file_with_limits(self):
- expected_files = [self.fs._parse_url(self.fs.join(self.tmpdir, filename))
+ expected_files = [self.fs.join(self.tmpdir, filename)
for filename in ['old_file1', 'old_file2']]
result = self.fs.match([self.tmpdir], [1])[0]
files = [f.path for f in result.metadata_list]
@@ -293,7 +287,7 @@ def test_match_file_error(self):
self.assertEqual(files, [self.fs._parse_url(url)])
def test_match_directory(self):
- expected_files = [self.fs._parse_url(self.fs.join(self.tmpdir, filename))
+ expected_files = [self.fs.join(self.tmpdir, filename)
for filename in ['old_file1', 'old_file2']]
result = self.fs.match([self.tmpdir])[0]
@@ -301,7 +295,7 @@ def test_match_directory(self):
self.assertItemsEqual(files, expected_files)
def test_match_directory_trailing_slash(self):
- expected_files = [self.fs._parse_url(self.fs.join(self.tmpdir, filename))
+ expected_files = [self.fs.join(self.tmpdir, filename)
for filename in ['old_file1', 'old_file2']]
result = self.fs.match([self.tmpdir + '/'])[0]
@@ -517,6 +511,52 @@ def test_delete_error(self):
self.assertFalse(self.fs.exists(url2))
+class HadoopFileSystemRuntimeValueProviderTest(unittest.TestCase):
+ """Tests pipeline_options, in the form of a
+ RuntimeValueProvider.runtime_options object."""
+
+ def test_dict_options(self):
+ self._fake_hdfs = FakeHdfs()
+ hdfs.hdfs.InsecureClient = (
+ lambda *args, **kwargs: self._fake_hdfs)
+ pipeline_options = {
+ 'hdfs_host': '',
+ 'hdfs_port': 0,
+ 'hdfs_user': '',
+ }
+
+ self.fs = hdfs.HadoopFileSystem(pipeline_options=pipeline_options)
+
+ def test_dict_options_missing(self):
+ self._fake_hdfs = FakeHdfs()
+ hdfs.hdfs.InsecureClient = (
+ lambda *args, **kwargs: self._fake_hdfs)
+
+ with self.assertRaisesRegexp(ValueError, r'hdfs_host'):
+ self.fs = hdfs.HadoopFileSystem(
+ pipeline_options={
+ 'hdfs_port': 0,
+ 'hdfs_user': '',
+ }
+ )
+
+ with self.assertRaisesRegexp(ValueError, r'hdfs_port'):
+ self.fs = hdfs.HadoopFileSystem(
+ pipeline_options={
+ 'hdfs_host': '',
+ 'hdfs_user': '',
+ }
+ )
+
+ with self.assertRaisesRegexp(ValueError, r'hdfs_user'):
+ self.fs = hdfs.HadoopFileSystem(
+ pipeline_options={
+ 'hdfs_host': '',
+ 'hdfs_port': 0,
+ }
+ )
+
+
if __name__ == '__main__':
logging.getLogger().setLevel(logging.INFO)
unittest.main()
diff --git a/sdks/python/apache_beam/io/hdfs_integration_test/Dockerfile
b/sdks/python/apache_beam/io/hdfs_integration_test/Dockerfile
index b5a5724e755..b7955e4c0f9 100644
--- a/sdks/python/apache_beam/io/hdfs_integration_test/Dockerfile
+++ b/sdks/python/apache_beam/io/hdfs_integration_test/Dockerfile
@@ -22,7 +22,9 @@
FROM python:2
WORKDIR /app
-RUN pip install --no-cache-dir holdup
+ENV HDFSCLI_CONFIG
/app/sdks/python/apache_beam/io/hdfs_integration_test/hdfscli.cfg
+RUN pip install --no-cache-dir holdup gsutil
+RUN gsutil cp gs://dataflow-samples/shakespeare/kinglear.txt .
