Merge pull request #399 from griffithlab/interaction_linkout

WIP: Add linkout to source's interaction claim pages
dgidb · Jul 21, 2020 · 4580f06 · 4580f06
2 parents 122cb6e + a9e3516
commit 4580f06
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Showing 32 changed files with 157 additions and 21 deletions.
diff --git a/app/controllers/interactions_controller.rb b/app/controllers/interactions_controller.rb
@@ -1,6 +1,6 @@
 class InteractionsController < ApplicationController
   def show
-    interaction = DataModel::Interaction.find(params[:id])
+    interaction = DataModel::Interaction.for_show.find(params[:id])
     @interaction = InteractionPresenter.new(interaction)
     @title = @interaction.display_name
   end

diff --git a/app/models/data_model/interaction.rb b/app/models/data_model/interaction.rb
@@ -31,5 +31,9 @@ def directionality
     def self.for_tsv
       eager_load(:gene, :drug, :interaction_types, :sources)
     end
+
+    def self.for_show
+      eager_load(:gene, :drug, :interaction_types, :interaction_attributes, :publications, interaction_claims: [:drug_claim, :gene_claim, :interaction_claim_types, :interaction_claim_attributes, :publications, :interaction_claim_links, source: [:source_type]])
+    end
   end
 end
diff --git a/app/models/data_model/interaction_claim.rb b/app/models/data_model/interaction_claim.rb
@@ -3,6 +3,7 @@ class InteractionClaim < ::ActiveRecord::Base
     include Genome::Extensions::UUIDPrimaryKey
 
     has_many :interaction_claim_attributes, inverse_of: :interaction_claim
+    has_many :interaction_claim_links, inverse_of: :interaction_claim
     belongs_to :gene_claim, inverse_of: :interaction_claims
     belongs_to :drug_claim, inverse_of: :interaction_claims
     belongs_to :source, inverse_of: :interaction_claims, counter_cache: true
@@ -11,7 +12,7 @@ class InteractionClaim < ::ActiveRecord::Base
     has_and_belongs_to_many :publications
 
     def self.for_show
-      eager_load(:interaction_claim_types, :interaction_claim_attributes, :source, :drug_claim, gene_claim: [:gene, :source])
+      eager_load(:interaction_claim_types, :interaction_claim_attributes, :source, :publications, :interaction_claim_links, :drug_claim, gene_claim: [:gene], interaction: [:gene, :drug])
     end
 
     def self.for_tsv

diff --git a/app/models/data_model/interaction_claim_link.rb b/app/models/data_model/interaction_claim_link.rb
@@ -0,0 +1,6 @@
+module DataModel
+  class InteractionClaimLink < ::ActiveRecord::Base
+    include Genome::Extensions::UUIDPrimaryKey
+    belongs_to :interaction_claim, inverse_of: :interaction_claim_attributes
+  end
+end
diff --git a/app/presenters/interaction_claim_presenter.rb b/app/presenters/interaction_claim_presenter.rb
@@ -24,6 +24,7 @@ def as_json
       interaction_types: @interaction_claim.interaction_claim_types.map{|t| t.type},
       attributes: @interaction_claim.interaction_claim_attributes.map{|a| ClaimAttributePresenter.new(a).as_json},
       publications: @interaction_claim.publications.map(&:pmid),
+      source_links: @interaction_claim.interaction_claim_links.map{|l| {url: l.link_url, text: l.link_text}  },
     }
   end
 end
diff --git a/app/views/interaction_claims/_interaction_claim.html.haml b/app/views/interaction_claims/_interaction_claim.html.haml
@@ -57,12 +57,22 @@
                                   %a{href: PMID.pubmed_url(publication.pmid)}
                                     = publication.citation
                     %div{class: "cell category", style: "float: right; width: 50%"}
-                      %div(class="item-panel")
+                      %div{class: "item-panel", style:"margin-bottom: 10px"}
                         %h4
                           Other Info:
-                        %div{style: "height: 456px; overflow-y: scroll; "}
+                        %div{style: "height: 197px; overflow-y: scroll; "}
                           %table{class: "table table-condensed table-striped", id: "table_info"}
                             -interaction_claim.interaction_claim_attributes.each do |attribute|
                               %tr
                                 %td{style: "width: 300px"}=attribute.name
                                 %td{style: "width: 350px"}=attribute.value
+                      %div(class="item-panel")
+                        %h4
+                          Source Links:
+                        %div{style: "height: 198px; overflow-y: scroll; "}
+                          %table{class: "table table-condensed table-striped", id: "table_info"}
+                            -interaction_claim.interaction_claim_links.each do |link|
+                              %tr
+                                %td
+                                  %a{href: link.link_url}
+                                    = link.link_text
diff --git a/app/views/interaction_claims/_interaction_claim_summary.html.haml b/app/views/interaction_claims/_interaction_claim_summary.html.haml
@@ -45,12 +45,21 @@
               %td=attribute.value
 
