Merge pull request #1049 from griffithlab/new-reports

Add additional reports

server/app/reports/diseases_with_icdo.rb

@@ -0,0 +1,48 @@
+require 'set'
+
+class DiseasesWithIcdo < Report
+  attr_reader :qualifying_disease_ids
+
+  def self.name
+    "Counts of Diseases and EIDs with and without DO and ICD-O terms"
+  end
+
+  def self.description
+    "Generate counts of Evidence Items and Diseases that have associated DOIDs and ICD-O terms"
+  end
+
+  def setup
+    @qualifying_disease_ids = Set.new
+    candidate_diseases = Disease.joins(:evidence_items)
+      .where.not(evidence_items: {status: 'rejected'})
+      .where.not(doid: nil).distinct
+
+    candidate_diseases.find_each do |disease|
+      resp = MyDiseaseInfo.new(disease).response
+      if resp && resp[:icdo].present?
+        @qualifying_disease_ids << disease.id
+      end
+      sleep 0.1
+    end
+
+
+  end
+
+  def headers
+    [
+      "Total Diseases",
+      "Total Diseases Associated with a DOID and ICD-O code",
+      "Total Non Rejected EIDs",
+      "Total Non Rejected EIDs Associated with a DOID and ICD-O code.",
+    ]
+  end
+
+  def execute
+    data << [
+      Disease.joins(:evidence_items).where.not(evidence_items: {status: 'rejected'}).distinct.count,
+      qualifying_disease_ids.size,
+      EvidenceItem.where.not(status: 'rejected').count,
+      EvidenceItem.where.not(status: 'rejected').where(disease_id: qualifying_disease_ids).count,
+    ]
+  end
+end

server/app/reports/eids_with_onset_terms.rb

@@ -0,0 +1,41 @@
+class EidsWithOnsetTerms < Report
+  attr_reader :onset_terms
+
+  def self.name
+    "EIDs with Onset Terms"
+  end
+
+  def self.description
+    "Generate a list of EIDs with any of the following onset terms: Young adult, early young adult, intermediate young adult, late young adult, childhood, juvenile, pediatric, congenital, and infantile."
+  end
+
+  def setup
+    @onset_terms = Phenotype.where(hpo_class: [
+      'Young adult onset',
+      'Intermediate young adult onset',
+      'Late young adult onset',
+      'Childhood onset',
+      'Juvenile onset',
+      'Pediatric onset',
+      'Congenital onset',
+      'Infantile onset'
+    ])
+  end
+
+  def headers
+    [
+      "EID",
+      "Link",
+      "HPO Term",
+      "HPO ID"
+    ]
+  end
+
+  def execute
+    onset_terms.each do |term|
+      term.evidence_items.each do |eid|
+        data << ["EID#{eid.id}", "https://civicdb.org/#{eid.link}", term.hpo_class, term.hpo_id]
+      end
+    end
+  end
+end

server/app/reports/reports.rb

@@ -1,5 +1,7 @@
 module Reports
   AVAILABLE_REPORTS = [
-    OrganizationContributions
+    OrganizationContributions,
+    EidsWithOnsetTerms,
+    DiseasesWithIcdo
   ]
 end