semtools 0.1.6 → 0.1.9

data/lib/semtools/parsers/file_parser.rb

@@ -0,0 +1,32 @@
+class FileParser
+	#############################################
+    # FIELDS
+    #############################################
+    # Handled class variables
+    # => @@basic_tags :: hash with main OBO structure tags
+    # => @@symbolizable_ids :: tags which can be symbolized
+    # => @@tags_with_trailing_modifiers :: tags which can include extra info after specific text modifiers
+
+	@@basic_tags = {ancestors: [:is_a], obsolete: :is_obsolete, alternative: [:replaced_by,:consider,:alt_id]}
+    @@symbolizable_ids = [:id, :alt_id, :replaced_by, :consider]
+    @@tags_with_trailing_modifiers = [:is_a, :union_of, :disjoint_from, :relationship, :subsetdef, :synonymtypedef, :property_value]
+    @@multivalue_tags = [:alt_id, :is_a, :subset, :synonym, :xref, :intersection_of, :union_of, :disjoint_from, :relationship, :replaced_by, :consider, :subsetdef, :synonymtypedef, :property_value, :remark]
+    @@symbolizable_ids.concat(@@tags_with_trailing_modifiers)
+
+    # Symboliza all values into hashs using symbolizable tags as keys
+    # ===== Parameters
+    # +item_hash+:: hash to be checked
+    def self.symbolize_ids(item_hash)
+        @@symbolizable_ids.each do |tag|
+            query = item_hash[tag] 
+            if !query.nil?
+                if query.kind_of?(Array)
+                    query.map!{|item| item.to_sym}
+                else
+                    item_hash[tag] = query.to_sym if !query.nil?
+                end
+            end
+        end
+    end
+
+end

