Bio-KBase
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lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
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'Annotation' => {
id => 1,
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id => 1,
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'BiomassCompound' => {
id => 1,
'coefficient' => 1,
},
'Compartment' => {
id => 1,
'abbr' => 1,
'mod_date' => 1,
'name' => 1,
'msid' => 1,
},
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id => 1,
'name' => 1,
'msid' => 1,
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},
'Compound' => {
id => 1,
'label' => 1,
'abbr' => 1,
'msid' => 1,
'ubiquitous' => 1,
'mod_date' => 1,
'uncharged_formula' => 1,
'formula' => 1,
'mass' => 1,
},
'Contig' => {
id => 1,
'source_id' => 1,
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'ContigChunk' => {
id => 1,
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lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
=back
=cut
sub all_entities_Complex
{
my $self = shift;
my($start, $count, $fields) = @_;
my @_bad_arguments;
(!ref($start)) or push(@_bad_arguments, "Invalid type for argument \"start\" (value was \"$start\")");
(!ref($count)) or push(@_bad_arguments, "Invalid type for argument \"count\" (value was \"$count\")");
(ref($fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"fields\" (value was \"$fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to all_entities_Complex:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'all_entities_Complex');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN all_entities_Complex
$return = $self->_all_entities($ctx, 'Complex', $start, $count, $fields);
#END all_entities_Complex
my @_bad_returns;
(ref($return) eq 'HASH') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to all_entities_Complex:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'all_entities_Complex');
}
return($return);
}
=head2 get_entity_Compound
$return = $obj->get_entity_Compound($ids, $fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
A compound is a chemical that participates in a reaction. Both
ligands and reaction components are treated as compounds.
It has the following fields:
=over 4
=item label
primary name of the compound, for use in displaying
reactions
=item abbr
shortened abbreviation for the compound name
=item msid
common modeling ID of this compound
=item ubiquitous
TRUE if this compound is found in most reactions, else FALSE
=item mod_date
date and time of the last modification to the
compound definition
=item uncharged_formula
a electrically neutral formula for the compound
=item formula
a pH-neutral formula for the compound
=item mass
atomic mass of the compound
=back
=back
=cut
sub get_entity_Compound
{
my $self = shift;
my($ids, $fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"fields\" (value was \"$fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_entity_Compound:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_entity_Compound');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_entity_Compound
$return = $self->_get_entity($ctx, 'Compound', $ids, $fields);
#END get_entity_Compound
my @_bad_returns;
(ref($return) eq 'HASH') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_entity_Compound:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_entity_Compound');
}
return($return);
}
=head2 query_entity_Compound
$return = $obj->query_entity_Compound($qry, $fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$qry is a reference to a list where each element is a reference to a list containing 3 items:
0: a string
1: a string
2: a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$qry is a reference to a list where each element is a reference to a list containing 3 items:
0: a string
1: a string
2: a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
=back
=cut
sub query_entity_Compound
{
my $self = shift;
my($qry, $fields) = @_;
my @_bad_arguments;
(ref($qry) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"qry\" (value was \"$qry\")");
(ref($fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"fields\" (value was \"$fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to query_entity_Compound:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'query_entity_Compound');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN query_entity_Compound
$return = $self->_query_entity($ctx, 'Compound', $qry, $fields);
#END query_entity_Compound
my @_bad_returns;
(ref($return) eq 'HASH') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to query_entity_Compound:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'query_entity_Compound');
}
return($return);
}
=head2 all_entities_Compound
$return = $obj->all_entities_Compound($start, $count, $fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$start is an int
$count is an int
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$start is an int
$count is an int
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
=back
=cut
sub all_entities_Compound
{
my $self = shift;
my($start, $count, $fields) = @_;
my @_bad_arguments;
(!ref($start)) or push(@_bad_arguments, "Invalid type for argument \"start\" (value was \"$start\")");
(!ref($count)) or push(@_bad_arguments, "Invalid type for argument \"count\" (value was \"$count\")");
(ref($fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"fields\" (value was \"$fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to all_entities_Compound:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'all_entities_Compound');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN all_entities_Compound
$return = $self->_all_entities($ctx, 'Compound', $start, $count, $fields);
#END all_entities_Compound
my @_bad_returns;
(ref($return) eq 'HASH') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to all_entities_Compound:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'all_entities_Compound');
}
return($return);
}
=head2 get_entity_Contig
$return = $obj->get_entity_Contig($ids, $fields)
=over 4
=item Parameter and return types
=begin html
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
msid has a value which is a string
abbr has a value which is a string
equation has a value which is a string
reversibility has a value which is a string
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Reaction
fields_Reaction is a reference to a hash where the following keys are defined:
id has a value which is a string
mod_date has a value which is a string
name has a value which is a string
msid has a value which is a string
abbr has a value which is a string
equation has a value which is a string
reversibility has a value which is a string
=end text
=item Description
A reaction is a chemical process that converts one set of
compounds (substrate) to another set (products).
