figshare_api_v2 0.9.3 → 0.9.7

checksums.yaml

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

@@ -1,3 +1,59 @@
+robertburrowes	Tue Nov 2 13:12:30 2021 +1300
+	Saner initialization option :)
+robertburrowes	Tue Sep 21 13:03:44 2021 +1200
+	Experimenting with fetching user accounts. Finding a 9000 limit on the total responses, resulting in odd differences in the numbers between  fetching everyone, just active, and just inactive accounts. None of which match using the figshare admin web pages
+robertburrowes	Tue Sep 21 13:01:16 2021 +1200
+	Rubocop'd
+robertburrowes	Tue Sep 21 13:00:57 2021 +1200
+	Rubocop'd Added chdir, so Atom starts in the right dir
+robertburrowes	Mon Sep 20 12:31:26 2021 +1200
+	Test for listing all institutional accounts, and getting individual account quota.
+robertburrowes	Mon Sep 20 12:30:34 2021 +1200
+	Ran through Rubocop to clean up formatting, picking up a few error in quote usage; extra args; and other misc errors.
+robertburrowes	Thu Sep 2 16:26:24 2021 +1200
+	Reserve DOIs
+robertburrowes	Thu Sep 2 16:22:36 2021 +1200
+	Reworked, to check if articles already exist and to reserve DOIs.
+robertburrowes	Thu Sep 2 16:20:53 2021 +1200
+	Look for duplicate files in the source directories.
+robertburrowes	Thu Sep 2 16:17:02 2021 +1200
+	Fetch article IDs, if the conf file has them set to 0
+robertburrowes	Sat Apr 24 09:17:14 2021 +1200
+	check local dir against figshare
+robertburrowes	Thu Apr 22 12:31:17 2021 +1200
+	exclude sub test dir
+robertburrowes	Thu Apr 22 12:31:06 2021 +1200
+	missing ,
+robertburrowes	Thu Apr 22 12:30:49 2021 +1200
+	delete tmp test scripts
+robertburrowes	Fri Mar 19 13:54:58 2021 +1300
+	tests of creation of articles, and upload, using config file
+robertburrowes	Fri Mar 19 13:54:18 2021 +1300
+	Iterate across just last upload
+robertburrowes	Fri Mar 19 13:51:08 2021 +1300
+	Look for duplicate files within upload set, as defined by upload config file
+robertburrowes	Fri Mar 19 13:26:46 2021 +1300
+	hash to json naming changes
+robertburrowes	Fri Mar 19 13:24:00 2021 +1300
+	changes from hash to json naming
+robertburrowes	Fri Mar 19 13:17:26 2021 +1300
+	run from json config file, to test this works
+robertburrowes	Fri Mar 19 13:15:52 2021 +1300
+	Creating generic upload, that uses json config
+robertburrowes	Thu Mar 18 11:59:15 2021 +1300
+	Testing with Peter and Danes articles
+robertburrowes	Tue Mar 16 14:08:00 2021 +1300
+	private articles create was broken: Added private article body method
+robertburrowes	Tue Dec 1 14:43:50 2020 +1300
+	more testing
+robertburrowes	Tue Dec 1 13:19:01 2020 +1300
+	bump build version
+robertburrowes	Tue Dec 1 13:18:27 2020 +1300
+	Shouldn't have had article_id in URL
+robertburrowes	Tue Dec 1 13:18:06 2020 +1300
+	More random tests
+robertburrowes	Tue Dec 1 13:17:40 2020 +1300
+	ignore test
 robertburrowes	Mon Nov 9 22:35:19 2020 +1300
 	Missed @ in trace
 robertburrowes	Mon Nov 9 22:27:11 2020 +1300

data/lib/authors.rb

@@ -12,23 +12,27 @@ module Figshare
     # @param order [String] "published_date" Default, "modified_date", "views", "cites", "shares"
     # @param order_direction [String] "desc" Default, "asc"
     # @yield [Hash] {id, first_name, last_name, full_name, url_name, is_active, is_public, orcid_id, institution_id, group_id, job_title}
-    def search(institute: false, group_id: nil, orcid: nil,
-                is_active: true, is_public: true,  
-                order: 'published_date', order_direction: 'desc',
-                search_for:,
+    def search( search_for:,
+                institute: false,
+                group_id: nil,
+                orcid: nil,
+                is_active: true,
+                is_public: true,
+                order: 'published_date',
+                order_direction: 'desc',
                 &block
               )
       args = { 'search_for' => search_for }
-      args['institution'] = @institute_id if ! institute.nil?
-      args['group_id'] = group_id if ! group_id.nil?
-      args['is_active'] = is_active if ! is_active.nil?
-      args['is_public'] = is_public if ! is_public.nil?
-      args['orcid'] = orcid if ! orcid.nil?
-      args['order'] = order if ! order.nil?
-      args['order_direction'] = order_direction if ! order_direction.nil?
+      args['institution'] = @institute_id unless institute.nil?
+      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?
+      args['orcid'] = orcid unless orcid.nil?
+      args['order'] = order unless order.nil?
+      args['order_direction'] = order_direction unless order_direction.nil?
       post(api_query: 'account/authors/search', args: args, &block)
     end
-    
+
     # Get an authors details
     #
     # @param author_id [Integer] Figshare Author ID
@@ -37,5 +41,4 @@ module Figshare
       get(api_query: "account/authors/#{author_id}",  &block)
     end
   end
-
 end

