Merge branch 'main' into joss

.github/workflows/tests.yml

@@ -7,7 +7,7 @@ jobs:
     continue-on-error: ${{ matrix.failure-allowed }}
     strategy:
       matrix:
-        ruby-version: ['3.0.7', '3.1.5', '3.2.4', '3.3.3']
+        ruby-version: ['3.0.7', '3.1.6', '3.2.5', '3.3.4']
         failure-allowed: [false]
         include:
         - ruby-version: 'truffleruby'

Gemfile.lock

@@ -9,7 +9,7 @@ GEM
       racc (~> 1.7)
     bigdecimal (3.1.8)
     cgi (0.4.1)
-    charlock_holmes (0.7.7)
+    charlock_holmes (0.7.9)
     chronic (0.10.2)
     concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
@@ -18,8 +18,9 @@ GEM
       rexml
     diff-lcs (1.5.1)
     dotenv (3.1.2)
-    faraday (2.9.2)
+    faraday (2.10.0)
       faraday-net_http (>= 2.0, < 3.2)
+      logger
     faraday-follow_redirects (0.1.0)
       faraday (>= 2, < 3)
     faraday-net_http (3.1.0)
@@ -42,6 +43,7 @@ GEM
       reverse_markdown (>= 1, < 3)
       rugged (>= 0.24, < 2.0)
       thor (>= 0.19, < 2.0)
+    logger (1.6.0)
     mini_mime (1.1.5)
     mini_portile2 (2.8.7)
     multi_json (1.15.0)
@@ -63,7 +65,7 @@ GEM
     puma (6.4.2)
       nio4r (~> 2.0)
     racc (1.8.0)
-    rack (3.1.4)
+    rack (3.1.7)
     rack-protection (4.0.0)
       base64 (>= 0.1.0)
       rack (>= 3.0.0, < 4)
@@ -75,7 +77,7 @@ GEM
       connection_pool
     reverse_markdown (2.1.1)
       nokogiri
-    rexml (3.3.1)
+    rexml (3.3.4)
       strscan
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
@@ -101,11 +103,12 @@ GEM
       multi_json (~> 1.15)
       rexml (~> 3.2, >= 3.2.5)
       thor (~> 1.2, >= 1.2.1)
-    sidekiq (7.2.4)
+    sidekiq (7.3.0)
       concurrent-ruby (< 2)
       connection_pool (>= 2.3.0)
+      logger
       rack (>= 2.2.4)
-      redis-client (>= 0.19.0)
+      redis-client (>= 0.22.2)
     sinatra (4.0.0)
       mustermann (~> 3.0)
       rack (>= 3.0.0, < 4)
@@ -120,7 +123,7 @@ GEM
       tilt (~> 2.0)
     strscan (3.1.0)
     thor (1.3.1)
-    tilt (2.3.0)
+    tilt (2.4.0)
     uri (0.13.0)
     webmock (3.23.1)
       addressable (>= 2.8.0)

README.md

@@ -2,7 +2,7 @@
 
 A service to provide a bot helping scientific journals and communities manage submission reviews.
 
-Buffy automates common editorial tasks like those needed by [The Journal of Open Source Software](https://joss.theoj.org/) or [rOpenSci](https://ropensci.org/).
+Buffy automates common editorial tasks like those needed by [The Journal of Open Source Software](https://joss.theoj.org/), [rOpenSci](https://ropensci.org/), [JuliaCon](https://proceedings.juliacon.org/) or [pyOpenSci](https://www.pyopensci.org/).
 
 [![Build Status](https://github.com/openjournals/buffy/actions/workflows/tests.yml/badge.svg)](https://github.com/openjournals/buffy/actions/workflows/tests.yml)
 [![Documentation Status](https://readthedocs.org/projects/buffy/badge/?version=latest)](https://buffy.readthedocs.io/en/latest/?badge=latest)

app/lib/doi_checker.rb

@@ -9,34 +9,52 @@ def initialize(entries=[])
   end
 
   def check_dois
-    doi_summary = {ok: [], missing: [], invalid: []}
+    doi_summary = {ok: [], skip: [], missing: [], invalid: []}
 
