view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

    - Fixed Segment features method to support API needed for GBrowse2
    - Fixed a bug that caused CDS inferrence to fail for single exon
      genes that have either a 5' or 3' UTR (but not both) to fail

0.22 Thu May 28 15:53:03 EDT 2009
    - Added a rel2abs method to the Segment feature so that uploaded
      annotations will work correctly.

0.23 Thu Jun  4 11:55:24 EDT 2009
    - Fixes to accomidate changes to the Chado GFF3 loader; there is still
      an outstanding bug associated with searching when the same ID

 view release on metacpan or  search on metacpan

bin/bp_bulk_load_gff  view on Meta::CPAN

The nature of the bulk load requires that the database be on the local
machine and that the indicated user have the "file" privilege to load
the tables and have enough room in /usr/tmp (or whatever is specified
by the \$TMPDIR environment variable), to hold the tables transiently.

Local data may now be uploaded to a remote server via the --local option
with the database host specified in the dsn, e.g. dbi:mysql:test:db_host

The adaptor used is dbi::mysqlopt.  There is currently no way to
change this.

 view release on metacpan or  search on metacpan

lib/Bio/Das/ProServer/SourceHydra.pm  view on Meta::CPAN

The SourceHydra's role is to clone a series of SourceAdaptors of the
same type but each configured in a (systematically) different way, but
with only one configuration file section.

For example the hydra is pivotal in the Ensembl upload service where
each data upload is of the same structure and loaded into a numbered
table in a database. In order to provide a valid DSN for each uploaded
source, the hydra then clones a series of dbi-based sources, pointing
them all at the upload database but each one at a different table.

The hydra can also be useful in situations such as the provision of
similar sources for different species where the data are in different
databases but have the same structure in each.

 view release on metacpan or  search on metacpan

lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm  view on Meta::CPAN

  return ($feature, $seq_region_id);
}


# The same function as _pre_store
# This one is used to store user uploaded features in XXX_userdata db

sub _pre_store_userdata {
  my $self    = shift;
  my $feature = shift;

 view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

0.07  2014-01-05T23:42:11
    - switch to Dist::Zilla

0.06  2004-03-05T07:59:23
    - a bug in my upload tool included the distro in the
      archive. this is now fixed...
    - switched to Artistic License 2.0
    - removed Exporter as dependency

0.05  2004-03-04T07:59:23

 view release on metacpan or  search on metacpan

lib/Bio/Glite.pm  view on Meta::CPAN

our $VERSION = '0.10';

# Preloaded methods go here.

my $prefix  = 'http://rest.g-language.org/';
my $upload  = $prefix . 'upload/upl.pl';
my $ua = LWP::UserAgent->new;

sub load {
    my $this = {};

    $_[0] =  $ua->post($upload, 'Content_Type'=>'form-data', 'Content'=>['file'=>[$_[0]]])->content if(-e $_[0]);

    foreach my $line (split(/\n/, $ua->get($prefix . $_[0] . '/disclose')->content)){
	my ($feat, $key, $val) = split(/\t/, $line);
	if(length $val){
	    $this->{$feat}->{$key} = $val;

 view release on metacpan or  search on metacpan

lib/Bio/Graphics/Wiggle/Loader.pm  view on Meta::CPAN

package Bio::Graphics::Wiggle::Loader;

=head1 SYNOPSIS

  my $loader = Bio::Graphics::Wiggle::Loader->new('/base/directory/for/wigfiles','wibfilename');
  my $fh = IO::File->new('uploaded_file.txt');
  $loader->load($fh);

  my $gff3_file   = $loader->featurefile('gff3',$method,$source);
  my $featurefile = $loader->featurefile('featurefile');
  my @features    = $loader->features();

 view release on metacpan or  search on metacpan

lib/Bio/MUST/Apps/FortyTwo/Manual.pod  view on Meta::CPAN

# Set reference banks suffix
# Set trim_max_shift
# Set candiate banks suffix
# En fait, il y a plus d'explications dans le fichier yaml lui-même, mais puisqu'on ne l'a pas encore quand on lance le premier wizzard, il faudrait que les explications arrivent plus tôt, soit dans le manuel soit dans le wizzard
# 
# [DONE] 6. Si je prépare un fichier config localement pour ensuite l'uploader sur un cluster, si je veux indiquer le path vers le dossier qui contient les génomes de référence, ou vers les génomes à miner sur le cluster, je vais me retrouver a...

