import ndjson into R skip first n lines
0
How to read a big ndjson (20GB) file by chunk into R?
I have a big data file that I want to read 1M rows at a time.
currently, I'm using below code to load data into R.
jsonlite::stream_in(
file(fileName)
)
But I don't need to load all data together. how can I split this file to chunk to load faster?
r ndjson
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
add a comment |
0
How to read a big ndjson (20GB) file by chunk into R?
I have a big data file that I want to read 1M rows at a time.
currently, I'm using below code to load data into R.
jsonlite::stream_in(
file(fileName)
)
But I don't need to load all data together. how can I split this file to chunk to load faster?
r ndjson
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
I'd highly suggest using Apache Drill along with the sergeant package rud.is/books/drill-sergeant-rstats/…. In fact, I'd highly suggest converting the ndjson to parquet with Drill and use the parquet version in Drill via the sergeant package.
– hrbrmstr
Nov 12 '18 at 20:51
add a comment |
0
0
0
How to read a big ndjson (20GB) file by chunk into R?
I have a big data file that I want to read 1M rows at a time.
currently, I'm using below code to load data into R.
jsonlite::stream_in(
file(fileName)
)
But I don't need to load all data together. how can I split this file to chunk to load faster?
r ndjson
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
How to read a big ndjson (20GB) file by chunk into R?
I have a big data file that I want to read 1M rows at a time.
currently, I'm using below code to load data into R.
jsonlite::stream_in(
file(fileName)
)
But I don't need to load all data together. how can I split this file to chunk to load faster?
r ndjson
r ndjson
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
edited Nov 12 '18 at 21:46
hrbrmstr
60.4k687148
60.4k687148
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
asked Nov 12 '18 at 20:43
Mahdi JadalihaMahdi Jadaliha
1,1561018
1,1561018
I'd highly suggest using Apache Drill along with the sergeant package rud.is/books/drill-sergeant-rstats/…. In fact, I'd highly suggest converting the ndjson to parquet with Drill and use the parquet version in Drill via the sergeant package.
– hrbrmstr
Nov 12 '18 at 20:51
add a comment |
I'd highly suggest using Apache Drill along with the sergeant package rud.is/books/drill-sergeant-rstats/…. In fact, I'd highly suggest converting the ndjson to parquet with Drill and use the parquet version in Drill via the sergeant package.
– hrbrmstr
Nov 12 '18 at 20:51
I'd highly suggest using Apache Drill along with the sergeant package rud.is/books/drill-sergeant-rstats/…. In fact, I'd highly suggest converting the ndjson to parquet with Drill and use the parquet version in Drill via the sergeant package.
– hrbrmstr
Nov 12 '18 at 20:51
I'd highly suggest using Apache Drill along with the sergeant package rud.is/books/drill-sergeant-rstats/…. In fact, I'd highly suggest converting the ndjson to parquet with Drill and use the parquet version in Drill via the sergeant package.
– hrbrmstr
Nov 12 '18 at 20:51
add a comment |
1 Answer
1
active
oldest
votes
1
If you don't want to level-up and use Drill, this will work on any system zcat (or gzcat) and sed live:
stream_in_range <- function(infile, start, stop, cat_kind = c("gzcat", "zcat")) {
infile <- path.expand(infile)
stopifnot(file.exists(infile))
gzip <- (tools::file_ext(infile) == "gz")
if (gzip) cat_kind <- match.arg(cat_kind, c("gzcat", "zcat"))
start <- as.numeric(start[1])
stop <- as.numeric(stop[1])
sed_arg <- sprintf("%s,%sp;", start, stop, (stop+1))
sed_command <- sprintf("sed -n '%s'", sed_arg)
if (gzip) {
command <- sprintf("%s %s | %s ", cat_kind, infile, sed_command)
} else {
command <- sprintf("%s %s", sed_command, infile)
}
ndjson::flatten(system(command, intern=TRUE), "tbl")
}
stream_in_range("a-big-compressed-ndjson-file.json.gz", 100, 200)
stream_in_range("a-big-uncompressed-nsjdon-file.json", 1, 10)
Choose and/or add a different cat_kind for whatever works for you.
