view release on metacpan or  search on metacpan

MANIFEST.SKIP  view on Meta::CPAN

# Avoid Module::Build generated and utility files.
\bBuild$
\b_build/

# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$

 view release on metacpan or  search on metacpan

TODO  view on Meta::CPAN

Write DTD for defaults; convert Adaptor.pm to parsing XML

Future items:
1. Option to backup software prior to install.

2 .starting and stopping of servers - is this working / robust
    during or after an install

3. server monitoring

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lib/Bio/MUST/Core/Tree.pm  view on Meta::CPAN

        $mode == 2 ? $tree->get_entities  :
        $mode == 1 ? $tree->get_internals :
                     $tree->get_terminals
    };

    # Note: old labels are backuped in specified attributes and vice-versa
    # TODO: allow appending acc for terminal nodes?
    for my $node (@nodes) {
        my $label     = $node->get_name;
        my $attribute = $node->get_generic($key);
        $node->set_generic($key => $label);

lib/Bio/MUST/Core/Tree.pm  view on Meta::CPAN

sub store_tpl {
    my $self    = shift;
    my $outfile = shift;

    # backup and discard branch lengths
    # Note: I have to do that since I cannot clone the tree (Bio::Phylo bug?)
    my @branch_lengths;
    for my $node ( @{ $self->tree->get_entities } ) {
        push @branch_lengths, $node->get_branch_length;
        $node->set_branch_length(undef);

 view release on metacpan or  search on metacpan

scripts/manipulate_datasets.pl  view on Meta::CPAN

	}
	else {
		# need to sort by the mean of provided column indices
		# we will generate a temporary column of the mean
		# first need to set the target of mean which is needed by combine function
		my $original = $opt_target;    # keep a backup just in case
		$opt_target = 'mean';
		combine_function(@indices);
		my $i = $Data->last_column;
		$opt_target = $original;       # restore backup just in case
		$Data->sort_data( $i, $direction );
		$Data->delete_column($i);      # delete the temporary column
	}

	# remove any pre-existing sorted metadata since no longer valid

scripts/manipulate_datasets.pl  view on Meta::CPAN

performed as specified using command line options. As such, the program can
be called in shell scripts.

The program keeps track of the number of manipulations performed, and if 
any are performed, will write out to file the changed data. Unless an 
output file name is provided, it will overwrite the input file (NO backup is
made!).

=head1 FUNCTIONS

This is a list of the functions available for manipulating columns. These may 

 view release on metacpan or  search on metacpan

lib/Bio/WGS2NCBI.pm  view on Meta::CPAN

		
		# have a FASTA file
		if ( $file =~ /(.+)\.fsa$/ ) {
			my $stem = $1;
		
			# make backup of FASTA file
			rename "${INDIR}/${file}", "${INDIR}/${file}.bak";
			
			# read file, look op non-missing residue positions, write truncated
			open my $fh,  '<', "${INDIR}/${file}.bak" or die $!;
			open my $out, '>', "${INDIR}/${file}"     or die $!;

lib/Bio/WGS2NCBI.pm  view on Meta::CPAN

				INFO "$id\t$i1 .. $i2";
				$coord{$id} = [ $i1, $i2  ];
				$seq->trunc( $i1 + 1, $i2 + 1 )->write_fasta($out);	
			}
			
			# make backup of TBL file, open handle for writing		
			rename "${INDIR}/${stem}.tbl", "${INDIR}/${stem}.tbl.bak";
			open my $outtbl, '>', "${INDIR}/${stem}.tbl" or die $!;
			
			# initialize variables
			my $tr = Bio::WGS2NCBI::TableReader->new( 

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lib/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm  view on Meta::CPAN

		              \s*(.*?)
		              \s*(?: \( (.*?) \) )?\.?
		              $}xms ) { 
        ($organelle, $abbr_name, $common) = ($1, $2, $3); # optional
    } else {
        $abbr_name = $get->('source'); # nothing caught; this is a backup!
    }

    # Convert data in classification lines into classification array.
    my @class = split(/; /, $get->('taxonomy'));

 view release on metacpan or  search on metacpan

Bio/SeqFeature/Tools/Unflattener.pm  view on Meta::CPAN

   # of genbank records
   #
   # if no resolver tag is specified, we revert to the normal
   # resolver_method
   if ($resolver_tag) {
       my $backup_resolver_method = $resolver_method;
       # closure: $resolver_tag is remembered by this sub
       my $sub = 
	 sub {
	     my ($self, $sf, @possible_container_sfs) = @_;
	     my @container_sfs = ();