data/lib/semtools/parsers/json_parser.rb

@@ -0,0 +1,84 @@
+class JsonParser < FileParser
+
+	def self.load(ontology, file, build: true)
+        read(ontology, file) 
+	end
+
+   # Read a JSON file with an OBO_Handler object stored
+    # ===== Parameters
+    # +file+:: with object info
+    # +file+:: if true, calculate indexes. Default: true
+    # ===== Return
+    # OBO_Handler internal fields 
+    def self.read(ontology, file, build: true)
+        # Read file
+        jsonFile = File.open(file)
+        jsonInfo = JSON.parse(jsonFile.read, :symbolize_names => true)
+        # Pre-process (Symbolize some hashs values)
+        jsonInfo[:terms].map{|id,info| symbolize_ids(info)} # STANZAS
+        # Optional
+        jsonInfo[:alternatives_index] = jsonInfo[:alternatives_index].map{|id,value| [id, value.to_sym]}.to_h unless jsonInfo[:alternatives_index].nil?
+        jsonInfo[:ancestors_index].map {|id,family_arr| family_arr.map!{|item| item.to_sym}} unless jsonInfo[:ancestors_index].nil?
+        jsonInfo[:descendants_index].map {|id,family_arr| family_arr.map!{|item| item.to_sym}} unless jsonInfo[:descendants_index].nil?
+        jsonInfo[:dicts] = jsonInfo[:dicts].each do |flag, dictionaries|
+            next if dictionaries.nil?
+            # Special case: byTerm
+            dictionaries[:byTerm] = dictionaries[:byTerm].map do |term, value| 
+                if !term.to_s.scan(/\A[-+]?[0-9]*\.?[0-9]+\Z/).empty?  # Numeric dictionary
+                    [term.to_s.to_i, value.map{|term| term.to_sym}]
+                elsif value.is_a? Numeric # Numeric dictionary
+                    [term.to_sym, value]
+                elsif value.kind_of?(Array) && flag == :is_a
+                    [term.to_sym, value.map{|v| v.to_sym}]
+                else
+                    [term.to_sym, value]
+                end
+            end
+            dictionaries[:byTerm] = dictionaries[:byTerm].to_h
+            # By value
+            dictionaries[:byValue] = dictionaries[:byValue].map do |value, term| 
+                if value.is_a? Numeric # Numeric dictionary
+                    [value, term.to_sym]
+                elsif term.is_a? Numeric # Numeric dictionary
+                    [value.to_s.to_sym, term]
+                elsif flag == :is_a
+                    [value.to_sym, term.map{|v| v.to_sym}]
+                elsif term.kind_of?(Array)
+                    [value.to_sym, term.map{|t| t.to_sym}]
+                else
+                    [value.to_s, term.to_sym]
+                end
+            end
+            dictionaries[:byValue] = dictionaries[:byValue].to_h
+        end 
+        if !jsonInfo[:profiles].nil?
+            jsonInfo[:profiles].map{|id,terms| terms.map!{|term| term.to_sym}}
+            jsonInfo[:profiles].keys.map{|id| jsonInfo[:profiles][id.to_s.to_i] = jsonInfo[:profiles].delete(id) if self.is_number?(id.to_s)}
+        end
+        jsonInfo[:removable_terms] = jsonInfo[:removable_terms].map{|term| term.to_sym} unless jsonInfo[:removable_terms].nil?
+        jsonInfo[:items].each{|k,v| jsonInfo[:items][k] = v.map{|item| item.to_sym}} unless jsonInfo[:items].nil?
+        jsonInfo[:term_paths].each{|term,info| jsonInfo[:term_paths][term][:paths] = info[:paths].map{|path| path.map{|t| t.to_sym}}} unless jsonInfo[:term_paths].nil?
+        
+        # Store info
+        ontology.terms = jsonInfo[:terms]
+        ontology.ancestors_index = jsonInfo[:ancestors_index]
+        ontology.descendants_index = jsonInfo[:descendants_index]
+        ontology.alternatives_index = jsonInfo[:alternatives_index]
+        jsonInfo[:structureType] = jsonInfo[:structureType].to_sym unless jsonInfo[:structureType].nil?
+        ontology.structureType = jsonInfo[:structureType]
+        ontology.ics = jsonInfo[:ics]
+        ontology.meta = jsonInfo[:meta]
+        ontology.max_freqs = jsonInfo[:max_freqs]
+        ontology.dicts = jsonInfo[:dicts]
+        ontology.profiles = jsonInfo[:profiles]
+        ontology.items = jsonInfo[:items]
+        ontology.term_paths = jsonInfo[:term_paths]
+
+        ontology.precompute() if build
+    end
+
+    def self.is_number? string
+          true if Float(string) rescue false
+    end
+
+end

