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Hi,
Following the discussion in http://apache-spark-developers-list.1001551.n3.nabble.com/python-converter-in-HBaseConverter-scala-spark-examples-td10001.html. I made some modification in three files in package examples:
1. HBaseConverters.scala: the new converter will converts all the records in an hbase results into a single string
2. hbase_input.py: as the value string may contain several records, we can use ast package to convert the string into dict
3. HBaseTest.scala: as the package examples use hbase 0.98.7 the original constructor HTableDescriptor is deprecated. The updation to new constructor is made
Author: GenTang <gen.tang86@gmail.com>
Closes #3920 from GenTang/master and squashes the following commits:
d2153df [GenTang] import JSONObject precisely
4802481 [GenTang] dump the result into a singl String
62df7f0 [GenTang] remove the comment
21de653 [GenTang] return the string in json format
15b1fe3 [GenTang] the modification of comments
5cbbcfc [GenTang] the improvement of pythonconverter
ceb31c5 [GenTang] the modification for adapting updation of hbase
3253b61 [GenTang] the modification accompanying the improvement of pythonconverter
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....py
Author: tedyu <yuzhihong@gmail.com>
Closes #5673 from tedyu/master and squashes the following commits:
ab7c72b [tedyu] SPARK-7107 Adjust indentation to pass Python style tests
6e25939 [tedyu] Adjust line length to be shorter than 100 characters
18d172a [tedyu] SPARK-7107 Add parameter for zookeeper.znode.parent to hbase_inputformat.py
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This PR update PySpark to support Python 3 (tested with 3.4).
Known issue: unpickle array from Pyrolite is broken in Python 3, those tests are skipped.
TODO: ec2/spark-ec2.py is not fully tested with python3.
Author: Davies Liu <davies@databricks.com>
Author: twneale <twneale@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes #5173 from davies/python3 and squashes the following commits:
d7d6323 [Davies Liu] fix tests
6c52a98 [Davies Liu] fix mllib test
99e334f [Davies Liu] update timeout
b716610 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
cafd5ec [Davies Liu] adddress comments from @mengxr
bf225d7 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
179fc8d [Davies Liu] tuning flaky tests
8c8b957 [Davies Liu] fix ResourceWarning in Python 3
5c57c95 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
4006829 [Davies Liu] fix test
2fc0066 [Davies Liu] add python3 path
71535e9 [Davies Liu] fix xrange and divide
5a55ab4 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
125f12c [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ed498c8 [Davies Liu] fix compatibility with python 3
820e649 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
e8ce8c9 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ad7c374 [Davies Liu] fix mllib test and warning
ef1fc2f [Davies Liu] fix tests
4eee14a [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
20112ff [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
59bb492 [Davies Liu] fix tests
1da268c [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ca0fdd3 [Davies Liu] fix code style
9563a15 [Davies Liu] add imap back for python 2
0b1ec04 [Davies Liu] make python examples work with Python 3
d2fd566 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
a716d34 [Davies Liu] test with python 3.4
f1700e8 [Davies Liu] fix test in python3
671b1db [Davies Liu] fix test in python3
692ff47 [Davies Liu] fix flaky test
7b9699f [Davies Liu] invalidate import cache for Python 3.3+
9c58497 [Davies Liu] fix kill worker
309bfbf [Davies Liu] keep compatibility
5707476 [Davies Liu] cleanup, fix hash of string in 3.3+
8662d5b [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
f53e1f0 [Davies Liu] fix tests
70b6b73 [Davies Liu] compile ec2/spark_ec2.py in python 3
a39167e [Davies Liu] support customize class in __main__
814c77b [Davies Liu] run unittests with python 3
7f4476e [Davies Liu] mllib tests passed
d737924 [Davies Liu] pass ml tests
375ea17 [Davies Liu] SQL tests pass
6cc42a9 [Davies Liu] rename
431a8de [Davies Liu] streaming tests pass
78901a7 [Davies Liu] fix hash of serializer in Python 3
24b2f2e [Davies Liu] pass all RDD tests
35f48fe [Davies Liu] run future again
1eebac2 [Davies Liu] fix conflict in ec2/spark_ec2.py
6e3c21d [Davies Liu] make cloudpickle work with Python3
2fb2db3 [Josh Rosen] Guard more changes behind sys.version; still doesn't run
1aa5e8f [twneale] Turned out `pickle.DictionaryType is dict` == True, so swapped it out
7354371 [twneale] buffer --> memoryview I'm not super sure if this a valid change, but the 2.7 docs recommend using memoryview over buffer where possible, so hoping it'll work.
