Class: Theoj::Submission

Inherits:
Object
  • Object
show all
Includes:
GitHub
Defined in:
lib/theoj/submission.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from GitHub

#can_be_assignee?, #github_access_token, #github_client, #github_headers, #is_collaborator?, #is_invited?, #issue, #issue_labels, #user_login, #username?

Constructor Details

#initialize(journal, review_issue, paper = nil) ⇒ Submission

Returns a new instance of Submission.



15
16
17
18
19
 
# File 'lib/theoj/submission.rb', line 15

def initialize(journal, review_issue, paper=nil)
  @journal = journal
  @review_issue = review_issue
  @paper = paper || @review_issue.paper
end

Instance Attribute Details

#journal ⇒ Object

Returns the value of attribute journal.



11
12
13
 
# File 'lib/theoj/submission.rb', line 11

def journal
  @journal
end

#paper ⇒ Object

Returns the value of attribute paper.



13
14
15
 
# File 'lib/theoj/submission.rb', line 13

def paper
  @paper
end

#review_issue ⇒ Object

Returns the value of attribute review_issue.



12
13
14
 
# File 'lib/theoj/submission.rb', line 12

def review_issue
  @review_issue
end

Instance Method Details

#all_metadata ⇒ Object

Removes archive_doi, adds neurolibre reproducibility assets DOIs.



124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
 
# File 'lib/theoj/submission.rb', line 124

def all_metadata
  metadata = {
    title: plaintext(paper.title),
    tags: paper.tags,
    languages: paper.languages,
    authors: paper.authors.collect { |a| a.to_h },
    doi: paper_doi,
    software_repository_url: review_issue.target_repository,
    review_issue_id: review_issue.issue_id,
    review_editor: review_issue.editor,
    reviewers: review_issue.reviewers,
    volume: journal.current_volume,
    issue: journal.current_issue,
    year: journal.current_year,
    page: review_issue.issue_id,
    journal_alias: journal.alias,
    journal_name: journal.name,
    software_review_url: journal.reviews_repository_url(review_issue.issue_id),
    
    # Context changes from archive --> doi
    repository_doi: review_issue.repository_archive,
    data_doi: review_issue.data_archive,
    book_doi: review_issue.book_archive,
    docker_doi: review_issue.docker_archive,
    # Context does not change for this
    book_exec_url: review_issue.book_exec_url,
    
    citation_author: paper.citation_author
  }
  # @NeuroLibre -- END

  metadata.merge!(editor_info, dates_info)
  metadata[:citation_string] = build_citation_string(metadata)
  metadata
end

#article_metadata ⇒ Object

Create metadata used to generate PDF/JATS outputs Removes archive_doi, adds neurolibre reproducibility assets DOIs.



72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
 
# File 'lib/theoj/submission.rb', line 72

def article_metadata
  {
    title: metadata_info[:title],
    tags: metadata_info[:tags],
    authors: metadata_info[:authors],
    doi: metadata_info[:doi],
    software_repository_url: metadata_info[:software_repository_url],
    reviewers: metadata_info[:reviewers].collect{|r| (r)},
    volume: metadata_info[:volume],
    issue: metadata_info[:issue],
    year: metadata_info[:year],
    page: metadata_info[:page],
    journal_alias: metadata_info[:journal_alias],
    software_review_url: metadata_info[:software_review_url],

    repository_doi: metadata_info[:repository_doi],
    book_exec_url: metadata_info[:book_exec_url],
    data_doi: metadata_info[:data_doi],
    book_doi: metadata_info[:book_doi],
    docker_doi: metadata_info[:docker_doi],
    
    citation_string: metadata_info[:citation_string],
    editor: metadata_info[:editor],
    submitted_at: metadata_info[:submitted_at],
    published_at: metadata_info[:published_at]
  }
end

