Copasi javascript support

app/assets/javascripts/application.js

@@ -78,3 +78,8 @@
 //= require select2.full.min
 //= require licenses
 //= require svg-pan-zoom-3.6.1/svg-pan-zoom.min
+//= require copasi/copasi
+//= require copasi/copasijs
+//= require copasi/copasi_simulation
+//= require plotly-2.27.0.min
+

app/assets/javascripts/copasi/copasi_simulation.js

@@ -0,0 +1,79 @@
+// app/assets/javascripts/copasi_simulation.js
+
+var copasi = null;
+
+function automaticChanged() {
+    var autoStepSize = document.getElementById("autoStepSize").checked;
+    document.getElementById("numPoints").disabled = autoStepSize;
+}
+
+function loadIntoCOPASI() {
+    var info = copasi.loadModel(document.getElementById("cps").value);
+    document.getElementById("model_name").innerHTML = "none";
+    if (info['status'] != "success") {
+        document.getElementById("simulation_error").innerHTML = "Error loading model: " + info['messages'];
+        document.getElementById('simulation_error').hidden = false;
+    }
+    document.getElementById("model_name").innerHTML = 'Model name: ' + info['model']['name'];
+    document.getElementById("copasi_version").innerHTML = 'Copasi version: ' + copasi.version;
+    document.getElementById('simulation_info').hidden = false;
+}
+
+function simulate() {
+    if (copasi == null) {
+        alert('There is a problem to load Copasi simulator.');
+        return;
+    }
+    loadIntoCOPASI();
+    runSimulation();
+}
+
+function runSimulation() {
+    var autoStepSize = document.getElementById("autoStepSize").checked;
+    var timeStart = parseFloat(document.getElementById("startTime").value);
+    var timeEnd = parseFloat(document.getElementById("endTime").value);
+
+    if (autoStepSize) {
+        var result = copasi.simulateYaml({
+            "problem": {
+                "AutomaticStepSize": true,
+                "Duration": timeEnd,
+                "OutputStartTime": timeStart
+            }
+        });
+        loadPlotFromResult(result);
+        return;
+    }
+
+    var numPoints = parseInt(document.getElementById("numPoints").value);
+    var result = copasi.simulateEx(timeStart, timeEnd, numPoints);
+    loadPlotFromResult(result);
+}
+
+function loadPlotFromResult(result) {
+    if (typeof result === 'string') {
+        result = JSON.parse(result);
+    }
+
+    clearResults();
+    document.getElementById("data").innerHTML = JSON.stringify(result);
+
+    var data = [];
+    for (var i = 1; i < result.num_variables; i++) {
+        data.push({
+            name: result.columns[i][0],
+            x: result.columns[0],
+            y: result.columns[i],
+            type: "scatter",
+            name: result.titles[i]
+        });
+    }
+
+    Plotly.newPlot('chart', data);
+}
+
+function clearResults() {
+    document.getElementById("data").innerHTML = "";
+    document.getElementById("chart").innerHTML = "";
+}
+

app/controllers/application_controller.rb

@@ -391,6 +391,7 @@ def log_event
         action = 'inline_view' if action == 'explore'
         action = 'download' if action == 'ro_crate'
         action = 'run' if action == 'simulate'
+        action = 'run' if action == 'copasi_simulate'
         if %w(show create update destroy download inline_view run).include?(action)
           check_log_exists(action, controller_name, object)
           ActivityLog.create(action: action,

app/controllers/models_controller.rb

@@ -12,6 +12,7 @@ class ModelsController < ApplicationController
   before_action :find_other_version, :only => [:compare_versions]
 
   include Seek::Jws::Simulator
+  include Seek::Copasi::Simulator
   include Seek::Publishing::PublishingCommon
 
   include Bives

app/helpers/assets_helper.rb

@@ -214,15 +214,26 @@ def download_or_link_button(asset, download_path, link_url, _human_name = nil, o
     end
   end
 
-  def open_with_copasi_button (asset)
+  def open_with_copasi_js_button
+
+    tooltip_text = "Simulate model in the browser with javascript library"
+    button_link_to 'Simulate Online', 'copasi', '#', class: 'btn btn-primary btn-block', onclick: 'simulate()', disabled: @blob.nil?, 'data-tooltip' => tooltip(tooltip_text)
+
+  end
+
+  def open_with_copasi_ui_button
+
+    blob  =   @display_model.copasi_supported_content_blobs.first
+
+    auth_code = @model.special_auth_codes.where('code LIKE ?', 'copasi_%').first.code unless @model.can_download?(nil)
+
+    download_path = polymorphic_path([@model, blob], action: :download, code: auth_code)
 