It has the following fields:
=over 4
=item mod_date
date and time of the last modification to this reaction's
definition
=item name
descriptive name of this reaction
=item msid
common modeling ID of this reaction
=item abbr
abbreviated name of this reaction
=item equation
displayable formula for the reaction
=item reversibility
direction of this reaction (> for forward-only,
< for backward-only, = for bidirectional)
=back
=back
=cut
sub get_entity_Reaction
{
my $self = shift;
my($ids, $fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"fields\" (value was \"$fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_entity_Reaction:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_entity_Reaction');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_entity_Reaction
$return = $self->_get_entity($ctx, 'Reaction', $ids, $fields);
#END get_entity_Reaction
my @_bad_returns;
(ref($return) eq 'HASH') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_entity_Reaction:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_entity_Reaction');
}
return($return);
}
=head2 query_entity_Reaction
$return = $obj->query_entity_Reaction($qry, $fields)
=over 4
=item Parameter and return types
=begin html
<pre>
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
=head2 get_entity_Reagent
$return = $obj->get_entity_Reagent($ids, $fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Reagent
fields_Reagent is a reference to a hash where the following keys are defined:
id has a value which is a string
stoichiometry has a value which is a float
cofactor has a value which is an int
compartment_index has a value which is an int
transport_coefficient has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Reagent
fields_Reagent is a reference to a hash where the following keys are defined:
id has a value which is a string
stoichiometry has a value which is a float
cofactor has a value which is an int
compartment_index has a value which is an int
transport_coefficient has a value which is a float
=end text
=item Description
This entity represents a compound as it is used by
a specific reaction. A reaction involves many compounds, and a
compound can be involved in many reactions. The reagent
describes the use of the compound by a specific reaction.
It has the following fields:
=over 4
=item stoichiometry
Number of molecules of the compound that participate
in a single instance of the reaction. For example, if a
reaction produces two water molecules, the stoichiometry of
water for the reaction would be two. When a reaction is
written on paper in chemical notation, the stoichiometry is
the number next to the chemical formula of the
compound. The value is negative for substrates and positive
for products.
=item cofactor
TRUE if the compound is a cofactor; FALSE if it is a major
component of the reaction.
=item compartment_index
Abstract number that groups this reagent into a
compartment. Each group can then be assigned to real
compartments when doing comparative analysis.
=item transport_coefficient
Number of reagents of this type transported.
A positive value implies transport into the reactions
default compartment; a negative value implies export
to the reagent's specified compartment.
