phenoscaperb 0.1.0

data/lib/phenoscaperb/Genes.rb

@@ -0,0 +1,83 @@
+require "faraday"
+require 'faraday_middleware'
+require "multi_json"
+require "phenoscaperb/error"
+require "phenoscaperb/request"
+require "phenoscaperb/constants"
+require 'phenoscaperb/helpers/configuration'
+require 'phenoscaperb/faraday'
+require 'phenoscaperb/utils'
+
+##
+# Phenoscape::Genes
+#
+# Class to perform HTTP requests to the Phenoscape API
+module Phenoscape
+  module Genes
+    ##
+    # Return detail info for a given gene
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] a gene IRI
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      ge = Phenoscape::Genes
+    #      ge.gene(iri: "http://www.informatics.jax.org/marker/MGI:104842")
+    def self.gene(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("gene", opts, verbose, options, nil).perform
+    end
+
+    # Search for genes by gene symbol.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param text [String] the input text to search
+    # @param taxon [String] NCBI IRI for taxon
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      ge = Phenoscape::Genes
+    #      ge.search(text: "coil")
+    def self.search(text:, taxon: nil, verbose: nil, options: nil)
+
+      arguments = { text: text, taxon: taxon }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("gene/search", opts, verbose, options, nil).perform
+    end
+
+    # Search for classes from a particular ontology.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] anatomical entity IRI
+    # @param quality [String] uality IRI
+    # @param parts [boolean] whether to include phenotypes of parts of the entity. default: false
+    # @param historical_homologs [boolean] whether to include historical homologs of the entity in the query. default: false
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      ge = Phenoscape::Genes
+    #      ge.affecting_entity_phenotype(iri: "http://purl.obolibrary.org/obo/UBERON_0003097")
+    def self.affecting_entity_phenotype(iri:, quality: nil, parts: nil, historical_homologs: nil,
+        serial_homologs: nil, limit: nil, offset: nil, total: nil, verbose: nil, options: nil)
+
+      arguments = { iri: iri, quality: quality, parts: parts, 
+        historical_homologs: historical_homologs, serial_homologs: serial_homologs, 
+        limit: limit, offset: offset, total: total }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("gene/affecting_entity_phenotype", opts, verbose, options, nil).perform
+    end
+
+  end
+end

data/lib/phenoscaperb/Ontotrace.rb

@@ -0,0 +1,46 @@
+require "faraday"
+require 'faraday_middleware'
+require "multi_json"
+require "xml/to/hash"
+require "phenoscaperb/error"
+require "phenoscaperb/request"
+require "phenoscaperb/constants"
+require 'phenoscaperb/helpers/configuration'
+require 'phenoscaperb/faraday'
+require 'phenoscaperb/utils'
+
+##
+# Phenoscape::Ontotrace
+#
+# Module to perform HTTP requests to the Phenoscape Ontotrace API
+module Phenoscape
+  module Ontotrace
+    ##
+    # Generate matrix of inferred presence/absence associations for anatomical structures subsumed by the provided entity class expression, for any taxa within the provided taxon class expression. Returns a NeXML-format evolutionary character matrix.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param taxon [String] Taxonomic class expression in OWL Manchester syntax
+    # @param entity [String] Anatomical class expression in OWL Manchester syntax
+    # @param variable_only [boolean] whether to restrict the matrix to characters with both ‘present’ and ‘absent’ values in the matrix. default: true
+    # @param ret [String] what to return, one of hash (default), text (raw xml [nexml] as text), or noko (class 'Nokogiri::XML::Document')
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      onto = Phenoscape::Ontotrace
+    #      onto.ontotrace(taxon: "<http://purl.obolibrary.org/obo/VTO_0058051>", entity: "<http://purl.obolibrary.org/obo/BFO_0000050>")
+    #      onto.ontotrace(taxon: "<http://purl.obolibrary.org/obo/VTO_0058051>", entity: "<http://purl.obolibrary.org/obo/BFO_0000050>", variable_only: false)
+    #.      
+    #.     # this one times out
+    #      # onto.ontotrace(taxon: "http://purl.obolibrary.org/obo/VTO_0033622", entity: "http://purl.obolibrary.org/obo/UBERON_0003097")
+    def self.ontotrace(taxon:, entity:, variable_only: nil, ret: "hash", verbose: nil, options: nil)
+
+      arguments = { taxon: taxon, entity: entity, variable_only: variable_only }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("ontotrace", opts, verbose, options, ret, "application/xml").perform
+    end
+    
+  end
+end

