Re: example of non-line oriented input data?

[Matei Zaharia <ma...@gmail.com>]

FYI, one thing we’ve added now is support for reading multiple text files from a directory as separate records: https://github.com/apache/spark/pull/327. This should remove the need for mapPartitions discussed here.

Avro and SequenceFiles look like they may not make it for 1.0, but there’s a chance that Parquet support with Spark SQL will, which should let you store binary data a bit better.

Matei

On Mar 19, 2014, at 3:12 PM, Jeremy Freeman <fr...@gmail.com> wrote:

> Another vote on this, support for simple SequenceFiles and/or Avro would be terrific, as using plain text can be very space-inefficient, especially for numerical data.
> 
> -- Jeremy
> 
> On Mar 19, 2014, at 5:24 PM, Nicholas Chammas <ni...@gmail.com> wrote:
> 
>> I'd second the request for Avro support in Python first, followed by Parquet.
>> 
>> 
>> On Wed, Mar 19, 2014 at 2:14 PM, Evgeny Shishkin <it...@gmail.com> wrote:
>> 
>> On 19 Mar 2014, at 19:54, Diana Carroll <dc...@cloudera.com> wrote:
>> 
>>> Actually, thinking more on this question, Matei: I'd definitely say support for Avro.  There's a lot of interest in this!!
>>> 
>> 
>> Agree, and parquet as default Cloudera Impala format.
>> 
>> 
>> 
>> 
>>> On Tue, Mar 18, 2014 at 8:14 PM, Matei Zaharia <ma...@gmail.com> wrote:
>>> BTW one other thing — in your experience, Diana, which non-text InputFormats would be most useful to support in Python first? Would it be Parquet or Avro, simple SequenceFiles with the Hadoop Writable types, or something else? I think a per-file text input format that does the stuff we did here would also be good.
>>> 
>>> Matei
>>> 
>>> 
>>> On Mar 18, 2014, at 3:27 PM, Matei Zaharia <ma...@gmail.com> wrote:
>>> 
>>>> Hi Diana,
>>>> 
>>>> This seems to work without the iter() in front if you just return treeiterator. What happened when you didn’t include that? Treeiterator should return an iterator.
>>>> 
>>>> Anyway, this is a good example of mapPartitions. It’s one where you want to view the whole file as one object (one XML here), so you couldn’t implement this using a flatMap, but you still want to return multiple values. The MLlib example you saw needs Python 2.7 because unfortunately that is a requirement for our Python MLlib support (see http://spark.incubator.apache.org/docs/0.9.0/python-programming-guide.html#libraries). We’d like to relax this later but we’re using some newer features of NumPy and Python. The rest of PySpark works on 2.6.
>>>> 
>>>> In terms of the size in memory, here both the string s and the XML tree constructed from it need to fit in, so you can’t work on very large individual XML files. You may be able to use a streaming XML parser instead to extract elements from the data in a streaming fashion, without every materializing the whole tree. http://docs.python.org/2/library/xml.sax.reader.html#module-xml.sax.xmlreader is one example.
>>>> 
>>>> Matei
>>>> 
>>>> On Mar 18, 2014, at 7:49 AM, Diana Carroll <dc...@cloudera.com> wrote:
>>>> 
>>>>> Well, if anyone is still following this, I've gotten the following code working which in theory should allow me to parse whole XML files: (the problem was that I can't return the tree iterator directly.  I have to call iter().  Why?)
>>>>> 
>>>>> import xml.etree.ElementTree as ET
>>>>> 
>>>>> # two source files, format <data> <country name="...">...</country>...</data>
>>>>> mydata=sc.textFile("file:/home/training/countries*.xml") 
>>>>> 
>>>>> def parsefile(iterator):
>>>>>     s = ''
>>>>>     for i in iterator: s = s + str(i)
>>>>>     tree = ET.fromstring(s)
>>>>>     treeiterator = tree.getiterator("country")
>>>>>     # why to I have to convert an iterator to an iterator?  not sure but required
>>>>>     return iter(treeiterator)
>>>>> 
>>>>> mydata.mapPartitions(lambda x: parsefile(x)).map(lambda element: element.attrib).collect()
>>>>> 
>>>>> The output is what I expect:
>>>>> [{'name': 'Liechtenstein'}, {'name': 'Singapore'}, {'name': 'Panama'}]
>>>>> 
>>>>> BUT I'm a bit concerned about the construction of the string "s".  How big can my file be before converting it to a string becomes problematic?
