Merge pull request #2231 from seek4science/project-default-data-ajax

Discipline annotations

Author: fbacall

app/assets/javascripts/sharing.js.erb

@@ -27,17 +27,6 @@ var Sharing = {
       }
     }
 
-    // This ensures that if a project permission is added, and that project is associated with the resource, it gains
-    //  the "isMandatory" flag.
-    if (permission.contributor_type === 'Project' && Sharing.projectsSelector) {
-      for (var j = 0; j < Sharing.projectsSelector.selected.length; j++) {
-        if (Sharing.projectsSelector.selected[j].id === permission.contributor_id) {
-          permission.isMandatory = true;
-          break;
-        }
-      }
-    }
-
     Sharing.permissionsTable.permissions.push(permission);
   },
 
@@ -47,20 +36,7 @@ var Sharing = {
         contributor_type: 'Project',
         contributor_id: project.id,
         title: project.title,
-        access_type: Sharing.associatedProjectAccessType,
-        isMandatory: true }, true);
-  },
-
-  removeMandatoryProjectPermissions: function () {
-    if (!Sharing.permissionsTable)
-      return;
-    var indices = [];
-    for (var i = Sharing.permissionsTable.permissions.length - 1; i >= 0; i--) {
-      if (Sharing.permissionsTable.permissions[i].contributor_type === 'Project' &&
-          Sharing.permissionsTable.permissions[i].isMandatory) {
-        Sharing.permissionsTable.permissions.splice(i, 1);
-      }
-    }
+        access_type: Sharing.associatedProjectAccessType }, true);
   },
 
   removePermissionForProject: function (project) {
@@ -72,13 +48,12 @@ var Sharing = {
     }
     if (confirm('Do you want to remove any permissions for ' + project.title + '?')) {
       Sharing.permissionsTable.permissions.splice(i, 1);
-    } else {
-      Sharing.permissionsTable.permissions[i].isMandatory = false;
     }
   },
 
   requestInstitutionsUrl: '<%= request_institutions_projects_path %>',
   requestAllInstitutionsUrl: '<%= request_all_sharing_form_institutions_path %>',
+  requestDefaultDataUrl: '<%= default_data_project_path('_replaceme_') %>',
 
   accessTypes: {
     noAccess: <%= Policy::NO_ACCESS %>,
@@ -120,15 +95,29 @@ var Sharing = {
   },
 
   // Ask if they want to use the default policy (if there is one)
-  defaultPolicyPrompt: function (project, skipPrompt) {
+  defaultPolicyPrompt: function (project, policy, skipPrompt) {
       if (!Sharing.permissionsTable)
           return;
 
-      if (Sharing.defaultPolicies[project.id] && (skipPrompt || confirm('' + project.title + ' has a default sharing policy specified, do you want to apply it?'))) {
-          Sharing.applyPolicy(Sharing.defaultPolicies[project.id]);
+      if (policy && (skipPrompt || confirm('' + project.title + ' has a default sharing policy specified, do you want to apply it?'))) {
+          Sharing.applyPolicy(policy);
       } else { // Otherwise just add a permission for the project
           Sharing.addPermissionForProject(project);
       }
+  },
+
+  fetchDefaultData: function (project) {
+      return new Promise((resolve, reject) => {
+        $j.ajax(Sharing.requestDefaultDataUrl.replace('_replaceme_', project.id), {
+                success: function (data) {
+                    resolve(data);
+                },
+                complete: function () {
+                    resolve({});
+                }
+            }
+        );
+      });
   }
 };
 
@@ -171,7 +160,8 @@ Vue.component('permissions-table', {
   computed: {
     sortedPermissions: function () {
       return this.permissions.sort(function (a, b) {
-        return (b.isMandatory || false) - (a.isMandatory || false);
+          return ((b.contributor_type === 'Project') && Sharing.getSelectedProjectIds().includes(b.contributor_id)) -
+                 ((a.contributor_type === 'Project') && Sharing.getSelectedProjectIds().includes(a.contributor_id));
       });
     }
   },
@@ -185,14 +175,14 @@ Vue.component('permissions-table', {
 Vue.component('permission-row', {
   props: ['index', 'permission', 'accessTypes', 'publicAccessType', 'fieldPrefixOrig'],
   template:
-  '<tr class="permission-row" :class="{ mandatory: permission.isMandatory, hidden: permission.contributor_type === \'FavouriteGroup\' }">' +
+  '<tr class="permission-row" :class="{ mandatory: mandatory, hidden: permission.contributor_type === \'FavouriteGroup\' }">' +
   '<td class="name-cell" :title="permission.title"><span class="type-icon-wrapper"><img :src="typeIcon" class="type-icon" :title="permission.contributor_type || \'All visitors\'"/></span> {{ permission.title }}' +
   '<input v-if="permission.contributor_type" type="hidden" :name="fieldPrefix+\'[contributor_type]\'" v-model="permission.contributor_type"/>' +
   '<input v-if="permission.contributor_id" type="hidden" :name="fieldPrefix+\'[contributor_id]\'" v-model="permission.contributor_id"/>' +
   '</td>' +
   '<td is="privilege-cell" v-for="accessType in accessTypes" :fieldPrefix="fieldPrefix" :permission="permission" :access-type="accessType" :public-access-type="publicAccessType"></td>' +
   '<td class="actions-cell">'+
-  '<a v-if="!permission.isMandatory" @click="$emit(\'delete-permission\')" class="clickable remove-button" title="Remove this permission">' +
+  '<a v-if="!mandatory" @click="$emit(\'delete-permission\')" class="clickable remove-button" title="Remove this permission">' +
   '<span class="glyphicon glyphicon-remove" aria-hidden="true"></span>' +
   '</a>' +
   '</td>' +
@@ -216,6 +206,15 @@ Vue.component('permission-row', {
       }
 