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
1
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to usesedfunction insystem(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters tondjson::stream_infunction?
– Mahdi Jadaliha
Nov 13 '18 at 18:20
sure. can you post that as an issue? i thought Rtools.exe install came w/sedbut I don't run Windows so I'm very likely wrong abt that.
– hrbrmstr
Nov 13 '18 at 18:53
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
1
If you don't want to level-up and use Drill, this will work on any system zcat (or gzcat) and sed live:
stream_in_range <- function(infile, start, stop, cat_kind = c("gzcat", "zcat")) {
infile <- path.expand(infile)
stopifnot(file.exists(infile))
gzip <- (tools::file_ext(infile) == "gz")
if (gzip) cat_kind <- match.arg(cat_kind, c("gzcat", "zcat"))
start <- as.numeric(start[1])
stop <- as.numeric(stop[1])
sed_arg <- sprintf("%s,%sp;", start, stop, (stop+1))
sed_command <- sprintf("sed -n '%s'", sed_arg)
if (gzip) {
command <- sprintf("%s %s | %s ", cat_kind, infile, sed_command)
} else {
command <- sprintf("%s %s", sed_command, infile)
}
ndjson::flatten(system(command, intern=TRUE), "tbl")
}
stream_in_range("a-big-compressed-ndjson-file.json.gz", 100, 200)
stream_in_range("a-big-uncompressed-nsjdon-file.json", 1, 10)
Choose and/or add a different cat_kind for whatever works for you.
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
1
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to usesedfunction insystem(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters tondjson::stream_infunction?
– Mahdi Jadaliha
Nov 13 '18 at 18:20
sure. can you post that as an issue? i thought Rtools.exe install came w/sedbut I don't run Windows so I'm very likely wrong abt that.
– hrbrmstr
Nov 13 '18 at 18:53
add a comment |
1
If you don't want to level-up and use Drill, this will work on any system zcat (or gzcat) and sed live:
stream_in_range <- function(infile, start, stop, cat_kind = c("gzcat", "zcat")) {
infile <- path.expand(infile)
stopifnot(file.exists(infile))
gzip <- (tools::file_ext(infile) == "gz")
if (gzip) cat_kind <- match.arg(cat_kind, c("gzcat", "zcat"))
start <- as.numeric(start[1])
stop <- as.numeric(stop[1])
sed_arg <- sprintf("%s,%sp;", start, stop, (stop+1))
sed_command <- sprintf("sed -n '%s'", sed_arg)
if (gzip) {
command <- sprintf("%s %s | %s ", cat_kind, infile, sed_command)
} else {
command <- sprintf("%s %s", sed_command, infile)
}
ndjson::flatten(system(command, intern=TRUE), "tbl")
}
stream_in_range("a-big-compressed-ndjson-file.json.gz", 100, 200)
stream_in_range("a-big-uncompressed-nsjdon-file.json", 1, 10)
Choose and/or add a different cat_kind for whatever works for you.
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
1
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to usesedfunction insystem(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters tondjson::stream_infunction?
– Mahdi Jadaliha
Nov 13 '18 at 18:20
sure. can you post that as an issue? i thought Rtools.exe install came w/sedbut I don't run Windows so I'm very likely wrong abt that.