data/lib/base.rb

@@ -1,4 +1,4 @@
-module Figshare  
+module Figshare
   # Supporting web calls to the API
   #
   class Base
@@ -8,23 +8,30 @@ module Figshare
     attr_accessor :hostname
     attr_accessor :api_url
     attr_accessor :institute_id
-  
+
     # Init reads the Json configuration files, setting @course_codes_to_faculty and @academic_department_code_to_faculty
     # Opens a connection to the LDAP server, setting @ldap for other methods to use.
     #
     # @param figshare_user [String] figshare user, in the figshare_keys.json
-    # @param conf_dir [String] directory for figshare_keys.json and figshare_site_params.json
-    def initialize(figshare_user:, conf_dir:)
-      figshare_token = load_json_file("#{conf_dir}/figshare_keys.json")
+    # @param conf_dir [String|nil] directory for figshare_keys.json and figshare_site_params.json
+    # @param key_file [String|nil] conf_dir/figshare_keys.json if nil
+    # @param conf_file [String|nil] conf_dir/figshare_site_params.json if nil
+    def initialize(figshare_user:, conf_dir: nil, key_file: nil, conf_file: nil)
+      raise 'Figshare_api_v2.initialize: Need to specify the conf_dir if key_file or conf_file are nil' if conf_dir.nil? && (key_file.nil? || conf_file.nil?)
+
+      conf_file ||= "#{conf_dir}/figshare_site_params.json"
+      key_file ||= "#{conf_dir}/figshare_keys.json"
+
+      figshare_token = load_json_file(key_file)
       @auth_token = figshare_token[figshare_user]
-    
-      figshare_site_params = load_json_file("#{conf_dir}/figshare_site_params.json")
-    
+
+      figshare_site_params = load_json_file(conf_file)
+
       @hostname = figshare_site_params['host']
       @api_url = figshare_site_params['api_url']
       @institute_id = figshare_site_params['institute_id']
     end
-  
+
     # Parse the config file
     #
     # @param filename [String] config file name to parse
@@ -32,7 +39,7 @@ module Figshare
     private def load_json_file(filename)
       JSON.parse(File.read(filename))
     end
-  
+
     # get iterates through the API response, yielding each value to the passed block
     # When Figshare API usually has no paging option.
     # If there is no block, then the results are printed (useful for debugging)
@@ -67,16 +74,16 @@ module Figshare
     private def get_paginate(api_query:, args: {}, debug: false, by_offset: false, &block)
       args = {} if args.nil?
       if ! args.is_a?(Hash)
-      raise "get_paginate(): Expecting args to be a Hash"
+        raise 'get_paginate(): Expecting args to be a Hash'
       end
- 
+
       offset = 0
       page = 1
       limit = page_size = 100
       result_count = 0
       loop do
         content_type = response = nil
-        form_args = by_offset ? {"limit"=>limit, "offset"=>offset} : {"page_size"=>page_size, "page"=>page}
+        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}",
@@ -88,10 +95,10 @@ module Figshare
         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
+        page += 1 # Ready to fetch next page
+        offset += limit # if we use offset, then mor
       end
-      
+
       return result_count
     end
 
