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* [SPARK-2079] Support batching when serializing SchemaRDD to PythonKan Zhang2014-06-141-1/+3
| | | | | | | | | | | Added batching with default batch size 10 in SchemaRDD.javaToPython Author: Kan Zhang <kzhang@apache.org> Closes #1023 from kanzhang/SPARK-2079 and squashes the following commits: 2d1915e [Kan Zhang] [SPARK-2079] Add batching in SchemaRDD.javaToPython 19b0c09 [Kan Zhang] [SPARK-2079] Removing unnecessary wrapping in SchemaRDD.javaToPython
* SPARK-1939 Refactor takeSample method in RDD to use ScaSRSDoris Xin2014-06-121-61/+106
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Modified the takeSample method in RDD to use the ScaSRS sampling technique to improve performance. Added a private method that computes sampling rate > sample_size/total to ensure sufficient sample size with success rate >= 0.9999. Added a unit test for the private method to validate choice of sampling rate. Author: Doris Xin <doris.s.xin@gmail.com> Author: dorx <doris.s.xin@gmail.com> Author: Xiangrui Meng <meng@databricks.com> Closes #916 from dorx/takeSample and squashes the following commits: 5b061ae [Doris Xin] merge master 444e750 [Doris Xin] edge cases 3de882b [dorx] Merge pull request #2 from mengxr/SPARK-1939 82dde31 [Xiangrui Meng] update pyspark's takeSample 48d954d [Doris Xin] remove unused imports from RDDSuite fb1452f [Doris Xin] allowing num to be greater than count in all cases 1481b01 [Doris Xin] washing test tubes and making coffee dc699f3 [Doris Xin] give back imports removed by accident in rdd.py 64e445b [Doris Xin] logwarnning as soon as it enters the while loop 55518ed [Doris Xin] added TODO for logging in rdd.py eff89e2 [Doris Xin] addressed reviewer comments. ecab508 [Doris Xin] "fixed checkstyle violation 0a9b3e3 [Doris Xin] "reviewer comment addressed" f80f270 [Doris Xin] Merge branch 'master' into takeSample ae3ad04 [Doris Xin] fixed edge cases to prevent overflow 065ebcd [Doris Xin] Merge branch 'master' into takeSample 9bdd36e [Doris Xin] Check sample size and move computeFraction e3fd6a6 [Doris Xin] Merge branch 'master' into takeSample 7cab53a [Doris Xin] fixed import bug in rdd.py ffea61a [Doris Xin] SPARK-1939: Refactor takeSample method in RDD 1441977 [Doris Xin] SPARK-1939 Refactor takeSample method in RDD to use ScaSRS
* SPARK-554. Add aggregateByKey.Sandy Ryza2014-06-122-1/+33
| | | | | | | | | | | | | | Author: Sandy Ryza <sandy@cloudera.com> Closes #705 from sryza/sandy-spark-554 and squashes the following commits: 2302b8f [Sandy Ryza] Add MIMA exclude f52e0ad [Sandy Ryza] Fix Python tests for real 2f3afa3 [Sandy Ryza] Fix Python test 0b735e9 [Sandy Ryza] Fix line lengths ae56746 [Sandy Ryza] Fix doc (replace T with V) c2be415 [Sandy Ryza] Java and Python aggregateByKey 23bf400 [Sandy Ryza] SPARK-554. Add aggregateByKey.
* fixed typo in docstring for min()Jeff Thompson2014-06-121-1/+1
| | | | | | | | | | Hi, I found this typo while learning spark and thought I'd do a pull request. Author: Jeff Thompson <jeffreykeatingthompson@gmail.com> Closes #1065 from jkthompson/docstring-typo-minmax and squashes the following commits: 29b6a26 [Jeff Thompson] fixed typo in docstring for min()
* HOTFIX: PySpark tests should be order insensitive.Patrick Wendell2014-06-111-4/+4
| | | | | | | | | | | This has been messing up the SQL PySpark tests on Jenkins. Author: Patrick Wendell <pwendell@gmail.com> Closes #1054 from pwendell/pyspark and squashes the following commits: 1eb5487 [Patrick Wendell] False change 06f062d [Patrick Wendell] HOTFIX: PySpark tests should be order insensitive
* HOTFIX: A few PySpark tests were not actually runAndrew Or2014-06-111-1/+4
| | | | | | | | | | | | | | | | This is a hot fix for the hot fix in fb499be1ac935b6f91046ec8ff23ac1267c82342. The changes in that commit did not actually cause the `doctest` module in python to be loaded for the following tests: - pyspark/broadcast.py - pyspark/accumulators.py - pyspark/serializers.py (@pwendell I might have told you the wrong thing) Author: Andrew Or <andrewor14@gmail.com> Closes #1053 from andrewor14/python-test-fix and squashes the following commits: d2e5401 [Andrew Or] Explain why these tests are handled differently 0bd6fdd [Andrew Or] Fix 3 pyspark tests not being invoked
* [SPARK-2091][MLLIB] use numpy.dot instead of ndarray.dotXiangrui Meng2014-06-111-3/+5
| | | | | | | | | | `ndarray.dot` is not available in numpy 1.4. This PR makes pyspark/mllib compatible with numpy 1.4. Author: Xiangrui Meng <meng@databricks.com> Closes #1035 from mengxr/numpy-1.4 and squashes the following commits: 7ad2f0c [Xiangrui Meng] use numpy.dot instead of ndarray.dot
* HOTFIX: Fix Python tests on Jenkins.Patrick Wendell2014-06-101-4/+7
| | | | | | | | | | Author: Patrick Wendell <pwendell@gmail.com> Closes #1036 from pwendell/jenkins-test and squashes the following commits: 9c99856 [Patrick Wendell] Better output during tests 71e7b74 [Patrick Wendell] Removing incorrect python path 74984db [Patrick Wendell] HOTFIX: Allow PySpark tests to run on Jenkins.