b69ccdf [twneale] Uses the pure python pickle._Pickler instead of c-extension _pickle.Pickler. It appears pyspark 2.7 uses the pure python pickler as well, so this shouldn't degrade pickling performance (?).
f40d925 [twneale] xrange --> range
e104215 [twneale] Replaces 2.7 types.InstsanceType with 3.4 `object`....could be horribly wrong depending on how types.InstanceType is used elsewhere in the package--see http://bugs.python.org/issue8206
79de9d0 [twneale] Replaces python2.7 `file` with 3.4 _io.TextIOWrapper
2adb42d [Josh Rosen] Fix up some import differences between Python 2 and 3
854be27 [Josh Rosen] Run `futurize` on Python code:
7c5b4ce [Josh Rosen] Remove Python 3 check in shell.py.
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This PR resolves [SPARK-3361](https://issues.apache.org/jira/browse/SPARK-3361) by expanding the PEP 8 checks to cover the remaining Python code base:
* The EC2 script
* All Python / PySpark examples
Author: Nicholas Chammas <nicholas.chammas@gmail.com>
Closes #2297 from nchammas/pep8-rulez and squashes the following commits:
1e5ac9a [Nicholas Chammas] PEP 8 fixes to Python examples
c3dbeff [Nicholas Chammas] PEP 8 fixes to EC2 script
65ef6e8 [Nicholas Chammas] expand PEP 8 checks
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Added examples for statistical summarization:
* Scala: StatisticalSummary.scala
** Tests: correlation, MultivariateOnlineSummarizer
* python: statistical_summary.py
** Tests: correlation (since MultivariateOnlineSummarizer has no Python API)
Added examples for random and sampled RDDs:
* Scala: RandomAndSampledRDDs.scala
* python: random_and_sampled_rdds.py
* Both test:
** RandomRDDGenerators.normalRDD, normalVectorRDD
** RDD.sample, takeSample, sampleByKey
Added sc.stop() to all examples.
CorrelationSuite.scala
* Added 1 test for RDDs with only 1 value
RowMatrix.scala
* numCols(): Added check for numRows = 0, with error message.
* computeCovariance(): Added check for numRows <= 1, with error message.
Python SparseVector (pyspark/mllib/linalg.py)
* Added toDense() function
python/run-tests script
* Added stat.py (doc test)
CC: mengxr dorx Main changes were examples to show usage across APIs.
Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>
Closes #1878 from jkbradley/mllib-stats-api-check and squashes the following commits:
ea5c047 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
dafebe2 [Joseph K. Bradley] Bug fixes for examples SampledRDDs.scala and sampled_rdds.py: Check for division by 0 and for missing key in maps.
8d1e555 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
60c72d9 [Joseph K. Bradley] Fixed stat.py doc test to work for Python versions printing nan or NaN.
b20d90a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
4e5d15e [Joseph K. Bradley] Changed pyspark/mllib/stat.py doc tests to use NaN instead of nan.
32173b7 [Joseph K. Bradley] Stats examples update.
c8c20dc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
cf70b07 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
0b7cec3 [Joseph K. Bradley] Small updates based on code review. Renamed statistical_summary.py to correlations.py
ab48f6e [Joseph K. Bradley] RowMatrix.scala * numCols(): Added check for numRows = 0, with error message. * computeCovariance(): Added check for numRows <= 1, with error message.
65e4ebc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
8195c78 [Joseph K. Bradley] Added examples for random and sampled RDDs: * Scala: RandomAndSampledRDDs.scala * python: random_and_sampled_rdds.py * Both test: ** RandomRDDGenerators.normalRDD, normalVectorRDD ** RDD.sample, takeSample, sampleByKey
064985b [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into mllib-stats-api-check
ee918e9 [Joseph K. Bradley] Added examples for statistical summarization: * Scala: StatisticalSummary.scala ** Tests: correlation, MultivariateOnlineSummarizer * python: statistical_summary.py ** Tests: correlation (since MultivariateOnlineSummarizer has no Python API)
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JIRA issue: https://issues.apache.org/jira/browse/SPARK-2024
This PR is a followup to #455 and adds capabilities for saving PySpark RDDs using SequenceFile or any Hadoop OutputFormats.
* Added RDD methods ```saveAsSequenceFile```, ```saveAsHadoopFile``` and ```saveAsHadoopDataset```, for both old and new MapReduce APIs.
* Default converter for converting common data types to Writables. Users may specify custom converters to convert to desired data types.
* No out-of-box support for reading/writing arrays, since ArrayWritable itself doesn't have a no-arg constructor for creating an empty instance upon reading. Users need to provide ArrayWritable subtypes. Custom converters for converting arrays to suitable ArrayWritable subtypes are also needed when writing. When reading, the default converter will convert any custom ArrayWritable subtypes to ```Object[]``` and they get pickled to Python tuples.
