package Bio::Root::IO;
use strict;
use Symbol;
use IO::Handle;
use File::Copy;
use Fcntl;
use base qw(Bio::Root::Root);
# as of 2016, worked on most systems, but will test this in a RC
my %modes = ( 0 => 'r', 1 => 'w', 2 => 'rw' );
=head1 SYNOPSIS
# Use stream I/O in your module
$self->{'io'} = Bio::Root::IO->new(-file => "myfile");
$self->{'io'}->_print("some stuff");
my $line = $self->{'io'}->_readline();
$self->{'io'}->_pushback($line);
$self->{'io'}->close();
# obtain platform-compatible filenames
$path = Bio::Root::IO->catfile($dir, $subdir, $filename);
# obtain a temporary file (created in $TEMPDIR)
($handle) = $io->tempfile();
=head1 DESCRIPTION
This module provides methods that will usually be needed for any sort
of file- or stream-related input/output, e.g., keeping track of a file
handle, transient printing and reading from the file handle, a close
method, automatically closing the handle on garbage collection, etc.
To use this for your own code you will either want to inherit from
this module, or instantiate an object for every file or stream you are
dealing with. In the first case this module will most likely not be
the first class off which your class inherits; therefore you need to
call _initialize_io() with the named parameters in order to set file
handle, open file, etc automatically.
Most methods start with an underscore, indicating they are private. In
OO speak, they are not private but protected, that is, use them in
your module code, but a client code of your module will usually not
want to call them (except those not starting with an underscore).
In addition this module contains a couple of convenience methods for
cross-platform safe tempfile creation and similar tasks. There are
some CPAN modules related that may not be available on all
platforms. At present, File::Spec and File::Temp are attempted. This
module defines $PATHSEP, $TEMPDIR, and $ROOTDIR, which will always be set,
and $OPENFLAGS, which will be set if either of File::Spec or File::Temp fails.
The -noclose boolean (accessed via the noclose method) prevents a
filehandle from being closed when the IO object is cleaned up. This
is special behavior when a object like a parser might share a
filehandle with an object like an indexer where it is not proper to
close the filehandle as it will continue to be reused until the end of the
stream is reached. In general you won't want to play with this flag.
=head1 AUTHOR Hilmar Lapp
=cut
our ($FILESPECLOADED, $FILETEMPLOADED,
$FILEPATHLOADED, $TEMPDIR,
$PATHSEP, $ROOTDIR,
$OPENFLAGS, $VERBOSE,
$ONMAC, $HAS_EOL, );
my $TEMPCOUNTER;
my $HAS_WIN32 = 0;
BEGIN {
$TEMPCOUNTER = 0;
$FILESPECLOADED = 0;
$FILETEMPLOADED = 0;
$FILEPATHLOADED = 0;
$VERBOSE = 0;
# try to load those modules that may cause trouble on some systems
eval {
require File::Path;
$FILEPATHLOADED = 1;
};
if( $@ ) {
print STDERR "Cannot load File::Path: $@" if( $VERBOSE > 0 );
# do nothing
}
# If on Win32, attempt to find Win32 package
if($^O =~ /mswin/i) {
eval {
require Win32;
$HAS_WIN32 = 1;
};
}
# Try to provide a path separator. Why doesn't File::Spec export this,
# or did I miss it?
if ($^O =~ /mswin/i) {
$PATHSEP = "\\";
} elsif($^O =~ /macos/i) {
$PATHSEP = ":";
} else { # unix
$PATHSEP = "/";
}
eval {
require File::Spec;
$FILESPECLOADED = 1;
$TEMPDIR = File::Spec->tmpdir();
$ROOTDIR = File::Spec->rootdir();
require File::Temp; # tempfile creation
$FILETEMPLOADED = 1;
};
if( $@ ) {
if(! defined($TEMPDIR)) { # File::Spec failed
# determine tempdir
if (defined $ENV{'TEMPDIR'} && -d $ENV{'TEMPDIR'} ) {
$TEMPDIR = $ENV{'TEMPDIR'};
} elsif( defined $ENV{'TMPDIR'} && -d $ENV{'TMPDIR'} ) {
$TEMPDIR = $ENV{'TMPDIR'};
}
if($^O =~ /mswin/i) {
$TEMPDIR = 'C:\TEMP' unless $TEMPDIR;
$ROOTDIR = 'C:';
} elsif($^O =~ /macos/i) {
$TEMPDIR = "" unless $TEMPDIR; # what is a reasonable default on Macs?