# Install Beam and dependencies.
ADD sdks/python /app/sdks/python
@@ -32,7 +34,11 @@ RUN cd sdks/python && \
pip install --no-cache-dir $(ls dist/apache-beam-*.tar.gz | tail -n1)[gcp]
# Run wordcount, and write results to HDFS.
-CMD holdup -t 45 http://namenode:50070 && \
+CMD holdup -t 45 http://namenode:50070 http://datanode:50075 && \
+ echo "Waiting for safe mode to end." && \
+ sleep 45 && \
+ hdfscli -v -v -v upload -f kinglear.txt / && \
python -m apache_beam.examples.wordcount \
- --output hdfs://tmp/py-wordcount-direct \
+ --input hdfs://kinglear.txt \
+ --output hdfs://py-wordcount-integration \
--hdfs_host namenode --hdfs_port 50070 --hdfs_user root
diff --git a/sdks/python/apache_beam/io/hdfs_integration_test/hdfscli.cfg
b/sdks/python/apache_beam/io/hdfs_integration_test/hdfscli.cfg
new file mode 100644
index 00000000000..cb9a5a43cb8
--- /dev/null
+++ b/sdks/python/apache_beam/io/hdfs_integration_test/hdfscli.cfg
@@ -0,0 +1,22 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You 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.
+#
+[global]
+default.alias = test
+
+[test.alias]
+url = http://namenode:50070
+user = root
diff --git a/sdks/python/run_postcommit.sh b/sdks/python/run_postcommit.sh
index 041ae035e9d..951579f4759 100755
--- a/sdks/python/run_postcommit.sh
+++ b/sdks/python/run_postcommit.sh
@@ -39,7 +39,7 @@ rm -rf sdks/python/target/.tox
pip install --user --upgrade virtualenv tox
# Tox runs unit tests in a virtual environment
-${LOCAL_PATH}/tox -e ALL -c sdks/python/tox.ini -v -v
+${LOCAL_PATH}/tox -e ALL -c sdks/python/tox.ini
# Virtualenv for the rest of the script to run setup & e2e tests
${LOCAL_PATH}/virtualenv sdks/python
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Issue Time Tracking
-------------------
Worklog Id: (was: 87773)
Time Spent: 3h 40m (was: 3.5h)
> HDFS read broken in python
> --------------------------
>
> Key: BEAM-3965
> URL: https://issues.apache.org/jira/browse/BEAM-3965
> Project: Beam
> Issue Type: Bug
> Components: sdk-py-core
> Reporter: Udi Meiri
> Assignee: Udi Meiri
> Priority: Major
> Time Spent: 3h 40m
> Remaining Estimate: 0h
>
> When running a command like:
> {noformat}
> python setup.py sdist > /dev/null && python -m apache_beam.examples.wordcount
> --output gs://.../py-wordcount-output \
> --hdfs_host ... --hdfs_port 50070 --hdfs_user ehudm --runner DataflowRunner
> --project ... \
> --temp_location gs://.../temp-hdfs-int --staging_location
> gs://.../staging-hdfs-int \
> --sdk_location dist/apache-beam-2.5.0.dev0.tar.gz --input
> hdfs://kinglear.txt
> {noformat}
> I get:
> {noformat}
> Traceback (most recent call last):
> File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
> "__main__", fname, loader, pkg_name)
> File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
> File
> "/usr/local/google/home/ehudm/src/beam/sdks/python/apache_beam/examples/wordcount.py",
> line 136, in <module>
> run()
> File
> "/usr/local/google/home/ehudm/src/beam/sdks/python/apache_beam/examples/wordcount.py",
> line 90, in run
> lines = p | 'read' >> ReadFromText(known_args.input)
> File "apache_beam/io/textio.py", line 522, in __init__
> skip_header_lines=skip_header_lines)
> File "apache_beam/io/textio.py", line 117, in __init__
> validate=validate)
> File "apache_beam/io/filebasedsource.py", line 119, in __init__
> self._validate()
> File "apache_beam/options/value_provider.py", line 124, in _f
> return fnc(self, *args, **kwargs)
> File "apache_beam/io/filebasedsource.py", line 176, in _validate
> match_result = FileSystems.match([pattern], limits=[1])[0]
> File "apache_beam/io/filesystems.py", line 159, in match
> return filesystem.match(patterns, limits)
> File "apache_beam/io/hadoopfilesystem.py", line 221, in match
> raise BeamIOError('Match operation failed', exceptions)
> apache_beam.io.filesystem.BeamIOError: Match operation failed with exceptions
> {'hdfs://kinglear.txt': KeyError('name',)}
> {noformat}
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