#citation_string ⇒ Object 



110
111
112
 
# File 'lib/theoj/submission.rb', line 110

def citation_string
  metadata_info[:citation_string]
end

#dates_info ⇒ Object 



182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
 
# File 'lib/theoj/submission.rb', line 182

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

    if dates_info[:published_at]
      yvi = journal.year_volume_issue_for_date(Date.parse(dates_info[:published_at]))
      dates_info[:year] = yvi[0]
      dates_info[:volume] = yvi[1]
      dates_info[:issue] = yvi[2]
    end
  end

  dates_info
end

#deposit!(secret) ⇒ Object 



105
106
107
108
 
# File 'lib/theoj/submission.rb', line 105

def deposit!(secret)
  parameters = deposit_payload.merge(secret: secret)
  Faraday.post(journal.data[:deposit_url], parameters.to_json, {"Content-Type" => "application/json"})
end

#deposit_payload ⇒ Object

Removes archive_doi, adds neurolibre reproducibility assets DOIs.



23
24
25
26
27
28
29
30
31
32
33
34
35
36
 
# File 'lib/theoj/submission.rb', line 23

def deposit_payload
  {
    id: metadata_info[:review_issue_id],
    metadata: Base64.encode64(metadata_payload),
    doi: metadata_info[:doi],
    repository_doi: metadata_info[:repository_doi],
    book_exec_url: metadata_info[:book_exec_url],
    data_doi: metadata_info[:data_doi],
    book_doi: metadata_info[:book_doi],
    docker_doi: metadata_info[:docker_doi],
    citation_string: citation_string,
    title: metadata_info[:title]
  }
end

#editor_info ⇒ Object 



160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
 
# File 'lib/theoj/submission.rb', line 160

def editor_info
  editor_info = { editor: {
                    github_user: (review_issue.editor),
                    name: nil,
                    url: nil,
                    orcid: nil
                    }
                }

  if review_issue.editor
    editor_lookup = Faraday.get(journal.url + "/editors/lookup/" + (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

#metadata_info ⇒ Object 



101
102
103
 
# File 'lib/theoj/submission.rb', line 101

def metadata_info
  @metadata_info ||= all_metadata
end

#metadata_payload ⇒ Object

Create a metadata json payload Removes archive_doi, adds neurolibre reproducibility assets DOIs.



42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
 
# File 'lib/theoj/submission.rb', line 42

def metadata_payload
  {
    paper: {
      title: metadata_info[:title],
      tags: metadata_info[:tags],
      languages: metadata_info[:languages],
      authors: metadata_info[:authors],
      doi: metadata_info[:doi],
      
      repository_doi: metadata_info[:repository_doi],
      book_exec_url: metadata_info[:book_exec_url],
      data_doi: metadata_info[:data_doi],
      book_doi: metadata_info[:book_doi],
      docker_doi: metadata_info[:docker_doi],

      repository_address: metadata_info[:software_repository_url],
      editor: metadata_info[:review_editor],
      reviewers: metadata_info[:reviewers].collect(&:strip),
      volume: metadata_info[:volume],
      issue: metadata_info[:issue],
      year: metadata_info[:year],
      page: metadata_info[:page]
    }
  }.to_json
end

#paper_doi ⇒ Object 



118
119
120
 
# File 'lib/theoj/submission.rb', line 118

def paper_doi
  journal.paper_doi_for_id(paper_id)
end

#paper_id ⇒ Object 



114
115
116
 
# File 'lib/theoj/submission.rb', line 114

def paper_id
  journal.paper_id_from_issue(review_issue.issue_id)
end

#track ⇒ Object 



204
205
206
207
208
209
210
211
212
213
214
215
 
# File 'lib/theoj/submission.rb', line 204

def track
  track_info = { name: nil, short_name: nil, code: nil, label: nil, parameterized: nil}

  if review_issue.issue_id
    track_lookup = Faraday.get(journal.url + "/papers/" + review_issue.issue_id.to_s + "/lookup_track" )
    if track_lookup.status == 200
      track_info = JSON.parse(track_lookup.body, symbolize_names: true)
    end
  end

  track_info
end