From 2101c2d694f44c6adaaac5123258e6fef3b6ffe6 Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Thu, 18 Apr 2024 16:32:12 -0500
Subject: [PATCH 1/6] tweak admin to get working with features

---
 server/app/admin/assertions_admin.rb          |  4 +--
 server/app/admin/evidence_items_admin.rb      |  6 ++--
 .../{genes_admin.rb => features_admin.rb}     | 36 +++++++++----------
 server/app/admin/variants_admin.rb            | 13 ++-----
 server/config/environments/development.rb     |  2 +-
 server/config/initializers/trestle.rb         |  1 -
 6 files changed, 26 insertions(+), 36 deletions(-)
 rename server/app/admin/{genes_admin.rb => features_admin.rb} (71%)

diff --git a/server/app/admin/assertions_admin.rb b/server/app/admin/assertions_admin.rb
index ecb619639..0957b5567 100644
--- a/server/app/admin/assertions_admin.rb
+++ b/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
diff --git a/server/app/admin/evidence_items_admin.rb b/server/app/admin/evidence_items_admin.rb
index 3c456003b..c518461f8 100644
--- a/server/app/admin/evidence_items_admin.rb
+++ b/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
 
diff --git a/server/app/admin/genes_admin.rb b/server/app/admin/features_admin.rb
similarity index 71%
rename from server/app/admin/genes_admin.rb
rename to server/app/admin/features_admin.rb
index 342f2dc2b..4f6c9f2f9 100644
--- a/server/app/admin/genes_admin.rb
+++ b/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)
+    Fature.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, -> { Features.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
diff --git a/server/app/admin/variants_admin.rb b/server/app/admin/variants_admin.rb
index d219ce4d9..41736867a 100644
--- a/server/app/admin/variants_admin.rb
+++ b/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
diff --git a/server/config/environments/development.rb b/server/config/environments/development.rb
index c129b5ff8..4961004f1 100644
--- a/server/config/environments/development.rb
+++ b/server/config/environments/development.rb
@@ -69,5 +69,5 @@
   # config.action_view.annotate_rendered_view_with_filenames = true
 
   # Raise error when a before_action's only/except options reference missing actions
-  config.action_controller.raise_on_missing_callback_actions = true
+  config.action_controller.raise_on_missing_callback_actions = false
 end
diff --git a/server/config/initializers/trestle.rb b/server/config/initializers/trestle.rb
index c2365ef4a..6b6276d24 100644
--- a/server/config/initializers/trestle.rb
+++ b/server/config/initializers/trestle.rb
@@ -79,7 +79,6 @@
     unless current_user && Role.user_is_at_least_a?(current_user, :admin)
       redirect_to '/'
     end
-    ActiveStorage::Current.host = request.base_url
   end
   #
   # config.after_action do |controller|

From 80c982c94f9b2ae7c0ce95045e430f1dbc1f8f11 Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Thu, 18 Apr 2024 16:33:02 -0500
Subject: [PATCH 2/6] rudimentary reporting framework for custom reports

---
 server/app/admin/reports_admin.rb             | 58 +++++++++++++++
 server/app/admin/utilities_admin.rb           | 35 ++++++++++
 server/app/models/actions/merge_accounts.rb   | 44 ++++++------
 server/app/reports/clingen_counts.rb          | 58 +++++++++++++++
 server/app/reports/report.rb                  | 70 +++++++++++++++++++
 server/app/utilities/action_wrapper.rb        | 28 ++++++++
 server/app/utilities/merge_accounts.rb        | 21 ++++++
 server/app/views/admin/reports/index.html.erb | 17 +++++
 .../app/views/admin/reports/result.html.erb   | 32 +++++++++
 server/app/views/admin/reports/show.html.erb  | 30 ++++++++
 server/app/views/admin/shared/_field.html.erb | 13 ++++
 .../app/views/admin/utilities/index.html.erb  | 17 +++++
 .../app/views/admin/utilities/result.html.erb | 32 +++++++++
 .../app/views/admin/utilities/show.html.erb   | 19 +++++
 14 files changed, 451 insertions(+), 23 deletions(-)
 create mode 100644 server/app/admin/reports_admin.rb
 create mode 100644 server/app/admin/utilities_admin.rb
 create mode 100644 server/app/reports/clingen_counts.rb
 create mode 100644 server/app/reports/report.rb
 create mode 100644 server/app/utilities/action_wrapper.rb
 create mode 100644 server/app/utilities/merge_accounts.rb
 create mode 100644 server/app/views/admin/reports/index.html.erb
 create mode 100644 server/app/views/admin/reports/result.html.erb
 create mode 100644 server/app/views/admin/reports/show.html.erb
 create mode 100644 server/app/views/admin/shared/_field.html.erb
 create mode 100644 server/app/views/admin/utilities/index.html.erb
 create mode 100644 server/app/views/admin/utilities/result.html.erb
 create mode 100644 server/app/views/admin/utilities/show.html.erb

