Sparklyr: List contents of directory in R using invoke methods

user_508440 0
Viewed 850

Unable to find a sparklyr built in for listing the contents of a directory via Spark, I am attempting to use invoke:

sc <- spark_connect(master = "yarn", config=config)
path <- 'gs:// ***path to bucket on google cloud*** '
spath <- sparklyr::invoke_new(sc, 'org.apache.hadoop.fs.Path', path) 
fs <- sparklyr::invoke(spath, 'getFileSystem')
list <- sparklyr:: invoke(fs, 'listLocatedStatus') 

Error: java.lang.Exception: No matched method found for class org.apache.hadoop.fs.Path.getFileSystem
    at sparklyr.Invoke.invoke(invoke.scala:134)
    at sparklyr.StreamHandler.handleMethodCall(stream.scala:123)
    at sparklyr.StreamHandler.read(stream.scala:66) ...

Note: Are there guidelines for reproducible examples with distributed code? I don't know how to make an example others could follow, given I am running against a particular Spark environment.

sparklyr apache-spark r
1 Answers

getFileSystem method takes org.apache.hadoop.conf.Configuration object as the first argument:

public FileSystem getFileSystem(Configuration conf)
                     throws IOException

Return the FileSystem that owns this Path.

Parameters:

conf - the configuration to use when resolving the FileSystem

So the code to retrieve FileSystem instance should looks more or less like this:

# Retrieve Spark's Hadoop configuration
hconf <- sc %>% spark_context() %>% invoke("hadoopConfiguration")
fs <- sparklyr::invoke(spath, 'getFileSystem', hconf)

Additionally listLocatedStatus takes either Path

public org.apache.hadoop.fs.RemoteIterator<LocatedFileStatus> listLocatedStatus(Path f)
                                                                     throws FileNotFoundException,
                                                                            IOException

or Path and PathFilter (note that this implementation is protected):

public org.apache.hadoop.fs.RemoteIterator<LocatedFileStatus> listLocatedStatus(Path f)
                                                                    throws FileNotFoundException,
                                                                            IOException

So if you want to structure your code as shown above you'll have to provide at least a path

sparklyr:: invoke(fs, "listLocatedStatus", spath)

In practice it might be easier to just get FileSystem directly:

fs <- invoke_static(sc, "org.apache.hadoop.fs.FileSystem", "get",  hconf)

and use globStatus

lls <- invoke(fs, "globStatus", spath)

where spath is a path with wildcard, like:

sparklyr::invoke_new(sc, 'org.apache.hadoop.fs.Path', "/some/path/*")

The result will be an R list, which can be easily iterated:

lls  %>%
    purrr::map(function(x) invoke(x, "getPath") %>% invoke("toString"))

Credits:

The answer to How can one list all csv files in an HDFS location within the Spark Scala shell? by @jaime

Notes:

  • In general, if you interact with non-trivial Java API, it makes much more sense to write your code in Java or Scala, and provide a minimal R interface.
  • For interactions with specific file object store it might be easier to use a dedicated package. For Google Cloud Storage you can take a look at googleCloudStorageR.
user_15600620
Related