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