Update BinaryClassificationEvaluator to use setRawPredictionCol, rather than setScoreCol. Deprecated setScoreCol.
I don't think setScoreCol was actually used anywhere (based on search).
CC: mengxr
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#7921 from jkbradley/binary-eval-rawpred and squashes the following commits:
e5d7dfa [Joseph K. Bradley] Update BinaryClassificationEvaluator to use setRawPredictionCol
This PR adds the RowMatrix, IndexedRowMatrix, and CoordinateMatrix distributed matrices to PySpark. Each distributed matrix class acts as a wrapper around the Scala/Java counterpart by maintaining a reference to the Java object. New distributed matrices can be created using factory methods added to DistributedMatrices, which creates the Java distributed matrix and then wraps it with the corresponding PySpark class. This design allows for simple conversion between the various distributed matrices, and lets us re-use the Scala code. Serialization between Python and Java is implemented using DataFrames as needed for IndexedRowMatrix and CoordinateMatrix for simplicity. Associated documentation and unit-tests have also been added. To facilitate code review, this PR implements access to the rows/entries as RDDs, the number of rows & columns, and conversions between the various distributed matrices (not including BlockMatrix), and does not implement the other linear algebra functions of the matrices, although this will be very simple to add now.
Author: Mike Dusenberry <mwdusenb@us.ibm.com>
Closes#7554 from dusenberrymw/SPARK-6485_Add_CoordinateMatrix_RowMatrix_IndexedMatrix_to_PySpark and squashes the following commits:
bb039cb [Mike Dusenberry] Minor documentation update.
b887c18 [Mike Dusenberry] Updating the matrix conversion logic again to make it even cleaner. Now, we allow the 'rows' parameter in the constructors to be either an RDD or the Java matrix object. If 'rows' is an RDD, we create a Java matrix object, wrap it, and then store that. If 'rows' is a Java matrix object of the correct type, we just wrap and store that directly. This is only for internal usage, and publicly, we still require 'rows' to be an RDD. We no longer store the 'rows' RDD, and instead just compute it from the Java object when needed. The point of this is that when we do matrix conversions, we do the conversion on the Scala/Java side, which returns a Java object, so we should use that directly, but exposing 'java_matrix' parameter in the public API is not ideal. This non-public feature of allowing 'rows' to be a Java matrix object is documented in the '__init__' constructor docstrings, which are not part of the generated public API, and doctests are also included.
7f0dcb6 [Mike Dusenberry] Updating module docstring.
cfc1be5 [Mike Dusenberry] Use 'new SQLContext(matrix.rows.sparkContext)' rather than 'SQLContext.getOrCreate', as the later doesn't guarantee that the SparkContext will be the same as for the matrix.rows data.
687e345 [Mike Dusenberry] Improving conversion performance. This adds an optional 'java_matrix' parameter to the constructors, and pulls the conversion logic out into a '_create_from_java' function. Now, if the constructors are given a valid Java distributed matrix object as 'java_matrix', they will store those internally, rather than create a new one on the Scala/Java side.
3e50b6e [Mike Dusenberry] Moving the distributed matrices to pyspark.mllib.linalg.distributed.
308f197 [Mike Dusenberry] Using properties for better documentation.
1633f86 [Mike Dusenberry] Minor documentation cleanup.
f0c13a7 [Mike Dusenberry] CoordinateMatrix should inherit from DistributedMatrix.
ffdd724 [Mike Dusenberry] Updating doctests to make documentation cleaner.
3fd4016 [Mike Dusenberry] Updating docstrings.
27cd5f6 [Mike Dusenberry] Simplifying input conversions in the constructors for each distributed matrix.
a409cf5 [Mike Dusenberry] Updating doctests to be less verbose by using lists instead of DenseVectors explicitly.
d19b0ba [Mike Dusenberry] Updating code and documentation to note that a vector-like object (numpy array, list, etc.) can be used in place of explicit Vector object, and adding conversions when necessary to RowMatrix construction.
4bd756d [Mike Dusenberry] Adding param documentation to IndexedRow and MatrixEntry.
c6bded5 [Mike Dusenberry] Move conversion logic from tuples to IndexedRow or MatrixEntry types from within the IndexedRowMatrix and CoordinateMatrix constructors to separate _convert_to_indexed_row and _convert_to_matrix_entry functions.
329638b [Mike Dusenberry] Moving the Experimental tag to the top of each docstring.
0be6826 [Mike Dusenberry] Simplifying doctests by removing duplicated rows/entries RDDs within the various tests.
c0900df [Mike Dusenberry] Adding the colons that were accidentally not inserted.
4ad6819 [Mike Dusenberry] Documenting the and parameters.
3b854b9 [Mike Dusenberry] Minor updates to documentation.
10046e8 [Mike Dusenberry] Updating documentation to use class constructors instead of the removed DistributedMatrices factory methods.
119018d [Mike Dusenberry] Adding static methods to each of the distributed matrix classes to consolidate conversion logic.
4d7af86 [Mike Dusenberry] Adding type checks to the constructors. Although it is slightly verbose, it is better for the user to have a good error message than a cryptic stacktrace.
93b6a3d [Mike Dusenberry] Pulling the DistributedMatrices Python class out of this pull request.
f6f3c68 [Mike Dusenberry] Pulling the DistributedMatrices Scala class out of this pull request.
6a3ecb7 [Mike Dusenberry] Updating pattern matching.
08f287b [Mike Dusenberry] Slight reformatting of the documentation.
a245dc0 [Mike Dusenberry] Updating Python doctests for compatability between Python 2 & 3. Since Python 3 removed the idea of a separate 'long' type, all values that would have been outputted as a 'long' (ex: '4L') will now be treated as an 'int' and outputed as one (ex: '4'). The doctests now explicitly convert to ints so that both Python 2 and 3 will have the same output. This is fine since the values are all small, and thus can be easily represented as ints.
4d3a37e [Mike Dusenberry] Reformatting a few long Python doctest lines.
