Merge pull request #5336 from aignatov-bio/ai-sci-8233-add-backend-for-navigator

Add backend for navigator [SCI-8233]

app/assets/javascripts/sidebar.js

@@ -12,11 +12,6 @@ var Sidebar = (function() {
 
   function reloadSidebar(params) {
     let url = $(SIDEBAR_CONTAINER).data('sidebar-url');
-    $.get(url, params, function(result) {
-      $(SIDEBAR_CONTAINER).find('.sidebar-body').html(result.html);
-      showSelectedLeaf();
-      $(SIDEBAR_CONTAINER).data('scrollBar').update();
-    });
   }
 
   function initSideBar() {

app/assets/javascripts/sidebar_toggle.js

@@ -9,7 +9,6 @@ var SideBarToggle = (function() {
     $(SIDEBAR_CONTAINER).removeClass('collapsed');
     $(WRAPPER).css('paddingLeft', 'var(--wrapper-width)');
     $('.navbar-secondary').removeClass("navbar-without-sidebar");
-    $.post($(LAYOUT).data('navitgator-state-url'), {state: 'open'});
     $(WRAPPER).trigger('sideBar::show');
     $(WRAPPER).one("transitionend", function() {
       $(WRAPPER).trigger('sideBar::shown');
@@ -21,7 +20,6 @@ var SideBarToggle = (function() {
     $(SIDEBAR_CONTAINER).addClass('collapsed');
     $(WRAPPER).css('paddingLeft', '0');
     $('.navbar-secondary').addClass("navbar-without-sidebar");
-    $.post($(LAYOUT).data('navitgator-state-url'), {state: 'collapsed'});
     $(WRAPPER).trigger('sideBar::hide');
     $(WRAPPER).one("transitionend", function() {
       $(WRAPPER).trigger('sideBar::hidden');

app/assets/stylesheets/shared_styles/constants/colors.scss

@@ -116,3 +116,7 @@ $color-dd-hover: #f5f5f5;
 .sn-color-primary {
   color: var(--sn-blue);
 }
+
+.sn-background-background-violet {
+  background-color: var(--sn-light-grey);
+}

app/controllers/experiments_controller.rb

@@ -663,6 +663,9 @@ class ExperimentsController < ApplicationController
   end
 
   def set_navigator
-    @navigator = true
+    @navigator = {
+      url: tree_navigator_experiment_path(@experiment),
+      id: @experiment.code
+    }
   end
 end

app/controllers/my_modules_controller.rb

@@ -612,6 +612,9 @@ class MyModulesController < ApplicationController
   end
 
   def set_navigator
-    @navigator = true
+    @navigator = {
+      url: tree_navigator_my_module_path(@my_module),
+      id: @my_module.code
+    }
   end
 end

