Class: FAIRChampionHarvester::Core

Inherits:
Object
  • Object
show all
Defined in:
lib/harvester.rb

Constant Summary collapse

@@distillerknown =

global, hash of sha256 keys of message bodies - have they been seen before t/f

{}

Class Method Summary collapse

Class Method Details

.convertToURL(guid) ⇒ Object 



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# File 'lib/harvester.rb', line 50

def self.convertToURL(guid)
  FAIRChampionHarvester::Utils::GUID_TYPES.each do |pair|
    k, regex = pair
    if k == "inchi" and regex.match(guid)
      return "inchi", "https://pubchem.ncbi.nlm.nih.gov/rest/rdf/inchikey/#{guid}"
    elsif k == "handle1" and regex.match(guid)
      return "handle", "http://hdl.handle.net/#{guid}"
    elsif k == "handle2" and regex.match(guid)
      return "handle", "http://hdl.handle.net/#{guid}"
    elsif k == "uri" and regex.match(guid)
      return "uri", guid
    elsif k == "doi" and regex.match(guid)
      return "doi", "https://doi.org/#{guid}"
    elsif k == "ark_url" and regex.match(guid)
      return "ark_url", guid
    elsif k == "ark" and regex.match(guid)
      return "ark", "https://n2t.net/#{guid}"
    end
  end
  [nil, nil]
end

.deep_dive_properties(myHash, property = nil, props = []) ⇒ Array<Array>

Recursively collects **every key-value pair** from a nested Hash structure as [key, value] arrays.

Traverses the entire nested hash in depth-first order and records every key-value pair encountered — including pairs where the value is itself a Hash.

Note: The ‘property` parameter is currently **not used** (dead code). Both branches of the conditional do the same thing, so every pair is collected regardless of `property`.

Examples:

h = {
  user: "bob42",
  config: {
    theme: "dark",
    alerts: { email: true, push: false }
  }
}

deep_dive_properties(h)
# => [[:user, "bob42"],
#     [:config, {theme: "dark", alerts: {email: true, push: false}}],
#     [:theme, "dark"],
#     [:alerts, {email: true, push: false}],
#     [:email, true],
#     [:push, false]]

deep_dive_properties(h, :email)   # ← currently returns the same as above (bug)

Parameters:

  • myHash (Hash) —

    the nested hash to traverse

  • property (Symbol, String, nil) (defaults to: nil) —

    intended filter key (currently ineffective)

  • props (Array) (defaults to: []) —

    accumulator for [key, value] pairs (mutable)

Returns:

  • (Array<Array>) —

    flat list of [key, value] tuples in depth-first order



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# File 'lib/harvester.rb', line 354

def self.deep_dive_properties(myHash, property = nil, props = [])
  return props unless myHash.is_a?(Hash)

  myHash.each_pair do |key, value|
    # The conditional is redundant — both branches are identical
    # This is very likely a bug or unfinished implementation.
    props << if property && property == key
               [key, value]
             else
               [key, value]
             end

    if value.is_a?(Hash)
      # $stderr.puts "key: #{key} recursing..."   # uncomment for debugging
      deep_dive_properties(value, property, props)
    end
  end

  props
end

.deep_dive_values(myHash, value = nil, vals = []) ⇒ Array

Recursively collects **all non-Hash values** (leaf values) from a nested Hash structure.

Traverses the hash in depth-first order and gathers every value that is not itself a Hash into a flat array. Keys are completely ignored.

Examples:

h = {
  name: "Alice",
  info: {
    age: 34,
    address: { city: "Madrid", coords: { lat: 40.4168, lon: -3.7038 } },
    hobbies: ["reading", "hiking"]
  }
}

deep_dive_values(h)
# => ["Alice", 34, "Madrid", 40.4168, -3.7038, "reading", "hiking"]

Parameters:

  • myHash (Hash) —

    the nested hash to traverse

  • value (Object) (defaults to: nil) —

    currently unused (likely legacy or placeholder parameter)

  • vals (Array) (defaults to: []) —

    accumulator for collected values (mutable, passed by reference)

Returns:

