figshare_api_v2 0.9.9 → 0.9.11

checksums.yaml

@@ -1,7 +1,7 @@
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data/History.txt

@@ -1,3 +1,39 @@
+robertburrowes	Tue Sep 27 15:24:24 2022 +1300
+	Added in collection handling. Shifted author processing to figshare library
+robertburrowes	Tue Sep 27 14:39:31 2022 +1300
+	Authors shoud be an array of Hash records.
+robertburrowes	Tue Sep 27 14:39:06 2022 +1300
+	Added body() for creating the body Hash needed for creating a new Collection
+robertburrowes	Tue Sep 27 14:38:25 2022 +1300
+	typo in name
+robertburrowes	Tue Sep 27 12:11:20 2022 +1300
+	Bumped version for 'institute' needing to be an Integer in json
+robertburrowes	Tue Sep 27 12:09:20 2022 +1300
+	institute has to be an Integer. A string now generates an exception
+robertburrowes	Tue Sep 27 09:04:43 2022 +1300
+	Debugging bulk user info request. Still getting inconsistent numbers of users being returned.
+robertburrowes	Tue Sep 27 09:03:55 2022 +1300
+	Testing what comes back
+robertburrowes	Fri May 13 08:40:05 2022 +1200
+	Bumped minor version
+robertburrowes	Thu May 12 17:25:07 2022 +1200
+	Moved the accounts_wrapper() into institution.accounts(), less the debugging stuff
+robertburrowes	Thu May 12 17:06:48 2022 +1200
+	Comment
+robertburrowes	Thu May 12 16:52:57 2022 +1200
+	Check returned account IDs are in order (they do seem to be)
+robertburrowes	Thu May 12 16:32:58 2022 +1200
+	Incorporate the new id_gte into institute.accounts, as page/page_size pagination has a 9000 record limit.
+robertburrowes	Thu May 12 16:22:48 2022 +1200
+	return earlier, in _paginate, to not set 'page'
+robertburrowes	Thu May 12 15:56:44 2022 +1200
+	Added 'once_only' to the post and get _pagination calls, so we don't automatically move onto the next page.
+robertburrowes	Thu May 12 11:18:45 2022 +1200
+	Refactored _pagination response code to see if it helped fix the duplicate record issue. It didn't.
+robertburrowes	Thu May 12 09:43:45 2022 +1200
+	Added debug output of updated Figshare API.
+robertburrowes	Wed May 11 09:07:42 2022 +1200
+	update comments
 robertburrowes	Tue May 10 10:42:27 2022 +1200
 	Comment
 robertburrowes	Tue May 10 10:40:02 2022 +1200

data/lib/authors.rb

@@ -31,7 +31,7 @@ module Figshare
                 &block
               )
       args = { 'search_for' => search_for }
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group_id'] = group_id unless group_id.nil?
       args['is_active'] = is_active unless is_active.nil?
       args['is_public'] = is_public unless is_public.nil?

data/lib/base.rb

@@ -71,41 +71,53 @@ module Figshare
     # @param by_offset [Boolean] use offset/limit rather than page/page_size in API calls
     # @yield [String] if given a block, iterates through the result from figshare
     # @return [Integer] number of results.
-    private def get_paginate(api_query:, args: {}, debug: false, by_offset: false, &block)
+    private def get_paginate(api_query:, args: {}, debug: false, by_offset: false, once_only: false, &block)
       args = {} if args.nil?
-      if ! args.is_a?(Hash)
-        raise 'get_paginate(): Expecting args to be a Hash'
-      end
-
-      # Loop variables, if we are using pages
-      page = args['page'].nil? ? 1 : args['page']
-      page_size = args['page_size'].nil? ? 100 : args['page_size']
-
-      # Loop variables, if we are using offsets
-      offset = args['offset'].nil? ? 0 : args['offset']
-      limit = args['limit'].nil? ? 100 : args['limit']
+      raise 'get_paginate(): Expecting args to be a Hash' unless args.is_a?(Hash)
 
       by_offset = true if args['page'].nil? && ! args['offset'].nil?
+      if by_offset
+        # Loop variables, if we are using offsets
+        offset = args['offset'].nil? ? 0 : args['offset']
+        limit = args['limit'].nil? ? 100 : args['limit']
+        args['offset'] = offset
+        args['limit'] = limit
+      else
+        page = args['page'].nil? ? 1 : args['page']
+        page_size = args['page_size'].nil? ? 100 : args['page_size']
+        args['page'] = page
+        args['page_size'] = page_size
+      end
 
