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implemented the first pass at bmir-radx/radx-project#37
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| require 'logger' | ||
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| module NcboCron | ||
| module Helpers | ||
| module OntologyHelper | ||
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| REDIS_SUBMISSION_ID_PREFIX = "sub:" | ||
| PROCESS_QUEUE_HOLDER = "parseQueue" | ||
| PROCESS_ACTIONS = { | ||
| :process_rdf => true, | ||
| :generate_labels => true, | ||
| :index_search => true, | ||
| :index_properties => true, | ||
| :run_metrics => true, | ||
| :process_annotator => true, | ||
| :diff => true, | ||
| :remote_pull => false | ||
| } | ||
|
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| class RemoteFileException < StandardError | ||
| attr_reader :submission | ||
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| def initialize(submission) | ||
| super | ||
| @submission = submission | ||
| end | ||
| end | ||
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| def self.do_ontology_pull(ontology_acronym, enable_pull_umls = false, umls_download_url = '', logger = nil, | ||
| add_to_queue = true) | ||
| logger ||= Logger.new($stdout) | ||
| ont = LinkedData::Models::Ontology.find(ontology_acronym).include(:acronym).first | ||
| new_submission = nil | ||
| raise StandardError, "Ontology #{ontology_acronym} not found" if ont.nil? | ||
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| last = ont.latest_submission(status: :any) | ||
| raise StandardError, "No submission found for #{ontology_acronym}" if last.nil? | ||
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| last.bring(:hasOntologyLanguage) if last.bring?(:hasOntologyLanguage) | ||
| if !enable_pull_umls && last.hasOntologyLanguage.umls? | ||
| raise StandardError, "Pull umls not enabled" | ||
| end | ||
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| last.bring(:pullLocation) if last.bring?(:pullLocation) | ||
| raise StandardError, "#{ontology_acronym} has no pullLocation" if last.pullLocation.nil? | ||
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| last.bring(:uploadFilePath) if last.bring?(:uploadFilePath) | ||
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| if last.hasOntologyLanguage.umls? && umls_download_url && !umls_download_url.empty? | ||
| last.pullLocation = RDF::URI.new(umls_download_url + last.pullLocation.split("/")[-1]) | ||
| logger.info("Using alternative download for umls #{last.pullLocation.to_s}") | ||
| logger.flush | ||
| end | ||
|
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| if last.remote_file_exists?(last.pullLocation.to_s) | ||
| logger.info "Checking download for #{ont.acronym}" | ||
| logger.info "Location: #{last.pullLocation.to_s}"; logger.flush | ||
| file, filename = last.download_ontology_file | ||
| file, md5local, md5remote, new_file_exists = self.new_file_exists?(file, last) | ||
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| if new_file_exists | ||
| logger.info "New file found for #{ont.acronym}\nold: #{md5local}\nnew: #{md5remote}" | ||
| logger.flush() | ||
| new_submission = self.create_submission(ont, last, file, filename, logger, add_to_queue) | ||
| else | ||
| logger.info "There is no new file found for #{ont.acronym}" | ||
| logger.flush() | ||
| end | ||
|
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| file.close | ||
| new_submission | ||
| else | ||
| raise self::RemoteFileException.new(last) | ||
| end | ||
| end | ||
|
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| def self.create_submission(ont, sub, file, filename, logger = nil, add_to_queue = true, new_version = nil, | ||
| new_released = nil) | ||
| logger ||= Kernel.const_defined?("LOGGER") ? Kernel.const_get("LOGGER") : Logger.new(STDOUT) | ||
| new_sub = LinkedData::Models::OntologySubmission.new | ||
|
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| sub.bring_remaining | ||
| sub.loaded_attributes.each do |attr| | ||
| new_sub.send("#{attr}=", sub.send(attr)) | ||
| end | ||
|
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| submission_id = ont.next_submission_id() | ||
