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* [SPARK-11820][ML][PYSPARK] PySpark LiR & LoR should support weightColYanbo Liang2015-11-182-16/+17
| | | | | | | | [SPARK-7685](https://issues.apache.org/jira/browse/SPARK-7685) and [SPARK-9642](https://issues.apache.org/jira/browse/SPARK-9642) have already supported setting weight column for ```LogisticRegression``` and ```LinearRegression```. It's a very important feature, PySpark should also support. mengxr Author: Yanbo Liang <ybliang8@gmail.com> Closes #9811 from yanboliang/spark-11820.
* [SPARK-11720][SQL][ML] Handle edge cases when count = 0 or 1 for Stats functionJihongMa2015-11-181-1/+1
| | | | | | | | return Double.NaN for mean/average when count == 0 for all numeric types that is converted to Double, Decimal type continue to return null. Author: JihongMa <linlin200605@gmail.com> Closes #9705 from JihongMA/SPARK-11720.
* [SPARK-11804] [PYSPARK] Exception raise when using Jdbc predicates opt…Jeff Zhang2015-11-182-5/+18
| | | | | | | | …ion in PySpark Author: Jeff Zhang <zjffdu@apache.org> Closes #9791 from zjffdu/SPARK-11804.
* [SPARK-9065][STREAMING][PYSPARK] Add MessageHandler for Kafka Python APIjerryshao2015-11-172-12/+134
| | | | | | | | | | | | Fixed the merge conflicts in #7410 Closes #7410 Author: Shixiong Zhu <shixiong@databricks.com> Author: jerryshao <saisai.shao@intel.com> Author: jerryshao <sshao@hortonworks.com> Closes #9742 from zsxwing/pr7410.
* [SPARK-11740][STREAMING] Fix the race condition of two checkpoints in a batchShixiong Zhu2015-11-171-5/+4
| | | | | | | | We will do checkpoint when generating a batch and completing a batch. When the processing time of a batch is greater than the batch interval, checkpointing for completing an old batch may run after checkpointing for generating a new batch. If this happens, checkpoint of an old batch actually has the latest information, so we want to recovery from it. This PR will use the latest checkpoint time as the file name, so that we can always recovery from the latest checkpoint file. Author: Shixiong Zhu <shixiong@databricks.com> Closes #9707 from zsxwing/fix-checkpoint.
* [SPARK-6328][PYTHON] Python API for StreamingListenerDaniel Jalova2015-11-164-2/+210
| | | | | | Author: Daniel Jalova <djalova@us.ibm.com> Closes #9186 from djalova/SPARK-6328.
* [SPARK-11745][SQL] Enable more JSON parsing optionsReynold Xin2015-11-161-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | This patch adds the following options to the JSON data source, for dealing with non-standard JSON files: * `allowComments` (default `false`): ignores Java/C++ style comment in JSON records * `allowUnquotedFieldNames` (default `false`): allows unquoted JSON field names * `allowSingleQuotes` (default `true`): allows single quotes in addition to double quotes * `allowNumericLeadingZeros` (default `false`): allows leading zeros in numbers (e.g. 00012) To avoid passing a lot of options throughout the json package, I introduced a new JSONOptions case class to define all JSON config options. Also updated documentation to explain these options. Scala ![screen shot 2015-11-15 at 6 12 12 pm](https://cloud.githubusercontent.com/assets/323388/11172965/e3ace6ec-8bc4-11e5-805e-2d78f80d0ed6.png) Python ![screen shot 2015-11-15 at 6 11 28 pm](https://cloud.githubusercontent.com/assets/323388/11172964/e23ed6ee-8bc4-11e5-8216-312f5983acd5.png) Author: Reynold Xin <rxin@databricks.com> Closes #9724 from rxin/SPARK-11745.
* [SPARK-11690][PYSPARK] Add pivot to python apiAndrew Ray2015-11-131-1/+23
| | | | | | | | This PR adds pivot to the python api of GroupedData with the same syntax as Scala/Java. Author: Andrew Ray <ray.andrew@gmail.com> Closes #9653 from aray/sql-pivot-python.