* Added HBase and Cassandra output examples to show how custom output formats and converters can be used.
cc MLnick mateiz ahirreddy pwendell
Author: Kan Zhang <kzhang@apache.org>
Closes #1338 from kanzhang/SPARK-2024 and squashes the following commits:
c01e3ef [Kan Zhang] [SPARK-2024] code formatting
6591e37 [Kan Zhang] [SPARK-2024] renaming pickled -> pickledRDD
d998ad6 [Kan Zhang] [SPARK-2024] refectoring to get method params below 10
57a7a5e [Kan Zhang] [SPARK-2024] correcting typo
75ca5bd [Kan Zhang] [SPARK-2024] Better type checking for batch serialized RDD
0bdec55 [Kan Zhang] [SPARK-2024] Refactoring newly added tests
9f39ff4 [Kan Zhang] [SPARK-2024] Adding 2 saveAsHadoopDataset tests
0c134f3 [Kan Zhang] [SPARK-2024] Test refactoring and adding couple unbatched cases
7a176df [Kan Zhang] [SPARK-2024] Add saveAsSequenceFile to PySpark
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So I finally resurrected this PR. It seems the old one against the incubator mirror is no longer available, so I cannot reference it.
This adds initial support for reading Hadoop ```SequenceFile```s, as well as arbitrary Hadoop ```InputFormat```s, in PySpark.
# Overview
The basics are as follows:
1. ```PythonRDD``` object contains the relevant methods, that are in turn invoked by ```SparkContext``` in PySpark
2. The SequenceFile or InputFormat is read on the Scala side and converted from ```Writable``` instances to the relevant Scala classes (in the case of primitives)
3. Pyrolite is used to serialize Java objects. If this fails, the fallback is ```toString```
4. ```PickleSerializer``` on the Python side deserializes.
This works "out the box" for simple ```Writable```s:
* ```Text```
* ```IntWritable```, ```DoubleWritable```, ```FloatWritable```
* ```NullWritable```
* ```BooleanWritable```
* ```BytesWritable```
* ```MapWritable```
It also works for simple, "struct-like" classes. Due to the way Pyrolite works, this requires that the classes satisfy the JavaBeans convenstions (i.e. with fields and a no-arg constructor and getters/setters). (Perhaps in future some sugar for case classes and reflection could be added).
I've tested it out with ```ESInputFormat``` as an example and it works very nicely:
```python
conf = {"es.resource" : "index/type" }
rdd = sc.newAPIHadoopRDD("org.elasticsearch.hadoop.mr.EsInputFormat", "org.apache.hadoop.io.NullWritable", "org.elasticsearch.hadoop.mr.LinkedMapWritable", conf=conf)
rdd.first()
```
I suspect for things like HBase/Cassandra it will be a bit trickier to get it to work out the box.
# Some things still outstanding:
1. ~~Requires ```msgpack-python``` and will fail without it. As originally discussed with Josh, add a ```as_strings``` argument that defaults to ```False```, that can be used if ```msgpack-python``` is not available~~
2. ~~I see from https://github.com/apache/spark/pull/363 that Pyrolite is being used there for SerDe between Scala and Python. @ahirreddy @mateiz what is the plan behind this - is Pyrolite preferred? It seems from a cursory glance that adapting the ```msgpack```-based SerDe here to use Pyrolite wouldn't be too hard~~
3. ~~Support the key and value "wrapper" that would allow a Scala/Java function to be plugged in that would transform whatever the key/value Writable class is into something that can be serialized (e.g. convert some custom Writable to a JavaBean or ```java.util.Map``` that can be easily serialized)~~
4. Support ```saveAsSequenceFile``` and ```saveAsHadoopFile``` etc. This would require SerDe in the reverse direction, that can be handled by Pyrolite. Will work on this as a separate PR
Author: Nick Pentreath <nick.pentreath@gmail.com>
Closes #455 from MLnick/pyspark-inputformats and squashes the following commits:
268df7e [Nick Pentreath] Documentation changes mer @pwendell comments
761269b [Nick Pentreath] Address @pwendell comments, simplify default writable conversions and remove registry.
