I have a code sample in Ruby that pipes data to a pager in order to print it in portions to STDOUT:
input = File.read "some_long_file"
pager = "less"
IO.popen(pager, mode="w") do |io|
io.write input
io.close
end
I have no problem in adopting this to Crystal like this:
input = File.read "some_long_file"
pager = "less"
Process.run(pager, output: STDOUT) do |process|
process.input.puts input
process.input.close
end
But if I change pager = "more" than the Ruby example still works fine, but the Crystal snippet dumps all the data, instead of serving it in portions. How can I fix it?
Crystal 0.25.0 [7fb783f7a] (2018-06-11)
LLVM: 4.0.0
Default target: x86_64-unknown-linux-gnu
The more command tries to write it's user interface to stderr, so you need to forward that as well:
Process.run(pager, output: STDOUT, error: STDERR) do |process|
process.input.puts input
process.input.close
end
Since you are reading a long file, you might consider not reading it into memory, but instead to pass the file descriptor to the pipe:
input = File.open("log/development.log")
pager = "more"
Process.run(pager, input: input, output: STDOUT, error: STDERR)
Related
I am getting a java.nio.file.ProviderMismatchException when I run the following script:
process a {
output:
file _biosample_id optional true into biosample_id
script:
"""
touch _biosample_id
"""
}
process b {
input:
file _biosample_id from biosample_id.ifEmpty{file("_biosample_id")}
script:
def biosample_id_option = _biosample_id.isEmpty() ? '' : "--biosample_id \$(cat _biosample_id)"
"""
echo \$(cat ${_biosample_id})
"""
}
i'm using a slightly modified version of Optional Input pattern.
Any ideas on why I'm getting the java.nio.file.ProviderMismatchException?
In your script block, _biosample_id is actually an instance of the nextflow.processor.TaskPath class. So to check if the file (or directory) is empty you can just call it's .empty() method. For example:
script:
def biosample_id_option = _biosample_id.empty() ? '' : "--biosample_id \$(< _biosample_id)"
I like your solution - I think it's neat. And I think it should be robust (but I haven't tested it). The optional input pattern that is recommended will fail when attempting to stage missing input files to a remote filesystem/object store. There is a solution however, which is to keep an empty file in your $baseDir and point to it in your scripts. For example:
params.inputs = 'prots/*{1,2,3}.fa'
params.filter = "${baseDir}/assets/null/NO_FILE"
prots_ch = Channel.fromPath(params.inputs)
opt_file = file(params.filter)
process foo {
input:
file seq from prots_ch
file opt from opt_file
script:
def filter = opt.name != 'NO_FILE' ? "--filter $opt" : ''
"""
your_commad --input $seq $filter
"""
}
I'm trying to run the sample program from this RedisLabs page.
I chose Option A - which was to set up the free Redis cloud server.
(Seems like if you install manually, then you have to add the JSON as a plugin.)
I'm able to connect and use other "set" commands, but getting error on JSON:
File "C:\Users\nwalt\.virtualenvs\TDAmeritradeGetQuotes\lib\site-packages\redis\client.py", line 901, in execute_command
return self.parse_response(conn, command_name, **options)
File "C:\Users\nwalt\.virtualenvs\TDAmeritradeGetQuotes\lib\site-packages\redis\client.py", line 915, in parse_response
response = connection.read_response()
File "C:\Users\nwalt\.virtualenvs\TDAmeritradeGetQuotes\lib\site-packages\redis\connection.py", line 756, in read_response
raise response
redis.exceptions.ResponseError: unknown command 'JSON.SET'
My Python test program (except put in the sample endpoint before posting):
import redis
import json
import pprint
host_info = "redis.us-east-1-1.ec2.cloud.redislabs.com"
redisObj = redis.Redis(host=host_info, port=18274, password='xxx')
print ("Normal call to Redis")
redisObj.set('foo', 'bar')
value = redisObj.get('foo')
print(value)
capitals = {
"Lebanon": "Beirut",
"Norway": "Oslo",
"France": "Paris"
}
print ("capitals - before call to Redis")
pprint.pprint(capitals)
print("JSON call to Redis")
redisObj.execute_command('JSON.SET', 'doc', '.', json.dumps(capitals))
print("Data Saved, now fetch data back from redis")
reply = json.loads(redisObj.execute_command('JSON.GET', 'doc'))
print("reply from Redis get")
pprint.pprint(reply)
This is the screen shot from their website where I created the database. I didn't see any option to enable JSON or add any modules.