* [SPARK-11706][STREAMING] Fix the bug that Streaming Python tests cannot ↵Shixiong Zhu2015-11-131-10/+20
| | | | | | | | | | report failures This PR just checks the test results and returns 1 if the test fails, so that `run-tests.py` can mark it fail. Author: Shixiong Zhu <shixiong@databricks.com> Closes #9669 from zsxwing/streaming-python-tests.
* [SPARK-11658] simplify documentation for PySpark combineByKeyChris Snow2015-11-121-1/+0
| | | | | | Author: Chris Snow <chsnow123@gmail.com> Closes #9640 from snowch/patch-3.
* [SPARK-11671] documentation code example typoChris Snow2015-11-121-1/+1
| | | | | | | | Example for sqlContext.createDataDrame from pandas.DataFrame has a typo Author: Chris Snow <chsnow123@gmail.com> Closes #9639 from snowch/patch-2.
* [SPARK-11420] Updating Stddev support via Imperative AggregateJihongMa2015-11-121-1/+1
| | | | | | | | switched stddev support from DeclarativeAggregate to ImperativeAggregate. Author: JihongMa <linlin200605@gmail.com> Closes #9380 from JihongMA/SPARK-11420.
* [SPARK-11463] [PYSPARK] only install signal in main threadDavies Liu2015-11-101-1/+4
| | | | | | | | Only install signal in main thread, or it will fail to create context in not-main thread. Author: Davies Liu <davies@databricks.com> Closes #9574 from davies/python_signal.
* [SPARK-11566] [MLLIB] [PYTHON] Refactoring GaussianMixtureModel.gaussians in ↵Yu ISHIKAWA2015-11-101-1/+1
| | | | | | | | | | Python cc jkbradley Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #9534 from yu-iskw/SPARK-11566.
* [SPARK-11567] [PYTHON] Add Python API for corr Aggregate functionfelixcheung2015-11-101-0/+16
| | | | | | | | | | like `df.agg(corr("col1", "col2")` davies Author: felixcheung <felixcheung_m@hotmail.com> Closes #9536 from felixcheung/pyfunc.
* [SPARK-9830][SQL] Remove AggregateExpression1 and Aggregate Operator used to ↵Yin Huai2015-11-103-3/+3
| | | | | | | | | | | | | | | | | | | evaluate AggregateExpression1s https://issues.apache.org/jira/browse/SPARK-9830 This PR contains the following main changes. * Removing `AggregateExpression1`. * Removing `Aggregate` operator, which is used to evaluate `AggregateExpression1`. * Removing planner rule used to plan `Aggregate`. * Linking `MultipleDistinctRewriter` to analyzer. * Renaming `AggregateExpression2` to `AggregateExpression` and `AggregateFunction2` to `AggregateFunction`. * Updating places where we create aggregate expression. The way to create aggregate expressions is `AggregateExpression(aggregateFunction, mode, isDistinct)`. * Changing `val`s in `DeclarativeAggregate`s that touch children of this function to `lazy val`s (when we create aggregate expression in DataFrame API, children of an aggregate function can be unresolved). Author: Yin Huai <yhuai@databricks.com> Closes #9556 from yhuai/removeAgg1.
* [SPARK-11610][MLLIB][PYTHON][DOCS] Make the docs of LDAModel.describeTopics ↵Yu ISHIKAWA2015-11-091-0/+6
| | | | | | | | | | in Python more specific cc jkbradley Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #9577 from yu-iskw/SPARK-11610.