=back
=back
=cut
sub get_entity_Reagent
{
my $self = shift;
my($ids, $fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"fields\" (value was \"$fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_entity_Reagent:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_entity_Reagent');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_entity_Reagent
$return = $self->_get_entity($ctx, 'Reagent', $ids, $fields);
#END get_entity_Reagent
my @_bad_returns;
(ref($return) eq 'HASH') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_entity_Reagent:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_entity_Reagent');
}
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_WasGeneratedFrom:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_WasGeneratedFrom');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_WasGeneratedFrom
$return = $self->_get_relationship($ctx, 'WasGeneratedFrom', 'GeneratedLevelsFor', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_WasGeneratedFrom
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_WasGeneratedFrom:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_WasGeneratedFrom');
}
return($return);
}
=head2 get_relationship_HasCompoundAliasFrom
$return = $obj->get_relationship_HasCompoundAliasFrom($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Source
1: a fields_HasCompoundAliasFrom
2: a fields_Compound
fields_Source is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
id has a value which is a string
alias has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Source
1: a fields_HasCompoundAliasFrom
2: a fields_Compound
fields_Source is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
id has a value which is a string
alias has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
This relationship connects a source (database or organization)
with the compounds for which it has assigned names (aliases).
The alias itself is stored as intersection data.
It has the following fields:
=over 4
=item alias
alias for the compound assigned by the source
=back
=back
=cut
sub get_relationship_HasCompoundAliasFrom
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_HasCompoundAliasFrom:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasCompoundAliasFrom');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_HasCompoundAliasFrom
$return = $self->_get_relationship($ctx, 'HasCompoundAliasFrom', 'HasCompoundAliasFrom', 0, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_HasCompoundAliasFrom
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_HasCompoundAliasFrom:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasCompoundAliasFrom');
}
return($return);
}
=head2 get_relationship_UsesAliasForCompound
$return = $obj->get_relationship_UsesAliasForCompound($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_HasCompoundAliasFrom
2: a fields_Source
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
id has a value which is a string
alias has a value which is a string
fields_Source is a reference to a hash where the following keys are defined:
id has a value which is a string
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_HasCompoundAliasFrom
2: a fields_Source
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
id has a value which is a string
alias has a value which is a string
fields_Source is a reference to a hash where the following keys are defined:
id has a value which is a string
=end text
=item Description
=back
=cut
sub get_relationship_UsesAliasForCompound
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_UsesAliasForCompound:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_UsesAliasForCompound');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_UsesAliasForCompound
$return = $self->_get_relationship($ctx, 'UsesAliasForCompound', 'HasCompoundAliasFrom', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_UsesAliasForCompound
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_UsesAliasForCompound:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_UsesAliasForCompound');
}
return($return);
}
=head2 get_relationship_HasIndicatedSignalFrom
$return = $obj->get_relationship_HasIndicatedSignalFrom($ids, $from_fields, $rel_fields, $to_fields)
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_ParticipatesIn');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_ParticipatesIn
$return = $self->_get_relationship($ctx, 'ParticipatesIn', 'HasParticipant', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_ParticipatesIn
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_ParticipatesIn:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_ParticipatesIn');
}
return($return);
}
=head2 get_relationship_HasPresenceOf
$return = $obj->get_relationship_HasPresenceOf($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Media
1: a fields_HasPresenceOf
2: a fields_Compound
fields_Media is a reference to a hash where the following keys are defined:
id has a value which is a string
mod_date has a value which is a string
name has a value which is a string
type has a value which is a string
fields_HasPresenceOf is a reference to a hash where the following keys are defined:
id has a value which is a string
concentration has a value which is a float
minimum_flux has a value which is a float
maximum_flux has a value which is a float
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Media
1: a fields_HasPresenceOf
2: a fields_Compound
fields_Media is a reference to a hash where the following keys are defined:
id has a value which is a string
mod_date has a value which is a string
name has a value which is a string
type has a value which is a string
fields_HasPresenceOf is a reference to a hash where the following keys are defined:
id has a value which is a string
concentration has a value which is a float
minimum_flux has a value which is a float
maximum_flux has a value which is a float
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
This relationship connects a media to the compounds that
occur in it. The intersection data describes how much of each
compound can be found.
