Difficulty with encoding while reading data in Spark - apache-spark

In connection with my earlier question, when I give the command,
filePath = sc.textFile("/user/cloudera/input/Hin*/datafile.txt")
filePath.collect()
some part of the data has '\xa0' prefixed to every word, and other part of the data doesn't have that special character. I am attaching 2 pictures, one with '\xa0', and another without '\xa0'. The content shown in 2 pictures belong to same file. Only some part of the data from same file is read that way by Spark. I have checked the original data file present in HDFS, and it was problem free.
I feel that it has something to do with encoding. I tried all methods like using replaceoption in flatMap like flatMap(lambda line: line.replace(u'\xa0', ' ').split(" ")), flatMap(lambda line: line.replace(u'\xa0', u' ').split(" ")), but none worked for me. This question might sound dump, but I am newbie in using Apache Spark, and I require some assistance to overcome this problem.
Can anyone please help me? Thanks in advance.

Check the encoding of your file. When you use sc.textFile, spark expects an UTF-8 encoded file.
One of the solution is to acquire your file with sc.binaryFiles and then apply the expected encoding.
sc.binaryFile create a key/value rdd where key is the path to file and value is the content as a byte.
If you need to keep only the text and apply an decoding function, :
filePath = sc.binaryFile("/user/cloudera/input/Hin*/datafile.txt")
filePath.map(lambda x :x[1].decode('utf-8')) #or another encoding depending on your file

Related

SPARK encoding issue while reading a csv with multiline=true option

I am stuck in an issue while trying to read a csv file with multiline=true option in spark that has characters like Ř and Á. The csv is read in utf-8 format ; But when we try to read the data by using multiline=true we get characters that are not equivalent to the ones that we had read. We get something like ŘÃ�. So essentially a word read as ZŘÁKO gets transformed to ZŘÃ�KO.I went through several other questions asked on stack overflow around the same issue but none of solution actually works !
I tried the following encodings while read/write operations : ‘US-ASCII’
‘ISO-8859-1’,‘UTF-8’,‘UTF-16BE’,‘UTF-16LE’,‘UTF-16’,SJIS and couple more but none of them could give me the expected result. But multiline=false generates the correct output somehow.
I cannot read/write the file as text as the current framework policy of project is around an ingestion framework where we read the file only once and then everything is expected to be done in-memory and I must use multiline as true.
I would really appreciate any thoughts on this matter. Thank You !
sample data:
id|name
1|ZŘÁKO
df=spark.read.format('csv').option('header',true).
option('delimter','|').option('multiline',true).option('encoding','utf-8').load()
df.show()
ouptut :
1|Z�KO
#trying to force utf-8 encoding as below :
df.withColumn("name", sql.functions.encode("name", 'utf-8'))
gives me this :
1|[22 5A c3..]
I tried the above steps with all the supported encodings in spark

Special characters not encoded properly when creating Spark dataframe from parquet

My input parquet file has a column defined as optional binary title (UTF8);, which may include special characters such as the German umlat (i.e. Schrödinger).
When using Spark to load the contents of the parquet to a DataFrame, the contents of the row are loading the value Schrödinger as Schrödinger. I believe the best explanation of why this could be happening is answered here, though I was under the impression that Spark will read the parquet file as UTF-8 by default anyway.
I have attempted to force UTF-8 encoding by using the option argument as described here, but still no luck. Any suggestions?
Can you try with encoding CP1252. It worked for us for most of the special characters which are not supported in UTF8.

Converting 2TB of gziped multiline JSONs to NDJSONs

For my research I have a dataset of about 20,000 gziped multiline json files (~2TB, all have the same schema). I need to process and clean this data (I should say I'm very new to data analytics tools).
After spending a few days reading about Spark and Apache Beam I'm convinced that the first step would be to first convert this dataset to NDJSONs. In most books and tutorials they always assume you are working with some new line delimited file.
What is the best way to go about converting this data?
I've tried to just launch a large instance on gcloud and just use gunzip and jq to do this. Not surprisingly, it seems that this will take a long time.
Thanks in advance for any help!
Apache Beam supports unzipping file if you use TextIO.
But the delimiter remains to be New Line.
For multiline json you can read complete file using in parallel and then convert the json string to pojo and eventually reshuffle the data to utilize parallelism.
So the steps would be
Get the file list > Read individual files > Parse file content to json objects > Reshuffle > ...
You can get the file list by FileSystems.match("gcs://my_bucker").metadata().
Read individual files by Compression Compression.detect((fileResouceId).getFilename()).readDecompressed(FileSystems.open(fileResouceId))
Converting to NDJSON is not necessary if you use sc.wholeTextFiles. Point this method at a directory, and you'll get back an RDD[(String, String)] where ._1 is the filename and ._2 is the content of the file.

