diff options
Diffstat (limited to 'reach_reports/reach_persistance.rb')
| -rwxr-xr-x | reach_reports/reach_persistance.rb | 1216 |
1 files changed, 0 insertions, 1216 deletions
diff --git a/reach_reports/reach_persistance.rb b/reach_reports/reach_persistance.rb deleted file mode 100755 index 1226d95..0000000 --- a/reach_reports/reach_persistance.rb +++ /dev/null @@ -1,1216 +0,0 @@ - -['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types', 'dm-migrations', 'dm-validations' ].each{|lib| require lib } -db_dir = File.join(File.join(ENV['HOME'], ".opentox"), "db") -FileUtils.mkdir_p db_dir -DataMapper::setup(:default, "sqlite3://#{db_dir}/reach_reports.sqlite3") - -DataMapper::Model.raise_on_save_failure = true - -module REXML - - class Element - def self.find_or_create(parent_node, name) - if parent_node.elements[name] - parent_node.elements[name] - else - node = Element.new(name) - parent_node << node - node - end - end - end - - class TextElement < Element - def initialize(name, text) - super(name) - self.text = text - end - - def self.find_or_create(parent_node, name, text) - elem = Element.find_or_create(parent_node, name) - elem.text = text - elem - end - end -end - - -class Symbol - - XML_ALIAS = { - :qsar_identifier => "QSAR_identifier", :qsar_title => "QSAR_title", :qsar_software => "QSAR_software", - :qsar_models => "QSAR_models", :qsar_general_information => "QSAR_General_information", - :qsar_endpoint => "QSAR_Endpoint", :qmrf_author => "qmrf_authors", :qsar_algorithm => "QSAR_Algorithm", - :qsar_applicability_domain => "QSAR_Applicability_domain", :qsar_robustness => "QSAR_Robustness", - :qsar_predictivity => "QSAR_Predictivity", :qsar_interpretation => "QSAR_Interpretation", - :qsar_miscellaneous => "QSAR_Miscelaneous", :qmrf_summary => "QMRF_Summary", :qmrf_number => "QMRF_number" } - - def xml_alias - XML_ALIAS[self] ? XML_ALIAS[self] : self.to_s - end -end - -class DataMapper::Associations::OneToMany::Relationship - def get_child_model - @child_model - end -end - -module DataMapper::Resource - - def association_class( property ) - relationship = relationships[property] - raise "no relationship found for "+property.to_s+" "+relationships.inspect unless relationship - raise "not a many-to-one or one-to-one association for "+property.to_s+" "+relationship.inspect unless - relationship.is_a?(DataMapper::Associations::OneToMany::Relationship) or - relationship.is_a?(DataMapper::Associations::OneToOne::Relationship) - relationship.get_child_model - end - - def from_xml(node) - - raise "node is nil ("+self.class.to_s+".from_xml)" unless node - #puts "FROM xml: "+self.class.to_s #+", NODE: "+node.to_s - - dbg_check = { :attributes => Set.new(), :nodes => Set.new(), :subnodes => Set.new() } - - xml_infos.each do |xml_info| - - if xml_info.is_a?(ReachReports::TextNodeProperty) - text_node = node.elements[ xml_info.xml_prop ] - raise "node not found: "+ xml_info.xml_prop+" ("+self.class.to_s+".from_xml)" unless text_node - self.send( xml_info.prop.to_s+"=", text_node.text ) - dbg_check[:nodes] << text_node.name - - elsif xml_info.is_a?(ReachReports::CatalogReference) - root_node = node.elements[ xml_info.xml_prop ] - raise "node not found: "+ xml_info.xml_prop+" ("+self.class.to_s+".from_xml)" unless root_node - dbg_check[:nodes] << root_node.name - - self.send(xml_info.prop).each{ |s| s.destroy } if self.send(xml_info.prop) - self.send(xml_info.prop).clear() #otherwise the content is tmp still here - - catalog_node = $catalogs_node.elements[xml_info.catalog_name] - - root_node.each_element(xml_info.catalog_element+"_ref") do |n| - ref = nil - catalog_node.each_element_with_attribute("id", n.attribute("idref").to_s) do |e| - ref = e - break - end - raise "referenced node not found for "+xml_info.xml_prop+" in catalog "+xml_info.catalog_name+" ref-node was "+n.to_s unless ref - dbg_check[:subnodes] << n - - entry = self.association_class(xml_info.prop).new - entry.from_xml( ref ) - self.send(xml_info.prop) << entry - end - - elsif xml_info.is_a?(ReachReports::AttributeProperty) - #puts "attr "+xml_info.prop.to_s - self.send(xml_info.prop.to_s+"=", node.attribute(xml_info.xml_prop)) - dbg_check[:attributes] << xml_info.prop - - elsif xml_info.is_a?(ReachReports::TextSubnodeProperty) - parent_node = node.elements[ xml_info.parent_prop.xml_alias ] - raise "parent node not found: '"+ xml_info.parent_prop.xml_alias+"' ("+self.class.to_s+".from_xml)" unless parent_node - text_node = parent_node.elements[ xml_info.xml_prop ] - raise "node not found: "+ xml_info.xml_prop+" ("+self.class.to_s+".from_xml)" unless text_node - self.send( xml_info.prop.to_s+"=", text_node.text ) - dbg_check[:nodes] << parent_node.name - dbg_check[:subnodes] << text_node - - elsif xml_info.is_a?