>>>>> 
>>>>> 
>>>>> 
>>>>> On Tue, Mar 18, 2014 at 9:41 AM, Diana Carroll <dc...@cloudera.com> wrote:
>>>>> Thanks, Matei.
>>>>> 
>>>>> In the context of this discussion, it would seem mapParitions is essential, because it's the only way I'm going to be able to process each file as a whole, in our example of a large number of small XML files which need to be parsed as a whole file because records are not required to be on a single line.
>>>>> 
>>>>> The theory makes sense but I'm still utterly lost as to how to implement it.  Unfortunately there's only a single example of the use of mapPartitions in any of the Python example programs, which is the log regression example, which I can't run because it requires Python 2.7 and I'm on Python 2.6.  (aside: I couldn't find any statement that Python 2.6 is unsupported...is it?)
>>>>> 
>>>>> I'd really really love to see a real life example of a Python use of mapPartitions.  I do appreciate the very simple examples you provided, but (perhaps because of my novice status on Python) I can't figure out how to translate those to a real world situation in which I'm building RDDs from files, not inline collections like [(1,2),(2,3)].
>>>>> 
>>>>> Also, you say that the function called in mapPartitions can return a collection OR an iterator.  I tried returning an iterator by calling ElementTree getiterator function, but still got the error telling me my object was not an iterator. 
>>>>> 
>>>>> If anyone has a real life example of mapPartitions returning a Python iterator, that would be fabulous.
>>>>> 
>>>>> Diana
>>>>> 
>>>>> 
>>>>> On Mon, Mar 17, 2014 at 6:17 PM, Matei Zaharia <ma...@gmail.com> wrote:
>>>>> Oh, I see, the problem is that the function you pass to mapPartitions must itself return an iterator or a collection. This is used so that you can return multiple output records for each input record. You can implement most of the existing map-like operations in Spark, such as map, filter, flatMap, etc, with mapPartitions, as well as new ones that might do a sliding window over each partition for example, or accumulate data across elements (e.g. to compute a sum).
>>>>> 
>>>>> For example, if you have data = sc.parallelize([1, 2, 3, 4], 2), this will work:
>>>>> 
>>>>> >>> data.mapPartitions(lambda x: x).collect()
>>>>> [1, 2, 3, 4]   # Just return the same iterator, doing nothing
>>>>> 
>>>>> >>> data.mapPartitions(lambda x: [list(x)]).collect()
>>>>> [[1, 2], [3, 4]]   # Group together the elements of each partition in a single list (like glom)
>>>>> 
>>>>> >>> data.mapPartitions(lambda x: [sum(x)]).collect()
>>>>> [3, 7]   # Sum each partition separately
>>>>> 
>>>>> However something like data.mapPartitions(lambda x: sum(x)).collect() will *not* work because sum returns a number, not an iterator. That’s why I put sum(x) inside a list above.
>>>>> 
>>>>> In practice mapPartitions is most useful if you want to share some data or work across the elements. For example maybe you want to load a lookup table once from an external file and then check each element in it, or sum up a bunch of elements without allocating a lot of vector objects.
>>>>> 
>>>>> Matei
>>>>> 
>>>>> 
>>>>> On Mar 17, 2014, at 11:25 AM, Diana Carroll <dc...@cloudera.com> wrote:
>>>>> 
>>>>> > "There’s also mapPartitions, which gives you an iterator for each partition instead of an array. You can then return an iterator or list of objects to produce from that."
>>>>> >
>>>>> > I confess, I was hoping for an example of just that, because i've not yet been able to figure out how to use mapPartitions.  No doubt this is because i'm a rank newcomer to Python, and haven't fully wrapped my head around iterators.  All I get so far in my attempts to use mapPartitions is the darned "suchnsuch is not an iterator" error.