Bio/SeqFeature/Tools/Unflattener.pm  view on Meta::CPAN

		       }
		       $match;
		   } @possible_container_sfs;
	     } 
	     else {
		 return $backup_resolver_method->($sf, @possible_container_sfs);
	     }
	     return map {$_=>0} @container_sfs;
	 };
       $resolver_method = $sub;
   }

 view release on metacpan or  search on metacpan

MANIFEST.SKIP  view on Meta::CPAN

\bbuild.com$

# and Module::Build::Tiny generated files
\b_build_params$

# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$

 view release on metacpan or  search on metacpan

lib/BioX/Workflow/Plugin/Drake.pm  view on Meta::CPAN

    global:
        - indir: /home/user/workflow
        - outdir: /home/user/workflow/output
        - file_rule: (.csv)$
    rules:
        - backup:
            local:
                - INPUT: "{$self->indir}/{$sample}.csv"
                - OUTPUT: "{$self->outdir}/{$sample}.csv"
                - thing: "other thing"
            process: |

lib/BioX/Workflow/Plugin/Drake.pm  view on Meta::CPAN

    ;
    ; Starting Workflow
    ;

    ;
    ; Starting backup
    ;


    ;
    ; Variables
    ; Indir: /home/guests/jir2004/workflow
    ; Outdir: /home/guests/jir2004/workflow/output/backup
    ; Local Variables:
    ;	INPUT: {$self->indir}/{$sample}.csv
    ;	OUTPUT: {$self->outdir}/{$sample}.csv
    ;	thing: other thing
    ;

    /home/guests/jir2004/workflow/output/backup/$[SAMPLE].csv <- /home/guests/jir2004/workflow/$[SAMPLE].csv
        cp $INPUT $OUTPUT


    ;
    ; Ending backup
    ;


    ;
    ; Starting grep_VARA

lib/BioX/Workflow/Plugin/Drake.pm  view on Meta::CPAN

Run drake

    drake --workflow workflow.full.drake

    The following steps will be run, in order:
      1: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv [timestamped]
      2: /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv [timestamped]
      3: /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv [projected timestamped]
      4: /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv [projected timestamped]
      5: /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv [projected timestamped]
      6: /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv [projected timestamped]
    Confirm? [y/n] y
    Running 6 steps with concurrence of 1...

    --- 0. Running (timestamped): /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv
    --- 0: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv -> done in 0.02s

    --- 1. Running (timestamped): /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv
    --- 1: /home/user/workflow/output/backup/test2.csv <- /home/user/workflow/test2.csv -> done in 0.01s

    --- 2. Running (timestamped): /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv
    Working on /home/user/workflow/output/backup/test1csv
    --- 2: /home/user/workflow/output/grep_vara/test1.grep_VARA.csv <- /home/user/workflow/output/backup/test1.csv -> done in 0.01s

    --- 3. Running (timestamped): /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv
    Working on /home/user/workflow/output/backup/test2csv
    --- 3: /home/user/workflow/output/grep_vara/test2.grep_VARA.csv <- /home/user/workflow/output/backup/test2.csv -> done in 0.01s

    --- 4. Running (timestamped): /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv
    --- 4: /home/user/workflow/output/grep_varb/test1.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test1.grep_VARA.csv -> done in 0.01s

    --- 5. Running (timestamped): /home/user/workflow/output/grep_varb/test2.grep_VARA.grep_VARB.csv <- /home/user/workflow/output/grep_vara/test2.grep_VARA.csv

lib/BioX/Workflow/Plugin/Drake.pm  view on Meta::CPAN

    cat drake.log #Here is the log for the first run

    2015-06-21 14:02:47,543 INFO Running 3 steps with concurrence of 1...
    2015-06-21 14:02:47,568 INFO
    2015-06-21 14:02:47,570 INFO --- 0. Running (timestamped): /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv
    2015-06-21 14:02:47,592 INFO --- 0: /home/user/workflow/output/backup/test1.csv <- /home/user/workflow/test1.csv -> done in 0.02s

    #So on and so forth

If you look in the example directory you will see a few png files, these are outputs of the drake workflow.

