DiaColloDB::Utils - diachronic collocation database, generic utilities
##======================================================================== ## PRELIMINARIES use DiaColloDB::Utils; ##======================================================================== ## Functions: Fcntl $flags = PACKAGE::fcflags($flags); $flags = PACKAGE::fcgetfl($fh); $bool = fcread($flags); $bool = fcwrite($flags); $bool = fctrunc($flags); $bool = fccreat($flags); $fh_or_undef = fcopen($file,$flags); ##======================================================================== ## JSON: load $data = PACKAGE::loadJsonString( $string,%opts); $data = PACKAGE::loadJsonFile($filename_or_handle,%opts); ##======================================================================== ## JSON: save $str = PACKAGE::saveJsonString($data); $bool = PACKAGE::saveJsonFile($data,$filename_or_handle,%opts); ##======================================================================== ## Functions: env \%setenv = PACKAGE::env_set(%setenv); \%restored = PACKAGE::env_pop(%setenv); ##======================================================================== ## Functions: run $fh_or_undef = PACKAGE::opencmd($cmd); $bool = crun(@IPC_Run_args); $bool = csort_to(\@sortargs, \&catcher); $bool = csortuc_to(\@sortargs, \&catcher); ##======================================================================== ## Functions: pack filters $len = PACKAGE::packsize($packfmt); \&filter_sub = PACKAGE::packFilterStore($pack_template); \&filter_sub = PACKAGE::packFilterFetch($pack_template); ##======================================================================== ## Math stuff $log2 = log2($x); $max2 = max2($x,$y); $min2 = min2($x,$y); ##======================================================================== ## Functions: lists \@l_uniq = luniq(\@l); \@l_sorted_uniq = sluniq(\@l_sorted); \@l_uniq = xluniq(\@l,\&keyfunc); ##======================================================================== ## Functions: regexes $re = regex($re_str); ##======================================================================== ## Functions: html $escaped = htmlesc($str); ##======================================================================== ## Functions: time $hms = PACKAGE::s2hms($seconds,$sfmt="%06.3f"); $timestr = PACKAGE::s2timestr($seconds,$sfmt="%f"); $rfc_timestamp = PACAKGE->timestamp(); ##======================================================================== ## Functions: file $mtime = PACKAGE->file_mtime($file_or_fh); $timestamp = PACKAGE->file_timestamp($file_or_fh); $nbytes = du_file(@filenames_or_fh); $nbytes = du_glob(@globs); $bool = PACKAGE->copyto ($src_filename_or_array, $dstdir, %opts); $bool = PACKAGE->copyto_a($src_filename_or_array, $dstdir, %opts); $bool = PACKAGE->moveto ($src_filename_or_array, $dstdir, %opts); $bool = PACKAGE->cp_a ($src_filename_or_array, $dstdir); ##======================================================================== ## Utils: SI $str = si_str($float); ##======================================================================== ## Functions: pdl: setops $pi = CLASS::_intersect_p($p1,$p2); $pu = CLASS::_union_p($p1,$p2); $pneg = CLASS::_complement_p($p,$N); $pdiff = CLASS::_setdiff_p($a,$b,$N); ##======================================================================== ## Functions: pdl $pdl_or_undef = CLASS->readPdlFile($basename, %opts); $bool = CLASS->writePdlFile($pdl_or_undef, $basename, %opts); $bool = CLASS->writePdlHeader($filename, $type, $ndims, @dims); $bool = CLASS->writeCcsHeader($filename, $itype, $vtype, $pdims, %opts); $pdl = mmzeroes($file?, $type?, @dims, \%opts?); $bool = mmunlink(@mmfiles); $type = CLASS->mintype($pdl, @types); $maxval = $type->maxval(); ($vals,$counts) = $pdl->valcounts(); ##======================================================================== ## Functions: temporaries $tmpdir = CLASS->tmpdir(); $fh = CLASS->tmpfh(); $filename = CLASS->tmpfile(); \@tmparray = CLASS->tmparray($template, %opts); \@tmparrayp = CLASS->tmparrayp($template, $packas, %opts); \%tmphash = CLASS->tmphash($class, $template, %opts); ##======================================================================== ## Functions: parallelization $ncores = CLASS->nCores(); $njobs = CLASS->nJobs(); $sortjobs = CLASS->sortJobs();
DiaColloDB::Utils inherits from Exporter and DiaColloDB::Logger.
