common names list

app/assets/javascripts/cns.coffee

@@ -0,0 +1,3 @@
+# Place all the behaviors and hooks related to the matching controller here.
+# All this logic will automatically be available in application.js.
+# You can use CoffeeScript in this file: http://coffeescript.org/

app/assets/stylesheets/cns.scss

@@ -0,0 +1,3 @@
+// Place all the styles related to the cns controller here.
+// They will automatically be included in application.css.
+// You can use Sass (SCSS) here: http://sass-lang.com/

app/controllers/cns_controller.rb

@@ -0,0 +1,94 @@
+class CnsController < ApplicationController
+  def new
+    @cn = Cn.new
+  end
+
+  def create
+    @cn = current_or_guest_user.cns.build(cn_params)
+    if @cn.save
+      name = params[:name].empty? ? @cn.file.original_filename : params[:name]
+      @list = @cn.create_list(name: name, description: params[:description])
+      flash[:success] = @list.name + " list is created!"
+
+      loaded_from_file = {}
+      raw = Paperclip.io_adapters.for(@cn.file).read.split("\n")
+      loaded_from_file["commonnames"] = raw.map do |n|
+        n.to_s.strip.encode('UTF-8', {
+          :invalid => :replace,
+          :undef   => :replace,
+          :replace => '?'
+        })
+      end
+
+      loaded_from_file["multiple_match"] = @cn.multiple_match
+
+      mapping_response = {}
+      mapping_response = Req.post( Rails.configuration.x.sv_NCBI_common_name,
+                                   loaded_from_file.to_json,
+                                   :content_type => :json )
+      if mapping_response.empty?
+        mapping_response = Req.post( Rails.configuration.x.sv_ITIS_common_name,
+                                     loaded_from_file.to_json,
+                                     :content_type => :json )
+      end
+
+      if mapping_response.empty?
+        mapping_response = Req.post( Rails.configuration.x.sv_TROPICOS_commmon_name,
+                                     loaded_from_file.to_json,
+                                     :content_type => :json )
+      end
+
+      extracted_response = {}
+      begin 
+        extracted_response["scientificNames"] = mapping_response["result"].map do |n|
+          n["matched_names"].map do |m|
+            m["scientific_name"]
+          end
+        end.flatten
+      rescue
+        extracted_response["scientificNames"] = []
+      end
+
+      @list.update_attributes(extracted: extracted_response.to_json)
+
+      resolved_response = Req.post( Rails.configuration.x.sv_OToL_TNRS_wrapper,
+                                    extracted_response.to_json,
+                                    :content_type => :json )
+
+      if resolved_response.empty?
+        extracted_for_gnr = extracted_response
+        extracted_for_gnr["fuzzy_match"]    = true
+        extracted_for_gnr["multiple_match"] = false
+        resolved_response = Req.post( Rails.configuration.x.sv_GNR_TNRS_wrapper,
+                                      extracted_for_gnr.to_json,
+                                      :content_type => :json )
+      end
+
+      if resolved_response.empty?
+        error = Req.post( Rails.configuration.x.sv_OToL_TNRS_wrapper,
+                          extracted_response.to_json,
+                          {:content_type => :json},
+                          true )
+        fail_record = Failure.last.id
+      end     
+
+      @list.update_attributes(resolved: resolved_response.to_json, 
+                              resolving_error: error, 
+                              possible_failure_record: fail_record)
+
+      redirect_to list_path(@list)
+    else
+      render action: "new"
+    end
+  end
+
+  private
+
+    def cn_params
+      begin
+        params.require(:cn).permit(:file, :multiple_match)
+      rescue
+        {}
+      end
+    end
+end

app/helpers/cns_helper.rb

@@ -0,0 +1,2 @@
+module CnsHelper
+end

app/models/cn.rb

@@ -0,0 +1,24 @@
+class Cn < ApplicationRecord
+  belongs_to :user
+
+  has_one :list, as: :resource, dependent: :destroy
+
+  has_attached_file :file, default_url: "/images/:style/missing.png"
+
+  default_scope -> { order(created_at: :desc) }
+
+  validates_attachment :file, 
+    content_type: { content_type: [ "application/pdf", 
+                                    "text/plain", 
+                                    "application/vnd.ms-excel", 
+                                    "application/vnd.openxmlformats-officedocument.wordprocessingml.document", 
+                                    "application/msword",
+                                    "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" ] },
+    size: { in: 0..2.megabytes, :message => "must be less than 2MB" }
+
+  validates_attachment_presence :file
+
+  def meta_origin
+    file.original_filename
+  end
+end