 view release on metacpan or  search on metacpan

config.yml  view on Meta::CPAN

    - outdir: data/processed
    - file_rule: (.*)csv$
    - plugins:
        - FileExists
rules:
    - backup:
        local:
            - wait: 0
        process: cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv
    - grep_VARA:
        process: |

 view release on metacpan or  search on metacpan

t/lib/TestsFor/BioX/Workflow/Test001.pm  view on Meta::CPAN

global:
    - indir: t/example/data/raw/test001
    - outdir: t/example/data/processed/test001
    - file_rule: (.*).csv\$
rules:
    - backup:
        process: cp {\$self->indir}/{\$sample}.csv {\$self->outdir}/{\$sample}.csv
    - grep_VARA:
        process: |
            echo "Working on {\$self->{indir}}/{\$sample}.csv"
            grep -i "VARA" {\$self->indir}/{\$sample}.csv >> {\$self->outdir}/{\$sample}.grep_VARA.csv

t/lib/TestsFor/BioX/Workflow/Test001.pm  view on Meta::CPAN

    my $cmd3 = <<EOF;
grep -i "VARB" {\$self->indir}/{\$sample}.grep_VARA.csv >> {\$self->outdir}/{\$sample}.grep_VARA.grep_VARB.csv
EOF

    my $process_exp = [
        {   backup => {
                process =>
                    'cp {$self->indir}/{$sample}.csv {$self->outdir}/{$sample}.csv'
            }
        },
        { grep_VARA => { process => $cmd2 } },

t/lib/TestsFor/BioX/Workflow/Test001.pm  view on Meta::CPAN

    #return;

    is( $got, $expected, "Got expected output!" );
    ok( -d "$Bin/example/data/processed/test001" );

    my @processes = qw(backup grep_VARA grep_VARB);

    foreach my $process (@processes) {
        ok( -d "$Bin/example/data/processed/test001/$process" );
    }
}

 view release on metacpan or  search on metacpan

Bioinf.pl  view on Meta::CPAN

        if(@file>0){
            if($file[0]=~/\S\.[n]?fa/){ ## to handle .nfa and .fa files
                $output_file = $file[0];   $out_file_name_provided=1;
                if(-s $output_file){
                    rename($output_file, "$output_file\.bak");
                    print "\n# (INFO) $output_file is present. $output_file\.bak will be created for backup\n";
                }
            }elsif($file[0]=~/(\S+)\.\S+/){
                $output_file = "$1\.fa";   $out_file_name_provided=1;
            }
	}else{ $output_file='default_out.fa'; }

Bioinf.pl  view on Meta::CPAN

	my %correct_head_box_entry = %{&read_correct_head_box()};
	for($p=0; $p < @file; $p++){
	  $in_file = $file[$p];

	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  ##  Make backup of the input file
	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  &cp( "$in_file", "$in_file\.bak$$");
	  print "\n $in_file\.bak$$ is created as a backup \n\n";
	  print chr(7);

	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  ##  Open files
	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

 view release on metacpan or  search on metacpan

MANIFEST.SKIP  view on Meta::CPAN

# Avoid Module::Build generated and utility files.
\bBuild$
\b_build

# Avoid temp and backup files.
~$
\.gz$
\.old$
\.bak$
\.swp$

 view release on metacpan or  search on metacpan

lib/Bitcoin/Crypto/Key/ExtPrivate.pm  view on Meta::CPAN

=head1 DESCRIPTION

This class allows you to create an extended private key instance. Extended keys
can be used to securely generate as many addresses as needed through key
derivation. This allows for long-term, reusable wallet with a single backup.

Moreover, you can use an extended private key to:

=over

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ppport.h  view on Meta::CPAN

av_top_index|5.017009|5.003007|p
av_top_index_skip_len_mg|5.025010||Viu
av_undef|5.003007|5.003007|
av_unshift|5.003007|5.003007|
ax|5.003007|5.003007|
backup_one_GCB|5.025003||Viu
backup_one_LB|5.023007||Viu
backup_one_SB|5.021009||Viu
backup_one_WB|5.021009||Viu
bad_type_gv|5.019002||Viu
bad_type_pv|5.016000||Viu
BADVERSION|5.011004||Viu
BASEOP|5.003007||Viu
BhkDISABLE|5.013003||xV