  • (Array) —

    flat list of all leaf (non-Hash) values in depth-first traversal order



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# File 'lib/harvester.rb', line 309

def self.deep_dive_values(myHash, value = nil, vals = [])
  myHash.each_pair do |_key, value|
    if value.is_a?(Hash)
      # $stderr.puts "key: #{_key} recursing..."   # uncomment for debugging
      deep_dive_values(value, value, vals)
    else
      vals << value
    end
  end

  vals
end

.fetch(guid:, headers: FAIRChampionHarvester::Utils::AcceptHeader, meta: nil) ⇒ Object

we will try to retrieve turtle whenever possible



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# File 'lib/harvester.rb', line 403

def self.fetch(guid:, headers: FAIRChampionHarvester::Utils::AcceptHeader, meta: nil) # we will try to retrieve turtle whenever possible
  head, body, finalURI = FAIRChampionHarvester::Cache.checkCache(guid, headers)
  return false if head and head == "ERROR"

  meta.finalURI |= [finalURI] if meta && finalURI

  warn meta.finalURI.inspect if meta
  if head and body
    warn "Retrieved from cache, returning data to code"
    return [head, body]
  end

  warn "In fetch routine now.  "
  begin
    warn "executing call over the Web to #{guid}"
    # response = RestClient::Request.execute(
    #   method: :get,
    #   url: guid.to_s,
    #   # user: user,
    #   # password: pass,
    #   headers: headers
    # )
    response = HTTP
               .headers(headers).follow
               .get(guid.to_s) # or full URL

    if response.status.success?
      final_url = response.uri.to_s
      meta.finalURI |= [final_url] if meta
      warn "There was a response to the call #{guid}"
      FAIRChampionHarvester::Cache.writeToCache(guid, headers, response.headers, response.body.to_s,
                                                response.uri.to_s)
      [response.headers, response.body.to_s] # return headers, body, and final URL
    else
      # Handle HTTP error status codes (4xx, 5xx, etc.)
      warn "HTTP Error #{response.status} for #{url}"
      warn "Final URL: #{response.uri}" if response.uri
      FAIRChampionHarvester::Cache.writeErrorToCache(guid, headers)
      meta.comments << "WARN: HTTP error #{response.status} encountered when trying to resolve #{guid}\n" if meta
      false
    end
  rescue HTTP::Error => e
    # This catches network errors, timeouts, connection failures, DNS errors, etc.
    warn "HTTP Request Failed for #{guid}: #{e.message}"
    FAIRChampionHarvester::Cache.writeErrorToCache(guid, headers)
    meta.comments << "WARN: HTTP error #{e.message} encountered when trying to resolve #{guid}\n" if meta
    false
  rescue StandardError => e
    # Catch any other unexpected errors
    warn "Unexpected error while fetching #{guid}: #{e.class} - #{e.message}"
    warn e.backtrace.first(5).join("\n") if ENV["DEBUG"]
    FAIRChampionHarvester::Cache.writeErrorToCache(guid, headers)
    meta.comments << "WARN: HTTP error #{e.message} encountered when trying to resolve #{guid}\n" if meta
    false
  end
  # rescue RestClient::ExceptionWithResponse => e
  #   warn "ERROR! #{e.response}"
  #   FAIRChampionHarvester::Cache.writeErrorToCache(guid, headers)
  #   meta.comments << "WARN: HTTP error #{e} encountered when trying to resolve #{guid}\n" if meta
  #   false
  #   # now we are returning 'False', and we will check that with an \"if\" statement in our main code
  # rescue RestClient::Exception => e
  #   warn "ERROR! #{e}"
  #   meta.comments << "WARN: HTTP error #{e} encountered when trying to resolve #{guid}\n" if meta
  #   FAIRChampionHarvester::Cache.writeErrorToCache(guid, headers)
  #   false
  #   # now we are returning 'False', and we will check that with an \"if\" statement in our main code
  # rescue Exception => e
  #   warn "ERROR! #{e}"
  #   meta.comments << "WARN: HTTP error #{e} encountered when trying to resolve #{guid}\n" if meta
  #   FAIRChampionHarvester::Cache.writeErrorToCache(guid, headers)
  #   false
  #   # now we are returning 'False', and we will check that with an \"if\" statement in our main code
  # end # you can capture the Exception and do something useful with it!\n",
end

.figure_out_type(head) ⇒ Object 



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# File 'lib/harvester.rb', line 375

def self.figure_out_type(head)
  type = head[:content_type]
  if type.nil?
    warn "\n\nSTRANGE - headers had no content-type\n\n"
    return nil, nil
  end
  type.match(%r{([\w+.]+/[\w+.]+):?;?}im)
  type = ::Regexp.last_match(1)
  # $stderr.puts "\n\nsearching for #{type}\n\n"

  FAIRChampionHarvester::Utils::RDF_FORMATS.each do |parser, types|
    return parser, type if types.include? type
  end
  FAIRChampionHarvester::Utils::JSON_FORMATS.each do |parser, types|
    return parser, type if types.include? type
  end
  FAIRChampionHarvester::Utils::TEXT_FORMATS.each do |parser, types|
    return parser, type if types.include? type
  end
  FAIRChampionHarvester::Utils::XML_FORMATS.each do |parser, types|
    return parser, type if types.include? type
  end
  FAIRChampionHarvester::Utils::HTML_FORMATS.each do |parser, types|
    return parser, type if types.include? type
  end
  [nil, nil]
end

.head(url, headers = FAIRChampionHarvester::Utils::AcceptHeader) ⇒ Object

this returns the URI that results from all redirects, etc.



