view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use File::Path ();
use FindBin;
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
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lib/Bio/BioVeL/AsynchronousService.pm view on Meta::CPAN
package Bio::BioVeL::AsynchronousService;
use strict;
use warnings;
use File::Path 'make_path';
use Scalar::Util 'refaddr';
use Bio::BioVeL::Service;
lib/Bio/BioVeL/AsynchronousService.pm view on Meta::CPAN
use constant DONE => 'done';
use constant ERROR => 'error';
=head1 NAME
Bio::BioVeL::AsynchronousService - base class for asynchronous web services
=head1 SYNOPSIS
use Bio::BioVeL::AsynchronousService::Mock; # example class
# this static method returns a writable directory into which
# service objects are persisted between request/response cycles
my $wd = Bio::BioVeL::AsynchronousService::Mock->workdir;
# when instantiating objects, values for the 'parameters' that are defined
# in their constructors can be provided as named arguments
my $mock = Bio::BioVeL::AsynchronousService::Mock->new( 'seconds' => 1 );
# every async service has a record of when it started
my $epoch_time = $mock->timestamp;
# can be RUNNING, ERROR or DONE
if ( $mock->status eq Bio::BioVeL::AsynchronousService::DONE ) {
print $mock->response_body;
}
=head1 DESCRIPTION
Asynchronous services need to subclass this class and implement at least the following
methods: C<launch> and C<response_body>. The parent class makes sure that launch()
forks off a process and returns immediately with enough information, stored as object
properties, so that update() can check how things are going and update the status().
Once the status set to C<DONE>, C<response_body> is executed to generate the output.
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lib/Bio/Chado/Schema/Test.pm view on Meta::CPAN
if ($args{storage_type}) {
$schema->storage_type($args{storage_type});
}
$schema = $schema->connect($self->_database(%args));
$schema->storage->on_connect_do(['PRAGMA synchronous = OFF']) unless $self->has_custom_dsn;
unless ( -e _sqlite_dbfilename() ) {
__PACKAGE__->deploy_schema( $schema, $args{deploy_args} ) if $should_deploy;
__PACKAGE__->populate_schema( $schema ) if $args{populate};
}
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lib/Bio/DB/GenBank.pm view on Meta::CPAN
Function: Gets a Seq object by accession numbers
Returns : a Bio::Seq object
Args : the accession number as a string
Note : For GenBank, this just calls the same code for get_Seq_by_id().
Caveat: this normally works, but in rare cases simply passing the
accession can lead to odd results, possibly due to unsynchronized
NCBI ID servers. Using get_Seq_by_version() is slightly better, but
using the unique identifier (GI) and get_Seq_by_id is the most
consistent
Throws : "id does not exist" exception
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lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
This method is the back end for fetch(). It accepts a primary_id and
returns a feature object. It must be implemented by the adaptor.
In practice, the implementation will retrieve the serialized
Bio::SeqfeatureI object from the database and pass it to the thaw()
method to unserialize it and synchronize the primary_id.
=cut
# _fetch($id)
sub _fetch { shift->throw_not_implemented }
view release on metacpan or search on metacpan
lib/Bio/DB/Taxonomy/sqlite.pm view on Meta::CPAN
# down the way
my $dbh = DBI->connect("dbi:SQLite:dbname=$db_name","","") or die $!;
$self->debug("Running SQLite version:".$dbh->{sqlite_version}."\n");
#$dbh->do('PRAGMA synchronous = 0'); # Non transaction safe!!!