       # How many results so far.
       result_count = 0
 
       loop do
         content_type = response = nil
-        form_args = by_offset ? { 'limit' => limit, 'offset' => offset } : { 'page_size' => page_size, 'page' => page }
         WIKK::WebBrowser.https_session( host: @hostname, verify_cert: false ) do |ws|
           response = ws.get_page( query: "#{@api_url}#{api_query}",
                                   authorization: "token #{@auth_token}",
-                                  form_values: form_args.merge(args)
+                                  form_values: args
                                 )
           content_type = ws.header_value(key: 'Content-Type')
         end
+        # File.write("/tmp/debug_#{args['id_gte']}_#{page}.json", response)
         page_count = iterate_json_response(response: response, content_type: content_type, debug: debug, &block)
         result_count += page_count
-        break if page_count < page_size # Got less results than we asked for, so it was the last page
 
-        page += 1 # Ready to fetch next page
-        offset += limit # if we use offset, then mor
+        return result_count if once_only
+
+        if by_offset
+          break if page_count < limit # Got less results than we asked for, so it was the last page
+
+          offset += limit # if we use offset
+          args['offset'] = offset
+        else
+          break if page_count < page_size # Got less results than we asked for, so it was the last page
+
+          page += 1 # Ready to fetch next page
+          args['page'] = page
+        end
       end
 
       return result_count
@@ -156,42 +168,54 @@ module Figshare
     # @param by_offset [Boolean] use offset/limit rather than page/page_size in API calls
     # @yield [String] if given a block, iterates through the result from figshare
     # @return [Integer] number of results.
-    private def post_paginate(api_query:, args: {}, debug: false, by_offset: false, &block)
+    private def post_paginate(api_query:, args: {}, debug: false, by_offset: false, once_only: false, &block)
       # Loop variables, if we are using pages
-      page = args['page'].nil? ? 1 : args['page']
-      page_size = args['page_size'].nil? ? 100 : args['page_size']
+      args = {} if args.nil?
+      raise 'post_paginate(): Expecting args to be a Hash' unless args.is_a?(Hash)
 
-      # Loop variables, if we are using offsets
-      offset = args['offset'].nil? ? 0 : args['offset']
-      limit = args['limit'].nil? ? 100 : args['limit']
+      by_offset = true if args['page'].nil? && ! args['offset'].nil?
+      if by_offset
+        # Loop variables, if we are using offsets
+        offset = args['offset'].nil? ? 0 : args['offset']
+        limit = args['limit'].nil? ? 100 : args['limit']
+        args['offset'] = offset
+        args['limit'] = limit
+      else
+        page = args['page'].nil? ? 1 : args['page']
+        page_size = args['page_size'].nil? ? 100 : args['page_size']
+        args['page'] = page
+        args['page_size'] = page_size
+      end
 
       # How many results so far.
       result_count = 0
 
-      by_offset = true if args['page'].nil? && ! args['offset'].nil?
-
-      args = {} if args.nil?
-      if ! args.is_a?(Hash)
-        raise 'post_paginate(): Expecting args to be a Hash'
-      end
-
       loop do
         content_type = response = nil
-        form_args = by_offset ? { 'limit' => limit, 'offset' => offset } : { 'page_size' => page_size, 'page' => page }
         WIKK::WebBrowser.https_session( host: @hostname, verify_cert: false ) do |ws|
           response = ws.post_page(  query: "#{@api_url}#{api_query}",
                                     content_type: 'application/json; charset=UTF-8',
                                     authorization: "token #{@auth_token}",
-                                    data: args.merge(form_args).to_j
+                                    data: args.to_j
                                  )
           content_type = ws.header_value(key: 'Content-Type')
         end
         page_count = iterate_json_response(response: response, content_type: content_type, debug: debug, &block)
         result_count += page_count
-        break if page_count < page_size # Got less results than we asked for, so it was the last page
 
-        page += 1 # Ready to fetch next page
-        offset += limit # if we use offset
+        return result_count if once_only
+
+        if by_offset
+          break if page_count < limit # Got less results than we asked for, so it was the last page
+
+          offset += limit # if we use offset
+          args['offset'] = offset
+        else
+          break if page_count < page_size # Got less results than we asked for, so it was the last page
+
+          page += 1 # Ready to fetch next page
+          args['page'] = page
+        end
       end
       return result_count
     end

data/lib/figshare_api_v2.rb

@@ -1,7 +1,7 @@
 module Figshare # :nodoc:
   # Figshare module initialization
   #
-  VERSION = '0.9.9'
+  VERSION = '0.9.11'
 
   require 'wikk_webbrowser'
   require 'wikk_json'

data/lib/institutions.rb

@@ -14,9 +14,9 @@ module Figshare
       end
     end
 
-    # Get the institional account details
+    # Get the institional account's details (not a person's account details)
     #
-    # @yield [Hash]
+    # @yield [Hash] {id:, name: "institute"}
     def account(&block)
       get(api_query: 'account/institution', &block)
     end
@@ -137,12 +137,13 @@ module Figshare
     end
 