data/lib/semtools/parsers/oboparser.rb

@@ -0,0 +1,511 @@
+class OboParser < FileParser
+
+    #############################################
+    # FIELDS
+    #############################################
+    # => @header :: file header (if is available)
+    # => @stanzas :: OBO stanzas {:terms,:typedefs,:instances}
+    # => @ancestors_index :: hash of ancestors per each term handled with any structure relationships
+    # => @descendants_index :: hash of descendants per each term handled with any structure relationships
+    # => @alternatives_index :: has of alternative IDs (include alt_id and obsoletes)
+    # => @special_tags :: set of special tags to be expanded (:is_a, :obsolete, :alt_id)
+    # => @structureType :: type of ontology structure depending on ancestors relationship. Allowed: {atomic, sparse, circular, hierarchical}
+    # => @dicts :: bidirectional dictionaries with three levels <key|value>: 1º) <tag|hash2>; 2º) <(:byTerm/:byValue)|hash3>; 3º) dictionary <k|v>
+    # => @removable_terms :: array of terms to not be considered
+
+    @@header = nil
+    @@stanzas = {terms: {}, typedefs: {}, instances: {}}
+    @@removable_terms = []
+    @@alternatives_index = {}
+    @@obsoletes = {}
+    @@structureType = nil
+    @@ancestors_index = {}
+    @@descendants_index = {}
+    @@reroot = false
+    @@dicts = {}
+
+    def self.reset
+        @@header = nil
+        @@stanzas = {terms: {}, typedefs: {}, instances: {}}
+        @@removable_terms = []
+        @@alternatives_index = {}
+        @@obsoletes = {}
+        @@structureType = nil
+        @@ancestors_index = {}
+        @@descendants_index = {}
+        @@reroot = false
+        @@dicts = {}
+    end
+
+    def self.each(att = false, only_main = true)
+        warn('stanzas terms empty') if @@stanzas[:terms].empty?
+        @@stanzas[:terms].each do |id, tags|            
+            next if only_main && (@@alternatives_index.include?(id) || @@obsoletes.include?(id))
+            if att
+               yield(id, tags)
+            else
+               yield(id)
+            end
+        end
+    end
+
+	def self.load(ontology, file, build: true, black_list: [], extra_dicts: [])
+        reset # Clean class variables to avoid the mix of several obo loads
+        @@removable_terms = black_list
+		_, header, stanzas = self.load_obo(file)
+        @@header = header
+        @@stanzas = stanzas
+        self.remove_black_list_terms() if !@@removable_terms.empty?
+        self.build_index(ontology, extra_dicts: extra_dicts) if build
+	end
+
+	# Class method to load an OBO format file (based on OBO 1.4 format). Specially focused on load
+    # the Header, the Terms, the Typedefs and the Instances.
+    # ===== Parameters
+    # +file+:: OBO file to be loaded
+    # ===== Returns 
+    # Hash with FILE, HEADER and STANZAS info
+    def self.load_obo(file) 
+        raise("File is not defined") if file.nil?
+        # Data variables
+        header = ''
+        stanzas = {terms: {}, typedefs: {}, instances: {}}
+        # Auxiliar variables
+        infoType = 'Header'
+        currInfo = []
+        stanzas_flags = %w[[Term] [Typedef] [Instance]]
+        # Read file
+        File.open(file).each do |line|
+            line.chomp!
+            next if line.empty?
+            fields = line.split(':', 2)
+            # Check if new instance is found
+            if stanzas_flags.include?(line)
+                header = self.process_entity(header, infoType, stanzas, currInfo)
+                # Update info variables
+                currInfo = []
+                infoType = line.gsub!(/[\[\]]/, '')
+                next
+            end
+            # Concat info
+            currInfo << fields  
+        end
+        # Store last loaded info
+        header = self.process_entity(header, infoType, stanzas, currInfo) if !currInfo.empty?
+        # Prepare to return
+        finfo = {:file => file, :name => File.basename(file, File.extname(file))}
+        return finfo, header, stanzas
+    end
+
+    # Handle OBO loaded info and stores it into correct container and format
+    # ===== Parameters
+    # +header+:: container
+    # +infoType+:: current ontology item type detected
+    # +stanzas+:: container
+    # +currInfo+:: info to be stored
+    # ===== Returns 
+    # header newly/already stored
+    def self.process_entity(header, infoType, stanzas, currInfo)
+        info = self.info2hash(currInfo)
+        # Store current info
+        if infoType.eql?('Header')
+            header = info
+        else
+            id = info[:id]
+            case infoType
+                when 'Term'
+                    stanzas[:terms][id] = info
+                when 'Typedef'
+                    stanzas[:typedefs][id] = info
+                when 'Instance'
+                    stanzas[:instances][id] = info
+            end
+        end
+        return header
+    end
+
+    # Class method to transform string with <tag : info> into hash structure
+    # ===== Parameters
+    # +attributes+:: array tuples with info to be transformed into hash format
+    # ===== Returns 
+    # Attributes stored into hash structure
+    def self.info2hash(attributes, split_char = " ! ", selected_field = 0)
+        # Load info
+        info_hash = {}
+        # Only TERMS multivalue tags (future add Typedefs and Instance)
+        # multivalue_tags = [:alt_id, :is_a, :subset, :synonym, :xref, :intersection_of, :union_of, :disjoint_from, :relationship, :replaced_by, :consider]