app/models/user.rb

@@ -10,6 +10,7 @@ class User < ApplicationRecord
   has_many  :links, dependent: :destroy
   has_many  :documents, dependent: :destroy
   has_many  :onpls, dependent: :destroy
+  has_many  :cns, dependent: :destroy
   has_many  :dcas, dependent: :destroy
   has_many  :taxonomies, dependent: :destroy
   has_many  :trees, dependent: :destroy
@@ -25,6 +26,9 @@ def lists
     onpl_resource_lists = self.onpls.map {|l| l.list}
     lists.concat onpl_resource_lists
 
+    cn_resource_lists = self.cns.map {|l| l.list}
+    lists.concat cn_resource_lists
+
     dca_resource_lists = self.dcas.map {|l| l.list}
     lists.concat dca_resource_lists
 

app/views/cns/new.html.erb

@@ -0,0 +1,59 @@
+<% provide(:title, "Create trees from common names in files that have one name per line") %>
+
+<div class="container">
+  <h1>Extract common names from files that have one name per line</h1>
+  <%= form_for @cn, html: {multipart: true, class: "form-horizontal"} do |f| %>
+
+    <div class="row">
+      <div class="col-sm-6 col-sm-offset-3">
+        <%= render 'shared/error_messages', object: f.object %>
+      </div>
+    </div>
+
+    <div class="form-group">
+      <%= f.label :file, for: "cn_file", class: "col-sm-3 control-label" do %>
+        <span data-toggle="tooltip" title="Accepted file extensions: .pdf, .txt, .doc, .docs, .xls or .xlsx">
+          <%= fa_icon "info-circle" %>
+        </span>
+        <span data-toggle="tooltip" title="Required field"><%= fa_icon "asterisk", text: "File" %></span>
+      <% end %>
+      <div class="col-sm-7">
+        <%= f.file_field :file, id: "file-dropzone" %>
+      </div>
+    </div>
+
+    <div class="form-group">
+      <%= label_tag "cn[multiple_match]", class: "col-sm-3 control-label" do %>
+        <span data-toggle="tooltip" title="The system will return multiple matches (if available) for each common name in the input list.">
+          <%= fa_icon "info-circle" %>
+        </span>
+        Multiple match
+      <% end %>
+      <div class="col-sm-4" style="margin-top: 7px;">
+        <%= f.check_box :multiple_match, {}, true, false %>
+      </div>
+    </div>
+
+    <div class="form-group">
+      <%= label_tag :name, for: "name", class: "col-sm-3 control-label" do %>
+        Name for list
+      <% end %>
+      <div class="col-sm-4">
+        <%= text_field_tag :name, nil, placeholder: "Name", class: "form-control" %>
+      </div>
+    </div>
+
+    <div class="form-group">
+      <%= label_tag :description, "Description", for: "description_", class: "col-sm-3 control-label" %>
+      <div class="col-sm-7">
+        <%= text_area :description, "", placeholder: "Description", class: "form-control", rows: 5 %>
+      </div>
+    </div>
+
+    <div class="form-group">
+      <div class="col-sm-offset-3 col-sm-9">
+        <%= f.submit "Submit", class: "btn btn-default btn-lg btn-primary" %>
+      </div>
+    </div>
+  <% end %>
+</div>

app/views/lists/_new_list.html.erb

@@ -27,7 +27,8 @@
       <div class="modal-body">
         <div class="panel panel-primary emphasize-panel">
           <div class="list-group">
-            <%= link_to "I have a text file with one name per line", new_onpl_path, class:"list-group-item" %>
+            <%= link_to raw("I have a text file with one <strong>scientific name</strong> per line"), new_onpl_path, class:"list-group-item" %>
+            <%= link_to raw("I have a text file with one <strong>common name</strong> per line"), new_cn_path, class:"list-group-item" %>
             <%= link_to "I have a Darwin Core Archive (.zip)", new_dca_path, class:"list-group-item" %>
           </div>
         </div>