@@ -105,26 +112,26 @@ module Figshare
     # @param content_type [String] Assuming Json, but might need binary ('application/octet-stream')
     # @yield [String] if given a block, iterates through the result from figshare
     # @return [Integer] number of results.
-    private def post(api_query:, args: {}, data: nil, debug: false, content_type: 'application/json; charset=UTF-8', &block)      
+    private def post(api_query:, args: {}, data: nil, debug: false, content_type: 'application/json; charset=UTF-8', &block)
       body = nil
-      if data.is_a?(Hash)
-        # Convert hash to json, and merge in additional args
-        body = data.merge(args).to_j
-      elsif data.nil? && ! args.empty?
-        # No data, but args, so just use the args
-        body = args.to_j
-      else
-        # Data isn't a Hash, so just pass it through (might be nil)
-        body = data
-      end
-      
-      content_type = response = nil
+      body = if data.is_a?(Hash)
+               # Convert hash to json, and merge in additional args
+               data.merge(args).to_j
+             elsif data.nil? && ! args.empty?
+               # No data, but args, so just use the args
+               args.to_j
+             else
+               # Data isn't a Hash, so just pass it through (might be nil)
+               data
+             end
+
+      response = nil
       WIKK::WebBrowser.https_session( host: @hostname, verify_cert: false ) do |ws|
         response = ws.post_page(  query: "#{@api_url}#{api_query}",
                                   content_type: content_type,
                                   authorization: "token #{@auth_token}",
                                   data: body
-                              )
+                               )
         content_type = ws.header_value(key: 'Content-Type')
       end
       return iterate_json_response(response: response, content_type: content_type, debug: debug, &block)
@@ -140,34 +147,34 @@ 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, &block)
       page = 1
       offset = 0
       limit = page_size = 100
       result_count = 0
-      
+
       args = {} if args.nil?
       if ! args.is_a?(Hash)
-       raise "post_paginate(): Expecting args to be 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}
+        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
-                                  )
+                                 )
           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
+        page += 1 # Ready to fetch next page
+        offset += limit # if we use offset
       end
       return result_count
     end
@@ -181,27 +188,27 @@ module Figshare
     # @param debug [Boolean] print result to stdout
     # @param content_type [String] Assuming Json, but might need binary ('application/octet-stream')
     # @yield [String] if given a block, iterates through the result from figshare
-    # @return [Integer] number of results 
+    # @return [Integer] number of results
     private def put(api_query:, args: {}, data: nil, debug: false, content_type: 'application/json; charset=UTF-8', &block)
       body = nil
-      if data.is_a?(Hash)
-        # Convert hash to json, and merge in additional args
-        body = data.merge(args).to_j
-      elsif data.nil? && ! args.empty?
-        # No data, but args, so just use the args
-        body = args.to_j
-      else
-        # Data isn't a Hash, so just pass it through (might be nil)
-        body = data
-      end
+      body = if data.is_a?(Hash)
+               # Convert hash to json, and merge in additional args
+               data.merge(args).to_j
+             elsif data.nil? && ! args.empty?
+               # No data, but args, so just use the args
+               args.to_j
+             else
+               # Data isn't a Hash, so just pass it through (might be nil)
+               data
+             end
 
-      content_type = response = nil
+      response = nil
       WIKK::WebBrowser.https_session( host: @hostname, verify_cert: false ) do |ws|
-        response = ws.put_page( query: "#{@api_url}#{api_query}",
-                                content_type: content_type,
-                                authorization: "token #{@auth_token}",
-                                data: body
-                              )
+        response = ws.put_req( query: "#{@api_url}#{api_query}",
+                               content_type: content_type,
+                               authorization: "token #{@auth_token}",
+                               data: body
+                             )
         content_type = ws.header_value(key: 'Content-Type')
       end
       return iterate_json_response(response: response, content_type: content_type, debug: debug, &block)
@@ -214,18 +221,18 @@ module Figshare
     # @param debug [Boolean] print result to stdout
     # @yield [Hash] Unlikely to have a result from delete calls, but if we do, we see it here
     # @return [Integer] number of results (usually 0)
-    private def delete(api_query:, args: {}, debug: false, &block)
-      #ignoring args for the moment. Not sure what to do with them, if we do get them.
-      content_type = response = nil
+    private def delete(api_query:, args: {}, debug: false, content_type: 'application/json; charset=UTF-8', &block)
+      response = nil
       WIKK::WebBrowser.https_session( host: @hostname, verify_cert: false ) do |ws|
         response = ws.delete_req( query: "#{@api_url}#{api_query}",
-                                authorization: "token #{@auth_token}"
-                              )
+                                  authorization: "token #{@auth_token}",
+                                  form_values: args
+                                )
         content_type = ws.header_value(key: 'Content-Type')
       end
       return iterate_json_response(response: response, content_type: content_type, debug: debug, &block)
     end
-    
+
     # For iterate through the api response
     #
     # @param response [String] response from the API call
@@ -234,25 +241,25 @@ module Figshare
     # @yield [Hash] each array member in the response (or the entire response, if not iteratable)
     private def iterate_json_response(response:, content_type:, debug: false )
       return 0 if response.nil? # got no responses
-      
+
       if content_type =~ /application\/json/
         response_array = JSON.parse(response)
-        #If we don't have an Array, turn the response into an Array so we can iterate over this one response.
-        response_array = [ response_array ] if ! (response_array.class == Array)
+        # If we don't have an Array, turn the response into an Array so we can iterate over this one response.
+        response_array = [ response_array ] unless response_array.instance_of?(Array)
         return 0 if response_array.empty? # got empty array of responses
-            
+
         count = 0
         response_array.each do |r|
           yield r if block_given?
           p r if debug
           count += 1
         end
-    
+
         return count
-      else #just dump the entire response on the caller :)
-        yield response  if block_given?
+      else # just dump the entire response on the caller :)
+        yield response if block_given?
         return response.length
       end
     end
   end
-end
+end