diff --git a/server/app/admin/reports_admin.rb b/server/app/admin/reports_admin.rb
new file mode 100644
index 000000000..1b3a9a2e1
--- /dev/null
+++ b/server/app/admin/reports_admin.rb
@@ -0,0 +1,58 @@
+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
+      report_instance = @report.new(report_params.symbolize_keys)
+      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
diff --git a/server/app/admin/utilities_admin.rb b/server/app/admin/utilities_admin.rb
new file mode 100644
index 000000000..c099b77a5
--- /dev/null
+++ b/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
diff --git a/server/app/models/actions/merge_accounts.rb b/server/app/models/actions/merge_accounts.rb
index 90c8d52b2..752423ec6 100644
--- a/server/app/models/actions/merge_accounts.rb
+++ b/server/app/models/actions/merge_accounts.rb
@@ -2,12 +2,12 @@ module Actions
   class MergeAccounts
     include Actions::Transactional
 
-    attr_reader :account_to_keep, :accounts_to_merge, :old_account_ids
+    attr_reader :account_to_keep, :account_to_merge, :old_account_id
 
-    def initialize(account_to_keep:, accounts_to_merge_in:)
-      @account_to_keep = account_to_keep
-      @accounts_to_merge = Array(accounts_to_merge_in)
-      @old_account_ids = @accounts_to_merge.map(&:id)
+    def initialize(account_id_to_keep:, account_id_to_merge_in:)
+      @account_to_keep = User.find(account_id_to_keep)
+      @old_account_id = account_id_to_merge_in
+      @account_to_merge = User.find(account_id_to_merge_in)
     end
 
     def execute
@@ -24,12 +24,12 @@ def execute
       merge_organizations
       move_legacy_changes
       account_to_keep.save!
-      accounts_to_merge.each { |u| u.destroy! }
+      account_to_merge.destroy!
     end
 
     private
     def move_authorizations
-      auths = Authorization.where(user_id: old_account_ids)
+      auths = Authorization.where(user_id: old_account_id)
       auths.each do |a|
         a.user_id = account_to_keep.id
         a.save!
@@ -37,7 +37,7 @@ def move_authorizations
     end
 
     def move_activities
-      activities = Activity.where(user_id: old_account_ids)
+      activities = Activity.where(user_id: old_account_id)
       activities.each do |a|
         a.user_id = account_to_keep.id
         a.save!
@@ -45,7 +45,7 @@ def move_activities
     end
 
     def move_events
-      events = Event.where(originating_user_id: old_account_ids)
+      events = Event.where(originating_user_id: old_account_id)
       events.each do |e|
         e.originating_user_id = account_to_keep.id
         e.save!
@@ -53,7 +53,7 @@ def move_events
     end
 
     def move_comments
-      comments = Comment.where(user_id: old_account_ids)
+      comments = Comment.where(user_id: old_account_id)
       comments.each do |c|
         c.user_id = account_to_keep.id
         c.save!
@@ -61,13 +61,13 @@ def move_comments
     end
 
     def move_flags
-      flagging = Flag.where(flagging_user_id: old_account_ids)
+      flagging = Flag.where(flagging_user_id: old_account_id)
       flagging.each do |f|
         f.flagging_user_id = account_to_keep.id
         f.save!
       end
 