app/controllers/navigator/base_controller.rb

@@ -0,0 +1,155 @@
+# frozen_string_literal: true
+
+module Navigator
+  class BaseController < ApplicationController
+    private
+
+    def project_serializer(project)
+      {
+        id: project.code,
+        name: project.name,
+        url: project_path(project),
+        archived: project.archived,
+        type: :project,
+        has_children: project.has_children,
+        children_url: navigator_project_path(project)
+      }
+    end
+
+    def folder_serializer(folder)
+      {
+        id: folder.code,
+        name: folder.name,
+        url: projects_path(project_folder_id: folder.id),
+        archived: folder.archived,
+        type: :folder,
+        has_children: folder.has_children,
+        children_url: navigator_project_folder_path(folder)
+      }
+    end
+
+    def experiment_serializer(experiment)
+      {
+        id: experiment.code,
+        name: experiment.name,
+        url: canvas_experiment_path(experiment),
+        archived: experiment.archived,
+        type: :experiment,
+        has_children: experiment.has_children,
+        children_url: navigator_experiment_path(experiment)
+      }
+    end
+
+    def my_module_serializer(my_module)
+      {
+        id: my_module.code,
+        name: my_module.name,
+        type: :my_module,
+        url: protocols_my_module_path(my_module),
+        archived: my_module.archived,
+        has_children: false
+      }
+    end
+
+    def fetch_projects(folder = nil, archived = false)
+      has_children_sql = if !archived
+                           'SUM(CASE WHEN experiments.archived IS FALSE THEN 1 ELSE 0 END) > 0 AS has_children'
+                         else
+                           'SUM(CASE WHEN experiments.archived IS TRUE OR my_modules.archived IS TRUE
+                                THEN 1 ELSE 0 END) > 0 AS has_children'
+                         end
+      current_team.projects
+                  .where(project_folder_id: folder)
+                  .viewable_by_user(current_user, current_team)
+                  .with_children_viewable_by_user(current_user)
+                  .where('
+                    projects.archived = :archived OR
+                    (
+                      (
+                        experiments.archived = :archived OR
+                        my_modules.archived = :archived
+                      ) AND
+                      :archived IS TRUE
+                    )
+                  ', archived: archived)
+                  .select(
+                    'projects.id',
+                    'projects.name',
+                    'projects.archived',
+                    has_children_sql
+                  ).group('projects.id')
+    end
+
+    def fetch_project_folders(folder = nil, archived = false)
+      current_team.project_folders.where(parent_folder: folder)
+                  .left_outer_joins(projects: { user_assignments: :user_role }, project_folders: {})
+                  .where(project_folders: { archived: archived })
+                  .where('
+                    user_assignments.user_id = ? AND
+                    user_roles.permissions @> ARRAY[?]::varchar[] OR
+                    projects.id IS NULL
+                  ', current_user.id, ProjectPermissions::READ)
+                  .select(
+                    'project_folders.id',
+                    'project_folders.name',
+                    'project_folders.archived',
+                    'SUM(CASE WHEN projects.id IS NOT NULL OR project_folders_project_folders.id IS NOT NULL
+                              THEN 1 ELSE 0 END) > 0 AS has_children'
+                  ).group('project_folders.id')
+    end
+
+    def fetch_experiments(project, archived = false)
+      has_children_sql = if !archived
+                           'SUM(CASE WHEN my_modules.archived IS FALSE THEN 1 ELSE 0 END) > 0 AS has_children'
+                         else
+                           'SUM(CASE WHEN my_modules.archived IS TRUE THEN 1 ELSE 0 END) > 0 AS has_children'
+                         end
+      project.experiments
+             .viewable_by_user(current_user, current_team)
+             .with_children_viewable_by_user(current_user)
+             .where('
+              experiments.archived = :archived OR
+              my_modules.archived = :archived AND
+              :archived IS TRUE
+            ', archived: archived)
+             .select(
+               'experiments.id',
+               'experiments.name',
+               'experiments.archived',
+               has_children_sql
+             ).group('experiments.id')
+    end
+
+    def fetch_my_modules(experiment, archived = false)
+      experiment.my_modules
+                .viewable_by_user(current_user, current_team)
+                .where(archived: archived)
+    end
+
+    def build_folder_tree(folder, children, archived = false)
+      parent_folder = folder.parent_folder
+      tree = fetch_projects(parent_folder, archived).map { |i| project_serializer(i) } +
+             fetch_project_folders(parent_folder, archived).map { |i| folder_serializer(i) }
+      tree.find { |i| i[:id] == folder.code }[:children] = children
+      tree = build_folder_tree(parent_folder, tree, archived) if parent_folder.present?
+      tree
+    end
+
+    def project_level_branch(folder = nil, archived = false)
+      fetch_projects(folder, archived)
+        .map { |i| project_serializer(i) } +
+        fetch_project_folders(folder, archived)
+        .map { |i| folder_serializer(i) }
+    end
+
+    def experiment_level_branch(project, archived = false)
+      fetch_experiments(project, archived)
+        .map { |i| experiment_serializer(i) }
+    end
+
+    def my_module_level_branch(experiment, archived = false)
+      fetch_my_modules(experiment, archived)
+        .map { |i| my_module_serializer(i) }
+    end
+  end
+end

