Release 1.108.0

Gemfile

@@ -90,6 +90,8 @@ gem 'benchmark'
 gem 'drb'
 gem 'reline'
 gem 'irb'
+gem 'json_schemer'
+gem 'faraday-multipart', require: 'faraday/multipart'
 
 group :development, :test do
   # Access an IRB console on exception pages or by using <%= console %> in views

Gemfile.lock

@@ -229,6 +229,7 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
+    hana (1.3.7)
     hashie (4.1.0)
     http-accept (1.7.0)
     http-cookie (1.0.3)
@@ -254,6 +255,11 @@ GEM
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
     json (2.6.2)
+    json_schemer (2.5.0)
+      bigdecimal
+      hana (~> 1.3)
+      regexp_parser (~> 2.0)
+      simpleidn (~> 0.2)
     jwt (2.7.0)
     listen (3.5.1)
       rb-fsevent (~> 0.10, >= 0.10.3)
@@ -489,6 +495,7 @@ GEM
     simplecov-html (0.13.1)
     simplecov-lcov (0.8.0)
     simplecov_json_formatter (0.1.4)
+    simpleidn (0.2.3)
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -575,6 +582,7 @@ DEPENDENCIES
   drb
   exponential-backoff
   factory_bot_rails
+  faraday-multipart
   flamegraph
   font-awesome-sass!
   gibberish
@@ -587,6 +595,7 @@ DEPENDENCIES
   jquery-datatables-rails!
   jquery-fileupload-rails
   jquery-rails
+  json_schemer
   listen
   logger
   memory_profiler

app/javascript/lib/metrics-api.js

@@ -98,10 +98,6 @@ export function logClick(event) {
     return
   }
 
-  if (window.Appcues) {
-    logAppcuesClicks()
-  }
-
   // we use closest() so we don't lose clicks on, e.g. icons within a link/button
   // (and we have to use $.closest since IE still doesn't have built-in support for it)
   if (target.closest('a').length) {
@@ -115,44 +111,6 @@ export function logClick(event) {
   }
 }
 
-/**
- * Logs Appcues public events to Mixpanel
- * https://docs.appcues.com/article/161-javascript-api
- *
- * Event prop building borrowed from Terra UI
- * https://github.com/DataBiosphere/terra-ui/pull/2463/files
- */
-function logAppcuesClicks() {
-  window.Appcues.on('all', (eventName, event) => {
-    const eventProps = {
-      'appcues.flowId': event.flowId,
-      'appcues.flowName': event.flowName,
-      'appcues.flowType': event.flowType,
-      'appcues.flowVersion': event.flowVersion,
-      'appcues.id': event.id,
-      'appcues.interaction.category': event.interaction?.category,
-      'appcues.interaction.destination': event.interaction?.destination,
-      'appcues.interaction.element': event.interaction?.element,
-      'appcues.interaction.fields': JSON.stringify(event.interaction?.fields),
-      'appcues.interaction.formId': event.interaction?.formId,
-      'appcues.interaction.text': event.interaction?.text, // not documented by Appcues, but observed and useful
-      'appcues.interactionType': event.interactionType,
-      'appcues.localeId': event.localeId,
-      'appcues.localeName': event.localeName,
-      'appcues.name': event.name,
-      'appcues.sessionId': event.sessionId,
-      'appcues.stepChildId': event.stepChildId,
-      'appcues.stepChildNumber': event.stepChildNumber,
-      'appcues.stepId': event.stepId,
-      'appcues.stepNumber': event.stepNumber,
-      'appcues.stepType': event.stepType,
-      'appcues.timestamp': event.timestamp
-    }
-    log(eventName, eventProps)
-    log('appcues:event', eventProps)
-  })
-}
-
 /** Log clicks on SVG element of analytics interest */
 export function logClickOther(target) {
   const props = {
@@ -522,8 +480,6 @@ export function log(name, props = {}) {
 
   init = Object.assign(init, body)
 