-      resolving = Flag.where(resolving_user_id: old_account_ids)
+      resolving = Flag.where(resolving_user_id: old_account_id)
       resolving.each do |f|
         f.resolving_user_id = account_to_keep.id
         f.save!
@@ -75,7 +75,7 @@ def move_flags
     end
 
     def move_subscriptions
-      subs = Subscription.where(user_id: old_account_ids)
+      subs = Subscription.where(user_id: old_account_id)
       subs.each do |s|
         if Subscription.where(subscribable: s.subscribable, user_id: account_to_keep.id).exists?
           s.destroy!
@@ -87,7 +87,7 @@ def move_subscriptions
     end
 
     def move_notifications
-      notified = Notification.where(notified_user_id: old_account_ids)
+      notified = Notification.where(notified_user_id: old_account_id)
       notified.each do |n|
         if Notification.where(event_id: n.event_id, notified_user_id: account_to_keep.id).exists?
           n.destroy!
@@ -97,7 +97,7 @@ def move_notifications
         end
       end
 
-      notifier = Notification.where(originating_user_id: old_account_ids)
+      notifier = Notification.where(originating_user_id: old_account_id)
       notifier.each do |n|
         if Notification.where(event_id: n.event_id, originating_user_id: account_to_keep.id).exists?
           n.destroy!
@@ -109,7 +109,7 @@ def move_notifications
     end
 
     def move_mentions
-      mentions = UserMention.where(user_id: old_account_ids)
+      mentions = UserMention.where(user_id: old_account_id)
       mentions.each do |m|
         if UserMention.where(user_id: account_to_keep.id, comment_id: m.comment_id)
           m.destroy!
@@ -121,11 +121,11 @@ def move_mentions
     end
 
     def merge_roles
-      account_to_keep.role = Role.highest_role_for_users(account_to_keep, *accounts_to_merge)
+      account_to_keep.role = Role.highest_role_for_users(account_to_keep, account_to_merge)
     end
 
     def move_source_suggestions
-      suggestions = SourceSuggestion.where(user_id: old_account_ids)
+      suggestions = SourceSuggestion.where(user_id: old_account_id)
       suggestions.each do |s|
         s.user_id = account_to_keep.id
         s.save!
@@ -133,10 +133,8 @@ def move_source_suggestions
     end
 
     def merge_organizations
-      orgs_to_add = accounts_to_merge.flat_map(&:organizations)
-      accounts_to_merge.each do |user|
-        user.organizations = []
-      end
+      orgs_to_add = account_to_merge.organizations
+      account_to_merge.organizations = []
       existing_orgs = account_to_keep.organizations
       all_orgs = orgs_to_add + existing_orgs
       account_to_keep.organizations = all_orgs.uniq
@@ -144,7 +142,7 @@ def merge_organizations
 