__END__

=pod

lib/Bio/MUST/Apps/FortyTwo/Manual.pod  view on Meta::CPAN

C<ref_bank_suffix> options, respectively. If your banks are built from protein
sequences, use C<.psq>; otherwise, for nucleotide sequences, use C<.nsq>.

Because of this scanning behavior, it is better to prepare your files directly
on the computer on which you plan to run C<42>. If you try to prepare your
C<config> file locally (for subsequent upload on a remote computer), it is very
likely that the wizard complains about some directories not being found.

=head3 Command-line options

Since the configuration (C<config>) file specifies all the details, running

 view release on metacpan or  search on metacpan

bin/export-itol.pl  view on Meta::CPAN

=item <infiles>

Path to input TSV tree id files [repeatable argument].

Such files are generated when uploading trees with the script L<import-itol.pl>.

=for Euclid: infiles.type: readable
    repeatable

=back

 view release on metacpan or  search on metacpan

lib/Bio/Maxd.pm  view on Meta::CPAN

                  -experiment=>'experimentName', -array_type=>'geneChipName');
  $maxd_db->disconnect();

=head1 DESCRIPTION

B<Bio::Maxd> provides methods for uploading and retrieving
data to/from a maxd (MySQL) database.

"maxd" is a data warehouse and visualization environment for microarray
expression data developed by the Microarray Group at
Manchester Bioinformatics (http://www.bioinf.man.ac.uk/microarray/)

 view release on metacpan or  search on metacpan

lib/Bio/NEXUS/Tools/NexPlotter.pm  view on Meta::CPAN

	my $table_name = ($dir_param eq 'pandit') ? 'sptr_taxa' : 'cds';
	my $field_name = ($dir_param eq 'pandit') ? 'sptr_id' : 'prot_id';
	my $search_cond=($dir_param eq 'pandit') ? "= ?" : "like ?";
	my $sql_statement; 

	if($dir_param eq 'uploads') {
		$sql_statement=qq{ 
			SELECT kingdom,name
				from taxon_name 
				where name_class='scientific name' and
				taxon_id= ? limit 10};

lib/Bio/NEXUS/Tools/NexPlotter.pm  view on Meta::CPAN

		protist		   => lc $runtime_options->{'kingdom'}->{'protist'}
	};
	for my $taxlabel (@$taxlabels) {
		my $taxlabel_tmp=(split(/\//,$taxlabel))[0];
		(my $id=$taxlabel_tmp)=~s/^.*_//g;
		if ($dir_param eq 'uploads') {
## some conditions
		}else {
			chop($id) if ($dir_param eq 'NEXUS' or  $dir_param eq 'uploads');
			chop($id) if ($dir_param eq 'NEXUS' or $dir_param eq 'uploads');
			$id = ($dir_param eq 'pandit') ? $id : "$id%";
		}
		my $sth 	= $dbh->prepare($sql_statement) || die "Can't prepare statement: $DBI::errstr"; 
		my $rc 		= $sth->execute($id) || die "Can't execute statement: $DBI::errstr";
		my $num_of_rows = $sth->rows;

 view release on metacpan or  search on metacpan

lib/Bio/Phylo/CIPRES.pm  view on Meta::CPAN

=over

=item * B<Launch a job>
This is done by issuing an HTTP POST request that includes: 1) HTTP authentication (i.e.
a user name and password that is registered to the realm), 2) uploading input data, 3)
configuration options for the job. The result value is an XML document that reports the
status. If all goes well, this will report that the job was launched successfully, and it
gives a URL to visit to check up on the status.