$ROOTDIR = ""; # what is reasonable??
} else { # unix
$TEMPDIR = "/tmp" unless $TEMPDIR;
$ROOTDIR = "/";
}
if (!( -d $TEMPDIR && -w $TEMPDIR )) {
$TEMPDIR = '.'; # last resort
}
}
# File::Temp failed (alone, or File::Spec already failed)
# determine open flags for tempfile creation using Fcntl
$OPENFLAGS = O_CREAT | O_EXCL | O_RDWR;
for my $oflag (qw/FOLLOW BINARY LARGEFILE EXLOCK NOINHERIT TEMPORARY/){
my ($bit, $func) = (0, "Fcntl::O_" . $oflag);
no strict 'refs';
$OPENFLAGS |= $bit if eval { $bit = &$func(); 1 };
}
}
$ONMAC = "\015" eq "\n";
}
=head2 new
Title : new
Usage : my $io = Bio::Root::IO->new( -file => 'data.txt' );
Function: Create new class instance. It automatically calls C<_initialize_io>.
Args : Same named parameters as C<_initialize_io>.
Returns : A Bio::Root::IO object
=cut
sub new {
my ($caller, @args) = @_;
my $self = $caller->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 _initialize_io
Title : _initialize_io
Usage : $io->_initialize_io(@params);
Function: Initializes filehandle and other properties from the parameters.
Args : The following named parameters are currently recognized:
-file name of file to read or write to
-fh file handle to read or write to (mutually exclusive
with -file and -string)
-input name of file, or filehandle (GLOB or IO::Handle object)
to read of write to
-string string to read from (will be converted to filehandle)
-url name of URL to open
-flush boolean flag to autoflush after each write
-noclose boolean flag, when set to true will not close a
filehandle (must explicitly call close($io->_fh)
-retries number of times to try a web fetch before failure
-ua_parms when using -url, hashref of key => value parameters
to pass to LWP::UserAgent->new(). A useful value might
be, for example, {timeout => 60 } (ua defaults to 180s)
Returns : True
=cut
sub _initialize_io {
my($self, @args) = @_;
$self->_register_for_cleanup(\&_io_cleanup);
my ($input, $noclose, $file, $fh, $string,
$flush, $url, $retries, $ua_parms) =
$self->_rearrange([qw(INPUT NOCLOSE FILE FH STRING FLUSH URL RETRIES UA_PARMS)],
@args);
my $mode;
if ($url) {
$retries ||= 5;
require LWP::UserAgent;
my $ua = LWP::UserAgent->new(%$ua_parms);
my $http_result;
my ($handle, $tempfile) = $self->tempfile();
CORE::close($handle);
for (my $try = 1 ; $try <= $retries ; $try++) {
$http_result = $ua->get($url, ':content_file' => $tempfile);
$self->warn("[$try/$retries] tried to fetch $url, but server ".
"threw ". $http_result->code . ". retrying...")
if !$http_result->is_success;
last if $http_result->is_success;
}
$self->throw("Failed to fetch $url, server threw ".$http_result->code)
if !$http_result->is_success;
$file = $tempfile;
$mode = '>';
}
delete $self->{'_readbuffer'};
delete $self->{'_filehandle'};
$self->noclose( $noclose) if defined $noclose;
# determine whether the input is a file(name) or a stream
if ($input) {
if (ref(\$input) eq 'SCALAR') {
# we assume that a scalar is a filename
if ($file && ($file ne $input)) {
$self->throw("Input file given twice: '$file' and '$input' disagree");
}
$file = $input;
} elsif (ref($input) &&
((ref($input) eq 'GLOB') || $input->isa('IO::Handle'))) {
# input is a stream
$fh = $input;
} else {
# let's be strict for now
$self->throw("Unable to determine type of input $input: ".
"not string and not GLOB");
}
}
if (defined($file) && defined($fh)) {
$self->throw("Providing both a file and a filehandle for reading - ".