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# File 'lib/harvester.rb', line 510

def self.head(url, headers = FAIRChampionHarvester::Utils::AcceptHeader)
  response = RestClient::Request.execute({
                                           method: :head,
                                           url: url.to_s,
                                           # user: user,
                                           # password: pass,
                                           headers: headers
                                         })
  response.headers
rescue RestClient::ExceptionWithResponse => e
  warn e.response
  false
# now we are returning 'False', and we will check that with an \"if\" statement in our main code
rescue RestClient::Exception => e
  warn e.response
  false
# now we are returning 'False', and we will check that with an \"if\" statement in our main code
rescue Exception => e
  warn e
  false
  # now we are returning 'False', and we will check that with an \"if\" statement in our main code
  # you can capture the Exception and do something useful with it!\n",
end

.parse_html(meta, body) ⇒ Object 



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# File 'lib/harvester.rb', line 104

def self.parse_html(meta, body)
  # just use extruct and distiller instead
end

.parse_json(meta, body) ⇒ Object 



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# File 'lib/harvester.rb', line 93

def self.parse_json(meta, body)
  hash = JSON.parse(body)
  # warn body
  # warn hash.inspect
  # warn hash.class

  meta.hash.merge!(hash)
  #      warn meta.hash
  meta.hash
end

.parse_link_body_headers(url, body) ⇒ Object 



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# File 'lib/harvester.rb', line 225

def self.parse_link_body_headers(url, body)
  # Parse the HTML body (Nokogiri is tolerant of malformed HTML)
  doc = Nokogiri::HTML(body)

  # Focus on <link> tags inside <head> (MetaInspector's head_links equivalent)
  # We use css selector for simplicity and readability
  link_nodes = doc.css('head link[rel="alternate"][type]') # only those with rel=alternate AND type attr

  # Your format lists – assuming these are constants/hashes like:
  # FAIRChampionHarvester::Utils::RDF_FORMATS  => { jsonld: "application/ld+json", ... }
  # We flatten them once for efficiency
  allowed_types = [
    FAIRChampionHarvester::Utils::RDF_FORMATS.values,
    FAIRChampionHarvester::Utils::XML_FORMATS.values,
    FAIRChampionHarvester::Utils::JSON_FORMATS.values
  ].flatten.uniq # uniq to avoid duplicates if any overlap

  # Filter and extract hrefs
  urls = link_nodes.filter_map do |link|
    type = link["type"]&.strip
    next unless type && allowed_types.include?(type)

    href = link["href"]&.strip
    href if href && !href.empty?
  end

  # Optional: make relative URLs absolute (MetaInspector usually does this)
  base_uri = begin
    URI.parse(url)
  rescue StandardError
    nil
  end
  if base_uri
    urls.map! do |href|
      URI.join(base_uri, href).to_s
    rescue StandardError
      href
    end
  end

  warn "\n\nGOT BODY LINKS #{urls}\n\n"

  urls
end

.parse_link_http_headers(headers) ⇒ Object 



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# File 'lib/harvester.rb', line 193

def self.parse_link_http_headers(headers)
  # we can be sure that a Link header is a URL
  # code stolen from https://gist.github.com/thesowah/0ca5e1b4b3c61bfe8e13 with a few tweaks

  links = headers[:link]
  return [] unless links

  parts = links.split(",")

  urls = []
  # Parse each part into a named link
  parts.each do |part, _index|
    section = part.split(";")
    next unless section[0]

    url = section[0][/<(.*)>/, 1]
    next unless section[1]

    type = ""
    section[1..].each do |s|
      type = s[/rel="?(\w+)"?/, 1]
      break if type
    end
    next unless type
    # "meta" headers are for old versions of Virtuoso LDP - not in link relations standared
    next unless %w[meta alternate].include?(type.downcase)

    urls << url
  end
  urls
end

.parse_rdf(meta, body, format = nil) ⇒ Object 



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# File 'lib/harvester.rb', line 108

