module ProtocolsIoHelper #============================================================================= # Protocols.io limits #============================================================================= TEXT_MAX_LENGTH = Constants::TEXT_MAX_LENGTH PIO_ELEMENT_RESERVED_LENGTH_BIG = TEXT_MAX_LENGTH * 0.015 PIO_ELEMENT_RESERVED_LENGTH_MEDIUM = TEXT_MAX_LENGTH * 0.01 PIO_ELEMENT_RESERVED_LENGTH_SMALL = TEXT_MAX_LENGTH * 0.005 # PROTOCOLS.IO PROTOCOL ATTRIBUTES PIO_P_AVAILABLE_LENGTH = TEXT_MAX_LENGTH - (PIO_ELEMENT_RESERVED_LENGTH_SMALL * 2 + PIO_ELEMENT_RESERVED_LENGTH_MEDIUM * 8 + PIO_ELEMENT_RESERVED_LENGTH_BIG * 2) # -- 2 small = created at , publish date PROTOCOL ATTRIBUTES # -- 8 medium = description,tags,before_start,warning,guidelines, # manuscript_citation,keywords,vendor_name PROTOCOL ATTRIBUTES # -- 2 big = vendor_link, link PROTOCOL ATTRIBUTES # PROTOCOLS.IO STEP ATTRIBUTES PIO_S_AVAILABLE_LENGTH = TEXT_MAX_LENGTH - (PIO_ELEMENT_RESERVED_LENGTH_SMALL * 20) # -- 20 small = description,expected_result,safety_information # software_package version, software_package os_name, # software_package os_version,software_package link, # software_package repository,software_package developer,software_package name # commands os_version,commands os_name, commands name,commands description, # sub protocol full name (author), sub protocol name, sub protocol link, # dataset link,dataset name, safety_information link, # -- 0 medium = # -- 0 big = PIO_TITLE_TOOLONG_LEN = I18n.t('protocols.protocols_io_import.title_too_long').length + 5 PIO_STEP_TOOLONG_LEN = I18n.t('protocols.protocols_io_import.too_long').length # The + 2 above (in title) is there because if the length was at the limit, # the cutter method had issues, this gives it some space # below are default min table settings (minimum 5x5) PIO_TABLE_MIN_WIDTH = 5 PIO_TABLE_MIN_HEIGHT = 5 def protocolsio_string_to_table_element(description_string) string_without_tables = string_html_table_remove(description_string) table_regex = %r{]*>(.*?)<\/table>}m tr_regex = %r{]*>(.*?)<\/tr>}m td_regex = %r{]*>(.*?)<\/td>}m tables = {} description_string.gsub! '', '' description_string.gsub! '', '' table_strings = description_string.scan(table_regex) table_strings.each_with_index do |table, table_counter| tables[table_counter.to_s] = {} tr_number = table[0].scan(tr_regex).count diff = PIO_TABLE_MIN_HEIGHT - tr_number # always tables have atleast 5 row table_fix_str = table[0] table_fix_str += '' * diff if tr_number < PIO_TABLE_MIN_HEIGHT tr_strings = table_fix_str.scan(tr_regex) contents = {} contents['data'] = [] tr_strings.each_with_index do |tr, tr_counter| td_strings = tr[0].scan(td_regex) contents['data'][tr_counter] = [] td_counter = td_strings.count diff = PIO_TABLE_MIN_WIDTH - td_counter td_strings.each do |td| td_stripped = ActionController::Base.helpers.strip_tags(td[0]) contents['data'][tr_counter].push(td_stripped) end next if td_counter >= PIO_TABLE_MIN_WIDTH diff.times { contents['data'][tr_counter].push(' ') } end tables[table_counter.to_s]['contents'] = Base64.encode64( contents.to_s.sub('=>', ':') ) tables[table_counter.to_s]['name'] = ' ' end return tables, string_without_tables end def string_html_table_remove(description_string) description_string.remove!("\n", "\t", "\r", "\f") table_whole_regex = %r{(]*>.*?<\/table>)}m table_pattern_array = description_string.scan(table_whole_regex) string_without_tables = description_string table_pattern_array.each do |table_pattern| string_without_tables = string_without_tables.gsub( table_pattern[0], t('protocols.protocols_io_import.comp_append.table_moved').html_safe ) end string_without_tables end def pio_eval_prot_desc(text, attribute_name) case attribute_name when 'published_on' pio_eval_len(text, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL) when 'vendor_link', 'link' pio_eval_len(text, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_BIG) else pio_eval_len(text, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_MEDIUM) end end def pio_eval_title_len(text) if text text += ' ' if text.length < Constants::NAME_MIN_LENGTH if text.length > Constants::NAME_MAX_LENGTH text = text[0..(Constants::NAME_MAX_LENGTH - PIO_TITLE_TOOLONG_LEN)] + t('protocols.protocols_io_import.title_too_long') @toolong = true end text else '' end end def pio_eval_len(text, reserved) if text text_end = reserved + @remaining - PIO_STEP_TOOLONG_LEN text_end = 2 if text_end < 2 # Since steps have very low reserved values now (below 100), # the above sets their index to 1 if its negative # (length of toolong text is about 90 chars, and if remaining is 0, # then the negative index just gets set to 1. this is a workaround # it would also be possible to not count the length of the "too long" text # or setting the import reserved value to 95,but then available characters # will be like before (around 7600) if text.length - reserved > @remaining text = close_open_html_tags( text[0..text_end] + t('protocols.protocols_io_import.too_long') ) @toolong = true @remaining = 0 elsif (text.length - reserved) > 0 @remaining -= text.length - reserved end text else '' end end def pio_eval_authors(text) # Extract authors names from the JSON text.map { |auth| auth['name'] }.join(', ') rescue StandardError [] end def eval_last_modified(steps) timestamps = steps.map do |step| step['modified_on'] if step['modified_on'].present? end I18n.l(Time.at(timestamps.max), format: :full) rescue StandardError I18n.l(Time.at(0), format: :full) end # Checks so that null values are returned as zero length strings # Did this so views arent as ugly (i avoid using if present statements) def not_null(attribute) if attribute attribute else '' end end def close_open_html_tags(text) Nokogiri::HTML::DocumentFragment.parse(text).to_html end def step_hash_null?(step_json) step_json.dig( 0, 'components', 0, 'type_id' ).nil? && step_json.dig( 0, 'components', '0', 'type_id' ).nil? end # Images are allowed in: # Step: description, expected result # Protocol description : description before_start warning # guidelines manuscript_citation def prepare_for_view( attribute_text1, size, table = 'no_table', image_allowed = false ) image_tag = image_allowed ? Array('img') : Array(nil) image_tag.push('br') if table == 'no_table' attribute_text = sanitize_input(not_null(attribute_text1), image_tag) elsif table == 'table' attribute_text = sanitize_input( string_html_table_remove(not_null(attribute_text1)), image_tag ) end pio_eval_len( attribute_text, size ) end def fill_attributes(attribute_name, attribute_text, step_component) output_string = '' trans_string = step_component trans_string += if attribute_name != 'os_name' && attribute_name != 'os_version' attribute_name else 'os' end output_string += if attribute_name != 'os_version' t(trans_string) else ' , ' end if attribute_name == 'protocol_name' output_string += pio_eval_title_len(attribute_text) else output_string += prepare_for_view( attribute_text, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL ) end output_string end # pio_stp_x means protocols io step (id of component) parser # protocols io description parser def pio_stp_1(iterating_key) br = '
' append = if iterating_key.present? br + prepare_for_view( iterating_key, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL, 'table', true ) + br else t('protocols.protocols_io_import.comp_append.missing_desc') end append end def pio_stp_6(iterating_key) if iterating_key.present? # protocols io section(title) parser return pio_eval_title_len(CGI.unescapeHTML(sanitize_input(iterating_key))) end t('protocols.protocols_io_import.comp_append.missing_step') end def pio_stp_17(iterating_key) # protocols io expected result parser if iterating_key.present? append = t('protocols.protocols_io_import.comp_append.expected_result') + prepare_for_view( iterating_key, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL, 'table', true ) + '
' return append end '' end # protocols io software package,dataset,commands, # sub_protocol and safety_information parser def pio_stp(iterating_key, parse_elements_array, en_local_text) append = '' parse_elements_array.each do |element| next unless iterating_key[element] append += fill_attributes( element, iterating_key[element], en_local_text ) end append end def protocols_io_fill_desc(json_hash) unshortened_string_for_tables = '' description_array = %w[ ( before_start warning guidelines manuscript_citation published_on vendor_name vendor_link keywords tags link created_on ) ] allowed_image_attributes = %w[ ( before_start warning guidelines manuscript_citation ) ] if json_hash['description'].present? unshortened_string_for_tables += json_hash['description'] description_string = '' + t('protocols.protocols_io_import.preview.description') + '' + prepare_for_view( json_hash['description'], ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_MEDIUM, 'table', true ).html_safe else description_string = '' + t('protocols.protocols_io_import.preview.description') + '' + t('protocols.protocols_io_import.comp_append.missing_desc') end description_string += '
' description_array.each do |e| if e == 'created_on' && json_hash[e].present? new_e = '' + e.humanize + '' description_string += new_e.to_s + ': ' + prepare_for_view( params['protocol']['created_at'].to_s, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_SMALL ) + + '
' elsif e == 'tags' && json_hash[e].present? \ && json_hash[e].any? && json_hash[e] != '' new_e = '' + e.humanize + '' description_string += new_e.to_s + ': ' tags_length_checker = '' json_hash[e].each do |tag| tags_length_checker += sanitize_input(tag['tag_name']) + ' , ' end description_string += prepare_for_view( tags_length_checker, ProtocolsIoHelper::PIO_ELEMENT_RESERVED_LENGTH_MEDIUM ) description_string += '