   %div(class="cell category")
-    %div(class="item-panel")
+    %div{class: "item-panel", style: "margin-bottom:10px"}
       %h4
         Publications:
         %table{class: "table table-condensed table-striped", style: "table-layout:fixed;" }
           -interaction_claim.publications[0..2].each do |publication|
             %tr
               %td
                 %a{href: PMID.pubmed_url(publication.pmid)}
-                  = publication.citation
+                  = publication.citation
+    %div(class="item-panel")
+      %h4
+        Source Links:
+        %table{class: "table table-condensed table-striped", style: "table-layout:fixed;" }
+          -interaction_claim.interaction_claim_links.each do |link|
+            %tr
+              %td
+                %a{href: link.link_url}
+                  = link.link_text
diff --git a/data b/data
diff --git a/db/migrate/20200615173440_add_interaction_claim_linkout.rb b/db/migrate/20200615173440_add_interaction_claim_linkout.rb
@@ -0,0 +1,12 @@
+class AddInteractionClaimLinkout < ActiveRecord::Migration[6.0]
+  def change
+    create_table :interaction_claim_links, id: false do |t|
+      t.text :id, null: false, primary_key: true
+      t.text :interaction_claim_id, null: false
+      t.string :link_text, null: false
+      t.string :link_url, null: false
+    end
+
+    add_foreign_key :interaction_claim_links, :interaction_claims
+  end
+end
diff --git a/db/structure.sql b/db/structure.sql
@@ -26,7 +26,7 @@ CREATE FUNCTION public.clean(text) RETURNS text
 
 SET default_tablespace = '';
 
-SET default_with_oids = false;
+SET default_table_access_method = heap;
 
 --
 -- Name: ar_internal_metadata; Type: TABLE; Schema: public; Owner: -
@@ -495,6 +495,18 @@ CREATE TABLE public.interaction_claim_attributes (
 );
 
 
+--
+-- Name: interaction_claim_links; Type: TABLE; Schema: public; Owner: -
+--
+
+CREATE TABLE public.interaction_claim_links (
+    id text NOT NULL,
+    interaction_claim_id text NOT NULL,
+    link_text character varying NOT NULL,
+    link_url character varying NOT NULL
+);
+
+
 --
 -- Name: interaction_claim_types; Type: TABLE; Schema: public; Owner: -
 --
@@ -924,6 +936,14 @@ ALTER TABLE ONLY public.interaction_claim_attributes
     ADD CONSTRAINT interaction_claim_attributes_pkey PRIMARY KEY (id);
 
 
+--
+-- Name: interaction_claim_links interaction_claim_links_pkey; Type: CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY public.interaction_claim_links
+    ADD CONSTRAINT interaction_claim_links_pkey PRIMARY KEY (id);
+
+
 --
 -- Name: interaction_claim_types_interaction_claims interaction_claim_types_interaction_claims_pkey; Type: CONSTRAINT; Schema: public; Owner: -
 --
@@ -1866,6 +1886,14 @@ ALTER TABLE ONLY public.drug_aliases
     ADD CONSTRAINT fk_rails_4d255ac147 FOREIGN KEY (drug_id) REFERENCES public.drugs(id) ON DELETE CASCADE;
 
