SysMO-DB/seek

Similar blocks of code found in 2 locations. Consider refactoring.

Open

                        context.strokeRect(
                            data.select[0],
                            data.select[1],
                            data.select[2] - data.select[0],
                            data.select[3] - data.select[1]);

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

                    context.fillRect(
                        data.select[0],
                        data.select[1],
                        data.select[2] - data.select[0],
                        data.select[3] - data.select[1]);

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Function updateRoles has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function updateRoles(editable,group_id) {

    role_ids=new Array();
    role_text=""

Method update has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def update
    # remove protected columns (including a "link" to content blob - actual data cannot be updated!)
    if params[:data_file]
      [:contributor_id, :contributor_type, :original_filename, :content_type, :content_blob_id, :created_at, :updated_at, :last_used_at].each do |column_name|
        params[:data_file].delete(column_name)

Method create has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def create
    if handle_upload_data

      @data_file = DataFile.new params[:data_file]

Similar blocks of code found in 3 locations. Consider refactoring.

Open

    def set_rna_extractions sheet, rna_extraction_protocol, rna_attribute_names       # not used anymore
      sheet_name = sheet.attributes["name"]

      row = rna_extraction_protocol.attributes["row"].to_i
      col = rna_extraction_protocol.attributes["column"].to_i

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Similar blocks of code found in 3 locations. Consider refactoring.

Open

    def set_sequencing sheet, sequencing_protocol, sequencing_attribute_names   # not used anymore
      sheet_name = sheet.attributes["name"]

      row = sequencing_protocol.attributes["row"].to_i
      col = sequencing_protocol.attributes["column"].to_i

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Similar blocks of code found in 3 locations. Consider refactoring.

Open

    def set_treatments sheet, treatment_protocol, treatment_attribute_names         # not used anymore
      sheet_name = sheet.attributes["name"]

      row = treatment_protocol.attributes["row"].to_i
      col = treatment_protocol.attributes["column"].to_i

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Function setTheDivStyle has 42 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function setTheDivStyle() {
if(!readCookie('name_panel')) {
// if cookie not found display the div and create the cookie
//document.getElementById("name_panel").style.display="block";
//createCookie('name_panel', 1);  // 1 day = 24 hours persistence

Function addAll has 42 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function addAll(resource_type, source) {

    if (source == "target") {
        for(var key in allLinks[resource_type]) {
            $(resource_type +"_" + key + "_target_row").hide();

Similar blocks of code found in 2 locations. Consider refactoring.

Open

    if (link_hash == null) {
        link_hash = {};
        allLinks[resource_type] = link_hash;
        var source_map = {};
        checkedSourceMap[resource_type] = source_map

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    if (link_data == null) {
        link_data = {};
        allLinksData[resource_type] = link_data;
        var target_map = {};
        checkedTargetMap[resource_type] = target_map

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Method specimen_row_data has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def specimen_row_data specimen
    id_column = Seek::Config.is_virtualliver ? 8 : 6
    creators = []
    specimen.creators.each do |creator|
      creators << link_to(h(creator.name), person_path(creator.id))

Method tree_editor_display has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def tree_editor_display type, show_edit=true, show_delete=true, selected_id=nil, related_resource_type="Person",selective_display=false, foldable=false

    selected_display_items = nil

    if selected_id && selective_display

Method send_policy_data has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def send_policy_data
    request_type = white_list(params[:policy_type])
    entity_type = white_list(params[:entity_type])
    entity_id = white_list(params[:entity_id])
    

Method update_rdf has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        def update_rdf(item)
          if configured?
            connect_to_repository
            graphs = rdf_graph_uris(item)
            rdf_file_path = last_rdf_file_path(item)

Method clone_versioned_model has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

          def clone_versioned_model(orig_model, new_model, process_file_columns=true)
            self.versioned_attributes.each do |key|
              # Make sure to ignore file columns, white list columns, timestamp columns and any other ignore columns
              unless self.file_columns.include?(key) ||
                     self.white_list_columns.include?(key) ||

Method populate_treatment has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def populate_treatment treatment_json, specimen=nil, sample=nil

        start_value = treatment_json["start value"]
        end_value = treatment_json["end value"]
        standard_deviation = treatment_json["standard deviation"]

Similar blocks of code found in 2 locations. Consider refactoring.

Open

  def fs_search_fields
    flds = studied_factors.collect do |fs|
      [fs.measured_item.title,
       fs.substances.collect do |sub|
         #FIXME: this makes the assumption that the synonym.substance appears like a Compound

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    if @strain.save
      if @strain.from_biosamples=='true'
        #reload to get updated nested attributes,e.g. genotypes/phenotypes
        @strain.reload
        render :partial => "biosamples/back_to_biosamples", :locals => {:action => 'update', :object => @strain}

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