Merge pull request #292 from Merfoo/gene-sequences-import

Gene sequences import for Maddison Lab

app/controllers/descriptors_controller.rb

@@ -1,8 +1,8 @@
 class DescriptorsController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
-
+  
   before_action :set_descriptor, only: [:show, :edit, :update, :destroy, :annotations]
-
+  
   # GET /descriptors
   # GET /descriptors.json
   def index
@@ -16,30 +16,30 @@ def index
       }
     end 
   end
-
+  
   # GET /descriptors/1
   # GET /descriptors/1.json
   def show
   end
-
+  
   def list
     @descriptor = Descriptor.with_project_id(sessions_current_project_id).page(params[:page])
   end
-
+  
   # GET /descriptors/new
   def new
     @descriptor = Descriptor.new
   end
-
+  
   # GET /descriptors/1/edit
   def edit
   end
-
+  
   # POST /descriptors
   # POST /descriptors.json
   def create
     @descriptor = Descriptor.new(descriptor_params)
-
+    
     respond_to do |format|
       if @descriptor.save
         format.html { redirect_to @descriptor.metamorphosize, notice: 'Descriptor was successfully created.' }
@@ -50,7 +50,7 @@ def create
       end
     end
   end
-
+  
   # PATCH/PUT /descriptors/1
   # PATCH/PUT /descriptors/1.json
   def update
@@ -64,7 +64,7 @@ def update
       end
     end
   end
-
+  
   # DELETE /descriptors/1
   # DELETE /descriptors/1.json
   def destroy
@@ -74,21 +74,21 @@ def destroy
       format.json { head :no_content }
     end
   end
-
+  
   def autocomplete
     t = "#{params[:term]}%"
     @descriptors = Descriptor.where(project_id: sessions_current_project_id).where('name like ? or short_name like ?', t, t)
     data = @descriptors.collect do |t|
       {id:              t.id,
-       label:           t.name, 
-       gid: t.to_global_id.to_s,
-       response_values: {
-         params[:method] => t.id
-       },
-       label_html:      t.name 
-      }
-    end
-    render :json => data
+      label:           t.name, 
+      gid: t.to_global_id.to_s,
+      response_values: {
+        params[:method] => t.id
+      },
+      label_html:      t.name 
+    }
+  end
+  render :json => data
   end
 
   def search
@@ -105,15 +105,46 @@ def annotations
     render '/shared/data/all/annotations'
   end
 
+  def batch_load
+  end
 
+  def preview_modify_gene_descriptor_batch_load 
+    if params[:file] 
+      @result = BatchLoad::Import::Descriptors::ModifyGeneDescriptorInterpreter.new(batch_params)
+      digest_cookie(params[:file].tempfile, :modify_gene_descriptor_batch_load_descriptors_md5)
+      render 'descriptors/batch_load/modify_gene_descriptor/preview'
+    else
+      flash[:notice] = "No file provided!"
+      redirect_to action: :batch_load 
+    end
+  end
+
+  def create_modify_gene_descriptor_batch_load
+    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :modify_gene_descriptor_batch_load_descriptors_md5)
+      @result = BatchLoad::Import::Descriptors::ModifyGeneDescriptorInterpreter.new(batch_params)
+      if @result.create
+        flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} Gene Descriptors were modified."
+        render 'descriptors/batch_load/modify_gene_descriptor/create' and return
+      else
+        flash[:alert] = 'Batch import failed.'
+      end
+    else
+      flash[:alert] = 'File to batch upload must be supplied.'
+    end
+    render :batch_load
+  end
+
+private
 
-  private
-
   def set_descriptor
     @descriptor = Descriptor.find(params[:id])
   end
 
   def descriptor_params
     params.require(:descriptor).permit(:name, :short_name, :type)
   end
+
+  def batch_params
+    params.permit(:file).merge(user_id: sessions_current_user_id, project_id: sessions_current_project_id).to_h.symbolize_keys
+  end
 end

app/views/collection_objects/batch_load/castor/_batch_load.html.erb

@@ -18,7 +18,7 @@
         <li>Assumes a namespace with name "GenBank" and shortname "GBK" exists</li>
         <li>Identifier Global::Uri will be attached with the value of the "guid" column if not blank to each collection object</li>
         <li>Identifier Global::MorphbankSpecimenNumber will be attached with the value of the "morphbank_specimen_id" column if not blank to each collection object</li>
-        <li>Identifier with namespace DRMLabVoucher will be attached with the value of the "voucher_number_prefix" + "voucher_number_string" column if not blank to each collection object</li>
+        <li>Identifier with namespace DRMLabVoucher will be attached with the value of the "voucher_number_prefix" + "voucher_number_string" column once if not blank to each collection object</li>
         <li>Identifier with namespace DRMDNAVoucher will be attached with the value of the "sample_code_prefix" and "sample_code" column if not blank to each collection object</li>
         <li>Identifier with namespace GenBank will be attached with the value of the "sample_code_prefix" and "sample_code" columns if not blank to each extract</li>
         <li>DataAttribute of predicate "SpecimenNumber" with value of "specimen_number" will be attached if not blank to each collection object.</li>

