store uploaded datasets

4 files changed, 132 insertions, 47 deletions

diff --git a/application.rb b/application.rb
index 04b5aa3..8f78845 100644
--- a/application.rb
+++ b/application.rb
@@ -33,6 +33,7 @@ get '/predict/?' do
   rescue
     nil
   end
+  @existing_datasets = dataset_storage
   @models = Model::Validation.all
   @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/}
   @endpoints = @models.collect{|m| m.endpoint}.sort.uniq
@@ -136,6 +137,22 @@ get '/predict/dataset/:name' do
   csv
 end
 
+get '/download/dataset/:id' do
+  response['Content-Type'] = "text/csv"
+  dataset = Dataset.find params[:id]
+  tempfile = Tempfile.new
+  tempfile.write(File.read("tmp/"+dataset.name+".csv"))
+  tempfile.rewind
+  send_file tempfile, :filename => dataset.name+".csv", :type => "text/csv", :disposition => "attachment"
+end
+
+get '/delete/dataset/:id' do
+  dataset = Dataset.find params[:id]
+  dataset.delete
+  File.delete File.join("tmp/"+dataset.name+".csv")
+  redirect to("/")
+end
+
 get '/predict/csv/:task/:model/:filename/?' do
   response['Content-Type'] = "text/csv"
   task = Task.find params[:task].to_s
@@ -156,35 +173,49 @@ get '/predict/csv/:task/:model/:filename/?' do
 end
 
 post '/predict/?' do
-
   # process batch prediction
-  if !params[:fileselect].blank?
-    if params[:fileselect][:filename] !~ /\.csv$/
-      bad_request_error "Wrong file extension for '#{params[:fileselect][:filename]}'. Please upload a CSV file."
+  if !params[:fileselect].blank? || !params[:existing].blank?
+    if !params[:existing].blank?
+      @dataset = Dataset.find params[:existing].keys[0]
+      @compounds = @dataset.compounds
+      @filename = @dataset.name
     end
-    File.open('tmp/' + params[:fileselect][:filename], "w") do |f|
-      f.write(params[:fileselect][:tempfile].read)
-    end
-    @filename = params[:fileselect][:filename]
-    begin
-      input = Dataset.from_csv_file File.join("tmp", params[:fileselect][:filename]), true
-      $logger.debug "save dataset #{params[:fileselect][:filename]}"
-      if input.class == OpenTox::Dataset
-        @dataset = Dataset.find input
-        @compounds = @dataset.compounds
-      else
+    if !params[:fileselect].blank?
+      if params[:fileselect][:filename] !~ /\.csv$/
+        bad_request_error "Wrong file extension for '#{params[:fileselect][:filename]}'. Please upload a CSV file."
+      end
+      @filename = params[:fileselect][:filename]
+      begin
+        @dataset = Dataset.find_by(:name => params[:fileselect][:filename].sub(/\.csv$/,""))
+        if @dataset
+          $logger.debug "Take file from database."
+          @compounds = @dataset.compounds
+        else
+          File.open('tmp/' + params[:fileselect][:filename], "w") do |f|
+            f.write(params[:fileselect][:tempfile].read)
+          end
+          input = Dataset.from_csv_file File.join("tmp", params[:fileselect][:filename]), true
+          $logger.debug "Processing '#{params[:fileselect][:filename]}'"
+          if input.class == OpenTox::Dataset
+            @dataset = input
+            @compounds = input.compounds
+          else
+            File.delete File.join("tmp", params[:fileselect][:filename])
+            bad_request_error "Could not serialize file '#{@filename}'."
+          end
+        end
+      rescue
+        File.delete File.join("tmp", params[:fileselect][:filename])
         bad_request_error "Could not serialize file '#{@filename}'."
       end
-    rescue
-      bad_request_error "Could not serialize file '#{@filename}'."
-    end
 
-    if @compounds.size == 0
-      message = dataset[:warnings]
-      @dataset.delete
-      bad_request_error message
+      if @compounds.size == 0
+        message = dataset[:warnings]
+        @dataset.delete
+        bad_request_error message
+      end
     end
-    
+      
     @models = params[:selection].keys
     # for single predictions in batch
     @tasks = []
@@ -322,7 +353,7 @@ post '/predict/?' do
     @pid = task.pid
 
     #@dataset.delete
-    File.delete File.join("tmp", params[:fileselect][:filename])
+    #File.delete File.join("tmp", params[:fileselect][:filename])
     return haml :batch
   end
 
diff --git a/helper.rb b/helper.rb
index fd3b9f4..dc4b695 100644
--- a/helper.rb
+++ b/helper.rb
@@ -122,4 +122,11 @@ helpers do
     csv
   end
 