| new_sub.submissionId = submission_id | ||
| file_location = LinkedData::Models::OntologySubmission.copy_file_repository(ont.acronym, submission_id, file, filename) | ||
| new_sub.uploadFilePath = file_location | ||
|
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| unless new_version.nil? | ||
| new_sub.version = new_version | ||
| end | ||
|
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| if new_released.nil? | ||
| new_sub.released = DateTime.now | ||
| else | ||
| new_sub.released = DateTime.parse(new_released) | ||
| end | ||
| new_sub.submissionStatus = nil | ||
| new_sub.creationDate = nil | ||
| new_sub.missingImports = nil | ||
| new_sub.metrics = nil | ||
| full_file_path = File.expand_path(file_location) | ||
|
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| # check if OWLAPI is able to parse the file before creating a new submission | ||
| owlapi = LinkedData::Parser::OWLAPICommand.new( | ||
| full_file_path, | ||
| File.expand_path(new_sub.data_folder.to_s), | ||
| logger: logger) | ||
| owlapi.disable_reasoner | ||
| parsable = true | ||
|
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| begin | ||
| owlapi.parse | ||
| rescue Exception => e | ||
| logger.error("The new file for ontology #{ont.acronym}, submission id: #{submission_id} did not clear OWLAPI: #{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}") | ||
| logger.error("A new submission has NOT been created.") | ||
| logger.flush | ||
| parsable = false | ||
| end | ||
|
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| if parsable | ||
| if new_sub.valid? | ||
| new_sub.save() | ||
|
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| if add_to_queue | ||
| self.queue_submission(new_sub, { all: true }) | ||
| logger.info("OntologyPull created a new submission (#{submission_id}) for ontology #{ont.acronym}") | ||
| end | ||
| else | ||
| logger.error("Unable to create a new submission for ontology #{ont.acronym} with id #{submission_id}: #{new_sub.errors}") | ||
| logger.flush | ||
| end | ||
| else | ||
| # delete the bad file | ||
| File.delete full_file_path if File.exist? full_file_path | ||
| end | ||
| new_sub | ||
| end | ||
|
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| def self.queue_submission(submission, actions={:all => true}) | ||
| redis = Redis.new(:host => NcboCron.settings.redis_host, :port => NcboCron.settings.redis_port) | ||
|
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| if actions[:all] | ||
| actions = PROCESS_ACTIONS.dup | ||
| else | ||
| actions.delete_if {|k, v| !PROCESS_ACTIONS.has_key?(k)} | ||
| end | ||
| actionStr = MultiJson.dump(actions) | ||
| redis.hset(PROCESS_QUEUE_HOLDER, get_prefixed_id(submission.id), actionStr) unless actions.empty? | ||
| end | ||
|
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| def self.get_prefixed_id(id) | ||
| "#{REDIS_SUBMISSION_ID_PREFIX}#{id}" | ||
| end | ||
|
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| def self.last_fragment_of_uri(uri) | ||
| uri.to_s.split("/")[-1] | ||
| end | ||
|
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| def self.acronym_from_submission_id(submissionID) | ||
| submissionID.to_s.split("/")[-3] | ||
| end | ||
|
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| def self.new_file_exists?(file, last) | ||
| file = File.open(file.path, "rb") | ||
| remote_contents = file.read | ||
| md5remote = Digest::MD5.hexdigest(remote_contents) | ||
|
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| if last.uploadFilePath && File.exist?(last.uploadFilePath) | ||
| file_contents = open(last.uploadFilePath) { |f| f.read } | ||
| md5local = Digest::MD5.hexdigest(file_contents) | ||
| new_file_exists = (not md5remote.eql?(md5local)) | ||
| else | ||
| # There is no existing file, so let's create a submission with the downloaded one | ||
| new_file_exists = true | ||
| end | ||
| return file, md5local, md5remote, new_file_exists | ||
| end | ||
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| end | ||
| end | ||
| end |
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