(ReachReports::SingleAttributeNodeProperty) - attr_node = node.elements[ xml_info.xml_prop ] - self.send(xml_info.prop.to_s+"=", attr_node.attribute(xml_info.attribute)) - dbg_check[:nodes] << attr_node.name - - elsif xml_info.is_a?(ReachReports::AttributeNodeProperty) - attr_node = node.elements[ xml_info.xml_prop ] - entry = self.association_class( xml_info.prop ).new - entry.from_xml(attr_node) - self.send(xml_info.prop.to_s+"=",entry) - dbg_check[:nodes] << attr_node.name - - elsif xml_info.is_a?(ReachReports::AttributeSubNodeListProperty) - - parent_node = node.elements[ xml_info.parent_prop.xml_alias ] - raise "parent node not found: '"+ xml_info.parent_prop.xml_alias+"' ("+self.class.to_s+".from_xml)" unless parent_node - #puts "parent node "+xml_info.parent_prop.xml_alias - prop_node = parent_node.elements[ xml_info.xml_prop ] - if prop_node - #puts "prop node "+xml_info.xml_prop.to_s - prop_node.each_element do |n| - #puts "elem node "+n.name.to_s - raise "illegal node '"+n.name.to_s+"' should be '"+xml_info.list_element.to_s+"'" unless n.name==xml_info.list_element.to_s - entry = self.association_class( xml_info.prop ).new - entry.from_xml( n ) - self.send(xml_info.prop) << entry - end - dbg_check[:subnodes] << prop_node - end - dbg_check[:nodes] << parent_node.name - - else - raise "type not supported yet: "+xml_info.inspect - end - end - - ##raise "not a qsar_identifier" unless qsar_identifier.is_a?(QsarIdentifier) - - #puts node.elements.inspect - #puts "there we go: "+qsar_identifier.qsar_software.to_s - #qsar_identifier.qsar_software = QsarSoftware.new - #puts "there we go: "+qsar_identifier.qsar_software.to_s - #exit - - # if defined?(self.class.text_properties) -# self.class.text_properties.each do |p| -# puts "set "+p.to_s -# raise "node not found: "+p.xml_alias.to_s+" ("+self.class.to_s+".from_xml)" unless node.elements[p.xml_alias] -# #puts "set "+p.to_s+" to: "+node.elements[p.xml_alias].text.to_s -# self.send(p.to_s+"=", node.elements[p.xml_alias].text) -# #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text -# dbg_check[:nodes] << node.elements[p.xml_alias].name -# end -# - - -# if defined?(self.class.subsection_properties) -# self.class.subsection_properties.each do |section_p, subsection_p| -# #puts "set "+p.to_s -# #raise "node not found: "+p.xml_alias.to_s+" ("+self.class.to_s+".from_xml)" unless node.elements[p.xml_alias] -# #puts "set "+p.to_s+" to: "+node.elements[p.xml_alias].text.to_s -# section = node.elements[section_p.xml_alias] -# subsection = section.elements[subsection_p.xml_alias] -# self.send(subsection_p.to_s+"=", subsection.text) -# -# dbg_check[:nodes] << section.name -# dbg_check[:subnodes] << subsection -# -# #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text -# #dbg_check[:text_nodes] << node.elements[p.xml_alias].name -# end -# end - -# if defined?(self.class.attribute_properties) -# self.class.attribute_properties.each do |p| -# puts "read attribute "+p.to_s -# #self.update(p => node.attribute(p.xml_alias)) -# self.send(p.to_s+"=", node.attribute(p.xml_alias)) -# dbg_check[:attributes] << p -# #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text -# end -# end - - #qsar_identifier.qsar_title = node.elements["qsar_title".xml_alias].text - #qsar_identifier.qsar_models = node.elements["qsar_models".xml_alias].text - - - - ignore_attribs =[ "id", "name", "help", "chapter" ] - node.attributes.each do |a,v| - unless (ignore_attribs.include?(a.to_s)) || dbg_check[:attributes].include?(a.to_sym) - raise "not handled : attribute '"+a.to_s+"' -> '"+v.to_s+"'" + - "\n("+self.class.to_s+".from_xml)" + - "\nchecked:\n"+dbg_check[:attributes].to_yaml+ - "\nnode-attribtues:\n"+node.attributes.to_yaml - end - end - - node.each_element do |n| -# if n.text!=nil and n.text.to_s.size>0 and -# !dbg_check[:text_nodes].include?(n.name) and -# (!dbg_check[:catalog_nodes].has_key?(n.name)) - - valid = dbg_check[:nodes].include?(n.name) - if (valid) - refs = dbg_check[:subnodes] - #puts "sub "+refs.inspect - n.each_element do |nn| - #puts "lookin for ref "+nn.to_s - unless refs.include?