roboneuro 0.1.2 → 0.1.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 229efd4a36c74c79d4bd13b049d5fabc490755ba1cfd3c6b4975d7d3a679f6ee
+  metadata.gz: 0ae582272abc421d012bce9b43d328adf2b5c50aaf9122c64f3f13b360b1fb2c
+  data.tar.gz: 8dffcf7ea86fae1e5edbaf5a99500fe193d51123775762e417dea7d6406ee90e
 SHA512:
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-  data.tar.gz: 6bb0ccf1b8a1f58f3217505e05c548bc97efbe1f0151b397a0fabd8e6bd53be1e935ab16329933f27f218e7a369d131881ddd981b557eafe53822189c4548d8d
+  metadata.gz: d0e3be3dcfc6a31b9d4a36c9241e4042371b7ec3c4c5bcf6718370e90901c7a55f0fee06287b219f0c878f2582f64b1675766f8a2f06d9a67fa5241fbf101d11
+  data.tar.gz: 5d8d2e1719bcf688cbe163d8ed05f22e7fd449c3d973cc0e62fef656bf0a00e5e3f53826e424b23b63d14b183b188236cec4e80fa7171479226d83a36743c4cc

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    roboneuro (0.1.2)
+    roboneuro (0.1.5)
       bibtex-ruby (~> 6.0.0)
       dotenv
       github-linguist (~> 5.3)
@@ -102,7 +102,7 @@ GEM
       rspec-support (~> 3.10.0)
     rspec-support (3.10.2)
     ruby2_keywords (0.0.5)
-    rugged (1.4.2)
+    rugged (1.4.3)
     sawyer (0.8.2)
       addressable (>= 2.3.5)
       faraday (> 0.8, < 2.0)

data/README.md

@@ -1,3 +1,5 @@
+Modified for NeuroLibre.
+
 # What is Whedon?
 
 Whedon is a collection of command-line utilities to manage JOSS submissions. Whedon is used by the [Whedon-API bot](https://github.com/openjournals/whedon-api) to interact with authors and reviewers during the review process on https://github.com/openjournals/joss-reviews
@@ -14,6 +16,8 @@ Hopefully...
 
 [![Build Status](https://github.com/openjournals/whedon/actions/workflows/tests.yml/badge.svg)](https://github.com/openjournals/whedon/actions/workflows/tests.yml)
 
+[![Gem Version](https://badge.fury.io/rb/roboneuro.svg)](https://badge.fury.io/rb/roboneuro)
+
 ## Installation
 
 Depending on how Ruby is installed on your system there might slightly different steps be necessary. Note that Whedon is only tested for reasonably modern versions of Ruby (i.e. > 2.1) [Bundler](http://bundler.io/) is used to install dependencies.

data/lib/whedon/compilers.rb

@@ -106,7 +106,6 @@ module Compilers
   def pdf_from_markdown(custom_branch=nil, draft=true, paper_issue=nil, paper_volume=nil, paper_year=nil)
     latex_template_path = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/latex.template"
     csl_file = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/apa.csl"
-    book_exec_icon = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/logo_link.png"
 
     url = "#{ENV['JOURNAL_URL']}/papers/lookup/#{@review_issue_id}"
     response = RestClient.get(url)
@@ -115,7 +114,7 @@ module Compilers
     published = parsed['accepted']
 
     # TODO - remove this once JOSE has their editors hooked up in the system
-    if ENV['JOURNAL_ALIAS'] == "joss" && !paper.editor.nil?
+    if ENV['JOURNAL_ALIAS'] == "neurolibre" && !paper.editor.nil?
       editor_lookup_url = "#{ENV['JOURNAL_URL']}/editors/lookup/#{paper.editor}"
       response = RestClient.get(editor_lookup_url)
       parsed = JSON.parse(response)
@@ -148,7 +147,6 @@ module Compilers
       "book_doi" => book_doi,
       "docker_doi" => docker_doi,
       "book_exec_url" => book_exec_url,
-      "book_exec_icon" => book_exec_icon,
       "paper_url" => paper.pdf_url,
       "journal_name" => ENV['JOURNAL_NAME'],
       "review_issue_url" => paper.review_issue_url,
@@ -178,7 +176,6 @@ module Compilers
     -V book_doi="#{book_doi}" \
     -V docker_doi="#{docker_doi}" \
     -V book_exec_url="#{book_exec_url}" \
-    -V book_exec_icon="#{book_exec_icon}" \
     -V review_issue_url="#{paper.review_issue_url}" \
     -V editor_url="#{editor_url}" \
     -V graphics="true" \
@@ -230,7 +227,7 @@ module Compilers
     -V paper_url=#{paper.pdf_url} \
     -V joss_resource_url=#{paper.joss_resource_url} \
     -V journal_alias=#{ENV['JOURNAL_ALIAS']} \
-    -V journal_abbrev_title=#{ENV['JOURNAL_ALIAS'].upcase} \
+    -V journal_abbrev_title=#{ENV['JOURNAL_ABBRV_TITLE']} \
     -V journal_url=#{ENV['JOURNAL_URL']} \
     -V journal_name='#{ENV['JOURNAL_NAME']}' \
     -V journal_issn=#{ENV['JOURNAL_ISSN']} \
@@ -300,7 +297,7 @@ module Compilers
       "paper_url" => paper.pdf_url,
       "joss_resource_url" => paper.joss_resource_url,
       "journal_alias" => ENV['JOURNAL_ALIAS'],
-      "journal_abbrev_title" => ENV['JOURNAL_ALIAS'].upcase,
+      "journal_abbrev_title" => ENV['JOURNAL_ABBRV_TITLE'],
       "journal_url" => ENV['JOURNAL_URL'],
       "journal_name" => ENV['JOURNAL_NAME'],
       "journal_issn"=> ENV['JOURNAL_ISSN'],