* SPARK-1416: PySpark support for SequenceFile and Hadoop InputFormatsNick Pentreath2014-06-092-0/+282
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* [SPARK-1308] Add getNumPartitions to pyspark RDDSyed Hashmi2014-06-091-18/+27
| | | | | | | | | | Add getNumPartitions to pyspark RDD to provide an intuitive way to get number of partitions in RDD like we can do in scala today. Author: Syed Hashmi <shashmi@cloudera.com> Closes #995 from syedhashmi/master and squashes the following commits: de0ed5e [Syed Hashmi] [SPARK-1308] Add getNumPartitions to pyspark RDD
* [SPARK-1752][MLLIB] Standardize text format for vectors and labeled pointsXiangrui Meng2014-06-044-51/+129
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | We should standardize the text format used to represent vectors and labeled points. The proposed formats are the following: 1. dense vector: `[v0,v1,..]` 2. sparse vector: `(size,[i0,i1],[v0,v1])` 3. labeled point: `(label,vector)` where "(..)" indicates a tuple and "[...]" indicate an array. `loadLabeledPoints` is added to pyspark's `MLUtils`. I didn't add `loadVectors` to pyspark because `RDD.saveAsTextFile` cannot stringify dense vectors in the proposed format automatically. `MLUtils#saveLabeledData` and `MLUtils#loadLabeledData` are deprecated. Users should use `RDD#saveAsTextFile` and `MLUtils#loadLabeledPoints` instead. In Scala, `MLUtils#loadLabeledPoints` is compatible with the format used by `MLUtils#loadLabeledData`. CC: @mateiz, @srowen Author: Xiangrui Meng <meng@databricks.com> Closes #685 from mengxr/labeled-io and squashes the following commits: 2d1116a [Xiangrui Meng] make loadLabeledData/saveLabeledData deprecated since 1.0.1 297be75 [Xiangrui Meng] change LabeledPoint.parse to LabeledPointParser.parse to maintain binary compatibility d6b1473 [Xiangrui Meng] Merge branch 'master' into labeled-io 56746ea [Xiangrui Meng] replace # by . 623a5f0 [Xiangrui Meng] merge master f06d5ba [Xiangrui Meng] add docs and minor updates 640fe0c [Xiangrui Meng] throw SparkException 5bcfbc4 [Xiangrui Meng] update test to add scientific notations e86bf38 [Xiangrui Meng] remove NumericTokenizer 050fca4 [Xiangrui Meng] use StringTokenizer 6155b75 [Xiangrui Meng] merge master f644438 [Xiangrui Meng] remove parse methods based on eval from pyspark a41675a [Xiangrui Meng] python loadLabeledPoint uses Scala's implementation ce9a475 [Xiangrui Meng] add deserialize_labeled_point to pyspark with tests e9fcd49 [Xiangrui Meng] add serializeLabeledPoint and tests aea4ae3 [Xiangrui Meng] minor updates 810d6df [Xiangrui Meng] update tokenizer/parser implementation 7aac03a [Xiangrui Meng] remove Scala parsers c1885c1 [Xiangrui Meng] add headers and minor changes b0c50cb [Xiangrui Meng] add customized parser d731817 [Xiangrui Meng] style update 63dc396 [Xiangrui Meng] add loadLabeledPoints to pyspark ea122b5 [Xiangrui Meng] Merge branch 'master' into labeled-io cd6c78f [Xiangrui Meng] add __str__ and parse to LabeledPoint a7a178e [Xiangrui Meng] add stringify to pyspark's Vectors 5c2dbfa [Xiangrui Meng] add parse to pyspark's Vectors 7853f88 [Xiangrui Meng] update pyspark's SparseVector.__str__ e761d32 [Xiangrui Meng] make LabelPoint.parse compatible with the dense format used before v1.0 and deprecate loadLabeledData and saveLabeledData 9e63a02 [Xiangrui Meng] add loadVectors and loadLabeledPoints 19aa523 [Xiangrui Meng] update toString and add parsers for Vectors and LabeledPoint
* [SPARK-1161] Add saveAsPickleFile and SparkContext.pickleFile in PythonKan Zhang2014-06-032-8/+39
| | | | | | | | | | Author: Kan Zhang <kzhang@apache.org> Closes #755 from kanzhang/SPARK-1161 and squashes the following commits: 24ed8a2 [Kan Zhang] [SPARK-1161] Fixing doc tests 44e0615 [Kan Zhang] [SPARK-1161] Adding an optional batchSize with default value 10 d929429 [Kan Zhang] [SPARK-1161] Add saveAsObjectFile and SparkContext.objectFile in Python
* [SPARK-1468] Modify the partition function used by partitionBy.Erik Selin2014-06-031-1/+4
| | | | | | | | | | | | | | Make partitionBy use a tweaked version of hash as its default partition function since the python hash function does not consistently assign the same value to None across python processes. Associated JIRA at https://issues.apache.org/jira/browse/SPARK-1468 Author: Erik Selin <erik.selin@jadedpixel.com> Closes #371 from tyro89/consistent_hashing and squashes the following commits: 201c301 [Erik Selin] Make partitionBy use a tweaked version of hash as its default partition function since the python hash function does not consistently assign the same value to None across python processes.