data/lib/figshare_api_v2.rb

@@ -1,8 +1,10 @@
-module Figshare
-  VERSION = '0.9.3'
+module Figshare # :nodoc:
+  # Figshare module initialization
+  #
+  VERSION = '0.9.7'
 
-  require "wikk_webbrowser"
-  require "wikk_json"
+  require 'wikk_webbrowser'
+  require 'wikk_json'
   require 'time'
 
   require_relative 'base.rb'
@@ -18,8 +20,8 @@ module Figshare
   require_relative 'upload.rb'
   require_relative 'stats.rb'
   require_relative 'oai_pmh.rb'
-  
-  # Hack :) to do a lazy initialization of the Figshare subclasses. i.e. only if they get called.
+
+  # HACK: to do a lazy initialization of the Figshare subclasses. i.e. only if they get called.
   # Usage:
   #  @figshare = Figshare::Init.new(figshare_user: 'figshare_admin', conf_dir: "#{__dir__}/conf")
   #
@@ -31,95 +33,98 @@ module Figshare
     # Intitialize the Init class, so it can dynamically initialize the Figshare subclasses
     #
     # @param figshare_user [String] figshare user, in the figshare_keys.json
-    # @param conf_dir [String] directory for figshare_keys.json and figshare_site_params.json
-    def initialize(figshare_user:, conf_dir:)
+    # @param conf_dir [String|nil] directory for figshare_keys.json and figshare_site_params.json
+    # @param key_file [String|nil] conf_dir/figshare_keys.json if nil
+    # @param conf_file [String|nil] conf_dir/figshare_site_params.json if nil
+    def initialize(figshare_user:, conf_dir: nil, key_file: nil, conf_file: nil)
       @figshare_user = figshare_user
       @conf_dir = conf_dir
+      @key_file = key_file
+      @conf_file = conf_file
     end
-    
+
     # Create Figshare::Authors, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::Authors]
     def authors
-      @authors ||= Authors.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @authors ||= Authors.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
 
     # Create Figshare::Institutions, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::Institutions]
     def institutions
-      @institutions ||= Institutions.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @institutions ||= Institutions.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::Other, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::Other]
     def other
-      @other ||= Other.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @other ||= Other.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::PrivateArticles, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::PrivateArticles]
     def private_articles
-      @private_articles ||= PrivateArticles.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @private_articles ||= PrivateArticles.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::PrivateCollections, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::PrivateCollections]
     def private_collections
-      @private_collections ||= PrivateCollections.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @private_collections ||= PrivateCollections.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::PrivateProjects, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::PrivateProjects]
     def private_projects
-      @private_projects ||= PrivateProjects.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @private_projects ||= PrivateProjects.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::PublicArticles, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::PublicArticles]
     def public_articles
-      @public_articles ||= PublicArticles.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @public_articles ||= PublicArticles.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::PublicCollections, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::PublicCollections]
     def public_collections
-      @public_collections ||= PublicCollections.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @public_collections ||= PublicCollections.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::PublicProjects, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::PublicProjects]
     def public_projects
-      @public_projects ||= PublicProjects.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @public_projects ||= PublicProjects.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
 
     # Create Figshare::Upload, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::Upload]
     def upload
-      @upload ||= Upload.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @upload ||= Upload.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::Stats, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::Stats]
     def stats
-      @stats ||= Stats.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @stats ||= Stats.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
+
     # Create Figshare::OAI_PMH, if it doesn't exist. Initialized with @figshare_user and @conf_dir
     #
     # @return [Figshare::OAI_PMH]
     def oai_pmh
-      @oai_pmh ||= OAI_PMH.new(figshare_user: @figshare_user, conf_dir: @conf_dir)
+      @oai_pmh ||= OAI_PMH.new(figshare_user: @figshare_user, conf_dir: @conf_dir, key_file: @key_file, conf_file: @conf_file)
     end
-    
   end
-end # module
+end