if ($self->cache_size) {
my $cs = $self->cache_size;
$self->debug("Setting cache size $cs\n");
$dbh->do("PRAGMA cache_size = $cs")
lib/Bio/DB/Taxonomy/sqlite.pm view on Meta::CPAN
$self->debug("Creating taxon name table index\n");
$dbh->do("CREATE INDEX taxon_name_idx ON names (taxon_id)") or $self->throw($dbh->errstr);
$dbh->do("PRAGMA foreign_keys = ON");
#$dbh->do('PRAGMA synchronous = 1');
$self->{dbh} = $dbh;
$self->{'_initialized'} = 1;
}
1;
}
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inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
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inc/Module/Install.pm view on Meta::CPAN
use 5.004;
use strict 'vars';
use vars qw{$VERSION};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
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lib/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm view on Meta::CPAN
# Retrieve the newly assigned dbID
my $rp_dbID = $self->last_insert_id('rnaproduct_id', undef, 'rnaproduct');
# Store attributes
$rnaproduct->synchronise_attributes();
my $attr_adaptor = $db->get_AttributeAdaptor();
$attr_adaptor->store_on_RNAProduct($rp_dbID,
$rnaproduct->get_all_Attributes());
# Store xrefs
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GMOD/Admin/Update.pm view on Meta::CPAN
=item $mod->prepare_tmp_dir(@options)
Options:
-tmp_path full path to a temporary download directory
-sync_to site to synchronize to (live || dev)
Prepare the temporary directory for downloading. The temporary
directory is supplied by Bio::GMOD::Adaptor::* or can be overridden by
passing a "-tmp_path=" option. If provided with
"-sync_to=[live|dev]", this method will prepare a temporary directory
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data/controlled_vocab/SMP_DevelopmentStageName.xml view on Meta::CPAN
<controlled_vocabulary db_table="Sample" db_column="dev_stage_name" cv_table="SMP_DevelopmentStageName">
<comment type="definition">This table provides the restricted vocabulary for the column developmental stage name in the table sample and is used to provide the stage as agreed upon by researchers in the particular field unless there is a more gener...
</comment>
<term name="stationary_phase"
description="appropriate to single-celled organisms"/>
<term name="synchronized_g0"
description="appropriate to single-celled organisms"/>
<term name="synchronized_g1"
description="appropriate to single-celled organisms"/>
<term name="synchronized_s1"
description="appropriate to single-celled organisms"/>
<term name="synchronized_g2"
description="appropriate to single-celled organisms"/>
<term name="synchronized_m_phase"
description="appropriate to single-celled organisms"/>
<term name="early_log"
description="appropriate to single-celled organisms"/>
<term name="mid_log"
description="appropriate to single-celled organisms"/>
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inc/Module/Install.pm view on Meta::CPAN
use 5.004;
use strict 'vars';
use vars qw{$VERSION};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
or alternatively
http://www.ensembl.org/info/docs/api/api_cvs.html
B<NOTE 1 - > The Ensembl Vertebrate and Ensembl Genomes DB releases are usually not synchronised: an Ensembl Genomes DB release usually follows the corresponding Ensembl Vertebrates
release by a number of weeks. This means that if you install a bleeding-edge Ensembl Vertebrate API, while the corresponding Ensembl Vertebrate DB will exist, I<a matching EnsemblGenomes DB release might
not be available yet>: you will still be able to use C<Bio::Homology::InterologWalk> to run an orthology walk using exclusively Ensembl Vertebrate DBs, but you
will get an error if you try to choose an Ensembl Genomes databases. In such cases, please install the most recent API compatible with Ensembl Genomes Metazoa, from
http://metazoa.ensembl.org/info/docs/api/api_installation.html
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
lib/Bio/Palantir/Parser/Root.pm view on Meta::CPAN
}
# fix antiSMASH 5.1 and its module delineation
if ($self->_root->{modulelist}) { # Add new module feature from version 5.1
# TODO see how synchronize domain rank in @genes and @modules
my @cluster_modules =
sort {$a->genomic_prot_begin <=> $b->genomic_prot_begin }
grep { $_->genomic_dna_begin < $end
&& $_->genomic_dna_end > $begin }
@modules;
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
Bio/DB/GenBank.pm view on Meta::CPAN
Function: Gets a Seq object by accession numbers
Returns : a Bio::Seq object
Args : the accession number as a string
Note : For GenBank, this just calls the same code for get_Seq_by_id().
Caveat: this normally works, but in rare cases simply passing the
accession can lead to odd results, possibly due to unsynchronized
NCBI ID servers. Using get_Seq_by_version() is slightly better, but
using the unique identifier (GI) and get_Seq_by_id is the most
consistent
Throws : "id does not exist" exception
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lib/BioX/Workflow/Plugin/Drake.pm view on Meta::CPAN
=head1 SYNOPSIS
The main documentation for this module is at L<BioX::Workflow>. This module extends Workflow in order to add functionality for outputing workflows in drake format.
biox-workflow.pl --workflow workflow.yml > workflow.drake
drake --workflow workflow.drake #with other functionality such as --jobs for asynchronous output, etc.