7e3ca16 [Mike Dusenberry] Fixing long lines.
f721ead [Mike Dusenberry] Updating documentation for each of the distributed matrices.
ab0e8b6 [Mike Dusenberry] Updating unit test to be more useful.
dda2f89 [Mike Dusenberry] Added wrappers for the conversions between the various distributed matrices. Added logic to be able to access the rows/entries of the distributed matrices, which requires serialization through DataFrames for IndexedRowMatrix and CoordinateMatrix types. Added unit tests.
0cd7166 [Mike Dusenberry] Implemented the CoordinateMatrix API in PySpark, following the idea of the IndexedRowMatrix API, including using DataFrames for serialization.
3c369cb [Mike Dusenberry] Updating the architecture a bit to make conversions between the various distributed matrix types easier. The different distributed matrix classes are now only wrappers around the Java objects, and take the Java object as an argument during construction. This way, we can call for example on an , which returns a reference to a Java RowMatrix object, and then construct a PySpark RowMatrix object wrapped around the Java object. This is analogous to the behavior of PySpark RDDs and DataFrames. We now delegate creation of the various distributed matrices from scratch in PySpark to the factory methods on .
4bdd09b [Mike Dusenberry] Implemented the IndexedRowMatrix API in PySpark, following the idea of the RowMatrix API. Note that for the IndexedRowMatrix, we use DataFrames to serialize the data between Python and Scala/Java, so we accept PySpark RDDs, then convert to a DataFrame, then convert back to RDDs on the Scala/Java side before constructing the IndexedRowMatrix.
23bf1ec [Mike Dusenberry] Updating documentation to add PySpark RowMatrix. Inserting newline above doctest so that it renders properly in API docs.
b194623 [Mike Dusenberry] Updating design to have a PySpark RowMatrix simply create and keep a reference to a wrapper over a Java RowMatrix. Updating DistributedMatrices factory methods to accept numRows and numCols with default values. Updating PySpark DistributedMatrices factory method to simply create a PySpark RowMatrix. Adding additional doctests for numRows and numCols parameters.
bc2d220 [Mike Dusenberry] Adding unit tests for RowMatrix methods.
d7e316f [Mike Dusenberry] Implemented the RowMatrix API in PySpark by doing the following: Added a DistributedMatrices class to contain factory methods for creating the various distributed matrices. Added a factory method for creating a RowMatrix from an RDD of Vectors. Added a createRowMatrix function to the PythonMLlibAPI to interface with the factory method. Added DistributedMatrix, DistributedMatrices, and RowMatrix classes to the pyspark.mllib.linalg api.
Small cleanups to recent LDA additions and docs.
CC: feynmanliang
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#7916 from jkbradley/lda-cleanups and squashes the following commits:
f7021d9 [Joseph K. Bradley] broadcasting large matrices for LDA in local model and online learning
97947aa [Joseph K. Bradley] a few more cleanups
5b03f88 [Joseph K. Bradley] reverted split of lda log likelihood
c566915 [Joseph K. Bradley] small edit to make review easier
63f6c7d [Joseph K. Bradley] clarified log likelihood for lda models
Added HasRawPredictionCol, HasProbabilityCol to RandomForestClassifier, plus doc tests for those columns.
CC: holdenk yanboliang
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#7903 from jkbradley/rf-prob-python and squashes the following commits:
c62a83f [Joseph K. Bradley] made unit test more robust
14eeba2 [Joseph K. Bradley] added HasRawPredictionCol, HasProbabilityCol to RandomForestClassifier in PySpark
https://issues.apache.org/jira/browse/SPARK-9602
Although we have hidden Akka behind RPC interface, I found that the Akka/Actor-related comments are still spreading everywhere. To make it consistent, we shall remove "actor"/"akka" words from the comments...
Author: CodingCat <zhunansjtu@gmail.com>
Closes#7936 from CodingCat/SPARK-9602 and squashes the following commits:
e8296a3 [CodingCat] remove actor words from comments
This patch extends UnsafeExternalSorter to support records larger than the page size. The basic strategy is the same as in #7762: store large records in their own overflow pages.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7891 from JoshRosen/large-records-in-sql-sorter and squashes the following commits:
967580b [Josh Rosen] Merge remote-tracking branch 'origin/master' into large-records-in-sql-sorter
948c344 [Josh Rosen] Add large records tests for KV sorter.
3c17288 [Josh Rosen] Combine memory and disk cleanup into general cleanupResources() method
380f217 [Josh Rosen] Merge remote-tracking branch 'origin/master' into large-records-in-sql-sorter
27eafa0 [Josh Rosen] Fix page size in PackedRecordPointerSuite
a49baef [Josh Rosen] Address initial round of review comments
3edb931 [Josh Rosen] Remove accidentally-committed debug statements.
2b164e2 [Josh Rosen] Support large records in UnsafeExternalSorter.
Author: Wenchen Fan <cloud0fan@outlook.com>
Closes#7890 from cloud-fan/minor and squashes the following commits:
c3b1be3 [Wenchen Fan] fix style
b0cbe2e [Wenchen Fan] remove the createCode and createStructCode, and replace the usage of them by createStructCode
Author: Michael Armbrust <michael@databricks.com>
Closes#7939 from marmbrus/turnOffThriftTests and squashes the following commits:
80d618e [Michael Armbrust] [SPARK-9606][SQL] Ignore flaky thrift server tests
This PR replaces the old "threshold" with a generalized "thresholds" Param. We keep getThreshold,setThreshold for backwards compatibility for binary classification.
Note that the primary author of this PR is holdenk
Author: Holden Karau <holden@pigscanfly.ca>
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#7909 from jkbradley/holdenk-SPARK-8069-add-cutoff-aka-threshold-to-random-forest and squashes the following commits:
3952977 [Joseph K. Bradley] fixed pyspark doc test
85febc8 [Joseph K. Bradley] made python unit tests a little more robust
7eb1d86 [Joseph K. Bradley] small cleanups
6cc2ed8 [Joseph K. Bradley] Fixed remaining merge issues.
0255e44 [Joseph K. Bradley] Many cleanups for thresholds, some more tests
7565a60 [Holden Karau] fix pep8 style checks, add a getThreshold method similar to our LogisticRegression.scala one for API compat
be87f26 [Holden Karau] Convert threshold to thresholds in the python code, add specialized support for Array[Double] to shared parems codegen, etc.