It has the following fields:
=over 4
=item concentration
concentration of the compound in the media
=item minimum_flux
minimum flux of the compound for this media
=item maximum_flux
maximum flux of the compound for this media
=back
=back
=cut
sub get_relationship_HasPresenceOf
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_HasPresenceOf:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasPresenceOf');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_HasPresenceOf
$return = $self->_get_relationship($ctx, 'HasPresenceOf', 'HasPresenceOf', 0, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_HasPresenceOf
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_HasPresenceOf:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasPresenceOf');
}
return($return);
}
=head2 get_relationship_IsPresentIn
$return = $obj->get_relationship_IsPresentIn($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_HasPresenceOf
2: a fields_Media
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_HasPresenceOf is a reference to a hash where the following keys are defined:
id has a value which is a string
concentration has a value which is a float
minimum_flux has a value which is a float
maximum_flux has a value which is a float
fields_Media is a reference to a hash where the following keys are defined:
id has a value which is a string
mod_date has a value which is a string
name has a value which is a string
type has a value which is a string
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_HasPresenceOf
2: a fields_Media
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_HasPresenceOf is a reference to a hash where the following keys are defined:
id has a value which is a string
concentration has a value which is a float
minimum_flux has a value which is a float
maximum_flux has a value which is a float
fields_Media is a reference to a hash where the following keys are defined:
id has a value which is a string
mod_date has a value which is a string
name has a value which is a string
type has a value which is a string
=end text
=item Description
=back
=cut
sub get_relationship_IsPresentIn
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsPresentIn:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsPresentIn');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsPresentIn
$return = $self->_get_relationship($ctx, 'IsPresentIn', 'HasPresenceOf', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsPresentIn
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsPresentIn:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsPresentIn');
}
return($return);
}
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsLocated:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsLocated');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsLocated
$return = $self->_get_relationship($ctx, 'IsLocated', 'HasUnits', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsLocated
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsLocated:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsLocated');
}
return($return);
}
=head2 get_relationship_HasUsage
$return = $obj->get_relationship_HasUsage($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_HasUsage
2: a fields_BiomassCompound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_BiomassCompound is a reference to a hash where the following keys are defined:
id has a value which is a string
coefficient has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_HasUsage
2: a fields_BiomassCompound
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_BiomassCompound is a reference to a hash where the following keys are defined:
id has a value which is a string
coefficient has a value which is a float
=end text
=item Description
This relationship connects a biomass compound specification
to the compounds for which it is relevant.
It has the following fields:
=over 4
=back
=back
=cut
sub get_relationship_HasUsage
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_HasUsage:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasUsage');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_HasUsage
$return = $self->_get_relationship($ctx, 'HasUsage', 'HasUsage', 0, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_HasUsage
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_HasUsage:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasUsage');
}
return($return);
}
=head2 get_relationship_IsUsageOf
$return = $obj->get_relationship_IsUsageOf($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_BiomassCompound
1: a fields_HasUsage
2: a fields_Compound
fields_BiomassCompound is a reference to a hash where the following keys are defined:
id has a value which is a string
coefficient has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_BiomassCompound
1: a fields_HasUsage
2: a fields_Compound
fields_BiomassCompound is a reference to a hash where the following keys are defined:
id has a value which is a string
coefficient has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
=back
=cut
sub get_relationship_IsUsageOf
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsUsageOf:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsUsageOf');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsUsageOf
$return = $self->_get_relationship($ctx, 'IsUsageOf', 'HasUsage', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsUsageOf
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsUsageOf:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsUsageOf');
}
return($return);
}
=head2 get_relationship_HasValueFor
$return = $obj->get_relationship_HasValueFor($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsInTaxa:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsInTaxa');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsInTaxa
$return = $self->_get_relationship($ctx, 'IsInTaxa', 'IsTaxonomyOf', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsInTaxa
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsInTaxa:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsInTaxa');
}
return($return);
}
=head2 get_relationship_IsTerminusFor
$return = $obj->get_relationship_IsTerminusFor($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_IsTerminusFor
2: a fields_Scenario
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_IsTerminusFor is a reference to a hash where the following keys are defined:
id has a value which is a string
group_number has a value which is an int
fields_Scenario is a reference to a hash where the following keys are defined:
id has a value which is a string
common_name has a value which is a string
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_IsTerminusFor
2: a fields_Scenario
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_IsTerminusFor is a reference to a hash where the following keys are defined:
id has a value which is a string
group_number has a value which is an int
fields_Scenario is a reference to a hash where the following keys are defined:
id has a value which is a string
common_name has a value which is a string
=end text
=item Description
A terminus for a scenario is a compound that acts as its
input or output. A compound can be the terminus for many scenarios,
and a scenario will have many termini. The relationship attributes
indicate whether the compound is an input to the scenario or an
output. In some cases, there may be multiple alternative output
groups. This is also indicated by the attributes.