def self.parse_rdf(meta, body, format = nil)
  unless body
    meta.comments << "CRITICAL: The response message body component appears to have no content.\n"
    return meta
  end
  unless body.match(/\w/)
    meta.comments << "CRITICAL: The response message body component appears to have no content.\n"
    return meta
  end

  warn "\n\n\nSANITY CHECK \n\n#{body[0..300]}\n\n"
  # sanitycheck = RDF::Format.for({ sample: body[0..5000] })
  # unless sanitycheck
  #   meta.comments << "CRITICAL: The Evaluator found what it believed to be RDF (sample:  #{body[0..300].delete!("\n")}), but it could not find a parser.  Please report this error, along with the GUID of the resource, to the maintainer of the system.\n"
  #   return meta
  # end

  graph = FAIRChampionHarvester::Cache.checkRDFCache(body)
  if graph.size > 0
    warn "\n\n\n unmarshalling graph from cache\n\n"
    warn "\n\ngraph size #{graph.size} #{graph.inspect}\n\n"
    meta.merge_rdf(graph.to_a)
    return meta
  end

  formattype = nil
  warn "\n\n\ndeclared format #{format}\n\n"
  if format.nil?
    formattype = RDF::Format.for({ sample: body[0..3000] })
    warn "\n\n\ndetected format #{formattype}\n\n"
  else
    warn "\n\n\ntesting declared format #{format}\n\n"
    formattype = RDF::Format.for(content_type: format)
    warn "\n\n\nfound format #{formattype}\n\n"
  end
  warn "\n\n\nfinal format #{formattype}\n\n"
  # $stderr.puts "\n\n\nBODY #{body}\n\n"

  unless formattype
    meta.comments << "CRITICAL: Unable to find an RDF reader type that matches the content that was returned from resolution.  Here is a sample #{body[0..100]}  Please send your GUID to the dev team so we can investigate!\n"
    return meta
  end
  meta.comments << "INFO: The response message body component appears to contain #{formattype}.\n"
  reader = ""
  begin
    reader = formattype.reader.new(body)
  rescue StandardError
    meta.comments << "WARN: Though linked data was found, it failed to parse.  This likely indicates some syntax error in the data.  As a result, no metadata will be extracted from this message.\n"
    return meta
  end

  begin
    # $stderr.puts "Reader Class #{reader.class}\n\n #{reader.inspect}"
    if reader.size == 0
      meta.comments << "WARN: Though linked data was found, it failed to parse.  This likely indicates some syntax error in the data.  As a result, no metadata will be extracted from this message.\n"
      return meta
    end
    #       reader.rewind!
    # for some reason, the rewind method isn't working here...??
    reader = formattype.reader.new(body) # have to re-read it here, but now its safe because we have already caught errors
    warn "WRITING TO CACHE"
    FAIRChampionHarvester::Cache.writeRDFCache(reader, body) # write to the special RDF graph cache
    warn "WRITING DONE"
    reader = formattype.reader.new(body)
    warn "RE-READING DONE"
    meta.merge_rdf(reader.to_a)
    warn "MERGE DONE"
  rescue RDF::ReaderError => e
    meta.comments << "CRITICAL: The Linked Data was malformed and caused the parser to crash with error message: #{e.message} ||  (sample of what was parsed:  #{body[0..300].delete("\n")})\n"
    warn "CRITICAL: The Linked Data was malformed and caused the parser to crash with error message: #{e.message} ||  (sample of what was parsed:  #{body[0..300].delete("\n")})\n"
    nil
  rescue Exception => e
    meta.comments << "CRITICAL: An unknown error occurred while parsing the (apparent) Linked Data (sample of what was parsed:  #{body[0..300].delete("\n")}).  Moving on...\n"
    warn "\n\nCRITICAL: #{e.inspect} An unknown error occurred while parsing the (apparent) Linked Data (full body:  #{body}).  Moving on...\n\n"
    nil
  end
end

.parse_text(meta, body) ⇒ Object 



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# File 'lib/harvester.rb', line 86

def self.parse_text(meta, body)
  meta.comments << "WARTN: Plain Text cannot be mapped to any parser.  No structured metadata found.\n"
  meta.comments << "INFO: Using Apache Tika to attempt to extract metadata from plaintext.\n"

  FAIRChampionHarvester::Tika.do_tika(meta, body)
end

.parse_xml(meta, body) ⇒ Object 



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# File 'lib/harvester.rb', line 186

def self.parse_xml(meta, body)
  hash = XmlSimple.xml_in(body)
  meta.comments << "INFO: The XML is being converted into a simple hash structure.\n"
  meta.hash.merge hash
  meta.hash
end

.resolve(url, headers = FAIRChampionHarvester::Utils::AcceptHeader) ⇒ Object

this returns the URI that results from all redirects, etc.