.csv is empty after reading it with pd.read_csv()

After running
df = pd.read_csv('my_file.csv'),
my original .csv file goes blank. Is there a way to read the .csv data without emptying the original file?
pd.read_csv() does not modify the file!
Here, the file before using pd.read_csv():
Using it:
And now if we check it again, the file hasn't changed (as expected):
So the problem isn't with pd.read_csv(). I would assume that you have other code that's messing things up. Take a look and tell us, so we can help you better.

How to read sequence files exported from HBase

I used the following code to export an HBase table and save the output to HDFS:
hbase org.apache.hadoop.hbase.mapreduce.Export \
MyHbaseTable1 hdfs://nameservice1/user/ken/data/exportTable1
Output files are binary files. If I use pyspark to read the file folder:
test1 = sc.textFile('hdfs://nameservice1/user/ken/data/exportTable1')
test1.show(5)
It shows:
u'SEQ\x061org.apache.hadoop.hbase.io.ImmutableBytesWritable%org.apache.hadoop.hbase.client.Result\x00\x00\x00\x00\x00\x00\ufffd-\x10A\ufffd~lUE\u025bt\ufffd\ufffd\ufffd&\x00\x00\x04\ufffd\x00\x00\x00'
u'\x00\x00\x00\x067-2010\ufffd\t'
u'|'
u'\x067-2010\x12\x01r\x1a\x08clo-0101 \ufffd\ufffd\ufffd*(\x042\\6.67|10|10|10|7.33|6.67|6.67|6.67|6.67|6.67|6.67|5.83|3.17|0|0|0.67|0.67|0.67|0.67|0|0|0|0|0'
u'u'
I can tell that
'7-2010' in the 2nd line is the Rowkey,
'r' in the 4th line is the column family,
'clo-0101' in the 4th line is the column name,
'6.67|10|10|10|7.33|6.67|6.67|6.67|6.67|6.67|6.67|5.83|3.17|0|0|0.67|0.67|0.67|0.67|0|0|0|0|0' is the value.
I don't know where 3rd and 5th line came from. It seems like Hbase-export followed its own rule to generate the file, if I use my own way to decode it, data might got corrupted.
Question:
How can I convert this file back to a readable format? For example:
7-2010, r, clo-0101, 6.67|10|10|10|7.33|6.67|6.67|6.67|6.67|6.67|6.67|5.83|3.17|0|0|0.67|0.67|0.67|0.67|0|0|0|0|0
I have tried:
test1 = sc.sequenceFile('/user/youyang/data/hbaseSnapshot1/', keyClass=None, valueClass=None, keyConverter=None, valueConverter=None, minSplits=None, batchSize=0)
test1.show(5)
and
test1 = sc.sequenceFile('hdfs://nameservice1/user/ken/data/exportTable1'
, keyClass='org.apache.hadoop.hbase.mapreduce.TableInputFormat'
, valueClass='org.apache.hadoop.hbase.io.ImmutableBytesWritable'
, keyConverter='org.apache.spark.examples.pythonconverters.ImmutableBytesWritableToStringConverter'
, valueConverter='org.apache.spark.examples.pythonconverters.HBaseResultToStringCon verter'
, minSplits=None
, batchSize=100)
No luck, the code did not work, ERROR:
Caused by: java.io.IOException: Could not find a deserializer for the Value class: 'org.apache.hadoop.hbase.client.Result'. Please ensure that the configuration 'io.serializations' is properly configured, if you're using custom serialization.
Any suggestions? Thank you!
I had this problem recently myself. I solved it by going away from sc.sequenceFile, and instead using sc.newAPIHadoopFile (or just hadoopFile if you're on the old API). The Spark SequenceFile-reader appears to only handle keys/values that are Writable types (it's stated in the docs).
If you use newAPIHadoopFile it uses the Hadoop deserialization logic, and you can specify which Serialization types you need in the config-dictionary you give it:
hadoop_conf = {"io.serializations": "org.apache.hadoop.io.serializer.WritableSerialization,org.apache.hadoop.hbase.mapreduce.ResultSerialization"}
sc.newAPIHadoopFile(
<input_path>,
'org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat',
keyClass='org.apache.hadoop.hbase.io.ImmutableBytesWritable',
valueClass='org.apache.hadoop.hbase.client.Result',
keyConverter='org.apache.spark.examples.pythonconverters.ImmutableBytesWritableToStringConverter',
valueConverter='org.apache.spark.examples.pythonconverters.HBaseResultToStringConverter',
conf=hadoop_conf)
Note that the value in hadoop_conf for "io.serializations" is a comma separated list which includes "org.apache.hadoop.hbase.mapreduce.ResultSerialization". That is the key configuration you need to be able to deserialize the Result. The WritableSerialization is also needed in order to be able to deserialize ImmutableBytesWritable.
You can also use sc.newAPIHadoopRDD, but then you also need to set a value for "mapreduce.input.fileinputformat.inputdir" in the config dictionary.

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