+  def dataset_storage
+    all = Dataset.where(:source => /^tmp/)
+    out = Hash.new
+    all.reverse.each{|d| out[d.id] = [d.name, d.created_at]}
+    out
+  end  
+
 end
diff --git a/views/predict.haml b/views/predict.haml
index 6b1c462..054bfa2 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -26,7 +26,14 @@
   function getInput(){
     identifier = document.getElementById("identifier").value.trim();
     fileselect = document.getElementById("fileselect").value;
-    if (fileselect != ""){
+    allexisting = document.querySelectorAll('[id^="existing"]');
+    existingcsv = false
+    for (var index = 0; index < allexisting.length; index++) {
+      if(allexisting[index].checked == true) {
+        existingcsv = true;
+      };
+    };
+    if (fileselect != "" || existingcsv == true){
       return 1;
     };
     if (identifier != ""){
@@ -70,6 +77,12 @@
       //TODO check file type is csv
       return true;
     };
+    allexisting = document.querySelectorAll('[id^="existing"]');
+    for (var index = 0; index < allexisting.length; index++) {
+      if(allexisting[index].checked == true) {
+        return true;
+      };
+    };
     alert("Please select a file (csv).");
     return false;
   };
@@ -85,11 +98,12 @@
   };
   function checkboxes () {
     var checked = false;
-    $('input[type="checkbox"]').each(function() {
-      if ($(this).is(":checked")) {
+    models = document.querySelectorAll('[id^="selection"]');
+    for (var index = 0; index < models.length; index++) {
+      if(models[index].checked == true) {
         checked = true;
       };
-    });
+    };
     if (checked == false){
       alert("Please select an endpoint.");
       $("img.circle").hide();
@@ -114,23 +128,43 @@
 %form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" }
   %fieldset#top.well
     %h2 1. Draw a chemical structure
-    #insert
-      %label &nbsp;
-      #appletContainer
-      %br
-      %label{:for => 'identifier'}
-        or enter the
-        %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
-        string:
-      %br
-      %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
-      %p
-      %label{:for=>"fileselect"}
-        or upload a CSV file for batch predictions
-      %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}}
-      %br
-      %span.btn.btn-default.btn-file
-        %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :autocomplete=>"off", :accept=>"text/csv"}
+    %div.row
+      %div.col-md-6
+        #insert
+          %label &nbsp;
+          #appletContainer
+          %br
+          %label{:for => 'identifier'}
+            or enter the
+            %a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
+            string:
+          %br
+          %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'}
+          %p
+          %label{:for=>"fileselect"}
+            or upload a CSV file for batch predictions
+          %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"First column must contain a header with \"SMILES\" or \"InChI\" and the compounds. Also note that a file with the same name of a file that already exists won't be processed."}}
+          %br
+          %span.btn.btn-default.btn-file
+            %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :autocomplete=>"off", :accept=>"text/csv"}
+      %div.col-md-6
+        - if !@existing_datasets.blank?
+          %label{:for=>"storage"} or select an uploaded CSV file
+          #storage.storage-list
+            - @existing_datasets.each do |id,values|
+              %div.p2
+                %input.checkDataset{:type => "checkbox", :name => "existing[#{id}]", :id => "existing[#{id}]", :value => true, :disabled => false}
+                %div.btn-group{:role=>"group", :aria=>{:label=>"remove-download"}}
+                  %a.btn.btn-secondary{:role=>"button", :href=>to("/delete/dataset/#{id}")}
+                    %i.glyphicon.glyphicon-trash
+                  %a.btn.btn-secondary{:role=>"button", :href=>to("/download/dataset/#{id}")}
+                    %i.glyphicon.glyphicon-save
+              %div.p2
+                %label{:for => "existing[#{id}]"}
+                  = values[0]
+              %div.p2
+                = values[1].strftime("%Y-%m-%d %H:%M:%S")
+              %hr
 
   %fieldset#middle.well
     %h2 2. Select one or more endpoints
@@ -146,6 +180,9 @@
             $(".check").prop('checked', false);
           };
         });
+        $(".checkDataset").click(function () {
+          $('.checkDataset').not(this).prop('checked', false);
+        });
       - @endpoints.each do |endpoint|
         %div{:id=>endpoint.gsub(/\s+/, "_")}
           %h4.head-back=endpoint
@@ -197,6 +234,7 @@
       %div.col-md-2
         %h2
           3. Predict
-      %div.col-md-10
-        %input.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>">>", :onclick => "getsmiles()"}
+      %div.col-md-10.input-group
+        %button.has-feedback.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>"", :onclick => "getsmiles()"}
+          %span.glyphicon.glyphicon-play
         %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle", :class=>"circle", :alt=>"wait", :style=>"display:none;"}
diff --git a/views/style.scss b/views/style.scss
index 46c57c6..fc6f8f2 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -26,6 +26,10 @@
 }
 body {
   background-color:#E7E7E7;
+  
+  a {
+    color: inherit;
+  }
 }
 table.table-borderless tbody tr td{
   border-top: none;
@@ -111,3 +115,8 @@ tr.hide-top > td {
 .footer{
   margin-top:3em;
 }
+.storage-list {
+    height: 400px;
+    overflow-y: auto;
+    overflow-x: auto;
+}