data/lib/whedon/processor.rb

@@ -118,11 +118,13 @@ module Whedon
     end
 
     def deposit
-      crossref_deposit
+      #crossref_deposit
       joss_deposit
 
       puts "p=dat #{@review_issue_id};p.doi='#{paper.formatted_doi}';"\
-           "p.archive_doi=#{archive_doi};p.accepted_at=Time.now;"\
+           "p.repository_doi=#{repository_doi};p.accepted_at=Time.now;"\
+           "p.data_doi=#{data_doi};p.book_doi=#{book_doi};"\
+           "p.docker_doi=#{docker_doi};p.book_exec_url=#{book_exec_url};"\
            "p.citation_string='#{citation_string}';"\
            "p.authors='#{paper.authors_string}';p.title='#{paper.title}';"
     end
@@ -131,18 +133,24 @@ module Whedon
       puts "Depositing with JOSS..."
       request = RestClient::Request.new(
                 :method => :post,
-                :url => "#{ENV['JOURNAL_URL']}/papers/api_deposit",
+                :url => "http://neurolibre.herokuapp.com/papers/api_deposit",
+                verify_ssl: false,
                 :payload => {
                   :id => paper.review_issue_id,
                   :metadata => Base64.encode64(paper.deposit_payload.to_json),
                   :doi => paper.formatted_doi,
-                  :archive_doi => archive_doi,
+                  :repository_doi => repository_doi,
+                  :data_doi => data_doi,
+                  :book_doi => book_doi,
+                  :docker_doi => docker_doi,
+                  :book_exec_url => book_exec_url,
                   :citation_string => citation_string,
                   :title => paper.plain_title,
                   :secret => ENV['WHEDON_SECRET']
                 })
 
       response = request.execute
+      puts response.body
       if response.code == 201
         puts "Deposit looks good."
       else
@@ -155,6 +163,7 @@ module Whedon
         puts "Depositing with Crossref..."
         request = RestClient::Request.new(
                   :method => :post,
+                  #:url => "https://test.crossref.org/servlet/deposit",
                   :url => "https://doi.crossref.org/servlet/deposit",
                   :payload => {
                     :multipart => true,

data/lib/whedon/version.rb

@@ -1,3 +1,3 @@
 module Whedon
-  VERSION = "0.1.2"
+  VERSION = "0.1.5"
 end

data/lib/whedon.rb

@@ -185,6 +185,7 @@ module Whedon
       payload['paper']['data_doi'] = review_issue_body[ARCHIVE_DATA_REGEX].gsub('"', '')
       payload['paper']['book_doi'] = review_issue_body[ARCHIVE_BOOK_REGEX].gsub('"', '')
       payload['paper']['docker_doi'] = review_issue_body[ARCHIVE_DOCKER_REGEX].gsub('"', '')
+      payload['paper']['book_exec_url'] = review_issue_body[BOOK_EXEC_REGEX].gsub('"', '')
       payload['paper']['repository_address'] = review_issue_body[REPO_REGEX].gsub('"', '')
       payload['paper']['editor'] = "@#{editor}"
       payload['paper']['reviewers'] = reviewers.collect(&:strip)