app/controllers/navigator/experiments_controller.rb

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+module Navigator
+  class ExperimentsController < BaseController
+    before_action :load_experiment
+    before_action :check_read_permissions
+
+    def show
+      my_modules = my_module_level_branch(@experiment, params[:archived] == 'true')
+      render json: { items: my_modules }
+    end
+
+    def tree
+      my_modules = my_module_level_branch(@experiment, params[:archived] == 'true')
+      experiments = experiment_level_branch(@experiment.project, params[:archived] == 'true')
+      experiments.find { |i| i[:id] == @experiment.code }[:children] = my_modules
+
+      tree = project_level_branch(@experiment.project.project_folder, params[:archived] == 'true')
+      tree.find { |i| i[:id] == @experiment.project.code }[:children] = experiments
+
+      tree = build_folder_tree(@experiment.project.project_folder, tree) if @experiment.project.project_folder
+
+      render json: { items: tree }
+    end
+
+    private
+
+    def load_experiment
+      @experiment = Experiment.find_by(id: params[:id])
+    end
+
+    def check_read_permissions
+      render_403 and return unless can_read_experiment?(@experiment)
+    end
+  end
+end

app/controllers/navigator/my_modules_controller.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+module Navigator
+  class MyModulesController < BaseController
+    before_action :load_my_module
+    before_action :check_read_permissions
+
+    def tree
+      my_modules = my_module_level_branch(@experiment, params[:archived] == 'true')
+      experiments = experiment_level_branch(@experiment.project, params[:archived] == 'true')
+      experiments.find { |i| i[:id] == @experiment.code }[:children] = my_modules
+
+      tree = project_level_branch(@experiment.project.project_folder, params[:archived] == 'true')
+      tree.find { |i| i[:id] == @experiment.project.code }[:children] = experiments
+
+      tree = build_folder_tree(@experiment.project.project_folder, tree) if @experiment.project.project_folder
+
+      render json: { items: tree }
+    end
+
+    private
+
+    def load_my_module
+      @my_module = MyModule.find_by(id: params[:id])
+
+      @experiment = @my_module.experiment
+    end
+
+    def check_read_permissions
+      render_403 and return unless can_read_my_module?(@my_module)
+    end
+  end
+end

app/controllers/navigator/project_folders_controller.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module Navigator
+  class ProjectFoldersController < BaseController
+    before_action :load_project_folder
+
+    def show
+      folder = project_level_branch(@project_folder, params[:archived] == 'true')
+      render json: { items: folder }
+    end
+
+    def tree
+      tree = folder_tree_branch(@project_folder, tree)
+      render json: { items: tree }
+    end
+
+    private
+
+    def load_project_folder
+      @project_folder = current_team.project_folders.find_by(id: params[:id])
+    end
+  end
+end

app/controllers/navigator/projects_controller.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module Navigator
+  class ProjectsController < BaseController
+    before_action :load_project
+    before_action :check_read_permissions, except: :index
+
+    def index
+      project_and_folders = project_level_branch(nil, params[:archived] == 'true')
+      render json: { items: project_and_folders }
+    end
+
+    def show
+      experiments = experiment_level_branch(@project, params[:archived] == 'true')
+      render json: { items: experiments }
+    end
+
+    def tree
+      experiments = experiment_level_branch(@project, params[:archived] == 'true')
+      tree = project_level_branch(@project.project_folder, params[:archived] == 'true')
+      tree.find { |i| i[:id] == @project.code }[:children] = experiments
+
+      tree = build_folder_tree(@project.project_folder, tree) if @project.project_folder
+
+      render json: { items: tree }
+    end
+
+    private
+
+    def load_project
+      @project = current_team.projects.find_by(id: params[:id])
+    end
+
+    def check_read_permissions
+      render_403 and return unless can_read_project?(@project)
+    end
+  end
+end

