Concat Avro files using avro-tools - hadoop

Im trying to merge avro files into one big file, the problem is concat command does not accept the wildcard
hadoop jar avro-tools.jar concat /input/part* /output/bigfile.avro
I get:
Exception in thread "main" java.io.FileNotFoundException: File does
not exist: /input/part*
I tried to use "" and '' but no chance.

I quickly checked Avro's source code (1.7.7) and it seems that concat does not support glob patterns (basically, they call FileSystem.open() on each argument except the last one).
It means that you have to explicitly provide all the filenames as argument. It is cumbersome, but following command should do what you want:
IN=$(hadoop fs -ls /input/part* | awk '{printf "%s ", $NF}')
hadoop jar avro-tools.jar concat ${IN} /output/bigfile.avro
It would be a nice addition to add support of glob pattern to this command.

Instead of hadoop jar avro-tools.jar one can run java -jar avro-tools.jar, since you don't need hadoop for this operation.

Related

How to delete a directory in hadoop which has the '[' character in its name

I accidentally uploaded a file to the "/hadoo[-workshop" path and I am trying to delete it.
I am using the hadoop fs -rmr <path> Hadoop 0.20.2 .
I have tried every permutation of putting the file path in single quotes ('), double quotes ("), and escaping the "[" character with a backslash (), but every time i get an error saying
rmr: Illegal file pattern: Expecting set closure character or end of range, or } for glob hadoo[-workshop at 15
I managed to delete it by using a wildcard (*) in the command.
hadoop fs -rmr /hadoo*
I guess "deleting everything that start with the string before faulty character" is good enough.
NOTE: If you use this and you have other directories with a similar name don't use -skipTrash to be able to recover the other directories

Extend parsing command to multiple files

There are a number of files I use which can all be parsed into three files (per input file) with:
third_file_1_1.txt
first_file_1_2.txt....
in an automated process?
You can use the FILENAME builtin variable to know what file you are currently processing. This allows you to do:
awk '/^[01]+$/ {print > "third_"FILENAME; next}/ [...]' $(<list.txt)

Load multiple files with PigLatin (Hadoop)

I have a hdfs file list of csv files with same format. I need to be able to LOAD them with pig together. Eg:
/path/to/files/2013/01-01/qwe123.csv
/path/to/files/2013/01-01/asd123.csv
/path/to/files/2013/01-01/zxc321.csv
/path/to/files/2013/01-02/ert435.csv
/path/to/files/2013/01-02/fgh987.csv
/path/to/files/2013/01-03/vbn764.csv
They can not be globed as their name is "random" hash and their directories might contain more csv files.
As suggested in other comments, you can do this by pre-processing the file. Suppose your HDFS file is called file_list.txt, then you can do the following:
pig -param flist=`hdfs dfs -cat file_list.txt | awk 'BEGIN{ORS="";}{if (NR == 1) print; else print ","$0;}'` script.pig
The awk code gets rid of the newline characters and uses commas to separate the file names.
In your script (called script.pig in my example), you should use parameter substitution to load the data:
data = LOAD '$flist';
You aren't restricted to globbing. Use this:
LOAD '/path/to/files/2013/01-{01/qwe123,01/asd123,01/zxc321,02/ert435,02/fgh987,03/vbn764}.csv';

How does Pig use Hadoop Globs in a 'load' statement?

As I've noted previously, Pig doesn't cope well with empty (0-byte) files. Unfortunately, there are lots of ways that these files can be created (even within Hadoop utilitities).
I thought that I could work around this problem by explicitly loading only files that match a given naming convention in the LOAD statement using Hadoop's glob syntax. Unfortunately, this doesn't seem to work, as even when I use a glob to filter down to known-good input files, I still run into the 0-byte failure mentioned earlier.
Here's an example: Assume I have the following files in S3:
mybucket/a/b/ (0 bytes)
mybucket/a/b/myfile.log (>0 bytes)
mybucket/a/b/yourfile.log (>0 bytes)
If I use a LOAD statement like this in my pig script:
myData = load 's3://mybucket/a/b/*.log as ( ... )
I would expect that Pig would not choke on the 0-byte file, but it still does. Is there a trick to getting Pig to actually only look at files that match the expected glob pattern?
This is a fairly ugly solution, but globs that don't rely on the * wildcard syntax appear to work. So, in our workflow (before calling our pig script), we list all of the files below the prefix we're interested, and then create a specific glob that consists of only the paths we're interested in.
For example, in the example above, we list "mybucket/a":
hadoop fs -lsr s3://mybucket/a
Which returns a list of files, plus other metadata. We can then create the glob from that data:
myData = load 's3://mybucket/a/b{/myfile.log,/yourfile.log}' as ( ... )
This requires a bit more front-end work, but allows us to specifically target files we're interested and avoid 0-byte files.
Update: Unfortunately, I've found that this solution fails when the glob pattern gets long; Pig ends up throwing an exception "Unable to create input slice".