     class SuggestedChange < ActiveRecord::Base; end
     def move_legacy_changes
-      changes = SuggestedChange.where(user_id: old_account_ids)
+      changes = SuggestedChange.where(user_id: old_account_id)
       changes.each do |sc|
         sc.user_id = account_to_keep.id
         sc.save!
diff --git a/server/app/reports/clingen_counts.rb b/server/app/reports/clingen_counts.rb
new file mode 100644
index 000000000..22fdb4d77
--- /dev/null
+++ b/server/app/reports/clingen_counts.rb
@@ -0,0 +1,58 @@
+class ClingenCounts < Report
+  attr_reader :start_date, :end_date, :all_org_ids
+  CLINGEN_ORG_ID = 2
+
+  def self.name
+    "ClinGen Contributions"
+  end
+
+  def self.description
+    "Count contributions from ClinGen member orgs over a specified timespan."
+  end
+
+  def self.inputs
+    {
+      start_date: :date,
+      end_date: :date,
+      include_suborgs: :boolean
+    }
+  end
+
+  def setup(start_date:, end_date:, include_suborgs:)
+    @start_date = Date.parse(start_date)
+    @end_date = Date.parse(end_date)
+
+    clingen_org = Organization.find(CLINGEN_ORG_ID)
+    if include_suborgs
+      sub_groups = clingen_org.groups
+      @all_org_ids = [clingen_org.id] + sub_groups.map(&:id)
+    else
+      @all_org_ids = clingen_org.id
+    end
+  end
+
+  def headers
+    ["Contribution Type", "Count"]
+  end
+
+  def execute
+    data << ["Assertions Submitted", SubmitAssertionActivity.where(organization_id: all_org_ids, created_at: (start_date..end_date)).count]
+    data << ["Evidence Submitted", SubmitEvidenceItemActivity.where(organization_id: all_org_ids, created_at: (start_date..end_date)).count]
+    data << ["Comments Made", CommentActivity.where(organization_id: all_org_ids, created_at: (start_date..end_date)).count]
+    data << ["Revisions Suggested", Event.where(organization_id: all_org_ids, action: 'revision suggested', created_at: (start_date..end_date)).count]
+    data << ["Proposed Revisions Accepted", calculate_contribution('revision suggested', 'revision suggested')]
+    data << ["Submitted Evidence Accepted", calculate_contribution('accepted', 'submitted')]
+    data << ["Submitted Assertions Accepted", calculate_contribution('assertion accepted', 'assertion submitted')]
+  end
+
+  private
+  def calculate_contribution(submission_event_name, accept_event_name)
+    contributed_by_clingen = 0
+    Event.where(action: accept_event_name, created_at: (start_date..end_date)).find_each do |e|
+      if Event.where(action: submission_event_name, organization_id: all_org_ids, subject: e.subject).exists?
+        contributed_by_clingen += 1
+      end
+    end
+    contributed_by_clingen
+  end
+end
diff --git a/server/app/reports/report.rb b/server/app/reports/report.rb
new file mode 100644
index 000000000..4a7cde6a9
--- /dev/null
+++ b/server/app/reports/report.rb
@@ -0,0 +1,70 @@
+class Report
+  AVAILABLE_REPORTS = [
+    ClingenCounts
+  ]
+
+  def initialize(params)
+    setup(**params)
+  rescue => e
+    errors << e.message
+  end
+
+  attr_reader :data, :headers, :errors
+
+  def self.name
+    raise NotImplementedError.new("Specify in subclass")
+  end
+
+  def self.description
+    raise NotImplementedError.new("Specify in subclass")
+  end
+
+  # Can users download this as a TSV
+  def self.downloadable?
+    true
+  end
+
+  # Can users view this directly in the admin UI
+  def self.viewable?
+    true
+  end
+
+  def self.inputs
+    #format input_name: :type
+    #supported types :text, :date, :boolean, :int
+    {}
+  end
+
+  # Column headers for the report
+  def headers
+    raise NotImplementedError.new("Specify in subclass")
+  end
+
+  # Data rows. #execute should append rows to this list
+  def data
+    @data ||= []
+  end
+
+  # Append any errors here
+  def errors
+    @errors ||= []
+  end
+
+  def perform
+    execute
+  rescue => e
+    errors << e.message
+  end
+
+  # Called from constructor.
+  # Will receive named arguments from the form inputs
+  # specified by self.inputs
+  def setup