-  window.Appcues && window.Appcues.identify(window.SCP.userId)
-
   if (('SCP' in window && !window.SCP.isTest) || metricsApiMock) {
     const url = `${bardDomain}/api/event/`
     fetch(url, init).then(response => {

app/lib/duos_registration_service.rb

@@ -0,0 +1,117 @@
+# service containing business logic for managing Study registrations as datasets in DUOS
+class DuosRegistrationService
+
+  # pointer to DUOS UI for auto-completing URLs
+  #
+  # * *returns*
+  #   - (String) DUOS UI base URL, based on environment
+  def self.duos_ui_url
+    Rails.env.production? ? 'https://duos.org' : 'https://duos-k8s.dsde-dev.broadinstitute.org/'
+  end
+
+  # API client
+  #
+  # * *returns*
+  #   - (DuosClient)
+  def self.client
+    @client ||= DuosClient.new
+  end
+
+  # determine if study is eligible for registering as a dataset in DUOS
+  # must meet all the following criteria:
+  # * public
+  # * initialized
+  # * has all required metadata for DUOS
+  #
+  # * *params*
+  #   - +study+ (Study)
+  #
+  # * *returns*
+  #   - (Boolean)
+  def self.study_eligible?(study)
+    has_required = required_metadata(study).map do |field, value|
+      if field == :donor_count
+        value > 0
+      else
+        value.any?
+      end
+    end.flatten.uniq == [true]
+
+    study.public && study.initialized && study.duos_dataset_id.blank? && has_required
+  end
+
+  # metadata values required for DUOS dataset registration
+  #
+  # * *params*
+  #   - +study+ (Study)
+  #
+  # * *returns*
+  #   - (Hash)
+  def self.required_metadata(study)
+    {
+      diseases: study.diseases,
+      species: study.species_list,
+      donor_count: study.donor_count,
+      data_types: study.data_types
+    }
+  end
+
+  # get a list of accessions for studies eligible for DUOS registration
+  #
+  # * *returns*
+  #   - (Array<String>) list of study accessions
+  def self.eligible_studies
+    studies = Study.where(public: true, initialized: true, duos_dataset_id: nil, duos_study_id: nil)
+    studies.select { |study| study_eligible?(study) }.map(&:accession)
+  end
+
+  # register a study as a new dataset in DUOS
+  #
+  #
+  # * *params*
+  #   - +study+ (Study)
+  #
+  # * *returns*
+  #   - (Hash) DUOS dataset registration object
+  def self.register_study(study)
+    raise ArgumentError, "#{study.accession} is not eligible for DUOS registration" unless study_eligible?(study)
+
+    begin
+      dataset = client.create_dataset(study)
+      ids = client.identifiers_from_dataset(dataset)
+      study.update(**ids)
+      Rails.logger.info "Registered #{study.accession} in DUOS as #{ids}"
+      dataset
+    rescue ArgumentError => e
+      Rails.logger.error "Cannot validate #{study.accession} for DUOS: #{e.message}"
+    rescue Faraday::Error => e
+      Rails.logger.error "Unable to register #{study.accession} in DUOS: #{e.message} (#{e.try(:response_body)})"
+      ErrorTracker.report_exception(e, client.issuer, { study: })
+      nil
+    end
+  end
+
+  # redact a DUOS dataset registration
+  # in non-production environments, this is a deletion, otherwise publicVisibility is set to false
+  #
+  # * *params*
+  #   - +study+ (Study)
+  #
+  # * *returns*
+  #   - (Boolean)
+  def self.redact_study(study)
+    if Rails.env.production?
+      client.update_study(study.duos_study_id, publicVisibility: false)
+    else
+      client.delete_study(study.duos_study_id)
+      study.update(duos_dataset_id: nil, duos_study_id: nil)
+    end
+
+    Rails.logger.info "Redacted #{study.accession} in DUOS"
+    true
+  rescue Faraday::Error => e
+    Rails.logger.error "Unable to redact #{study.accession} in DUOS: (#{e.message}) #{e.try(:response_body)}"
+    ErrorTracker.report_exception(e, client.issuer, { study: })
+    false
+  end
+end