* [SPARK-1942] Stop clearing spark.driver.port in unit testsSyed Hashmi2014-06-031-4/+0
| | | | | | | | | | | | | | | | | | | stop resetting spark.driver.port in unit tests (scala, java and python). Author: Syed Hashmi <shashmi@cloudera.com> Author: CodingCat <zhunansjtu@gmail.com> Closes #943 from syedhashmi/master and squashes the following commits: 885f210 [Syed Hashmi] Removing unnecessary file (created by mergetool) b8bd4b5 [Syed Hashmi] Merge remote-tracking branch 'upstream/master' b895e59 [Syed Hashmi] Revert "[SPARK-1784] Add a new partitioner" 57b6587 [Syed Hashmi] Revert "[SPARK-1784] Add a balanced partitioner" 1574769 [Syed Hashmi] [SPARK-1942] Stop clearing spark.driver.port in unit tests 4354836 [Syed Hashmi] Revert "SPARK-1686: keep schedule() calling in the main thread" fd36542 [Syed Hashmi] [SPARK-1784] Add a balanced partitioner 6668015 [CodingCat] SPARK-1686: keep schedule() calling in the main thread 4ca94cc [Syed Hashmi] [SPARK-1784] Add a new partitioner
* SPARK-1917: fix PySpark import of scipy.special functionsUri Laserson2014-05-312-1/+25
| | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-1917 Author: Uri Laserson <laserson@cloudera.com> Closes #866 from laserson/SPARK-1917 and squashes the following commits: d947e8c [Uri Laserson] Added test for scipy.special importing 1798bbd [Uri Laserson] SPARK-1917: fix PySpark import of scipy.special
* SPARK-1839: PySpark RDD#take() shouldn't always read from driverAaron Davidson2014-05-312-21/+64
| | | | | | | | | | This patch simply ports over the Scala implementation of RDD#take(), which reads the first partition at the driver, then decides how many more partitions it needs to read and will possibly start a real job if it's more than 1. (Note that SparkContext#runJob(allowLocal=true) only runs the job locally if there's 1 partition selected and no parent stages.) Author: Aaron Davidson <aaron@databricks.com> Closes #922 from aarondav/take and squashes the following commits: fa06df9 [Aaron Davidson] SPARK-1839: PySpark RDD#take() shouldn't always read from driver
* Added doctest and method description in context.pyJyotiska NK2014-05-281-1/+14
| | | | | | | | | | | Added doctest for method textFile and description for methods _initialize_context and _ensure_initialized in context.py Author: Jyotiska NK <jyotiska123@gmail.com> Closes #187 from jyotiska/pyspark_context and squashes the following commits: 356f945 [Jyotiska NK] Added doctest for textFile method in context.py 5b23686 [Jyotiska NK] Updated context.py with method descriptions
* Fix PEP8 violations in Python mllib.Reynold Xin2014-05-258-88/+78
| | | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #871 from rxin/mllib-pep8 and squashes the following commits: 848416f [Reynold Xin] Fixed a typo in the previous cleanup (c -> sc). a8db4cd [Reynold Xin] Fix PEP8 violations in Python mllib.
* Python docstring update for sql.py.Reynold Xin2014-05-251-61/+63
| | | | | | | | | | | | | | Mostly related to the following two rules in PEP8 and PEP257: - Line length < 72 chars. - First line should be a concise description of the function/class. Author: Reynold Xin <rxin@apache.org> Closes #869 from rxin/docstring-schemardd and squashes the following commits: 7cf0cbc [Reynold Xin] Updated sql.py for pep8 docstring. 0a4aef9 [Reynold Xin] Merge branch 'master' into docstring-schemardd 6678937 [Reynold Xin] Python docstring update for sql.py.
* SPARK-1822: Some minor cleanup work on SchemaRDD.count()Reynold Xin2014-05-251-1/+4
| | | | | | | | | | Minor cleanup following #841. Author: Reynold Xin <rxin@apache.org> Closes #868 from rxin/schema-count and squashes the following commits: 5442651 [Reynold Xin] SPARK-1822: Some minor cleanup work on SchemaRDD.count()
* [SPARK-1822] SchemaRDD.count() should use query optimizerKan Zhang2014-05-251-1/+13
| | | | | | | | | | Author: Kan Zhang <kzhang@apache.org> Closes #841 from kanzhang/SPARK-1822 and squashes the following commits: 2f8072a [Kan Zhang] [SPARK-1822] Minor style update cf4baa4 [Kan Zhang] [SPARK-1822] Adding Scaladoc e67c910 [Kan Zhang] [SPARK-1822] SchemaRDD.count() should use optimizer
* [SPARK-1900 / 1918] PySpark on YARN is brokenAndrew Or2014-05-241-2/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | If I run the following on a YARN cluster ``` bin/spark-submit sheep.py --master yarn-client ``` it fails because of a mismatch in paths: `spark-submit` thinks that `sheep.py` resides on HDFS, and balks when it can't find the file there. A natural workaround is to add the `file:` prefix to the file: ``` bin/spark-submit file:/path/to/sheep.py --master yarn-client ``` However, this also fails. This time it is because python does not understand URI schemes. This PR fixes this by automatically resolving all paths passed as command line argument to `spark-submit` properly. This has the added benefit of keeping file and jar paths consistent across different cluster modes. For python, we strip the URI scheme before we actually try to run it. Much of the code is originally written by @mengxr. Tested on YARN cluster. More tests pending. Author: Andrew Or <andrewor14@gmail.com> Closes #853 from