+    raise NotImplementedError.new("Specify in subclass")
+  end
+
+  # Invoke the report logic. Must set data, headers, or errors
+  def execute
+    raise NotImplementedError.new("Specify in subclass")
+  end
+end
diff --git a/server/app/utilities/action_wrapper.rb b/server/app/utilities/action_wrapper.rb
new file mode 100644
index 000000000..97c6db572
--- /dev/null
+++ b/server/app/utilities/action_wrapper.rb
@@ -0,0 +1,28 @@
+class ActionWrapper
+  AVAILABLE_ACTIONS = [
+    MergeAccounts
+  ]
+
+  def self.name
+    raise NotImplementedError.new("Specify in subclass")
+  end
+
+  def self.description
+    raise NotImplementedError.new("Specify in subclass")
+  end
+
+  def self.inputs
+    #format input_name: :type
+    #supported types :text, :date, :boolean, :int
+    {}
+  end
+
+  def perform(params)
+    instance = action_class.new(**params)
+    instance.perform
+  end
+
+  def action_class
+    raise NotImplementedError.new("Implement in Subclass")
+  end
+end
diff --git a/server/app/utilities/merge_accounts.rb b/server/app/utilities/merge_accounts.rb
new file mode 100644
index 000000000..a8662b258
--- /dev/null
+++ b/server/app/utilities/merge_accounts.rb
@@ -0,0 +1,21 @@
+class MergeAccounts < ActionWrapper
+
+  def self.name
+    "Merge User Accounts"
+  end
+
+  def self.description
+    "Merge two user accounts, removing one and transfering the authorizations and events to the remaining one."
+  end
+
+  def self.inputs
+    {
+      account_id_to_keep: :int,
+      account_id_to_merge_in: :int,
+    }
+  end
+
+  def action_class
+    Actions::MergeAccounts
+  end
+end
diff --git a/server/app/views/admin/reports/index.html.erb b/server/app/views/admin/reports/index.html.erb
new file mode 100644
index 000000000..94f15ab3e
--- /dev/null
+++ b/server/app/views/admin/reports/index.html.erb
@@ -0,0 +1,17 @@
+<%= content_for(:title, "Reports") %>
+<%= render "header" %>
+
+<div class="main-content-area">
+  <div class="utilities">
+  </div>
+  <div class="main-content-container">
+    <div class="main-content">
+      <%= table(@reports) do
+        column :name do |report|
+          link_to report.name, "/admin/reports/#{report.name}"
+        end
+        column :description, truncate: false
+      end %>
+    </div>
+  </div>
+</div>
diff --git a/server/app/views/admin/reports/result.html.erb b/server/app/views/admin/reports/result.html.erb
new file mode 100644
index 000000000..d8d9fe08e
--- /dev/null
+++ b/server/app/views/admin/reports/result.html.erb
@@ -0,0 +1,32 @@
+<%= content_for(:title, @report.name) %>
+<%= render "header" %>
+
+<div class="main-content-area">
+  <div class="utilities">
+      Results:
+  </div>
+  <div class="main-content-container">
+    <div class="main-content">
+      <div class="table-container">
+        <table class="trestle-table">
+          <thead>
+            <tr>
+              <% @headers.each do |header| %>
+                <th><%= header %></th>
+              <% end %>
+            </tr>
+          </thead>
+          <tbody>
+            <% @data.each do |row| %>
+              <tr>
+                <% row.each do |col| %>
+                  <td><%= col %></td>
+                <% end %>
+              </tr>
+            <% end %>
+          </tbody>
+        </table>
+      </div>
+    </div>
+  </div>
+</div>
diff --git a/server/app/views/admin/reports/show.html.erb b/server/app/views/admin/reports/show.html.erb
new file mode 100644
index 000000000..efbfa724e
--- /dev/null
+++ b/server/app/views/admin/reports/show.html.erb
@@ -0,0 +1,30 @@
+<%= content_for(:title, @report.name) %>
+<%= render "header" %>
+
+<div class="main-content-area">
+  <%= render "trestle/flash/flash" %>
+  <div class="utilities">
+      Configure your report:
+  </div>
+  <div class="main-content-container">
+    <div class="main-content">
+      <%= form_with do |f| %>
+        <% @report.inputs.each do |f_name, f_type| %>
+          <%= render 'admin/shared/field', name: f_name, type: f_type, form: f  %>
+        <% end %>
+        <div class="form-group">