* [SPARK-9301][SQL] Add collect_set and collect_list aggregate functionsNick Buroojy2015-11-092-11/+31
| | | | | | | | | | | | | | | | | | | | | For now they are thin wrappers around the corresponding Hive UDAFs. One limitation with these in Hive 0.13.0 is they only support aggregating primitive types. I chose snake_case here instead of camelCase because it seems to be used in the majority of the multi-word fns. Do we also want to add these to `functions.py`? This approach was recommended here: https://github.com/apache/spark/pull/8592#issuecomment-154247089 marmbrus rxin Author: Nick Buroojy <nick.buroojy@civitaslearning.com> Closes #9526 from nburoojy/nick/udaf-alias. (cherry picked from commit a6ee4f989d020420dd08b97abb24802200ff23b2) Signed-off-by: Michael Armbrust <michael@databricks.com>
* [SPARK-10280][MLLIB][PYSPARK][DOCS] Add @since annotation to ↵Yu ISHIKAWA2015-11-091-0/+56
| | | | | | | | pyspark.ml.classification Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #8690 from yu-iskw/SPARK-10280.
* [SPARK-8467] [MLLIB] [PYSPARK] Add LDAModel.describeTopics() in PythonYu ISHIKAWA2015-11-061-15/+18
| | | | | | | | | | | | | Could jkbradley and davies review it? - Create a wrapper class: `LDAModelWrapper` for `LDAModel`. Because we can't deal with the return value of`describeTopics` in Scala from pyspark directly. `Array[(Array[Int], Array[Double])]` is too complicated to convert it. - Add `loadLDAModel` in `PythonMLlibAPI`. Since `LDAModel` in Scala is an abstract class and we need to call `load` of `DistributedLDAModel`. [[SPARK-8467] Add LDAModel.describeTopics() in Python - ASF JIRA](https://issues.apache.org/jira/browse/SPARK-8467) Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #8643 from yu-iskw/SPARK-8467-2.
* [HOTFIX] Fix python tests after #9527Michael Armbrust2015-11-061-1/+1
| | | | | | | | #9527 missed updating the python tests. Author: Michael Armbrust <michael@databricks.com> Closes #9533 from marmbrus/hotfixTextValue.
* [SPARK-11410] [PYSPARK] Add python bindings for repartition and sortW…Nong Li2015-11-061-16/+101
| | | | | | | | …ithinPartitions. Author: Nong Li <nong@databricks.com> Closes #9504 from nongli/spark-11410.
* [SPARK-10116][CORE] XORShiftRandom.hashSeed is random in high bitsImran Rashid2015-11-064-18/+18
| | | | | | | | | | | | https://issues.apache.org/jira/browse/SPARK-10116 This is really trivial, just happened to notice it -- if `XORShiftRandom.hashSeed` is really supposed to have random bits throughout (as the comment implies), it needs to do something for the conversion to `long`. mengxr mkolod Author: Imran Rashid <irashid@cloudera.com> Closes #8314 from squito/SPARK-10116.
* [SPARK-11473][ML] R-like summary statistics with intercept for OLS via ↵Yanbo Liang2015-11-051-8/+8
| | | | | | | | | | normal equation solver Follow up [SPARK-9836](https://issues.apache.org/jira/browse/SPARK-9836), we should also support summary statistics for ```intercept```. Author: Yanbo Liang <ybliang8@gmail.com> Closes #9485 from yanboliang/spark-11473.
* [SPARK-11527][ML][PYSPARK] PySpark AFTSurvivalRegressionModel should expose ↵Yanbo Liang2015-11-051-0/+24
| | | | | | | | | | coefficients/intercept/scale PySpark ```AFTSurvivalRegressionModel``` should expose coefficients/intercept/scale. mengxr vectorijk Author: Yanbo Liang <ybliang8@gmail.com> Closes #9492 from yanboliang/spark-11527.
* [SPARK-11378][STREAMING] make StreamingContext.awaitTerminationOrTimeout ↵Nick Evans2015-11-052-1/+8
| | | | | | | | | | | | return properly This adds a failing test checking that `awaitTerminationOrTimeout` returns the expected value, and then fixes that failing test with the addition of a `return`. tdas zsxwing Author: Nick Evans <me@nicolasevans.org> Closes #9336 from manygrams/fix_await_termination_or_timeout.
