Merge pull request #1 from ontoportal-lirmm/master

Merge the lastes version of Agroportal into the branch ontoportal-lirmm
ontoportal · Sep 12, 2023 · 6d3d046 · 6d3d046
2 parents 3d73f62 + a5f0c71
commit 6d3d046
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diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 6010ff60b99dc1282822b8a1fb59bd59f453755f
+  revision: d0ac992c88bd417f2f2137ba62934c3c41b6db7c
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -11,8 +11,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 92968978e5d2436c648bf7956e25aff05440b59d
-  branch: master
+  revision: cda6aff2338e2a2831e4e7bf716abdf8fa8483d2
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -37,13 +37,13 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: d09999177235029ba30a00cd59d10f7ca1a1fa93
+  revision: 8db3481116c57d2a21dc8f32bcd1695d95442280
   branch: master
   specs:
     ncbo_cron (0.0.1)
       dante
       goo
-      google-api-client
+      google-apis-analytics_v3
       mlanett-redis-lock
       multi_json
       ncbo_annotator
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 9c5c56cf7b4546ccc45431a82bbce9a33184e4cc
-  branch: master
+  revision: e9b708c40b2b22b935fb48d18ed19de8148fca35
+  branch: development
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -125,16 +125,16 @@ GEM
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.1.10)
+    concurrent-ruby (1.2.0)
     cube-ruby (0.0.3)
     dante (0.2.0)
-    date (3.3.2)
+    date (3.3.3)
     declarative (0.0.20)
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     ed25519 (1.3.0)
-    faraday (1.10.2)
+    faraday (1.10.3)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
@@ -160,22 +160,24 @@ GEM
     ffi (1.15.5)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-api-client (0.52.0)
+    google-apis-analytics_v3 (0.12.0)
+      google-apis-core (>= 0.9.1, < 2.a)
+    google-apis-core (0.11.0)
       addressable (~> 2.5, >= 2.5.1)
-      googleauth (~> 0.9)
-      httpclient (>= 2.8.1, < 3.0)
+      googleauth (>= 0.16.2, < 2.a)
+      httpclient (>= 2.8.1, < 3.a)
       mini_mime (~> 1.0)
       representable (~> 3.0)
-      retriable (>= 2.0, < 4.0)
+      retriable (>= 2.0, < 4.a)
       rexml
-      signet (~> 0.12)
-    googleauth (0.17.1)
-      faraday (>= 0.17.3, < 2.0)
+      webrick
+    googleauth (1.3.0)
+      faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
       memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
-      signet (~> 0.15)
+      signet (>= 0.16, < 2.a)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
@@ -189,13 +191,13 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.6.3)
-    jwt (2.5.0)
+    jwt (2.7.0)
     kgio (2.11.4)
-    libxml-ruby (3.2.4)
+    libxml-ruby (4.0.0)
     logger (1.5.3)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
-    mail (2.8.0)
+    mail (2.8.1)
       mini_mime (>= 0.1.1)
       net-imap
       net-pop
@@ -211,9 +213,9 @@ GEM
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    multipart-post (2.2.3)
+    multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.2)
+    net-imap (0.3.4)
       date
       net-protocol
     net-pop (0.1.2)
@@ -226,15 +228,15 @@ GEM
       net-protocol
     net-ssh (7.0.1)
     netrc (0.11.0)
-    newrelic_rpm (8.14.0)
+    newrelic_rpm (8.16.0)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
-    pry (0.14.1)
+    pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.1)
@@ -258,8 +260,8 @@ GEM
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redcarpet (3.5.1)
-    redis (4.8.0)
+    redcarpet (3.6.0)
+    redis (4.8.1)
     redis-activesupport (5.3.0)
       activesupport (>= 3, < 8)
       redis-store (>= 1.3, < 2)
@@ -292,7 +294,7 @@ GEM
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    simplecov (0.21.2)
+    simplecov (0.22.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
@@ -318,11 +320,11 @@ GEM
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
-    temple (0.9.1)
+    temple (0.10.0)
     tilt (2.0.11)
-    timeout (0.3.1)
+    timeout (0.3.2)
     trailblazer-option (0.1.2)
-    tzinfo (2.0.5)
+    tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
     unf (0.1.4)
@@ -336,8 +338,10 @@ GEM
       unicorn (>= 4, < 7)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webrick (1.8.1)
 