app/controllers/projects_controller.rb

@@ -482,6 +482,20 @@ class ProjectsController < ApplicationController
   end
 
   def set_navigator
-    @navigator = true
+    @navigator = if @project
+                   {
+                     url: tree_navigator_project_path(@project),
+                     id: @project.code
+                   }
+                 elsif current_folder
+                   {
+                     url: tree_navigator_project_folder_path(current_folder),
+                     id: current_folder.code
+                   }
+                 else
+                   {
+                     url: navigator_projects_path
+                   }
+                 end
   end
 end

app/javascript/packs/vue/navigation/navigator.js

@@ -8,7 +8,10 @@ Vue.use(PerfectScrollbar);
 
 Vue.prototype.i18n = window.I18n;
 
-window.addEventListener('DOMContentLoaded', () => {
+window.addEventListener('turbolinks:load', () => {
+  if ($('#sciNavigationNavigatorContainer').length === 0) return;
+  if ($('.navigator-container').length > 0) return;
+
   const navigator = new Vue({
     el: '#sciNavigationNavigatorContainer',
     components: {

app/javascript/vue/navigation/navigator.vue

@@ -1,5 +1,5 @@
 <template>
-  <div class="w-72 h-full border rounded bg-white flex flex-col right-0 absolute">
+  <div class="w-72 h-full border rounded bg-white flex flex-col right-0 absolute navigator-container">
     <div class="p-3 flex items-center">
       <i class="fas fa-bars p-2 cursor-pointer"></i>
       <div class="font-bold text-base">
@@ -7,9 +7,9 @@
       </div>
       <i @click="$emit('navigator:colapse')" class="fas fa-times ml-auto cursor-pointer"></i>
     </div>
-    <div class="grow px-2 py-4">
-      <NavigatorItem v-for="item in sortedMenuItems" :key="item.id" :item="item" />
-    </div>
+    <perfect-scrollbar class="grow px-2 py-4 relative">
+      <NavigatorItem v-for="item in sortedMenuItems" :key="item.id" :currentItemId="currentItemId" :item="item" />
+    </perfect-scrollbar>
   </div>
 </template>
 
@@ -25,28 +25,39 @@ export default {
   data() {
     return {
       menuItems: [],
-      navigatorCollapsed: false
+      navigatorCollapsed: false,
+      navigatorUrl: null,
+      currentItemId: null
     }
   },
   computed: {
     sortedMenuItems() {
-
       return this.menuItems.sort((a, b) => a.name - b.name)
     }
   },
   created() {
-    this.menuItems = [
-      {id: 'p1', name: 'Project 1', url: '/', archive: false, children: [
-        {id: 'e1', name: 'Experiment 1', url: '/', archive: false}
-      ]},
-      {id: 'f1', name: 'Folder', url: '/', archive: false, icon: 'fas fa-folder', children: [
-        {id: 'p2', name: 'Project 2', url: '/', archive: false, children: [
-          {id: 'e2', name: 'Experiment 2', url: '/', archive: false, children: [
-            {id: 't1', name: 'Task', url: '/', archive: false}
-        ]}
-      ]}
-      ]}
-    ]
-  }
+    this.changePage();
+    this.loadTree();
+
+    $(document).on('turbolinks:load', () => {
+      this.changePage();
+      if ($(`[navigator-item-id="${this.currentItemId}"]`).length === 0) {
+        this.loadTree();
+      }
+    });
+  },
+  methods: {
+    changePage() {
+      this.navigatorUrl = $('#active_navigator_url').val();
+      this.currentItemId = $('#active_navigator_item').val();
+    },
+    loadTree() {
+      if (!this.navigatorUrl) return;
+
+      $.get(this.navigatorUrl, {archived: false}, (data) => {
+        this.menuItems = data.items
+      })
+    }
+  },
 }
 </script>

