Merge branch 'main' into release

server/app/admin/assertions_admin.rb

@@ -1,10 +1,10 @@
 Trestle.resource(:assertions) do
   collection do
-    Assertion.eager_load(:flags, molecular_profile: {variants: [:gene]}).order(id: :asc)
+    Assertion.eager_load(:flags, molecular_profile: {variants: [:feature]}).order(id: :asc)
   end
 
   search do |q|
-    q ? collection.where("genes.name ILIKE ?", "#{q}%").or(collection.where("variants.name ILIKE ?", "#{q}%")) : collection
+    q ? collection.where("features.name ILIKE ?", "#{q}%").or(collection.where("variants.name ILIKE ?", "#{q}%")) : collection
   end
 
   remove_action :destroy

server/app/admin/evidence_items_admin.rb

@@ -1,6 +1,6 @@
 Trestle.resource(:evidence_items) do
   collection do
-    EvidenceItem.eager_load(:flags, molecular_profile: {variants: [:gene]}).order(id: :asc)
+    EvidenceItem.eager_load(:flags, molecular_profile: {variants: [:feature]}).order(id: :asc)
   end
 
   remove_action :destroy
@@ -37,7 +37,7 @@
     tab :evidence_item do
       row do
         col(sm: 1) { static_field :id }
-        col(sm: 1) { static_field evidence_item.molecular_profile.display_name }
+        col(sm: 1) { evidence_item.molecular_profile.display_name }
         col(sm: 2) do
           variant_origins = EvidenceItem.variant_origins.keys.map { |variant_origin| [variant_origin, variant_origin] }
           select :variant_origin, variant_origins
@@ -95,7 +95,7 @@
 
       select :phenotype_ids, Phenotype.order(:hpo_class), { label: "Phenotypes" }, multiple: true
 
-      collection_select :source_id, Source.order(:description), :id, :display_name
+      collection_select :source_id, Source.order(:citation), :id, :display_name
 
       divider
 

server/app/admin/genes_admin.rb → server/app/admin/features_admin.rb

@@ -1,41 +1,39 @@
-Trestle.resource(:genes, model: Features::Gene) do
+Trestle.resource(:features) do
   collection do
-    Fatures::Gene.includes(:flags).order(name: :asc)
+    Feature.includes(:flags).order(name: :asc)
   end
 
   search do |q|
-    q ? collection.where("genes.name ILIKE ?", "#{q}%") : collection
+    q ? collection.where("features.name ILIKE ?", "#{q}%") : collection
   end
 
   remove_action :destroy
   remove_action :new
 
   menu do
-    item :genes, icon: "fa fa-align-center" #TODO: see if we can use our custom icons here
+    item :features, icon: "fa fa-align-center" #TODO: see if we can use our custom icons here
   end
 
   scope :all
-  scope :with_variants, -> { Features::Gene.joins(:variants).distinct }, default: true
-  scope :flagged, -> { Features::Gene.where(flagged: true) }
+  scope :with_variants, -> { Feature.joins(:variants).distinct }, default: true
+  scope :flagged, -> { Feature.where(flagged: true) }
 
   # Customize the table columns shown on the index view.
   table do
     column :id
-    column :entrez_id
     column :name
-    column :official_name
+    column :full_name
     column :flagged
   end
 
   # Customize the form fields shown on the new/edit views.
-  form do |gene|
-    tab :gene do
+  form do |feature|
+    tab :feature do
       row do
         col(sm: 1) { static_field :id }
-        col(sm: 1) { static_field :entrez_id }
         col(sm: 1) { static_field :name }
-        col(sm: 8) { static_field :official_name }
-        if gene.flagged
+        col(sm: 8) { static_field :full_name }
+        if feature.flagged
           col do
             static_field :flagged do
               status_tag(icon("fa fa-flag"), :danger)
@@ -54,8 +52,8 @@
       end
     end
 
-    tab :comments, badge: gene.comments.size do
-      table gene.comments do
+    tab :comments, badge: feature.comments.size do
+      table feature.comments do
         column :id do |comment|
           link_to comment.id, CommentsAdmin.instance_path(comment)
         end
@@ -67,8 +65,8 @@
       end
     end
 
-    tab :flags, badge: gene.flags.where(state: 'open').exists? do
-      table gene.flags do
+    tab :flags, badge: feature.flags.where(state: 'open').exists? do
+      table feature.flags do
         column :id do |flag|
           link_to flag.id, FlagsAdmin.instance_path(flag)
         end
@@ -82,8 +80,8 @@
       end
     end
 