+        attributes.each do |tag, value|
+            value.gsub!(/{[\\\":A-Za-z0-9\/\.\-, =?&_]+} /, '') if tag == 'is_a' # To delete extra attributes (source, xref) in is_a tag of MONDO ontology
+            # Check
+            raise EncodingError, 'Info element incorrect format' if (tag.nil?) || (value.nil?)
+            # Prepare
+            tag = tag.lstrip.to_sym
+            value.lstrip!
+            value = value.split(split_char)[selected_field].to_sym if @@tags_with_trailing_modifiers.include?(tag)
+            
+            # Store
+            query = info_hash[tag]
+            if !query.nil? # Tag already exists
+                if !query.kind_of?(Array) # Check that tag is multivalue
+                    raise('Attempt to concatenate plain text with another. The tag is not declared as multivalue. [' + tag.to_s + '](' + query + ')')
+                else
+                    query << value    # Add new value to tag
+                end
+            else # New entry
+                if @@multivalue_tags.include?(tag)
+                    info_hash[tag] = [value]
+                else
+                    info_hash[tag] = value
+                end
+            end
+        end
+        self.symbolize_ids(info_hash)
+        return info_hash
+    end
+
+    def self.remove_black_list_terms()
+        @@removable_terms.each{|removableID| @@stanzas[:terms].delete(removableID)}
+    end
+
+    # Executes basic expansions of tags (alternatives, obsoletes and parentals) with default values
+    # ===== Returns 
+    # true if eprocess ends without errors and false in other cases
+    def self.build_index(ontology, extra_dicts: [])
+        self.get_index_obsoletes
+        self.get_index_alternatives
+        self.remove_obsoletes_in_terms
+        self.get_index_child_parent_relations
+        @@alternatives_index.transform_values!{|v| self.extract_id(v)}
+        @@alternatives_index.compact!
+        @@ancestors_index.each{|k,v| @@ancestors_index[k] = v.map{|t| self.extract_id(t)}.compact}
+        @@descendants_index.each{|k,v| @@descendants_index[k] = v.map{|t| self.extract_id(t)}.compact}
+        self.calc_dictionary(:name)
+        self.calc_dictionary(:synonym, select_regex: /\"(.*)\"/)
+        self.calc_ancestors_dictionary
+        extra_dicts.each do |dict_tag, extra_parameters|
+            self.calc_dictionary(dict_tag, **extra_parameters) # https://www.justinweiss.com/articles/fun-with-keyword-arguments/
+        end
+        ontology.terms = @@stanzas[:terms]
+        ontology.alternatives_index = @@alternatives_index
+        ontology.obsoletes = @@obsoletes
+        ontology.ancestors_index = @@ancestors_index
+        ontology.descendants_index = @@descendants_index
+        ontology.reroot = @@reroot
+        ontology.structureType = @@structureType
+        ontology.dicts = @@dicts
+
+    end
+
+    def self.remove_obsoletes_in_terms() # once alternative and obsolete indexes are loaded, use this to keep only working terms
+        terms = @@stanzas[:terms]
+        @@obsoletes.each do |term, val|
+            terms.delete(term)
+        end
+    end
+
+
+    # Expand obsoletes set and link info to their alternative IDs
+    # ===== Parameters
+    # +obs_tags+:: tags to be used to find obsoletes
+    # +alt_tags+:: tags to find alternative IDs (if are available)
+    # ===== Returns 
+    # true if process ends without errors and false in other cases
+    def self.get_index_obsoletes(obs_tag: @@basic_tags[:obsolete], alt_tags: @@basic_tags[:alternative])
+        each(att = true) do |id, term_tags|
+            obs_value = term_tags[obs_tag]
+            if obs_value == 'true' # Obsolete tag presence, must be checked as string
+                alt_ids = alt_tags.map{|alt| term_tags[alt]}.compact # Check if alternative value is available
+                if !alt_ids.empty?
+                    alt_id = alt_ids.first.first #FIRST tag, FIRST id 
+                    @@alternatives_index[id] = alt_id
+                end
+                @@obsoletes[id] = true
+            end
+        end
+    end
+
+    # Expand alternative IDs arround all already stored terms
+    # ===== Parameters
+    # +alt_tag+:: tag used to expand alternative IDs
+    # ===== Returns 
+    # true if process ends without errors and false in other cases
+    def self.get_index_alternatives(alt_tag: @@basic_tags[:alternative].last)
+        each(att = true) do |id, tags|
+            alt_ids = tags[alt_tag]
+            if !alt_ids.nil?
+                alt_ids = alt_ids - @@removable_terms - [id]
+                alt_ids.each do |alt_term|
+                    @@alternatives_index[alt_term] = id
+                end
+            end
+        end
+    end
+
+    # Expand parentals set. Also launch frequencies process
+    # ===== Parameters
+    # +tag+:: tag used to expand parentals
+    # ===== Returns 
+    # true if process ends without errors and false in other cases
+    def self.get_index_child_parent_relations(tag: @@basic_tags[:ancestors][0])
+        structType, parentals = self.get_related_ids_by_tag(terms: @@stanzas[:terms],
+                                                        target_tag: tag,
+                                                        reroot: @@reroot)    
+        if structType.nil? || parentals.nil?
+            raise('Error expanding parentals')
+        elsif ![:atomic,:sparse].include?(structType) # Check structure
+            structType = structType == :circular ? :circular : :hierarchical
+        end