 view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

    [Improvements]
    - Major refactoring
0.009
    - fix minor documentation bugs
    - tuple signature check
    - remove tidy backup and cache
0.008
    - private methods, correct package name
0.007
    - remove required test dependencies
0.006

 view release on metacpan or  search on metacpan

MANIFEST  view on Meta::CPAN

src/boost/utility/value_init.hpp
src/boost/variant/apply_visitor.hpp
src/boost/variant/detail/apply_visitor_binary.hpp
src/boost/variant/detail/apply_visitor_delayed.hpp
src/boost/variant/detail/apply_visitor_unary.hpp
src/boost/variant/detail/backup_holder.hpp
src/boost/variant/detail/bool_trait_def.hpp
src/boost/variant/detail/bool_trait_undef.hpp
src/boost/variant/detail/cast_storage.hpp
src/boost/variant/detail/config.hpp
src/boost/variant/detail/enable_recursive_fwd.hpp

 view release on metacpan or  search on metacpan

MANIFEST  view on Meta::CPAN

include/boost/variant/apply_visitor.hpp
include/boost/variant/bad_visit.hpp
include/boost/variant/detail/apply_visitor_binary.hpp
include/boost/variant/detail/apply_visitor_delayed.hpp
include/boost/variant/detail/apply_visitor_unary.hpp
include/boost/variant/detail/backup_holder.hpp
include/boost/variant/detail/bool_trait_def.hpp
include/boost/variant/detail/bool_trait_undef.hpp
include/boost/variant/detail/cast_storage.hpp
include/boost/variant/detail/config.hpp
include/boost/variant/detail/enable_recursive.hpp

 view release on metacpan or  search on metacpan

lib/Bot/BasicBot/Pluggable/Module/Excuse.pm  view on Meta::CPAN

SIMM crosstalk.
IRQ dropout
Collapsed Backbone
Power company testing new voltage spike (creation) equipment
operators on strike due to broken coffee machine
backup tape overwritten with copy of system manager's favourite CD
UPS interrupted the server's power
The electrician didn't know what the yellow cable was so he yanked the ethernet out.
The keyboard isn't plugged in
The air conditioning water supply pipe ruptured over the machine room
The electricity substation in the car park blew up.

lib/Bot/BasicBot/Pluggable/Module/Excuse.pm  view on Meta::CPAN

Change your language to Finnish.
Fluorescent lights are generating negative ions. If turning them off doesn't work, take them out and put tin foil on the ends.
High nuclear activity in your area.
What office are you in? Oh, that one.  Did you know that your building was built over the universities first nuclear research site? And wow, aren't you the lucky one, your office is right over where the core is buried!
The MGs ran out of gas.
The UPS doesn't have a battery backup.
Recursivity.  Call back if it happens again.
Someone thought The Big Red Button was a light switch.
The mainframe needs to rest.  It's getting old, you know.
I'm not sure.  Try calling the Internet's head office -- it's in the book.
The lines are all busy (busied out, that is -- why let them in to begin with?).

lib/Bot/BasicBot/Pluggable/Module/Excuse.pm  view on Meta::CPAN

Root name servers corrupted.
Budget cuts forced us to sell all the power cords for the servers.
Someone hooked the twisted pair wires into the answering machine.
Operators killed by year 2000 bug bite.
We've picked COBOL as the language of choice.
Operators killed when huge stack of backup tapes fell over.
Robotic tape changer mistook operator's tie for a backup tape.
Someone was smoking in the computer room and set off the halon systems.
Your processor has taken a ride to Heaven's Gate on the UFO behind Hale-Bopp's comet.
it's an ID-10-T error
Dyslexics retyping hosts file on servers
The Internet is being scanned for viruses.

 view release on metacpan or  search on metacpan

lib/Bot/BasicBot/Pluggable/Module/Notify.pm  view on Meta::CPAN

Each line in the file should consist of 3 fields. The first being the 'nick', 
the second being the ident of the account connection, and the third being the 
email address to send mail to.