     # Get the accounts for which the account has administrative privileges (assigned and inherited).
+    # Accounts are returned in account id order, and there is a 9000 user upper limit. See id_gte.
     #
     # @param is_active [Boolean] user account is active
     # @param institution_user_id [String] As set in the HR upload
     # @param email [String] as set in the HR upload
-    # @param id_lte [Integer] ID is <=
-    # @param id_gte [Integer] ID is >=
+    # @param id_lte [Integer] ID is <= Introduced to get around the buffer limit of 9000 users
+    # @param id_gte [Integer] ID is >= Introduced to get around the buffer limit of 9000 users
     # @param page [Numeric] Pages start at 1. Page and Page size go together
     # @param page_size [Numeric]
     # @param offset [Numeric] offset is 0 based.  Offset and Limit go together
@@ -157,6 +158,7 @@ module Figshare
                   page_size: nil,
                   offset: nil,
                   limit: nil,
+                  cursor_pagination: true,
                   &block
                 )
       args = {}
@@ -169,7 +171,26 @@ module Figshare
       args['page_size'] = page_size unless page_size.nil?
       args['offset'] = offset unless offset.nil?
       args['limit'] = limit unless limit.nil?
-      get_paginate(api_query: 'account/institution/accounts', args: args, &block)
+      if cursor_pagination
+        highest_id_gte = 0
+        args['id_lte'] = nil
+        args['page_size'] = 100
+        loop do
+          count = 0
+          args['page'] = 1
+          args['id_gte'] = highest_id_gte + 1
+          get_paginate(api_query: 'account/institution/accounts', args: args, once_only: true) do |account|
+            next if account.nil? || account['id'].nil?
+
+            count += 1
+            highest_id_gte = account['id'].to_i if highest_id_gte < account['id'].to_i
+            yield account
+          end
+          break if count < 100 # Didn't reach the page_size limit.
+        end
+      else # Do it the old broken way (Pagination only works for the first 9000 entries)
+        get_paginate(api_query: 'account/institution/accounts', args: args, &block)
+      end
     end
 
     # Create new Institution Account

data/lib/private_articles.rb

@@ -67,7 +67,7 @@ module Figshare
               )
       args = { 'search_for' => search_for }
       args['impersonate'] = impersonate unless impersonate.nil?
-      args['institution'] = @institute_id unless institute.nil? # Inconsistent use. Other calls use institute_id
+      args['institution'] = @institute_id.to_i if institute # Inconsistent use. Other calls use institute_id
       args['group'] = group_id unless group_id.nil? # Not sure if this changed from group_id to group
       args['item_type'] = item_type unless item_type.nil?
       args['resource_id'] = resource_id unless resource_id.nil?
@@ -138,7 +138,17 @@ module Figshare
       body_['references'] = references unless references.nil?
       body_['categories'] = categories unless categories.nil?
       body_['categories_by_source_id'] = categories_by_source_id unless categories_by_source_id.nil?
-      body_['authors'] = authors unless authors.nil?
+      authors_array = []
+      if authors.instance_of?(Array)
+        authors.each do |author|
+          authors_array << if author.instance_of?(Hash)
+                             author
+                           else
+                             { 'name' => author }
+                           end
+        end
+      end
+      body_['authors'] = authors_array
       body_['custom_fields'] = custom_fields unless custom_fields.nil?
       body_['custom_fields_list'] = custom_fields_list unless custom_fields_list.nil?
       body_['defined_type'] = defined_type unless defined_type.nil?

data/lib/private_collections.rb

@@ -70,7 +70,7 @@ module Figshare
               )
       args = { 'search_for' => search_for }
       args['impersonate'] = impersonate unless impersonate.nil?
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group'] = group_id unless group_id.nil?
       args['resource_id'] = resource_id unless resource_id.nil?
       args['resource_doi'] = resource_doi unless resource_doi.nil?
@@ -87,6 +87,89 @@ module Figshare
       post_paginate(api_query: 'account/collections/search', args: args, &block)
     end
 