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# File 'lib/harvester.rb', line 535

def self.resolve(url, headers = FAIRChampionHarvester::Utils::AcceptHeader)
  response = RestClient::Request.execute({
                                           method: :head,
                                           url: url.to_s,
                                           # user: user,
                                           # password: pass,
                                           headers: headers
                                         })
  response.request.url
rescue RestClient::ExceptionWithResponse => e
  warn e.response
  false
# now we are returning 'False', and we will check that with an \"if\" statement in our main code
rescue RestClient::Exception => e
  warn e.response
  false
# now we are returning 'False', and we will check that with an \"if\" statement in our main code
rescue Exception => e
  warn e
  false
  # now we are returning 'False', and we will check that with an \"if\" statement in our main code
  # you can capture the Exception and do something useful with it!\n",
end

.resolveit(guid) ⇒ Object 



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# File 'lib/harvester.rb', line 19

def self.resolveit(guid)
  # if meta = FAIRChampionHarvester::Utils::retrieveMetaObject(guid)
  #    return meta
  # end

  meta = FAIRChampionHarvester::MetadataObject.new

  FAIRChampionHarvester::Utils::GUID_TYPES.each do |pair| # meta object gets updated in each case
    k, regex = pair
    if k == "inchi" and regex.match(guid)
      FAIRChampionHarvester::INCHI.resolve_inchi(guid, meta)
    elsif k == "handle1" and regex.match(guid)
      FAIRChampionHarvester::Handle.resolve_handle(guid, meta)
    elsif k == "handle2" and regex.match(guid)
      FAIRChampionHarvester::Handle.resolve_handle(guid, meta)
    elsif k == "uri" and regex.match(guid)
      FAIRChampionHarvester::Uri.resolve_uri(guid, meta)
    elsif k == "doi" and regex.match(guid)
      FAIRChampionHarvester::DOI.resolve_doi(guid, meta)
    end
  end

  if meta.comments.empty? # didn't match any of the types, so no comments were added
    meta.guidtype = "unknown"
    meta.comments << "CRITICAL: The guid '#{guid}' did not correspond to any known GUID format. Tested #{FAIRChampionHarvester::Utils::GUID_TYPES.keys}. Halting.\n"
  end
  meta.comments << "INFO: END OF HARVESTING\n"
  # FAIRChampionHarvester::Utils::cacheMetaObject(meta, guid)
  meta
end

.simplefetch(url, headers = FAIRChampionHarvester::Utils::AcceptHeader, _meta = nil) ⇒ Object

we will try to retrieve turtle whenever possible



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# File 'lib/harvester.rb', line 479

def self.simplefetch(url, headers = FAIRChampionHarvester::Utils::AcceptHeader, _meta = nil) # we will try to retrieve turtle whenever possible
  # head = FAIRChampionHarvester::Utils::head(url, headers)
  # $stderr.puts "content length " + head[:content_length].to_s
  # if head[:content_length] and head[:content_length].to_f > 300000 and meta
  #    meta.comments << "WARN: The size of the content at #{url} reports itself to be >300kb.  This service will not download something so large.  This does not mean that the content is not FAIR, only that this service will not test it.  Sorry!\n"
  #    return false
  # end

  response = HTTP
             .headers(headers).follow
             .get(guid.to_s) # or full URL

  if response.status.success?
    [response.headers, response.body.to_s] # return headers, body, and final URL
  else
    # Handle HTTP error status codes (4xx, 5xx, etc.)
    warn "HTTP Error #{response.status} for #{url}"
    warn "Final URL: #{response.uri}" if response.uri
    false
  end
rescue HTTP::Error => e
  # This catches network errors, timeouts, connection failures, DNS errors, etc.
  warn "HTTP Request Failed for #{guid}: #{e.message}"
  false
rescue StandardError => e
  # Catch any other unexpected errors
  warn "Unexpected error while fetching #{guid}: #{e.class} - #{e.message}"
  false
end

.typeit(guid) ⇒ Object 



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# File 'lib/harvester.rb', line 72

def self.typeit(guid)
  FAIRChampionHarvester::Utils::GUID_TYPES.each do |pair|
    type, regex = pair
    return type if regex.match(guid)
  end
  false
end