Pig Latin: Load multiple files from a date range (part of the directory structure)

I have the following scenario-
Pig version used 0.70
Sample HDFS directory structure:
/user/training/test/20100810/<data files>
/user/training/test/20100811/<data files>
/user/training/test/20100812/<data files>
/user/training/test/20100813/<data files>
/user/training/test/20100814/<data files>
As you can see in the paths listed above, one of the directory names is a date stamp.
Problem: I want to load files from a date range say from 20100810 to 20100813.
I can pass the 'from' and 'to' of the date range as parameters to the Pig script but how do I make use of these parameters in the LOAD statement. I am able to do the following
temp = LOAD '/user/training/test/{20100810,20100811,20100812}' USING SomeLoader() AS (...);
The following works with hadoop:
hadoop fs -ls /user/training/test/{20100810..20100813}
But it fails when I try the same with LOAD inside the pig script. How do I make use of the parameters passed to the Pig script to load data from a date range?
Error log follows:
Backend error message during job submission
-------------------------------------------
org.apache.pig.backend.executionengine.ExecException: ERROR 2118: Unable to create input splits for: hdfs://<ServerName>.com/user/training/test/{20100810..20100813}
at org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.PigInputFormat.getSplits(PigInputFormat.java:269)
at org.apache.hadoop.mapred.JobClient.writeNewSplits(JobClient.java:858)
at org.apache.hadoop.mapred.JobClient.writeSplits(JobClient.java:875)
at org.apache.hadoop.mapred.JobClient.access$500(JobClient.java:170)
at org.apache.hadoop.mapred.JobClient$2.run(JobClient.java:793)
at org.apache.hadoop.mapred.JobClient$2.run(JobClient.java:752)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1062)
at org.apache.hadoop.mapred.JobClient.submitJobInternal(JobClient.java:752)
at org.apache.hadoop.mapred.JobClient.submitJob(JobClient.java:726)
at org.apache.hadoop.mapred.jobcontrol.Job.submit(Job.java:378)
at org.apache.hadoop.mapred.jobcontrol.JobControl.startReadyJobs(JobControl.java:247)
at org.apache.hadoop.mapred.jobcontrol.JobControl.run(JobControl.java:279)
at java.lang.Thread.run(Thread.java:619)
Caused by: org.apache.hadoop.mapreduce.lib.input.InvalidInputException: Input Pattern hdfs://<ServerName>.com/user/training/test/{20100810..20100813} matches 0 files
at org.apache.hadoop.mapreduce.lib.input.FileInputFormat.listStatus(FileInputFormat.java:231)
at org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.PigTextInputFormat.listStatus(PigTextInputFormat.java:36)
at org.apache.hadoop.mapreduce.lib.input.FileInputFormat.getSplits(FileInputFormat.java:248)
at org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.PigInputFormat.getSplits(PigInputFormat.java:258)
... 14 more
Pig Stack Trace
---------------
ERROR 2997: Unable to recreate exception from backend error: org.apache.pig.backend.executionengine.ExecException: ERROR 2118: Unable to create input splits for: hdfs://<ServerName>.com/user/training/test/{20100810..20100813}
org.apache.pig.impl.logicalLayer.FrontendException: ERROR 1066: Unable to open iterator for alias test
at org.apache.pig.PigServer.openIterator(PigServer.java:521)
at org.apache.pig.tools.grunt.GruntParser.processDump(GruntParser.java:544)
at org.apache.pig.tools.pigscript.parser.PigScriptParser.parse(PigScriptParser.java:241)
at org.apache.pig.tools.grunt.GruntParser.parseStopOnError(GruntParser.java:162)
at org.apache.pig.tools.grunt.GruntParser.parseStopOnError(GruntParser.java:138)
at org.apache.pig.tools.grunt.Grunt.run(Grunt.java:75)
at org.apache.pig.Main.main(Main.java:357)
Caused by: org.apache.pig.backend.executionengine.ExecException: ERROR 2997: Unable to recreate exception from backend error: org.apache.pig.backend.executionengine.ExecException: ERROR 2118: Unable to create input splits for: hdfs://<ServerName>.com/user/training/test/{20100810..20100813}
at org.apache.pig.backend.hadoop.executionengine.mapReduceLayer.Launcher.getStats(Launcher.java:169)
Do I need to make use of a higher language like Python to capture all date stamps in the range and pass them to LOAD as a comma separated list?
cheers
As zjffdu said, the path expansion is done by the shell. One common way to solve your problem is to simply use Pig parameters (which is a good way to make your script more resuable anyway):
shell:
pig -f script.pig -param input=/user/training/test/{20100810..20100812}
script.pig:
temp = LOAD '$input' USING SomeLoader() AS (...);