(nn) - valid = false - break - end - end - end - - unless valid - raise puts "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\nnot handled node : "+n.to_s+ - "\n("+self.class.to_s+".from_xml)" -# raise "not handled node : "+n.to_s+ -# "\n("+self.class.to_s+".from_xml)" + -# "\nchecked text nodes:\n"+dbg_check[:text_nodes].to_yaml+ -# "\nchecked catalog nodes:\n"+dbg_check[:catalog_nodes].to_yaml+ -# "\nnode-attribtues:\n"+n.attributes.to_yaml - end - end - - - #self.save! - #self.reload -# unless self.save -# self.errors.each do |e| -# puts "Error: "+e.to_s -# end -# end - #puts "self id: "+self.id.to_s - -# qsar_identifier.qsar_software.each{ |s| s.destroy } if qsar_identifier.qsar_software -# qsar_identifier.qsar_software.update({}) #otherwise the content is tmp still here -# -# catalog_node = $catalogs_node.elements["software_catalog"] -# -# node.elements[:qsar_software.xml_alias].each_element do |n| -# -# puts "reading software ref "+n.to_s -# ref = nil -# catalog_node.each_element_with_attribute("id", n.attribute("idref").to_s) do |e| -# ref = e -# break -# end -# software = QsarSoftware.new -# QsarSoftware.from_xml( software, ref ) -# qsar_identifier.qsar_software << software -# end -# #qsar_identifier.qsar_software = QsarSoftware.new unless qsar_identifier.qsar_software -# #QsarSoftware.from_xml( qsar_identifier.qsar_software, node.elements["qsar_software".xml_alias] ) - - end - - def to_XML(node, chapter=nil ) - - xml_infos.each do |xml_info| - if xml_info.is_a?(ReachReports::TextNodeProperty) - new_node = REXML::TextElement.find_or_create(node, xml_info.xml_prop,self.send(xml_info.prop)) - - elsif xml_info.is_a?(ReachReports::CatalogReference) - - new_node = REXML::Element.find_or_create( node, xml_info.xml_prop ) - catalog_node = $catalogs_node.elements[ xml_info.catalog_name ] - - self.send(xml_info.prop.to_s+"=",[self.association_class(xml_info.prop).new]) unless self.send(xml_info.prop) and self.send(xml_info.prop).size>0 - - self.send( xml_info.prop ).each do |elem| - elem_node = REXML::Element.new(xml_info.catalog_element ) - elem.to_XML( elem_node ) - # if not saved, i.e. the element was only created for a complete xml, count elements in catalog for id - element_id = xml_info.catalog_element+"_"+(elem.id ? elem.id.to_s : (catalog_node.elements.size+1).to_s) - elem_node.add_attribute("id",element_id) - catalog_node << elem_node - - ref_node = REXML::Element.new(xml_info.catalog_element+"_ref" ) - ref_node.add_attributes("idref"=>element_id,"catalog"=>xml_info.catalog_name) - new_node << ref_node - end - - elsif xml_info.is_a?(ReachReports::AttributeProperty) - node.add_attribute( xml_info.xml_prop, self.send(xml_info.prop).to_s ) - - elsif xml_info.is_a?(ReachReports::TextSubnodeProperty) - new_node = REXML::Element.find_or_create( node, xml_info.parent_prop.xml_alias) - REXML::TextElement.find_or_create( new_node, xml_info.xml_prop,self.send(xml_info.prop)) - - elsif xml_info.is_a?(ReachReports::SingleAttributeNodeProperty) - new_node = REXML::Element.find_or_create(node, xml_info.xml_prop) - new_node.add_attribute(xml_info.attribute, self.send(xml_info.prop).to_s) - - elsif xml_info.is_a?(ReachReports::AttributeNodeProperty) - new_node = REXML::Element.find_or_create(node, xml_info.xml_prop) - self.send(xml_info.prop.to_s+"=",self.association_class(xml_info.prop).new) unless self.send(xml_info.prop) - self.send(xml_info.prop).to_XML(new_node) - - elsif xml_info.is_a?(ReachReports::AttributeSubNodeListProperty) - new_node = REXML::Element.find_or_create( node, xml_info.parent_prop.xml_alias ) - #puts "new parent "+xml_info.parent_prop.xml_alias - prop_node = REXML::Element.find_or_create( new_node, xml_info.xml_prop ) - #puts "new prop "+xml_info.xml_prop - self.send( xml_info.prop ).each do |elem| - #puts "elem "+elem.to_yaml - elem_node = REXML::Element.new( xml_info.list_element.xml_alias ) - elem.to_XML( elem_node ) - prop_node << elem_node - end - - else - raise "type not supported yet: "+xml_info.inspect - end - - new_node.add_attribute("chapter", chapter.to_s+"."+node.elements.size.to_s) if chapter and new_node and new_node.attribute("chapter")==nil - end - -# if defined?(self.class.text_properties) -# self.class.text_properties.each do |p| -# node << REXML::TextElement.new(p.xml_alias,self.send(p)) -# end -# end - #node << REXML::TextElement.new(:qsar_title.xml_alias,qsar_title) - #node << REXML::TextElement.new(:qsar_models.xml_alias,qsar_models) - -# if defined?(self.class.catalog_entries) -# self.class.catalog_entries.each do |p| #,associatedClass| -# -# assoc_node = REXML::Element.new( p.xml_alias ) -# self.send(p).each{ |s| s.to_XML( assoc_node ) } -# node << assoc_node -# end -# end -# -# if defined?