=item * B<Check job status>

 view release on metacpan or  search on metacpan

contrib/roary_plots/roary.html  view on Meta::CPAN

<style type="text/css">
    /*!
*
* Twitter Bootstrap
*
*//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary...
*
* Font Awesome
*
*//*!
 *  Font Awesome 4.3.0 by @davegandy - http://fontawesome.io - @fontawesome
 *  License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License)
 */@font-face{font-family:'FontAwesome';src:url('../components/font-awesome/fonts/fontawesome-webfont.eot?v=4.3.0');src:url('../components/font-awesome/fonts/fontawesome-webfont.eot?#iefix&v=4.3.0') format('embedded-opentype'),url('../components/font...
*
* IPython base
*
*/.modal.fade .modal-dialog{-webkit-transform:translate(0, 0);-ms-transform:translate(0, 0);-o-transform:translate(0, 0);transform:translate(0, 0)}code{color:#000}pre{font-size:inherit;line-height:inherit}label{font-weight:normal}.border-box-sizing{b...
*

contrib/roary_plots/roary.html  view on Meta::CPAN

*
*/.center-nav{display:inline-block;margin-bottom:-4px}/*!
*
* IPython tree view
*
*/.alternate_upload{background-color:none;display:inline}.alternate_upload.form{padding:0;margin:0}.alternate_upload input.fileinput{display:inline;opacity:0;z-index:2;width:12ex;margin-right:-12ex}.alternate_upload .input-overlay{display:inline-bloc...
*
* IPython text editor webapp
*
*/.selected-keymap i.fa{padding:0 5px}.selected-keymap i.fa:before{content:"\f00c"}#mode-menu{overflow:auto;max-height:20em}.edit_app #header{-webkit-box-shadow:0 0 12px 1px rgba(87,87,87,0.2);box-shadow:0 0 12px 1px rgba(87,87,87,0.2)}.edit_app #men...
*

 view release on metacpan or  search on metacpan

lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

  #check arguments
  croak ("ERROR [$this_function] \$fasta_path does not exist\n") 
    unless (-e $fasta_path);
  croak ("ERROR [$this_function] \$basedir does not exist\n") 
    unless (-d $basedir);
  croak ("ERROR [$this_function]: no URL (network location for upload to UCSC) provided") 
    unless(defined $baseURL);

  unless ($baseURL =~ /\/$/) { $baseURL .= "/"; }

  my $tmp_path = dist_file('Bio-ViennaNGS', "hub.txt" );

lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

  #check arguments
  croak ("ERROR [$this_function] \no species provided\n")
    unless ($species);
  croak ("ERROR [$this_function] \$basedir does not exist\n")
    unless (-d $basedir);
  croak ("ERROR [$this_function]: no URL (network location for upload to UCSC) provided")
    unless(defined $baseURL);

  if (defined $log){
    open(LOG, ">>", $log) or croak "$!";
  }

lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

=item 1 chromosome id as used in existing ucsc assembly hub (e.g. chr1)

=item 2 path to the ouput directory (e.g. /home/user/assemblyhubs/)

=item 3 base URL where the output folder will be placed for upload to the UCSC genome browser (e.g. http://www.foo.com/folder/)

=item 4 path for the log file (/home/user/logs/assemblyhubconstructionlog)

=back

 view release on metacpan or  search on metacpan

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

}

=head1 compress

The C<compress> action bundles the ASN.1 files produced by C<Bio::WGS2NCBI/convert> into
a .tar.gz archive that can be uploaded to NCBI. This requires the following configuration 
settings:

=over

=item C<outdir>

 view release on metacpan or  search on metacpan

lib/Bio/WebService/LANL/SequenceLocator/Server.pm  view on Meta::CPAN

                return $self->locate_sequences_from_fasta($fasta, $base, $format);
            },
            sub (*fasta=) {
                my ($self, $fasta) = @_;
                return error(422 => $fasta->reason)
                    unless $fasta->is_upload;
                return $self->locate_sequences_from_fasta(path($fasta->path)->slurp, $base, $format);
            },
            sub (%@sequence~) {
                my ($self, $sequences) = @_;
                return $self->locate_sequences($sequences, $base, $format);

 view release on metacpan or  search on metacpan

scripts/biosql/load_ontology.pl  view on Meta::CPAN

one is found by lookup, removing and re-adding has essentially the
same result as leaving it untouched).