 
+--
+-- Name: interaction_claim_links fk_rails_af235a7f08; Type: FK CONSTRAINT; Schema: public; Owner: -
+--
+
+ALTER TABLE ONLY public.interaction_claim_links
+    ADD CONSTRAINT fk_rails_af235a7f08 FOREIGN KEY (interaction_claim_id) REFERENCES public.interaction_claims(id);
+
+
 --
 -- Name: drugs fk_rails_de0c74dec1; Type: FK CONSTRAINT; Schema: public; Owner: -
 --
@@ -2027,6 +2055,7 @@ INSERT INTO "schema_migrations" (version) VALUES
 ('20170913202927'),
 ('20170914145053'),
 ('20191016180948'),
-('20191107152512');
+('20191107152512'),
+('20200615173440');
 
 
diff --git a/lib/genome/importers/cgi/new_cgi.rb b/lib/genome/importers/cgi/new_cgi.rb
@@ -55,6 +55,7 @@ def create_interaction_claims
                 if row['Source'].include?('PMID')
                   add_interaction_claim_publications(interaction_claim, row['Source'])
                 end
+                create_interaction_claim_link(interaction_claim, 'Cancer Biomarkers database', 'https://www.cancergenomeinterpreter.org/biomarkers')
               end
             else
               gene_claim = create_gene_claim(row['Gene'], 'CGI Gene Name')
@@ -65,6 +66,7 @@ def create_interaction_claims
               if row['Source'].include?('PMID')
                 add_interaction_claim_publications(interaction_claim, row['Source'])
               end
+              create_interaction_claim_link(interaction_claim, 'Cancer Biomarkers database', 'https://www.cancergenomeinterpreter.org/biomarkers')
             end
           end
         if row['Drug'].include?(';')
@@ -81,6 +83,7 @@ def create_interaction_claims
                 if row['Source'].include?('PMID')
                   add_interaction_claim_publications(interaction_claim, row['Source'])
                 end
+                create_interaction_claim_link(interaction_claim, 'Cancer Biomarkers database', 'https://www.cancergenomeinterpreter.org/biomarkers')
               end
             else
               gene_claim = create_gene_claim(row['Gene'], 'CGI Gene Name')
@@ -91,6 +94,7 @@ def create_interaction_claims
               if row['Source'].include?('PMID')
                 add_interaction_claim_publications(interaction_claim, row['Source'])
               end
+              create_interaction_claim_link(interaction_claim, 'Cancer Biomarkers database', 'https://www.cancergenomeinterpreter.org/biomarkers')
             end
           end
         end
@@ -105,6 +109,7 @@ def create_interaction_claims
               if row['Source'].include?('PMID')
                 add_interaction_claim_publications(interaction_claim, row['Source'])
               end
+              create_interaction_claim_link(interaction_claim, 'Cancer Biomarkers database', 'https://www.cancergenomeinterpreter.org/biomarkers')
             end
           else
             gene_claim = create_gene_claim(row['Gene'], 'CGI Gene Name')
@@ -114,6 +119,7 @@ def create_interaction_claims
             if row['Source'].include?('PMID')
               add_interaction_claim_publications(interaction_claim, row['Source'])
             end
+            create_interaction_claim_link(interaction_claim, 'Cancer Biomarkers database', 'https://www.cancergenomeinterpreter.org/biomarkers')
           end
         end
       end
@@ -137,4 +143,4 @@ def add_interaction_claim_publications(interaction_claim, source_string)
       end
     end
   end
-end; end; end
+end; end; end
diff --git a/lib/genome/importers/chembl/chembl_tsv_importer.rb b/lib/genome/importers/chembl/chembl_tsv_importer.rb
@@ -43,7 +43,11 @@ def self.run(tsv_path)
             attribute :action_type, name: 'Interaction Type', transform: downcase, unless: blank_filter
           end
         end.save!
+        s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+        s.interaction_claims.each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, 'Drug Mechanisms', "https://www.ebi.ac.uk/chembl/compound_report_card/#{ic.drug_claim.name}/#MechanismOfAction")
+        end
       end
     end
   end
-end
+end
diff --git a/lib/genome/importers/drug_bank/new_drug_bank.rb b/lib/genome/importers/drug_bank/new_drug_bank.rb
@@ -78,6 +78,7 @@ def import_claims
         row['pmid'].split(DELIMITER).each do |pmid|
           create_interaction_claim_publication(interaction_claim, pmid) unless pmid == 'N/A'
         end
+        create_interaction_claim_link(interaction_claim, "Drug Target", "https://www.drugbank.ca/drugs/#{row['drug_id']}#targets")
         interaction_claim.save
       end
     end