Not sure this was available when I created the REDIS database, but it is now. When you create it on redislabs.com, you can turn on the modules, and pick one from the list.
Then use this library: "rejson" from https://pypi.org/project/rejson/ to get the method "jsonset" method, using such code such as this:
rj = Client(host=config_dict['REDIS_CONFIG_HOST'], port=config_dict['REDIS_CONFIG_PORT'], password=config_dict['REDIS_CONFIG_PASSWORD'], decode_responses=True)
out_doc = {}
out_doc['firstname'] = "John"
out_doc['lastname'] = "Doe"
rj.jsonset('config', Path.rootPath(), out_doc)
get_doc = rj.jsonget('config', Path.rootPath())
pprint.pprint(get_doc)
I'm not used the cloud redis, in my local the Python don't load the JSON.SET
I just so make done, in this sample https://onelinerhub.com/python-redis/save-json-to-redis
I have the following code.
import lib
var stat = false
when isMainModule:
while stat != true:
echo("Option: ")
var opt = readChar(stdin)
case opt
of 'q':
stat = true
of 'n':
echo("Salu: ")
var ss = readLine(stdin)
echo("Nam: ")
var nn = readLine(stdin)
let k = prompt("Rust")
else: discard
What I am trying to achieve is, prompting and receiving user input one after another for two variables. Upon choosing n I am expecting Salu first and once user input is supplied then Nam.
However, what I receive when I execute the following nim code by issuing the following command is, nim c -r src/mycode.nim
~~> nim c -r src/cmdparsing.nim
...
...
...
CC: stdlib_system.nim
CC: cmdparsing.nim
Hint: [Link]
Hint: operation successful (48441 lines compiled; 2.338 sec total; 66.824MiB peakmem; Debug Build) [SuccessX]
Hint: /home/XXXXX/Development/nim_devel/mycode/src/mycode [Exec]
Option:
n
Salu:
Nam:
Salu is being echoed, but readLine doesn't wait for my input and immediately echoes Nam. But, stacked readLine commands from the prompt procedure appears one after the other for receiving user input.
I was wondering what is that I am missing to understand here. Could someone enlighten me?
Code for prompt lives in lib.nim which is as follows,
proc prompt*(name: string): bool =
echo("Salutation: ")
var nn = readLine(stdin)
echo(nn&"."&name)
echo("Diesel")
var dd = readLine(stdin)
echo(dd)
return true
You do a readChar to get the opt value, and then you input two chars: n and \n. The first is the opt value, the second gets buffered or retained in the stdin waiting for further reading. The next time you try to read a line, the \n that's still hanging is interpreted as a new line, and immediately assigned to ss. You don't see anything because the line is empty except for the newline char.
E.g.
var opt = readChar(stdin)
case opt
of 'n':
var ss = readLine(stdin)
echo ss
else:
discard
Compile and run, but in the input write something like "ntest". n fires the first branch of case, test (the remainder of stdin) is assigned to ss, and echoed.
You have two options to solve the problem:
Read a line instead of a char, and store only the first char with something like var opt = readLine(stdin)[0].
Use the rdstdin module:
import rdstdin
var ss = readLineFromStdin("Salu:")
I'm trying to read a gz file line by line in Perl6, however, I'm getting blocked:
How to read gz file line by line in Perl6 however, this method, reading everything into :out uses far too much RAM to be usable except on very small files.
I don't understand how to use Perl6's Compress::Zlib to get everything line by line, although I opened an issue on their github https://github.com/retupmoca/P6-Compress-Zlib/issues/17
I'm trying Perl5's Compress::Zlib to translate this code, which works perfectly in Perl5:
use Compress::Zlib;
my $file = "data.txt.gz";
my $gz = gzopen($file, "rb") or die "Error reading $file: $gzerrno";
while ($gz->gzreadline($_) > 0) {
# Process the line read in $_
}
die "Error reading $file: $gzerrno" if $gzerrno != Z_STREAM_END ;
$gz->gzclose() ;
to something like this using Inline::Perl5 in Perl6:
use Compress::Zlib:from<Perl5>;
my $file = 'chrMT.1.vcf.gz';
my $gz = Compress::Zlib::new(gzopen($file, 'r');
while ($gz.gzreadline($_) > 0) {
print $_;
}
$gz.gzclose();
but I can't see how to translate this :(
I'm confused by Lib::Archive example https://github.com/frithnanth/perl6-Archive-Libarchive/blob/master/examples/readfile.p6 I don't see how I can get something like item 3 here
There should be something like
for $file.IO.lines(gz) -> $line { or something like that in Perl6, if it exists, I can't find it.