data/lib/phenoscaperb/Studies.rb

@@ -0,0 +1,102 @@
+require "faraday"
+require 'faraday_middleware'
+require "multi_json"
+require "phenoscaperb/error"
+require "phenoscaperb/request"
+require "phenoscaperb/constants"
+require 'phenoscaperb/helpers/configuration'
+require 'phenoscaperb/faraday'
+require 'phenoscaperb/utils'
+
+##
+# Phenoscape::Studies
+#
+# Class to perform HTTP requests to the Phenoscape API
+module Phenoscape
+  module Studies
+    ##
+    # Return studies containing taxa which are members of the optional input taxon expression and are have annotated phenotypes which are relevant to the optional input entity expression.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param taxon [String] Taxonomic class expression in OWL Manchester syntax
+    # @param entity [String] Anatomical class expression in OWL Manchester syntax
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      st = Phenoscape::Studies
+    #      st.query(taxon: "<http://purl.obolibrary.org/obo/VTO_0037519>", entity: "<http://purl.obolibrary.org/obo/UBERON_0001703>")
+    def self.query(taxon:, entity:, verbose: nil, options: nil)
+
+      arguments = { taxon: taxon, entity: entity }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("study/query", opts, verbose, options, nil).perform
+    end
+
+    # Taxa annotated within a study
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] the study IRI
+    # @param limit [Integer] maximum results to return
+    # @param offset [Integer] index of results to begin returning
+    # @param total [boolean] whether to return the total result count rather than the results
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Studies
+    #      st.taxa(iri: "http://www.pfeilbook.com/07pala/pdf/2_48d15.pdf")
+    def self.taxa(iri:, limit: 20, offset: 0, total: false, verbose: nil, options: nil)
+
+      arguments = { iri: iri, limit: limit, offset: offset, total: total }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("study/taxa", opts, verbose, options, nil).perform
+    end
+
+    # Character states and their phenotypes annotated within a study
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] the study IRI
+    # @param limit [Integer] maximum results to return
+    # @param offset [Integer] index of results to begin returning
+    # @param total [boolean] whether to return the total result count rather than the results
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Studies
+    #      st.phenotypes(iri: "http://www.pfeilbook.com/07pala/pdf/2_48d15.pdf")
+    def self.phenotypes(iri:, limit: 20, offset: 0, total: false, verbose: nil, options: nil)
+
+      arguments = { iri: iri, limit: limit, offset: offset, total: total }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("study/phenotypes", opts, verbose, options, nil).perform
+    end
+
+    # Return a data matrix in NeXML format containing the data for a given study.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] the study IRI
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Studies
+    #      st.matrix(iri: "http://www.pfeilbook.com/07pala/pdf/2_48d15.pdf")
+    def self.matrix(iri:, ret: "hash", verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("study/matrix", opts, verbose, options, ret, "text/plain").perform
+    end
+    
+  end
+end