-    tab :revisions, badge: gene.revisions.where(status: 'new').exists? do
-      table gene.revisions do
+    tab :revisions, badge: feature.revisions.where(status: 'new').exists? do
+      table feature.revisions do
         column :id do |revision|
           link_to revision.id, RevisionsAdmin.instance_path(revision)
         end

server/app/admin/organizations_admin.rb

@@ -1,4 +1,8 @@
 Trestle.resource(:organizations) do
+  controller do
+    include ActiveStorage::SetCurrent
+  end
+
   menu do
     item :organizations, icon: "fa fa-users"
   end

server/app/admin/reports_admin.rb

@@ -0,0 +1,65 @@
+Trestle.admin(:reports) do
+  menu do
+    item :reports, icon: "fas fa-file-alt"
+  end
+
+  controller do
+    def index
+      @reports = Report::AVAILABLE_REPORTS
+    end
+
+    def show
+      @report = Report::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
+    end
+
+    def generate_report
+      @report = Report::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
+      report_params = params.permit(@report.inputs.keys).to_h.symbolize_keys
+      #checkbox will come in as 0 or 1
+      #cast it to a boolean here so reports dont have to worry about that
+      report_params.each do |key, val|
+        if @report.inputs[key] == :boolean
+          report_params[key] =  ActiveRecord::Type::Boolean.new.cast(val)
+        end
+      end
+      report_instance = @report.new(report_params)
+      report_instance.perform unless report_instance.errors.any?
+
+      if report_instance.errors.any?
+        flash[:error] = report_instance.errors.join("\n")
+        render :show
+      else
+        if params[:format] == "download"
+          stream_table(report_instance)
+        else
+          @data = report_instance.data
+          @headers = report_instance.headers
+          render :result
+        end
+      end
+    end
+
+    private
+    def stream_table(report)
+      require 'csv'
+      headers.delete("Content-Length")
+      headers["Cache-Control"] = "no-cache"
+      headers["Content-Type"] = "text/csv"
+      headers["Content-Disposition"] = "attachment; filename=\"#{report.class.name}-#{Date.today}.tsv\""
+      headers["X-Accel-Buffering"] = "no"
+      response.status = 200
+
+      self.response_body = Enumerator.new do |stream|
+        stream << CSV.generate_line(report.headers, col_sep: "\t")
+        report.data.each do |row|
+          stream << CSV.generate_line(row, col_sep: "\t")
+        end
+      end
+    end
+  end
+
+  routes do
+    get '/:name', action: :show
+    post '/:name', action: :generate_report
+  end
+end

server/app/admin/users_admin.rb

@@ -1,4 +1,8 @@
 Trestle.resource(:users) do
+  controller do
+    include ActiveStorage::SetCurrent
+  end
+
   menu do
     item :users, icon: "fa fa-user"
   end

server/app/admin/utilities_admin.rb

@@ -0,0 +1,35 @@
+Trestle.admin(:utilities) do
+  menu do
+    item :utilities, icon: "fas fa-cogs"
+  end
+
+  controller do
+    def index
+      @utilities = ActionWrapper::AVAILABLE_ACTIONS
+    end
+
+    def show
+      @util = ActionWrapper::AVAILABLE_ACTIONS.find { |x| params[:name] == x.name }
+    end
+
+    def perform_action
+      @util = ActionWrapper::AVAILABLE_ACTIONS.find { |x| params[:name] == x.name }
+      util_params = params.permit(@util.inputs.keys).to_h
+      action = @util.new
+      res = action.perform(util_params.symbolize_keys)
+
+      if res.errors.any?
+        flash[:error] = res.errors.join("\n")
+      else
+        flash[:message] = "#{@util.name} Succeeded"
+      end
+
+      render :show
+    end
+  end
+
+  routes do
+    get '/:name', action: :show
+    post '/:name', action: :perform_action
+  end
+end

server/app/admin/variants_admin.rb

@@ -20,7 +20,7 @@
   table do
     column :id
     column :name
-    column :gene
+    column :feature
     column :variant_aliases do |variant|
       variant.variant_aliases.map {|a| a.name }.join(', ')
     end
@@ -37,15 +37,8 @@
         col(sm: 1) { static_field :id }
         col(sm: 1) { static_field :name }
         col(sm: 1) do
-          static_field :gene do
-            link_to variant.gene.name, GenesAdmin.instance_path(variant.gene)
-          end
-        end
-        if variant.secondary_gene.present?
-          col(sm: 1) do
-            static_field :secondary_gene do
-              link_to variant.secondary_gene.name, GenesAdmin.instance_path(variant.secondary_gene)
-            end
+          static_field :variant do
+            link_to variant.feature.name, FeaturesAdmin.instance_path(variant.feature)
           end
         end
         if variant.flagged