"only one please!");
}
if ($string) {
if (defined($file) || defined($fh)) {
$self->throw("File or filehandle provided with -string, ".
"please unset if you are using -string as a file");
}
open $fh, '<', \$string or $self->throw("Could not read string: $!");
}
if (defined($file) && ($file ne '')) {
$self->file($file);
($mode, $file) = $self->cleanfile;
$mode ||= '<';
my $action = ($mode =~ m/>/) ? 'write' : 'read';
$fh = Symbol::gensym();
open $fh, $mode, $file or $self->throw("Could not $action file '$file': $!");
}
if (defined $fh) {
# check filehandle to ensure it's one of:
# a GLOB reference, as in: open(my $fh, "myfile");
# an IO::Handle or IO::String object
# the UNIVERSAL::can added to fix Bug2863
unless ( ( ref $fh and ( ref $fh eq 'GLOB' ) )
or ( ref $fh and ( UNIVERSAL::can( $fh, 'can' ) )
and ( $fh->isa('IO::Handle')
or $fh->isa('IO::String') ) )
) {
$self->throw("Object $fh does not appear to be a file handle");
}
if ($HAS_EOL) {
binmode $fh, ':raw:eol(LF-Native)';
}
$self->_fh($fh); # if $fh not provided, defaults to STDIN and STDOUT
}
$self->_flush_on_write(defined $flush ? $flush : 1);
return 1;
}
=head2 _fh
Title : _fh
Usage : $io->_fh($newval);
Function: Get or set the file handle for the stream encapsulated.
Args : Optional filehandle to use
Returns : Filehandle for the stream
=cut
sub _fh {
my ($self, $value) = @_;
if ( defined $value) {
$self->{'_filehandle'} = $value;
}
return $self->{'_filehandle'};
}
=head2 mode
Title : mode
Usage : $io->mode();
$io->mode(-force => 1);
Function: Determine if the object was opened for reading or writing
Args : -force: Boolean. Once mode() has been called, the mode is cached for
further calls to mode(). Use this argument to override this
behavior and re-check the object's mode.
Returns : Mode of the object:
'r' for readable
'w' for writable
'rw' for readable and writable
'?' if mode could not be determined (e.g. for a -url)
=cut
sub mode {
my ($self, %arg) = @_;
# Method 1: IO::Handle::fdopen
# my $iotest = new IO::Handle;
# $iotest->fdopen( dup(fileno($fh)) , 'r' );
# if ($iotest->error == 0) { ... }
# It did not actually seem to work under any platform, since there would no
# error if the filehandle had been opened writable only. It could not be
# hacked around when dealing with unseekable (piped) filehandles.
# Method 2: readline, a.k.a. the <> operator
# no warnings "io";
# my $line = <$fh>;
# if (defined $line) {
# $self->{'_mode'} = 'r';
# ...
# It did not work well either because <> returns undef, i.e. querying the
# mode() after having read an entire file returned 'w'.
if ( $arg{-force} || not exists $self->{'_mode'} ) {
# Determine stream mode
my $mode;
my $fh = $self->_fh;
if (defined $fh) {
# use fcntl if not Windows-based
if ($^O !~ /MSWin32/) {
my $m = fcntl($fh, F_GETFL, 0);
$mode = exists $modes{$m & 3} ? $modes{$m & 3} : '?';
} else {
# Determine read/write status of filehandle
no warnings 'io';
if ( defined( read $fh, my $content, 0 ) ) {
# Successfully read 0 bytes
$mode = 'r'
}
if ( defined( syswrite $fh, '') ) {
# Successfully wrote 0 bytes
$mode ||= '';
$mode .= 'w';
}
}
} else {
# Stream does not have a filehandle... cannot determine mode
$mode = '?';
}
# Save mode for future use
$self->{'_mode'} = $mode;
}
return $self->{'_mode'};
}
=head2 file
Title : file
Usage : $io->file('>'.$file);
my $file = $io->file;
Function: Get or set the name of the file to read or write.
Args : Optional file name (including its mode, e.g. '<' for reading or '>'
for writing)
Returns : A string representing the filename and its mode.