Exportable tags:
fcntl => [qw(fcflags fcgetfl fcread fcwrite fctrunc fccreat fcperl fcopen)], json => [qw(loadJsonString loadJsonFile saveJsonString saveJsonFile)], sort => [qw(csort_to csortuc_to)], run => [qw(crun opencmd)], env => [qw(env_set env_push env_pop)], pack => [qw(packsize packsingle packFilterFetch packFilterStore)], math => [qw($LOG2 log2 min2 max2)], list => [qw(luniq sluniq xluniq)], regex => [qw(regex)], html => [qw(htmlesc)], time => [qw(s2hms s2timestr timestamp)], file => [qw(file_mtime file_timestamp du_file du_glob copyto copyto_a moveto cp_a fh_flush fh_reopen)], si => [qw(si_str)], pdl => [qw(_intersect_p _union_p _complement_p _setdiff_p), qw(readPdlFile writePdlFile writePdlHeader writeCcsHeader mmzeroes mmtemp), qw(maxval mintype), ], temp => [qw($TMPDIR tmpdir tmpfh tmpfile tmparray tmparrayp tmphash)], jobs => [qw(nCores nJobs sortJobs)],
All symbols in %EXPORT_TAGS are exportable
All symbols in %EXPORT_TAGS are exported by default.
$flags = PACKAGE::fcflags($flags);
returns Fcntl flags for symbolic string $flags
$flags = PACKAGE::fcgetfl($fh);
returns Fcntl flags for filehandle $fh
$bool = fcread($flags);
returns true if any read-bits are set for $flags
$bool = fcwrite($flags);
returns true if any write-bits are set for $flags
$bool = fctrunc($flags);
returns true if truncate-bits are set for $flags
$bool = fccreat($flags);
returns true iff creation flag is set for $flags.
$str = fcperl($flags);
returns perl mode-string corresponding to $flags.
$fh_or_undef = fcopen($file,$flags); $fh_or_undef = fcopen($file,$flags,$mode,$perms)
opens $file with Fcntl-style flags $flags.
$data = PACKAGE::loadJsonString( $string,%opts); $data = PACKAGE::loadJsonString(\$string,%opts)
decodes JSON string. %opts are passed to JSON::from_json().
$data = PACKAGE::loadJsonFile($filename_or_handle,%opts);
loads JSON data from a file or filehandle. %opts are passed to loadJsonString().
$str = PACKAGE::saveJsonString($data); $str = PACKAGE::saveJsonString($data,%opts);
Encode data as a JSON string. %opts are passed to JSON::to_json(), e.g. (pretty=>0, canonical=>0)'.
$bool = PACKAGE::saveJsonFile($data,$filename_or_handle,%opts);
Save JSON data to a file. %opts are passed to saveJsonString().
Stack of temporary environment variables.
\%setenv = PACKAGE::env_set(%setenv);
Set or clear environment variables.
\%oldvals = PACKAGE::env_push(%setenv);
Push old values for keys(%setenv) to @env_stack and calls env_set(%setenv).
\%restored = PACKAGE::env_pop(%setenv);
Pops the most recent variable bindings from @env_stack and restores them to the environment.
$fh_or_undef = PACKAGE::opencmd($cmd); $fh_or_undef = PACKAGE::opencmd($mode,@argv);
does log trace at level $TRACE_RUNCMD
$bool = crun(@IPC_Run_args);
wrapper for IPC::Run::run(@IPC_Run_args) with $ENV{LC_ALL}='C'
$bool = csort_to(\@sortargs, \&catcher);
runs system sort and feeds resulting lines to \&catcher
$bool = csortuc_to(\@sortargs, \&catcher);
runs system sort | uniq -c and feeds resulting lines to \&catcher
$len = PACKAGE::packsize($packfmt); $len = PACKAGE::packsize($packfmt,@args);
get pack-size for $packfmt with args @args
\&filter_sub = PACKAGE::packFilterStore($pack_template); \&filter_sub = PACKAGE::packFilterStore([$pack_template_store, $pack_template_fetch]); \&filter_sub = PACKAGE::packFilterStore([\&pack_code_store, \&pack_code_fetch]);
returns a DB_File-style STORE-filter sub for transparent packing of data to $pack_template
\&filter_sub = PACKAGE::packFilterFetch($pack_template); \&filter_sub = PACKAGE::packFilterFetch([$pack_template_store, $pack_template_fetch]); \&filter_sub = PACKAGE::packFilterFetch([\&pack_code_store, \&pack_code_fetch]);
returns a DB_File-style FETCH-filter sub for transparent unpacking of data from $pack_template.
constant: log(2) for binary logarithms.
log(2)
$log2 = log2($x);
binary logarithm function.