How can I read a large file line by line without reading everything into RAM in Perl6?
Update Now tested, which revealed an error, now fixed.
Solution #2
use Compress::Zlib;
my $file = "data.txt.gz" ;
my $handle = try open $file or die "Error reading $file: $!" ;
my $zwrap = zwrap($handle, :gzip) ;
for $zwrap.lines {
.print
}
CATCH { default { die "Error reading $file: $_" } }
$handle.close ;
I've tested this with a small gzipped text file.
I don't know much about gzip etc. but figured this out based on:
Knowing P6;
Reading Compress::Zlib's README and choosing the zwrap routine;
Looking at the module's source code, in particular the signature of the zwrap routine our sub zwrap ($thing, :$zlib, :$deflate, :$gzip);
And trial and error, mainly to guess that I needed to pass the :gzip adverb.
Please comment on whether my code works for you. I'm guessing the main thing is whether it's fast enough for the large files you have.
A failed attempt at solution #5
With solution #2 working I would have expected to be able to write just:
use Compress::Zlib ;
.print for "data.txt.gz".&zwrap(:gzip).lines ;
But that fails with:
No such method 'eof' for invocant of type 'IO::Path'
This is presumably because this module was written before the reorganization of the IO classes.
That led me to #MattOates' IO::Handle like object with .lines ? issue. I note no response and I saw no related repo at https://github.com/MattOates?tab=repositories.
I am focusing on the Inline::Perl5 solution that you tried.
For the call to $gz.gzreadline($_): it seems like gzreadline tries to return the line read from the zip file by modifying its input argument $_ (treated as an output argument, but it is not a true Perl 5 reference variable[1]), but the modified value is not returned to the Perl 6 script.
Here is a possoble workaround:
Create a wrapper module in the curent directory, e.g. ./MyZlibWrapper.pm:
package MyZlibWrapper;
use strict;
use warnings;
use Compress::Zlib ();
use Exporter qw(import);
our #EXPORT = qw(gzopen);
our $VERSION = 0.01;
sub gzopen {
my ( $fn, $mode ) = #_;
my $gz = Compress::Zlib::gzopen( $fn, $mode );
my $self = {gz => $gz};
return bless $self, __PACKAGE__;
}
sub gzreadline {
my ( $self ) = #_;
my $line = "";
my $res = $self->{gz}->gzreadline($line);
return [$res, $line];
}
sub gzclose {
my ( $self ) = #_;
$self->{gz}->gzclose();
}
1;
Then use Inline::Perl5 on this wrapper module instead of Compress::Zlib. For example ./p.p6:
use v6;
use lib:from<Perl5> '.';
use MyZlibWrapper:from<Perl5>;
my $file = 'data.txt.gz';
my $mode = 'rb';
my $gz = gzopen($file, $mode);
loop {
my ($res, $line) = $gz.gzreadline();
last if $res == 0;
print $line;
}
$gz.gzclose();
[1]
In Perl 5 you can modify an input argument that is not a reference, and the change will be reflected in the caller. This is done by modifying entries in the special #_ array variable. For example: sub quote { $_[0] = "'$_[0]'" } $str = "Hello"; quote($str) will quote $str even if $str is not passed by reference.
I am attempting to set up a small test environment (homelab) using CentOS 6.6, Rancid 3.1, Looking Glass, and some Cisco Switches/Routers, with httpd acting as the handler. I have picked up a little perl by means of this endeavor, but python (more 2 than 3) is my background. Right now, everything on the rancid side of things works without issue: bin/clogin successfully logs into all of the equipment in the router.db file, and logging of the configs is working as expected. All switches/routers to be accessed are available and online, verified by ssh connection to devices as well as using bin/clogin.