6747dad [Holden Karau] Override raw2prediction for ProbabilisticClassifier, fix some tests
25df168 [Holden Karau] Fix handling of thresholds in LogisticRegression
c02d6c0 [Holden Karau] No default for thresholds
5e43628 [Holden Karau] CR feedback and fixed the renamed test
f3fbbd1 [Holden Karau] revert the changes to random forest :(
51f581c [Holden Karau] Add explicit types to public methods, fix long line
f7032eb [Holden Karau] Fix a java test bug, remove some unecessary changes
adf15b4 [Holden Karau] rename the classifier suite test to ProbabilisticClassifierSuite now that we only have it in Probabilistic
398078a [Holden Karau] move the thresholding around a bunch based on the design doc
4893bdc [Holden Karau] Use numtrees of 3 since previous result was tied (one tree for each) and the switch from different max methods picked a different element (since they were equal I think this is ok)
638854c [Holden Karau] Add a scala RandomForestClassifierSuite test based on corresponding python test
e09919c [Holden Karau] Fix return type, I need more coffee....
8d92cac [Holden Karau] Use ClassifierParams as the head
3456ed3 [Holden Karau] Add explicit return types even though just test
a0f3b0c [Holden Karau] scala style fixes
6f14314 [Holden Karau] Since hasthreshold/hasthresholds is in root classifier now
ffc8dab [Holden Karau] Update the sharedParams
0420290 [Holden Karau] Allow us to override the get methods selectively
978e77a [Holden Karau] Move HasThreshold into classifier params and start defining the overloaded getThreshold/getThresholds functions
1433e52 [Holden Karau] Revert "try and hide threshold but chainges the API so no dice there"
1f09a2e [Holden Karau] try and hide threshold but chainges the API so no dice there
efb9084 [Holden Karau] move setThresholds only to where its used
6b34809 [Holden Karau] Add a test with thresholding for the RFCS
74f54c3 [Holden Karau] Fix creation of vote array
1986fa8 [Holden Karau] Setting the thresholds only makes sense if the underlying class hasn't overridden predict, so lets push it down.
2f44b18 [Holden Karau] Add a global default of null for thresholds param
f338cfc [Holden Karau] Wait that wasn't a good idea, Revert "Some progress towards unifying threshold and thresholds"
634b06f [Holden Karau] Some progress towards unifying threshold and thresholds
85c9e01 [Holden Karau] Test passes again... little fnur
099c0f3 [Holden Karau] Move thresholds around some more (set on model not trainer)
0f46836 [Holden Karau] Start adding a classifiersuite
f70eb5e [Holden Karau] Fix test compile issues
a7d59c8 [Holden Karau] Move thresholding into Classifier trait
5d999d2 [Holden Karau] Some more progress, start adding a test (maybe try and see if we can find a better thing to use for the base of the test)
1fed644 [Holden Karau] Use thresholds to scale scores in random forest classifcation
31d6bf2 [Holden Karau] Start threading the threshold info through
0ef228c [Holden Karau] Add hasthresholds
The analysis rule has a bug and we ended up making the sorter still capable of doing evaluation, so lets revert this for now.
Author: Michael Armbrust <michael@databricks.com>
Closes#7906 from marmbrus/revertSortProjection and squashes the following commits:
2da6972 [Michael Armbrust] unrevert unrelated changes
4f2b00c [Michael Armbrust] Revert "[SPARK-9251][SQL] do not order by expressions which still need evaluation"
cc srowen pwendell nchammas
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#7899 from shivaram/spark-ec2-move and squashes the following commits:
7cc22c9 [Shivaram Venkataraman] Change reference to amplab/spark-ec2 from mesos/
This is based on #7485 , thanks to NathanHowell
Tests were copied from Hive, but do not seem to be super comprehensive. I've generally replicated Hive's unusual behavior rather than following a JSONPath reference, except for one case (as noted in the comments). I don't know if there is a way of fully replicating Hive's behavior without a slower TreeNode implementation, so I've erred on the side of performance instead.
Author: Davies Liu <davies@databricks.com>
Author: Yin Huai <yhuai@databricks.com>
Author: Nathan Howell <nhowell@godaddy.com>
Closes#7901 from davies/get_json_object and squashes the following commits:
3ace9b9 [Davies Liu] Merge branch 'get_json_object' of github.com:davies/spark into get_json_object
98766fc [Davies Liu] Merge branch 'master' of github.com:apache/spark into get_json_object
a7dc6d0 [Davies Liu] Update JsonExpressionsSuite.scala
c818519 [Yin Huai] new results.
18ce26b [Davies Liu] fix tests
6ac29fb [Yin Huai] Golden files.
25eebef [Davies Liu] use HiveQuerySuite
e0ac6ec [Yin Huai] Golden answer files.
940c060 [Davies Liu] tweat code style
44084c5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into get_json_object
9192d09 [Nathan Howell] Match Hive’s behavior for unwrapping arrays of one element
8dab647 [Nathan Howell] [SPARK-8246] [SQL] Implement get_json_object
This PR is based on #7186 (just fix the conflict), thanks to tarekauel .
find_in_set(string str, string strList): int
Returns the first occurance of str in strList where strList is a comma-delimited string. Returns null if either argument is null. Returns 0 if the first argument contains any commas. For example, find_in_set('ab', 'abc,b,ab,c,def') returns 3.
Only add this to SQL, not DataFrame.
