SysMO-DB/seek

# BioCatalogue: app/helpers/api_helper.rb
#
# Copyright (c) 2008-2009, University of Manchester, The European Bioinformatics 
# Institute (EMBL-EBI) and the University of Southampton.
# See license.txt for details.

module ApiHelper
  
  def xml_root_attributes
    { "xmlns" => "http://www.sysmo-db.org/2010/xml/rest",
      "xmlns:xsi" => "http://www.w3.org/2001/XMLSchema-instance",
      "xsi:schemaLocation" => "http://www.sysmo-db.org/2010/xml/rest/schema-v1.xsd",
      "xmlns:xlink" => "http://www.w3.org/1999/xlink",
      "xmlns:dc" => "http://purl.org/dc/elements/1.1/",
      "xmlns:dcterms" => "http://purl.org/dc/terms/" }
  end
  
  def uri_for_path(path, *args)
    Seek::Api.uri_for_path(path, *args)
  end
  
  def api_partial_path_for_item object
    Seek::Api.api_partial_path_for_item(object)
  end
  
  def uri_for_collection(resource_name, *args)
    Seek::Api.uri_for_collection(resource_name, *args)
  end
  
  def uri_for_object(resource_obj, *args)
    Seek::Api.uri_for_object(resource_obj, *args)
  end
  
  def previous_link_xml_attributes(resource_uri)
    xlink_attributes(resource_uri, :title => xlink_title("Previous page of results"))
  end
  
  def next_link_xml_attributes(resource_uri)
    xlink_attributes(resource_uri, :title => xlink_title("Next page of results"))
  end

  def assay_type_xlink assay
    xlink = xlink_attributes(assay.assay_type_uri)
    xlink["xlink:title"] = assay.assay_type_label
    xlink["resourceType"] = "AssayType"
    xlink
  end

  def technology_type_xlink assay
    xlink = xlink_attributes(assay.technology_type_uri)
    xlink["xlink:title"] = assay.technology_type_label
    xlink["resourceType"] = "TechnologyType"
    xlink
  end

  def core_xlink object,include_title=true
    if (object.class.name.include?("::Version"))
      xlink=xlink_attributes(uri_for_object(object.parent,{:params=>{:version=>object.version}}))
    else
      xlink=xlink_attributes(uri_for_object(object))  
    end
    
    xlink["xlink:title"]=xlink_title(object) unless !include_title || display_name(object,false).nil?
    xlink["id"]=object.id
    xlink["uuid"]=object.uuid if object.respond_to?("uuid")
    xlink["resourceType"] = object.class.name.include?("::Version") ? object.parent.class.name : object.class.name
    return xlink
  end
  
  #requires a slightly different handling to core_xlink because the route is nested
  def avatar_xlink avatar
    return {"xsi:nil"=>"true"} if avatar.nil?    
    uri=uri_for_object(avatar.owner)
    uri="#{uri}/avatars/#{avatar.id}"
    xlink=xlink_attributes(uri)
    xlink["id"]=avatar.id
    xlink["resourceType"]=avatar.class.name
    return xlink
  end
  
  def xlink_attributes(resource_uri, *args)
    attribs = { }
    
    attribs_in = args.extract_options!
    
    attribs["xlink:href"] = resource_uri
    
    attribs_in.each do |k,v|
      attribs["xlink:#{k.to_s}"] = v
    end
    
    return attribs
  end
  
  def xlink_title(item, item_type_name=nil)
    case item
      when String
      return item
    else
      if item_type_name.blank?
        item_type_name = case item
          when User
              "User"
        else
          if (item.class.name.include?("::Version"))
            item.parent.class.name
          else
            item.class.name  
          end              
        end
      end