       return '<%= asset_path icon_filename_for_key('world') %>';
+    },
+    mandatory: function () {
+        if (this.permission.isPublic) {
+            return true;
+        }
+        if (this.permission.contributor_type === 'Project') {
+            return Sharing.getSelectedProjectIds().includes(this.permission.contributor_id);
+        }
+        return false;
     }
   }
 });

app/controllers/projects_controller.rb

@@ -18,14 +18,16 @@ class ProjectsController < ApplicationController
                                         :administer_create_project_request, :respond_create_project_request,
                                         :administer_import_project_request, :respond_import_project_request,
                                         :import_from_fairdata_station, :submit_fairdata_station,
-                                        :project_join_requests, :project_creation_requests, :project_importation_requests, :typeahead]
+                                        :project_join_requests, :project_creation_requests, :project_importation_requests,
+                                        :typeahead, :default_data]
 
   before_action :find_requested_item, only: %i[show admin edit update destroy admin_members
                                                asset_report populate populate_from_spreadsheet
                                                admin_member_roles update_members storage_report
                                                overview administer_join_request respond_join_request
                                                import_from_fairdata_station submit_fairdata_station
-                                               fair_data_station_import_status hide_fair_data_station_import_status]
+                                               fair_data_station_import_status hide_fair_data_station_import_status
+                                               default_data]
 
   before_action :has_spreadsheets, only: %i[:populate populate_from_spreadsheet]
 
@@ -36,7 +38,8 @@ class ProjectsController < ApplicationController
   before_action :administerable_by_user, only: %i[admin admin_members admin_member_roles destroy update_members storage_report administer_join_request respond_join_request populate populate_from_spreadsheet]
 
   before_action :member_of_this_project, only: [:asset_report, :import_from_fairdata_station, :submit_fairdata_station,
-                                                :fair_data_station_import_status, :hide_fair_data_station_import_status], unless: :admin_logged_in?
+                                                :fair_data_station_import_status, :hide_fair_data_station_import_status,
+                                                :default_data], unless: :admin_logged_in?
 
   before_action :validate_message_log_for_join, only: [:administer_join_request, :respond_join_request]
   before_action :validate_message_log_for_create, only: [:administer_create_project_request, :respond_create_project_request]
@@ -977,6 +980,12 @@ def typeahead
     end
   end
 
+  def default_data
+    respond_to do |format|
+      format.json
+    end
+  end
+
   private
 
   def project_role_params
@@ -993,7 +1002,7 @@ def project_role_params
   def project_params
     permitted_params = [:title, :web_page, :wiki_page, :description, { organism_ids: [] }, :parent_id, :start_date,
                         :end_date,
-                        { funding_codes: [] }, { human_disease_ids: [] }, topic_annotations: [],
+                        { funding_codes: [] }, { human_disease_ids: [] }, { topic_annotations: [] }, { discipline_annotations: [] },
                         discussion_links_attributes:[:id, :url, :label, :_destroy], extended_metadata_attributes: determine_extended_metadata_keys ]
 
     if User.admin_logged_in?
@@ -1089,10 +1098,10 @@ def member_of_this_project
     @project = Project.find(params[:id])
     if @project.nil? || !@project.has_member?(current_user)
       flash[:error] = "You are not a member of this #{t('project')}, so cannot access this page."
-      redirect_to project_path(@project)
-      false
-    else
-      true
+      respond_to do |format|
+        format.html { redirect_to project_path(@project) }
+        format.json { head :forbidden }
+      end
     end
   end
 

app/controllers/workflows_controller.rb

@@ -377,7 +377,7 @@ def workflow_params
                                      { publication_ids: [] }, { presentation_ids: [] }, { document_ids: [] }, { data_file_ids: [] }, { sop_ids: [] },
                                      { workflow_data_files_attributes:[:id, :data_file_id, :workflow_data_file_relationship_id, :_destroy] },
                                      :internals, :maturity_level, :source_link_url, :execution_instance_url,
-                                     { topic_annotations: [] }, { operation_annotations: [] },
+                                     { topic_annotations: [] }, { operation_annotations: [] }, { discipline_annotations: [] },
                                      { discussion_links_attributes: [:id, :url, :label, :_destroy] },
                                      { git_version_attributes: [:name, :comment, :ref, :commit, :root_path,
                                                                 :git_repository_id, :main_workflow_path,

app/helpers/license_helper.rb

@@ -54,12 +54,6 @@ def default_license_for_current_user
     current_user.person.projects_with_default_license.any?
   end
 