The connection ident is optional, and only used as a backup check in the event 
that the user may be roaming and their nick may be automatically switched to 
something like '_barbie' instead of 'barbie'. An connection ident is used 
within a regex pattern, but should not be a regex itself. Any regex characters
will be treated as literal string characters.

 view release on metacpan or  search on metacpan

bin/bot-basicbot-pluggable-infobot-upgrade  view on Meta::CPAN

unless (-e "Infobot.storable") {
  die "I can't see Infobot.storable in ./\n";
}

if (-e "Infobot.storable.backup") {
  die "There's already a backup of Infobot.storable in ./\n";
}

cp("Infobot.storable", "Infobot.storable.backup")
  or die "Can't back up Infobot.storable: $!\n";

unless (-s "Infobot.storable" == -s "Infobot.storable.backup") {
  die "Infobot.storable backup isn't the same size!\n"
}

my $data = retrieve("Infobot.storable")
  or die "Can't load Infobot.storable for some reason\n";

 view release on metacpan or  search on metacpan

MANIFEST.SKIP  view on Meta::CPAN

\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$

# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$

 view release on metacpan or  search on metacpan

COPYRIGHT  view on Meta::CPAN

 examples/classes/Admin/apt/init.yml
 examples/classes/Admin/apt/popcon.yml
 examples/classes/Admin/apt/tools/changes.yml
 examples/classes/Admin/apt/tools/init.yml
 examples/classes/Admin/auto.yml
 examples/classes/Admin/backup/init.yml
 examples/classes/Admin/backup/remote.yml
 examples/classes/Admin/base.yml
 examples/classes/Admin/disk/lvm.yml
 examples/classes/Admin/etc/functions.yml
 examples/classes/Admin/etc/track.yml
 examples/classes/Admin/harden/account/init.yml

 view release on metacpan or  search on metacpan

lib/Brackup/Target/Gmail.pm  view on Meta::CPAN

# returns bool
sub has_chunk {
    my ($self, $chunk) = @_;
    my $dig = $chunk->backup_digest;   # "sha1:sdfsdf" format scalar

    if (my $dbh = $self->{dbh}) {
        my $ans = $dbh->selectrow_array("SELECT COUNT(*) FROM ${CACHE_TABLE} WHERE key=?", undef, $dig);
        warn "gmail database for $dig is = $ans\n";
        return 1 if $ans;

lib/Brackup/Target/Gmail.pm  view on Meta::CPAN

sub store_chunk {
    my ($self, $chunk) = @_;
    my ($fh, $filename) = tempfile( UNLINK => 1 );
    print $fh ${ $chunk->chunkref };
    close($fh);
    $self->{_gmail}->store($filename, $chunk->backup_digest);
}

sub store_backup_meta {
    my ($self, $name, $file) = @_;
    my ($fh, $filename) = tempfile( UNLINK => 1 );
    print $fh $file;
    close($fh);
    $self->{_gmail}->store($filename, $name);

 view release on metacpan or  search on metacpan

lib/Brackup.pm  view on Meta::CPAN

__END__

=head1 NAME

Brackup - Flexible backup tool.  Slices, dices, encrypts, and sprays across the net.

=head1 FURTHER READING

L<Brackup::Manual::Overview>

 view release on metacpan or  search on metacpan

t/05-defaults.t  view on Meta::CPAN

# Test that defaults don't apply to required parameters that fail
$b->register_schema('required_no_default', {
    params => {
        name => { required => 1 },
        backup_name => { default => 'unnamed' }
    }
});

{
    my $params = {}; # Missing required name
    my $rejects = $b->process('required_no_default', $params);
    is($rejects, { name => { required => 1 } }, 'Required parameter failure');
    is($params->{backup_name}, 'unnamed', 'Default still applied to non-required params');
}

# Edge case: empty string and zero values should not trigger defaults
$b->register_schema('edge_cases', {
    params => {

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README.pod  view on Meta::CPAN

the source repository: L<https://github.com/briandfoy/brick>

If you find a problem, file a ticket in the L<issue
tracker|https://github.com/briandfoy/brick/issues>.

There are also backup repositories hosted on other services. These
reflect the state of the main repo and exist only for redundancy:

=over 4

=item * L<https://bitbucket.com/briandfoy/brick>

 view release on metacpan or  search on metacpan

MANIFEST.SKIP  view on Meta::CPAN

\bbuild.com$

# and Module::Build::Tiny generated files
\b_build_params$

# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$

 view release on metacpan or  search on metacpan

MANIFEST.SKIP  view on Meta::CPAN

\bBuild.bat$
\bBuild.COM$
\bBUILD.COM$
\bbuild.com$

# Avoid temp and backup files.
~$
\.old$
\#$
\b\.#
\.bak$