>>>>> >
>>>>> > def myfunction(iterator): return [1,2,3]
>>>>> > mydata.mapPartitions(lambda x: myfunction(x)).take(2)
>>>>> >
>>>>> >
>>>>> >
>>>>> >
>>>>> >
>>>>> > On Mon, Mar 17, 2014 at 1:57 PM, Matei Zaharia <ma...@gmail.com> wrote:
>>>>> > Here’s an example of getting together all lines in a file as one string:
>>>>> >
>>>>> > $ cat dir/a.txt
>>>>> > Hello
>>>>> > world!
>>>>> >
>>>>> > $ cat dir/b.txt
>>>>> > What's
>>>>> > up??
>>>>> >
>>>>> > $ bin/pyspark
>>>>> > >>> files = sc.textFile(“dir”)
>>>>> >
>>>>> > >>> files.collect()
>>>>> > [u'Hello', u'world!', u"What's", u'up??’]   # one element per line, not what we want
>>>>> >
>>>>> > >>> files.glom().collect()
>>>>> > [[u'Hello', u'world!'], [u"What's", u'up??’]]   # one element per file, which is an array of lines
>>>>> >
>>>>> > >>> files.glom().map(lambda a: "\n".join(a)).collect()
>>>>> > [u'Hello\nworld!', u"What's\nup??”]    # join back each file into a single string
>>>>> >
>>>>> > The glom() method groups all the elements of each partition of an RDD into an array, giving you an RDD of arrays of objects. If your input is small files, you always have one partition per file.
>>>>> >
>>>>> > There’s also mapPartitions, which gives you an iterator for each partition instead of an array. You can then return an iterator or list of objects to produce from that.
>>>>> >
>>>>> > Matei
>>>>> >
>>>>> >
>>>>> > On Mar 17, 2014, at 10:46 AM, Diana Carroll <dc...@cloudera.com> wrote:
>>>>> >
>>>>> > > Thanks Matei.  That makes sense.  I have here a dataset of many many smallish XML files, so using mapPartitions that way would make sense.  I'd love to see a code example though ...It's not as obvious to me how to do that as I probably should be.
>>>>> > >
>>>>> > > Thanks,
>>>>> > > Diana
>>>>> > >
>>>>> > >
>>>>> > > On Mon, Mar 17, 2014 at 1:02 PM, Matei Zaharia <ma...@gmail.com> wrote:
>>>>> > > Hi Diana,
>>>>> > >
>>>>> > > Non-text input formats are only supported in Java and Scala right now, where you can use sparkContext.hadoopFile or .hadoopDataset to load data with any InputFormat that Hadoop MapReduce supports. In Python, you unfortunately only have textFile, which gives you one record per line. For JSON, you’d have to fit the whole JSON object on one line as you said. Hopefully we’ll also have some other forms of input soon.
>>>>> > >
>>>>> > > If your input is a collection of separate files (say many .xml files), you can also use mapPartitions on it to group together the lines because each input file will end up being a single dataset partition (or map task). This will let you concatenate the lines in each file and parse them as one XML object.
>>>>> > >
>>>>> > > Matei
>>>>> > >
>>>>> > > On Mar 17, 2014, at 9:52 AM, Diana Carroll <dc...@cloudera.com> wrote:
>>>>> > >
>>>>> > >> Thanks, Krakna, very helpful.  The way I read the code, it looks like you are assuming that each line in foo.log contains a complete json object?  (That is, that the data doesn't contain any records that are split into multiple lines.)  If so, is that because you know that to be true of your data?  Or did you do as Nicholas suggests and have some preprocessing on the text input to flatten the data in that way?
>>>>> > >>
>>>>> > >> Thanks,
>>>>> > >> Diana
>>>>> > >>
>>>>> > >>
>>>>> > >> On Mon, Mar 17, 2014 at 12:09 PM, Krakna H <sh...@gmail.com> wrote:
>>>>> > >> Katrina,
>>>>> > >>
>>>>> > >> Not sure if this is what you had in mind, but here's some simple pyspark code that I recently wrote to deal with JSON files.