Closes#7186
Author: Tarek Auel <tarek.auel@googlemail.com>
Author: Davies Liu <davies@databricks.com>
Closes#7900 from davies/find_in_set and squashes the following commits:
4334209 [Davies Liu] Merge branch 'master' of github.com:apache/spark into find_in_set
8f00572 [Davies Liu] Merge branch 'master' of github.com:apache/spark into find_in_set
243ede4 [Tarek Auel] [SPARK-8244][SQL] hive compatibility
1aaf64e [Tarek Auel] [SPARK-8244][SQL] unit test fix
e4093a4 [Tarek Auel] [SPARK-8244][SQL] final modifier for COMMA_UTF8
0d05df5 [Tarek Auel] Merge branch 'master' into SPARK-8244
208d710 [Tarek Auel] [SPARK-8244] address comments & bug fix
71b2e69 [Tarek Auel] [SPARK-8244] find_in_set
66c7fda [Tarek Auel] Merge branch 'master' into SPARK-8244
61b8ca2 [Tarek Auel] [SPARK-8224] removed loop and split; use unsafe String comparison
4f75a65 [Tarek Auel] Merge branch 'master' into SPARK-8244
e3b20c8 [Tarek Auel] [SPARK-8244] added type check
1c2bbb7 [Tarek Auel] [SPARK-8244] findInSet
This allows build/mvn to be used by make-distribution.sh.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#7915 from vanzin/SPARK-9583 and squashes the following commits:
6469e60 [Marcelo Vanzin] [SPARK-9583] [build] Do not print mvn debug messages to stdout.
This PR removes the dependency reduced POM hack brought back by #7191
Author: tedyu <yuzhihong@gmail.com>
Closes#7919 from tedyu/master and squashes the following commits:
1bfbd7b [tedyu] [BUILD] Remove dependency reduced POM hack
Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process.
I'll explain several of the changes inline in comments.
Author: Sean Owen <sowen@cloudera.com>
Closes#7862 from srowen/SPARK-9534 and squashes the following commits:
ea51618 [Sean Owen] Enable most javac lint warnings; fix a lot of build warnings. In a few cases, touch up surrounding code in the process.
SPARK-3190 was originally fixed by 96df929069, but a5ef581136 introduced a regression during refactoring. This commit fixes the regression.
Author: Ankur Dave <ankurdave@gmail.com>
Closes#7923 from ankurdave/SPARK-3190-reopening and squashes the following commits:
a3e1b23 [Ankur Dave] Fix VertexRDD.count() overflow regression
Follow on for #7852: Building Spark doc needs to refer to new Maven requirement too
Author: Sean Owen <sowen@cloudera.com>
Closes#7905 from srowen/SPARK-9521.2 and squashes the following commits:
73285df [Sean Owen] Follow on for #7852: Building Spark doc needs to refer to new Maven requirement too
We often return abstract iterator types in various sort-related classes (e.g. UnsafeKVExternalSorter). It is actually better to return a more concrete type, so the callsite uses that type and JIT can inline the iterator calls.
Author: Reynold Xin <rxin@databricks.com>
Closes#7911 from rxin/surface-concrete-type and squashes the following commits:
0422add [Reynold Xin] [SPARK-9577][SQL] Surface concrete iterator types in various sort classes.
https://issues.apache.org/jira/browse/SPARK-8416
To facilitate debugging, I made this patch with three changes:
* render the executor-thread and non executor-thread entries with different background colors
* put the executor threads on the top of the list
* sort the threads alphabetically
Author: CodingCat <zhunansjtu@gmail.com>
Closes#7808 from CodingCat/SPARK-8416 and squashes the following commits:
34fc708 [CodingCat] fix className
d7b79dd [CodingCat] lowercase threadName
d032882 [CodingCat] sort alphabetically and change the css class name
f0513b1 [CodingCat] change the color & group threads by name
2da6e06 [CodingCat] small fix
3fc9f36 [CodingCat] define classes in webui.css
8ee125e [CodingCat] highlight and put on top the executor threads in thread dumping page
While the functionality is there to exclude packages, there are no flags that allow users to exclude dependencies, in case of dependency conflicts. We should provide users with a flag to add dependency exclusions in case the packages are not resolved properly (or not available due to licensing).
The flag I added was --packages-exclude, but I'm open on renaming it. I also added property flags in case people would like to use a conf file to provide dependencies, which is possible if there is a long list of dependencies or exclusions.
cc andrewor14 vanzin pwendell
Author: Burak Yavuz <brkyvz@gmail.com>
Closes#7599 from brkyvz/packages-exclusions and squashes the following commits:
636f410 [Burak Yavuz] addressed nits
6e54ede [Burak Yavuz] is this the culprit
b5e508e [Burak Yavuz] Merge branch 'master' of github.com:apache/spark into packages-exclusions
154f5db [Burak Yavuz] addressed initial comments
1536d7a [Burak Yavuz] Added flags to exclude packages using --packages-exclude
Previous code assumed little-endian.
Author: Matthew Brandyberry <mbrandy@us.ibm.com>
Closes#7902 from mtbrandy/SPARK-9483 and squashes the following commits:
ec31df8 [Matthew Brandyberry] [SPARK-9483] Changes from review comments.
17d54c6 [Matthew Brandyberry] [SPARK-9483] Fix UTF8String.getPrefix for big-endian.
This puts all the install commands that need to be run in one section instead of being spread over many paragraphs
cc rxin
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Closes#7912 from shivaram/docs-setup-readme and squashes the following commits:
cf7a204 [Shivaram Venkataraman] Add a prerequisites section for building docs
Add missing methods
1. getVectors
2. findSynonyms
to W2Vec scala and python API
mengxr
Author: MechCoder <manojkumarsivaraj334@gmail.com>
Closes#7263 from MechCoder/missing_methods_w2vec and squashes the following commits:
149d5ca [MechCoder] minor doc
69d91b7 [MechCoder] [SPARK-8874] [ML] Add missing methods in Word2Vec
Cherry picked the parts of the initial SPARK-8064 WiP branch needed to get sql/hive to compile against hive 1.2.1. That's the ASF release packaged under org.apache.hive, not any fork.