+          <%= f.label :format, "Format", class: "control-label" %>
+          <div class="custom-control custom-radio custom-control-inline">
+            <%= f.radio_button :format, "view", disabled: !@report.viewable?, class: "custom-control-input" %>
+            <%= f.label :format_view, "View on Web", class: "custom-control-label" %>
+          </div>
+          <div class="custom-control custom-radio custom-control-inline">
+            <%= f.radio_button :format, "download", checked: true, disabled: !@report.downloadable?, class: "custom-control-input" %>
+            <%= f.label :format_download, "Download TSV", class: "custom-control-label"  %>
+          </div>
+        </div>
+        <%= f.submit "Generate Report", class: "btn btn-success" %>
+      <% end %>
+    </div>
+  </div>
+</div>
diff --git a/server/app/views/admin/shared/_field.html.erb b/server/app/views/admin/shared/_field.html.erb
new file mode 100644
index 000000000..4813efb62
--- /dev/null
+++ b/server/app/views/admin/shared/_field.html.erb
@@ -0,0 +1,13 @@
+<%# locals: (form:, name:, type:) %>
+<div class="form-group">
+  <%= form.label name, class: "control-label" %>
+  <% if type == :text %>
+    <%= form.text_field name, required: true %>
+  <% elsif type == :date %>
+    <%= form.date_field name, required: true %>
+  <% elsif type == :boolean %>
+    <%= form.check_box name, checked: true %>
+  <% elsif type == :int %>
+    <%= form.text_field name, required: true, pattern: "\\d+" %>
+  <% end %>
+</div>
diff --git a/server/app/views/admin/utilities/index.html.erb b/server/app/views/admin/utilities/index.html.erb
new file mode 100644
index 000000000..445a43894
--- /dev/null
+++ b/server/app/views/admin/utilities/index.html.erb
@@ -0,0 +1,17 @@
+<%= content_for(:title, "Utilities") %>
+<%= render "header" %>
+
+<div class="main-content-area">
+  <div class="utilities">
+  </div>
+  <div class="main-content-container">
+    <div class="main-content">
+      <%= table(@utilities) do
+        column :name do |util|
+          link_to util.name, "/admin/utilities/#{util.name}"
+        end
+        column :description, truncate: false
+      end %>
+    </div>
+  </div>
+</div>
diff --git a/server/app/views/admin/utilities/result.html.erb b/server/app/views/admin/utilities/result.html.erb
new file mode 100644
index 000000000..d8d9fe08e
--- /dev/null
+++ b/server/app/views/admin/utilities/result.html.erb
@@ -0,0 +1,32 @@
+<%= content_for(:title, @report.name) %>
+<%= render "header" %>
+
+<div class="main-content-area">
+  <div class="utilities">
+      Results:
+  </div>
+  <div class="main-content-container">
+    <div class="main-content">
+      <div class="table-container">
+        <table class="trestle-table">
+          <thead>
+            <tr>
+              <% @headers.each do |header| %>
+                <th><%= header %></th>
+              <% end %>
+            </tr>
+          </thead>
+          <tbody>
+            <% @data.each do |row| %>
+              <tr>
+                <% row.each do |col| %>
+                  <td><%= col %></td>
+                <% end %>
+              </tr>
+            <% end %>
+          </tbody>
+        </table>
+      </div>
+    </div>
+  </div>
+</div>
diff --git a/server/app/views/admin/utilities/show.html.erb b/server/app/views/admin/utilities/show.html.erb
new file mode 100644
index 000000000..73693edbd
--- /dev/null
+++ b/server/app/views/admin/utilities/show.html.erb
@@ -0,0 +1,19 @@
+<%= content_for(:title, @util.name) %>
+<%= render "header" %>
+
+<div class="main-content-area">
+  <%= render "trestle/flash/flash" %>
+  <div class="utilities">
+      Configure your utility:
+  </div>
+  <div class="main-content-container">
+    <div class="main-content">
+      <%= form_with do |f| %>
+        <% @util.inputs.each do |f_name, f_type| %>
+          <%= render 'admin/shared/field', name: f_name, type: f_type, form: f  %>
+        <% end %>
+        <%= f.submit @util.name, class: "btn btn-success" %>
+      <% end %>
+    </div>
+  </div>
+</div>