     if @entries.any?
       @entries.each do |entry|
-        if entry.has_field?('doi') && !entry.doi.empty?
+        # handle special cases first
+        if special_case = handle_special_case(entry)
+          doi_validity = special_case
+        elsif entry.has_field?('doi') && !entry.doi.empty?
+          # Validate entries with DOIs
           doi_validity = validate_doi(entry.doi.value)
-          doi_summary[doi_validity[:validity]].push(doi_validity[:msg])
-        # If there's no DOI present, check Crossref to see if we can find a candidate DOI for this entry.
         elsif entry.has_field?('title')
-            candidate_doi = crossref_lookup(entry.title.value)
-            truncated_title = entry.title.to_s[0,50]
-            truncated_title += "..." if truncated_title.length < entry.title.to_s.length
-            if candidate_doi == "CROSSREF-ERROR"
-              doi_summary[:missing].push("Errored finding suggestions for \"#{truncated_title}\", please try later")
-            elsif candidate_doi
-              doi_summary[:missing].push("#{candidate_doi} may be a valid DOI for title: #{truncated_title}")
-            else
-              doi_summary[:missing].push("No DOI given, and none found for title: #{truncated_title}")
-            end
+          # Try and find candidate entries if doi absent, but title present
+          doi_validity = handle_missing_doi(entry)
         else
-          doi_summary[:missing].push("Entry without DOI or title found")
+          doi_validity = {validity: :missing, msg: "Entry without DOI or title found"}
         end
+
+        doi_summary[doi_validity[:validity]].push(doi_validity[:msg])
       end
     end
 
     doi_summary
   end
 
+  # any special case should return false if not applicable, and an object like
+  # {:validity => :ok, :msg => "whatever"} otherwise.
+  # Add additional special cases as private methods and chain in a tidy sequence plz <3
+  def handle_special_case(entry)
+    acm_105555_prefix(entry) || false
+  end
+
+
+  # If there's no DOI present, check Crossref to see if we can find a candidate DOI for this entry.
+  def handle_missing_doi(entry)
+    candidate_doi = crossref_lookup(entry.title.value)
+    truncated_title = entry.title.to_s[0,50]
+    truncated_title += "..." if truncated_title.length < entry.title.to_s.length
+    if candidate_doi == "CROSSREF-ERROR"
+      { validity: :missing, msg: "Errored finding suggestions for \"#{truncated_title}\", please try later" }
+    elsif candidate_doi
+      { validity: :missing, msg: "#{candidate_doi} may be a valid DOI for title: #{truncated_title}" }
+    else
+      { validity: :skip, msg: "No DOI given, and none found for title: #{truncated_title}" }
+    end
+  end
+
   def validate_doi(doi_string)
     return { validity: :invalid, msg: "Empty DOI string" } if doi_string.nil? || doi_string.empty?
 
@@ -112,4 +130,16 @@ def levenshtein_distance(s, t)
   def similar?(string_1, string_2)
     levenshtein_distance(string_1, string_2) < 3
   end
+
+  private
+
+  def acm_105555_prefix(entry)
+    if entry.has_field?('doi') && entry.doi.include?("10.5555/")
+      { validity: :invalid, msg: "#{entry.doi} is INVALID - 10.5555 is a known broken prefix, replace with https://dl.acm.org/doi/{doi} in the {url} field" }
+    elsif entry.has_field?('url') && entry.url.include?("https://dl.acm.org/doi/10.5555")
+      { validity: :skip, msg: "#{entry.url} - correctly put 10.5555 prefixed doi in the url field, editor should ensure this resolves" }
+    else
+      false
+    end
+  end
 end