data/lib/phenoscaperb/Taxa.rb

@@ -0,0 +1,115 @@
+require "faraday"
+require 'faraday_middleware'
+require "multi_json"
+require "phenoscaperb/error"
+require "phenoscaperb/request"
+require "phenoscaperb/constants"
+require 'phenoscaperb/helpers/configuration'
+require 'phenoscaperb/faraday'
+require 'phenoscaperb/utils'
+
+##
+# Phenoscape::Taxa
+#
+# Class to perform HTTP requests to the Phenoscape API
+module Phenoscape
+  module Taxa
+    ##
+    # Return detail info for a given taxon. Currently this is the label, extinction status, and an optional rank.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] a taxon IRI
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Taxa
+    #      tax.taxon(iri: "http://purl.obolibrary.org/obo/VTO_0067193")
+    def self.taxon(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("taxon", opts, verbose, options, nil).perform
+    end
+
+    # Retrieve all taxa with a given taxonomic rank, within the given super-taxon. Ranks are term IRIs from the taxonomic rank ontology such as order, family, genus, species.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param rank [String] a rank IRI
+    # @param in_taxon [String] a taxon IRI
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Taxa
+    #      tax.taxon_with_rank(rank: "http://purl.obolibrary.org/obo/TAXRANK_0000003", in_taxon: "http://purl.obolibrary.org/obo/VTO_0000009")
+    def self.taxon_with_rank(rank:, in_taxon:, verbose: nil, options: nil)
+
+      arguments = { rank: rank, in_taxon: in_taxon }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("taxon/with_rank", opts, verbose, options, nil).perform
+    end
+
+    # Retrieve taxa with annotated phenotypes related to the given anatomical entity or quality.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param entity [String] Anatomical class expression in OWL Manchester syntax
+    # @param quality [String] Quality class expression in OWL Manchester syntax
+    # @param in_taxon [String] A taxon group to limit the results
+    # @param parts [boolean] whether to include phenotypes of parts of the entity. default: false
+    # @param historical_homologs [boolean] whether to include historical homologs of the entity in the query. default: false
+    # @param serial_homologs [boolean] whether to include serial homologs of the entity in the query. default: false
+    # @param total [boolean] whether to return the total result count rather than the results. default: false
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Taxa
+    #      tax.with_phenotype(entity: "<http://purl.obolibrary.org/obo/UBERON_0008897>", quality: "<http://purl.obolibrary.org/obo/PATO_0000052>", in_taxon: "http://purl.obolibrary.org/obo/VTO_0059975")
+    #      tax.with_phenotype(entity: "<http://purl.obolibrary.org/obo/UBERON_0008897>", quality: "<http://purl.obolibrary.org/obo/PATO_0000052>", in_taxon: "http://purl.obolibrary.org/obo/VTO_0059975", total: true)
+    def self.with_phenotype(entity: nil, quality: nil, in_taxon: nil, parts: false, historical_homologs: false,
+        serial_homologs: false, limit: 20, offset: 0, total: false, verbose: nil, options: nil)
+
+      arguments = { entity: entity, quality: quality, in_taxon: in_taxon, parts: parts, 
+        historical_homologs: historical_homologs, serial_homologs: serial_homologs, 
+        limit: limit, offset: offset, total: total }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("taxon/with_phenotype", opts, verbose, options, nil).perform
+    end
+
+    # Retrieve taxa annotations
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param entity [String] Anatomical class expression
+    # @param quality [String] Quality class expression
+    # @param in_taxon [String] A taxon group to limit the results
+    # @param parts [boolean] whether to include phenotypes of parts of the entity. default: false
+    # @param historical_homologs [boolean] whether to include historical homologs of the entity in the query. default: false
+    # @param serial_homologs [boolean] whether to include serial homologs of the entity in the query. default: false
+    # @param total [boolean] whether to return the total result count rather than the results. default: false
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tax = Phenoscape::Taxa
+    #      tax.annotations(entity: "http://purl.obolibrary.org/obo/UBERON_0001703", quality: "http://purl.obolibrary.org/obo/PATO_0000052", in_taxon: "http://purl.obolibrary.org/obo/VTO_0037519", parts: true, historical_homologs: false, serial_homologs: false, limit: 20, offset: 0, total: true)
+    def self.annotations(entity: nil, quality: nil, in_taxon: nil, parts: false, historical_homologs: false,
+        serial_homologs: false, limit: 20, offset: 0, total: false, verbose: nil, options: nil)
+
+      arguments = { entity: entity, quality: quality, in_taxon: in_taxon, parts: parts, 
+        historical_homologs: historical_homologs, serial_homologs: serial_homologs, 
+        limit: limit, offset: offset, total: total }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("taxon/annotations", opts, verbose, options, nil).perform
+    end
+    
+  end
+end