Tests not run yet: that's what the machines are for
Author: Steve Loughran <stevel@hortonworks.com>
Author: Cheng Lian <lian@databricks.com>
Author: Michael Armbrust <michael@databricks.com>
Author: Patrick Wendell <patrick@databricks.com>
Closes#7191 from steveloughran/stevel/feature/SPARK-8064-hive-1.2-002 and squashes the following commits:
7556d85 [Cheng Lian] Updates .q files and corresponding golden files
ef4af62 [Steve Loughran] Merge commit '6a92bb09f46a04d6cd8c41bdba3ecb727ebb9030' into stevel/feature/SPARK-8064-hive-1.2-002
6a92bb0 [Cheng Lian] Overrides HiveConf time vars
dcbb391 [Cheng Lian] Adds com.twitter:parquet-hadoop-bundle:1.6.0 for Hive Parquet SerDe
0bbe475 [Steve Loughran] SPARK-8064 scalastyle rejects the standard Hadoop ASF license header...
fdf759b [Steve Loughran] SPARK-8064 classpath dependency suite to be in sync with shading in final (?) hive-exec spark
7a6c727 [Steve Loughran] SPARK-8064 switch to second staging repo of the spark-hive artifacts. This one has the protobuf-shaded hive-exec jar
376c003 [Steve Loughran] SPARK-8064 purge duplicate protobuf declaration
2c74697 [Steve Loughran] SPARK-8064 switch to the protobuf shaded hive-exec jar with tests to chase it down
cc44020 [Steve Loughran] SPARK-8064 remove hadoop.version from runtest.py, as profile will fix that automatically.
6901fa9 [Steve Loughran] SPARK-8064 explicit protobuf import
da310dc [Michael Armbrust] Fixes for Hive tests.
a775a75 [Steve Loughran] SPARK-8064 cherry-pick-incomplete
7404f34 [Patrick Wendell] Add spark-hive staging repo
832c164 [Steve Loughran] SPARK-8064 try to supress compiler warnings on Complex.java pasted-thrift-code
312c0d4 [Steve Loughran] SPARK-8064 maven/ivy dependency purge; calcite declaration needed
fa5ae7b [Steve Loughran] HIVE-8064 fix up hive-thriftserver dependencies and cut back on evicted references in the hive- packages; this keeps mvn and ivy resolution compatible, as the reconciliation policy is "by hand"
c188048 [Steve Loughran] SPARK-8064 manage the Hive depencencies to that -things that aren't needed are excluded -sql/hive built with ivy is in sync with the maven reconciliation policy, rather than latest-first
4c8be8d [Cheng Lian] WIP: Partial fix for Thrift server and CLI tests
314eb3c [Steve Loughran] SPARK-8064 deprecation warning noise in one of the tests
17b0341 [Steve Loughran] SPARK-8064 IDE-hinted cleanups of Complex.java to reduce compiler warnings. It's all autogenerated code, so still ugly.
d029b92 [Steve Loughran] SPARK-8064 rely on unescaping to have already taken place, so go straight to map of serde options
23eca7e [Steve Loughran] HIVE-8064 handle raw and escaped property tokens
54d9b06 [Steve Loughran] SPARK-8064 fix compilation regression surfacing from rebase
0b12d5f [Steve Loughran] HIVE-8064 use subset of hive complex type whose types deserialize
fce73b6 [Steve Loughran] SPARK-8064 poms rely implicitly on the version of kryo chill provides
fd3aa5d [Steve Loughran] SPARK-8064 version of hive to d/l from ivy is 1.2.1
dc73ece [Steve Loughran] SPARK-8064 revert to master's determinstic pushdown strategy
d3c1e4a [Steve Loughran] SPARK-8064 purge UnionType
051cc21 [Steve Loughran] SPARK-8064 switch to an unshaded version of hive-exec-core, which must have been built with Kryo 2.21. This currently looks for a (locally built) version 1.2.1.spark
6684c60 [Steve Loughran] SPARK-8064 ignore RTE raised in blocking process.exitValue() call
e6121e5 [Steve Loughran] SPARK-8064 address review comments
aa43dc6 [Steve Loughran] SPARK-8064 more robust teardown on JavaMetastoreDatasourcesSuite
f2bff01 [Steve Loughran] SPARK-8064 better takeup of asynchronously caught error text
8b1ef38 [Steve Loughran] SPARK-8064: on failures executing spark-submit in HiveSparkSubmitSuite, print command line and all logged output.
5a9ce6b [Steve Loughran] SPARK-8064 add explicit reason for kv split failure, rather than array OOB. *does not address the issue*
642b63a [Steve Loughran] SPARK-8064 reinstate something cut briefly during rebasing
97194dc [Steve Loughran] SPARK-8064 add extra logging to the YarnClusterSuite classpath test. There should be no reason why this is failing on jenkins, but as it is (and presumably its CP-related), improve the logging including any exception raised.
335357f [Steve Loughran] SPARK-8064 fail fast on thrive process spawning tests on exit codes and/or error string patterns seen in log.
3ed872f [Steve Loughran] SPARK-8064 rename field double to dbl
bca55e5 [Steve Loughran] SPARK-8064 missed one of the `date` escapes
41d6479 [Steve Loughran] SPARK-8064 wrap tests with withTable() calls to avoid table-exists exceptions
2bc29a4 [Steve Loughran] SPARK-8064 ParquetSuites to escape `date` field name
1ab9bc4 [Steve Loughran] SPARK-8064 TestHive to use sered2.thrift.test.Complex
bf3a249 [Steve Loughran] SPARK-8064: more resubmit than fix; tighten startup timeout to 60s. Still no obvious reason why jersey server code in spark-assembly isn't being picked up -it hasn't been shaded
c829b8f [Steve Loughran] SPARK-8064: reinstate yarn-rm-server dependencies to hive-exec to ensure that jersey server is on classpath on hadoop versions < 2.6
0b0f738 [Steve Loughran] SPARK-8064: thrift server startup to fail fast on any exception in the main thread
13abaf1 [Steve Loughran] SPARK-8064 Hive compatibilty tests sin sync with explain/show output from Hive 1.2.1
d14d5ea [Steve Loughran] SPARK-8064: DATE is now a predicate; you can't use it as a field in select ops
26eef1c [Steve Loughran] SPARK-8064: HIVE-9039 renamed TOK_UNION => TOK_UNIONALL while adding TOK_UNIONDISTINCT
3d64523 [Steve Loughran] SPARK-8064 improve diagns on uknown token; fix scalastyle failure
d0360f6 [Steve Loughran] SPARK-8064: delicate merge in of the branch vanzin/hive-1.1
1126e5a [Steve Loughran] SPARK-8064: name of unrecognized file format wasn't appearing in error text
8cb09c4 [Steve Loughran] SPARK-8064: test resilience/assertion improvements. Independent of the rest of the work; can be backported to earlier versions
dec12cb [Steve Loughran] SPARK-8064: when a CLI suite test fails include the full output text in the raised exception; this ensures that the stdout/stderr is included in jenkins reports, so it becomes possible to diagnose the cause.