-    files =   asset.content_blobs
-    download_path = polymorphic_path([files.first.asset, files.first], action: :download, code: params[:code])
     copasi_download_path =  "copasi://process?downloadUrl=http://"+request.host_with_port+download_path+"&activate=Time%20Course&createPlot=Concentrations%2C%20Volumes%2C%20and%20Global%20Quantity%20Values&runTask=Time-Course"
 
-    tooltip_text_copasi_button = "Simulate the publicly accessible model in your local installed Copasi. "
+    tooltip_text_copasi_button = "Simulate your model locally using desk application CopasiUI."
 
-    button= button_link_to('Simulate Model in Copasi', 'copasi', copasi_download_path, class: 'btn btn-default', disabled: asset.download_disabled?, 'data-tooltip' => tooltip(tooltip_text_copasi_button))
+    button= button_link_to('Simulate in CopasiUI', 'copasi', copasi_download_path, class: 'btn btn-primary btn-block', disabled: @blob.nil?, 'data-tooltip' => tooltip(tooltip_text_copasi_button))
 
     button
   end

app/helpers/models_helper.rb

@@ -40,6 +40,6 @@ def jws_online_logo
   end
 
   def show_copasi_button?
-    Seek::Config.copasi_enabled && (@display_model.policy.access_type == Policy::ALL_USERS) && @display_model.is_copasi_supported?
+    Seek::Config.copasi_enabled && @display_model.is_copasi_supported? && @display_model.is_downloadable? && @display_model.can_download?(current_user)
   end
 end

app/models/model.rb

@@ -112,9 +112,17 @@ def model_format
   end
 
   def can_run?
+    can_run_jws? || can_run_copasi?
+  end
+
+  def can_run_jws?
     Seek::Config.jws_enabled && can_download? && is_jws_supported?
   end
 
+  def can_run_copasi?
+    Seek::Config.copasi_enabled && can_download? && is_copasi_supported?
+  end
+
   private
 
   def check_for_sbml_format

app/views/models/_buttons.html.erb

@@ -1,21 +1,21 @@
 <% if show_copasi_button? %>
-  <%= open_with_copasi_button @display_model %>
+  <%= button_link_to("Simulate #{t('model')} on Copasi", 'copasi', copasi_simulate_model_path(version: @display_model.version, code: params[:code]),method: :get) %>
 <% end %>
 
 <% if show_jws_simulate? %>
     <%= button_link_to("Simulate #{t('model')} on JWS", 'execute',
-                       simulate_model_path(item, :version => @display_model.version, :code => params[:code]), :method=>:post,:title => "Simulate #{t('model')} on JWS") %>
+                       simulate_model_path(item, version: @display_model.version, code: params[:code]), method: :post, title: "Simulate #{t('model')} on JWS") %>
 <% end %>
 
 <% if Seek::Config.sycamore_enabled && @display_model.contains_sbml? %>
     <% excutable_content_blob =  @display_model.content_blobs.detect{|cb| cb.is_sbml?}
        if excutable_content_blob.is_in_simulatable_size_limit? && can_download_asset?(@model, params[:code]) -%>
-        <%= form_tag("http://sycamore.eml.org/sycamore/submission.jsp", :id => 'sycamore-form', :target => '_blank') do -%>
+        <%= form_tag("http://sycamore.eml.org/sycamore/submission.jsp", id: 'sycamore-form', target: '_blank') do -%>
             <%= hidden_field_tag 'sbml_model' -%>
             <%= hidden_field_tag 'sender', 'seek' -%>
-            <%= button_link_to "Simulate #{t('model')} on Sycamore", 'execute', url_for(:action => 'submit_to_sycamore', :id => @model.id, :version => @display_model.version), :remote => true, :method => :post -%>
+            <%= button_link_to "Simulate #{t('model')} on Sycamore", 'execute', url_for(action: 'submit_to_sycamore', id: @model.id, version: @display_model.version), remote: true, method: :post -%>
         <% end -%>
     <% end -%>
 <% end %>
 