$max2 = max2($x,$y);
maximum
$min2 = min2($x,$y);
minimum
\@l_uniq = luniq(\@l);
returns sorted list of unique defined elements of @l; @l need not be sorted.
\@l_sorted_uniq = sluniq(\@l_sorted);
returns unique defined elements of pre-sorted list @l_sorted.
\@l_uniq = xluniq(\@l,\&keyfunc);
returns elements of @l with unique defined keys according to \&keyfunc (default=\&overload::StrVal); returned list is sorted by \&keyfunc.
\&keyfunc
\&overload::StrVal
$re = regex($re_str);
parses regex $re_str, which can optionally be "/"-quoted. parses modifiers /[gimsadlu]. /g modifier is parsed a la ddc (match whole word).
$escaped = htmlesc($str);
escape an HTML string.
$hms = PACKAGE::s2hms($seconds,$sfmt="%06.3f"); ($h,$m,$s) = PACKAGE::s2hms($seconds,$sfmt="%06.3f");
convert a time value in seconds to HH:MM:SS.SSSS format
$timestr = PACKAGE::s2timestr($seconds,$sfmt="%f");
convert a time value in seconds to H?M?S.SSSS format
$rfc_timestamp = PACAKGE->timestamp(); $rfc_timestamp = PACAKGE->timestamp($time);
Return a UTC ISO-8601 timestamp format "%Y-%m-%dT%H:%M%SZ" for the UNIX time $time.
$mtime = PACKAGE->file_mtime($file_or_fh);
get mtime (last modification time) for $file_or_fh.
$timestamp = PACKAGE->file_timestamp($file_or_fh);
get an ISO-8601 timestamp for mtime of $file_or_fh.
$nbytes = du_file(@filenames_or_fhs);
return number of bytes used by @filesnames_or_fhs
$nbytes = du_glob(@globs);
return number of bytes used by files matching and $glob in @globs
$bool = PACKAGE->moveto($src_filename_or_array, $dstdir, %opts);
Copies source file(s) to $dstdir, creating $dstdir if it doesn't already exist. Argument $src_filename_or_array may be either a ARRAY-ref of filenames to be copied or a single scalar filename. By default, files are copied using File::Copy::copy(). Options %opts:
$dstdir
$src_filename_or_array
from => $from, ##-- replace prefix $from in file(s) with $todir; default=undef: flat copy to $todir method => \&method, ##-- use CODE-ref \&method as underlying copy routing; default=\&File::Copy::copy label => $label, ##-- report errors as '$label'; (default='copyto()')
$bool = PACKAGE->copyto_a($src_filename_or_array, $dstdir, %opts);
Wrapper for PACKAGE->copyto($src_filename_or_array, $dstdir, %opts, method=>\&cp_a, label=>'moveto()').
PACKAGE->copyto($src_filename_or_array, $dstdir, %opts, method=>\&cp_a, label=>'moveto()')
Wrapper for PACKAGE->copyto($src_filename_or_array, $dstdir, %opts, method=>\&File::Copy::move, label=>'moveto()').
PACKAGE->copyto($src_filename_or_array, $dstdir, %opts, method=>\&File::Copy::move, label=>'moveto()')
$bool = PACKAGE->cp_a($src,$dst);
Copies a single file $src to $dst, attempting to preserve ownership, permissions, and timestamps; used by copyto_a(). Uses File::Copy::syscopy() if available and distinct from File::Copy::copy(), otherwise first copies the file using File::Copy::copy() and subsequently propagates file attributes using the core perl functions chown(), chmod(), and utime().
$src
$dst
$fh_or_undef = PACKAGE->fh_flush($fh);
flushes filehandle $fh using its flush() method if available
$fh_or_undef = PACKAGE->fh_reopen($fh,$file);
closes and re-opens filehandle $fh, should be an expensive flush even if system doesn't support the IO::Handle::flush method.
$str = si_str($float);
returns an SI string for $float.
$pi = CLASS::_intersect_p($p1,$p2); $pi = CLASS->_intersect_p($p1,$p2);
computes intersection of 2 piddles; undef is treated as the universal set; argument piddles MUST be sorted in ascending order.