=item --noobsolete

Flag to exclude from upload terms marked as obsolete. Note that with
this flag, any update, removal, or object merge that you specify using
other parameters will not apply to obsolete terms. I.e., if you have
terms existing in your database that are marked as obsolete in the
input file, using this flag will prevent the existing terms from being
updated to reflect the obsolete status. Therefore, this flag is best

scripts/biosql/load_ontology.pl  view on Meta::CPAN

Note that relationships found in the input file(s) that reference an
obsolete term will be omitted from loading with this flag in effect.

=item --updobsolete

Flag to exclude from upload terms marked as obsolete unless they are
already present in the database. If they are, they will be updated,
and the --mergeobjs procedure will apply. If they are not, they will
be treated as if --noobsolete had been specified. Note that
relationships will not be updated for obsolete terms.

scripts/biosql/load_ontology.pl  view on Meta::CPAN

        $ont->name($namespace) unless $ont->name();
        
        print STDERR "Loading ontology ",$ont->name(),":\n\t... terms\n";

        # in order to allow callbacks to the user and generally a
        # better ability to interfere with and customize the upload
        # process, we load all terms first here instead of simply
        # going for the relationships

        foreach my $term ($ont->get_all_terms()) {
            # call the persistence handler - there is only one right now

 view release on metacpan or  search on metacpan

scripts/Bio-DB-GFF/bp_bulk_load_gff.pl  view on Meta::CPAN

The nature of the bulk load requires that the database be on the local
machine and that the indicated user have the "file" privilege to load
the tables and have enough room in /usr/tmp (or whatever is specified
by the \$TMPDIR environment variable), to hold the tables transiently.

Local data may now be uploaded to a remote server via the --local option
with the database host specified in the dsn, e.g. dbi:mysql:test:db_host

The adaptor used is dbi::mysqlopt.  There is currently no way to
change this.

 view release on metacpan or  search on metacpan

Build.PL  view on Meta::CPAN

    my $tarball = $self->dist_dir() . '.tar.gz';
    die "tarball not found"
        if (! -e $tarball);
    print "Uploading $tarball\n";
    CPAN::Uploader->upload_file( $tarball, {
        user     => $ENV{PAUSE_USER},
        password => $ENV{PAUSE_PASS},
    } );
}
SUBCLASS

 view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

0.11  2016-08-31 20:09:59 GST
    - Bugfix for filedetails - no basename was causing it to crash

0.10  2016-06-17 08:53:13 GST

    - Made more changes to formatting for easy upload to JIRA

0.09  2016-06-17 08:49:31 GST
    - Bugfix in filedetails.pl added predicate has_line_count
    - Changed format of output

 view release on metacpan or  search on metacpan

README  view on Meta::CPAN

Credits:
--------

Many thanks to Andreas Koenig <andreas.koenig@mind.de> (as always!)
for his relentless support and efforts as upload manager of the CPAN!

Also many thanks to Jon Orwant <orwant@media.mit.edu> and Tim Bunce
<Tim.Bunce@ig.co.uk> for their suggestions concerning this module's
name and its implementation!

 view release on metacpan or  search on metacpan

CREDITS.txt  view on Meta::CPAN

Credits:
--------

Many thanks to Andreas Koenig <upload@franz.ww.tu-berlin.de> for his
efforts as upload-manager for the CPAN, his patience, and lots of good
advice and suggestions! Thank you for doing such a tremendous (and time-
consuming) job!!