-  # JSON that creates a lookup for project license by id
-  def project_licenses_json
-    projects = current_user.person.projects_with_default_license
-    Hash[projects.collect { |proj| [proj.id, proj.default_license] }].to_json.html_safe
-  end
-
   private
 
   def license_description_content(license)

app/helpers/policy_helper.rb

@@ -120,7 +120,6 @@ def policy_hash(policy, associated_projects)
       # Mark associated project permissions as "mandatory"
       if permission.contributor_type == 'Project' && project_ids.include?(permission.contributor_id)
         project_ids.delete(permission.contributor_id)
-        h[:isMandatory] = true
       end
 
       h[:title] = permission_title(permission)
@@ -133,8 +132,7 @@ def policy_hash(policy, associated_projects)
       hash[:permissions] << { access_type: policy.access_type,
                               contributor_id: project.id,
                               contributor_type: 'Project',
-                              title: project.title,
-                              isMandatory: true }
+                              title: project.title }
     end
 
     hash
@@ -144,16 +142,6 @@ def policy_json(policy, associated_projects)
     policy_hash(policy, associated_projects).to_json.html_safe
   end
 
-  def project_policies_json(projects)
-    hash = {}
-
-    projects.each do |p|
-      hash[p.id] = policy_hash(p.default_policy, [p]) if p.use_default_policy
-    end
-
-    hash.to_json.html_safe
-  end
-
   def project_policy_json(project)
     hash = policy_hash(project.default_policy, [project]) if project.use_default_policy
     hash.to_json.html_safe

app/models/concerns/has_controlled_vocabulary_annotations.rb

@@ -92,6 +92,7 @@ def associate_controlled_vocab_annotation_values(vals, property)
       vocab = annotation_controlled_vocab(property)
       values = Array(vals.split(',').flatten).map do |value|
         value = value.strip
+        next if value.blank?
         vocab.sample_controlled_vocab_terms.find_by_label(value) ||
           vocab.sample_controlled_vocab_terms.find_by_iri(value)
       end.compact.uniq

app/models/project.rb

@@ -75,7 +75,7 @@ class Project < ApplicationRecord
   #  is to be used)
   belongs_to :default_policy, class_name: 'Policy', dependent: :destroy, autosave: true
 
-  has_controlled_vocab_annotations :topics
+  has_controlled_vocab_annotations :topics, :disciplines
 
   # FIXME: temporary handler, projects need to support multiple programmes
   def programmes
@@ -93,6 +93,9 @@ def programmes
 
   has_many :dependent_permissions, class_name: 'Permission', as: :contributor, dependent: :destroy
 
+  before_save :check_disciplines
+  after_save :propagate_disciplines
+
   def assets
     data_files | sops | models | publications | presentations | documents | workflows | collections
   end
@@ -282,4 +285,20 @@ def ro_crate_metadata
     end
   end
 
+  def check_disciplines
+    @_disciplines = discipline_annotation_labels.sort
+  end
+
+  def propagate_disciplines
+    new_disciplines = discipline_annotation_labels.sort
+    unless @_disciplines == new_disciplines
+      disable_authorization_checks do
+        workflows.find_each do |workflow|
+          next if workflow.discipline_annotations.any?
+          workflow.discipline_annotations = new_disciplines
+          workflow.save(touch: false)
+        end
+      end
+    end
+  end
 end

app/models/sample_controlled_vocab.rb

@@ -116,7 +116,8 @@ class SystemVocabs
       topics: 'topic_annotations',
       operations: 'operation_annotations',
       data_formats: 'data_format_annotations',
-      data_types: 'data_type_annotations'
+      data_types: 'data_type_annotations',
+      disciplines: 'discipline_annotations',
     }
 
     def self.vocab_for_property(property)

app/models/workflow.rb

@@ -14,7 +14,7 @@ class Workflow < ApplicationRecord
 
   acts_as_doi_parent
 
-  has_controlled_vocab_annotations :topics, :operations
+  has_controlled_vocab_annotations :topics, :operations, :disciplines
 
   validates :projects, presence: true, projects: { self: true }
 

app/views/assays/_form.html.erb

@@ -19,11 +19,13 @@
 
 <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:f,resource:@assay} %>
 
-<div class="form-group">
-  <label class="required"><%= t('study') -%></label>
+<% if show_form_manage_specific_attributes? %>
+  <div class="form-group">
+    <label class="required"><%= t('study') -%></label>
 
-  <%= resource_study_selection('assay[study_id]', @assay.study) %>
-</div>
+    <%= resource_study_selection('assay[study_id]', @assay.study) %>
+  </div>
+<% end %>
 
 <div class="form-group">
   <%= f.label "Assay position" -%><br/>