 PLATFORMS
+  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES

diff --git a/controllers/classes_controller.rb b/controllers/classes_controller.rb
@@ -9,7 +9,7 @@ class ClassesController < ApplicationController
       cls_count = submission.class_count(LOGGER)
       error 403, "Unable to display classes due to missing metrics for #{submission.id.to_s}. Please contact the administrator." if cls_count < 0
 
-      attributes, page, size, filter_by_label, order_by_hash, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
+      attributes, page, size, order_by_hash, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
       check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
 
       index = LinkedData::Models::Class.in(submission)

diff --git a/controllers/collection_controller.rb b/controllers/collection_controller.rb
@@ -30,7 +30,7 @@ class CollectionsController < ApplicationController
 
       get '/members' do
         ont, submission = get_ontology_and_submission
-        attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
+        attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
         collection_uri = get_collection_uri(params)
         data = LinkedData::Models::Class.where(memberOf: collection_uri).in(submission).include(attributes).page(page,size).all
         reply data

diff --git a/controllers/instances_controller.rb b/controllers/instances_controller.rb
@@ -7,8 +7,8 @@ class InstancesController < ApplicationController
     check_last_modified_segment(LinkedData::Models::Instance, [ont.acronym])
     cls = get_class(sub)
     error 404 if cls.nil?
-
-    attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Instance)
+    filter_by_label = label_regex_filter
+    attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Instance)
 
 
 
@@ -20,7 +20,7 @@ class InstancesController < ApplicationController
     page_data.order_by(order_by) unless order_by.nil?
     page_data = page_data.page(page,size).all
 
-    bring_unmapped_to page_data , sub if bring_unmapped_needed
+    bring_unmapped_to page_data , sub, LinkedData::Models::Instance if bring_unmapped_needed
 
     reply page_data
   end
@@ -30,8 +30,8 @@ class InstancesController < ApplicationController
     get do
       ont, sub = get_ontology_and_submission
       check_last_modified_segment(LinkedData::Models::Instance, [ont.acronym])
-
-      attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Instance)
+      filter_by_label = label_regex_filter
+      attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Instance)
 
 
       page_data = LinkedData::Models::Instance.where
@@ -42,7 +42,7 @@ class InstancesController < ApplicationController
       page_data.order_by(order_by) unless order_by.nil?
       page_data = page_data.page(page,size).all
 
-      bring_unmapped_to page_data , sub if bring_unmapped_needed
+      bring_unmapped_to page_data , sub, LinkedData::Models::Instance if bring_unmapped_needed
 
       reply page_data
     end
@@ -51,11 +51,11 @@ class InstancesController < ApplicationController
       ont, sub = get_ontology_and_submission
       check_last_modified_segment(LinkedData::Models::Instance, [ont.acronym])
 
-      attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Instance)
+      attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Instance)
 
       page_data = LinkedData::Models::Instance.find(@params["inst"]).include(attributes).in(sub).first
 
-      bring_unmapped_to [page_data] , sub if bring_unmapped_needed
+      bring_unmapped_to [page_data] , sub, LinkedData::Models::Instance if bring_unmapped_needed
 
       reply page_data
     end

diff --git a/controllers/skos_xl_label_controller.rb b/controllers/skos_xl_label_controller.rb
@@ -3,7 +3,7 @@ class SkosXlLabelController < ApplicationController
   namespace "/ontologies/:ontology/skos_xl_labels" do
     get  do
       ont, submission = get_ontology_and_submission
-      attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::SKOS::Label)
+      attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::SKOS::Label)
       labels = LinkedData::Models::SKOS::Label.where.in(submission).include(attributes).page(page, size).all
       if labels && bring_unmapped_needed
         LinkedData::Models::SKOS::Label.in(submission).models(labels).include(:unmapped).all
@@ -13,7 +13,7 @@ class SkosXlLabelController < ApplicationController
 
     get '/:id' do
       ont, submission = get_ontology_and_submission
-      attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::SKOS::Label)
+      attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::SKOS::Label)
       label = LinkedData::Models::SKOS::Label.find(params[:id]).in(submission).include(attributes).first
       if label && bring_unmapped_needed
         LinkedData::Models::SKOS::Label.in(submission).models([label]).include(:unmapped).all