andrewor14/submit-paths and squashes the following commits: 0bb097a [Andrew Or] Format path correctly before adding it to PYTHONPATH 323b45c [Andrew Or] Include --py-files on PYTHONPATH for pyspark shell 3c36587 [Andrew Or] Improve error messages (minor) 854aa6a [Andrew Or] Guard against NPE if user gives pathological paths 6638a6b [Andrew Or] Fix spark-shell jar paths after #849 went in 3bb0359 [Andrew Or] Update more comments (minor) 2a1f8a0 [Andrew Or] Update comments (minor) 6af2c77 [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-paths a68c4d1 [Andrew Or] Handle Windows python file path correctly 427a250 [Andrew Or] Resolve paths properly for Windows a591a4a [Andrew Or] Update tests for resolving URIs 6c8621c [Andrew Or] Move resolveURIs to Utils db8255e [Andrew Or] Merge branch 'master' of github.com:apache/spark into submit-paths f542dce [Andrew Or] Fix outdated tests 691c4ce [Andrew Or] Ignore special primary resource names 5342ac7 [Andrew Or] Add missing space in error message 02f77f3 [Andrew Or] Resolve command line arguments to spark-submit properly
* [SPARK-1519] Support minPartitions param of wholeTextFiles() in PySparkKan Zhang2014-05-211-2/+10
| | | | | | | | Author: Kan Zhang <kzhang@apache.org> Closes #697 from kanzhang/SPARK-1519 and squashes the following commits: 4f8d1ed [Kan Zhang] [SPARK-1519] Support minPartitions param of wholeTextFiles() in PySpark
* [SPARK-1808] Route bin/pyspark through Spark submitAndrew Or2014-05-162-5/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | **Problem.** For `bin/pyspark`, there is currently no other way to specify Spark configuration properties other than through `SPARK_JAVA_OPTS` in `conf/spark-env.sh`. However, this mechanism is supposedly deprecated. Instead, it needs to pick up configurations explicitly specified in `conf/spark-defaults.conf`. **Solution.** Have `bin/pyspark` invoke `bin/spark-submit`, like all of its counterparts in Scala land (i.e. `bin/spark-shell`, `bin/run-example`). This has the additional benefit of making the invocation of all the user facing Spark scripts consistent. **Details.** `bin/pyspark` inherently handles two cases: (1) running python applications and (2) running the python shell. For (1), Spark submit already handles running python applications. For cases in which `bin/pyspark` is given a python file, we can simply call pass the file directly to Spark submit and let it handle the rest. For case (2), `bin/pyspark` starts a python process as before, which launches the JVM as a sub-process. The existing code already provides a code path to do this. All we needed to change is to use `bin/spark-submit` instead of `spark-class` to launch the JVM. This requires modifications to Spark submit to handle the pyspark shell as a special case. This has been tested locally (OSX and Windows 7), on a standalone cluster, and on a YARN cluster. Running IPython also works as before, except now it takes in Spark submit arguments too. Author: Andrew Or <andrewor14@gmail.com> Closes #799 from andrewor14/pyspark-submit and squashes the following commits: bf37e36 [Andrew Or] Minor changes 01066fa [Andrew Or] bin/pyspark for Windows c8cb3bf [Andrew Or] Handle perverse app names (with escaped quotes) 1866f85 [Andrew Or] Windows is not cooperating 456d844 [Andrew Or] Guard against shlex hanging if PYSPARK_SUBMIT_ARGS is not set 7eebda8 [Andrew Or] Merge branch 'master' of github.com:apache/spark into pyspark-submit b7ba0d8 [Andrew Or] Address a few comments (minor) 06eb138 [Andrew Or] Use shlex instead of writing our own parser 05879fa [Andrew Or] Merge branch 'master' of github.com:apache/spark into pyspark-submit a823661 [Andrew Or] Fix --die-on-broken-pipe not propagated properly 6fba412 [Andrew Or] Deal with quotes + address various comments fe4c8a7 [Andrew Or] Update --help for bin/pyspark afe47bf [Andrew Or] Fix spark shell f04aaa4 [Andrew Or] Merge branch 'master' of github.com:apache/spark into pyspark-submit a371d26 [Andrew Or] Route bin/pyspark through Spark submit
* Documentation: Encourage use of reduceByKey instead of groupByKey.Patrick Wendell2014-05-141-0/+4
| | | | | | | | | Author: Patrick Wendell <pwendell@gmail.com> Closes #784 from pwendell/group-by-key and squashes the following commits: 9b4505f [Patrick Wendell] Small fix 6347924 [Patrick Wendell] Documentation: Encourage use of reduceByKey instead of groupByKey.
* [FIX] do not load defaults when testing SparkConf in pysparkXiangrui Meng2014-05-141-1/+1
| | | | | | | | | | The default constructor loads default properties, which can fail the test. Author: Xiangrui Meng <meng@databricks.com> Closes #775 from mengxr/pyspark-conf-fix and squashes the following commits: 83ef6c4 [Xiangrui Meng] do not load defaults when testing SparkConf in pyspark
* [SQL] Make it possible to create Java/Python SQLContexts from an existing ↵Michael Armbrust2014-05-131-2/+5
| | | | | | | | | | Scala SQLContext. Author: Michael Armbrust <michael@databricks.com> Closes #761 from marmbrus/existingContext and squashes the following commits: 4651051 [Michael Armbrust] Make it possible to create Java/Python SQLContexts from an existing Scala SQLContext.