=cut
sub file {
my ($self, $value) = @_;
if ( defined $value) {
$self->{'_file'} = $value;
}
return $self->{'_file'};
}
=head2 cleanfile
Title : cleanfile
Usage : my ($mode, $file) = $io->cleanfile;
Function: Get the name of the file to read or write, stripped of its mode
('>', '<', '+>', '>>', etc).
Args : None
Returns : In array context, an array of the mode and the clean filename.
=cut
sub cleanfile {
my ($self) = @_;
return ($self->{'_file'} =~ m/^ (\+?[><]{1,2})?\s*(.*) $/x);
}
=head2 format
Title : format
Usage : $io->format($newval)
Function: Get the format of a Bio::Root::IO sequence file or filehandle. Every
object inheriting Bio::Root::IO is guaranteed to have a format.
Args : None
Returns : Format of the file or filehandle, e.g. fasta, fastq, genbank, embl.
=cut
sub format {
my ($self) = @_;
my $format = (split '::', ref($self))[-1];
return $format;
}
=head2 variant
Title : format
Usage : $io->format($newval)
Function: Get the variant of a Bio::Root::IO sequence file or filehandle.
The format variant depends on the specific format used. Note that
not all formats have variants. Also, the Bio::Root::IO-implementing
modules that require access to variants need to define a global hash
that has the allowed variants as its keys.
Args : None
Returns : Variant of the file or filehandle, e.g. sanger, solexa or illumina for
the fastq format, or undef for formats that do not have variants.
=cut
sub variant {
my ($self, $variant) = @_;
if (defined $variant) {
$variant = lc $variant;
my $var_name = '%'.ref($self).'::variant';
my %ok_variants = eval $var_name; # e.g. %Bio::Assembly::IO::ace::variant
if (scalar keys %ok_variants == 0) {
$self->throw("Could not validate variant because global variant ".
"$var_name was not set or was empty\n");
}
if (not exists $ok_variants{$variant}) {
$self->throw("$variant is not a valid variant of the " .
$self->format . ' format');
}
$self->{variant} = $variant;
}
return $self->{variant};
}
=head2 _print
Title : _print
Usage : $io->_print(@lines)
Function: Print lines of text to the IO stream object.
Args : List of strings to print
Returns : True on success, undef on failure
=cut
sub _print {
my $self = shift;
my $fh = $self->_fh() || \*STDOUT;
my $ret = print $fh @_;
return $ret;
}
=head2 _insert
Title : _insert
Usage : $io->_insert($string,1)
Function: Insert some text in a file at the given line number (1-based).
Args : * string to write in file
* line number to insert the string at
Returns : True
=cut
sub _insert {
my ($self, $string, $line_num) = @_;
# Line number check
if ($line_num < 1) {
$self->throw("Could not insert text at line $line_num: the minimum ".
"line number possible is 1.");
}
# File check
my ($mode, $file) = $self->cleanfile;
if (not defined $file) {
$self->throw('Could not insert a line: IO object was initialized with '.
'something else than a file.');
}
# Everything that needs to be written is written before we read it
$self->flush;
# Edit the file line by line (no slurping)
$self->close;
my $temp_file;
my $number = 0;
while (-e "$file.$number.temp") {
$number++;
}
$temp_file = "$file.$number.temp";
copy($file, $temp_file);
open my $fh1, '<', $temp_file or $self->throw("Could not read temporary file '$temp_file': $!");
open my $fh2, '>', $file or $self->throw("Could not write file '$file': $!");
while (my $line = <$fh1>) {
if ($. == $line_num) { # right line for new data
print $fh2 $string . $line;
}
else {
print $fh2 $line;
}
}
CORE::close $fh1;
CORE::close $fh2;
unlink $temp_file or $self->throw("Could not delete temporary file '$temp_file': $!");
# Line number check (again)
if ( $. > 0 && $line_num > $. ) {
$self->throw("Could not insert text at line $line_num: there are only ".
"$. lines in file '$file'");
}
# Re-open the file in append mode to be ready to add text at the end of it
# when the next _print() statement comes
open my $new_fh, '>>', $file or $self->throw("Could not append to file '$file': $!");
$self->_fh($new_fh);
# If file is empty and we're inserting at line 1, simply append text to file
if ( $. == 0 && $line_num == 1 ) {
$self->_print($string);
}
return 1;
}
=head2 _readline
Title : _readline
Usage : local $Bio::Root::IO::HAS_EOL = 1;
my $io = Bio::Root::IO->new(-file => 'data.txt');
my $line = $io->_readline();
$io->close;
Function: Read a line of input and normalize all end of line characters.