      "#{display_name(item, false)}"
    end
  end
  
  def display_name item,escape_html=false          
    result = nil
    result = item.title if item.respond_to?("title")
    result = item.name if item.respond_to?("name") && result.nil?
    result = h(result) if escape_html && !result.nil?
    return result
  end
  
  def dc_xml_tag(builder, term, value)
    builder.tag! "dc:#{term}", value
  end
  
  def dcterms_xml_tag(builder, term, value)
    # For dates...
    if [ :created, :modified, "created", "modified" ].include?(term)
      value = value.iso8601
    end

    builder.tag! "dcterms:#{term}", value
  end
  
  def core_xml builder,object
    builder.tag! "id",object.id
    dc_core_xml builder,object
    builder.tag! "uuid",object.uuid if object.respond_to?("uuid")    
  end  
  
  def extended_xml builder,object        
    
    submitter = determine_submitter object
    builder.tag! "submitter" do 
      api_partial(builder,submitter)
    end if submitter
    
    builder.tag! "organisms" do
      organisms=[]
      organisms=object.organisms if object.respond_to?("organisms")
      organisms << object.organism if object.respond_to?("organism") && object.organism
      api_partial_collection builder,organisms
    end if object.respond_to?("organism") || object.respond_to?("organisms")
        
    builder.tag! "creators" do
      api_partial_collection builder,(object.creators || [])
    end if !object.instance_of?(Publication) && object.respond_to?("creators")

    unless hide_contact_details?
      builder.tag! "email",object.email if object.respond_to?("email")
      builder.tag! "webpage",object.webpage if object.respond_to?("webpage")
      builder.tag! "internal_webpage",object.internal_webpage if object.respond_to?("internal_webpage")
      builder.tag! "phone",object.phone if object.respond_to?("phone")
    end
    
    builder.tag! "bioportal_concepts" do
      concepts=[]
      concepts=object.bioportal_concepts if object.respond_to?("bioportal_concepts")
      concept = object.bioportal_concept if object.respond_to?("bioportal_concept")
      concepts.compact.each do |concept|
        builder.tag! "bioportal_concept" do
          builder.tag! "ontology_id",concept.ontology_id
          builder.tag! "concept_uri",concept.concept_uri
        end
      end
    end if object.respond_to?("bioportal_concept") || object.respond_to?("bioportal_concepts")

    builder.tag! "version",object.version if object.respond_to?("version")
    builder.tag! "revision_comments",object.revision_comments if object.respond_to?("revision_comments")
    builder.tag! "latest_version",core_xlink(object.latest_version) if object.respond_to?("latest_version")           
    
    if (object.respond_to?("versions"))
      builder.tag! "versions" do
        object.versions.each do |v|
          builder.tag! "version",core_xlink(v)
        end
      end
    end
    
    policy_xml builder,object if User.admin_logged_in? && object.respond_to?("policy")
    if object.respond_to?("content_blobs")
      builder.tag! "blobs" do
        object.content_blobs.each do |cb|
          blob_xml builder, cb
        end
      end
    elsif object.respond_to?("content_blob")
      blob_xml builder, object.content_blob
    end

    if object.respond_to?("avatar")
      builder.tag! "avatars" do
        builder.tag! "avatar",avatar_xlink(object.avatar) unless object.avatar.nil?
      end      
    end
    tags_xml builder,object

  end

  def tags_xml builder,object
    object = object.parent if object.class.name.include?("::Version")
    if object.respond_to?(:annotations_as_text_array)
      builder.tag! "tags" do
        object.annotations.each do |annotation|
          builder.tag! "tag",annotation.value.text,{:context=>annotation.attribute.name}
        end
      end
    end
  end
  
  def policy_xml builder,asset
    policy = asset.policy
    unless policy.nil?
      builder.tag! "policy" do
        dc_core_xml builder,policy
        builder.tag! "sharing_scope",policy.sharing_scope
        builder.tag! "access_type",policy.access_type
        builder.tag! "use_blacklist",policy.use_blacklist ? policy.use_blacklist : false
        builder.tag! "use_whitelist",policy.use_whitelist ? policy.use_whitelist : false
        builder.tag! "permissions" do
          policy.permissions.select{|p| p.contributor_type!="FavouriteGroup"}.each do |permission|
            builder.tag! "permission" do
              dc_core_xml builder,permission
              builder.tag! "contributor",core_xlink(permission.contributor)              
              builder.tag! "access_type",permission.access_type
            end
          end
        end
      end
    else
      builder.tag! "policy",{"xsi:nil"=>"true"}
    end
  end
  