+        @@structureType = structType 
+
+        parentals.each do |id, parents|
+            parents = parents - @@removable_terms
+            @@ancestors_index[id] = parents
+            parents.each{|anc_id| self.add2hash(@@descendants_index, anc_id, id)}
+        end
+    end
+
+
+    # Expand terms using a specific tag and return all extended terms into an array and
+    # the relationship structuture observed (hierarchical or circular). If circular structure is
+    # foumd, extended array will be an unique vector without starting term (no loops) 
+    # ===== Parameters
+    # +terms+:: set to be used to expand
+    # +target_tag+:: tag used to expand
+    # ===== Returns 
+    # A vector with the observed structure (string) and the hash with extended terms
+    def self.get_related_ids_by_tag(terms:, target_tag:, reroot: false)
+        structType = :hierarchical
+        related_ids = {}
+        terms.each do |id, tags|
+            if !tags[target_tag].nil?
+                set_structure, _ = self.get_related_ids(id, terms, target_tag, related_ids)
+                structType = :circular if set_structure == :circular # Check structure
+            end
+        end
+
+        # Check special case
+        structType = :atomic if related_ids.length <= 0
+        structType = :sparse if reroot || (related_ids.length > 0 && ((terms.length - related_ids.length ) >= 2) )
+        return structType, related_ids
+    end
+
+    # Expand a (starting) term using a specific tag and return all extended terms into an array and
+    # the relationship structuture observed (hierarchical or circular). If circular structure is
+    # foumd, extended array will be an unique vector without starting term (no loops).
+    # +Note+: we extremly recomend use get_related_ids_by_tag function instead of it (directly)
+    # ===== Parameters
+    # +start+:: term where start to expand
+    # +terms+:: set to be used to expand
+    # +target_tag+:: tag used to expand
+    # +eexpansion+:: already expanded info
+    # ===== Returns 
+    # A vector with the observed structure (string) and the array with extended terms.
+    def self.get_related_ids(start_id, terms, target_tag, related_ids = {})
+        # Take start_id term available info and already accumulated info
+        current_associations = related_ids[start_id]
+        current_associations = [] if current_associations.nil? 
+        return [:no_term,[]] if terms[start_id].nil?
+        id_relations = terms[start_id][target_tag]
+        return [:source,[]] if id_relations.nil?
+
+        struct = :hierarchical
+
+        # Study direct extensions
+        id_relations.each do |id| 
+            # Handle
+            if current_associations.include?(id) # Check if already have been included into this expansion
+                next
+                #struct = :circular # Old code that give circular status in real obo files. The apparent logic no makes sense. The change gives no error in tests.
+                # TODO: CHECK CAREFULLY THIS METHOD.
+            else
+                current_associations << id 
+                if related_ids.include?(id) # Check if current already has been expanded
+                    current_associations = current_associations | related_ids[id]
+                    if current_associations.include?(start_id) # Check circular case
+                        struct = :circular
+                        current_associations = current_associations - [id, start_id]
+                    end    
+                else # Expand
+                    related_ids[start_id] = current_associations
+                    structExp, current_related_ids = self.get_related_ids(id, terms, target_tag, related_ids) # Expand current
+                    current_associations = current_associations | current_related_ids                                     
+                    struct = :circular if structExp == :circular # Check struct
+                    if current_associations.include?(start_id) # Check circular case
+                        struct = :circular
+                        current_associations.delete(start_id)
+                    end
+                end
+            end
+        end
+        related_ids[start_id] = current_associations
+
+        return struct, current_associations
+    end
+
+    # Calculates :is_a dictionary 
+    def self.calc_ancestors_dictionary
+        self.calc_dictionary(:is_a, self_type_references: true, multiterm: true)
+    end
+
+    # Generate a bidirectinal dictionary set using a specific tag and terms stanzas set
+    # This functions stores calculated dictionary into @dicts field.
+    # This functions stores first value for multivalue tags
+    # This function does not handle synonyms for byValue dictionaries
+    # ===== Parameters
+    # +tag+:: to be used to calculate dictionary
+    # +select_regex+:: gives a regfex that can be used to modify value to be stored
+    # +store_tag+:: flag used to store dictionary. If nil, mandatory tag given will be used
+    # +multiterm+:: if true, byValue will allows multi-term linkage (array)
+    # +self_type_references+:: if true, program assumes that refrences will be between Ontology terms, and it term IDs will be checked
+    # ===== Return
+    # hash with dict data. And stores calcualted bidirectional dictonary into dictionaries main container
+    def self.calc_dictionary(tag, select_regex: nil, store_tag: nil, multiterm: false, self_type_references: false)
+        tag = tag.to_sym