End of line characters are typically "\n" on Linux platforms, "\r\n"
on Windows and "\r" on older Mac OS. By default, the _readline()
method uses the value of $/, Perl's input record separator, to
detect the end of each line. This means that you will not get the
expected lines if your input has Mac-formatted end of line characters.
Also, note that the current implementation does not handle pushed
back input correctly unless the pushed back input ends with the
value of $/. For each line parsed, its line ending, e.g. "\r\n" is
converted to "\n", unless you provide the -raw argument.
Altogether it is easier to let the PerlIO::eol module automatically
detect the proper end of line character and normalize it to "\n". Do
so by setting $Bio::Root::IO::HAS_EOL to 1.
Args : -raw : Avoid converting end of line characters to "\n" This option
has no effect when using $Bio::Root::IO::HAS_EOL = 1.
Returns : Line of input, or undef when there is nothing to read anymore
=cut
sub _readline {
my ($self, %param) = @_;
my $fh = $self->_fh or return;
my $line;
# if the buffer been filled by _pushback then return the buffer
# contents, rather than read from the filehandle
if( @{$self->{'_readbuffer'} || [] } ) {
$line = shift @{$self->{'_readbuffer'}};
} else {
$line = <$fh>;
}
# Note: In Windows the "-raw" parameter has no effect, because Perl already discards
# the '\r' from the line when reading in text mode from the filehandle
# ($line = <$fh>), and put it back automatically when printing
if( !$HAS_EOL && !$param{-raw} && (defined $line) ) {
# don't strip line endings if -raw or $HAS_EOL is specified
$line =~ s/\015\012/\012/g; # Change all CR/LF pairs to LF
$line =~ tr/\015/\n/ unless $ONMAC; # Change all single CRs to NEWLINE
}
return $line;
}
=head2 _pushback
Title : _pushback
Usage : $io->_pushback($newvalue)
Function: Puts a line previously read with _readline back into a buffer.
buffer can hold as many lines as system memory permits.
Note that this is only supported for pushing back data ending with
the current, localized value of $/. Using this method to push
modified data back onto the buffer stack is not supported; see bug
843.
Args : newvalue
Returns : True
=cut
# fix for bug 843, this reveals some unsupported behavior
#sub _pushback {
# my ($self, $value) = @_;
# if (index($value, $/) >= 0) {
# push @{$self->{'_readbuffer'}}, $value;
# } else {
# $self->throw("Pushing modifed data back not supported: $value");
# }
#}
sub _pushback {
my ($self, $value) = @_;
return unless $value;
unshift @{$self->{'_readbuffer'}}, $value;
return 1;
}
=head2 close
Title : close
Usage : $io->close()
Function: Closes the file handle associated with this IO instance,
excepted if -noclose was specified.
Args : None
Returns : True
=cut
sub close {
my ($self) = @_;
# do not close if we explicitly asked not to
return if $self->noclose;
if( defined( my $fh = $self->{'_filehandle'} )) {
$self->flush;
return if ref $fh eq 'GLOB' && (
\*STDOUT == $fh || \*STDERR == $fh || \*STDIN == $fh
);
# don't close IO::Strings
CORE::close $fh unless ref $fh && $fh->isa('IO::String');
}
$self->{'_filehandle'} = undef;
delete $self->{'_readbuffer'};
return 1;
}
=head2 flush
Title : flush
Usage : $io->flush()
Function: Flushes the filehandle
Args : None
Returns : True
=cut
sub flush {
my ($self) = shift;
if( !defined $self->{'_filehandle'} ) {
$self->throw("Flush failed: no filehandle was active");
}
if( ref($self->{'_filehandle'}) =~ /GLOB/ ) {
my $oldh = select($self->{'_filehandle'});
$| = 1;
select($oldh);
} else {
$self->{'_filehandle'}->flush();
}
return 1;
}
=head2 noclose
Title : noclose
Usage : $io->noclose($newval)
Function: Get or set the NOCLOSE flag - setting this to true will prevent a
filehandle from being closed when an object is cleaned up or
explicitly closed.