463a670 [Steve Loughran] SPARK-8064 run-tests.py adds a hadoop-2.6 profile, and changes info messages to say "w/Hive 1.2.1" in console output
2531099 [Steve Loughran] SPARK-8064 successful attempt to get rid of pentaho as a transitive dependency of hive-exec
1d59100 [Steve Loughran] SPARK-8064 (unsuccessful) attempt to get rid of pentaho as a transitive dependency of hive-exec
75733fc [Steve Loughran] SPARK-8064 change thrift binary startup message to "Starting ThriftBinaryCLIService on port"
3ebc279 [Steve Loughran] SPARK-8064 move strings used to check for http/bin thrift services up into constants
c80979d [Steve Loughran] SPARK-8064: SparkSQLCLIDriver drops remote mode support. CLISuite Tests pass instead of timing out: undetected regression?
27e8370 [Steve Loughran] SPARK-8064 fix some style & IDE warnings
00e50d6 [Steve Loughran] SPARK-8064 stop excluding hive shims from dependency (commented out , for now)
cb4f142 [Steve Loughran] SPARK-8054 cut pentaho dependency from calcite
f7aa9cb [Steve Loughran] SPARK-8064 everything compiles with some commenting and moving of classes into a hive package
6c310b4 [Steve Loughran] SPARK-8064 subclass Hive ServerOptionsProcessor to make it public again
f61a675 [Steve Loughran] SPARK-8064 thrift server switched to Hive 1.2.1, though it doesn't compile everywhere
4890b9d [Steve Loughran] SPARK-8064, build against Hive 1.2.1
Add Python API for RFormula. Similar to other feature transformers in Python. This is just a thin wrapper over the Scala implementation. ericl MechCoder
Author: Xiangrui Meng <meng@databricks.com>
Closes#7879 from mengxr/SPARK-9544 and squashes the following commits:
3d5ff03 [Xiangrui Meng] add an doctest for . and -
5e969a5 [Xiangrui Meng] fix pydoc
1cd41f8 [Xiangrui Meng] organize imports
3c18b10 [Xiangrui Meng] add Python API for RFormula
Add ml.PCA user guide document and code examples for Scala/Java/Python.
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#7522 from yanboliang/ml-pca-md and squashes the following commits:
60dec05 [Yanbo Liang] address comments
f992abe [Yanbo Liang] Add ml.PCA doc and examples
Now the memory defaults of master and slave in Standalone mode and History Server is 1g, not 512m. So let's update docs.
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#7896 from sarutak/update-doc-for-daemon-memory and squashes the following commits:
a77626c [Kousuke Saruta] Fix docs to follow the update of increase of memory defaults
Added featureImportance to RandomForestClassifier and Regressor.
This follows the scikit-learn implementation here: [a95203b249/sklearn/tree/_tree.pyx (L3341)]
CC: yanboliang Would you mind taking a look? Thanks!
Author: Joseph K. Bradley <joseph@databricks.com>
Author: Feynman Liang <fliang@databricks.com>
Closes#7838 from jkbradley/dt-feature-importance and squashes the following commits:
72a167a [Joseph K. Bradley] fixed unit test
86cea5f [Joseph K. Bradley] Modified RF featuresImportances to return Vector instead of Map
5aa74f0 [Joseph K. Bradley] finally fixed unit test for real
33df5db [Joseph K. Bradley] fix unit test
42a2d3b [Joseph K. Bradley] fix unit test
fe94e72 [Joseph K. Bradley] modified feature importance unit tests
cc693ee [Feynman Liang] Add classifier tests
79a6f87 [Feynman Liang] Compare dense vectors in test
21d01fc [Feynman Liang] Added failing SKLearn test
ac0b254 [Joseph K. Bradley] Added featureImportance to RandomForestClassifier/Regressor. Need to add unit tests
Author: Cheng Lian <lian@databricks.com>
Closes#7895 from liancheng/spark-9554/enable-in-memory-partition-pruning and squashes the following commits:
67c403e [Cheng Lian] Enables in-memory partition pruning by default
Author: Reynold Xin <rxin@databricks.com>
Closes#7897 from rxin/calculateBitSetWidthInBytes and squashes the following commits:
2e73b3a [Reynold Xin] [SQL][minor] Simplify UnsafeRow.calculateBitSetWidthInBytes.
The issue was that the tokenizer was parsing "1one" into the numeric 1 using the code on line 110. I added another case to accept strings that start with a number and then have a letter somewhere else in it as well.
Author: Joseph Batchik <joseph.batchik@cloudera.com>
Closes#7844 from JDrit/parse_error and squashes the following commits:
b8ca12f [Joseph Batchik] fixed parsing issue by adding another case
Certain use cases of Spark involve RDDs with long lineages that must be truncated periodically (e.g. GraphX). The existing way of doing it is through `rdd.checkpoint()`, which is expensive because it writes to HDFS. This patch provides an alternative to truncate lineages cheaply *without providing the same level of fault tolerance*.
**Local checkpointing** writes checkpointed data to the local file system through the block manager. It is much faster than replicating to a reliable storage and provides the same semantics as long as executors do not fail. It is accessible through a new operator `rdd.localCheckpoint()` and leaves the old one unchanged. Users may even decide to combine the two and call the reliable one less frequently.
The bulk of this patch involves refactoring the checkpointing interface to accept custom implementations of checkpointing. [Design doc](https://issues.apache.org/jira/secure/attachment/12741708/SPARK-7292-design.pdf).