4c972d8 [Nick Pentreath] Add license headers
d150431 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
cde6af9 [Nick Pentreath] Parameterize converter trait
5ebacfa [Nick Pentreath] Update docs for PySpark input formats
a985492 [Nick Pentreath] Move Converter examples to own package
365d0be [Nick Pentreath] Make classes private[python]. Add docs and @Experimental annotation to Converter interface.
eeb8205 [Nick Pentreath] Fix path relative to SPARK_HOME in tests
1eaa08b [Nick Pentreath] HBase -> Cassandra app name oversight
3f90c3e [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
2c18513 [Nick Pentreath] Add examples for reading HBase and Cassandra InputFormats from Python
b65606f [Nick Pentreath] Add converter interface
5757f6e [Nick Pentreath] Default key/value classes for sequenceFile asre None
085b55f [Nick Pentreath] Move input format tests to tests.py and clean up docs
43eb728 [Nick Pentreath] PySpark InputFormats docs into programming guide
94beedc [Nick Pentreath] Clean up args in PythonRDD. Set key/value converter defaults to None for PySpark context.py methods
1a4a1d6 [Nick Pentreath] Address @mateiz style comments
01e0813 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
15a7d07 [Nick Pentreath] Remove default args for key/value classes. Arg names to camelCase
9fe6bd5 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
84fe8e3 [Nick Pentreath] Python programming guide space formatting
d0f52b6 [Nick Pentreath] Python programming guide
7caa73a [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
93ef995 [Nick Pentreath] Add back context.py changes
9ef1896 [Nick Pentreath] Recover earlier changes lost in previous merge for serializers.py
077ecb2 [Nick Pentreath] Recover earlier changes lost in previous merge for context.py
5af4770 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
35b8e3a [Nick Pentreath] Another fix for test ordering
bef3afb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
e001b94 [Nick Pentreath] Fix test failures due to ordering
78978d9 [Nick Pentreath] Add doc for SequenceFile and InputFormat support to Python programming guide
64eb051 [Nick Pentreath] Scalastyle fix
e7552fa [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
44f2857 [Nick Pentreath] Remove msgpack dependency and switch serialization to Pyrolite, plus some clean up and refactoring
c0ebfb6 [Nick Pentreath] Change sequencefile test data generator to easily be called from PySpark tests
1d7c17c [Nick Pentreath] Amend tests to auto-generate sequencefile data in temp dir
17a656b [Nick Pentreath] remove binary sequencefile for tests
f60959e [Nick Pentreath] Remove msgpack dependency and serializer from PySpark
450e0a2 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
31a2fff [Nick Pentreath] Scalastyle fixes
fc5099e [Nick Pentreath] Add Apache license headers
4e08983 [Nick Pentreath] Clean up docs for PySpark context methods
b20ec7e [Nick Pentreath] Clean up merge duplicate dependencies
951c117 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
f6aac55 [Nick Pentreath] Bring back msgpack
9d2256e [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
1bbbfb0 [Nick Pentreath] Clean up SparkBuild from merge
a67dfad [Nick Pentreath] Clean up Msgpack serialization and registering
7237263 [Nick Pentreath] Add back msgpack serializer and hadoop file code lost during merging
25da1ca [Nick Pentreath] Add generator for nulls, bools, bytes and maps
65360d5 [Nick Pentreath] Adding test SequenceFiles
0c612e5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
d72bf18 [Nick Pentreath] msgpack
dd57922 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
e67212a [Nick Pentreath] Add back msgpack dependency
f2d76a0 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
41856a5 [Nick Pentreath] Merge branch 'master' into pyspark-inputformats
97ef708 [Nick Pentreath] Remove old writeToStream
2beeedb [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
795a763 [Nick Pentreath] Change name to WriteInputFormatTestDataGenerator. Cleanup some var names. Use SPARK_HOME in path for writing test sequencefile data.
174f520 [Nick Pentreath] Add back graphx settings
703ee65 [Nick Pentreath] Add back msgpack
619c0fa [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
1c8efbc [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
eb40036 [Nick Pentreath] Remove unused comment lines
4d7ef2e [Nick Pentreath] Fix indentation
f1d73e3 [Nick Pentreath] mergeConfs returns a copy rather than mutating one of the input arguments
0f5cd84 [Nick Pentreath] Remove unused pair UTF8 class. Add comments to msgpack deserializer
4294cbb [Nick Pentreath] Add old Hadoop api methods. Clean up and expand comments. Clean up argument names
818a1e6 [Nick Pentreath] Add seqencefile and Hadoop InputFormat support to PythonRDD
4e7c9e3 [Nick Pentreath] Merge remote-tracking branch 'upstream/master' into pyspark-inputformats
c304cc8 [Nick Pentreath] Adding supporting sequncefiles for tests. Cleaning up
4b0a43f [Nick Pentreath] Refactoring utils into own objects. Cleaning up old commented-out code
d86325f [Nick Pentreath] Initial WIP of PySpark support for SequenceFile and arbitrary Hadoop InputFormat
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