app/javascript/vue/navigation/navigator_item.vue

@@ -1,15 +1,19 @@
 <template>
-  <div class="sn-color-primary pl-7 pt-4 flex items-center flex-wrap">
-    <div class="w-5 mr-2 flex justify-start">
-      <i v-if="haveChildren"
-        class="fas cursor-pointer"
-        :class="{'fa-chevron-right': !childrenOpen, 'fa-chevron-down': childrenOpen }"
-        @click="childrenOpen = !childrenOpen"></i>
+  <div class="sn-color-primary pl-7 w-64 flex justify-center flex-col" :navigator-item-id="item.id">
+    <div class="p-2 flex items-center whitespace-nowrap" :class="{ 'sn-background-background-violet': activeItem }">
+      <div class="w-5 mr-2 flex justify-start shrink-0">
+        <i v-if="hasChildren"
+          class="fas cursor-pointer"
+          :class="{'fa-chevron-right': !childrenExpanded, 'fa-chevron-down': childrenExpanded }"
+          @click="toggleChildren"></i>
+      </div>
+      <i v-if="itemIcon" class="mr-2" :class="itemIcon"></i>
+      <a :href="item.url" class="text-ellipsis overflow-hidden">
+        {{ item.name }}
+      </a>
     </div>
-    <i v-if="item.icon" class="mr-2" :class="item.icon"></i>
-    {{ item.name }}
-    <div v-if="childrenOpen" class="basis-full">
-      <NavigatorItem v-for="item in sortedMenuItems" :key="item.id" :item="item" />
+    <div class="basis-full" :class="{'hidden': !childrenExpanded}">
+      <NavigatorItem v-for="item in sortedMenuItems" @item:expand="treeExpand" :key="item.id" :currentItemId="currentItemId" :item="item" />
     </div>
   </div>
 </template>
@@ -18,20 +22,67 @@
 export default {
   name: 'NavigatorItem',
   props: {
-    item: Object
+    item: Object,
+    currentItemId: String
   },
   data: function() {
     return {
-      childrenOpen: false
-    }
+      childrenExpanded: false,
+      children: []
+    };
   },
   computed: {
-    haveChildren: function() {
-      return this.item.children && this.item.children.length > 0
+    hasChildren: function() {
+      return this.item.has_children;
     },
     sortedMenuItems: function() {
-      if (!this.haveChildren) return []
-      return this.item.children.sort((a, b) => a.name - b.name)
+      return this.children.sort((a, b) => a.name - b.name);
+    },
+    activeItem: function() {
+      return this.item.id == this.currentItemId;
+    },
+    itemIcon: function() {
+      switch(this.item.type) {
+        case 'folder':
+          return 'fas fa-folder';
+        default:
+          return null;
+      }
+    }
+  },
+  created: function() {
+    if (this.item.children) this.children = this.item.children;
+  },
+  mounted: function() {
+    this.selectItem();
+  },
+  watch: {
+    currentItemId: function() {
+      this.selectItem();
+    }
+  },
+  methods: {
+    toggleChildren: function() {
+      this.childrenExpanded = !this.childrenExpanded;
+      if (this.childrenExpanded) this.loadChildren();
+    },
+    loadChildren: function() {
+      $.get(this.item.children_url, {archived: false}, (data) => {
+        this.children = data.items;
+      });
+    },
+    treeExpand: function() {
+      this.childrenExpanded = true;
+      this.$emit('item:expand');
+    },
+    selectItem: function() {
+      if (this.activeItem && !this.childrenExpanded) {
+        this.$emit('item:expand');
+        if (this.hasChildren) {
+          this.childrenExpanded = true;
+          this.loadChildren();
+        }
+      }
     }
   },
 }

app/models/experiment.rb

@@ -89,6 +89,21 @@ class Experiment < ApplicationRecord
       .where(project: Project.viewable_by_user(user, teams))
   end
 