Author: Andrew Or <andrew@databricks.com>
Closes#7279 from andrewor14/local-checkpoint and squashes the following commits:
729600f [Andrew Or] Oops, fix tests
34bc059 [Andrew Or] Avoid computing all partitions in local checkpoint
e43bbb6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
3be5aea [Andrew Or] Address comments
bf846a6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
ab003a3 [Andrew Or] Fix compile
c2e111b [Andrew Or] Address comments
33f167a [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
e908a42 [Andrew Or] Fix tests
f5be0f3 [Andrew Or] Use MEMORY_AND_DISK as the default local checkpoint level
a92657d [Andrew Or] Update a few comments
e58e3e3 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
4eb6eb1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
1bbe154 [Andrew Or] Simplify LocalCheckpointRDD
48a9996 [Andrew Or] Avoid traversing dependency tree + rewrite tests
62aba3f [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
db70dc2 [Andrew Or] Express local checkpointing through caching the original RDD
87d43c6 [Andrew Or] Merge branch 'master' of github.com:apache/spark into local-checkpoint
c449b38 [Andrew Or] Fix style
4a182f3 [Andrew Or] Add fine-grained tests for local checkpointing
53b363b [Andrew Or] Rename a few more awkwardly named methods (minor)
e4cf071 [Andrew Or] Simplify LocalCheckpointRDD + docs + clean ups
4880deb [Andrew Or] Fix style
d096c67 [Andrew Or] Fix mima
172cb66 [Andrew Or] Fix mima?
e53d964 [Andrew Or] Fix style
56831c5 [Andrew Or] Add a few warnings and clear exception messages
2e59646 [Andrew Or] Add local checkpoint clean up tests
4dbbab1 [Andrew Or] Refactor CheckpointSuite to test local checkpointing
4514dc9 [Andrew Or] Clean local checkpoint files through RDD cleanups
0477eec [Andrew Or] Rename a few methods with awkward names (minor)
2e902e5 [Andrew Or] First implementation of local checkpointing
8447454 [Andrew Or] Fix tests
4ac1896 [Andrew Or] Refactor checkpoint interface for modularity
RandomForestClassifier now outputs rawPrediction based on tree probabilities, plus probability column computed from normalized rawPrediction.
CC: holdenk
Author: Joseph K. Bradley <joseph@databricks.com>
Closes#7859 from jkbradley/rf-prob and squashes the following commits:
6c28f51 [Joseph K. Bradley] Changed RandomForestClassifier to extend ProbabilisticClassifier
Currently, when copy the bitsets, we didn't consider that the row1 may not sit in the beginning of byte array.
cc rxin
Author: Davies Liu <davies@databricks.com>
Closes#7892 from davies/clean_join and squashes the following commits:
14cce9e [Davies Liu] cleanup generated UnsafeRowJoiner and fix bug
Author: Wenchen Fan <cloud0fan@outlook.com>
Closes#7885 from cloud-fan/cheap-copy and squashes the following commits:
0900ca1 [Wenchen Fan] replace == with ===
73f4ada [Wenchen Fan] add tests
07b865a [Wenchen Fan] add a cheap version of copy
This patch builds directly on #7820, which is largely written by tnachen. The only addition is one commit for cleaning up the code. There should be no functional differences between this and #7820.
Author: Timothy Chen <tnachen@gmail.com>
Author: Andrew Or <andrew@databricks.com>
Closes#7881 from andrewor14/tim-cleanup-mesos-shuffle and squashes the following commits:
8894f7d [Andrew Or] Clean up code
2a5fa10 [Andrew Or] Merge branch 'mesos_shuffle_clean' of github.com:tnachen/spark into tim-cleanup-mesos-shuffle
fadff89 [Timothy Chen] Address comments.
e4d0f1d [Timothy Chen] Clean up external shuffle data on driver exit with Mesos.
This PR adds a base aggregation iterator `AggregationIterator`, which is used to create `SortBasedAggregationIterator` (for sort-based aggregation) and `UnsafeHybridAggregationIterator` (first it tries hash-based aggregation and falls back to the sort-based aggregation (using external sorter) if we cannot allocate memory for the map). With these two iterators, we will not need existing iterators and I am removing those. Also, we can use a single physical `Aggregate` operator and it internally determines what iterators to used.
https://issues.apache.org/jira/browse/SPARK-9240
Author: Yin Huai <yhuai@databricks.com>
Closes#7813 from yhuai/AggregateOperator and squashes the following commits:
e317e2b [Yin Huai] Remove unnecessary change.
74d93c5 [Yin Huai] Merge remote-tracking branch 'upstream/master' into AggregateOperator
ba6afbc [Yin Huai] Add a little bit more comments.
c9cf3b6 [Yin Huai] update
0f1b06f [Yin Huai] Remove unnecessary code.
21fd15f [Yin Huai] Remove unnecessary change.
964f88b [Yin Huai] Implement fallback strategy.
b1ea5cf [Yin Huai] wip
7fcbd87 [Yin Huai] Add a flag to control what iterator to use.
533d5b2 [Yin Huai] Prepare for fallback!
33b7022 [Yin Huai] wip
bd9282b [Yin Huai] UDAFs now supports UnsafeRow.
f52ee53 [Yin Huai] wip
3171f44 [Yin Huai] wip
d2c45a0 [Yin Huai] wip
f60cc83 [Yin Huai] Also check input schema.
af32210 [Yin Huai] Check iter.hasNext before we create an iterator because the constructor of the iterato will read at least one row from a non-empty input iter.
299008c [Yin Huai] First round cleanup.
3915bac [Yin Huai] Create a base iterator class for aggregation iterators and add the initial version of the hybrid iterator.
JIRA: https://issues.apache.org/jira/browse/SPARK-9549
This PR fix the following bugs:
1. `UnaryMinus`'s codegen version would fail to compile when the input is `Long.MinValue`
2. `BinaryComparison` would fail to compile in codegen mode when comparing Boolean types.
3. `AddMonth` would fail if passed a huge negative month, which would lead accessing negative index of `monthDays` array.
4. `Nanvl` with different type operands.
Author: Yijie Shen <henry.yijieshen@gmail.com>
Closes#7882 from yjshen/minor_bug_fix and squashes the following commits:
41bbd2c [Yijie Shen] fix bug in Nanvl type coercion
3dee204 [Yijie Shen] address comments
4fa5de0 [Yijie Shen] fix bugs in expressions
This PR adds a UnsafeArrayData, current we encode it in this way:
first 4 bytes is the # elements
then each 4 byte is the start offset of the element, unless it is negative, in which case the element is null.
followed by the elements themselves
an example: [10, 11, 12, 13, null, 14] will be encoded as:
5, 28, 32, 36, 40, -44, 44, 10, 11, 12, 13, 14
Note that, when we read a UnsafeArrayData from bytes, we can read the first 4 bytes as numElements and take the rest(first 4 bytes skipped) as value region.
unsafe map data just use 2 unsafe array data, first 4 bytes is # of elements, second 4 bytes is numBytes of key array, the follows key array data and value array data.