app/responses/doi_checks.erb

@@ -1,14 +1,18 @@
 ```
 Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
 <% doi_summary.each do |type, messages| -%>
-
-<%= type.to_s.upcase %> DOIs
-
+<% if type.to_s === "ok" %>
+✅ <%= type.to_s.upcase %> DOIs
+<% elsif type.to_s === "skip" %>
+🟡 <%= type.to_s.upcase %> DOIs
+<% else %>
+❌ <%= type.to_s.upcase %> DOIs
+<% end %>
 <%  if messages.empty? -%>
 - None
 <%  else -%>
-<%    messages.each do |message| -%>
-- <%= message%>
+<% messages.each do |message| -%>
+- <%= message %>
 <%    end -%>
 <%  end -%>
 <% end -%>

spec/doi_checker_spec.rb

@@ -11,6 +11,7 @@
       expect(doi_summary[:ok]).to be_empty
       expect(doi_summary[:invalid]).to be_empty
       expect(doi_summary[:missing]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
     end
 
     it "should classify as invalid entries with invalid DOI" do
@@ -25,6 +26,7 @@
       expect(doi_summary[:invalid].size).to eq(1)
       expect(doi_summary[:invalid].first).to eq(validity[:msg])
       expect(doi_summary[:missing]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
     end
 
     it "should classify as ok entries with valid DOI" do
@@ -39,6 +41,7 @@
       expect(doi_summary[:ok].first).to eq(validity[:msg])
       expect(doi_summary[:invalid]).to be_empty
       expect(doi_summary[:missing]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
     end
 
     it "should classify as missing entries without DOI but with a candidate crossref entry" do
@@ -50,6 +53,7 @@
       doi_summary = doi_checker.check_dois
       expect(doi_summary[:ok]).to be_empty
       expect(doi_summary[:invalid]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
       expect(doi_summary[:missing].size).to eq(1)
       expect(doi_summary[:missing][0]).to eq("10.maybe/doi may be a valid DOI for title: No DOI")
     end
@@ -63,6 +67,7 @@
       doi_summary = doi_checker.check_dois
       expect(doi_summary[:ok]).to be_empty
       expect(doi_summary[:invalid]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
       expect(doi_summary[:missing].size).to eq(1)
       expect(doi_summary[:missing][0]).to eq('Errored finding suggestions for "No DOI", please try later')
     end
@@ -78,6 +83,7 @@
       doi_summary = doi_checker.check_dois
       expect(doi_summary[:ok]).to be_empty
       expect(doi_summary[:invalid]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
       expect(doi_summary[:missing].size).to eq(1)
       expect(doi_summary[:missing][0]).to eq("Errored finding suggestions for \"#{expected_title}\", please try later")
     end
@@ -93,7 +99,9 @@
 
       expect(doi_summary[:ok]).to be_empty
       expect(doi_summary[:invalid]).to be_empty
-      expect(doi_summary[:missing][0]).to eq("No DOI given, and none found for title: #{title}")
+      expect(doi_summary[:missing]).to be_empty
+      expect(doi_summary[:skip].size).to eq(1)
+      expect(doi_summary[:skip][0]).to eq("No DOI given, and none found for title: #{title}")
     end
 
     it "should report entries with no DOI or title as missing both" do
@@ -103,10 +111,38 @@
       doi_summary = doi_checker.check_dois
       expect(doi_summary[:ok]).to be_empty
       expect(doi_summary[:invalid]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
       expect(doi_summary[:missing][0]).to eq("Entry without DOI or title found")
     end
   end
 
+  describe "#handle_special_case" do
+    it "should treat DOIs with a 10.5555 prefix as invalid" do
+      entry = BibTeX::Entry.new(doi: "10.5555/xxxxxxx.yyyyyyyyy")
+      validity = subject.handle_special_case(entry)
+      expect(validity[:validity]).to eq(:invalid)
+      expect(validity[:msg]).to include("replace with https://dl.acm.org/doi")
+    end
+
+    it "should treat URLs with a 10.5555 prefix as a skip" do
+      entry = BibTeX::Entry.new(url: "https://dl.acm.org/doi/10.5555/2827719.2827740")
+      validity = subject.handle_special_case(entry)
+      expect(validity[:validity]).to eq(:skip)
+      expect(validity[:msg]).to eq("https://dl.acm.org/doi/10.5555/2827719.2827740 - correctly put 10.5555 prefixed doi in the url field, editor should ensure this resolves")
+    end
+
+    it "should handle special cases separately from normal DOI checking" do
+      entry = BibTeX::Entry.new(doi: "10.5555/xxxxxxx.yyyyyyyyy")
+      doi_checker = DOIChecker.new([entry])
+
+      doi_summary = doi_checker.check_dois
+      expect(doi_summary[:ok]).to be_empty
+      expect(doi_summary[:missing]).to be_empty
+      expect(doi_summary[:skip]).to be_empty
+      expect(doi_summary[:invalid][0]).to include("is INVALID - 10.5555 is a known broken prefix, replace with https://dl.acm.org/doi/")
+    end
+  end
+
   describe "#validate_doi" do
 
     it "should invalidate empty doi strings" do