  def resource_xml builder,resource 
    builder.tag! "resource",core_xlink(resource)
  end
  
  def blob_xml builder,blob
    builder.tag! "blob",core_xlink(blob) do      
      builder.tag! "uuid",blob.uuid
      builder.tag! "md5sum",blob.md5sum
      builder.tag! "url",blob.url
      builder.tag! "original_filename",blob.original_filename
      builder.tag! "content_type",blob.content_type
      builder.tag! "is_remote",!blob.file_exists?
    end
  end
  
  def assets_list_xml builder,assets,tag="assets",include_core=true,include_resource=true
    builder.tag! tag do
      assets.each do |asset|
        asset_xml builder,asset,include_core,include_resource
      end
    end
  end
  
  def associated_resources_xml builder, object
    object=object.parent if (object.class.name.include?("::Version"))
    associated = get_related_resources(object)
    to_ignore = ignore_associated_types.collect{|t| t.name}
    associated.delete_if {|k,v| to_ignore.include?(k)}
    builder.tag! "associated" do
      associated.keys.sort.each do |key|
        attr={}
        attr[:total]=associated[key][:items].count
        if (associated[key][:hidden_count])
          attr[:total]=attr[:total]+associated[key][:hidden_count]
          attr[:hidden_count]=associated[key][:hidden_count]
        end
        generic_list_xml(builder, associated[key][:items],key.underscore.pluralize,attr)        
      end
    end    
  end

  #types that should be ignored from the related resources. It may be desirable to add items in this list to the schema
  def ignore_associated_types
    [Strain,TavernaPlayer::Run,Workflow,Sweep]
  end
  
  def generic_list_xml builder,list,tag,attr={}
    builder.tag! tag,attr do 
      list.each do |item|
        if (item.class.name.include?("::Version")) #versioned items need to be handled slightly differently.
          parent=item.parent
          builder.tag! parent.class.name.underscore,core_xlink(item)
        else
          builder.tag! item.class.name.underscore,core_xlink(item)  
        end        
      end
    end
  end
  
  def api_partial builder,object, is_root=false
    parent_object =  object.class.name.include?("::Version") ? object.parent : object
    path=api_partial_path_for_item(parent_object)
    classname=parent_object.class.name.underscore
    render :partial=>path,:locals=>{:parent_xml => builder,:is_root=>is_root,classname.to_sym=>object}
  end
  
  def api_partial_collection builder,objects,is_root=false
    objects.each{|o| api_partial builder,o,is_root}
  end
  
  def parent_child_elements builder,object
    builder.tag! "parents" do
      api_partial_collection(builder, object.parents, is_root = false)  
    end
    
    builder.tag! "children" do
      api_partial_collection(builder, object.children, is_root = false)
    end
  end
  
  def dc_core_xml builder,object
    submitter = determine_submitter object
    dc_xml_tag builder,:title,object.title if object.respond_to?("title")
    dc_xml_tag builder,:description,object.description if object.respond_to?("description")    
    dcterms_xml_tag builder,:created,object.created_at if object.respond_to?("created_at")
    dcterms_xml_tag builder,:modified,object.updated_at if object.respond_to?("updated_at")
    dc_xml_tag builder,:creator,submitter.name if submitter
  end
  
  def determine_submitter object
    #FIXME: needs to be the creators for assets
    return object.owner if object.respond_to?("owner")
    result = object.contributor if object.respond_to?("contributor") && !object.kind_of?(Permission)
    if (result)
      return result if result.instance_of?(Person)
      return result.person if result.instance_of?(User)      
    end
    
    return nil
  end
  
  def assay_data_relationships_xml builder,assay
    relationships={}
    assay.assay_assets.each do |aa|
      if aa.relationship_type
        relationships[aa.relationship_type.title] ||= []
        relationships[aa.relationship_type.title] << aa.asset
      end
    end
    
    builder.tag! "data_relationships" do
      relationships.keys.each do |k|        
        generic_list_xml(builder, relationships[k],"data_relationship",{:type=>k})                 
      end
    end
  end
  
end