diff --git a/lib/genome/importers/fda/fda.rb b/lib/genome/importers/fda/fda.rb
@@ -47,13 +47,15 @@ def create_drug_claims(row, gene_claim, fusion_protein)
         if not fusion_protein.nil?
           create_interaction_claim_attribute(interaction_claim, 'Fusion protein', fusion_protein)
         end
+        create_interaction_claim_link(interaction_claim, 'Table of Pharmacogenomic Biomarkers in Drug Labeling', 'https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling')
       end
     else
       drug_claim = create_drug_claim(row['Drug'], row['Drug'], 'FDA Drug Name')
       interaction_claim = create_interaction_claim(gene_claim, drug_claim)
       if not fusion_protein.nil?
         create_interaction_claim_attribute(interaction_claim, 'Fusion protein', fusion_protein)
       end
+      create_interaction_claim_link(interaction_claim, 'Table of Pharmacogenomic Biomarkers in Drug Labeling', 'https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling')
     end
   end
 
@@ -72,4 +74,4 @@ def create_interaction_claims
     end
   end
 end
-end; end; end
+end; end; end
diff --git a/lib/genome/importers/guide_to_pharmacology_interactions/new_guide_to_pharmacology.rb b/lib/genome/importers/guide_to_pharmacology_interactions/new_guide_to_pharmacology.rb
@@ -36,6 +36,7 @@ def import_claims
             end
           end
           create_interaction_claim_attributes(interaction_claim, line)
+          create_interaction_claim_link(interaction_claim, "Ligand Biological Activity", "https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=#{line['ligand_id']}&tab=biology")
         end
       end
     end

diff --git a/lib/genome/importers/my_cancer_genome/my_cancer_genome_tsv_importer.rb b/lib/genome/importers/my_cancer_genome/my_cancer_genome_tsv_importer.rb
@@ -36,6 +36,10 @@ def self.run(tsv_path)
             attribute :interaction_type, name: 'Interaction Type', unless: blank_filter
           end
         end.save!
+        s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+        s.interaction_claims.each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, 'Overview of Targeted Therapies for Cancer', "https://www.mycancergenome.org/content/page/overview-of-targeted-therapies-for-cancer/")
+        end
       end
     end
   end

diff --git a/...importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb b/...importers/my_cancer_genome_clinical_trial/my_cancer_genome_clinical_trial_tsv_importer.rb
@@ -37,6 +37,10 @@ def self.run(tsv_path)
               attribute :indication_of_interaction, name: 'Indication of Interaction'
             end
           end.save!
+          s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+          s.interaction_claims.each do |ic|
+            Genome::OnlineUpdater.new.create_interaction_claim_link(ic, 'Clinical Trials', "https://www.mycancergenome.org/content/clinical_trials/")
+          end
         end
       end
     end