* [SPARK-1690] Tolerating empty elements when saving Python RDD to text filesKan Zhang2014-05-101-0/+8
| | | | | | | | | | | Tolerate empty strings in PythonRDD Author: Kan Zhang <kzhang@apache.org> Closes #644 from kanzhang/SPARK-1690 and squashes the following commits: c62ad33 [Kan Zhang] Adding Python doctest 473ec4b [Kan Zhang] [SPARK-1690] Tolerating empty elements when saving Python RDD to text files
* Add Python includes to path before depickling broadcast valuesBouke van der Bijl2014-05-101-7/+7
| | | | | | | | | | | | This fixes https://issues.apache.org/jira/browse/SPARK-1731 by adding the Python includes to the PYTHONPATH before depickling the broadcast values @airhorns Author: Bouke van der Bijl <boukevanderbijl@gmail.com> Closes #656 from bouk/python-includes-before-broadcast and squashes the following commits: 7b0dfe4 [Bouke van der Bijl] Add Python includes to path before depickling broadcast values
* [SPARK-1743][MLLIB] add loadLibSVMFile and saveAsLibSVMFile to pysparkXiangrui Meng2014-05-072-2/+178
| | | | | | | | | | | | | Make loading/saving labeled data easier for pyspark users. Also changed type check in `SparseVector` to allow numpy integers. Author: Xiangrui Meng <meng@databricks.com> Closes #672 from mengxr/pyspark-mllib-util and squashes the following commits: 2943fa7 [Xiangrui Meng] format docs d61668d [Xiangrui Meng] add loadLibSVMFile and saveAsLibSVMFile to pyspark
* SPARK-1579: Clean up PythonRDD and avoid swallowing IOExceptionsAaron Davidson2014-05-072-2/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch includes several cleanups to PythonRDD, focused around fixing [SPARK-1579](https://issues.apache.org/jira/browse/SPARK-1579) cleanly. Listed in order of approximate importance: - The Python daemon waits for Spark to close the socket before exiting, in order to avoid causing spurious IOExceptions in Spark's `PythonRDD::WriterThread`. - Removes the Python Monitor Thread, which polled for task cancellations in order to kill the Python worker. Instead, we do this in the onCompleteCallback, since this is guaranteed to be called during cancellation. - Adds a "completed" variable to TaskContext to avoid the issue noted in [SPARK-1019](https://issues.apache.org/jira/browse/SPARK-1019), where onCompleteCallbacks may be execution-order dependent. Along with this, I removed the "context.interrupted = true" flag in the onCompleteCallback. - Extracts PythonRDD::WriterThread to its own class. Since this patch provides an alternative solution to [SPARK-1019](https://issues.apache.org/jira/browse/SPARK-1019), I did test it with ``` sc.textFile("latlon.tsv").take(5) ``` many times without error. Additionally, in order to test the unswallowed exceptions, I performed ``` sc.textFile("s3n://<big file>").count() ``` and cut my internet during execution. Prior to this patch, we got the "stdin writer exited early" message, which was unhelpful. Now, we get the SocketExceptions propagated through Spark to the user and get proper (though unsuccessful) task retries. Author: Aaron Davidson <aaron@databricks.com> Closes #640 from aarondav/pyspark-io and squashes the following commits: b391ff8 [Aaron Davidson] Detect "clean socket shutdowns" and stop waiting on the socket c0c49da [Aaron Davidson] SPARK-1579: Clean up PythonRDD and avoid swallowing IOExceptions
* [SPARK-1460] Returning SchemaRDD instead of normal RDD on Set operations...Kan Zhang2014-05-071-0/+29
| | | | | | | | | | | | ... that do not change schema Author: Kan Zhang <kzhang@apache.org> Closes #448 from kanzhang/SPARK-1460 and squashes the following commits: 111e388 [Kan Zhang] silence MiMa errors in EdgeRDD and VertexRDD 91dc787 [Kan Zhang] Taking into account newly added Ordering param 79ed52a [Kan Zhang] [SPARK-1460] Returning SchemaRDD on Set operations that do not change schema
* SPARK-1637: Clean up examples for 1.0Sandeep2014-05-0610-574/+0
| | | | | | | | | | | | | | | | | | - [x] Move all of them into subpackages of org.apache.spark.examples (right now some are in org.apache.spark.streaming.examples, for instance, and others are in org.apache.spark.examples.mllib) - [x] Move Python examples into examples/src/main/python - [x] Update docs to reflect these changes Author: Sandeep <sandeep@techaddict.me> This patch had conflicts when merged, resolved by Committer: Matei Zaharia <matei@databricks.com> Closes #571 from techaddict/SPARK-1637 and squashes the following commits: 47ef86c [Sandeep] Changes based on Discussions on PR, removing use of RawTextHelper from examples 8ed2d3f [Sandeep] Docs Updated for changes, Change for java examples 5f96121 [Sandeep] Move Python examples into examples/src/main/python 0a8dd77 [Sandeep] Move all Scala Examples to org.apache.spark.examples (some are in org.apache.spark.streaming.examples, for instance, and others are in org.apache.spark.examples.mllib)
* [SPARK-1549] Add Python support to spark-submitMatei Zaharia2014-05-063-58/+168