$pu = CLASS::_union_p($p1,$p2); $pu = CLASS-E<gt>_intersect_p($p1,$p2);
computes union of 2 piddles; undef is treated as the universal set; argument piddles MUST be sorted in ascending order.
$pneg = CLASS::_complement_p($p,$N); $pneg = CLASS-E<gt>_complement_p($p,$N);
computes complement of an index-piddle $p; undef is treated as the universal set; $N is the total number of elements in the index-universe.
$p
$N
$pdiff = CLASS::_setdiff_p($a,$b,$N); $pdiff = CLASS-E<gt>_setdiff_p($a,$b,$N);
index-piddle difference; undef is treated as the universal set. $N is the total number of elements in the index-universe.
$pdl_or_undef = CLASS->readPdlFile($basename, %opts);
Load or mmap a PDL file from disk using PDL::IO::FastRaw; %opts:
class=>$class, # one of qw(PDL PDL::CCS::Nd) mmap =>$bool, # use mapfraw() (default=1) log =>$level, # log-level (default=undef: off) #... # other keys passed to CLASS->mapfraw() rsp. CLASS->readfraw()
$bool = CLASS->writePdlFile($pdl_or_undef, $basename, %opts);
Write a PDL file to disk using PDL::IO::FastRaw. Unlinks target file(s) if $pdl_or_undef is not defined. %opts:
$pdl_or_undef
log => $bool, # log-level (default=undef: off) #... # other keys passed to $pdl->writefraw()
$bool = CLASS->writePdlHeader($filename, $type, $ndims, @dims);
writes a PDL::IO::FastRaw-style header $filename (e.g. "pdl.hdr"); adapted from PDL::IO::FastRaw::_writefrawhdr(). Arguments:
$filename
"pdl.hdr"
$type ##-- PDL::Type or integer $ndims ##-- number of piddle dimensions @dims ##-- dimension size list, piddle, or ARRAY-ref
$bool = CLASS->writeCcsHeader($filename, $itype, $vtype, $pdims, %opts);
writes a PDL::CCS::IO::FastRaw-style header $filename (e.g. "pdl.hdr"). Arguments:
$itype, ##-- PDL::Type for index (default: PDL::CCS::Utils::ccs_indx()) $vtype, ##-- PDL::Type for values (default: $PDL::IO::Misc::deftype) $pdims, ##-- dimension piddle or ARRAY-ref %opts ##-- passed to PDL::CCS::Nd-E<gt>newFromWich
$pdl = mmzeroes ($file?, $type?, @dims, \%opts?); $pdl = $pdl->mmzeroes($file?, $type?, \%opts?);
create a (temporary) mmap()ed pdl using DiaColloDB::PDL::MM; wraps DiaColloDB::PDL::MM->new(). %opts:
file => $template, ##-- file basename or File::Temp template; default='pdlXXXX' suffix => $suffix, ##-- File::Temp::tempfile() suffix (default='.pdl') log => $level, ##-- logging verbosity (default=undef: off) temp => $bool, ##-- delete on END (default: $file =~ /X{4}/)
$pdl = mmtemp ($file?, $type?, @dims, \%opts?); $pdl = $pdl->mmtemp($file?, $type?, \%opts?);
Like mmzeroes(), but wraps DiaColloDB::PDL::MM->mmtemp(), implicitly setting $opts->{temp}=1.
$opts->{temp}=1
$bool = mmunlink(@mmfiles); $bool = mmunlink($mmpdl,@mmfiles);
unlinks file(s) generated by mmzeroes($basename) or mmtemp($basename); wraps DiaColloDB::PDL::MM::unlink().
$type = CLASS->mintype ($pdl, @types); $type = CLASS->mintype($maxval, @types);
returns minimum PDL::Types type from @types required for representing $maxval, which in turn defaults to $maxval->max if $maxval is passed as a PDL; @types defaults to all known PDL types.
@types
$maxval
$maxval->max
$maxval = $type->maxval(); $maxval = CLASS::maxval($type_or_name)
returns maximum value representable by PDL::Type $type (first form) or $type_or_name (second form); really only meaningful for integer types.
$type
$type_or_name
($vals,$counts) = $pdl->valcounts();
wrapper for $pdl->flat->qsort->rle() with masking of zero-counts lifted from MUDL::PDL::Smooth.
Global temp directory to use. If undefined (the default), File::Spec::tmpdir() will be used.
list of temporary files created by this process to be unlinked in an END block.