Args : Optional new value (a scalar or undef)
Returns : Value of noclose (a scalar)
=cut
sub noclose {
my $self = shift;
return $self->{'_noclose'} = shift if @_;
return $self->{'_noclose'};
}
=head2 _io_cleanup
=cut
sub _io_cleanup {
my ($self) = @_;
$self->close();
my $v = $self->verbose;
# we are planning to cleanup temp files no matter what
if ( exists($self->{'_rootio_tempfiles'})
and ref($self->{'_rootio_tempfiles'}) =~ /array/i
and not $self->save_tempfiles
) {
if( $v > 0 ) {
warn( "going to remove files ",
join(",", @{$self->{'_rootio_tempfiles'}}),
"\n");
}
unlink (@{$self->{'_rootio_tempfiles'}} );
}
# cleanup if we are not using File::Temp
if ( $self->{'_cleanuptempdir'}
and exists($self->{'_rootio_tempdirs'})
and ref($self->{'_rootio_tempdirs'}) =~ /array/i
and not $self->save_tempfiles
) {
if( $v > 0 ) {
warn( "going to remove dirs ",
join(",", @{$self->{'_rootio_tempdirs'}}),
"\n");
}
$self->rmtree( $self->{'_rootio_tempdirs'});
}
}
=head2 exists_exe
Title : exists_exe
Usage : $exists = $io->exists_exe('clustalw');
$exists = Bio::Root::IO->exists_exe('clustalw')
$exists = Bio::Root::IO::exists_exe('clustalw')
Function: Determines whether the given executable exists either as file
or within the path environment. The latter requires File::Spec
to be installed.
On Win32-based system, .exe is automatically appended to the program
name unless the program name already ends in .exe.
Args : Name of the executable
Returns : 1 if the given program is callable as an executable, and 0 otherwise
=cut
sub exists_exe {
my ($self, $exe) = @_;
$self->throw("Must pass a defined value to exists_exe") unless defined $exe;
$exe = $self if (!(ref($self) || $exe));
$exe .= '.exe' if(($^O =~ /mswin/i) && ($exe !~ /\.(exe|com|bat|cmd)$/i));
return $exe if ( -f $exe && -x $exe ); # full path and exists
# Ewan's comment. I don't think we need this. People should not be
# asking for a program with a pathseparator starting it
# $exe =~ s/^$PATHSEP//;
# Not a full path, or does not exist. Let's see whether it's in the path.
if($FILESPECLOADED) {
for my $dir (File::Spec->path()) {
my $f = Bio::Root::IO->catfile($dir, $exe);
return $f if( -f $f && -x $f );
}
}
return 0;
}
=head2 tempfile
Title : tempfile
Usage : my ($handle,$tempfile) = $io->tempfile();
Function: Create a temporary filename and a handle opened for reading and
writing.
Caveats: If you do not have File::Temp on your system you should
avoid specifying TEMPLATE and SUFFIX.
Args : Named parameters compatible with File::Temp: DIR (defaults to
$Bio::Root::IO::TEMPDIR), TEMPLATE, SUFFIX.
Returns : A 2-element array, consisting of temporary handle and temporary
file name.
=cut
sub tempfile {
my ($self, @args) = @_;
my ($tfh, $file);
my %params = @args;
# map between naming with and without dash
for my $key (keys(%params)) {
if( $key =~ /^-/ ) {
my $v = $params{$key};
delete $params{$key};
$params{uc(substr($key,1))} = $v;
} else {
# this is to upper case
my $v = $params{$key};
delete $params{$key};
$params{uc($key)} = $v;
}
}
$params{'DIR'} = $TEMPDIR if(! exists($params{'DIR'}));
unless (exists $params{'UNLINK'} &&
defined $params{'UNLINK'} &&
! $params{'UNLINK'} ) {
$params{'UNLINK'} = 1;
} else {
$params{'UNLINK'} = 0;
}
if($FILETEMPLOADED) {
if(exists($params{'TEMPLATE'})) {
my $template = $params{'TEMPLATE'};
delete $params{'TEMPLATE'};
($tfh, $file) = File::Temp::tempfile($template, %params);
} else {
($tfh, $file) = File::Temp::tempfile(%params);
}
} else {
my $dir = $params{'DIR'};
$file = $self->catfile(
$dir,
(exists($params{'TEMPLATE'}) ?
