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Merged
merged 13 commits into from
Nov 25, 2025
Merged

Extend publication type list #2408

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998bef9
use publication_types.yml to populate publication types
whomingbird Nov 13, 2025
2d4d86e
Check consistency between DB and YAML
whomingbird Nov 13, 2025
32480b5
Update publication types to align with the DataCite Metadata Schema.
whomingbird Nov 14, 2025
b067202
Add Project Deliverable publication type and update naming for readab…
whomingbird Nov 17, 2025
a373a28
Synchronize publication types with YAML definitions, migrate legacy t…
whomingbird Nov 17, 2025
0ee7837
add seed:005_publication_types to upgrade task
whomingbird Nov 17, 2025
b690cfb
Refactor publication code to adopt the new publication types.
whomingbird Nov 17, 2025
27ce570
update and add new tests
whomingbird Nov 17, 2025
c41af8d
update publication type in api responses
whomingbird Nov 17, 2025
d539480
code update according to copilot review
whomingbird Nov 18, 2025
38eb875
Merge branch 'seek-1.17' into extended-publication-type
whomingbird Nov 19, 2025
e363eda
update code according to the PR review.
whomingbird Nov 24, 2025
109393a
remove unnecessary code
whomingbird Nov 25, 2025
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62 changes: 16 additions & 46 deletions app/models/publication.rb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -248,7 +248,7 @@ def extract_bibtex_metadata(bibtex_record)
month = bibtex_record[:month].try(:to_s)
year = bibtex_record[:year].try(:to_s)
self.published_date = Date.new(bibtex_record.year.try(:to_i) || 1, bibtex_record.month_numeric || 1, bibtex_record[:day].try(:to_i) || 1)
self.published_date = nil if self.published_date.to_s == "0001-01-01"
self.published_date = nil if self.published_date.to_s == '0001-01-01'
self.doi = bibtex_record[:doi].try(:to_s)
self.pubmed_id = bibtex_record[:pubmed_id].try(:to_s)
self.booktitle = bibtex_record[:booktitle].try(:to_s)
Expand Down Expand Up @@ -326,7 +326,7 @@ def generate_citation(bibtex_record)
self.citation = ''
month = bibtex_record[:month].try(:to_s)
year = bibtex_record[:year].try(:to_s)
page_or_pages = (bibtex_record[:pages].try(:to_s).match?(/[^0-9]/) ? "pp." : "p." ) unless bibtex_record[:pages].nil?
page_or_pages = (bibtex_record[:pages].try(:to_s).match?(/[^0-9]/) ? 'pp.' : 'p.' ) unless bibtex_record[:pages].nil?
pages = bibtex_record[:pages].try(:to_s)
volume = bibtex_record[:volume].try(:to_s)
series = bibtex_record[:series].try(:to_s)
Expand All @@ -344,25 +344,16 @@ def generate_citation(bibtex_record)
url = parse_bibtex_url(bibtex_record).try(:to_s)
publication_type = PublicationType.find(self.publication_type_id)

if publication_type.is_journal?
case publication_type.key
when 'journalarticle'
self.citation += self.journal.nil? ? '':self.journal
self.citation += volume.blank? ? '': " #{volume}"
self.citation += number.nil? ? '' : "(#{number})"
self.citation += pages.blank? ? '' : (":#{pages}")
=begin
unless year.nil?
self.citation += year.nil? ? '' : (' '+year)
end
=end
elsif publication_type.is_booklet?
when 'booklet'
self.citation += howpublished.blank? ? '': "#{howpublished}"
self.citation += address.nil? ? '' : (", #{address}")
=begin
unless year.nil?
self.citation += year.nil? ? '' : (' '+year)
end
=end
elsif publication_type.is_inbook?
when 'bookchapter'
self.citation += self.booktitle.nil? ? '' : ("In #{self.booktitle}")
self.citation += volume.blank? ? '' : (", volume #{volume}")
self.citation += series.blank? ? '' : (" of #{series}")
Expand All @@ -372,14 +363,7 @@ def generate_citation(bibtex_record)
unless address.nil? || (self.booktitle.try(:include?, address))
self.citation += address.nil? ? '' : (", #{address}")
end
=begin
unless self.booktitle.try(:include?, year)
unless year.nil?
self.citation += year.nil? ? '' : (' '+year)
end
end
=end
elsif publication_type.is_inproceedings? || publication_type.is_incollection? || publication_type.is_book?
when 'conferencepaper', 'collection', 'book'
# InProceedings / InCollection
self.citation += self.booktitle.nil? ? '' : ("In #{self.booktitle}")
self.citation += volume.blank? ? '' : (", vol. #{volume}")
Expand All @@ -390,39 +374,25 @@ def generate_citation(bibtex_record)
unless address.nil? || (self.booktitle.try(:include?, address))
self.citation += address.nil? ? '' : (", #{address}")
end
=begin
unless self.booktitle.try(:include?, year)
unless year.nil?
self.citation += year.nil? ? '' : (', '+year)
end
end
=end
elsif publication_type.is_phd_thesis? || publication_type.is_masters_thesis? || publication_type.is_bachelor_thesis?
when 'bachelorsthesis', 'mastersthesis', 'phdthesis'
#PhD/Master Thesis
self.citation += school.nil? ? '' : (" #{school}")
self.errors.add(:base,'A thesis need to have a school') if school.nil?
self.citation += year.nil? ? '' : (", #{year}")
self.citation += tutor.nil? ? '' : (", #{tutor}(Tutor)")
self.citation += tutorhits.nil? ? '' : (", #{tutorhits}(HITS Tutor)")
self.citation += url.nil? ? '' : (", #{url}")
elsif publication_type.is_proceedings?
when 'conferenceproceeding'
# Proceedings are conference proceedings, it has no authors but editors
# Book
self.journal = self.title
self.citation += volume.blank? ? '' : ("vol. #{volume}")
self.citation += series.blank? ? '' : (" of #{series}")
self.citation += self.publisher.blank? ? '' : (", #{self.publisher}")
=begin
unless month.nil? && year.nil?
self.citation += self.citation.blank? ? '' : ','
self.citation += month.nil? ? '' : (' '+ month.capitalize)
self.citation += year.nil? ? '' : (' '+year)
end
=end
elsif publication_type.is_tech_report?
when 'report'
self.citation += institution.blank? ? ' ': institution
self.citation += type.blank? ? ' ' : (", #{type}")
elsif publication_type.is_unpublished?
when 'preprint'
self.citation += note.blank? ? ' ': note
end

