Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::DbCmd:

Public Member Functions
public	param_defaults ()

public	fetch_input ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
public	param_defaults ()

public	run ()

public	write_output ()

public Void	complete_early_if_branch_connected ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::Process
public	new ()

public	life_cycle ()

public	say_with_header ()

public	enter_status ()

public	warning ()

public	param_defaults ()

public	fetch_input ()

public	run ()

public	write_output ()

public Bio::EnsEMBL::Hive::Worker	worker ()

public	execute_writes ()

public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection	dbc ()

public Bio::EnsEMBL::Hive::DBSQL::DBConnection	data_dbc ()

public Returns	run_system_command ()

public Bio::EnsEMBL::Hive::AnalysisJob	input_job ()

public	input_id ()

public	param ()

public	param_required ()

public	param_exists ()

public	param_is_defined ()

public	param_substitute ()

public	dataflow_output_id ()

public	dataflow_output_ids_from_json ()

public	throw ()

public This	complete_early ()

public Int	debug ()

public	worker_temp_directory ()

public	cleanup_worker_temp_directory ()

Detailed Description

Synopsis

standaloneJob.pl Bio::EnsEMBL::Hive::RunnableDB::DbCmd -db_conn mysql://ensro@ens-livemirror/ncbi_taxonomy -input_query "SELECT name FROM ncbi_taxa_name WHERE name_class = 'scientific name' AND taxon_id = 9606" --append '["-N"]' -output_file out.dat

Description

    This RunnableDB module acts as a wrapper around a database connection. It interfaces with the database the same way as you would
    on the command line (i.e. with redirections and / or pipes to other commands) but with hive parameters instead.
    The database connection is created from the "data_dbc" parameter, if provided, or the current hive database.

Definition at line 19 of file DbCmd.pm.

Member Function Documentation

◆ fetch_input()

public Bio::EnsEMBL::Hive::RunnableDB::DbCmd::fetch_input ( )

    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
                  Here it deals with finding the command line, doing parameter substitution and storing the result in a predefined place.

    param('cmd'): The recommended way of passing in the command line. It can be either a string, or an array-ref of strings. The later is safer if some of the
                  arguments contain white-spaces.

    param('*'):   Any other parameters can be freely used for parameter substitution.

Code:

click to view

sub fetch_input {
    my $self = shift;
 
    # Validate the arguments
    # There can be only 1 input
    if (not $self->param('executable') and not ($self->param('input_file') or $self->param('input_query') or $self->param('command_in'))) {
        die "No input defined (missing 'input_file', 'input_query' and 'command_in')\n";
    } elsif (($self->param('input_file') and ($self->param('input_query') or $self->param('command_in'))) or ($self->param('input_query') and $self->param('command_in'))) {
        die "Only 1 input ('input_file', 'input_query' and 'command_in') can be defined\n";
    }
    # And 1 output
    if ($self->param('output_file') and $self->param('command_out')) {
        die "'output_file' and 'command_out' cannot be set together\n";
    }
 
    # If there is any of those, system() will need a shell to deal with
    # the pipes / redirections, and we need to hide the passwords
    my $need_a_shell = ($self->param('input_file') or $self->param('command_in') or $self->param('output_file') or $self->param('command_out')) ? 1 : 0;
 
    my @cmd = @{ $self->data_dbc->to_cmd(
        $self->param('executable'),
        [grep {defined $_} @{$self->param('prepend')}],
        [grep {defined $_} @{$self->param('append')}],
        $self->param('input_query'),
        $need_a_shell,
    ) };
 
    # Add the input data
    my $prefix = '';
    if ($self->param('input_file')) {
        push @cmd, '<', $self->param('input_file');
    } elsif ($self->param('input_query')) {
        # the query as already been fed into @cmd by to_cmd()
    } elsif ($self->param('command_in')) {
        $prefix = (join_command_args($self->param('command_in')))[1] . ' | ';
    }
 
    # Add the output data
    my $postfix = '';
    if ($self->param('output_file')) {
        push @cmd, '>', $self->param('output_file');
    } elsif ($self->param('command_out')) {
        $postfix = ' | ' . (join_command_args($self->param('command_out')))[1];
    }
 
    if ($need_a_shell) {
        my ($join_needed, $flat_cmd) = join_command_args(\@cmd);
        $flat_cmd =~ s/ '(\S*\$EHIVE_TMP_PASSWORD_\d+)' / $1 /g;
        $self->param('cmd', $prefix.$flat_cmd.$postfix);
    } else {
        $self->param('cmd', \@cmd);
    }
}

◆ param_defaults()

public Bio::EnsEMBL::Hive::RunnableDB::DbCmd::param_defaults ( )

Undocumented method