theoj 1.0.0 → 1.2.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,5 +1,27 @@
 # Changelog
 
+## 1.2.1 (2021-11-30)
+
+- Changed metadata dates format to ISO
+- Changed editor and reviewers metadata values to github login
+- Removed languages from article metadata
+
+## 1.2.0 (2021-11-23)
+
+- Added reviews_repository_url to Journal
+- Added article_metadata to Submission
+- Added editor and paper dates lookup information in Submission
+- Fixed error reading reviewers list from issue body
+
+## 1.1.1 (2021-11-05)
+
+- Added support for test-journal
+
+## 1.1.0 (2021-10-29)
+
+- Added Theoj::PublishedPaper object with metadata from Journal's API
+- Added custom Error class
+
 ## 1.0.0 (2021-10-20)
 
 - Added method to Journal to create paper_id from issue_id

data/lib/theoj/author.rb

@@ -62,7 +62,7 @@ module Theoj
       if validator.valid?
         return author_orcid.strip
       else
-        raise "Problem with ORCID (#{author_orcid}) for #{self.name}. #{validator.error}"
+        raise Theoj::Error, "Problem with ORCID (#{author_orcid}) for #{self.name}. #{validator.error}"
       end
     end
 
@@ -82,7 +82,7 @@ module Theoj
       # Raise if we can't parse the string, might be because of this bug :-(
       # https://bugs.ruby-lang.org/issues/12451
       affiliations.each do |a|
-        raise "Problem with affiliations for #{self.name}, perhaps the " +
+        raise Theoj::Error, "Problem with affiliations for #{self.name}, perhaps the " +
               "affiliations index need quoting?" unless affiliations_hash.has_key?(a)
 
         author_affiliations << affiliations_hash[a].strip

data/lib/theoj/github.rb

@@ -52,7 +52,7 @@ module Theoj
 
     # Returns the user login (removes the @ from the username)
     def user_login(username)
-      username.strip.sub(/^@/, "").downcase
+      username.to_s.strip.sub(/^@/, "").downcase
     end
 
     # Returns true if the string is a valid GitHub isername (starts with @)

data/lib/theoj/journal.rb

@@ -34,6 +34,14 @@ module Theoj
       "#@doi_prefix/#{paper_id}"
     end
 
+    def reviews_repository_url(issue_id=nil)
+      reviews_url = "https://github.com/#{data[:reviews_repository]}"
+      if issue_id
+        reviews_url += "/issues/" + issue_id.to_s
+      end
+      reviews_url
+    end
+
     private
 
     def set_data(custom_data)

data/lib/theoj/journals_data.rb

@@ -19,6 +19,16 @@ module Theoj
       papers_repository: "openjournals/jose-papers",
       reviews_repository: "openjournals/jose-reviews",
       deposit_url: "https://joss.theoj.org/papers/api_deposit"
+    },
+    test_journal: {
+      doi_prefix: "10.21105",
+      url: "https://test.joss.theoj.org/",
+      name: "Test Journal",
+      alias: "test_journal",
+      launch_date: "2016-05-05",
+      papers_repository: "openjournals/joss-papers-testing",
+      reviews_repository: "openjournals/joss-reviews-testing",
+      deposit_url: "https://test.joss.theoj.org/papers/api_deposit"
     }
   }
 end

data/lib/theoj/paper.rb

@@ -152,7 +152,7 @@ module Theoj
 
       def failure(msg)
         cleanup
-        raise(msg)
+        raise Theoj::Error, msg
       end
   end
 end

data/lib/theoj/published_paper.rb

@@ -0,0 +1,46 @@
+require "faraday"
+require "yaml"
+require "json"
+
+module Theoj
+  class PublishedPaper
+    include Theoj::Git
+
+    attr_accessor :metadata
+
+    def initialize(doi)
+      doi_url = "https://doi.org/#{doi}"
+      doi_response = Faraday.get(doi_url)
+      if doi_response.status == 302
+        paper_url = doi_response.headers[:location]
+      else
+        raise Theoj::Error, "The DOI is invalid, url does not resolve #{doi_url}"
+      end
+
+      paper_data = Faraday.get(paper_url + ".json")
+      if paper_data.status == 200
+        @metadata = JSON.parse(paper_data.body, symbolize_names: true)
+      else
+        raise Theoj::Error, "Could not find the paper data at #{paper_url + ".json"}"
+      end
+    end
+
+    [:title, :state, :submitted_at, :doi, :published_at,
+     :volume, :issue, :year, :page, :authors, :editor,
+     :editor_name, :editor_url, :editor_orcid, :reviewers,
+     :languages, :tags, :software_repository, :paper_review,
+     :pdf_url, :software_archive].each do |method_name|
+      define_method(method_name) { metadata[method_name] }
+      define_method("#{method_name}=") {|value| @metadata[method_name] = value }
+    end
+
+    def yaml_metadata
+      metadata.transform_keys(&:to_s).to_yaml
+    end
+
+    def json_metadata
+      metadata.to_json
+    end
+
+  end
+end