It has the following fields:
=over 4
=item group_number
If zero, then the compound is an input. If one, the compound is
an output. If two, the compound is an auxiliary output.
=back
=back
=cut
sub get_relationship_IsTerminusFor
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsTerminusFor:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsTerminusFor');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsTerminusFor
$return = $self->_get_relationship($ctx, 'IsTerminusFor', 'IsTerminusFor', 0, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsTerminusFor
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsTerminusFor:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsTerminusFor');
}
return($return);
}
=head2 get_relationship_HasAsTerminus
$return = $obj->get_relationship_HasAsTerminus($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Scenario
1: a fields_IsTerminusFor
2: a fields_Compound
fields_Scenario is a reference to a hash where the following keys are defined:
id has a value which is a string
common_name has a value which is a string
fields_IsTerminusFor is a reference to a hash where the following keys are defined:
id has a value which is a string
group_number has a value which is an int
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Scenario
1: a fields_IsTerminusFor
2: a fields_Compound
fields_Scenario is a reference to a hash where the following keys are defined:
id has a value which is a string
common_name has a value which is a string
fields_IsTerminusFor is a reference to a hash where the following keys are defined:
id has a value which is a string
group_number has a value which is an int
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
=back
=cut
sub get_relationship_HasAsTerminus
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_HasAsTerminus:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasAsTerminus');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_HasAsTerminus
$return = $self->_get_relationship($ctx, 'HasAsTerminus', 'IsTerminusFor', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_HasAsTerminus
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_HasAsTerminus:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_HasAsTerminus');
}
return($return);
}
=head2 get_relationship_IsTriggeredBy
$return = $obj->get_relationship_IsTriggeredBy($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IncludesPartOf:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IncludesPartOf');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IncludesPartOf
$return = $self->_get_relationship($ctx, 'IncludesPartOf', 'Overlaps', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IncludesPartOf
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IncludesPartOf:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IncludesPartOf');
}
return($return);
}
=head2 get_relationship_ParticipatesAs
$return = $obj->get_relationship_ParticipatesAs($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_ParticipatesAs
2: a fields_Reagent
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_Reagent is a reference to a hash where the following keys are defined:
id has a value which is a string
stoichiometry has a value which is a float
cofactor has a value which is an int
compartment_index has a value which is an int
transport_coefficient has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_ParticipatesAs
2: a fields_Reagent
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_Reagent is a reference to a hash where the following keys are defined:
id has a value which is a string
stoichiometry has a value which is a float
cofactor has a value which is an int
compartment_index has a value which is an int
transport_coefficient has a value which is a float
=end text
=item Description
This relationship connects a compound to the reagents
that represent its participation in reactions.
