Class: GenomerPluginValidate::Validator::BadProductField

Inherits:
Genomer::Plugin
  • Object
show all
Includes:
GenomerPluginValidate::Validator
Defined in:
lib/genomer-plugin-validate/validator/bad_product_field.rb

Constant Summary collapse

ERROR = 
"Bad product field for '%s:' "

Instance Method Summary collapse

Methods included from GenomerPluginValidate::Validator

#annotations_by_attribute, load, validators

Instance Method Details

#all_caps_products ⇒ Object 



39
40
41
42
43
 
# File 'lib/genomer-plugin-validate/validator/bad_product_field.rb', line 39

def all_caps_products
  products_matching(/^([A-Z\s-]+)$/).
    map(&:first).
    map{|i| (ERROR + "all caps product fields are not allowed.") % i}
end

#domain_related_like_ending_products ⇒ Object 



29
30
31
32
 
# File 'lib/genomer-plugin-validate/validator/bad_product_field.rb', line 29

def domain_related_like_ending_products
  products_matching(/([Dd]omain|[Rr]elated|[Ll]ike).?$/).
    map{|i| (ERROR + "products ending with '%s' are not allowed.") % i}
end

#hypothetical_products ⇒ Object 



24
25
26
27
 
# File 'lib/genomer-plugin-validate/validator/bad_product_field.rb', line 24

def hypothetical_products
  products_matching(/^([Hh]ypothetical)(?! protein)/).
    map{|i| (ERROR + "start with 'putative' instead of '%s.'") % i}
end

#nterm_products ⇒ Object 



34
35
36
37
 
# File 'lib/genomer-plugin-validate/validator/bad_product_field.rb', line 34

def nterm_products
  products_matching(/(?!\B)([Nn][-\s][Tt]erm(inal)?)/).
    map{|i| (ERROR + "'N-terminal' or variations are not allowed.") % i}
end

#products_matching(re) ⇒ Object 



15
16
17
18
19
20
21
22
 
# File 'lib/genomer-plugin-validate/validator/bad_product_field.rb', line 15

def products_matching(re)
  annotations_by_attribute("product").
    map{|(product,entries)| entries.map{|i| [i.id,product]}}.
    flatten(1).
    map{|(id,product)| [id, re.match(product)]}.
    select{|(_,match)| match}.
    map{|(id,match)| [id,match.to_a[1].downcase]}
end

#run ⇒ Object 



6
7
8
9
10
11
12
13
 
# File 'lib/genomer-plugin-validate/validator/bad_product_field.rb', line 6

def run
  [
    hypothetical_products,
    domain_related_like_ending_products,
    nterm_products,
    all_caps_products
  ].flatten
end