Pig is processing your file name pattern using the hadoop file glob utilities, not the shell's glob utilities. Hadoop's are documented here. As you can see, hadoop does not support the '..' operator for a range. It seems to me you have two options - either write out the {date1,date2,date2,...,dateN} list by hand, which if this is a rare use case is probably the way to go, or write a wrapper script which generates that list for you. Building such a list from a date range should be a trivial task for the scripting language of your choice. For my application, I've gone with the generated list route, and it's working fine (CHD3 distribution).
i ran across this answer when i was having trouble trying to create a file glob in a script and then pass it as a parameter into a pig script.
none of the current answers applied to my situation, but i did find a general answer that might be helpful here.
in my case, the shell expansion was happening and then passing that into the script - causing complete problems with the pig parser, understandably.
so by simply surrounding the glob in double-quotes protects it from being expanded by the shell, and passes it as is into the command.
WON'T WORK:
$ pig -f my-pig-file.pig -p INPUTFILEMASK='/logs/file{01,02,06}.log' -p OTHERPARAM=6
WILL WORK
$ pig -f my-pig-file.pig -p INPUTFILEMASK="/logs/file{01,02,06}.log" -p OTHERPARAM=6
i hope this saves someone some pain and agony.
So since this works:
temp = LOAD '/user/training/test/{20100810,20100811,20100812}' USING SomeLoader()
but this does not work:
temp = LOAD '/user/training/test/{20100810..20100812}' USING SomeLoader()
but if you want a date range that spans say 300 days and passing a full list to LOAD is not elegant to say the least. I came up with this and it works.
Say you want to load data from 2012-10-08 to today 2013-02-14, what you can do is
temp = LOAD '/user/training/test/{201210*,201211*,201212,2013*}' USING SomeLoader()
then do a filter after that
filtered = FILTER temp BY (the_date>='2012-10-08')
temp = LOAD '/user/training/test/2010081*/*' USING SomeLoader() AS (...);
load 20100810~20100819 data
temp = LOAD '/user/training/test/2010081{0,1,2}/*' USING SomeLoader() AS (...);
load 20100810~2010812 data
if the variable is in the middle of file path, concate subfolder name or use '*' for all files.
I found this problem is caused by linux shell. Linux shell will help you expand
{20100810..20100812}
to
20100810 20100811 20100812,
then you actually run command
bin/hadoop fs -ls 20100810 20100811 20100812
But in the hdfs api, it won't help you to expand the expression.
Thanks to dave campbell.
Some of the answer beyond are wrong since they got some votes.
Following is my test result:
Works
pig -f test.pig -param input="/test_{20120713,20120714}.txt"
Cannot have space before or after "," in the expression
pig -f test.pig -param input="/test_201207*.txt"
pig -f test.pig -param input="/test_2012071?.txt"
pig -f test.pig -param input="/test_20120713.txt,/test_20120714.txt"
pig -f test.pig -param input=/test_20120713.txt,/test_20120714.txt
Cannot have space before or after "," in the expression
Doesn't Work
pig -f test.pig -param input="/test_{20120713..20120714}.txt"
pig -f test.pig -param input=/test_{20120713,20120714}.txt
pig -f test.pig -param input=/test_{20120713..20120714}.txt
Do I need to make use of a higher language like Python to capture all date stamps in the range and pass them to LOAD as a comma separated list?
Probably you don't - this can be done using custom Load UDF, or try rethinking you directory structure (this will work good if your ranges are mostly static).
additionally: Pig accepts parameters, maybe this would help you (maybe you could do function that will load data from one day and union it to resulting set, but I don't know if it's possible)
edit: probably writing simple python or bash script that generates list of dates (folders) is the easiest solution, you than just have to pass it to Pig, and this should work fine
To Romain's answer, if you want to just parameterize the date, the shell will run like this:
pig -param input="$(echo {20100810..20100812} | tr ' ' ,)" -f script.pig
pig:
temp = LOAD '/user/training/test/{$input}' USING SomeLoader() AS (...);
Please note the quotes.
Pig support globe status of hdfs,
so I think pig can handle the pattern
/user/training/test/{20100810,20100811,20100812},
could you paste the error logs ?
Here's a script I'm using to generate a list of dates, and then put this list to pig script params. Very tricky, but works for me.
For example:
DT=20180101
DT_LIST=''
for ((i=0; i<=$DAYS; i++))
do
d=$(date +%Y%m%d -d "${DT} +$i days");
DT_LIST=${DT_LIST}$d','
done
size=${#DT_LIST}
DT_LIST=${DT_LIST:0:size-1}
pig -p input_data=xxx/yyy/'${DT_LIST}' script.pig

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