It has the following fields:
=over 4
=back
=back
=cut
sub get_relationship_ParticipatesAs
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_ParticipatesAs:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_ParticipatesAs');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_ParticipatesAs
$return = $self->_get_relationship($ctx, 'ParticipatesAs', 'ParticipatesAs', 0, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_ParticipatesAs
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_ParticipatesAs:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_ParticipatesAs');
}
return($return);
}
=head2 get_relationship_IsParticipationOf
$return = $obj->get_relationship_IsParticipationOf($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Reagent
1: a fields_ParticipatesAs
2: a fields_Compound
fields_Reagent is a reference to a hash where the following keys are defined:
id has a value which is a string
stoichiometry has a value which is a float
cofactor has a value which is an int
compartment_index has a value which is an int
transport_coefficient has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Reagent
1: a fields_ParticipatesAs
2: a fields_Compound
fields_Reagent is a reference to a hash where the following keys are defined:
id has a value which is a string
stoichiometry has a value which is a float
cofactor has a value which is an int
compartment_index has a value which is an int
transport_coefficient has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
=back
=cut
sub get_relationship_IsParticipationOf
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsParticipationOf:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsParticipationOf');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsParticipationOf
$return = $self->_get_relationship($ctx, 'IsParticipationOf', 'ParticipatesAs', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsParticipationOf
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsParticipationOf:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsParticipationOf');
}
return($return);
}
=head2 get_relationship_ProducedResultsFor
$return = $obj->get_relationship_ProducedResultsFor($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_WasProvidedBy:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_WasProvidedBy');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_WasProvidedBy
$return = $self->_get_relationship($ctx, 'WasProvidedBy', 'Provided', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_WasProvidedBy
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_WasProvidedBy:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_WasProvidedBy');
}
return($return);
}
=head2 get_relationship_Shows
$return = $obj->get_relationship_Shows($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Diagram
1: a fields_Shows
2: a fields_Compound
fields_Diagram is a reference to a hash where the following keys are defined:
id has a value which is a string
name has a value which is a string
content has a value which is a reference to a list where each element is a string
fields_Shows is a reference to a hash where the following keys are defined:
id has a value which is a string
location has a value which is a rectangle
rectangle is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Diagram
1: a fields_Shows
2: a fields_Compound
fields_Diagram is a reference to a hash where the following keys are defined:
id has a value which is a string
name has a value which is a string
content has a value which is a reference to a list where each element is a string
fields_Shows is a reference to a hash where the following keys are defined:
id has a value which is a string
location has a value which is a rectangle
rectangle is a string
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=item Description
This relationship indicates that a compound appears on a
particular diagram. The same compound can appear on many diagrams,
and a diagram always contains many compounds.
It has the following fields:
=over 4
=item location
Location of the compound's node on the diagram.
=back
=back
=cut
sub get_relationship_Shows
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_Shows:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_Shows');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_Shows
$return = $self->_get_relationship($ctx, 'Shows', 'Shows', 0, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_Shows
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_Shows:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_Shows');
}
return($return);
}
=head2 get_relationship_IsShownOn
$return = $obj->get_relationship_IsShownOn($ids, $from_fields, $rel_fields, $to_fields)
=over 4
=item Parameter and return types
=begin html
<pre>
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_Shows
2: a fields_Diagram
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_Shows is a reference to a hash where the following keys are defined:
id has a value which is a string
location has a value which is a rectangle
rectangle is a string
fields_Diagram is a reference to a hash where the following keys are defined:
id has a value which is a string
name has a value which is a string
content has a value which is a reference to a list where each element is a string
</pre>
=end html
=begin text
$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
0: a fields_Compound
1: a fields_Shows
2: a fields_Diagram
fields_Compound is a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