– hrbrmstr
Nov 13 '18 at 18:53
add a comment |
1
1
1
If you don't want to level-up and use Drill, this will work on any system zcat (or gzcat) and sed live:
stream_in_range <- function(infile, start, stop, cat_kind = c("gzcat", "zcat")) {
infile <- path.expand(infile)
stopifnot(file.exists(infile))
gzip <- (tools::file_ext(infile) == "gz")
if (gzip) cat_kind <- match.arg(cat_kind, c("gzcat", "zcat"))
start <- as.numeric(start[1])
stop <- as.numeric(stop[1])
sed_arg <- sprintf("%s,%sp;", start, stop, (stop+1))
sed_command <- sprintf("sed -n '%s'", sed_arg)
if (gzip) {
command <- sprintf("%s %s | %s ", cat_kind, infile, sed_command)
} else {
command <- sprintf("%s %s", sed_command, infile)
}
ndjson::flatten(system(command, intern=TRUE), "tbl")
}
stream_in_range("a-big-compressed-ndjson-file.json.gz", 100, 200)
stream_in_range("a-big-uncompressed-nsjdon-file.json", 1, 10)
Choose and/or add a different cat_kind for whatever works for you.
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
If you don't want to level-up and use Drill, this will work on any system zcat (or gzcat) and sed live:
stream_in_range <- function(infile, start, stop, cat_kind = c("gzcat", "zcat")) {
infile <- path.expand(infile)
stopifnot(file.exists(infile))
gzip <- (tools::file_ext(infile) == "gz")
if (gzip) cat_kind <- match.arg(cat_kind, c("gzcat", "zcat"))
start <- as.numeric(start[1])
stop <- as.numeric(stop[1])
sed_arg <- sprintf("%s,%sp;", start, stop, (stop+1))
sed_command <- sprintf("sed -n '%s'", sed_arg)
if (gzip) {
command <- sprintf("%s %s | %s ", cat_kind, infile, sed_command)
} else {
command <- sprintf("%s %s", sed_command, infile)
}
ndjson::flatten(system(command, intern=TRUE), "tbl")
}
stream_in_range("a-big-compressed-ndjson-file.json.gz", 100, 200)
stream_in_range("a-big-uncompressed-nsjdon-file.json", 1, 10)
Choose and/or add a different cat_kind for whatever works for you.
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
answered Nov 12 '18 at 21:46
hrbrmstrhrbrmstr
60.4k687148
60.4k687148
1
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to usesedfunction insystem(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters tondjson::stream_infunction?
– Mahdi Jadaliha
Nov 13 '18 at 18:20
sure. can you post that as an issue? i thought Rtools.exe install came w/sedbut I don't run Windows so I'm very likely wrong abt that.
– hrbrmstr
Nov 13 '18 at 18:53
add a comment |
1
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to usesedfunction insystem(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters tondjson::stream_infunction?
– Mahdi Jadaliha
Nov 13 '18 at 18:20
sure. can you post that as an issue? i thought Rtools.exe install came w/sedbut I don't run Windows so I'm very likely wrong abt that.
– hrbrmstr
Nov 13 '18 at 18:53
1
1
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to use
sed function in system(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters to ndjson::stream_in function?– Mahdi Jadaliha
Nov 13 '18 at 18:20
Thanks, @hrbrmstr. your answer helped a lot. I add this here for Windows users that you may install Cygwin as well to use
sed function in system(command, intern=TRUE). I have one more question: I see that you are the author of ndjson. Is this possible to add skip parameters to ndjson::stream_in function?– Mahdi Jadaliha
Nov 13 '18 at 18:20
sure. can you post that as an issue? i thought Rtools.exe install came w/
sed but I don't run Windows so I'm very likely wrong abt that.– hrbrmstr
Nov 13 '18 at 18:53
sure. can you post that as an issue? i thought Rtools.exe install came w/
sed but I don't run Windows so I'm very likely wrong abt that.– hrbrmstr
Nov 13 '18 at 18:53
add a comment |
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I'd highly suggest using Apache Drill along with the sergeant package rud.is/books/drill-sergeant-rstats/…. In fact, I'd highly suggest converting the ndjson to parquet with Drill and use the parquet version in Drill via the sergeant package.
– hrbrmstr
Nov 12 '18 at 20:51