$params{'TEMPLATE'} :
sprintf( "%s.%s.%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++))
);
# sneakiness for getting around long filenames on Win32?
if( $HAS_WIN32 ) {
$file = Win32::GetShortPathName($file);
}
# Try to make sure this will be marked close-on-exec
# XXX: Win32 doesn't respect this, nor the proper fcntl,
# but may have O_NOINHERIT. This may or may not be in Fcntl.
local $^F = 2;
# Store callers umask
my $umask = umask();
# Set a known umaskr
umask(066);
# Attempt to open the file
if ( sysopen($tfh, $file, $OPENFLAGS, 0600) ) {
# Reset umask
umask($umask);
} else {
$self->throw("Could not write temporary file '$file': $!");
}
}
if( $params{'UNLINK'} ) {
push @{$self->{'_rootio_tempfiles'}}, $file;
}
return wantarray ? ($tfh,$file) : $tfh;
}
=head2 tempdir
Title : tempdir
Usage : my ($tempdir) = $io->tempdir(CLEANUP=>1);
Function: Creates and returns the name of a new temporary directory.
Note that you should not use this function for obtaining "the"
temp directory. Use $Bio::Root::IO::TEMPDIR for that. Calling this
method will in fact create a new directory.
Args : args - ( key CLEANUP ) indicates whether or not to cleanup
dir on object destruction, other keys as specified by File::Temp
Returns : The name of a new temporary directory.
=cut
sub tempdir {
my ($self, @args) = @_;
if ($FILETEMPLOADED && File::Temp->can('tempdir')) {
return File::Temp::tempdir(@args);
}
# we have to do this ourselves, not good
# we are planning to cleanup temp files no matter what
my %params = @args;
print "cleanup is " . $params{CLEANUP} . "\n";
$self->{'_cleanuptempdir'} = ( defined $params{CLEANUP} &&
$params{CLEANUP} == 1);
my $tdir = $self->catfile( $TEMPDIR,
sprintf("dir_%s-%s-%s",
$ENV{USER} || 'unknown',
$$,
$TEMPCOUNTER++));
mkdir($tdir, 0755);
push @{$self->{'_rootio_tempdirs'}}, $tdir;
return $tdir;
}
=head2 catfile
Title : catfile
Usage : $path = Bio::Root::IO->catfile(@dirs, $filename);
Function: Constructs a full pathname in a cross-platform safe way.
If File::Spec exists on your system, this routine will merely
delegate to it. Otherwise it tries to make a good guess.
You should use this method whenever you construct a path name
from directory and filename. Otherwise you risk cross-platform
compatibility of your code.
You can call this method both as a class and an instance method.
Args : components of the pathname (directories and filename, NOT an
extension)
Returns : a string
=cut
sub catfile {
my ($self, @args) = @_;
return File::Spec->catfile(@args) if $FILESPECLOADED;
# this is clumsy and not very appealing, but how do we specify the
# root directory?
if($args[0] eq '/') {
$args[0] = $ROOTDIR;
}
return join($PATHSEP, @args);
}
=head2 rmtree
Title : rmtree
Usage : Bio::Root::IO->rmtree($dirname );
Function: Remove a full directory tree
If File::Path exists on your system, this routine will merely
delegate to it. Otherwise it runs a local version of that code.
You should use this method to remove directories which contain
files.
You can call this method both as a class and an instance method.
Args : roots - rootdir to delete or reference to list of dirs
verbose - a boolean value, which if TRUE will cause
C<rmtree> to print a message each time it
examines a file, giving the name of the file, and
indicating whether it's using C<rmdir> or
C<unlink> to remove it, or that it's skipping it.