| | | | | | | | | | | | | | | | | | | | | | This PR updates spark-submit to allow submitting Python scripts (currently only with deploy-mode=client, but that's all that was supported before) and updates the PySpark code to properly find various paths, etc. One significant change is that we assume we can always find the Python files either from the Spark assembly JAR (which will happen with the Maven assembly build in make-distribution.sh) or from SPARK_HOME (which will exist in local mode even if you use sbt assembly, and should be enough for testing). This means we no longer need a weird hack to modify the environment for YARN. This patch also updates the Python worker manager to run python with -u, which means unbuffered output (send it to our logs right away instead of waiting a while after stuff was written); this should simplify debugging. In addition, it fixes https://issues.apache.org/jira/browse/SPARK-1709, setting the main class from a JAR's Main-Class attribute if not specified by the user, and fixes a few help strings and style issues in spark-submit. In the future we may want to make the `pyspark` shell use spark-submit as well, but it seems unnecessary for 1.0. Author: Matei Zaharia <matei@databricks.com> Closes #664 from mateiz/py-submit and squashes the following commits: 15e9669 [Matei Zaharia] Fix some uses of path.separator property 051278c [Matei Zaharia] Small style fixes 0afe886 [Matei Zaharia] Add license headers 4650412 [Matei Zaharia] Add pyFiles to PYTHONPATH in executors, remove old YARN stuff, add tests 15f8e1e [Matei Zaharia] Set PYTHONPATH in PythonWorkerFactory in case it wasn't set from outside 47c0655 [Matei Zaharia] More work to make spark-submit work with Python: d4375bd [Matei Zaharia] Clean up description of spark-submit args a bit and add Python ones
* [SPARK-1594][MLLIB] Cleaning up MLlib APIs and guideXiangrui Meng2014-05-051-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Final pass before the v1.0 release. * Remove `VectorRDDs` * Move `BinaryClassificationMetrics` from `evaluation.binary` to `evaluation` * Change default value of `addIntercept` to false and allow to add intercept in Ridge and Lasso. * Clean `DecisionTree` package doc and test suite. * Mark model constructors `private[spark]` * Rename `loadLibSVMData` to `loadLibSVMFile` and hide `LabelParser` from users. * Add `saveAsLibSVMFile`. * Add `appendBias` to `MLUtils`. Author: Xiangrui Meng <meng@databricks.com> Closes #524 from mengxr/mllib-cleaning and squashes the following commits: 295dc8b [Xiangrui Meng] update loadLibSVMFile doc 1977ac1 [Xiangrui Meng] fix doc of appendBias 649fcf0 [Xiangrui Meng] rename loadLibSVMData to loadLibSVMFile; hide LabelParser from user APIs 54b812c [Xiangrui Meng] add appendBias a71e7d0 [Xiangrui Meng] add saveAsLibSVMFile d976295 [Xiangrui Meng] Merge branch 'master' into mllib-cleaning b7e5cec [Xiangrui Meng] remove some experimental annotations and make model constructors private[mllib] 9b02b93 [Xiangrui Meng] minor code style update a593ddc [Xiangrui Meng] fix python tests fc28c18 [Xiangrui Meng] mark more classes experimental f6cbbff [Xiangrui Meng] fix Java tests 0af70b0 [Xiangrui Meng] minor 6e139ef [Xiangrui Meng] Merge branch 'master' into mllib-cleaning 94e6dce [Xiangrui Meng] move BinaryLabelCounter and BinaryConfusionMatrixImpl to evaluation.binary df34907 [Xiangrui Meng] clean DecisionTreeSuite to use LocalSparkContext c81807f [Xiangrui Meng] set the default value of AddIntercept to false 03389c0 [Xiangrui Meng] allow to add intercept in Ridge and Lasso c66c56f [Xiangrui Meng] move tree md to package object doc a2695df [Xiangrui Meng] update guide for BinaryClassificationMetrics 9194f4c [Xiangrui Meng] move BinaryClassificationMetrics one level up 1c1a0e3 [Xiangrui Meng] remove VectorRDDs because it only contains one function that is not necessary for us to maintain
* SPARK-1004. PySpark on YARNSandy Ryza2014-04-295-11/+33
| | | | | | | | | | | | This reopens https://github.com/apache/incubator-spark/pull/640 against the new repo Author: Sandy Ryza <sandy@cloudera.com> Closes #30 from sryza/sandy-spark-1004 and squashes the following commits: 89889d4 [Sandy Ryza] Move unzipping py4j to the generate-resources phase so that it gets included in the jar the first time 5165a02 [Sandy Ryza] Fix docs fd0df79 [Sandy Ryza] PySpark on YARN
* [SPARK-1674] fix interrupted system call error in pyspark's RDD.pipeXiangrui Meng2014-04-291-3/+3
| | | | | | | | | | `RDD.pipe`'s doctest throws interrupted system call exception on Mac. It can be fixed by wrapping `pipe.stdout.readline` in an iterator. Author: Xiangrui Meng <meng@databricks.com> Closes #594 from mengxr/pyspark-pipe and squashes the following commits: cc32ac9 [Xiangrui Meng] fix interrupted system call error in pyspark's RDD.pipe
* Minor fix to python table caching API.Michael Armbrust2014-04-291-2/+2
| | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #585 from marmbrus/pythonCacheTable and squashes the following commits: 7ec1f91 [Michael Armbrust] Minor fix to python table caching API.