+    # Create a body for use with create and update methods
+    #
+    # @param title [String] Required
+    # @param description [String] The article description. In a publisher case, usually this is the remote article description
+    # @param tags [Array] List of tags (strings) to be associated with the article. Tags can be used instead
+    # @param keywords [Array] List of tags (strings) to be associated with the article. Tags can be used instead
+    # @param references [Array] List of links to be associated with the article (e.g ["http://link1", "http://link2", "http://link3"])
+    # @param categories [Array] List of category ids to be associated with the article(e.g [1, 23, 33, 66])
+    # @param categories_by_source_id [Array] List of category ids to be associated with the article(e.g ["300204", "400207"])
+    # @param authors [Array] List of authors to be associated with the article. The list can contain the following fields: id, name, first_name, last_name, email, orcid_id. If an id is supplied, it will take priority and everything else will be ignored. No more than 10 authors. For adding more authors use the specific authors endpoint. e.g. { "name" => "Joe X"} and or { "id" => 123 }
+    # @param custom_fields [Hash] List of key, values pairs to be associated with the article. eg. { "key" => "value"}
+    # @param custom_fields_list [Array] List of key, values pairs to be associated with the article. eg. [{ "key" => "value"}]
+    # @param defined_type [String] one of "figshare","media","dataset","poster","journal contribution", "presentation", "thesis", "software", "online resource", "preprint", "book", "conference contribution", "chapter", "peer review", "educational resource", "report", "standard", "composition", "funding", "physical object", "data management plan", "workflow", "monograph", "performance", "event", "service", "model", "registration"
+    # @param funding [String] Grant number or funding authority
+    # @param funding_list [Array] Funding creation / update items. eg {"id" => 0, "title" => "string"}
+    # @param license [Integer] License id for this article.
+    # @param doi [String] Not applicable for regular users. In an institutional case, make sure your group supports setting DOIs. This setting is applied by figshare via opening a ticket through our support/helpdesk system.
+    # @param handle [String] Not applicable for regular users. In an institutional case, make sure your group supports setting Handles. This setting is applied by figshare via opening a ticket through our support/helpdesk system.
+    # @param resource_doi [String] Not applicable to regular users. In a publisher case, this is the publisher article DOI.
+    # @param resource_title [String] Not applicable to regular users. In a publisher case, this is the publisher article title.
+    # @param timeline [Hash] Various timeline dates ie. { "firstOnline" => "date_string", "publisherPublication" => "date_string", "publisherAcceptance" => "date_string"},
+    # @param group_id [Integer] Not applicable to regular users. This field is reserved to institutions/publishers with access to assign to specific groups
+    def body( title:,
+              description: nil,
+              is_metadata_record: nil,
+              metadata_reason: nil,
+              tags: nil,
+              keywords: nil,
+              references: nil,
+              categories: nil,
+              categories_by_source_id: nil,
+              authors: nil,
+              custom_fields: nil,
+              custom_fields_list: nil,
+              defined_type: nil,
+              funding: nil,
+              funding_list: nil,
+              license: nil,
+              doi: nil,
+              handle: nil,
+              resource_doi: nil,
+              resource_title: nil,
+              timeline: nil,
+              group_id: nil
+            )
+      body_ = {
+        'title' => title
+      }
+      body_['description'] = description unless description.nil?
+      body_['is_metadata_record'] = is_metadata_record unless is_metadata_record.nil?
+      body_['metadata_reason'] = metadata_reason unless metadata_reason.nil?
+      body_['tags'] = tags unless tags.nil?
+      body_['keywords'] = keywords unless keywords.nil?
+      body_['references'] = references unless references.nil?
+      body_['categories'] = categories unless categories.nil?
+      body_['categories_by_source_id'] = categories_by_source_id unless categories_by_source_id.nil?
+      authors_array = []
+      if authors.instance_of?(Array)
+        authors.each do |author|
+          authors_array << if author.instance_of?(Hash)
+                             author
+                           else
+                             { 'name' => author }
+                           end
+        end
+      end
+      body_['authors'] = authors_array
+      body_['custom_fields'] = custom_fields unless custom_fields.nil?
+      body_['custom_fields_list'] = custom_fields_list unless custom_fields_list.nil?
+      body_['defined_type'] = defined_type unless defined_type.nil?
+      body_['funding'] = funding unless funding.nil?
+      body_['funding_list'] = funding_list unless funding_list.nil?
+      body_['license'] = license unless license.nil?
+      body_['doi'] = doi unless doi.nil?
+      body_['handle'] = handle unless handle.nil?
+      body_['resource_doi'] = resource_doi unless resource_doi.nil?
+      body_['resource_title'] = resource_title unless resource_title.nil?
+      body_['timeline'] = timeline unless timeline.nil?
+      body_['group_id'] = group_id unless group_id.nil?
+
+      return body_
+    end
+
     # Create a new private Collection by sending collection information
     #
     # @param body [Hash] See Figshare API docs
@@ -133,7 +216,7 @@ module Figshare
     #
     # @param collection_id [Integer] Figshare id of the collection
     # @param impersonate [Integer] Figshare account_id of the user we are making this call on behalf of
-    # @yield [Hash] { doi }
+    # @yield [Hash] { "doi" => "the_doi" }
     def reserve_doi(collection_id:, impersonate: nil, &block)
       args = {}
       args['impersonate'] = impersonate unless impersonate.nil?

