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require_relative "field_parser"
require_relative "line"
#
# Methods to validate the string representations of the GFA fields data
# @api private
#
module RGFA::FieldValidator
# Validation regular expressions, derived from the GFA specification
DATASTRING_VALIDATION_REGEXP = {
:A => /^[!-~]$/, # Printable character
:i => /^[-+]?[0-9]+$/, # Signed integer
:f => /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
# Single-precision floating number
:Z => /^[ !-~]+$/, # Printable string, including space
:J => /^[ !-~]+$/, # JSON, excluding new-line and tab characters
:H => /^[0-9A-F]+$/, # Byte array in the Hex format
:B => /^[cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+$/,
# Integer or numeric array
:lbl => /^[!-)+-<>-~][!-~]*$/, # segment/path label
:orn => /^\+|-$/, # segment orientation
:lbs => /^[!-)+-<>-~][!-~]*[+-](,[!-)+-<>-~][!-~]*[+-])+$/,
# multiple labels with orientations, comma-sep
:seq => /^\*$|^[A-Za-z=.]+$/, # nucleotide sequence
:pos => /^[0-9]*$/, # positive integer
:cig => /^(\*|(([0-9]+[MIDNSHPX=])+))$/, # CIGAR string
:cgs => /^(\*|(([0-9]+[MIDNSHPX=])+))(,(\*|(([0-9]+[MIDNSHPX=])+)))*$/,
# multiple CIGARs, comma-sep
:cmt => /.*/, # content of comment line, everything is allowed
}
# Validates the string according to the provided datatype
# @param datatype [RGFA::Line::FIELD_DATATYPE]
# @param fieldname [#to_s] Fieldname to use in the error msg
# @raise [RGFA::FieldParser::FormatError] if the string does not match
# the regexp for the provided datatype
# @return [void]
# @api private
def validate_gfa_field!(datatype, fieldname=nil)
regexp = DATASTRING_VALIDATION_REGEXP[datatype]
raise RGFA::FieldParser::UnknownDatatypeError if regexp.nil?
if (regexp !~ self)
fieldname ||= "Value"
raise RGFA::FieldParser::FormatError,
"Wrong format for field #{fieldname}: \n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}\n"+
"Expected regex: #{regexp}\n"
end
end
# Validates segment names, to check that they do not contain + or -
# followed by comma
# @raise [RGFA::FieldParser::FormatError] if the segment name is invalid
# @return [void]
# @api private
def validate_segment_name!
if self =~ /.*[+-],.*/
raise RGFA::FieldParser::FormatError,
"Segment names are not allowed to contain +/- followed by comma "+
"(found: #{self})"
end
end
end
class String
include RGFA::FieldValidator
end
class Object
# @!macro [new] validate_gfa_field
# Validates the object according to the provided datatype
# @param datatype [RGFA::Line::FIELD_DATATYPE]
# @param fieldname [#to_s] Fieldname to use in the error msg
# @raise [RGFA::FieldParser::FormatError] if the object type or content
# is not compatible to the provided datatype
# @return [void]
# @api private
def validate_gfa_field!(datatype, fieldname=nil)
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
end
class Symbol
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :lbl and datatype != :orn and datatype != :Z
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
self.to_s.validate_gfa_field!(datatype)
end
end
class Hash
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :J
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
end
end
class Array
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
begin
case datatype
when :J
return
when :Z
return
when :lbs
map!(&:to_oriented_segment).each(&:validate!)
return
when :cig
to_cigar.validate!
return
when :cgs
map(&:to_cigar).each(&:validate!)
return
when :B
to_numeric_array.validate!
return
when :H
to_byte_array.validate!
return
end
rescue => err
raise RGFA::FieldParser::FormatError,
"Invalid content for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}\n"+
"Error: #{err}"
end
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
end
class RGFA::ByteArray
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :H
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
begin
validate!
rescue => err
raise RGFA::FieldParser::FormatError,
"Invalid content for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}\n"+
"Error: #{err}"
end
end
end
class RGFA::CIGAR
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :cig
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
begin
validate!
rescue => err
raise RGFA::FieldParser::FormatError,
"Invalid content for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}\n"+
"Error: #{err}"
end
end
end
class RGFA::NumericArray
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :B
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
begin
validate!
rescue => err
raise RGFA::FieldParser::FormatError,
"Invalid content for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}\n"+
"Error: #{err}"
end
end
end
class Float
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :f and datatype != :Z
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
end
end
class Fixnum
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if (datatype == :pos and self < 0)
raise RGFA::FieldParser::FormatError,
"Invalid content for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
elsif ![:i, :f, :Z].include?(datatype)
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
end
end
class Integer
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if (datatype == :pos and self < 0)
raise RGFA::FieldParser::FormatError,
"Invalid content for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
elsif ![:i, :f, :Z].include?(datatype)
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: #{self.inspect}\n"+
"Datatype: #{datatype}"
end
end
end
class RGFA::Line::Segment
# @!macro validate_gfa_field
def validate_gfa_field!(datatype, fieldname=nil)
if datatype != :lbl
raise RGFA::FieldParser::FormatError,
"Wrong type (#{self.class}) for field #{fieldname}\n"+
"Content: <RGFA::Segment:#{self.to_s}>\n"+
"Datatype: #{datatype}"
end
end
end
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