Expand Down Expand Up @@ -583,7 +553,7 @@ def pubmed_entry
if pubmed_id
Rails.cache.fetch("bio-reference-#{pubmed_id}") do
entry = Bio::PubMed.efetch(pubmed_id).first
raise "PubMed entry was nil" if entry.nil?
raise 'PubMed entry was nil' if entry.nil?
entry
end
end
Expand Down Expand Up @@ -620,23 +590,23 @@ def check_bibtex_file (bibtex_record)


if self.title.blank?
errors.add(:base, "Please check your bibtex files, each publication should contain a title or a chapter name.")
errors.add(:base, 'Please check your bibtex files, each publication should contain a title or a chapter name.')
return false
end

if (%w[InCollection InProceedings].include? self.publication_type.title) && (bibtex_record[:booktitle].blank?)
if (['Collection','Conference Paper'].include? self.publication_type.title) && (bibtex_record[:booktitle].blank?)
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Copilot AI Nov 18, 2025

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[nitpick] Inconsistent spacing within array literals. Ruby style guides typically recommend spaces after commas in arrays for better readability:

if (['Collection', 'Conference Paper'].include? self.publication_type.title) && (bibtex_record[:booktitle].blank?)
Suggested change
if (['Collection','Conference Paper'].include? self.publication_type.title) && (bibtex_record[:booktitle].blank?)
if (['Collection', 'Conference Paper'].include? self.publication_type.title) && (bibtex_record[:booktitle].blank?)

Copilot uses AI. Check for mistakes.
errors.add(:base, "An #{self.publication_type.title} needs to have a booktitle.")
return false
end

unless %w[Booklet Manual Misc Proceedings].include? self.publication_type.title
unless ['Booklet','Text','Other','Conference Proceeding'].include? self.publication_type.title
if bibtex_record[:author].nil? && self.editor.nil?
self.errors.add(:base, "You need at least one author or editor for the #{self.publication_type.title}.")
return false
end
end

if self.publication_type.is_phd_thesis? || self.publication_type.is_masters_thesis? || self.publication_type.is_bachelor_thesis?
if publication_type.key == 'bachelorsthesis' || publication_type.key == 'mastersthesis' || publication_type.key == 'phdthesis'
if bibtex_record[:school].try(:to_s).nil?
self.errors.add(:base,"A #{self.publication_type.title} needs to have a school.")
return false
Expand Down
181 changes: 45 additions & 136 deletions app/models/publication_type.rb
View file
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Original file line number Diff line number Diff line change
@@ -1,143 +1,52 @@
class PublicationType < ActiveRecord::Base

class PublicationType < ActiveRecord::Base
has_many :publications

#this returns an instance of PublicationType according to one of the publication types
#if there is not a match nil is returned