(defaults to FALSE)
safe - a boolean value, which if TRUE will cause C<rmtree>
to skip any files to which you do not have delete
access (if running under VMS) or write access (if
running under another OS). This will change in the
future when a criterion for 'delete permission'
under OSs other than VMS is settled. (defaults to
FALSE)
Returns : number of files successfully deleted
=cut
# taken straight from File::Path VERSION = "1.0403"
sub rmtree {
my ($self, $roots, $verbose, $safe) = @_;
if ( $FILEPATHLOADED ) {
return File::Path::rmtree ($roots, $verbose, $safe);
}
my $force_writable = ($^O eq 'os2' || $^O eq 'dos' || $^O eq 'MSWin32' ||
$^O eq 'amigaos' || $^O eq 'cygwin');
my $Is_VMS = $^O eq 'VMS';
my @files;
my $count = 0;
$verbose ||= 0;
$safe ||= 0;
if ( defined($roots) && length($roots) ) {
$roots = [$roots] unless ref $roots;
} else {
$self->warn("No root path(s) specified\n");
return 0;
}
my $root;
for $root (@{$roots}) {
$root =~ s#/\z##;
(undef, undef, my $rp) = lstat $root or next;
$rp &= 07777; # don't forget setuid, setgid, sticky bits
if ( -d _ ) {
# notabene: 0777 is for making readable in the first place,
# it's also intended to change it to writable in case we have
# to recurse in which case we are better than rm -rf for
# subtrees with strange permissions
chmod(0777, ($Is_VMS ? VMS::Filespec::fileify($root) : $root))
or $self->warn("Could not make directory '$root' read+writable: $!")
unless $safe;
if (opendir DIR, $root){
@files = readdir DIR;
closedir DIR;
} else {
$self->warn("Could not read directory '$root': $!");
@files = ();
}
# Deleting large numbers of files from VMS Files-11 filesystems
# is faster if done in reverse ASCIIbetical order
@files = reverse @files if $Is_VMS;
($root = VMS::Filespec::unixify($root)) =~ s#\.dir\z## if $Is_VMS;
@files = map("$root/$_", grep $_!~/^\.{1,2}\z/s,@files);
$count += $self->rmtree([@files],$verbose,$safe);
if ($safe &&
($Is_VMS ? !&VMS::Filespec::candelete($root) : !-w $root)) {
print "skipped '$root'\n" if $verbose;
next;
}
chmod 0777, $root
or $self->warn("Could not make directory '$root' writable: $!")
if $force_writable;
print "rmdir '$root'\n" if $verbose;
if (rmdir $root) {
++$count;
}
else {
$self->warn("Could not remove directory '$root': $!");
chmod($rp, ($Is_VMS ? VMS::Filespec::fileify($root) : $root))
or $self->warn("and can't restore permissions to "
. sprintf("0%o",$rp) . "\n");
}
}
else {
if ( $safe
and ($Is_VMS ? !&VMS::Filespec::candelete($root)
: !(-l $root || -w $root))
) {
print "skipped '$root'\n" if $verbose;
next;
}
chmod 0666, $root
or $self->warn( "Could not make file '$root' writable: $!")
if $force_writable;
warn "unlink '$root'\n" if $verbose;
# delete all versions under VMS
for (;;) {
unless (unlink $root) {
$self->warn("Could not unlink file '$root': $!");
if ($force_writable) {
chmod $rp, $root
or $self->warn("and can't restore permissions to "
. sprintf("0%o",$rp) . "\n");
}
last;
}
++$count;
last unless $Is_VMS && lstat $root;
}
}
}
return $count;
}
=head2 _flush_on_write
Title : _flush_on_write
Usage : $io->_flush_on_write($newval)
Function: Boolean flag to indicate whether to flush
the filehandle on writing when the end of
a component is finished (Sequences, Alignments, etc)
Args : Optional new value
Returns : Value of _flush_on_write
=cut
sub _flush_on_write {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_flush_on_write'} = $value;
}
return $self->{'_flush_on_write'};
}
=head2 save_tempfiles
Title : save_tempfiles
Usage : $io->save_tempfiles(1)
Function: Boolean flag to indicate whether to retain tempfiles/tempdir
Args : Value evaluating to TRUE or FALSE
Returns : Boolean value : 1 = save tempfiles/tempdirs, 0 = remove (default)
=cut
sub save_tempfiles {
my $self = shift;
if (@_) {
my $value = shift;
$self->{save_tempfiles} = $value ? 1 : 0;
}
return $self->{save_tempfiles} || 0;
}
1;