List your plugins in your workflow.yml file
---
plugins:
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inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use 5.004;
use strict 'vars';
use vars qw{$VERSION};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use 5.004;
use strict 'vars';
use vars qw{$VERSION};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use 5.004;
use strict 'vars';
use vars qw{$VERSION};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
.idea/dbnavigator.xml view on Meta::CPAN
<mapping file-type-id="TYPE_BODY" extensions="tpb" />
</extensions>
<general>
<lookup-ddl-files value="true" />
<create-ddl-files value="false" />
<synchronize-ddl-files value="true" />
<use-qualified-names value="false" />
<make-scripts-rerunnable value="true" />
</general>
</ddl-file-settings>
<general-settings>
view release on metacpan or search on metacpan
- overcame MOJO_MAX_WEBSOCKET_SIZE limit for server-to-client messages
v0.0.7 2021-01-31T06:21:58Z
- fixed potential synchronicity issue
v0.0.6 2021-01-30T11:40:02Z
- overcame pg notify payload size limit
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inc/Module/Install.pm view on Meta::CPAN
use File::Find ();
use File::Path ();
use vars qw{$VERSION $MAIN};
BEGIN {
# All Module::Install core packages now require synchronised versions.
# This will be used to ensure we don't accidentally load old or
# different versions of modules.
# This is not enforced yet, but will be some time in the next few
# releases once we can make sure it won't clash with custom
# Module::Install extensions.
view release on metacpan or search on metacpan
src/boost/graph/distributed/crauser_et_al_shortest_paths.hpp view on Meta::CPAN
{
inherited::collect();
// If there are no suitable messages, wait until we get something
while (!has_suitable_vertex()) {
if (do_synchronize()) return true;
}
// Return true only if nobody has any messages; false if we
// have suitable messages
return false;
}
bool do_synchronize()
{
using boost::parallel::all_reduce;
using boost::parallel::minimum;
inherited::synchronize();
// TBD: could use combine here, but then we need to stop using
// minimum<distance_type>() as the function object.
distance_type local_distances[2];
local_distances[0] =
src/boost/graph/distributed/crauser_et_al_shortest_paths.hpp view on Meta::CPAN
put(min_in_weight, target(e, g), get(weight, e));
}
}
using boost::graph::parallel::process_group;
synchronize(process_group(g));
// Replace any infinities with zeros
BGL_FORALL_VERTICES_T(v, g, Graph) {
if (get(min_in_weight, v) == inf) put(min_in_weight, v, 0);
}
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include/boost/detail/atomic_count.hpp view on Meta::CPAN
// Returns: (long) zero if the new value of a is zero,
// unspecified non-zero value otherwise (usually the new value)
//
// Important note: when --a returns zero, it must act as a
// read memory barrier (RMB); i.e. the calling thread must
// have a synchronized view of the memory
//
// On Intel IA-32 (x86) memory is always synchronized, so this
// is not a problem.
//
// On many architectures the atomic instructions already act as
// a memory barrier.
//
// This property is necessary for proper reference counting, since
// a thread can update the contents of a shared object, then
// release its reference, and another thread may immediately
// release the last reference causing object destruction.
//
// The destructor needs to have a synchronized view of the
// object to perform proper cleanup.
//
// Original example by Alexander Terekhov:
//
// Given:
//
// - a mutable shared object OBJ;
// - two threads THREAD1 and THREAD2 each holding
// a private smart_ptr object pointing to that OBJ.
//
// t1: THREAD1 updates OBJ (thread-safe via some synchronization)
// and a few cycles later (after "unlock") destroys smart_ptr;
//
// t2: THREAD2 destroys smart_ptr WITHOUT doing any synchronization
// with respect to shared mutable object OBJ; OBJ destructors
// are called driven by smart_ptr interface...
//
#include <boost/config.hpp>