* [SPARK-10028][MLLIB][PYTHON] Add Python API for PrefixSpanYu ISHIKAWA2015-11-041-1/+68
| | | | | | Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #9469 from yu-iskw/SPARK-10028.
* [SPARK-11489][SQL] Only include common first order statistics in GroupedDataReynold Xin2015-11-031-88/+0
| | | | | | | | | | | | | | | | | | We added a bunch of higher order statistics such as skewness and kurtosis to GroupedData. I don't think they are common enough to justify being listed, since users can always use the normal statistics aggregate functions. That is to say, after this change, we won't support ```scala df.groupBy("key").kurtosis("colA", "colB") ``` However, we will still support ```scala df.groupBy("key").agg(kurtosis(col("colA")), kurtosis(col("colB"))) ``` Author: Reynold Xin <rxin@databricks.com> Closes #9446 from rxin/SPARK-11489.
* [SPARK-11467][SQL] add Python API for stddev/varianceDavies Liu2015-11-032-0/+105
| | | | | | | | Add Python API for stddev/stddev_pop/stddev_samp/variance/var_pop/var_samp/skewness/kurtosis Author: Davies Liu <davies@databricks.com> Closes #9424 from davies/py_var.
* [SPARK-10592] [ML] [PySpark] Deprecate weights and use coefficients instead ↵vectorijk2015-11-022-0/+25
| | | | | | | | | | in ML models Deprecated in `LogisticRegression` and `LinearRegression` Author: vectorijk <jiangkai@gmail.com> Closes #9311 from vectorijk/spark-10592.
* [SPARK-10286][ML][PYSPARK][DOCS] Add @since annotation to pyspark.ml.param ↵lihao2015-11-024-0/+230
| | | | | | | | and pyspark.ml.* Author: lihao <lihaowhu@gmail.com> Closes #9275 from lidinghao/SPARK-10286.
* [SPARK-11358][MLLIB] deprecate runs in k-meansXiangrui Meng2015-11-021-0/+4
| | | | | | | | | | This PR deprecates `runs` in k-means. `runs` introduces extra complexity and overhead in MLlib's k-means implementation. I haven't seen much usage with `runs` not equal to `1`. We don't have a unit test for it either. We can deprecate this method in 1.6, and void it in 1.7. It helps us simplify the implementation. cc: srowen Author: Xiangrui Meng <meng@databricks.com> Closes #9322 from mengxr/SPARK-11358.
* [SPARK-11437] [PYSPARK] Don't .take when converting RDD to DataFrame with ↵Jason White2015-11-021-7/+1
| | | | | | | | | | | | | | provided schema When creating a DataFrame from an RDD in PySpark, `createDataFrame` calls `.take(10)` to verify the first 10 rows of the RDD match the provided schema. Similar to https://issues.apache.org/jira/browse/SPARK-8070, but that issue affected cases where a schema was not provided. Verifying the first 10 rows is of limited utility and causes the DAG to be executed non-lazily. If necessary, I believe this verification should be done lazily on all rows. However, since the caller is providing a schema to follow, I think it's acceptable to simply fail if the schema is incorrect. marmbrus We chatted about this at SparkSummitEU. davies you made a similar change for the infer-schema path in https://github.com/apache/spark/pull/6606 Author: Jason White <jason.white@shopify.com> Closes #9392 from JasonMWhite/createDataFrame_without_take.
* [SPARK-11322] [PYSPARK] Keep full stack trace in captured exceptionLiang-Chi Hsieh2015-10-282-4/+21
| | | | | | | | | | JIRA: https://issues.apache.org/jira/browse/SPARK-11322 As reported by JoshRosen in [databricks/spark-redshift/issues/89](https://github.com/databricks/spark-redshift/issues/89#issuecomment-149828308), the exception-masking behavior sometimes makes debugging harder. To deal with this issue, we should keep full stack trace in the captured exception. Author: Liang-Chi Hsieh <viirya@appier.com> Closes #9283 from viirya/py-exception-stacktrace.