data/lib/phenoscaperb/Terms.rb

@@ -0,0 +1,200 @@
+require "faraday"
+require 'faraday_middleware'
+require "multi_json"
+require "phenoscaperb/error"
+require "phenoscaperb/request"
+require "phenoscaperb/constants"
+require 'phenoscaperb/helpers/configuration'
+require 'phenoscaperb/faraday'
+require 'phenoscaperb/utils'
+
+##
+# Phenoscape::Terms
+#
+# Class to perform HTTP requests to the Phenoscape API
+module Phenoscape
+  module Terms
+    ##
+    # Return detail info for a given term. Currently this is the label and an optional definition.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] a term IRI
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.term(iri: "http://purl.obolibrary.org/obo/UBERON_0011618")
+    def self.term(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term", opts, verbose, options, nil).perform
+    end
+
+    # Search for terms in the KB by text match on a property value.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param string [String] the input text to search
+    # @param type [String] the type of term to search for, e.g. http://www.w3.org/2002/07/owl#Class
+    # @param property [String] relation between term and text
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.search(text: "fin")
+    def self.search(text:, type: nil, property: nil, verbose: nil, options: nil)
+
+      arguments = { text: text, type: type, property: property }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/search", opts, verbose, options, nil).perform
+    end
+
+    # Search for classes from a particular ontology.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param text [String] the input text to search
+    # @param definedBy [String] the ontology identifier IRI in which the search terms are defined, e.g. http://purl.obolibrary.org/obo/uberon.owl
+    # @param limit [integer] limit records
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.search_classes(text: "fin", definedBy: "??")
+    def self.search_classes(text:, definedBy:, limit: nil, verbose: nil, options: nil)
+
+      arguments = { text: text, definedBy: definedBy, limit: limit }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/search_classes", opts, verbose, options, nil).perform
+    end
+
+    # Retrieve a label for a given term IRI.
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] a taxon IRI
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.label(iri: "http://purl.obolibrary.org/obo/UBERON_0011618")
+    def self.label(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/label", opts, verbose, options, nil).perform
+    end
+
+    # Retrieve a label for each term IRI in a list
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iris [String] one or more taxon IRIs
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.labels(iris: [
+    #        "http://purl.obolibrary.org/obo/UBERON_0011618"
+    #      ])
+    def self.labels(iris:, verbose: nil, options: nil)
+
+      arguments = { iris: iris }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/labels", opts, verbose, options, nil).perform
+    end
+
+    # Return direct superclasses, direct subclasses, and equivalent classes of a given term
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] one or more taxon IRIs
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.classification(iri: "http://purl.obolibrary.org/obo/UBERON_0011618")
+    def self.classification(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/classification", opts, verbose, options, nil).perform
+    end
+
+    # Return all ancestor superclasses of a given term
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] one or more taxon IRIs
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.all_ancestors(iri: "http://purl.obolibrary.org/obo/UBERON_0011618")
+    def self.all_ancestors(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/all_ancestors", opts, verbose, options, nil).perform
+    end
+
+    # Return all descendant subclasses of a given term
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iri [String] one or more taxon IRIs
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.all_descendants(iri: "http://purl.obolibrary.org/obo/UBERON_0011618")
+    def self.all_descendants(iri:, verbose: nil, options: nil)
+
+      arguments = { iri: iri }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/all_descendants", opts, verbose, options, nil).perform
+    end
+
+    # Return all descendant subclasses of a given term
+    #
+    # @!macro phenoscape_params
+    # @!macro phenoscape_options
+    # @param iris [String] one or more taxon IRIs
+    # @param definedBy [String] the ontology identifier IRI in which the search terms are defined, e.g. http://purl.obolibrary.org/obo/uberon.owl
+    # @return [Hash] A hash
+    #
+    # @example
+    #      require 'phenoscaperb'
+    #
+    #      tm = Phenoscape::Terms
+    #      tm.least_common_subsumers(
+    #         iris: "http://purl.obolibrary.org/obo/UBERON_0011618",
+    #.        definedBy: "??"
+    #      )
+    def self.least_common_subsumers(iris:, definedBy:, verbose: nil, options: nil)
+
+      arguments = { iris: iris, definedBy: definedBy }.tostrings
+      opts = arguments.delete_if { |k, v| v.nil? }
+      Request.new("term/least_common_subsumers", opts, verbose, options, nil).perform
+    end
+    
+  end
+end