' elsif json_hash[e].present? data = if e == 'published_on' Time.at(json_hash[e]).utc.to_datetime.to_s else json_hash[e] end unshortened_string_for_tables += data new_e = '' + e.humanize + '' image_tag = allowed_image_attributes.include?(e) ? Array('img') : Array(nil) description_string += new_e.to_s + ': ' + # intercept tables here, before cut pio_eval_prot_desc( sanitize_input(data, image_tag), e ).html_safe + '
' end end return description_string, unshortened_string_for_tables end def protocols_io_guid_reorder_step_json(unordered_step_json) return '' if unordered_step_json.blank? base_step = unordered_step_json.find { |step| step['previous_guid'].nil? } return unordered_step_json if base_step.nil? number_of_steps = unordered_step_json.size return unordered_step_json if number_of_steps == 1 step_order = [] step_counter = 0 step_order[step_counter] = base_step step_counter += 1 while step_order.length != number_of_steps step_order[step_counter] = unordered_step_json.find do |step| step['previous_guid'] == base_step['guid'] end base_step = step_order[step_counter] step_counter += 1 end step_order end def protocols_io_fill_step(original_json, newj) # newj = new json # (simple to map) id 1= step description, id 6= section (title), # id 17= expected result # (complex mapping with nested hashes) id 8 = software package, # id 9 = dataset, id 15 = command, id 18 = attached sub protocol # id 19= safety information , # id 20= regents (materials, like scinote samples kind of) original_json['steps'] = protocols_io_guid_reorder_step_json( original_json['steps'] ) newj['0'] = {} newj['0']['position'] = 0 newj['0']['name'] = 'Protocol info' @remaining = ProtocolsIoHelper::PIO_P_AVAILABLE_LENGTH shortened_string, unshortened_tables_string = protocols_io_fill_desc( original_json ) newj['0']['tables'] = protocolsio_string_to_table_element( sanitize_input(unshortened_tables_string).html_safe )[0] table_str = protocolsio_string_to_table_element( sanitize_input(shortened_string, Array('img')).html_safe )[1] newj['0']['description'] = table_str original_json['steps'].each_with_index do |step, pos_orig| # loop over steps i = pos_orig + 1 @remaining = ProtocolsIoHelper::PIO_S_AVAILABLE_LENGTH # position of step (first, second.... etc), newj[i.to_s] = {} # the json we will insert into db newj[i.to_s]['position'] = i newj[i.to_s]['description'] = '' unless newj[i.to_s].key?('description') newj[i.to_s]['name'] = '' unless newj[i.to_s].key?('name') unshortened_step_table_string = '' step['components'].each do |key, value| # sometimes there are random index values as keys # instead of hashes, this is a workaround to that buggy json format key = value if value.class == Hash # append is the string that we append values into for description # pio_stp_x means protocols io step (id of component) parser case key['type_id'] # intercept tables in all of below before cutting when 1 unshortened_step_table_string += key['source']['description'] newj[i.to_s]['description'] += pio_stp_1(key['source']['description']) when 6 newj[i.to_s]['name'] = pio_stp_6(key['source']['title']) when 17 unshortened_step_table_string += key['source']['body'] newj[i.to_s]['description'] += pio_stp_17(key['source']['body']) when 8 pe_array = %w( name developer version link repository os_name os_version ) trans_text = 'protocols.protocols_io_import.comp_append.soft_packg.' newj[i.to_s]['description'] += pio_stp( key['source'], pe_array, trans_text ) when 9 pe_array = %w( name link ) trans_text = 'protocols.protocols_io_import.comp_append.dataset.' newj[i.to_s]['description'] += pio_stp( key['source'], pe_array, trans_text ) when 15 pe_array = %w( name description os_name os_version ) key['source']['name'] = '
' +
            not_null(key['source']['name'].gsub(/\n/, '
')) + '
' trans_text = 'protocols.protocols_io_import.comp_append.command.' newj[i.to_s]['description'] += pio_stp( key['source'], pe_array, trans_text ) when 18 pe_array = %w( title title_html uri ) trans_text = 'protocols.protocols_io_import.comp_append.sub_protocol.' newj[i.to_s]['description'] += pio_stp( key['source'], pe_array, trans_text ) when 19 pe_array = %w( body link ) trans_text = 'protocols.protocols_io_import.comp_append.safety_infor.' newj[i.to_s]['description'] += pio_stp( key['source'], pe_array, trans_text ) end # case end end # finished looping over step components table_str = protocolsio_string_to_table_element( newj[i.to_s]['description'] )[1] newj[i.to_s]['description'] = table_str newj[i.to_s]['tables'] = protocolsio_string_to_table_element( sanitize_input(unshortened_step_table_string).html_safe )[0] end # steps newj end def get_steps(json) # Get steps of the given json_object if json.key?('steps') && json['steps'].respond_to?('each') json['steps'] else [] end end def get_components(step_json) # Get components of given step_json if step_json.key?('components') && step_json['components'].respond_to?('each') step_json['components'] else [] end end end