>>>>> > >>
>>>>> > >> from pyspark import SparkContext, SparkConf
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> from operator import add
>>>>> > >> import json
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> import random
>>>>> > >> import numpy as np
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> def concatenate_paragraphs(sentence_array):
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> return ' '.join(sentence_array).split(' ')
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> logFile = 'foo.json'
>>>>> > >> conf = SparkConf()
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> conf.setMaster("spark://cluster-master:7077").setAppName("example").set("spark.executor.memory", "1g")
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> sc = SparkContext(conf=conf)
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> logData = sc.textFile(logFile).cache()
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> num_lines = logData.count()
>>>>> > >> print 'Number of lines: %d' % num_lines
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> # JSON object has the structure: {"key": {'paragraphs': [sentence1, sentence2, ...]}}
>>>>> > >> tm = logData.map(lambda s: (json.loads(s)['key'], len(concatenate_paragraphs(json.loads(s)['paragraphs']))))
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> tm = tm.reduceByKey(lambda _, x: _ + x)
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> op = tm.collect()
>>>>> > >> for key, num_words in op:
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>      print 'state: %s, num_words: %d' % (state, num_words)
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> On Mon, Mar 17, 2014 at 11:58 AM, Diana Carroll [via Apache Spark User List] <[hidden email]> wrote:
>>>>> > >> I don't actually have any data.  I'm writing a course that teaches students how to do this sort of thing and am interested in looking at a variety of real life examples of people doing things like that.  I'd love to see some working code implementing the "obvious work-around" you mention...do you have any to share?  It's an approach that makes a lot of sense, and as I said, I'd love to not have to re-invent the wheel if someone else has already written that code.  Thanks!
>>>>> > >>
>>>>> > >> Diana
>>>>> > >>
>>>>> > >>
>>>>> > >> On Mon, Mar 17, 2014 at 11:35 AM, Nicholas Chammas <[hidden email]> wrote:
>>>>> > >> There was a previous discussion about this here:
>>>>> > >>
>>>>> > >> http://apache-spark-user-list.1001560.n3.nabble.com/Having-Spark-read-a-JSON-file-td1963.html
>>>>> > >>
>>>>> > >> How big are the XML or JSON files you're looking to deal with?
>>>>> > >>
>>>>> > >> It may not be practical to deserialize the entire document at once. In that case an obvious work-around would be to have some kind of pre-processing step that separates XML nodes/JSON objects with newlines so that you can analyze the data with Spark in a "line-oriented format". Your preprocessor wouldn't have to parse/deserialize the massive document; it would just have to track open/closed tags/braces to know when to insert a newline.
>>>>> > >>
>>>>> > >> Then you'd just open the line-delimited result and deserialize the individual objects/nodes with map().
>>>>> > >>
>>>>> > >> Nick
>>>>> > >>
>>>>> > >>
>>>>> > >> On Mon, Mar 17, 2014 at 11:18 AM, Diana Carroll <[hidden email]> wrote:
>>>>> > >> Has anyone got a working example of a Spark application that analyzes data in a non-line-oriented format, such as XML or JSON?  I'd like to do this without re-inventing the wheel...anyone care to share?  Thanks!
>>>>> > >>
>>>>> > >> Diana
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >>
>>>>> > >> If you reply to this email, your message will be added to the discussion below:
>>>>> > >> http://apache-spark-user-list.1001560.n3.nabble.com/example-of-non-line-oriented-input-data-tp2750p2752.html
>>>>> > >> To start a new topic under Apache Spark User List, email [hidden email]
>>>>> > >> To unsubscribe from Apache Spark User List, click here.
>>>>> > >> NAML
>>>>> > >>
>>>>> > >>
>>>>> > >> View this message in context: Re: example of non-line oriented input data?
>>>>> > >> Sent from the Apache Spark User List mailing list archive at Nabble.com.
>>>>> > >>
>>>>> > >
>>>>> > >
>>>>> >
>>>>> >
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
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