From 9140d52059d1f434db16a936e68d2c2a29014551 Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Thu, 18 Apr 2024 20:23:19 -0500
Subject: [PATCH 3/6] fix image uploading

---
 server/app/admin/organizations_admin.rb | 4 ++++
 server/app/admin/users_admin.rb         | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/server/app/admin/organizations_admin.rb b/server/app/admin/organizations_admin.rb
index bcf0d0d6f..98e53e066 100644
--- a/server/app/admin/organizations_admin.rb
+++ b/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
diff --git a/server/app/admin/users_admin.rb b/server/app/admin/users_admin.rb
index e2915c223..dd9e5b8e3 100644
--- a/server/app/admin/users_admin.rb
+++ b/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

From 13f5485447e93a3e9346e5183f2c1f71bdb4b7cd Mon Sep 17 00:00:00 2001
From: Adam Coffman <acoffman@wustl.edu>
Date: Fri, 19 Apr 2024 08:55:21 -0500
Subject: [PATCH 4/6] Update server/app/admin/features_admin.rb

Co-authored-by: Susanna Kiwala <susanna.kiwala@wustl.edu>
---
 server/app/admin/features_admin.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server/app/admin/features_admin.rb b/server/app/admin/features_admin.rb
index 4f6c9f2f9..f692d452f 100644
--- a/server/app/admin/features_admin.rb
+++ b/server/app/admin/features_admin.rb
@@ -1,6 +1,6 @@
 Trestle.resource(:features) do
   collection do
-    Fature.includes(:flags).order(name: :asc)
+    Feature.includes(:flags).order(name: :asc)
   end
 
   search do |q|

From a9dacb76076fa7ac765e5ca56c6bb1a84ab9c0c6 Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Fri, 19 Apr 2024 09:59:42 -0500
Subject: [PATCH 5/6] make org report generic, support select controls

---
 server/app/admin/reports_admin.rb             | 11 +++++--
 ...ounts.rb => organization_contributions.rb} | 32 +++++++++----------
 server/app/reports/report.rb                  |  5 +--
 server/app/views/admin/shared/_field.html.erb |  4 ++-
 4 files changed, 31 insertions(+), 21 deletions(-)
 rename server/app/reports/{clingen_counts.rb => organization_contributions.rb} (57%)

diff --git a/server/app/admin/reports_admin.rb b/server/app/admin/reports_admin.rb
index 1b3a9a2e1..d02ab0a60 100644
--- a/server/app/admin/reports_admin.rb
+++ b/server/app/admin/reports_admin.rb
@@ -14,8 +14,15 @@ def show
 
     def generate_report
       @report = Report::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
-      report_params = params.permit(@report.inputs.keys).to_h
-      report_instance = @report.new(report_params.symbolize_keys)
+      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?
diff --git a/server/app/reports/clingen_counts.rb b/server/app/reports/organization_contributions.rb
similarity index 57%
rename from server/app/reports/clingen_counts.rb
rename to server/app/reports/organization_contributions.rb
index 22fdb4d77..435226ddc 100644
--- a/server/app/reports/clingen_counts.rb
+++ b/server/app/reports/organization_contributions.rb
@@ -1,33 +1,33 @@
-class ClingenCounts < Report
+class OrganizationContributions < Report
   attr_reader :start_date, :end_date, :all_org_ids
-  CLINGEN_ORG_ID = 2
 
   def self.name
-    "ClinGen Contributions"
+    "Organization Contributions"
   end
 
   def self.description
-    "Count contributions from ClinGen member orgs over a specified timespan."
+    "Count contributions from an organization over a specified timespan."
   end
 
   def self.inputs
     {
+      organization_id: Organization.order(:name).all.to_a,
       start_date: :date,
       end_date: :date,
-      include_suborgs: :boolean
+      include_suborgs: :boolean,
     }
   end
 
-  def setup(start_date:, end_date:, include_suborgs:)
+  def setup(start_date:, end_date:, include_suborgs:, organization_id:)
     @start_date = Date.parse(start_date)
     @end_date = Date.parse(end_date)
 
-    clingen_org = Organization.find(CLINGEN_ORG_ID)
+    org = Organization.find(organization_id)
     if include_suborgs
-      sub_groups = clingen_org.groups
-      @all_org_ids = [clingen_org.id] + sub_groups.map(&:id)
+      sub_groups = org.groups
+      @all_org_ids = [org.id] + sub_groups.map(&:id)
     else
-      @all_org_ids = clingen_org.id
+      @all_org_ids = org.id
     end
   end
 