Also many thanks to David Jenkins <jenkins@sdm.de> for reviewing the
first version of the README file and the man page.

 view release on metacpan or  search on metacpan

script/torrent  view on Meta::CPAN

    my $sep = ($announce =~ /\?/) ? '&' : '?';
    my $url = $announce . $sep
        . 'info_hash='  . uri_escape($info_hash, "^A-Za-z0-9\\-_.!~*'()")
        . '&peer_id='   . uri_escape($peer_id,   "^A-Za-z0-9\\-_.!~*'()")
        . '&port=6881'
        . '&uploaded=0'
        . '&downloaded=0'
        . '&left=' . $left
        . '&compact=1';
    $url .= "&event=$event" if $event;

 view release on metacpan or  search on metacpan

ex/example.pl  view on Meta::CPAN

#     https://developer.bitcoin.org/reference/rpc/getnettotals.html
#
#{
#  "totalbytesrecv": 7137052851,
#  "totalbytessent": 211648636140,
#  "uploadtarget": {
#    "timeframe": 86400,
#    "target": 0
#  }
#}
$nettot = $btc->getnettotals;
$timeframe = $nettot->{uploadtarget}->{timeframe};
print $timeframe;
print "\n";
# 86400

# JSON arrays

 view release on metacpan or  search on metacpan

lib/BlankOnDev/Tutorial/id.pod  view on Meta::CPAN

=item 12.
Perintah C<B<boidev bzr2git bzr-cgit>> - Perintah ini merupakan perintah yang digunakan untuk mengkonversi format repositori bazaar ke format repositori github, berdasarkan nama paket yang sudah terdaftar pada system program B<BlankOnDev>

=item 13.
Perintah C<B<boidev bzr2git git-push>> - Perintah ini merupakan perintah yang digunakan untuk mendorong/upload yang sudah didownload, berdasarkan nama paket yang sudah terdaftar pada system program B<BlankOnDev>

=item 14.
Perintah C<B<boidev bzr2git git-push-new>> - Perintah ini merupakan perintah yang digunakan untuk mendorong/upload yang sudah didownload namum belum dikonversi ke format repositori github, berdasarkan nama paket yang sudah terdaftar pada system progr...

=item 15.
Perintah C<B<boidev bzr2git git-check>> - Perintah ini merupakan perintah yang digunakan untuk validasi repositori yang sudah diupload ke github.

=item 16.
Perintah C<B<boidev bzr2git re-branch>> - Perintah ini merupakan perintah untuk download ulang paket dari bazaar repositori.

=item 17.
Perintah C<B<boidev bzr2git re-gitpush>> - Perintah ini digunakan untuk memperbaiki kesalahan upload paket ke github yang dimana paket belum dilakukan convert format sebelumnya.

=back

=head3 Perintah help

lib/BlankOnDev/Tutorial/id.pod  view on Meta::CPAN

=begin html

<p><center>
<figure>
<img src="https://yusrideb.github.io/BlankOnDev/docs/source/img/pkg-github-no-convert.png" alt="Contoh paket yang diupload tanpa konversi format ke github" />
<figcaption>Gambar 3.1. <b>Contoh paket yang diupload tanpa konversi format ke github</b></figcaption>
</figure>
</center></p>

=end html

Untuk memperbaiki repositori ini, sebenarnya bisa langsung menghapus repositori di akun github, kemudian mengupload ulang paket yang sudah dikonversi ke format git.
Jika hanya 1 paket mungkin tidak masalah, namun jika sudah terdapat repositori yang harus dihapus kemudian diupload ulang ke Github, maka beresiko salah hapus repositori.