+  def self.with_children_viewable_by_user(user)
+    joins("
+      LEFT OUTER JOIN my_modules ON my_modules.experiment_id = experiments.id
+      LEFT OUTER JOIN user_assignments my_module_user_assignments
+        ON my_module_user_assignments.assignable_id = my_modules.id AND
+           my_module_user_assignments.assignable_type = 'MyModule'
+      LEFT OUTER JOIN user_roles my_module_user_roles
+        ON my_module_user_roles.id = my_module_user_assignments.user_role_id
+    ")
+      .where('
+        (my_module_user_assignments.user_id = ? AND my_module_user_roles.permissions @> ARRAY[?]::varchar[]
+          OR my_modules.id IS NULL)
+      ', user.id, MyModulePermissions::READ)
+  end
+
   def self.filter_by_teams(teams = [])
     return self if teams.blank?
 

app/models/project.rb

@@ -109,6 +109,29 @@ class Project < ApplicationRecord
             .or(projects.with_granted_permissions(user, ProjectPermissions::READ)).distinct
   end
 
+  def self.with_children_viewable_by_user(user)
+    joins("
+      LEFT OUTER JOIN experiments ON experiments.project_id = projects.id
+      LEFT OUTER JOIN user_assignments experiment_user_assignments
+        ON experiment_user_assignments.assignable_id = experiments.id AND
+           experiment_user_assignments.assignable_type = 'Experiment'
+      LEFT OUTER JOIN user_roles experiment_user_roles
+        ON experiment_user_roles.id = experiment_user_assignments.user_role_id
+      LEFT OUTER JOIN my_modules ON my_modules.experiment_id = experiments.id
+      LEFT OUTER JOIN user_assignments my_module_user_assignments
+        ON my_module_user_assignments.assignable_id = my_modules.id AND
+           my_module_user_assignments.assignable_type = 'MyModule'
+      LEFT OUTER JOIN user_roles my_module_user_roles
+        ON my_module_user_roles.id = my_module_user_assignments.user_role_id
+    ")
+      .where('
+        (experiment_user_assignments.user_id = ? AND experiment_user_roles.permissions @> ARRAY[?]::varchar[]
+          OR experiments.id IS NULL) AND
+        (my_module_user_assignments.user_id = ? AND my_module_user_roles.permissions @> ARRAY[?]::varchar[]
+          OR my_modules.id IS NULL)
+      ', user.id, ExperimentPermissions::READ, user.id, MyModulePermissions::READ)
+  end
+
   def self.filter_by_teams(teams = [])
     teams.blank? ? self : where(team: teams)
   end

app/models/project_folder.rb

@@ -1,6 +1,9 @@
 # frozen_string_literal: true
 
 class ProjectFolder < ApplicationRecord
+  ID_PREFIX = 'PF'
+  include PrefixedIdModel
+
   include ArchivableModel
   include SearchableModel
   include SearchableByNameModel

app/views/shared/navigation/_navigator.html.erb

@@ -1,4 +1,6 @@
 <% if @navigator %>
+  <%= hidden_field_tag :active_navigator_item, @navigator[:id] %>
+  <%= hidden_field_tag :active_navigator_url, @navigator[:url] %>
   <div id="sciNavigationNavigatorContainer"
        class="contents"
        data-navigator-state-url="<%= navigator_state_navigations_path %>"

config/routes.rb

@@ -292,6 +292,32 @@ Rails.application.routes.draw do
       resources :my_modules, only: %i(show update edit)
     end
 
+    namespace :navigator do
+      resources :project_folders, only: %i(show) do
+        member do
+          get :tree
+        end
+      end
+
+      resources :projects, only: %i(show index) do
+        member do
+          get :tree
+        end
+      end
+
+      resources :experiments, only: %i(show) do
+        member do
+          get :tree
+        end
+      end
+
+      resources :my_modules, only: %i(show) do
+        member do
+          get :tree
+        end
+      end
+    end
+
     resources :projects, except: [:destroy] do
       resources :project_comments,
                 path: '/comments',

config/tailwind.config.js

@@ -15,6 +15,10 @@ module.exports = {
       },
     },
   },
+  blocklist: [
+    'collapse',
+    'container'
+  ],
   plugins: [
     require('@tailwindcss/forms'),
     require('@tailwindcss/aspect-ratio'),