Right now, I have placed the lg.cgi and lgform.cgi files into var/www/cgi-bin/ which allows the forms to be run as cgi scripts. I had to modify the files to split on ';' instead of ':' due to the change in the .db file in Rancid 3.1:#record = split('\:', $_); was replaced with: #record = split('\;', $_); etc. Once that change was made, I was able to load the lgform.cgi with the proper router.db parsing. At this point, it seemed like everything should be good to go. When I attempt to ping from one of those devices out to 8.8.8.8, the file correctly redirects to lg.cgi, and the page loads, but with
main is unavailable. Try again later.
as the error, where 'main' is the router hostname. Using this output, I was able to find the function responsible for this output. Here it is before I added anything:
sub DoRsh
{
my ($router, $mfg, $cmd, $arg) = #_;
my($ctime) = time();
my($val);
my($lckobj) = LockFile::Simple->make(-delay => $lock_int,
-max => $max_lock_wait, -hold => $max_lock_hold);
if ($pingcmd =~ /\d$/) {
`$pingcmd $router`;
} else {
`$pingcmd $router 56 1`;
}
if ($?) {
print "$router is unreachable. Try again later.\n";
return(-1);
}
if ($LG_SINGLE) {
if (! $lckobj->lock("$cache_dir/$router")) {
print "$router is busy. Try again later.\n";
return(-1);
}
}
$val = &DoCmd($router, $mfg, $cmd, $arg);
if ($LG_SINGLE) {
$lckobj->unlock("$cache_dir/$router");
}
return($val);
}
In order to dig in a little deeper, I peppered that function with several print statements. Here is the modified function, followed by the output from the loaded lg.cgi page:
sub DoRsh
{
my ($router, $mfg, $cmd, $arg) = #_;
my($ctime) = time();
my($val);
my($lckobj) = LockFile::Simple->make(-delay => $lock_int,
-max => $max_lock_wait, -hold => $max_lock_hold);
if ($pingcmd =~ /\d$/) {
`$pingcmd $router`;
} else {
`$pingcmd $router 56 1`;
}
print "About to test the ($?) branch.\n";
print "Also who is the remote_user?:' $remote_user'\n";
print "What about the ENV{REMOTE_USER} '$ENV{REMOTE_USER}'\n";
print "Here is the ENV{HOME}: '$ENV{HOME}'\n";
if ($?) {
print "$lckobj is the lock object.\n";
print "#_ something else to look at.\n";
print "$? whatever this is suppose to be....\n";
print "Some variables:\n";
print "$mfg is the mfg.\n";
print "$cmd was the command passed in with $arg as the argument.\n";
print "$pingcmd $router\n";
print "$cloginrc - Is the cloginrc pointing correctly?\n";
print "$LG_SINGLE the next value to be tested.\n";
print "$router is unreachable. Try again later.\n";
return(-1);
}
if ($LG_SINGLE) {
if (! $lckobj->lock("$cache_dir/$router")) {
print "$router is busy. Try again later.\n";
return(-1);
}
}
$val = &DoCmd($router, $mfg, $cmd, $arg);
if ($LG_SINGLE) {
$lckobj->unlock("$cache_dir/$router");
}
return($val);
}
OUTPUT:
About to test the (512) branch.
Also who is the remote_user?:' '
What about the ENV{REMOTE_USER} ''
Here is the ENV{HOME}: '.'
LockFile::Simple=HASH(0x1a13650) is the lock object.
main cisco ping 8.8.8.8 something else to look at.
512 whatever this is suppose to be....
Some variables:
cisco is the mfg.
ping was the command passed in with 8.8.8.8 as the argument.
/bin/ping -c 1 main
./.cloginrc - Is the cloginrc pointing correctly?
1 the next value to be tested.
main is unreachable. Try again later.
I can provide the code for when DoRsh is called, if necessary, but it looks mostly like this:&DoRsh($router, $mfg, $cmd, $arg);.
From what I can tell the '$?' special variable (or at least according to
this reference it is a special var) is returning the 512 value, which is causing that fork to test true. The problem is I don't know what that 512 means, nor where it is coming from. Using the ref site's description ("The status returned by the last pipe close, backtick (``) command, or system operator.") and the formation of the conditional tree above, I can see that it is some error of some kind, but I don't know how else to proceed with this inspection. I'm wondering if maybe it is in response to some permission issue, since the remote_user variable is null, when I didn't expect it to be. Any guidance anyone may be able to provide would be helpful. Furthermore, if there is any information that I may have skipped over, that I didn't think to include, or that may prove helpful, please ask, and I will provide to the best of my ability
May be you put in something like
my $pingret=$pingcmd ...;
print 'Ping result was:'.$pingret;
And check the returned strings?