+        store_tag = tag if store_tag.nil?
+
+        byTerm = {}
+        byValue = {}
+        # Calc per term
+        each(att = true, only_main = false) do |term, tags|
+            referenceTerm = term
+            queryTag = tags[tag]
+            if !queryTag.nil?
+                # Pre-process
+                if !select_regex.nil?
+                    if queryTag.kind_of?(Array)
+                        queryTag = queryTag.map{|value| value.scan(select_regex).first}
+                        queryTag.flatten!
+                    else
+                        queryTag = queryTag.scan(select_regex).first
+                    end
+                    queryTag.compact!
+                end
+                if queryTag.kind_of?(Array) # Store
+                    if !queryTag.empty?
+                        if byTerm.include?(referenceTerm)
+                            byTerm[referenceTerm] = (byTerm[referenceTerm] + queryTag).uniq
+                        else
+                            byTerm[referenceTerm] = queryTag
+                        end
+                        if multiterm
+                            queryTag.each do |value|
+                                byValue[value] = [] if byValue[value].nil? 
+                                byValue[value] << referenceTerm
+                            end                                
+                        else
+                            queryTag.each{|value| byValue[value] = referenceTerm}
+                        end
+                    end
+                else
+                    if byTerm.include?(referenceTerm)
+                        byTerm[referenceTerm] = (byTerm[referenceTerm] + [queryTag]).uniq
+                    else
+                        byTerm[referenceTerm] = [queryTag]
+                    end
+                    if multiterm
+                        byValue[queryTag] = [] if byValue[queryTag].nil?
+                        byValue[queryTag] << referenceTerm
+                    else
+                        byValue[queryTag] = referenceTerm
+                    end
+                end
+            end
+        end
+        
+        # Check self-references
+        if self_type_references
+            byTerm.map do |term, references|
+                corrected_references = references.map do |t|
+                    checked = self.extract_id(t)
+                    if checked.nil?
+                        t
+                    else
+                        byValue[checked] = byValue.delete(t) if checked != t && byValue[checked].nil? # Update in byValue
+                        checked
+                    end
+                end
+                byTerm[term] = corrected_references.uniq
+            end
+        end
+
+        # Check order
+        byTerm.map do |term,values|
+            if self.exists?(term)
+                referenceValue = @@stanzas[:terms][term][tag]
+                if !referenceValue.nil?
+                    if !select_regex.nil?
+                        if referenceValue.kind_of?(Array)
+                            referenceValue = referenceValue.map{|value| value.scan(select_regex).first}
+                            referenceValue.flatten!
+                        else
+                            referenceValue = referenceValue.scan(select_regex).first
+                        end
+                        referenceValue.compact!
+                    end
+                    if self_type_references
+                        if referenceValue.kind_of?(Array)
+                            aux = referenceValue.map{|t| self.extract_id(t)}
+                        else
+                            aux = self.extract_id(referenceValue)
+                        end
+                        aux.compact! unless aux.nil?
+                        referenceValue = aux unless aux.nil?
+                    end
+                    referenceValue = [referenceValue] if !referenceValue.kind_of?(Array)
+                    byTerm[term] = referenceValue + (values - referenceValue)
+                end
+            end
+        end
+
+        # Store
+        dict = {byTerm: byTerm, byValue: byValue}
+        @@dicts[store_tag] = dict
+        return dict
+    end
+
+    # Check if a given ID is stored as term into this object
+    # ===== Parameters
+    # +id+:: to be checked 
+    # ===== Return
+    # True if term is allowed or false in other cases
+    def self.exists? id
+        return @@stanzas[:terms].include?(id)
+    end
+
+    # Check if a term given is marked as obsolete
+    def self.is_obsolete? term
+        return @@obsoletes.include?(term)
+    end
+
+    # Check if a term given is marked as alternative
+    def self.is_alternative? term
+        return @@alternatives_index.include?(term)
+    end
+
+    # This method assumes that a text given contains an allowed ID. And will try to obtain it splitting it
+    # ===== Parameters
+    # +text+:: to be checked 
+    # ===== Return
+    # The correct ID if it can be found or nil in other cases
+    def self.extract_id(text, splitBy: ' ')
+        if self.exists?(text)
+            return text
+        else
+            splittedText = text.to_s.split(splitBy).first.to_sym
+            return self.exists?(splittedText) ? splittedText : nil
+        end
+    end
+
+
+    private
+
+    def self.add2hash(hash, key, val)
+        query = hash[key]
+        if query.nil?
+            hash[key] = [val]
+        else
+            query << val
+        end
+    end    
+
+end

