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extract the submission metrics generation step to a file
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110 changes: 110 additions & 0 deletions
110
...gies_linked_data/services/submission_process/operations/submission_mertrics_calculator.rb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| module LinkedData | ||
| module Services | ||
| class SubmissionMetricsCalculator < OntologySubmissionProcess | ||
| def process(logger, options = nil) | ||
| process_metrics(logger) | ||
| end | ||
|
|
||
| def generate_umls_metrics_file(tr_file_path=nil) | ||
| tr_file_path ||= @submission.triples_file_path | ||
| class_count = 0 | ||
| indiv_count = 0 | ||
| prop_count = 0 | ||
|
|
||
| File.foreach(tr_file_path) do |line| | ||
| class_count += 1 if line =~ /owl:Class/ | ||
| indiv_count += 1 if line =~ /owl:NamedIndividual/ | ||
| prop_count += 1 if line =~ /owl:ObjectProperty/ | ||
| prop_count += 1 if line =~ /owl:DatatypeProperty/ | ||
| end | ||
| generate_metrics_file(class_count, indiv_count, prop_count) | ||
| end | ||
|
|
||
| private | ||
|
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| def process_metrics(logger) | ||
| status = LinkedData::Models::SubmissionStatus.find('METRICS').first | ||
| begin | ||
| compute_metrics(logger) | ||
| @submission.add_submission_status(status) | ||
| rescue StandardError => e | ||
| logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") | ||
| logger.flush | ||
| @submission.metrics = nil | ||
| @submission.add_submission_status(status.get_error_status) | ||
| ensure | ||
| @submission.save | ||
| end | ||
| end | ||
|
|
||
| def compute_metrics(logger) | ||
| metrics = metrics_for_submission(logger) | ||
| metrics.id = RDF::URI.new(@submission.id.to_s + '/metrics') | ||
| exist_metrics = LinkedData::Models::Metric.find(metrics.id).first | ||
| exist_metrics.delete if exist_metrics | ||
| metrics.save | ||
| @submission.metrics = metrics | ||
| @submission | ||
| end | ||
|
|
||
| def metrics_for_submission(logger) | ||
| logger.info('metrics_for_submission start') | ||
| logger.flush | ||
| begin | ||
| @submission.bring(:submissionStatus) if @submission.bring?(:submissionStatus) | ||
| cls_metrics = LinkedData::Metrics.class_metrics(@submission, logger) | ||
| logger.info('class_metrics finished') | ||
| logger.flush | ||
| metrics = LinkedData::Models::Metric.new | ||
|
|
||
| cls_metrics.each do |k,v| | ||
| unless v.instance_of?(Integer) | ||
| begin | ||
| v = Integer(v) | ||
| rescue ArgumentError | ||
| v = 0 | ||
| rescue TypeError | ||
| v = 0 | ||
| end | ||
| end | ||
| metrics.send("#{k}=",v) | ||
| end | ||
| indiv_count = LinkedData::Metrics.number_individuals(logger, @submission) | ||
| metrics.individuals = indiv_count | ||
| logger.info('individuals finished') | ||
| logger.flush | ||
| prop_count = LinkedData::Metrics.number_properties(logger, @submission) | ||
| metrics.properties = prop_count | ||
| logger.info('properties finished') | ||
| logger.flush | ||
| # re-generate metrics file | ||
| generate_metrics_file(cls_metrics[:classes], indiv_count, prop_count) | ||
| logger.info('generation of metrics file finished') | ||
| logger.flush | ||
| rescue StandardError => e | ||
| logger.error(e.message) | ||
| logger.error(e) | ||
| logger.flush | ||
| metrics = nil | ||
| end | ||
| metrics | ||
| end | ||
|
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| def generate_metrics_file(class_count, indiv_count, prop_count) | ||
| CSV.open(@submission.metrics_path, 'wb') do |csv| | ||
| csv << ['Class Count', 'Individual Count', 'Property Count'] | ||
| csv << [class_count, indiv_count, prop_count] | ||
| end | ||
| end | ||
|
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||
| # TODO to find usage in NCBO code | ||
| def generate_metrics_file2(class_count, indiv_count, prop_count, max_depth) | ||
| CSV.open(self.metrics_path, "wb") do |csv| | ||
| csv << ["Class Count", "Individual Count", "Property Count", "Max Depth"] | ||
| csv << [class_count, indiv_count, prop_count, max_depth] | ||
| end | ||
| end | ||
|
|
||
| end | ||
| end | ||
| end |