-<%= render :partial => 'assets/asset_buttons', :locals => {:asset => item, :version => version} -%>
+<%= render partial: 'assets/asset_buttons', locals: {asset: item, version: version} -%>

app/views/models/copasi_simulate.html.erb

@@ -0,0 +1,105 @@
+<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(version: @display_model.version, code: params[:code])) } %>
+<%= render partial: "general/item_title",locals: {item: @model, title_postfix: " - Copasi #{t('model')} Simulation"} %>
+
+<div class="container-fluid">
+  <div id="simulation_error" class="alert alert-danger" role="alert" hidden=""></div>
+  <div id="simulation_info" class="alert alert-info" role="alert" hidden="">
+    <div id="model_name"></div>
+    <div id="copasi_version"></div>
+  </div>
+  <div id="chart"></div>
+  <div class="panel panel-default">
+    <div class="panel-body">
+      <div class="row">
+        <div class="col-sm-2">
+          <%= label_tag :start_time, "Start Time" %>
+          <%= number_field_tag :start_time, 0, class: "form-control", placeholder: "Enter start time", id: "startTime" %>
+        </div>
+        <div class="col-sm-2">
+          <%= label_tag :end_time, "End Time:" %>
+          <%= number_field_tag :end_time, 10, class: "form-control", placeholder: "Enter end time", id: "endTime" %>
+        </div>
+        <div class="col-sm-2">
+          <%= label_tag :num_points, "Number of Points:" %>
+          <%= number_field_tag :num_points, 101, class: "form-control", placeholder: "Enter number of points", id: "numPoints" %>
+        </div>
+        <div class="col-sm-3">
+          <%= label_tag :simulate_js, "&nbsp;".html_safe %>
+          <%= open_with_copasi_js_button %>
+        </div>
+        <div class="col-sm-3">
+          <label for="simulate_ui"> &nbsp;</label>
+          <%= open_with_copasi_ui_button %>
+        </div>
+      </div>
+      <div class="row">
+        <div class="col-sm-3">
+          <%= label_tag :auto_step_size, "Automatic Step Size:" %>
+          <%= check_box_tag :auto_step_size, 1, false, onclick: "automaticChanged()", id: "autoStepSize" %>
+        </div>
+      </div>
+    </div>
+  </div>
+  <div>
+    <ul class="nav nav-tabs" role="tablist">
+      <li class="nav-item active in">
+        <a class="nav-link" data-toggle="tab" href="#cps_form" role="tab" aria-controls="cps_form" aria-selected="true">CPS Model</a>
+      </li>
+      <li class="nav-item">
+        <a class="nav-link" data-toggle="tab" href="#yaml_form" role="tab" aria-controls="yaml_form" aria-selected="false">YAML</a>
+      </li>
+      <li class="nav-item">
+        <a class="nav-link" data-toggle="tab" href="#data_form" role="tab" aria-controls="data_form" aria-selected="false">Data</a>
+      </li>
+    </ul>
+    <div class="tab-content">
+      <div class="tab-pane fade active in" id="cps_form" role="tabpanel">
+        <div class="form-group">
+          <%= label_tag :cps, "CPS Model:" %>
+          <%= text_area_tag :cps, nil, class: "form-control", id: "cps", rows: 150 %>
+        </div>
+      </div>
+      <div class="tab-pane fade" id="yaml_form" role="tabpanel">
+        <div class="form-group">
+          <%= label_tag :yaml, "Processing: " %>
+          <small>
+            Changes for processing in yaml for the problem:
+            <pre>{"problem":{"Duration": 100, "StepNumber": 100, "StepSize": 0.1}}</pre> or
+            <pre>{"method": {"name": "Stochastic (Gibson + Bruck)"}}</pre> or for changes of
+            initial values in the form of display names. So:
+            <ul>
+              <li>
+                <pre>[A]_0</pre> for initial concentration of species A
+              </li>
+              <li>
+                <pre>Values[t].InitialValue</pre> for initial value of parameter t
+              </li>
+              <li>
+                <pre>(r1).k</pre> for the value of k of reaction r1.
+              </li>
+            </ul>
+            <pre>{"initial_values": {"[A]_0": 10.0, "Values[t].InitialValue": 0.1, "(r1).k": 0.1}}</pre>
+          </small>
+          <%= text_area_tag :yaml, "{}", class: "form-control", id: "yaml", rows: 8 %>
+        </div>
+      </div>
+      <div class="tab-pane fade" id="data_form" role="tabpanel">
+        <div class="form-group">
+          <%= label_tag :data, "Data Yaml:" %>
+          <%= text_area_tag :data, nil, class: "form-control", id: "data", rows: 8 %>
+        </div>
+      </div>
+    </div>
+  </div>
+</div>
+
+<script>
+    $j(document).ready(function () {
+        createCpsModule().then(module => {
+            copasi = new COPASI(module);
+            console.log(copasi.version);
+        });
+
+        $j('#cps').val("<%= escape_javascript @blob.html_safe %>");
+    });
+</script>