data/lib/private_projects.rb

@@ -63,7 +63,7 @@ module Figshare
                 &block
               )
       args = { 'search_for' => search_for }
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group'] = group_id unless group_id.nil?
       args['impersonate'] = impersonate unless impersonate.nil?
       args['published_since'] = published_since unless published_since.nil?
@@ -363,7 +363,7 @@ module Figshare
     # @param project_id [Integer] Figshare id of the project
     # @param article_id [Integer] Figshare id of the article
     # @param impersonate [Integer] Figshare account_id of the user we are making this call on behalf of
-    # @yield [Array] See docs.figshare.com for article hash
+    # @yield [Array] See docs.figshare.com
     def artilce_files(project_id:, article_id:, impersonate: nil, &block)
       args = {}
       args['impersonate'] = impersonate unless impersonate.nil?

data/lib/public_articles.rb

@@ -36,7 +36,7 @@ module Figshare
               &block
             )
       args = {}
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group_id'] = group_id unless group_id.nil?  # Not sure if this should be 'group' or 'group_id'. API has conflicting info
       args['item_type'] = item_type unless item_type.nil?
       args['resource_doi'] = resource_doi unless resource_doi.nil?
@@ -80,7 +80,7 @@ module Figshare
                 &block
               )
       args = { 'search_for' => search_for }
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group_id'] = group_id unless group_id.nil?
       args['item_type'] = item_type unless item_type.nil?
       args['resource_doi'] = resource_doi unless resource_doi.nil?

data/lib/public_collections.rb

@@ -4,7 +4,7 @@ module Figshare
   class PublicCollections < Base
     # Requests a list of public collections
     #
-    # @param institution [Boolean] Just our institution
+    # @param institute [Boolean] Just our institution
     # @param group_id [Integer] Only return this group's collections
     # @param published_since [Time] Return results if published after this time
     # @param modified_since [Time] Return results if modified after this time
@@ -18,7 +18,7 @@ module Figshare
     # @param offset [Numeric] offset is 0 based.  Offset and Limit go together
     # @param limit [Numeric]
     # @yield [Hash] {id, title, doi, handle, url, published_date}
-    def list( institution: false,
+    def list( institute: false,
               group_id: nil,
               published_since: nil,
               modified_since: nil,
@@ -34,7 +34,7 @@ module Figshare
               &block
             )
       args = {}
-      args['institution'] = @institute_id unless institution.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group'] = group_id unless group_id.nil?
       args['resource_doi'] = resource_doi unless resource_doi.nil?
       args['doi'] = doi unless doi.nil?
@@ -76,7 +76,7 @@ module Figshare
                 &block
               )
       args = { 'search_for' => search_for }
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group_id'] = group_id unless group_id.nil?
       args['item_type'] = item_type unless item_type.nil?
       args['resource_doi'] = resource_doi unless resource_doi.nil?

data/lib/public_projects.rb

@@ -26,7 +26,7 @@ module Figshare
               &block
             )
       args = {}
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group'] = group_id unless group_id.nil?
       args['published_since'] = published_since unless published_since.nil?
       args['order'] = order unless order.nil?
@@ -57,7 +57,7 @@ module Figshare
                 &block
               )
       args = { 'search_for' => search_for }
-      args['institution'] = @institute_id unless institute.nil?
+      args['institution'] = @institute_id.to_i if institute
       args['group'] = group_id unless group_id.nil?
       args['published_since'] = published_since unless published_since.nil?
       args['modified_since'] = modified_since unless modified_since.nil?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: figshare_api_v2
 version: !ruby/object:Gem::Version
-  version: 0.9.9
+  version: 0.9.11
 platform: ruby
 authors:
 - Rob Burrowes
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-05-10 00:00:00.000000000 Z
+date: 2022-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: wikk_json
@@ -72,14 +72,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.23'
+        version: '3.25'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.23'
+        version: '3.25'
 description: |-
   Figshare version 2 API.
 
@@ -136,7 +136,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.22
+rubygems_version: 3.3.7
 signing_key:
 specification_version: 4
 summary: Figshare version 2 API