* SPARK-1242 Add aggregate to python rddHolden Karau2014-04-241-2/+29
| | | | | | | | | | | Author: Holden Karau <holden@pigscanfly.ca> Closes #139 from holdenk/add_aggregate_to_python_api and squashes the following commits: 0f39ae3 [Holden Karau] Merge in master 4879c75 [Holden Karau] CR feedback, fix issue with empty RDDs in aggregate 70b4724 [Holden Karau] Style fixes from code review 96b047b [Holden Karau] Add aggregate to python rdd
* [SPARK-986]: Job cancelation for PySparkAhir Reddy2014-04-241-3/+49
| | | | | | | | | | | | | | | | | | | | | | | * Additions to the PySpark API to cancel jobs * Monitor Thread in PythonRDD to kill Python workers if a task is interrupted Author: Ahir Reddy <ahirreddy@gmail.com> Closes #541 from ahirreddy/python-cancel and squashes the following commits: dfdf447 [Ahir Reddy] Changed success -> completed and made logging message clearer 6c860ab [Ahir Reddy] PR Comments 4b4100a [Ahir Reddy] Success flag adba6ed [Ahir Reddy] Destroy python workers 27a2f8f [Ahir Reddy] Start the writer thread... d422f7b [Ahir Reddy] Remove unnecesssary vals adda337 [Ahir Reddy] Busy wait on the ocntext.interrupted flag, and then kill the python worker d9e472f [Ahir Reddy] Revert "removed unnecessary vals" 5b9cae5 [Ahir Reddy] removed unnecessary vals 07b54d9 [Ahir Reddy] Fix canceling unit test 8ae9681 [Ahir Reddy] Don't interrupt worker 7722342 [Ahir Reddy] Monitor Thread for python workers db04e16 [Ahir Reddy] Added canceling api to PySpark
* SPARK-1438 RDD.sample() make seed param optionalArun Ramakrishnan2014-04-242-24/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | copying form previous pull request https://github.com/apache/spark/pull/462 Its probably better to let the underlying language implementation take care of the default . This was easier to do with python as the default value for seed in random and numpy random is None. In Scala/Java side it might mean propagating an Option or null(oh no!) down the chain until where the Random is constructed. But, looks like the convention in some other methods was to use System.nanoTime. So, followed that convention. Conflict with overloaded method in sql.SchemaRDD.sample which also defines default params. sample(fraction, withReplacement=false, seed=math.random) Scala does not allow more than one overloaded to have default params. I believe the author intended to override the RDD.sample method and not overload it. So, changed it. If backward compatible is important, 3 new method can be introduced (without default params) like this sample(fraction) sample(fraction, withReplacement) sample(fraction, withReplacement, seed) Added some tests for the scala RDD takeSample method. Author: Arun Ramakrishnan <smartnut007@gmail.com> This patch had conflicts when merged, resolved by Committer: Matei Zaharia <matei@databricks.com> Closes #477 from smartnut007/master and squashes the following commits: 07bb06e [Arun Ramakrishnan] SPARK-1438 fixing more space formatting issues b9ebfe2 [Arun Ramakrishnan] SPARK-1438 removing redundant import of random in python rddsampler 8d05b1a [Arun Ramakrishnan] SPARK-1438 RDD . Replace System.nanoTime with a Random generated number. python: use a separate instance of Random instead of seeding language api global Random instance. 69619c6 [Arun Ramakrishnan] SPARK-1438 fix spacing issue 0c247db [Arun Ramakrishnan] SPARK-1438 RDD language apis to support optional seed in RDD methods sample/takeSample
* fix bugs of dot in pythonXusen Yin2014-04-222-5/+5
| | | | | | | | | | | | | | If there are no `transpose()` in `self.theta`, a *ValueError: matrices are not aligned* is occurring. The former test case just ignore this situation. Author: Xusen Yin <yinxusen@gmail.com> Closes #463 from yinxusen/python-naive-bayes and squashes the following commits: fcbe3bc [Xusen Yin] fix bugs of dot in python
* [SPARK-1439, SPARK-1440] Generate unified Scaladoc across projects and JavadocsMatei Zaharia2014-04-211-2/+2
| | | | | | | | | | | | | | | | | | | | | | I used the sbt-unidoc plugin (https://github.com/sbt/sbt-unidoc) to create a unified Scaladoc of our public packages, and generate Javadocs as well. One limitation is that I haven't found an easy way to exclude packages in the Javadoc; there is a SBT task that identifies Java sources to run javadoc on, but it's been very difficult to modify it from outside to change what is set in the unidoc package. Some SBT-savvy people should help with this. The Javadoc site also lacks package-level descriptions and things like that, so we may want to look into that. We may decide not to post these right now if it's too limited compared to the Scala one. Example of the built doc site: http://people.csail.mit.edu/matei/spark-unified-docs/ Author: Matei Zaharia <matei@databricks.com> This patch had conflicts when merged, resolved by Committer: Patrick Wendell <pwendell@gmail.com> Closes #457 from mateiz/better-docs and squashes the following commits: a63d4a3 [Matei Zaharia] Skip Java/Scala API docs for Python package 5ea1f43 [Matei Zaharia] Fix links to Java classes in Java guide, fix some JS for scrolling to anchors on page load f05abc0 [Matei Zaharia] Don't include java.lang package names 995e992 [Matei Zaharia] Skip internal packages and class names with $ in JavaDoc a14a93c [Matei Zaharia] typo 76ce64d [Matei Zaharia] Add groups to Javadoc index page, and a first package-info.java ed6f994 [Matei Zaharia] Generate JavaDoc as well, add titles, update doc site to use unified docs acb993d [Matei Zaharia] Add Unidoc plugin for the projects we want Unidoced
* Add insertInto and saveAsTable to Python API.Michael Armbrust2014-04-191-0/+13
| | | | | | | | | Author: Michael Armbrust <michael@databricks.com> Closes #447 from marmbrus/pythonInsert and squashes the following commits: c7ab692 [Michael Armbrust] Keep docstrings < 72 chars. ff62870 [Michael Armbrust] Add insertInto and saveAsTable to Python API.