config/routes.rb

@@ -521,6 +521,7 @@
       post :execute
       get :simulate
       post :simulate
+      get :copasi_simulate
     end
     resources :model_images, only: [:show]
     resources :people, :programmes, :projects, :investigations, :assays, :studies, :publications, :events, :collections, :organisms, :human_diseases, only: [:index]

lib/seek/copasi/simulator.rb

@@ -0,0 +1,92 @@
+module Seek
+  module Copasi
+    module Simulator
+      extend ActiveSupport::Concern
+      include ERB::Util
+      included do
+        before_action :find_model, :find_display_asset_for_copasi, :select_model_file_for_simulation, only: [:copasi_simulate]
+        before_action :fetch_special_auth_code, if: -> { is_special_auth_code_required? }, only: [:copasi_simulate]
+        before_action :copasi_enabled, only: [:copasi_simulate]
+      end
+
+      def copasi_simulate
+        render 'copasi_simulate'
+      end
+
+      def find_model
+        @model = Model.find_by_id(params[:id])
+      end
+
+      # # If the content blob is not available locally, fetch a copy from the remote URL
+      def select_model_file_for_simulation
+
+        content_blob = select_copasi_content_blob
+
+        if content_blob.nil?
+          flash.now[:error] = 'The selected version does not contain a format supported by COPASI.'
+        else
+          if content_blob.file_exists?
+            @blob = (File.read(content_blob.file))
+          else
+            blob_url = content_blob.url
+            begin
+              handler = ContentBlob.remote_content_handler_for(blob_url)
+              data = handler.fetch
+              @blob = (File.read(data))
+              true
+            rescue Seek::DownloadHandling::BadResponseCodeException => e
+              flash.now[:error] = "URL could not be accessed: #{e.message}"
+              false
+            rescue StandardError => e
+              flash.now[:error] = 'There is a problem to load the model file.'
+              false
+            end
+          end
+        end
+      end
+
+      # select the first COPASI-compatible content_blob when multiple items are associated with the display model.
+      def select_copasi_content_blob
+        blob = @display_model.copasi_supported_content_blobs.first
+        blob
+      end
+
+      def find_display_asset_for_copasi
+        find_display_asset
+      end
+
+      def copasi_enabled
+        unless Seek::Config.copasi_enabled
+          respond_to do |format|
+            flash[:error] = "Interaction with Copasi Online is currently disabled"
+            format.html { redirect_to model_path(@model, :version => @display_model.version) }
+          end
+          return false
+        end
+      end
+
+      private
+
+      def special_auth_codes_with_copasi_prefix
+        @model.special_auth_codes.where('code LIKE ?', 'copasi_%')
+      end
+
+      def is_special_auth_code_required?
+        # If the model is not publicly accessible but can be downloaded by the current user, the special auth code will be required.
+        Seek::Config.copasi_enabled && @display_model.is_copasi_supported? && @model.can_download?(current_user) && [email protected]_download?(nil)
+      end
+
+      # fetches or generates a special auth code with a "copasi_" prefix, which is used by COPASI desk application to load the non public model
+      def fetch_special_auth_code
+        copasi_codes = special_auth_codes_with_copasi_prefix
+        return copasi_codes.first unless copasi_codes.empty?
+
+        auth_code = SpecialAuthCode.create(expiration_date: Time.now + 1.day, code: "copasi_#{SecureRandom.hex(10)}")
+        @model.special_auth_codes << auth_code
+        auth_code
+      end
+
+    end
+  end
+end
+