* [SPARK-11292] [SQL] Python API for text data sourceReynold Xin2015-10-282-2/+27
| | | | | | | | Adds DataFrameReader.text and DataFrameWriter.text. Author: Reynold Xin <rxin@databricks.com> Closes #9259 from rxin/SPARK-11292.
* [SPARK-11367][ML][PYSPARK] Python LinearRegression should support setting solverYanbo Liang2015-10-283-22/+37
| | | | | | | | [SPARK-10668](https://issues.apache.org/jira/browse/SPARK-10668) has provided ```WeightedLeastSquares``` solver("normal") in ```LinearRegression``` with L2 regularization in Scala and R, Python ML ```LinearRegression``` should also support setting solver("auto", "normal", "l-bfgs") Author: Yanbo Liang <ybliang8@gmail.com> Closes #9328 from yanboliang/spark-11367.
* [SPARK-11302][MLLIB] 2) Multivariate Gaussian Model with Covariance matrix ↵Sean Owen2015-10-271-2/+2
| | | | | | | | | | | | returns incorrect answer in some cases Fix computation of root-sigma-inverse in multivariate Gaussian; add a test and fix related Python mixture model test. Supersedes https://github.com/apache/spark/pull/9293 Author: Sean Owen <sowen@cloudera.com> Closes #9309 from srowen/SPARK-11302.2.
* [SPARK-10024][PYSPARK] Python API RF and GBT related params clear upvectorijk2015-10-272-338/+168
| | | | | | | | | implement {RandomForest, GBT, TreeEnsemble, TreeClassifier, TreeRegressor}Params for Python API in pyspark/ml/{classification, regression}.py Author: vectorijk <jiangkai@gmail.com> Closes #9233 from vectorijk/spark-10024.
* [SPARK-6488][MLLIB][PYTHON] Support addition/multiplication in PySpark's ↵Mike Dusenberry2015-10-271-0/+68
| | | | | | | | | | BlockMatrix This PR adds addition and multiplication to PySpark's `BlockMatrix` class via `add` and `multiply` functions. Author: Mike Dusenberry <mwdusenb@us.ibm.com> Closes #9139 from dusenberrymw/SPARK-6488_Add_Addition_and_Multiplication_to_PySpark_BlockMatrix.
* [SPARK-11270][STREAMING] Add improved equality testing for TopicAndPartition ↵Nick Evans2015-10-272-0/+20
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | from the Kafka Streaming API jerryshao tdas I know this is kind of minor, and I know you all are busy, but this brings this class in line with the `OffsetRange` class, and makes tests a little more concise. Instead of doing something like: ``` assert topic_and_partition_instance._topic == "foo" assert topic_and_partition_instance._partition == 0 ``` You can do something like: ``` assert topic_and_partition_instance == TopicAndPartition("foo", 0) ``` Before: ``` >>> from pyspark.streaming.kafka import TopicAndPartition >>> TopicAndPartition("foo", 0) == TopicAndPartition("foo", 0) False ``` After: ``` >>> from pyspark.streaming.kafka import TopicAndPartition >>> TopicAndPartition("foo", 0) == TopicAndPartition("foo", 0) True ``` I couldn't find any tests - am I missing something? Author: Nick Evans <me@nicolasevans.org> Closes #9236 from manygrams/topic_and_partition_equality.
* [SPARK-10271][PYSPARK][MLLIB] Added @since tags to pyspark.mllib.clusteringnoelsmith2015-10-261-1/+68
| | | | | | | | | | Duplicated the since decorator from pyspark.sql into pyspark (also tweaked to handle functions without docstrings). Added since to methods + "versionadded::" to classes (derived from the git file history in pyspark). Author: noelsmith <mail@noelsmith.com> Closes #8627 from noel-smith/SPARK-10271-since-mllib-clustering.
* [SPARK-11279][PYSPARK] Add DataFrame#toDF in PySparkJeff Zhang2015-10-261-0/+12
| | | | | | Author: Jeff Zhang <zjffdu@apache.org> Closes #9248 from zjffdu/SPARK-11279.