data/resources/crossref.template

@@ -7,14 +7,13 @@
       <depositor_name>NeuroLibre Admin</depositor_name>
       <email_address>roboneurolibre@gmail.com</email_address>
     </depositor>
-    <registrant>The Open Journal</registrant>
+    <registrant>Centre de Recherche de l'Institut Universitaire de Geriatrie de Montreal</registrant>
   </head>
   <body>
     <journal>
       <journal_metadata>
         <full_title>$journal_name$</full_title>
         <abbrev_title>$journal_abbrev_title$</abbrev_title>
-        <issn media_type="electronic">$journal_issn$</issn>
         <doi_data>
           <doi>10.55458/$journal_alias$</doi>
           <resource>$journal_url$</resource>
@@ -58,7 +57,7 @@
           </rel:related_item>
           <rel:related_item>
             <rel:description>Dataset archive</rel:description>
-            <rel:inter_work_relation relationship-type="hasPart" identifier-type="doi">$dataset_doi$</rel:inter_work_relation>
+            <rel:inter_work_relation relationship-type="hasPart" identifier-type="doi">$data_doi$</rel:inter_work_relation>
           </rel:related_item>
           <rel:related_item>
             <rel:description>Book archive</rel:description>

data/resources/{NeuroLibre → neurolibre}/defaults.yaml

@@ -4,9 +4,9 @@ csl: /usr/local/share/openjournals/NeuroLibre/apa.csl
 variables:
   joss_resource_url: 'N/A'
   journal_abbrev_title: 'NeuroLibre'
-  journal_alias: 'NeuroLibre'
+  journal_alias: 'neurolibre'
   journal_issn: '0000-0000'
-  journal_name: 'NeuroLibre Executable Preprint Server'
+  journal_name: 'NeuroLibre Reproducible Preprint Server'
   journal_url: 'https://neurolibre.org/'
 
 metadata:

data/resources/{NeuroLibre → neurolibre}/latex.template

@@ -431,29 +431,35 @@ $endif$
   %\hrule
   \sffamily\small
 
-  \href{$book_exec_url$}{\includegraphics[width=\marginparwidth]{$book_exec_icon$}}
-
-  \vspace{1mm}
+  \vspace{-4.5cm}
 
   {\bfseries DOI:} \href{https://doi.org/$formatted_doi$}{\color{red}{$formatted_doi$}}
 
   \vspace{2mm}
 
-  {\bfseries Jupyter Book}
+    {\bfseries Reproducible Preprint}
+  \begin{itemize}
+    \setlength\itemsep{0em}
+    \item \href{$book_exec_url$}{\color{red}{Jupyter Book}} \ExternalLink
+  \end{itemize}
+
+  \vspace{2mm}
+
+  {\bfseries Code}
   \begin{itemize}
     \setlength\itemsep{0em}
     \item \href{$review_issue_url$}{\color{red}{Technical Screening}} \ExternalLink
-    \item \href{$repository$}{\color{red}{Source}} \ExternalLink
+    \item \href{$repository$}{\color{red}{Submitted Repository}} \ExternalLink
   \end{itemize}
 
   \vspace{2mm}
 
-  {\bfseries Zenodo Archives}
+  {\bfseries Archives}
   \begin{itemize}
     \setlength\itemsep{0em}
     \item \href{$repository_doi$}{\color{red}{Repository}} \ExternalLink
     \item \href{$data_doi$}{\color{red}{Dataset}} \ExternalLink
-    \item \href{$book_doi$}{\color{red}{Built Book}} \ExternalLink
+    \item \href{$book_doi$}{\color{red}{Jupyter Book}} \ExternalLink
     \item \href{$docker_doi$}{\color{red}{Container}} \ExternalLink
   \end{itemize}
 
@@ -466,7 +472,7 @@ $endif$
   {\bfseries Editor:} \href{$editor_url$}{\color{red}$editor_name$} \ExternalLink \\
   \vspace{1mm}
   $if(reviewers)$
-  {\bfseries Reviewers:}
+  {\bfseries Reviewer(s):}
   \begin{itemize}
   \setlength\itemsep{0em}
   $for(reviewers)$

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: roboneuro
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.5
 platform: ruby
 authors:
 - Agah Karakuzu
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-12 00:00:00.000000000 Z
+date: 2022-04-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bibtex-ruby
@@ -315,12 +315,6 @@ files:
 - lib/whedon/version.rb
 - paperdraft.Dockerfile
 - pkg/roboneuro-0.1.0.gem
-- resources/NeuroLibre/aas-logo.png
-- resources/NeuroLibre/apa.csl
-- resources/NeuroLibre/defaults.yaml
-- resources/NeuroLibre/latex.template
-- resources/NeuroLibre/logo.png
-- resources/NeuroLibre/logo_link.png
 - resources/apa.csl
 - resources/crossref.template
 - resources/docker-defaults.yaml
@@ -337,6 +331,12 @@ files:
 - resources/joss/latex.template
 - resources/joss/logo.png
 - resources/latex.template
+- resources/neurolibre/aas-logo.png
+- resources/neurolibre/apa.csl
+- resources/neurolibre/defaults.yaml
+- resources/neurolibre/latex.template
+- resources/neurolibre/logo.png
+- resources/neurolibre/logo_link.png
 - resources/time.lua
 - roboneuro.gemspec
 - spec/auditor_spec.rb