#http://bib-it.sourceforge.net/help/fieldsAndEntryTypes.php#Entries

def self.for_type type
keys = { "Journal"=>"article",
"Book"=>"book",
"Booklet"=>"booklet",
"InBook"=>"inbook",
"InCollection"=>"incollection",
"InProceedings"=>"inproceedings",
"Manual"=>"manual",
"Masters_Thesis"=>"masters_thesis",
"Misc"=>"misc",
"Phd_Thesis"=>"phd_thesis",
"Bachelor_Thesis"=>"bachelorsthesis",
"Proceedings"=>"proceedings",
"Tech_Report"=>"tech_report",
"Unpublished"=>"unpublished" }
return PublicationType.find_by(key: keys[type])
end



# Map BibTeX keys → DataCite keys
BIBTEX_TO_DATACITE_KEY = {
'article' => 'journalarticle',
'book' => 'book',
'booklet' => 'booklet',
'inbook' => 'bookchapter',
'incollection' => 'collection',
'inproceedings' => 'conferencepaper',
'proceedings' => 'conferenceproceeding',
'manual' => 'text',
'misc' => 'other',
'unpublished' => 'preprint',
'techreport' => 'report',
'phdthesis' => 'phdthesis',
'mastersthesis' => 'mastersthesis',
'bachelorsthesis' => 'bachelorsthesis'
}.freeze


# Load expected publication types from YAML
def self.type_registry
@type_registry ||= begin
path = Rails.root.join('config/default_data/publication_types.yml')
YAML.load_file(path).values.index_by { |h| h['title'] }
end
end

def self.for_type(type)
yaml_entry = type_registry[type]
return nil unless yaml_entry
find_by(key: yaml_entry['key'])
end

# Extract publication type from BibTeX record
def self.get_publication_type_id(bibtex_record)
str_begin = "@"
str_end = "{"
publication_key = bibtex_record.try(:to_s)[/#{str_begin}(.*?)#{str_end}/m, 1]
unless PublicationType.find_by(key: publication_key).nil?
return PublicationType.find_by(key: publication_key).id
else
return PublicationType.find_by(key: "misc").id
end
end


def self.Journal
self.for_type('Journal')
end

def self.Book
self.for_type('Book')
end

def self.Booklet
self.for_type('Booklet')
end
def self.InBook
self.for_type('InBook')
end
def self.InCollection
self.for_type('InCollection')
end
def self.InProceedings
self.for_type('InProceedings')
end
def self.Manual
self.for_type('Manual')
end
def self.Masters_Thesis
self.for_type('Masters_Thesis')
end
def self.Misc
self.for_type('Misc')
end
def self.Bachelor_Thesis
self.for_type('Bachelor_Thesis')
end
def self.Phd_Thesis
self.for_type('Phd_Thesis')
end
def self.Proceedings
self.for_type('Proceedings')
end
def self.Tech_Report
self.for_type('Tech_Report')
end
def self.Unpublished
self.for_type('Unpublished')
end

def is_journal?
key == "article"
# Extract the BibTeX entry type, e.g. article, inbook, misc...
publication_key = bibtex_record.to_s[/@(.*?)\{/m, 1].to_s.downcase.strip
datacite_key = BIBTEX_TO_DATACITE_KEY[publication_key] || 'other'
pub_type = PublicationType.find_by(key: datacite_key)
pub_type.id
end

def is_book?
key == 'book'
end

def is_booklet?
key == 'booklet'
end

def is_inbook?
key == 'inbook'
end

def is_incollection?
key == 'incollection'
end

def is_inproceedings?
key == 'inproceedings'
end

def is_manual?
key == 'manual'
end

def is_masters_thesis?
key == 'mastersthesis'
end

def is_misc?
key == 'misc'
end

def is_phd_thesis?
key == 'phdthesis'
end

def is_bachelor_thesis?
key == 'bachelorsthesis'
end

def is_proceedings?
key == 'proceedings'
end

def is_tech_report?
key == 'techreport'
end

def is_unpublished?
key == 'unpublished'
type_registry.each_key do |title|
define_singleton_method(title.gsub(/\s+/, '')) do
find_by(key: type_registry[title]['key'])
end
end

end
end
4 changes: 2 additions & 2 deletions app/views/publications/new.html.erb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
<span id="publication_type_info" style="display:none;"></span>
<span id="publication_type_selection">
<%= collection_select :publication, :publication_type_id, PublicationType.order(:title), :id, :title,
{:selected => PublicationType.Journal.id},
{:selected => PublicationType.JournalArticle.id},
{:class => 'form-control'} -%>
</span>
</div>
Expand Down Expand Up @@ -79,7 +79,7 @@
<span id="publication_type_info" style="display:none;"></span>
<span id="publication_type_selection">
<%= collection_select :publication, :publication_type_id, PublicationType.order(:title), :id, :title,
{:selected => PublicationType.Journal.id},
{:selected => PublicationType.JournalArticle.id},
{:class => 'form-control'} -%>
</span>
</div>
Expand Down
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