Class: Parsers::BioanalysisCsvParser
- Inherits:
-
Object
- Object
- Parsers::BioanalysisCsvParser
- Defined in:
- app/models/parsers/bioanalysis_csv_parser.rb
Overview
rubocop:todo Style/Documentation
Defined Under Namespace
Classes: InvalidFile
Instance Attribute Summary collapse
-
#content ⇒ Object
readonly
Returns the value of attribute content.
Class Method Summary collapse
Instance Method Summary collapse
- #build_range(range) ⇒ Object
- #concentration(plate_position) ⇒ Object
- #each_well_and_parameters ⇒ Object
- #field_name_for(sym_name) ⇒ Object
- #get_group_content(group) ⇒ Object
-
#get_groups(regexp, range = nil) ⇒ Object
Finds groups of lines by range in which the beginning of the range contains the matching regexp as text in the first column and the end of the range is an empty line - regexp -> Regular expression to be matched in the first column as beginning of range - range -> In case it is specified, restricts the searching process to this range of lines instead of using all the content of the CSV file.
- #get_parsed_attribute(plate_position, field) ⇒ Object
-
#initialize(content) ⇒ BioanalysisCsvParser
constructor
A new instance of BioanalysisCsvParser.
- #molarity(plate_position) ⇒ Object
- #parse_cell(group) ⇒ Object
- #parse_overall(group) ⇒ Object
- #parse_peak_table(group) ⇒ Object
- #parse_region_table(group) ⇒ Object
- #parse_sample(group) ⇒ Object
- #parse_samples ⇒ Object
- #parsed_content ⇒ Object
- #table_content_hash(group) ⇒ Object
Constructor Details
#initialize(content) ⇒ BioanalysisCsvParser
Returns a new instance of BioanalysisCsvParser.
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 13 def initialize(content) @content = content end |
Instance Attribute Details
#content ⇒ Object (readonly)
Returns the value of attribute content
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 11 def content @content end |
Class Method Details
.parses?(content) ⇒ Boolean
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 155 def self.parses?(content) # We don't go through the whole file content[0..10].detect do |line| /Version Created/ === line[0] && /^B.*/ === line[1] end.present? end |
Instance Method Details
#build_range(range) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 48 def build_range(range) range = if range == nil [0, content.length - 1] else range.dup end range.push(content.length - 1) if (range.length == 1) range end |
#concentration(plate_position) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 24 def concentration(plate_position) get_parsed_attribute(plate_position, field_name_for(:concentration)) end |
#each_well_and_parameters ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 146 def each_well_and_parameters parsed_content.each do |well, values| yield(well, { 'concentration' => Unit.new(values[:peak_table][field_name_for(:concentration)], 'ng/ul'), 'molarity' => Unit.new(values[:peak_table][field_name_for(:molarity)], 'nmol/l') }) end end |
#field_name_for(sym_name) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 17 def field_name_for(sym_name) { concentration: 'Conc. [ng/µl]', molarity: 'Molarity [nmol/l]' }[sym_name] end |
#get_group_content(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 88 def get_group_content(group) content.slice(group[0], group[1] - group[0] + 1) end |
#get_groups(regexp, range = nil) ⇒ Object
Finds groups of lines by range in which the beginning of the range contains the matching regexp as text in the first column and the end of the range is an empty line
-
regexp -> Regular expression to be matched in the first column as beginning of range
-
range -> In case it is specified, restricts the searching process to this range of lines
instead of using all the content of the CSV file
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 63 def get_groups(regexp, range = nil) groups = [] group = [] range = build_range(range) group_contents = get_group_content(range) group_contents.each_with_index do |line, pos| if line[0].present? && line[0].match(regexp) && group.empty? group.push(pos) elsif (line.empty? && group.one?) group.push(pos - 1) end if group.length == 2 groups.push [group[0] + range[0], group[1] + range[0]] group = [] end if ((group.length == 1) && (pos == (group_contents.length - 1))) groups.push [group[0] + range[0], pos + range[0]] end end groups end |
#get_parsed_attribute(plate_position, field) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 140 def get_parsed_attribute(plate_position, field) return nil if parsed_content.nil? || parsed_content[plate_position].nil? parsed_content[plate_position][:peak_table][field] end |
#molarity(plate_position) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 28 def molarity(plate_position) get_parsed_attribute(plate_position, field_name_for(:molarity)) end |
#parse_cell(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 105 def parse_cell(group) get_group_content(group)[0][1] end |
#parse_overall(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 100 def parse_overall(group) # Number of peaks get_group_content(get_groups(/Overall.*/m, group)[0])[1][1] end |
#parse_peak_table(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 92 def parse_peak_table(group) table_content_hash(get_groups(/Peak Table/m, group)[0]) end |
#parse_region_table(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 96 def parse_region_table(group) table_content_hash(get_groups(/Region Table/m, group)[0]) end |
#parse_sample(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 109 def parse_sample(group) { parse_cell(group) => { peak_table: parse_peak_table(group), region_table: parse_region_table(group), overall: parse_overall(group) } } end |
#parse_samples ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 119 def parse_samples groups = get_groups(/Sample Name/) groups.each_with_index.map do |group, pos| next_index = if (pos == (groups.length - 1)) @content.length - 1 else groups[pos + 1][0] - 1 end [group[0], next_index] end.reduce({}) do |memo, group| memo.merge(parse_sample group) end end |
#parsed_content ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 134 def parsed_content @parsed_content ||= parse_samples rescue NoMethodError => e # Ugh! I want to catch these where they happen raise InvalidFile end |
#table_content_hash(group) ⇒ Object
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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 32 def table_content_hash(group) content_hash = {} starting_line = group[0] ending_line = group[1] type = content[starting_line][0] fields = content[starting_line + 1] ((starting_line + 2)..(ending_line)).each do |pos| values = content[pos] unless values.nil? && (values.length != fields.length) content_hash.merge!(fields.zip(values).to_h) end end content_hash end |