Untuk melesaikan permasalahan seperti ini I<BlankOnDev Tools> menyediakan fitur untuk perbaikan repositori github yaitu
dengan cara seperti yang ditunjukkan pada upabab I<L<2.4. Proses Migrasi Paket|https://metacpan.org/pod/distribution/BlankOnDev/lib/BlankOnDev/Tutorial/id.pod#Proses-Migrasi-Paket1>,
bagian L<2.4.1|https://metacpan.org/pod/distribution/BlankOnDev/lib/BlankOnDev/Tutorial/id.pod#Migrasi-Paket-dengan-Metode-Split>
dan bagian L<2.4.2|https://metacpan.org/pod/distribution/BlankOnDev/lib/BlankOnDev/Tutorial/id.pod#Migrasi-Paket-dengan-Skema-One-time>>. berikut Ilustrasi penyelesaian masalah :

lib/BlankOnDev/Tutorial/id.pod  view on Meta::CPAN

=begin html

<p><center>
<figure>
<img src="https://yusrideb.github.io/BlankOnDev/docs/source/img/pkg-github-1-branch.png" alt="Contoh paket yang diupload ke github, namun hanya memilik branch I<master>" />
<figcaption>Gambar 3.4. <b>Contoh paket yang diupload ke github, namun hanya memilik branch I<master></b></figcaption>
</figure>
</center></p>

=end html

 view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

0.004
    [Bug Fixes]
    - fix POD
0.003
    [Bug Fixes]
    - set version to encoder/decoder modules to avoid upload conflict after structure change
0.002
    [Bug Fixes]
    - set cpanfile Test::Fatal correct version
    [Improvements]
    - added clean for encode/decode functions

 view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

0.004
    [Bug Fixes]
    - fix POD
0.003
    [Bug Fixes]
    - set version to encoder/decoder modules to avoid upload conflict after structure change
0.002
    [Bug Fixes]
    - set cpanfile Test::Fatal correct version
    [Improvements]
    - added clean for encode/decode functions

 view release on metacpan or  search on metacpan

Makefile.old  view on Meta::CPAN

	$(RM_RF) inc MANIFEST.bak _build
	$(PERL) -I. "-MModule::Install::Admin" -e "remove_meta()"

reset :: purge

upload :: test dist
	cpan-upload -verbose $(DISTVNAME).tar$(SUFFIX)

grok ::
	perldoc Module::Install

distsign ::

 view release on metacpan or  search on metacpan

lib/Blosxom/Plugin/Web/Request.pm  view on Meta::CPAN

    my $self = shift;
    return $self->{query}->param( shift ) if @_;
    $self->{query}->param;
}

sub upload {
    my ( $self, $field ) = @_;

    $self->{upload} ||= do { 
        require Blosxom::Plugin::Web::Request::Upload;
        my $query = $self->{query};

        my %upload;
        for my $field ( $query->param ) {
            my @uploads;
            for my $fh ( $query->upload($field) ) {
                my $upload = Blosxom::Plugin::Web::Request::Upload->new(
                    fh     => $fh,
                    path   => $query->tmpFileName( $fh ),
                    header => $query->uploadInfo( $fh ),
                );

                push @uploads, $upload;
            }

            $upload{ $field } = \@uploads if @uploads;
        }

        \%upload;
    };

    if ( $field ) {
        if ( my $uploads = $self->{upload}{$field} ) {
            return wantarray ? @{ $uploads } : $uploads->[0];
        }
    }
    else {
        return keys %{ $self->{upload} };
    }

    return;
}

lib/Blosxom/Plugin/Web/Request.pm  view on Meta::CPAN

=item $request->protocol

Returns the protocol (HTTP/1.0 or HTTP/1.1) used for the current request.

=item $request->upload

Returns L<Blosxom::Plugin::Web::Request::Upload> objects.

  my $upload = $request->upload( 'field' );
  my @uploads = $request->upload( 'field' );
  my @fields = $request->upload;

=item $request->is_secure

Returns a Boolean value telling whether connection is secure.

 view release on metacpan or  search on metacpan

lib/BlueCoat/SGOS.pm  view on Meta::CPAN

our %_URL = (
	'archconf_expanded'    => '/archconf_expanded.txt',
	'contentfilter_status' => '/ContentFilter/Status',
	'sysinfo'              => '/SYSINFO',
	'send_command' =>
	  '/Secure/Local/console/install_upload_action/cli_post_setup.txt'
);

our %defaults = (
	'appliancehost'        => 'proxy',
	'applianceport'        => 8082,