diff --git a/lib/genome/importers/nci/nci.rb b/lib/genome/importers/nci/nci.rb
@@ -45,6 +45,7 @@ def create_interaction_claims
         create_drug_claim_alias(drug_claim, row['NCI drug code'], 'NCI drug code')
         interaction_claim = create_interaction_claim(gene_claim, drug_claim)
         create_interaction_claim_publication(interaction_claim, row['PMID'])
+        create_interaction_claim_link(interaction_claim, "The Cancer Gene Index Gene-Disease and Gene-Compound XML Documents", 'https://wiki.nci.nih.gov/display/cageneindex/The+Cancer+Gene+Index+Gene-Disease+and+Gene-Compound+XML+Documents')
       end
     end
   end

diff --git a/lib/genome/importers/pharmgkb/pharmgkb_tsv_importer.rb b/lib/genome/importers/pharmgkb/pharmgkb_tsv_importer.rb
@@ -44,6 +44,10 @@ def self.run(tsv_path)
             end
           end
         end
+        s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+        s.interaction_claims.each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, 'Drug Label Annotations', "https://www.pharmgkb.org/chemical/#{ic.drug_claim.name}/labelAnnotation")
+        end
       end
     end
   end

diff --git a/lib/genome/importers/talc/talc_tsv_importer.rb b/lib/genome/importers/talc/talc_tsv_importer.rb
@@ -36,7 +36,11 @@ def self.run(tsv_path)
 
           end
         end.save!
+        s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+        s.interaction_claims.each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, s.citation, "https://www.sciencedirect.com/science/article/pii/S1525730413002350")
+        end
       end
     end
   end
-end
+end
diff --git a/lib/genome/importers/tdg_clinical_trial/tdg_clinical_trial_tsv_importer.rb b/lib/genome/importers/tdg_clinical_trial/tdg_clinical_trial_tsv_importer.rb
@@ -36,6 +36,10 @@ def self.run(tsv_path)
             attribute :target_novelty, name: 'Novel drug target', unless: blank_filter
           end
         end.save!
+        s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+        s.interaction_claims.each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, s.citation, "https://www.annualreviews.org/doi/10.1146/annurev-pharmtox-011613-135943")
+        end
       end
     end
   end

diff --git a/lib/genome/importers/tend/tend_tsv_importer.rb b/lib/genome/importers/tend/tend_tsv_importer.rb
@@ -37,6 +37,10 @@ def self.run(tsv_path)
             end
           end
         end
+        s = DataModel::Source.where(source_db_name: source_info['source_db_name'])
+        DataModel::InteractionClaim.where(source_id: s.id).each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, 'Trends in the exploitation of novel drug targets, Table 1', "https://www.nature.com/articles/nrd3478/tables/1")
+        end
       end
     end
   end

diff --git a/lib/genome/importers/ttd/ttd_tsv_importer.rb b/lib/genome/importers/ttd/ttd_tsv_importer.rb
@@ -3,8 +3,8 @@ module Importers
     module TTD
       def source_info
         {
-          base_url:          'http://bidd.nus.edu.sg/group/cjttd/ZFTTD',
-          site_url:          'http://bidd.nus.edu.sg/group/ttd/ttd.asp',
+          base_url:          'http://db.idrblab.net/ttd/',
+          site_url:          'http://bidd.nus.edu.sg/group/cjttd/',
           citation:          "Update of TTD: Therapeutic Target Database. Zhu F, Han BC, ..., Zheng CJ, Chen YZ. Nucleic Acids Res. 38(suppl 1):D787-91, 2010. PMID: 19933260.",
           source_db_version:  '4.3.02 (2011.08.25)',
           source_type_id:    DataModel::SourceType.INTERACTION,
@@ -36,7 +36,11 @@ def self.run(tsv_path)
             end
           end
         end
+        s = DataModel::Source.find_by(source_db_name: source_info['source_db_name'])
+        s.interaction_claims.each do |ic|
+          Genome::OnlineUpdater.new.create_interaction_claim_link(ic, 'TTD Target Information', "http://idrblab.net/ttd/data/target/details/#{ic.gene_claim.name}")
+        end
       end
     end
   end
-end
+end