app/views/descriptors/batch_load.html.erb

@@ -0,0 +1 @@
+<%= render 'descriptors/batch_load/modify_gene_descriptor/batch_load' -%>

app/views/descriptors/batch_load/modify_gene_descriptor/_batch_load.html.erb

@@ -0,0 +1,35 @@
+<div>
+  <h2> Modify Gene Descriptor batch load </h2>
+
+  <div class="flexbox full_viewport_whitespace">
+    <div class="item item1 one_third_width">
+      <h3> Description and requirements </h3>
+
+      <p> Modifies each gene descriptors gene attribute logic to be at least one forward primer and one reverse primer. </p>
+      <ul>
+        <li>A tab-delimited, UTF-8 compatible text file is required.</li>
+        <li>Column headers are (see <%= link_to('sample template', asset_path('batch_load_templates/descriptors/modify_gene_descriptor_batch_load.tab'), target: '_blank') -%>).</li>
+        <li>Each primer is separated by a comma and space (", ")</li>
+        <li>Multiple uploads of the same data will X.</li>
+        <li>It is assumed each gene has one forward primer and one reverse primer.</li>
+        <li>There is currently some|no size limit to the file being loaded but this may change in the future.</li>
+      </ul>
+    </div>
+
+    <div class="item item2 one_third_width">
+      <h3> Example file </h3>
+
+      <p> A tab delimited formatted file 
+        In the example whitespace is a tab. View sample file template.</p>
+
+      <pre class="fixed_width_font">
+        gene_name forward_primers reverse_primers
+      </pre>
+    </div>
+
+    <div class="item item3">
+      <h3> Go! </h3>
+      <%= render partial: '/descriptors/batch_load/modify_gene_descriptor/form', locals: {url: preview_modify_gene_descriptor_batch_load_descriptors_path, submit: :preview} -%>
+    </div>
+  </div>
+</div>

app/views/descriptors/batch_load/modify_gene_descriptor/_form.html.erb

@@ -0,0 +1,10 @@
+<%= form_tag url, multipart: true do -%>
+    <div class="field">
+      <%= label_tag :file, 'Select a file' -%>
+      <br>
+      <%= file_field_tag :file -%>
+    </div>
+
+    <%= content_for :warn_level -%>
+    <%= submit_tag submit -%>
+<% end %>

app/views/descriptors/batch_load/modify_gene_descriptor/create.html.erb

@@ -0,0 +1 @@
+<%= render partial: '/shared/data/all/batch_load/create' -%>

app/views/descriptors/batch_load/modify_gene_descriptor/preview.html.erb

@@ -0,0 +1,33 @@
+<% content_for :warn_level do -%>
+    <%= warn_level_input(@result) -%>
+<% end %>
+
+<%= content_for :batch_form do -%>
+  <%= render partial: '/descriptors/batch_load/modify_gene_descriptor/form', locals: {url: create_modify_gene_descriptor_batch_load_descriptors_path, submit: :create} -%>
+<% end %>
+
+<%= content_for :line_breakdown do -%>
+  <table class="top_align_text"> 
+    <tr>
+      <th class="four_character_width">line</th>
+      <th class="four_character_width">data count</th>
+      <th> gene attribute logic </th>
+      <th class=""> data errors* </th>
+      <th class=""> parse errors </th>
+    </tr>
+
+    <% @result.sorted_processed_rows.each do |i, rp| -%>
+      <tr>
+        <%= batch_line_link_td(i) -%> 
+        <%= batch_all_objects_count_td(rp) -%>
+        <td>
+          <%= rp.objects[:descriptor].each_with_index.collect{|n, i| "#{i + 1}: " + n.gene_attribute_logic }.join('<br>').html_safe -%>
+        </td> 
+        <%= batch_data_errors_td(rp) -%>
+        <%= batch_parse_errors_td(rp) -%>
+      </tr>
+    <% end -%> 
+  </table>
+<% end %>
+
+<%= render partial: '/shared/data/all/batch_load/preview' -%>

app/views/sequence_relationships/batch_load/primers/_batch_load.html.erb

@@ -5,7 +5,7 @@
     <div class="item item1 one_third_width">
       <h3> Description and requirements </h3>
 
-      <p>Create sequence relationships between sequences and primer sequences</p>
+      <p>Create sequence relationships between sequences and primer sequences and creates gene descriptors and gene attributes</p>
       <ul>
         <li>A tab-delimited, UTF-8 compatible text file is required.</li>
         <li>Column headers are (see <%= link_to('sample template', asset_path('batch_load_templates/sequence_relationships/sequence_relationships_primers_batch_load.tab'), target: '_blank') -%>).</li>
@@ -20,7 +20,7 @@
       <p> A tab delimited formatted file. In the example whitespace is a tab. View sample file template.</p>
 
       <pre class="fixed_width_font">
-        identifier sample_code gene fragment publication taxon_name primers
+        identifier dna_number gene_name forward_primers reverse_primers
       </pre>
     </div>