* Fixed broken pyspark shell.Reynold Xin2014-04-181-2/+2
| | | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #444 from rxin/pyspark and squashes the following commits: fc11356 [Reynold Xin] Made the PySpark shell version checking compatible with Python 2.6. 571830b [Reynold Xin] Fixed broken pyspark shell.
* SPARK-1483: Rename minSplits to minPartitions in public APIsCodingCat2014-04-181-3/+3
| | | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-1483 From the original JIRA: " The parameter name is part of the public API in Scala and Python, since you can pass named parameters to a method, so we should name it to this more descriptive term. Everywhere else we refer to "splits" as partitions." - @mateiz Author: CodingCat <zhunansjtu@gmail.com> Closes #430 from CodingCat/SPARK-1483 and squashes the following commits: 4b60541 [CodingCat] deprecate defaultMinSplits ba2c663 [CodingCat] Rename minSplits to minPartitions in public APIs
* FIX: Don't build Hive in assembly unless running Hive tests.Patrick Wendell2014-04-171-1/+3
| | | | | | | | | | This will make the tests more stable when not running SQL tests. Author: Patrick Wendell <pwendell@gmail.com> Closes #439 from pwendell/hive-tests and squashes the following commits: 88a6032 [Patrick Wendell] FIX: Don't build Hive in assembly unless running Hive tests.
* [python alternative] pyspark require Python2, failing if system default is ↵AbhishekKr2014-04-161-6/+14
| | | | | | | | | | | | Py3 from shell.py Python alternative for https://github.com/apache/spark/pull/392; managed from shell.py Author: AbhishekKr <abhikumar163@gmail.com> Closes #399 from abhishekkr/pyspark_shell and squashes the following commits: 134bdc9 [AbhishekKr] pyspark require Python2, failing if system default is Py3 from shell.py
* [SQL] SPARK-1424 Generalize insertIntoTable functions on SchemaRDDsMichael Armbrust2014-04-151-4/+10
| | | | | | | | | | | | | | | | | This makes it possible to create tables and insert into them using the DSL and SQL for the scala and java apis. Author: Michael Armbrust <michael@databricks.com> Closes #354 from marmbrus/insertIntoTable and squashes the following commits: 6c6f227 [Michael Armbrust] Create random temporary files in python parquet unit tests. f5e6d5c [Michael Armbrust] Merge remote-tracking branch 'origin/master' into insertIntoTable 765c506 [Michael Armbrust] Add to JavaAPI. 77b512c [Michael Armbrust] typos. 5c3ef95 [Michael Armbrust] use names for boolean args. 882afdf [Michael Armbrust] Change createTableAs to saveAsTable. Clean up api annotations. d07d94b [Michael Armbrust] Add tests, support for creating parquet files and hive tables. fa3fe81 [Michael Armbrust] Make insertInto available on JavaSchemaRDD as well. Add createTableAs function.
* [WIP] SPARK-1430: Support sparse data in Python MLlibMatei Zaharia2014-04-1512-139/+1178
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This PR adds a SparseVector class in PySpark and updates all the regression, classification and clustering algorithms and models to support sparse data, similar to MLlib. I chose to add this class because SciPy is quite difficult to install in many environments (more so than NumPy), but I plan to add support for SciPy sparse vectors later too, and make the methods work transparently on objects of either type. On the Scala side, we keep Python sparse vectors sparse and pass them to MLlib. We always return dense vectors from our models. Some to-do items left: - [x] Support SciPy's scipy.sparse matrix objects when SciPy is available. We can easily add a function to convert these to our own SparseVector. - [x] MLlib currently uses a vector with one extra column on the left to represent what we call LabeledPoint in Scala. Do we really want this? It may get annoying once you deal with sparse data since you must add/subtract 1 to each feature index when training. We can remove this API in 1.0 and use tuples for labeling. - [x] Explain how to use these in the Python MLlib docs. CC @mengxr, @joshrosen Author: Matei Zaharia <matei@databricks.com> Closes #341 from mateiz/py-ml-update and squashes the following commits: d52e763 [Matei Zaharia] Remove no-longer-needed slice code and handle review comments ea5a25a [Matei Zaharia] Fix remaining uses of copyto() after merge b9f97a3 [Matei Zaharia] Fix test 1e1bd0f [Matei Zaharia] Add MLlib logistic regression example in Python 88bc01f [Matei Zaharia] Clean up inheritance of LinearModel in Python, and expose its parametrs 37ab747 [Matei Zaharia] Fix some examples and docs due to changes in MLlib API da0f27e [Matei Zaharia] Added a MLlib K-means example and updated docs to discuss sparse data c48e85a [Matei Zaharia] Added some tests for passing lists as input, and added mllib/tests.py to run-tests script. a07ba10 [Matei Zaharia] Fix some typos and calculation of initial weights 74eefe7 [Matei Zaharia] Added LabeledPoint class in Python 889dde8 [Matei Zaharia] Support scipy.sparse matrices in all our algorithms and models ab244d1 [Matei Zaharia] Allow SparseVectors to be initialized using a dict a5d6426 [Matei Zaharia] Add linalg.py to run-tests script 0e7a3d8 [Matei Zaharia] Keep vectors sparse in Java when reading LabeledPoints eaee759 [Matei Zaharia] Update regression, classification and clustering models for sparse data 2abbb44 [Matei Zaharia] Further work to get linear models working with sparse data 154f45d [Matei Zaharia] Update docs, name some magic values 881fef7 [Matei Zaharia] Added a sparse vector in Python and made Java-Python format more compact
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