data/lib/theoj/review_issue.rb

@@ -28,7 +28,7 @@ module Theoj
     end
 
     def reviewers
-      @reviewers ||= read_value_from_body("reviewers").split(",").map{|r| r.strip} - ["Pending", "TBD"]
+      @reviewers ||= read_value_from_body("reviewers-list").split(",").map{|r| r.strip} - ["Pending", "TBD"]
     end
 
     def editor

data/lib/theoj/submission.rb

@@ -1,9 +1,12 @@
 require "json"
+require "date"
 require "base64"
 require "faraday"
 
 module Theoj
   class Submission
+    include Theoj::GitHub
+
     attr_accessor :journal
     attr_accessor :review_issue
     attr_accessor :paper
@@ -49,6 +52,65 @@ module Theoj
       metadata.to_json
     end
 
+    # Create metadata used to generate PDF/JATS outputs
+    def article_metadata
+        metadata = {
+          title: paper.title,
+          tags: paper.tags,
+          authors: paper.authors.collect { |a| a.to_h },
+          doi: paper_doi,
+          software_repository_url: review_issue.target_repository,
+          reviewers: review_issue.reviewers.collect{|r| user_login(r)},
+          volume: journal.current_volume,
+          issue: journal.current_issue,
+          year: journal.current_year,
+          page: review_issue.issue_id,
+          journal_alias: journal.alias,
+          software_review_url: journal.reviews_repository_url(review_issue.issue_id),
+          archive_doi: review_issue.archive,
+          citation_string: citation_string
+        }
+
+        metadata.merge(editor_info, dates_info)
+    end
+
+    def editor_info
+      editor_info = { editor: {
+                        github_user: user_login(review_issue.editor),
+                        name: nil,
+                        url: nil,
+                        orcid: nil
+                        }
+                    }
+
+      if review_issue.editor
+        editor_lookup = Faraday.get(journal.url + "/editors/lookup/" + user_login(review_issue.editor))
+        if editor_lookup.status == 200
+          info = JSON.parse(editor_lookup.body, symbolize_names: true)
+          editor_info[:editor][:name] = info[:name]
+          editor_info[:editor][:url] = info[:url]
+          editor_info[:editor][:orcid] = info[:orcid]
+        end
+      end
+
+      editor_info
+    end
+
+    def dates_info
+      dates_info = { submitted_at: nil, published_at: nil }
+
+      if review_issue.issue_id
+        paper_lookup = Faraday.get(journal.url + "/papers/lookup/" + review_issue.issue_id.to_s)
+        if paper_lookup.status == 200
+          info = JSON.parse(paper_lookup.body, symbolize_names: true)
+          dates_info[:submitted_at] = format_date(info[:submitted]) if info[:submitted]
+          dates_info[:published_at] = format_date(info[:accepted]) if info[:accepted]
+        end
+      end
+
+      dates_info
+    end
+
     def deposit!(secret)
       parameters = deposit_payload.merge(secret: secret)
       Faraday.post(journal.data[:deposit_url], parameters.to_json, {"Content-Type" => "application/json"})
@@ -66,5 +128,12 @@ module Theoj
     def paper_doi
       journal.paper_doi_for_id(paper_id)
     end
+
+    private
+    def format_date(date_string)
+      Date.parse(date_string.to_s).strftime("%Y-%m-%d")
+    rescue Date::Error
+      nil
+    end
   end
 end

data/lib/theoj/version.rb

@@ -1,3 +1,3 @@
 module Theoj
-  VERSION = "1.0.0"
+  VERSION = "1.2.1"
 end

data/lib/theoj.rb

@@ -2,6 +2,7 @@ require_relative "theoj/version"
 require_relative "theoj/git"
 require_relative "theoj/github"
 require_relative "theoj/orcid"
+require_relative "theoj/published_paper"
 require_relative "theoj/submission"
 require_relative "theoj/journal"
 require_relative "theoj/review_issue"
@@ -9,4 +10,5 @@ require_relative "theoj/paper"
 require_relative "theoj/author"
 
 module Theoj
+  class Error < StandardError; end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: theoj
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.2.1
 platform: ruby
 authors:
 - Juanjo Bazán
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-10-20 00:00:00.000000000 Z
+date: 2021-11-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: octokit
@@ -126,6 +126,7 @@ files:
 - lib/theoj/journals_data.rb
 - lib/theoj/orcid.rb
 - lib/theoj/paper.rb
+- lib/theoj/published_paper.rb
 - lib/theoj/review_issue.rb
 - lib/theoj/submission.rb
 - lib/theoj/version.rb