Merge branch 'joss' into jose

.github/workflows/tests.yml

@@ -7,7 +7,7 @@ jobs:
     continue-on-error: ${{ matrix.failure-allowed }}
     strategy:
       matrix:
-        ruby-version: ['3.1.6', '3.2.6', '3.3.7', '3.4.1']
+        ruby-version: ['3.2.7', '3.3.7', '3.4.2']
         failure-allowed: [false]
         include:
         - ruby-version: 'truffleruby'

.ruby-version

@@ -1 +1 @@
-3.3.1
+3.3.3

Gemfile.lock

@@ -8,14 +8,14 @@ GEM
       latex-decode (~> 0.0)
       racc (~> 1.7)
     bigdecimal (3.1.9)
-    cgi (0.4.1)
+    cgi (0.4.2)
     charlock_holmes (0.7.9)
     chronic (0.10.2)
     connection_pool (2.5.0)
     crack (1.0.0)
       bigdecimal
       rexml
-    diff-lcs (1.5.1)
+    diff-lcs (1.6.0)
     dotenv (3.1.7)
     faraday (2.12.2)
       faraday-net_http (>= 2.0, < 3.5)
@@ -36,15 +36,15 @@ GEM
     issue (1.0.2)
       openssl (~> 3.2)
       rack (~> 3.1)
-    json (2.9.1)
+    json (2.10.1)
     latex-decode (0.4.0)
     licensee (9.18.0)
       dotenv (>= 2, < 4)
       octokit (>= 4.20, < 10.0)
       reverse_markdown (>= 1, < 4)
       rugged (>= 0.24, < 2.0)
       thor (>= 0.19, < 2.0)
-    logger (1.6.5)
+    logger (1.6.6)
     mini_mime (1.1.5)
     mini_portile2 (2.8.8)
     multi_json (1.15.0)
@@ -53,7 +53,7 @@ GEM
     net-http (0.6.0)
       uri
     nio4r (2.7.4)
-    nokogiri (1.18.1)
+    nokogiri (1.18.3)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     octokit (9.2.0)
@@ -63,10 +63,10 @@ GEM
       faraday (~> 2.9)
     openssl (3.3.0)
     public_suffix (6.0.1)
-    puma (6.5.0)
+    puma (6.6.0)
       nio4r (~> 2.0)
     racc (1.8.1)
-    rack (3.1.8)
+    rack (3.1.12)
     rack-protection (4.1.1)
       base64 (>= 0.1.0)
       logger (>= 1.6.0)
@@ -76,16 +76,16 @@ GEM
       rack (>= 3.0.0)
     rack-test (2.2.0)
       rack (>= 1.3)
-    redis-client (0.23.2)
+    redis-client (0.24.0)
       connection_pool
     reverse_markdown (3.0.0)
       nokogiri
-    rexml (3.4.0)
+    rexml (3.4.1)
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
       rspec-expectations (~> 3.13.0)
       rspec-mocks (~> 3.13.0)
-    rspec-core (3.13.2)
+    rspec-core (3.13.3)
       rspec-support (~> 3.13.0)
     rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
@@ -105,11 +105,12 @@ GEM
       multi_json (~> 1.15)
       rexml (~> 3.2, >= 3.2.5)
       thor (~> 1.2, >= 1.2.1)
-    sidekiq (7.3.7)
-      connection_pool (>= 2.3.0)
-      logger
-      rack (>= 2.2.4)
-      redis-client (>= 0.22.2)
+    sidekiq (8.0.1)
+      connection_pool (>= 2.5.0)
+      json (>= 2.9.0)
+      logger (>= 1.6.2)
+      rack (>= 3.1.0)
+      redis-client (>= 0.23.2)
     sinatra (4.1.1)
       logger (>= 1.6.0)
       mustermann (~> 3.0)
@@ -125,8 +126,8 @@ GEM
       tilt (~> 2.0)
     thor (1.3.2)
     tilt (2.6.0)
-    uri (1.0.2)
-    webmock (3.24.0)
+    uri (1.0.3)
+    webmock (3.25.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -156,4 +157,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.5.10
+   2.5.14

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} - non-DOI with 10.5555 correctly placed 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 -%>

docs/installation.md

@@ -1,7 +1,7 @@
 Installation
 ============
 
-Buffy functions by monitoring events that are sent from a GitHub repository (e.g., openjournals/joss-reviews). Based on the information in these events, Buffy determines whether and how to respond by passing the event data to different [Responders](https://api.rubyonrails.org/v4.1/classes/ActionController/Responder.html).
+Buffy functions by monitoring events that are sent from a GitHub repository (e.g., openjournals/joss-reviews). Based on the information in these events, Buffy determines whether and how to respond by passing the event data to different [Responders](./available_responders).
 
 You can fork Buffy and configure the responders you want to use for a particular repository, and the fork doesn't necessarily
 need to be hosted under the same GitHub user or organization (as the repository where it will be used). For Buffy to be operational, it must be running either through a local installation or deployment to a platform. The following components are necessary for this setup:

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 - non-DOI with 10.5555 correctly placed 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