fields_Shows is a reference to a hash where the following keys are defined:
id has a value which is a string
location has a value which is a rectangle
rectangle is a string
fields_Diagram is a reference to a hash where the following keys are defined:
id has a value which is a string
name has a value which is a string
content has a value which is a reference to a list where each element is a string
=end text
=item Description
=back
=cut
sub get_relationship_IsShownOn
{
my $self = shift;
my($ids, $from_fields, $rel_fields, $to_fields) = @_;
my @_bad_arguments;
(ref($ids) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"ids\" (value was \"$ids\")");
(ref($from_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"from_fields\" (value was \"$from_fields\")");
(ref($rel_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"rel_fields\" (value was \"$rel_fields\")");
(ref($to_fields) eq 'ARRAY') or push(@_bad_arguments, "Invalid type for argument \"to_fields\" (value was \"$to_fields\")");
if (@_bad_arguments) {
my $msg = "Invalid arguments passed to get_relationship_IsShownOn:\n" . join("", map { "\t$_\n" } @_bad_arguments);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsShownOn');
}
my $ctx = $Bio::KBase::CDMI::Service::CallContext;
my($return);
#BEGIN get_relationship_IsShownOn
$return = $self->_get_relationship($ctx, 'IsShownOn', 'Shows', 1, $ids, $from_fields, $rel_fields, $to_fields);
#END get_relationship_IsShownOn
my @_bad_returns;
(ref($return) eq 'ARRAY') or push(@_bad_returns, "Invalid type for return variable \"return\" (value was \"$return\")");
if (@_bad_returns) {
my $msg = "Invalid returns passed to get_relationship_IsShownOn:\n" . join("", map { "\t$_\n" } @_bad_returns);
Bio::KBase::Exceptions::ArgumentValidationError->throw(error => $msg,
method_name => 'get_relationship_IsShownOn');
}
return($return);
}
=head2 get_relationship_Submitted
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
=head2 role
=over 4
=item Description
The concept of "role" or "functional role" is basically an atomic functional unit.
The "function of a protein" is made up of one or more roles. That is, a bifunctional protein
with an assigned function of
5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.14)
would implement two distinct roles (the "function1 / function2" notation is intended to assert
that the initial part of the protein implements function1, and the terminal part of the protein
implements function2). It is worth noting that a protein often implements multiple roles due
to broad specificity. In this case, we suggest describing the protein function as
function1 @ function2
That is the ' / ' separator is used to represent multiple roles implemented by distinct
domains of the protein, while ' @ ' is used to represent multiple roles implemented by
distinct domains.
=item Definition
=begin html
<pre>
a string
</pre>
=end html
=begin text
a string
=end text
=back
=head2 subsystem
=over 4
=item Description
A substem is composed of two components: a set of roles that are gathered to be annotated
simultaneously and a spreadsheet depicting the proteins within each genome that implement
the roles. The set of roles may correspond to a pathway, a complex, an inventory (say, "transporters")
or whatever other principle an annotator used to formulate the subsystem.
The subsystem spreadsheet is a list of "rows", each representing the subsytem in a specific genome.
Each row includes a variant code (indicating what version of the molecular machine exists in the
genome) and cells. Each cell is a 2-tuple:
[role,protein-encoding genes that implement the role in the genome]
Annotators construct subsystems, and in the process impose a controlled vocabulary
for roles and functions.
=item Definition
=begin html
<pre>
a string
</pre>
=end html
=begin text
a string
=end text
=back
=head2 variant
=over 4
=item Definition
=begin html
<pre>
a string
</pre>
=end html
=begin text
a string
=end text
=back
=head2 variant_of_subsystem
=over 4
lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm view on Meta::CPAN
=end text
=back
=head2 fields_Complex
=over 4
=item Definition
=begin html
<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
name has a value which is a reference to a list where each element is a string
msid has a value which is a string
mod_date has a value which is a string
</pre>
=end html
=begin text
a reference to a hash where the following keys are defined:
id has a value which is a string
name has a value which is a reference to a list where each element is a string
msid has a value which is a string
mod_date has a value which is a string
=end text
=back
=head2 fields_Compound
=over 4
=item Definition
=begin html
<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
</pre>
=end html
=begin text
a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float
=end text
=back
=head2 fields_Contig
=over 4
=item Definition
=begin html
<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
source_id has a value which is a string
</pre>
=end html
=begin text
a reference to a hash where the following keys are defined:
id has a value which is a string
source_id has a value which is a string
=end text
=back
=head2 fields_ContigChunk
=over 4
=item Definition
=begin html
<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
sequence has a value which is a string
</pre>
=end html
( run in 1.093 second using v1.01-cache-2.11-cpan-39bf76dae61 )