data/lib/semtools/sim_handler.rb

@@ -92,7 +92,7 @@ end
 # +charsToRemove+:: char (or chars set) to be removed from texts to be compared
 # +unique+:: boolean flag which indicates if repeated elements must be removed
 # Returns the similarity percentage for all elements into array
-def similitude_network(items_array, splitChar = ";", charsToRemove = "", unique = false)
+def similitude_network(items_array, splitChar: ";", charsToRemove: "", unique: false)
   # Special cases
   return nil if items_array.nil?
   return nil if !items_array.is_a? Array

data/lib/semtools/version.rb

@@ -1,3 +1,3 @@
 module Semtools
-  VERSION = "0.1.6"
+  VERSION = "0.1.9"
 end

data/lib/semtools.rb

@@ -1,7 +1,9 @@
 require "semtools/version"
 require "semtools/sim_handler"
-require "semtools/math_methods"
 require "semtools/ontology"
+require "semtools/parsers/file_parser"
+require "semtools/parsers/json_parser"
+require "semtools/parsers/oboparser"
 
 module Semtools
   # Your code goes here...

data/semtools.gemspec

@@ -9,7 +9,7 @@ Gem::Specification.new do |spec|
   spec.authors       = ["seoanezonjic", "fmjabato"]
   spec.email         = ["seoanezonjic@hotmail.com", "fmjabato@gmail.com"]
 
-  spec.summary       = %q{Gem to handle semantic based calculations in text and defined ontologies as GO or HPO.}
+  spec.summary       = %q{DEPRECATED PROJECT. MIGRATED TO PYTHON: https://github.com/seoanezonjic/py_semtools. Gem to handle semantic based calculations in text and defined ontologies as GO or HPO.}
   spec.description   = %q{This gem allows to perform ontology based operations and calculation of Semantic similarity and information coefficient using different implementations.}
   spec.homepage      = "https://github.com/seoanezonjic/semtools"
   spec.license       = "MIT"
@@ -31,6 +31,8 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
   
   spec.add_dependency "text"
+  spec.add_dependency "down"
+  spec.add_dependency "expcalc"
 
   spec.add_development_dependency "rake"
   spec.add_development_dependency "rspec"