$tmpdir = CLASS->tmpdir(); $tmpdir = CLASS-t>tmpdir($template, %opts);
in first form, get name of global tempdir ($TMPDIR || File::Spec::tmpdir()). in second form, create and return a new temporary directory via File::Temp::tempdir().
$fh = CLASS->tmpfh(); $fh = CLASS->tmpfh($template_or_filename, %opts);
get a new temporary filehandle or undef on error; in list context, returns ($fh,$filename) or empty list on error. $template_or_filename defaults to "tmpXXXXX". uses File::Temp::tempfile() if $template_or_filename contains at least 4 "X" characters, otherwise uses literal $template_or_filename, honoring the DIR, TMPDIR, SUFFIX, and UNLINK options in %opts, which are interpreted as for File::Temp::tempfile().
undef
($fh,$filename)
$template_or_filename
"tmpXXXXX"
"X"
DIR
TMPDIR
SUFFIX
UNLINK
%opts
$filename = CLASS->tmpfile(); $filename = CLASS->tmpfile($template, %opts);
Wrapper for tmpfh which returns only the filename.
\@tmparray = CLASS->tmparray($template, %opts);
ties a new temporary array via DiaColloDB::Temp::Array and returns a reference to the newly tied array. wraps tmpfile($template,%opts) tie(my @tmparray, 'DiaColloDB::Temp::Array', $tmpfilename, %opts).
tmpfile($template,%opts)
tie(my @tmparray, 'DiaColloDB::Temp::Array', $tmpfilename, %opts)
\@tmparrayp = CLASS->tmparrayp($template, $packas, %opts);
ties a new temporary integer-array via DiaColloDB::PackedFile and returns a reference to the newly tied array. wraps tmpfile($template,%opts) and tie(my @tmparray, 'DiaColloDB::PackedFile', $tmpfilename, %opts).
tie(my @tmparray, 'DiaColloDB::PackedFile', $tmpfilename, %opts)
\%tmphash = CLASS->tmphash($template, %opts);
ties a new temporary hash via DiaColloDB::Temp::Hash and returns a reference to the newly tied hash. wraps tmpfile($template,%opts) and tie(my %tmphash, 'DiaColloDB::Temp::Hash', $tmpfilename, %opts).
tie(my %tmphash, 'DiaColloDB::Temp::Hash', $tmpfilename, %opts)
Cache for nCores() utility: ($cpuinfo_file=>$n, ...)
($cpuinfo_file=>$n, ...)
$ncores = PACKAGE::nCores(); $ncores = PACKAGE::nCores($proc_cpuinfo_filename);
Returns the number of CPU cores on the system according to the file $proc_cpuinfo_filename (by default /proc/cpuinfo) if available, otherwise according to the external program nproc if that is avaialble, and otherwise zero. Caches result as $NCORES{$proc_cpuinfo_filename}.
nproc
$NCORES{$proc_cpuinfo_filename}
$njobs = PACKAGE::nJobs(); $njobs = PACKAGE::nJobs($njobsRequest);
Gets non-negative number of parallel jobs (threads) for user request $njobsRequest, which defaults to the current value of the package variable $DiaColloDB::NJOBS, or -1 if it is undefined.
$njobsRequest
$DiaColloDB::NJOBS
If $njobsRequest is negative, returns the number of CPU cores on the system via nCores(). Otherwise, if (0 < $njobsRequest < 1), $njobsRequest is interpreted as the desired fraction of the number of available CPU cores to be used, and returns ($njobsRequest*nCores()). In all other cases, $njobsRequest is interpreted as an exact number of jobs to use, ans is returned as int($njobs+0).
($njobsRequest*nCores())
int($njobs+0)
$sort_parallel_option = sortJobs(); $sort_parallel_option = sortJobs($njobsRequest);
Returns an appropriate --parallel option for external sort system command calls to use <$njobsRequest> parallel jobs (assuming sort calling conventions as for GNU coreutils).
--parallel
sort
Bryan Jurish <moocow@cpan.org>
Copyright (C) 2015-2020 by Bryan Jurish
This package is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.14.2 or, at your option, any later version of Perl 5 you may have available.
DiaColloDB(3pm), perl(1), ...
To install DiaColloDB, copy and paste the appropriate command in to your terminal.
cpanm
cpanm DiaColloDB
CPAN shell
perl -MCPAN -e shell install DiaColloDB
For more information on module installation, please visit the detailed CPAN module installation guide.