config/environments/development.rb

@@ -81,5 +81,8 @@
     config.x.sv_Add_new_list = "http://phylo.cs.nmsu.edu:5005/phylotastic_ws/sls/insert_list"
     config.x.sv_OToL_scale_tree = "http://phylo.cs.nmsu.edu:5009/phylotastic_ws/sc/ot/scale"
     config.x.sv_Taxon_popular_species = "http://phylo.cs.nmsu.edu:5006/phylotastic_ws/ts/popular_species?taxon="
+    config.x.sv_NCBI_common_name = "http://phylo.cs.nmsu.edu:5013/phylotastic_ws/cs/ncbi/scientific_names"
+    config.x.sv_ITIS_common_name = "http://phylo.cs.nmsu.edu:5013/phylotastic_ws/cs/itis/scientific_names"
+    config.x.sv_TROPICOS_commmon_name = "http://phylo.cs.nmsu.edu:5013/phylotastic_ws/cs/tpcs/scientific_names"
   end
 end

config/environments/production.rb

@@ -115,5 +115,8 @@
     config.x.sv_Add_new_list = "http://phylo.cs.nmsu.edu:5007/phylotastic_ws/sls/insert_list"
     config.x.sv_OToL_scale_tree = "http://phylo.cs.nmsu.edu:5009/phylotastic_ws/sc/ot/scale"
     config.x.sv_Taxon_popular_species = "http://phylo.cs.nmsu.edu:5006/phylotastic_ws/ts/popular_species?taxon="
+    config.x.sv_NCBI_common_name = "http://phylo.cs.nmsu.edu:5013/phylotastic_ws/cs/ncbi/scientific_names"
+    config.x.sv_ITIS_common_name = "http://phylo.cs.nmsu.edu:5013/phylotastic_ws/cs/itis/scientific_names"
+    config.x.sv_TROPICOS_commmon_name = "http://phylo.cs.nmsu.edu:5013/phylotastic_ws/cs/tpcs/scientific_names"
   end
 end

config/routes.rb

@@ -1,5 +1,5 @@
 Rails.application.routes.draw do
-  
+
   mount ActionCable.server => '/cable'
 
   resources :trees, only: [:show, :update, :destroy] do
@@ -22,6 +22,7 @@
   resources :links, only: [:new, :create]
   resources :documents, only: [:new, :create]
   resources :onpls, only: [:new, :create]
+  resources :cns, only: [:new, :create]
   resources :dcas, only: [:new, :create] do
     member do
       get 'publish'

db/migrate/20181001224846_create_cns.rb

@@ -0,0 +1,10 @@
+class CreateCns < ActiveRecord::Migration[5.1]
+  def change
+    create_table :cns do |t|
+      t.references :user, foreign_key: true, index: true
+      t.boolean :multiple_match, :default => false
+
+      t.timestamps
+    end
+  end
+end

db/migrate/20181001225152_add_attachment_file_to_cns.rb

@@ -0,0 +1,11 @@
+class AddAttachmentFileToCns < ActiveRecord::Migration[5.1]
+  def self.up
+    change_table :cns do |t|
+      t.attachment :file
+    end
+  end
+
+  def self.down
+    remove_attachment :cns, :file
+  end
+end

interactive_test/common_names.txt

@@ -0,0 +1,4 @@
+cucumber
+tomato
+lettuce
+pea

interactive_test/common_names_2.txt

@@ -0,0 +1,9 @@
+cattle
+cat
+goat
+pig
+sheep
+duck
+chicken
+horse
+domestic dog

test/controllers/cns_controller_test.rb

@@ -0,0 +1,9 @@
+require 'test_helper'
+
+class CnsControllerTest < ActionDispatch::IntegrationTest
+  test "should get new" do
+    get cns_new_url
+    assert_response :success
+  end
+
+end

test/fixtures/cns.yml

@@ -0,0 +1,7 @@
+# Read about fixtures at http://api.rubyonrails.org/classes/ActiveRecord/FixtureSet.html
+
+one:
+  user: 
+
+two:
+  user: 

test/models/cn_test.rb

@@ -0,0 +1,7 @@
+require 'test_helper'
+
+class CnTest < ActiveSupport::TestCase
+  # test "the truth" do
+  #   assert true
+  # end
+end