diff --git a/helpers/application_helper.rb b/helpers/application_helper.rb
@@ -370,15 +370,14 @@ def retrieve_latest_submissions(options = {})
         end
 
         submissions_query = submissions_query.filter(Goo::Filter.new(ontology: [:viewOf]).unbound) unless include_views
+        submissions_query = submissions_query.filter(filter) if filter?
         # When asking to display all metadata, we are using bring_remaining on each submission. Slower but best way to retrieve all attrs
         if includes_param.first == :all
-          including = [:submissionId, {:contact=>[:name, :email], :ontology=>[:administeredBy, :acronym, :name, :summaryOnly, :ontologyType, :viewingRestriction, :acl,
+          includes = [:submissionId, {:contact=>[:name, :email], :ontology=>[:administeredBy, :acronym, :name, :summaryOnly, :ontologyType, :viewingRestriction, :acl,
                                        :group, :hasDomain, :views, :viewOf, :flat], :submissionStatus=>[:code], :hasOntologyLanguage=>[:acronym]}, :submissionStatus]
-          submissions = submissions_query.include(including).to_a
-        else
-          submissions = submissions_query.include(includes).to_a
         end
-
+        submissions = submissions_query.include(includes).to_a
+
         # Figure out latest parsed submissions using all submissions
         latest_submissions = {}
         submissions.each do |sub|
@@ -391,7 +390,7 @@ def retrieve_latest_submissions(options = {})
           latest_submissions[sub.ontology.acronym] ||= sub
           latest_submissions[sub.ontology.acronym] = sub if sub.submissionId.to_i > latest_submissions[sub.ontology.acronym].submissionId.to_i
         end
-        return latest_submissions
+        latest_submissions
       end
 
       def get_ontology_and_submission

diff --git a/helpers/collections_helper.rb b/helpers/collections_helper.rb
@@ -5,7 +5,7 @@ module Helpers
     module CollectionsHelper
       def collections_setting_params
         ont, submission = get_ontology_and_submission
-        attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::SKOS::Collection)
+        attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::SKOS::Collection)
         [submission, attributes, bring_unmapped_needed]
       end
 

diff --git a/helpers/instances_helper.rb b/helpers/instances_helper.rb
@@ -3,58 +3,12 @@
 module Sinatra
   module Helpers
     module InstancesHelper
-
-      # TODO: generalize this to all routes (maybe in application_helper)
-      def settings_params(klass)
-        page, size = page_params
-        attributes = get_attributes_to_include(includes_param, klass)
-        order_by = get_order_by_from(@params)
-        bring_unmapped = bring_unmapped?(includes_param)
-        filter_by_label = label_regex_filter
-
-        [attributes, page, size, filter_by_label, order_by, bring_unmapped]
-      end
-
-      def is_set?(param)
-        !param.nil? && param != ""
-      end
-
       def label_regex_filter
         (Goo::Filter.new(:label).regex(@params["search"])) if is_set?(@params["search"])
       end
 
       def filter_classes_by(class_uri)
-        class_uri.nil? ? nil :{types: RDF::URI.new(class_uri.to_s)}
-      end
-
-      def get_order_by_from(params, default_order = :asc)
-        if is_set?(params['sortby'])
-          orders = (params["order"] || default_order.to_s).split(',')
-          out = params['sortby'].split(',').map.with_index  do |param, index|
-            sort_order_item(param, orders[index] || default_order)
-          end
-          out.to_h
-        end
-
-      end
-
-      def get_attributes_to_include(includes_param, klass)
-        ld = klass.goo_attrs_to_load(includes_param)
-        ld.delete(:properties)
-        ld
-      end
-
-      def bring_unmapped?(includes_param)
-        (includes_param && includes_param.include?(:all))
-      end
-
-      def bring_unmapped_to(page_data, sub, klass = LinkedData::Models::Instance)
-        klass.in(sub).models(page_data).include(:unmapped).all
-      end
-
-      private
-      def sort_order_item(param , order)
-        [param.to_sym, order.to_sym]
+        class_uri.nil? ? nil : { types: RDF::URI.new(class_uri.to_s) }
       end
     end
   end