Feature: Add index all data step (#136)

* move the submission_all_data concern to a submission process service

* add index_all step to submission parsing steps

* add index all data submission status

lib/ontologies_linked_data/models/concerns/submission_process.rb

@@ -7,83 +7,47 @@ def process_submission(logger, options = {})
       end
 
       def generate_missing_labels(logger)
-        puts 'Start generate_mission_label'
-        time = Benchmark.realtime do
-          LinkedData::Services::GenerateMissingLabels.new(self).process(logger, file_path: self.master_file_path)
-        end
-        puts "generate_mission_label ended in #{time}"
+        LinkedData::Services::GenerateMissingLabels.new(self).process(logger, file_path: self.master_file_path)
       end
 
       def generate_obsolete_classes(logger)
-        puts 'Start submission_obsolete_classes'
-        time = Benchmark.realtime do
-          LinkedData::Services::ObsoleteClassesGenerator.new(self).process(logger, file_path: self.master_file_path)
-        end
-        puts "submission_obsolete_classes ended in #{time}"
+        LinkedData::Services::ObsoleteClassesGenerator.new(self).process(logger, file_path: self.master_file_path)
       end
 
       def extract_metadata(logger, options = {})
-        puts 'Start extract metadata'
-        time = Benchmark.realtime do
-          LinkedData::Services::SubmissionMetadataExtractor.new(self).process(logger, options)
-        end
-        puts "Extract metadata ended in #{time}"
+        LinkedData::Services::SubmissionMetadataExtractor.new(self).process(logger, options)
       end
 
       def diff(logger, older)
-        puts 'Start diff'
-        time = Benchmark.realtime do
-          LinkedData::Services::SubmissionDiffGenerator.new(self).diff(logger, older)
-        end
-        puts "Diff ended in #{time}"
+        LinkedData::Services::SubmissionDiffGenerator.new(self).diff(logger, older)
       end
 
       def generate_diff(logger)
-        puts 'Start diff'
-        time = Benchmark.realtime do
-          LinkedData::Services::SubmissionDiffGenerator.new(self).process(logger)
-        end
-        puts "Diff ended in #{time}"
+        LinkedData::Services::SubmissionDiffGenerator.new(self).process(logger)
+      end
+
+      def index_all(logger, commit: true)
+        LinkedData::Services::OntologySubmissionAllDataIndexer.new(self).process(logger, commit: commit)
       end
 
       def index_terms(logger, commit: true, optimize: true)
-        puts 'Start index terms'
-        time = Benchmark.realtime do
-          LinkedData::Services::OntologySubmissionIndexer.new(self).process(logger, commit: commit, optimize: optimize)
-        end
-        puts "Index terms ended in #{time}"
+        LinkedData::Services::OntologySubmissionIndexer.new(self).process(logger, commit: commit, optimize: optimize)
       end
 
       def index_properties(logger, commit: true, optimize: true)
-        puts 'Start index properties'
-        time = Benchmark.realtime do
-          LinkedData::Services::SubmissionPropertiesIndexer.new(self).process(logger, commit: commit, optimize: optimize)
-        end
-        puts "Index properties ended in #{time}"
+        LinkedData::Services::SubmissionPropertiesIndexer.new(self).process(logger, commit: commit, optimize: optimize)
       end
 
       def archive
-        puts 'Start archive'
-        time = Benchmark.realtime do
-          LinkedData::Services::OntologySubmissionArchiver.new(self).process
-        end
-        puts "Archive ended in #{time}"
+        LinkedData::Services::OntologySubmissionArchiver.new(self).process
       end
 
       def generate_rdf(logger, reasoning: true)
-        puts 'Start generate RDF'
-        time = Benchmark.realtime do
-          LinkedData::Services::SubmissionRDFGenerator.new(self).process(logger, reasoning: reasoning)
-        end
-        puts "Generate RDF ended in #{time}"
+        LinkedData::Services::SubmissionRDFGenerator.new(self).process(logger, reasoning: reasoning)
       end
 
       def generate_metrics(logger)
-        puts 'Start generate metrics'
-        time = Benchmark.realtime do
-          LinkedData::Services::SubmissionMetricsCalculator.new(self).process(logger)
-        end
-        puts "Generate metrics ended in #{time}"
+        LinkedData::Services::SubmissionMetricsCalculator.new(self).process(logger)
       end
 
     end

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -12,7 +12,6 @@ module Models
 
     class OntologySubmission < LinkedData::Models::Base
 
-      include LinkedData::Concerns::OntologySubmission::IndexAllData
       include LinkedData::Concerns::SubmissionProcessable
       include LinkedData::Concerns::OntologySubmission::Validators
       include LinkedData::Concerns::OntologySubmission::UpdateCallbacks
@@ -295,6 +294,16 @@ def self.copy_file_repository(acronym, submissionId, src, filename = nil)
         return dst
       end
 
+      def self.clear_indexed_content(ontology)
+        conn = Goo.init_search_connection(:ontology_data)
+        begin
+          conn.delete_by_query("ontology_t:\"#{ontology}\"")
+        rescue StandardError => e
+          #puts e.message
+        end
+        conn
+      end
+
       def valid?
         valid_result = super
         return false unless valid_result

lib/ontologies_linked_data/models/submission_status.rb

@@ -7,6 +7,7 @@ class SubmissionStatus < LinkedData::Models::Base
         "RDF_LABELS", "ERROR_RDF_LABELS",
         "OBSOLETE", "ERROR_OBSOLETE",
         "INDEXED", "ERROR_INDEXED",
+        "INDEXED_ALL_DATA", "ERROR_INDEXED_ALL_DATA",
         "INDEXED_PROPERTIES", "ERROR_INDEXED_PROPERTIES",
         "METRICS",  "ERROR_METRICS",
         "ANNOTATOR", "ERROR_ANNOTATOR",
@@ -18,6 +19,8 @@ class SubmissionStatus < LinkedData::Models::Base
         "RDF"                      => "Parsed successfully",
         "RDF_ERROR"                => "Error parsing",
         "INDEXED"                  => "Indexed terms for search",
+        "INDEXED_ALL_DATA"         => "Indexed all the data of the resource",
+        "ERROR_INDEXED_ALL_DATA"   => "Error indexeding all the data of the resource",
         "ERROR_INDEXED"            => "Error indexing terms for search",
         "INDEXED_PROPERTIES"       => "Indexed properties for search",
         "ERROR_INDEXED_PROPERTIES" => "Error indexing properties for search",