Fix reference logic in variant submission script

scripts/AGR/agr_variations.def

@@ -27,27 +27,26 @@ From 1
 Tag Reference   
 
 Colonne 3 
-Width 12 
-Optional 
-Hidden 
+Width 12
+Optional
+Hidden
 Show_Tag 
 From 2 
-Tag Database   
-Condition MEDLINE
+Tag Database
 
 Colonne 4 
 Width 12 
 Optional 
-Hidden 
+Visible
 Class 
 Class Text 
 Right_of 3 
-Tag HERE    
+Tag HERE
 
 Colonne 5 
 Width 12 
 Optional 
-Hidden 
+Visible
 Class 
 Class Text 
 Right_of 4 

scripts/AGR/make_agr_variations.rb

@@ -97,21 +97,23 @@ def execute_wquery(query,wquery,outfile='/tmp/tablemaker.outfile')
 	def parse_output(outfile)
 		results=Hash.new
 		File.open(outfile).each{|line|
-			line.chomp!
-			line.gsub!('"','')
-			c = line.split("\t")
-                        if !results[c[0]]
-			        results[c[0]]=Hash.new # WBVarXXX
-			        results[c[0]]["name"] = c[0] # WBVarXXX
-                        end
-			if !c[1].empty?
-				results[c[0]]["paper"]||=Hash.new # WBPaperXXX
-				results[c[0]]["paper"][c[1]] = (c[2].nil? or c[2].empty?) ? 'n/a' : c[2] # PubmedID
-			end
-			if c[3]
-				results[c[0]][:strains]||=[] # WBStrains
-				results[c[0]][:strains].push(c[3]) # adds WBStrainId
-			end
+		  line.chomp!
+		  line.gsub!('"','')
+                  if !line["Europe_PMC"]
+		    c = line.split("\t")
+                    if !results[c[0]]
+		      results[c[0]]=Hash.new # WBVarXXX
+		      results[c[0]]["name"] = c[0] # WBVarXXX
+                    end
+		    if !c[1].empty?
+		      results[c[0]]["paper"]||=Hash.new # WBPaperXXX
+		      results[c[0]]["paper"][c[1]] = (c[4].nil? or c[4].empty?) ? 'n/a' : c[4] # PubmedID
+		    end
+		    if c[5]
+		      results[c[0]][:strains]||=[] # WBStrains
+		      results[c[0]][:strains].push(c[5]) # adds WBStrainId
+		    end
+                  end
 		}
 #		File.unlink(outfile)
 		return results