@@ -40,19 +40,19 @@ def execute
     data << ["Evidence Submitted", SubmitEvidenceItemActivity.where(organization_id: all_org_ids, created_at: (start_date..end_date)).count]
     data << ["Comments Made", CommentActivity.where(organization_id: all_org_ids, created_at: (start_date..end_date)).count]
     data << ["Revisions Suggested", Event.where(organization_id: all_org_ids, action: 'revision suggested', created_at: (start_date..end_date)).count]
-    data << ["Proposed Revisions Accepted", calculate_contribution('revision suggested', 'revision suggested')]
-    data << ["Submitted Evidence Accepted", calculate_contribution('accepted', 'submitted')]
-    data << ["Submitted Assertions Accepted", calculate_contribution('assertion accepted', 'assertion submitted')]
+    data << ["Accepted Revisions Proposed by Organization", calculate_contribution('revision suggested', 'revision suggested')]
+    data << ["Accepted Evidence Submitted by Organization", calculate_contribution('accepted', 'submitted')]
+    data << ["Accepted Assertions Submitted by Organization", calculate_contribution('assertion accepted', 'assertion submitted')]
   end
 
   private
   def calculate_contribution(submission_event_name, accept_event_name)
-    contributed_by_clingen = 0
+    contributed_by_org = 0
     Event.where(action: accept_event_name, created_at: (start_date..end_date)).find_each do |e|
       if Event.where(action: submission_event_name, organization_id: all_org_ids, subject: e.subject).exists?
-        contributed_by_clingen += 1
+        contributed_by_org += 1
       end
     end
-    contributed_by_clingen
+    contributed_by_org
   end
 end
diff --git a/server/app/reports/report.rb b/server/app/reports/report.rb
index 4a7cde6a9..9905a8073 100644
--- a/server/app/reports/report.rb
+++ b/server/app/reports/report.rb
@@ -1,6 +1,6 @@
 class Report
   AVAILABLE_REPORTS = [
-    ClingenCounts
+    OrganizationContributions
   ]
 
   def initialize(params)
@@ -31,7 +31,8 @@ def self.viewable?
 
   def self.inputs
     #format input_name: :type
-    #supported types :text, :date, :boolean, :int
+    #supported primitive types :text, :date, :boolean, :int
+    #or you can provide an array of objects and a select will be rendered
     {}
   end
 
diff --git a/server/app/views/admin/shared/_field.html.erb b/server/app/views/admin/shared/_field.html.erb
index 4813efb62..c88d40a44 100644
--- a/server/app/views/admin/shared/_field.html.erb
+++ b/server/app/views/admin/shared/_field.html.erb
@@ -1,7 +1,9 @@
 <%# locals: (form:, name:, type:) %>
 <div class="form-group">
   <%= form.label name, class: "control-label" %>
-  <% if type == :text %>
+  <% if type.is_a?(Array) %>
+    <%= form.collection_select name, type, :id, :name %>
+  <% elsif type == :text %>
     <%= form.text_field name, required: true %>
   <% elsif type == :date %>
     <%= form.date_field name, required: true %>

From 8a2a80521f04ec02cece61400bf6675a2bdca8d8 Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Fri, 19 Apr 2024 10:04:33 -0500
Subject: [PATCH 6/6] fix typo

---
 server/app/admin/features_admin.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server/app/admin/features_admin.rb b/server/app/admin/features_admin.rb
index f692d452f..5e74c090f 100644
--- a/server/app/admin/features_admin.rb
+++ b/server/app/admin/features_admin.rb
@@ -16,7 +16,7 @@
 
   scope :all
   scope :with_variants, -> { Feature.joins(:variants).distinct }, default: true
-  scope :flagged, -> { Features.where(flagged: true) }
+  scope :flagged, -> { Feature.where(flagged: true) }
 
   # Customize the table columns shown on the index view.
   table do