fix: use docm snapshot data (#533)

server/lib/genome/importers/file_importers/docm.rb

@@ -0,0 +1,95 @@
+module Genome
+  module Importers
+    module FileImporters
+      module Docm
+        class Importer < Genome::Importers::Base
+          attr_reader :file_path
+
+          def initialize(tsv_root_path)
+            @tsv_root = if tsv_root_path.nil?
+                          'lib/data/docm/'
+                        else
+                          tsv_root_path
+                        end
+            @source_db_name = 'DoCM'
+            @drug_claims = {}
+            @gene_claims = {}
+            @interaction_claims = {}
+          end
+
+          def create_claims
+            create_drug_claims
+            create_gene_claims
+            create_interaction_claims
+          end
+
+          private
+
+          def create_new_source
+            @source ||= Source.create(
+              {
+                base_url: 'http://docm.info/',
+                site_url: 'http://docm.info/',
+                citation: 'Ainscough BJ, Griffith M, Coffman AC, Wagner AH, Kunisaki J, Choudhary MN, McMichael JF, Fulton RS, Wilson RK, Griffith OL, Mardis ER. DoCM: a database of curated mutations in cancer. Nat Methods. 2016 Sep 29;13(10):806-7. doi: 10.1038/nmeth.4000. PMID: 27684579; PMCID: PMC5317181.',
+                citation_short: 'Ainscough BJ, et al. DoCM: a database of curated mutations in cancer. Nat Methods. 2016 Sep 29;13(10):806-7.',
+                pmid: '27684579',
+                pmcid: 'PMC5317181',
+                doi: '10.1038/nmeth.4000',
+                source_db_version: '2024-10-02',
+                source_trust_level_id: SourceTrustLevel.EXPERT_CURATED,
+                source_db_name:,
+                full_name: 'Database of Curated Mutations',
+                license: License::CC_BY_4_0,
+                license_link: 'https://github.com/griffithlab/docm/blob/c8d2a8723f505689074d07841931475b9b7e914c/app/views/static/about.html.haml#L86'
+              }
+            )
+            @source.source_types << SourceType.find_by(type: 'interaction')
+            @source.save
+          end
+
+
+          def create_drug_claims
+            CSV.foreach("#{@tsv_root}drug_claim.csv", headers: true, col_sep: ',') do |row|
+              dc = create_drug_claim(row[0])
+              @drug_claims[row[0]] = dc
+            end
+          end
+
+          def create_gene_claims
+            CSV.foreach("#{@tsv_root}gene_claim.csv", headers: true, col_sep: ',') do |row|
+              gc = create_gene_claim(row[0], GeneNomenclature::NCBI_NAME)
+              @gene_claims[row[0]] = gc
+            end
+          end
+
+          def create_interaction_claims
+            CSV.foreach("#{@tsv_root}interaction_claim.csv", headers: true, col_sep: ',') do |row|
+              gc = @gene_claims[row[1]]
+              dc = @drug_claims[row[0]]
+              next if gc.nil? || dc.nil?
+
+              ic = create_interaction_claim(gc, dc)
+              @interaction_claims[[gc, dc]] = ic
+            end
+            CSV.foreach("#{@tsv_root}interaction_claim_attributes.csv", headers: true, col_sep: ',') do |row|
+              gc = @gene_claims[row[3]]
+              dc = @drug_claims[row[2]]
+              next if gc.nil? || dc.nil?
+
+              ic = @interaction_claims[[gc, dc]]
+              create_interaction_claim_attribute(ic, row[0], row[1])
+            end
+            CSV.foreach("#{@tsv_root}interaction_claim_publications.csv", headers: true, col_sep: ',') do |row|
+              gc = @gene_claims[row[3]]
+              dc = @drug_claims[row[2]]
+              next if gc.nil? || dc.nil?
+
+              ic = @interaction_claims[[gc, dc]]
+              create_interaction_claim_publication(ic, row[0])
+            end
+          end
+        end
+      end
+    end
+  end
+end

server/lib/genome/importers/file_importers/docm.sql

@@ -0,0 +1,41 @@
+-- It's a little tricky to grab data from the final DOCM dump;
+-- instead, these queries help us produce dumps from our last extraction in DGIdb
+
+-- gene claim
+SELECT gc.name, gc.nomenclature
+FROM gene_claims gc
+         LEFT JOIN sources s on gc.source_id = s.id
+WHERE source_db_name = 'DoCM';
+
+-- drug claim
+SELECT dc.name, dc.nomenclature
+FROM drug_claims dc
+         LEFT JOIN sources s on dc.source_id = s.id
+WHERE s.source_db_name = 'DoCM';
+
+-- interaction claim
+SELECT dc.name, gc.name
+FROM interaction_claims ic
+         LEFT JOIN sources s on ic.source_id = s.id
+         LEFT JOIN drug_claims dc on ic.drug_claim_id = dc.id
+         LEFT JOIN gene_claims gc on ic.gene_claim_id = gc.id
+WHERE s.source_db_name = 'DoCM';
+
+-- interaction claim attributes
+SELECT ica.name, ica.value, dc.name, gc.name
+FROM interaction_claims ic
+         LEFT JOIN sources s on ic.source_id = s.id
+         LEFT JOIN drug_claims dc on ic.drug_claim_id = dc.id
+         LEFT JOIN gene_claims gc on ic.gene_claim_id = gc.id
+         RIGHT JOIN interaction_claim_attributes ica on ic.id = ica.interaction_claim_id
+WHERE s.source_db_name = 'DoCM';
+
+-- interaction claim publications
+SELECT p.pmid, p.citation, dc.name, gc.name
+FROM interaction_claims ic
+         LEFT JOIN sources s on ic.source_id = s.id
+         LEFT JOIN drug_claims dc on ic.drug_claim_id = dc.id
+         LEFT JOIN gene_claims gc on ic.gene_claim_id = gc.id
+         RIGHT JOIN interaction_claims_publications icp ON icp.interaction_claim_id = ic.id
+         LEFT JOIN publications p ON p.id = icp.publication_id
+WHERE s.source_db_name = 'DoCM';