* [SPARK-10277] [MLLIB] [PYSPARK] Add @since annotation to ↵Yu ISHIKAWA2015-10-231-1/+101
| | | | | | | | pyspark.mllib.regression Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com> Closes #8684 from yu-iskw/SPARK-10277.
* [SPARK-7021] Add JUnit output for Python unit testsGábor Lipták2015-10-225-9/+48
| | | | | | | | WIP Author: Gábor Lipták <gliptak@gmail.com> Closes #8323 from gliptak/SPARK-7021.
* [SPARK-11205][PYSPARK] Delegate to scala DataFrame API rather than p…Jeff Zhang2015-10-201-1/+2
| | | | | | | | | | …rint in python No test needed. Verify it manually in pyspark shell Author: Jeff Zhang <zjffdu@apache.org> Closes #9177 from zjffdu/SPARK-11205.
* [MINOR][ML] fix doc warningsXiangrui Meng2015-10-201-0/+1
| | | | | | | | | | | | | Without an empty line, sphinx will treat doctest as docstring. holdenk ~~~ /Users/meng/src/spark/python/pyspark/ml/feature.py:docstring of pyspark.ml.feature.CountVectorizer:3: ERROR: Undefined substitution referenced: "label|raw |vectors | +-----+---------------+-------------------------+ |0 |[a, b, c] |(3,[0,1,2],[1.0,1.0,1.0])". /Users/meng/src/spark/python/pyspark/ml/feature.py:docstring of pyspark.ml.feature.CountVectorizer:3: ERROR: Undefined substitution referenced: "1 |[a, b, b, c, a]|(3,[0,1,2],[2.0,2.0,1.0])". ~~~ Author: Xiangrui Meng <meng@databricks.com> Closes #9188 from mengxr/py-count-vec-doc-fix.
* [SPARK-10767][PYSPARK] Make pyspark shared params codegen more consistentHolden Karau2015-10-203-65/+65
| | | | | | | | Namely "." shows up in some places in the template when using the param docstring and not in others Author: Holden Karau <holden@pigscanfly.ca> Closes #9017 from holdenk/SPARK-10767-Make-pyspark-shared-params-codegen-more-consistent.
* [SPARK-10269][PYSPARK][MLLIB] Add @since annotation to ↵noelsmith2015-10-201-4/+66
| | | | | | | | | | | | | | pyspark.mllib.classification Duplicated the since decorator from pyspark.sql into pyspark (also tweaked to handle functions without docstrings). Added since to methods + "versionadded::" to classes derived from the file history. Note - some methods are inherited from the regression module (i.e. LinearModel.intercept) so these won't have version numbers in the API docs until that model is updated. Author: noelsmith <mail@noelsmith.com> Closes #8626 from noel-smith/SPARK-10269-since-mlib-classification.
* [SPARK-10272][PYSPARK][MLLIB] Added @since tags to pyspark.mllib.evaluationnoelsmith2015-10-201-0/+41
| | | | | | | | | | | | Duplicated the since decorator from pyspark.sql into pyspark (also tweaked to handle functions without docstrings). Added since to public methods + "versionadded::" to classes (derived from the git file history in pyspark). Note - I added also the tags to MultilabelMetrics even though it isn't declared as public in the __all__ statement... if that's incorrect - I'll remove. Author: noelsmith <mail@noelsmith.com> Closes #8628 from noel-smith/SPARK-10272-since-mllib-evalutation.
* [SPARK-10447][SPARK-3842][PYSPARK] upgrade pyspark to py4j0.9Holden Karau2015-10-209-57/+25
| | | | | | | | | Upgrade to Py4j0.9 Author: Holden Karau <holden@pigscanfly.ca> Author: Holden Karau <holden@us.ibm.com> Closes #8615 from holdenk/SPARK-10447-upgrade-pyspark-to-py4j0.9.
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