Author: Wenchen Fan <cloud0fan@outlook.com>
Closes#7752 from cloud-fan/unsafe-array and squashes the following commits:
3269bd7 [Wenchen Fan] fix a bug
6445289 [Wenchen Fan] add unit tests
49adf26 [Wenchen Fan] add unsafe map
20d1039 [Wenchen Fan] add comments and unsafe converter
821b8db [Wenchen Fan] add unsafe array
This PR adds an optimization rule, `FilterNullsInJoinKey`, to add `Filter` before join operators to filter out rows having null values for join keys.
This optimization is guarded by a new SQL conf, `spark.sql.advancedOptimization`.
The code in this PR was authored by yhuai; I'm opening this PR to factor out this change from #7685, a larger pull request which contains two other optimizations.
Author: Yin Huai <yhuai@databricks.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7768 from JoshRosen/filter-nulls-in-join-key and squashes the following commits:
c02fc3f [Yin Huai] Address Josh's comments.
0a8e096 [Yin Huai] Update comments.
ea7d5a6 [Yin Huai] Make sure we do not keep adding filters.
be88760 [Yin Huai] Make it clear that FilterNullsInJoinKeySuite.scala is used to test FilterNullsInJoinKey.
8bb39ad [Yin Huai] Fix non-deterministic tests.
303236b [Josh Rosen] Revert changes that are unrelated to null join key filtering
40eeece [Josh Rosen] Merge remote-tracking branch 'origin/master' into filter-nulls-in-join-key
c57a954 [Yin Huai] Bug fix.
d3d2e64 [Yin Huai] First round of cleanup.
f9516b0 [Yin Huai] Style
c6667e7 [Yin Huai] Add PartitioningCollection.
e616d3b [Yin Huai] wip
7c2d2d8 [Yin Huai] Bug fix and refactoring.
69bb072 [Yin Huai] Introduce NullSafeHashPartitioning and NullUnsafePartitioning.
d5b84c3 [Yin Huai] Do not add unnessary filters.
2201129 [Yin Huai] Filter out rows that will not be joined in equal joins early.
Make the following ml.classification class support raw and probability prediction for PySpark:
```scala
NaiveBayesModel
DecisionTreeClassifierModel
LogisticRegressionModel
```
Author: Yanbo Liang <ybliang8@gmail.com>
Closes#7866 from yanboliang/spark-9536-9537 and squashes the following commits:
2934dab [Yanbo Liang] ml.NaiveBayes, ml.DecisionTreeClassifier and ml.LogisticRegression support probability prediction
This PR adds `PartitioningCollection`, which is used to represent the `outputPartitioning` for SparkPlans with multiple children (e.g. `ShuffledHashJoin`). So, a `SparkPlan` can have multiple descriptions of its partitioning schemes. Taking `ShuffledHashJoin` as an example, it has two descriptions of its partitioning schemes, i.e. `left.outputPartitioning` and `right.outputPartitioning`. So when we have a query like `select * from t1 join t2 on (t1.x = t2.x) join t3 on (t2.x = t3.x)` will only have three Exchange operators (when shuffled joins are needed) instead of four.
The code in this PR was authored by yhuai; I'm opening this PR to factor out this change from #7685, a larger pull request which contains two other optimizations.
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Author: Yin Huai <yhuai@databricks.com>
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7773 from JoshRosen/multi-way-join-planning-improvements and squashes the following commits:
5c45924 [Josh Rosen] Merge remote-tracking branch 'origin/master' into multi-way-join-planning-improvements
cd8269b [Josh Rosen] Refactor test to use SQLTestUtils
2963857 [Yin Huai] Revert unnecessary SqlConf change.
73913f7 [Yin Huai] Add comments and test. Also, revert the change in ShuffledHashOuterJoin for now.
4a99204 [Josh Rosen] Delete unrelated expression change
884ab95 [Josh Rosen] Carve out only SPARK-2205 changes.
247e5fa [Josh Rosen] Merge remote-tracking branch 'origin/master' into multi-way-join-planning-improvements
c57a954 [Yin Huai] Bug fix.
d3d2e64 [Yin Huai] First round of cleanup.
f9516b0 [Yin Huai] Style
c6667e7 [Yin Huai] Add PartitioningCollection.
e616d3b [Yin Huai] wip
7c2d2d8 [Yin Huai] Bug fix and refactoring.
69bb072 [Yin Huai] Introduce NullSafeHashPartitioning and NullUnsafePartitioning.
d5b84c3 [Yin Huai] Do not add unnessary filters.
2201129 [Yin Huai] Filter out rows that will not be joined in equal joins early.
This pull request creates two isOrderable functions in RowOrdering that can be used to check whether a data type or a sequence of expressions can be used in sorting.
Author: Reynold Xin <rxin@databricks.com>
Closes#7880 from rxin/SPARK-9546 and squashes the following commits:
f9e322d [Reynold Xin] Fixed tests.
0439b43 [Reynold Xin] [SPARK-9546][SQL] Centralize orderable data type checking.
#7142 made codegen enabled by default so let's modify the corresponding documents.
Closes#7142
Author: KaiXinXiaoLei <huleilei1@huawei.com>
Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>
Closes#7863 from sarutak/SPARK-9535 and squashes the following commits:
0884424 [Kousuke Saruta] Removed a line which mentioned about the effect of codegen enabled
3c11af0 [Kousuke Saruta] Merge branch 'sqlconfig' of https://github.com/KaiXinXiaoLei/spark into SPARK-9535
4ee531d [KaiXinXiaoLei] delete space
4cfd11d [KaiXinXiaoLei] change spark.sql.planner.externalSort
d624cf8 [KaiXinXiaoLei] sql config is wrong