(self.class.catalog_name) -# catalog_node = $catalogs_node.elements[self.class.catalog_name] -# node_ref = REXML::Element.new(self.class.catalog_element+"_ref") -# -# raise "id is nil" if self.id==nil || self.id.to_s.size==0 -# element_id = self.class.catalog_element+"_"+self.id.to_s -# node_ref.add_attributes("idref"=>element_id,"catalog"=>self.class.catalog_name) -# -# content_node = REXML::Element.new(self.class.catalog_element) -# content_node.add_attribute("id",element_id) -# self.class.attribute_properties.each do |p| -# content_node.add_attribute p.xml_alias,send(p) -# end -# catalog_node << content_node -# node << node_ref -# -## def catalog_to_xml(node, catalog_name, element_name, attributes) -## catalog_node = $catalogs_node.elements[catalog_name] -## node_ref = REXML::Element.new(element_name+"_ref") -## attributes["id"] = element_name+"_"+attributes.delete("id").to_s -## node_ref.add_attributes("idref"=>attributes["id"],"catalog"=>catalog_name) -## content_node = REXML::Element.new(element_name) -## #puts "my attribts: "+attributes.inspect -## attributes.each do |k,v| -## content_node.add_attribute k,v.to_s -## end -## catalog_node << content_node -## node << node_ref -## end -# end - - -# node << REXML::TextElement.new(:qsar_title.xml_alias,qsar_title) -# node << REXML::TextElement.new(:qsar_models.xml_alias,qsar_models) -# qsar_software_node = REXML::Element.new(:qsar_software.xml_alias) -# qsar_software.each{ |s| s.to_xml( qsar_software_node ) } -# node << qsar_software_node - end - -end - - -module ReachReports - - def self.get_uri( report ) - raise "internal error, id not set "+to_yaml if report.id==nil - return $url_provider.url_for("/"+File.join(report.type,report.id.to_s), :full).to_s - end - - - - -# module CatalogEntry -# -# def catalog_to_xml(node, catalog_name, element_name, attributes) -# catalog_node = $catalogs_node.elements[catalog_name] -# node_ref = REXML::Element.new(element_name+"_ref") -# attributes["id"] = element_name+"_"+attributes.delete("id").to_s -# node_ref.add_attributes("idref"=>attributes["id"],"catalog"=>catalog_name) -# content_node = REXML::Element.new(element_name) -# #puts "my attribts: "+attributes.inspect -# attributes.each do |k,v| -# content_node.add_attribute k,v.to_s -# end -# catalog_node << content_node -# node << node_ref -# end -# end - -# class QsarSoftware -# include DataMapper::Resource #, CatalogEntry -# -# property :id, Serial -# property :contact, String, :length => 255 -# property :description, String, :length => 255 -# property :name, String, :length => 255 -# property :number, String, :length => 255 -# property :url, String, :length => 255 -# -# def self.attribute_properties -# [ :contact, :description, :name, :number, :url ] -# end -# -# def self.catalog_name -# "software_catalog" -# end -# -# def self.catalog_element -# "software" -# end -# -# belongs_to :qsar_identifier -# end - - class Software - include DataMapper::Resource #, CatalogEntry - - property :id, Serial - property :contact, String, :length => 255 - property :description, String, :length => 255 - property :name, String, :length => 255 - property :number, String, :length => 255 - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:contact), - AttributeProperty.new(:description), - AttributeProperty.new(:name), - AttributeProperty.new(:number), - AttributeProperty.new(:url) ] - end - end - - class QsarSoftware < Software - #belongs_to :qsar_identifier, :key => false - property :qsar_identifier_id, Integer - end - - class XmlInfo - - attr_accessor :prop - - protected - def initialize( prop ) - @prop = prop - end - - public - def xml_prop - @prop.xml_alias - end - end - - class TextNodeProperty < XmlInfo - - end - - class TextSubnodeProperty < XmlInfo - attr_accessor :parent_prop - - def initialize( prop, parent_prop ) - super(prop) - @parent_prop = parent_prop - end - end - - class AttributeProperty < XmlInfo - - end - - class AttributeNodeProperty < XmlInfo - - end - - class AttributeSubNodeListProperty < XmlInfo - - attr_accessor :list_element, :parent_prop - - def initialize( prop, list_element, parent_prop ) - super(prop) - @list_element = list_element - @parent_prop = parent_prop - end - end - - class SingleAttributeNodeProperty < XmlInfo - attr_accessor :attribute - - def initialize( prop, attribute ) - super(prop) - @attribute = attribute - end - end - - class CatalogReference < XmlInfo - attr_accessor :catalog_name, :catalog_element - - def initialize( prop, catalog_name, catalog_element ) - super(prop) - @catalog_name = catalog_name - @catalog_element = catalog_element - end - end - - - class QsarIdentifier - include DataMapper::Resource - - property :id, Serial - property :qsar_title, Text - property :qsar_models, Text - - has n, :qsar_software - - def xml_infos - [ TextNodeProperty.new(:qsar_title), - TextNodeProperty.new(:qsar_models), - CatalogReference.new(:qsar_software, "software_catalog", "software") ] - end - - belongs_to :qmrf_report - end - - class Author - include DataMapper::Resource - - property :id, Serial - property :affiliation, String, :length => 255 - property :contact, String, :length => 255 - property :email, String, :length => 255 - property :name, String, :length => 255 - property :number, String, :length => 255 - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:affiliation), - AttributeProperty.new(:contact), - AttributeProperty.new(:email), - AttributeProperty.new(:name), - AttributeProperty.new(:number), - AttributeProperty.new(:url) ] - end - - belongs_to :qsar_general_information - end - - class QmrfAuthor < Author - property :type, String, :default => "QmrfAuthor" - end - - class ModelAuthor < Author - property :type, String, :default => "ModelAuthor" - end - - class Publication - include DataMapper::Resource - - property :id, Serial - property :title, Text - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:title), - AttributeProperty.new(:url) ] - end - end - - class Reference < Publication - #belongs_to :qsar_general_information - property :qsar_general_information_id, Integer - end - - - class QsarGeneralInformation - include DataMapper::Resource - - property :id, Serial - property :qmrf_date, Text #String, :length => 255 #PENDING -> datetime - property :model_date, Text #String, :length => 255 #PENDING -> datetime - property :qmrf_date_revision, Text #String, :length => 255 #PENDING -> datetime - property :qmrf_revision, Text - property :model_date, Text - property :info_availability, Text - property :related_models, Text - - # type is needed to distinguish between authors - # (the datamapper creates a table "Authors", the relation is defined by QsarGeneral.id and Author.id) - has n, :qmrf_authors, :type => "QmrfAuthor" - has n, :model_authors, :type => "ModelAuthor" - has n, :references - - def xml_infos - [ TextNodeProperty.new(:qmrf_date), - CatalogReference.new(:qmrf_authors, "authors_catalog", "author"), - TextNodeProperty.new(:qmrf_date_revision), - TextNodeProperty.new(:qmrf_revision), - CatalogReference.new(:model_authors, "authors_catalog", "author"), - TextNodeProperty.new(:model_date), - CatalogReference.new(:references, "publications_catalog", "publication"), - TextNodeProperty.new(:info_availability), - TextNodeProperty.new(:related_models) ] - end - - belongs_to :qmrf_report - end - - class ModelEndpoint - include DataMapper::Resource - - property :id, Serial - property :group, String, :length => 255 - property :name, String, :length => 255 - property :subgroup, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:group), - AttributeProperty.new(:name), - AttributeProperty.new(:subgroup) ] - end - - belongs_to :qsar_endpoint - end - - class QsarEndpoint - include DataMapper::Resource - - property :id, Serial - property :endpoint_variable, Text - property :model_species, Text - property :endpoint_comments, Text - property :endpoint_units, Text - property :endpoint_protocol, Text - property :endpoint_data_quality, Text - - has n, :model_endpoint - - def xml_infos - [ TextNodeProperty.new(:model_species), - CatalogReference.new(:model_endpoint, "endpoints_catalog", "endpoint"), - TextNodeProperty.new(:endpoint_comments), - TextNodeProperty.new(:endpoint_units), - TextNodeProperty.new(:endpoint_variable), - TextNodeProperty.new(:endpoint_protocol), - TextNodeProperty.new(:endpoint_data_quality) ] - end - - belongs_to :qmrf_report - end - - class AlgorithmExplicit - include DataMapper::Resource - - property :id, Serial - property :definition, Text - property :description, Text - property :publication_ref, Text - - def xml_infos - [ AttributeProperty.new(:definition), - AttributeProperty.new(:description), - AttributeProperty.new(:publication_ref) ] - end - - belongs_to :qsar_algorithm - end - - class AlgorithmsDescriptor - include DataMapper::Resource - - property :id, Serial - property :description, Text - property :name, Text - property :publication_ref, Text - property :units, Text - - def xml_infos - [ AttributeProperty.new(:description), - AttributeProperty.new(:name), - AttributeProperty.new(:publication_ref), - AttributeProperty.new(:units) ] - end - - belongs_to :qsar_algorithm - end - - class DescriptorsGenerationSoftware < Software - - #belongs_to :qsar_algorithm, :key => false - property :qsar_algorithm_id, Integer - end - - class QsarAlgorithm - include DataMapper::Resource - - property :id, Serial - - property :algorithm_type, Text - property :descriptors_selection, Text - property :descriptors_generation, Text - property :descriptors_chemicals_ratio, Text - property :equation, Text - - has n, :algorithm_explicit - has n, :algorithms_descriptors - has n, :descriptors_generation_software - - def xml_infos - [ TextNodeProperty.new(:algorithm_type), - CatalogReference.new(:algorithm_explicit, "algorithms_catalog", "algorithm"), - TextSubnodeProperty.new(:equation, :algorithm_explicit), - CatalogReference.new(:algorithms_descriptors, "descriptors_catalog", "descriptor"), - TextNodeProperty.new(:descriptors_selection), - TextNodeProperty.new(:descriptors_generation), - CatalogReference.new(:descriptors_generation_software, "software_catalog", "software"), - TextNodeProperty.new(:descriptors_chemicals_ratio), - ] - end - - belongs_to :qmrf_report - end - - class AppDomainSoftware < Software - - #belongs_to :qsar_algorithm, :key => false - property :qsar_applicability_domain_id, Integer - end - - class QsarApplicabilityDomain - include DataMapper::Resource - - property :id, Serial - property :app_domain_description, Text - property :app_domain_method, Text - property :applicability_limits, Text - - has n,:app_domain_software - - def xml_infos - [ TextNodeProperty.new(:app_domain_description), - TextNodeProperty.new(:app_domain_method), - CatalogReference.new(:app_domain_software, "software_catalog", "software"), - TextNodeProperty.new(:applicability_limits), ] - end - - belongs_to :qmrf_report - - end - - class DatasetData - include DataMapper::Resource - - property :id, Serial - property :chemname, String, :default => "No" - property :cas, String, :default => "No" - property :smiles, String, :default => "No" - property :inchi, String, :default => "No" - property :mol, String, :default => "No" - property :formula, String, :default => "No" - - def xml_infos - [ AttributeProperty.new(:chemname), - AttributeProperty.new(:cas), - AttributeProperty.new(:smiles), - AttributeProperty.new(:inchi), - AttributeProperty.new(:mol), - AttributeProperty.new(:formula) ] - end - - end - - class TrainingSetData < DatasetData - - #belongs_to :qsar_robustness - property :qsar_robustness_id, Integer - end - - - class QsarRobustness - include DataMapper::Resource - - property :id, Serial - property :training_set_availability, String, :default => "No" - property :training_set_descriptors, String, :default => "No" - property :dependent_var_availability, String, :default => "No" - property :other_info, Text - property :preprocessing, Text - property :goodness_of_fit, Text - property :loo, Text - property :lmo, Text - property :yscrambling, Text - property :bootstrap, Text - property :other_statistics, Text - - has 1, :training_set_data, :model => "TrainingSetData" - - def xml_infos - [ SingleAttributeNodeProperty.new(:training_set_availability, "answer"), - AttributeNodeProperty.new(:training_set_data), - SingleAttributeNodeProperty.new(:training_set_descriptors, "answer"), - SingleAttributeNodeProperty.new(:dependent_var_availability, "answer"), - TextNodeProperty.new(:other_info), - TextNodeProperty.new(:preprocessing), - TextNodeProperty.new(:goodness_of_fit), - TextNodeProperty.new(:loo), - TextNodeProperty.new(:lmo), - TextNodeProperty.new(:yscrambling), - TextNodeProperty.new(:bootstrap), - TextNodeProperty.new(:other_statistics), - ] - end - - belongs_to :qmrf_report - - end - - - class ValidationSetData < DatasetData - - #belongs_to :qsar_predictivity - property :qsar_predictivity_id, Integer - end - - class QsarPredictivity - include DataMapper::Resource - - property :id, Serial - - property :validation_set_availability, String, :default => "No" - property :validation_set_descriptors, String, :default => "No" - property :validation_dependent_var_availability, String, :default => "No" - property :validation_other_info, Text - property :experimental_design, Text - property :validation_predictivity, Text - property :validation_assessment, Text - property :validation_comments, Text - - has 1, :validation_set_data, :model => "ValidationSetData" - - def xml_infos - [ SingleAttributeNodeProperty.new(:validation_set_availability, "answer"), - AttributeNodeProperty.new(:validation_set_data), - SingleAttributeNodeProperty.new(:validation_set_descriptors, "answer"), - SingleAttributeNodeProperty.new(:validation_dependent_var_availability, "answer"), - TextNodeProperty.new(:validation_other_info), - TextNodeProperty.new(:experimental_design), - TextNodeProperty.new(:validation_predictivity), - TextNodeProperty.new(:validation_assessment), - TextNodeProperty.new(:validation_comments), - ] - end - - belongs_to :qmrf_report - end - - class QsarInterpretation - include DataMapper::Resource - - property :id, Serial - property :mechanistic_basis, Text - property :mechanistic_basis_comments, Text - property :mechanistic_basis_info, Text - - def xml_infos - [ TextNodeProperty.new(:mechanistic_basis), - TextNodeProperty.new(:mechanistic_basis_comments), - TextNodeProperty.new(:mechanistic_basis_info), - ] - end - - belongs_to :qmrf_report - end - - class Bibliography < Publication - - #belongs_to :qsar_miscellaneous - property :qsar_miscellaneous_id, Integer - end - - class Attachment - include DataMapper::Resource - - property :id, Serial - property :description, Text - property :filetype, String - property :url, String, :length => 255 - - def xml_infos - [ AttributeProperty.new(:description), - AttributeProperty.new(:filetype), - AttributeProperty.new(:url), - ] - end - - belongs_to :qsar_miscellaneous - end - - class AttachmentTrainingData < Attachment - property :type, String, :default => "AttachmentTrainingData" - end - - class AttachmentValidationData < Attachment - property :type, String, :default => "AttachmentValidationData" - end - - class AttachmentDocument < Attachment - property :type, String, :default => "AttachmentDocument" - end - - - class QsarMiscellaneous - include DataMapper::Resource - - property :id, Serial - property :comments, Text - - has n, :bibliography, Text - - # type is needed to distinguish between attachments - # (the datamapper creates a table "Attachments", the relation is defined by QsarMisc.id and Attachment.id) - has n, :attachment_training_data, :model => "AttachmentValidationData", :type => "AttachmentTrainingData" - has n, :attachment_validation_data, :model => "AttachmentValidationData", :type => "AttachmentValidationData" - has n, :attachment_documents, :type => "AttachmentDocument" - - def xml_infos - [ TextNodeProperty.new(:comments), - CatalogReference.new(:bibliography,"publications_catalog", "publication"), - AttributeSubNodeListProperty.new(:attachment_training_data, :molecules, :attachments), - AttributeSubNodeListProperty.new(:attachment_validation_data, :molecules, :attachments), - AttributeSubNodeListProperty.new(:attachment_documents, :documents, :attachments), - ] - end - - belongs_to :qmrf_report - end - - class QmrfSummary - include DataMapper::Resource - - property :id, Serial - property :qmrf_number, Text - property :date_publication, Text - property :keywords, Text - property :summary_comments, Text - - def xml_infos - [ TextNodeProperty.new(:qmrf_number), - TextNodeProperty.new(:date_publication), - TextNodeProperty.new(:keywords), - TextNodeProperty.new(:summary_comments), - ] - end - - belongs_to :qmrf_report - end - - class QmrfReport - include DataMapper::Resource, REXML - - property :id, Serial - property :model_uri, String, :length => 255 - - CHAPTERS = [ :qsar_identifier, :qsar_general_information, :qsar_endpoint, :qsar_algorithm, - :qsar_applicability_domain, :qsar_robustness, :qsar_predictivity, :qsar_interpretation, - :qsar_miscellaneous, :qmrf_summary ] - - CHAPTERS.each{ |c,clazz| has 1, c } - - attr_accessor :subjectid - - after :save, :check_policy - private - def check_policy - raise "no id" unless @id - #raise "no subjectid" unless subjectid - OpenTox::Authorization.check_policy(report_uri, subjectid) - end - - public - def to_yaml - super(:methods => CHAPTERS) - end - - def report_uri - return $url_provider.url_for("/reach_report/QMRF/"+@id.to_s, :full).to_s - end - - def self.from_xml(report, xml_data) - - raise "xml data size < 255, probably no qmrf report : '"+xml_data.to_s+"'" if xml_data.to_s.size<255 - doc = Document.new xml_data - - root = doc.elements["QMRF"] - raise "no QMRF node found" unless root - chapters = root.elements["QMRF_chapters"] - raise "no chapter node found" unless chapters - $catalogs_node = root.elements["Catalogs"] - raise "catalogs not found" unless $catalogs_node - - CHAPTERS.each do |p| #, chapterClass| - #unless report.send(p) - report.send(p).destroy if report.send(p) - c = report.association_class(p).new #chapterClass.new - #c.save - report.send(p.to_s+"=",c) - #end - report.send(p).from_xml( chapters.elements[p.xml_alias] ) - end - - #raise "already exists" if report.qsar_identifier - #report.qsar_general_information.destroy if report.qsar_general_information - #report.qsar_identifier.clear - #report.qsar_general_information = QsarGeneralInformation.new - #report.qsar_general_information.qmrf_date = "DateTime.now" - #report.qsar_general_information.model_authors << ModelAuthor.new - #report.qsar_general_information.qmrf_authors << QmrfAuthor.new - - #report.qsar_identifier = QsarIdentifier.new unless report.qsar_identifier - #report.qsar_identifier.from_xml( chapters.elements[:qsar_identifier.xml_alias] ) - - #report.qsar_general_information = QsarGeneralInformation.new unless report.qsar_general_information - #report.qsar_general_information.from_xml( chapters.elements[:qsar_general_information.xml_alias] ) - - - #QsarGeneralInformation.from_xml( report.qsar_general_information, chapters.elements["qsar_general_information".xml_alias] ) - - #puts "set qsar_identifier to "+report.qsar_identifier.class.to_s - -# begin - report.save -# rescue DataObjects::SQLError => e -# puts e.message -# exit -# rescue DataObjects::DataError => e -# puts e.message -# exit -# rescue DataMapper::SaveFailureError => e -# puts e.resource.errors.inspect -# exit -# end - -# puts "XXXXXXXxxxxx" -# -# puts "1" -# puts report.qsar_miscellaneous.attachment_training_data.inspect -# puts "2" -# puts report.qsar_miscellaneous.attachment_validation_data.inspect -# puts "3" -# puts report.qsar_miscellaneous.attachment_documents.inspect -# -# -# r = QmrfReport.get(report.id) -# -# puts "1" -# puts r.qsar_miscellaneous.attachment_training_data.inspect -# puts "2" -# puts r.qsar_miscellaneous.attachment_validation_data.inspect -# puts "3" -# puts r.qsar_miscellaneous.attachment_documents.inspect -# -# exit - - - end - - def to_xml - #puts "now qsar_identifier is "+self.qsar_identifier.class.to_s - - doc = Document.new - decl = XMLDecl.new - decl.encoding = "UTF-8" - doc << decl - type = DocType.new('QMRF SYSTEM "http://ambit.sourceforge.net/qmrf/jws/qmrf.dtd"') - doc << type - - root = Element.new("QMRF") - root.add_attributes( "version" => 1.2, "schema_version" => 1.0, "name" => "(Q)SAR Model Reporting Format", - "author" => "Joint Research Centre, European Commission", "contact" => "Joint Research Centre, European Commission", - "date" => "July 2007", "email" => "qsardb@jrc.it", "url" => "http://ecb.jrc.ec.europa.eu/qsar/" ) - - catalogs = Element.new("Catalogs") - [ "software_catalog", "algorithms_catalog", "descriptors_catalog", - "endpoints_catalog", "publications_catalog", "authors_catalog"].each do |c| - catalogs << Element.new(c) - end - $catalogs_node = catalogs - - chapters = Element.new("QMRF_chapters") - chapter_count = 1 - - CHAPTERS.each do |p| - node = Element.new( p.xml_alias ) - node.add_attribute("chapter",chapter_count) - self.send(p.to_s+"=", self.association_class(p).new) unless self.send(p) # create empy chapter, as xml must be complete - self.send(p).to_XML( node, chapter_count ) - chapters << node - chapter_count += 1 - end - -# qsar_identifier_node = Element.new(:qsar_identifier.xml_alias) -# self.qsar_identifier.to_XML( qsar_identifier_node ) -# chapters << qsar_identifier_node -# -# qsar_general_information_node = Element.new(:qsar_general_information.xml_alias) -# self.qsar_general_information.to_XML( qsar_general_information_node ) -# chapters << qsar_general_information_node - - - -# [ @qsar_identifier, @qsar_general_information, @qsar_endpoint ].each do |c| -# n = c.to_xml -# raise "no node "+n.to_s+" "+n.class.to_s unless n.is_a?(Element) -# chapters << n -# end - - root << chapters - root << catalogs - doc << root - - s = "" - doc.write(s, 2, false, false) - return s - - end - end - -#Profile2.auto_upgrade! - -# class QmrfReport < ActiveRecord::Base -# -# alias_attribute :date, :created_at -# -# QmrfProperties.serialized_properties.each do |p| -# serialize p -# end -# -# def type -# "QMRF" -# end -# -# def report_uri -# ReachReports.get_uri(self) -# end -# -# def get_content -# hash = {} -# [ :model_uri, :date ].each{ |p| hash[p] = self.send(p) } -# QmrfProperties.properties.each{ |p| hash[p] = self.send(p) } -# return hash -# end -# end -# -# -# class QprfReport < ActiveRecord::Base -# -# alias_attribute :date, :created_at -# -# def report_uri -# ReachReports.get_uri(self) -# end -# -# def type -# "QPRF" -# end -# end - - mysql_lite_retry do - [ QsarSoftware, QsarIdentifier, QmrfAuthor, ModelAuthor, Reference, QsarGeneralInformation, ModelEndpoint, QsarEndpoint, AlgorithmExplicit, - AlgorithmsDescriptor, DescriptorsGenerationSoftware, QsarAlgorithm, AppDomainSoftware, QsarApplicabilityDomain, TrainingSetData, - QsarRobustness, ValidationSetData, QsarPredictivity, QsarInterpretation, Bibliography, AttachmentTrainingData, AttachmentValidationData, - AttachmentDocument, QsarMiscellaneous, QmrfSummary, QmrfReport ].each do |model| - model.auto_upgrade! - model.raise_on_save_failure = true - end - - end - -end
\ No newline at end of file |