update delete zombie mapping counts to check also submission deletion

lib/ontologies_linked_data/concerns/mappings/mapping_counts.rb

@@ -16,9 +16,7 @@ def mapping_counts(enable_debug = false, logger = nil, reload_cache = false, arr
             exter_total += v
           end
           counts[external_uri.to_s] = exter_total
-          if enable_debug
-            logger.info("Time for External Mappings took #{Time.now - t0} sec. records #{exter_total}")
-          end
+          logger.info("Time for External Mappings took #{Time.now - t0} sec. records #{exter_total}") if enable_debug
           LinkedData.settings.interportal_hash ||= {}
           # Counting for Interportal mappings
           LinkedData.settings.interportal_hash.each_key do |acro|
@@ -93,8 +91,8 @@ def create_mapping_count_totals_for_ontologies(logger, arr_acronyms)
             persistent_counts[m.ontologies.first] = m
           end
 
-          ontologies = LinkedData::Models::Ontology.where.include(:acronym).all.map(&:acronym)
-          delete_zombie_mapping_count(persistent_counts.values, ontologies)
+          latest = self.retrieve_latest_submissions(options = { acronyms: arr_acronyms })
+          delete_zombie_mapping_count(persistent_counts.values, latest.values.compact.map { |sub| sub.ontology.acronym })
 
           num_counts = new_counts.keys.length
           ctr = 0
@@ -160,8 +158,6 @@ def create_mapping_count_pairs_for_ontologies(logger, arr_acronyms)
           # temp_dir = '/Users/mdorf/Downloads/test/'
           # temp_file_path = File.join(File.dirname(file_path), "test.ttl")
           # fsave = File.open(temp_file_path, "a")
-          ontologies = LinkedData::Models::Ontology.where.include(:acronym).all.map(&:acronym)
-
           latest_submissions.each do |acr, sub|
             self.handle_triple_store_downtime(logger) if Goo.backend_4s?
             new_counts = nil
@@ -175,14 +171,11 @@ def create_mapping_count_pairs_for_ontologies(logger, arr_acronyms)
             LinkedData::Models::MappingCount.where(pair_count: true).and(ontologies: acr)
                                             .include(:ontologies, :count).all.each do |m|
               other = m.ontologies.first
-
-              if other == acr
-                other = m.ontologies[1]
-              end
+              other = m.ontologies.last if other == acr
               persistent_counts[other] = m
             end
 
-            delete_zombie_mapping_count(persistent_counts.values, ontologies)
+            delete_zombie_mapping_count(persistent_counts.values, latest_submissions.values.compact.map { |s| s.ontology.acronym })
 
             num_counts = new_counts.keys.length
             logger.info("Ontology: #{acr}. #{num_counts} mapping pair counts to record...")
@@ -198,7 +191,7 @@ def create_mapping_count_pairs_for_ontologies(logger, arr_acronyms)
                 if new_count.zero?
                   inst.delete
                 elsif new_count != inst.count
-                  inst.bring_remaining
+                  inst.bring_remaining if inst.persistent?
                   inst.pair_count = true
                   inst.count = new_count
 
@@ -216,13 +209,12 @@ def create_mapping_count_pairs_for_ontologies(logger, arr_acronyms)
                   end
                 end
               else
-                next unless ontologies.include?(other)
+                next unless new_counts.key?(other)
 
                 m = LinkedData::Models::MappingCount.new
                 m.count = new_count
                 m.ontologies = [acr, other]
                 m.pair_count = true
-                puts "creating mapping count #{m.ontologies}"
                 begin
                   if m.valid?
                     m.save()
@@ -254,17 +246,16 @@ def create_mapping_count_pairs_for_ontologies(logger, arr_acronyms)
 
         private
 
-        def delete_zombie_mapping_count(mappings_count, ontologies)
+        def delete_zombie_mapping_count(existent_counts, submissions_ready)
           special_mappings = ["http://data.bioontology.org/metadata/ExternalMappings",
                               "http://data.bioontology.org/metadata/InterportalMappings/agroportal",
                               "http://data.bioontology.org/metadata/InterportalMappings/ncbo",
                               "http://data.bioontology.org/metadata/InterportalMappings/sifr"]
 
-          mappings_count.each do |mapping|
-            next mapping if mapping.ontologies.all? { |x| ontologies.include?(x) }
-            next mapping if mapping.ontologies.size == 1 && !(mapping.ontologies & special_mappings).empty?
-
-            next mapping unless mapping.persistent?
+          existent_counts.each do |mapping|
+            next if mapping.ontologies.size == 1 && !(mapping.ontologies & special_mappings).empty?
+            next if mapping.ontologies.all? { |x| submissions_ready.include?(x) }
+            next unless mapping.persistent?
 
             mapping.delete
           end

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -265,7 +265,11 @@ def bring_remaining
       def self.segment_instance(sub)
         sub.bring(:ontology) unless sub.loaded_attributes.include?(:ontology)
         sub.ontology.bring(:acronym) unless sub.ontology.loaded_attributes.include?(:acronym)
-        [sub.ontology.acronym] rescue []
+        begin
+          [sub.ontology.acronym]
+        rescue
+          []
+        end
       end
 
       def self.submission_id_generator(ss)
@@ -424,6 +428,9 @@ def data_folder
       end
 
       def zipped?(full_file_path = uploadFilePath)
+        return false if full_file_path.nil?
+        return false unless File.exist?(full_file_path)
+
         LinkedData::Utils::FileHelpers.zip?(full_file_path) || LinkedData::Utils::FileHelpers.gzip?(full_file_path)
       end
 

test/http_cache/test_http_cache.rb

@@ -57,6 +57,7 @@ def test_cache_segment_proper_setup
   end
 
   def test_cache_segment_invalidate
+    create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true)
     classes = LinkedData::Models::Class.where.include(:prefLabel).in(@@ontology.latest_submission).page(1, 100).to_a
     classes.each {|c| c.cache_write}
     last_modified_values = classes.map {|c| c.last_modified}
@@ -67,6 +68,7 @@ def test_cache_segment_invalidate
   end
 
   def test_cache_segment_invalidate_when_member_invalidates
+    create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true)
     classes = LinkedData::Models::Class.where.include(:prefLabel).in(@@ontology.latest_submission).page(1, 100).to_a
     classes.each {|c| c.cache_write}
     last_modified_values = classes.map {|c| c.last_modified}
@@ -137,4 +139,4 @@ def test_cache_invalidate_all
     assert_equal [], LinkedData::HTTPCache.keys_for_invalidate_all
   end
 
-end
+end