Merge pull request #1106 from StochSS/develop

2.3.1 Release

client/models/sweep-parameter.js

@@ -1,14 +1,17 @@
 /*
 StochSS is a platform for simulating biochemical systems
 Copyright (C) 2019-2020 StochSS developers.
+
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
+
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
+
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

client/models/sweep-parameters.js

@@ -1,14 +1,17 @@
 /*
 StochSS is a platform for simulating biochemical systems
 Copyright (C) 2019-2020 StochSS developers.
+
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
+
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
+
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

client/pages/file-browser.js

@@ -842,6 +842,24 @@ let FileBrowser = PageView.extend({
       }
     });
   },
+  extractAll: function (o) {
+    let self = this;
+    let queryStr = "?path=" + o.original._path;
+    let endpoint = path.join(app.getApiPath(), "file/unzip") + queryStr;
+    app.getXHR(endpoint, {
+      success: function (err, response, body) {
+        let node = $('#models-jstree').jstree().get_node(o.parent);
+        if(node.type === "root"){
+          self.refreshJSTree();
+        }else{          
+          $('#models-jstree').jstree().refresh_node(node);
+        }
+      },
+      error: function (err, response, body) {
+        let modal = $(modals.newProjectModelErrorHtml(body.Reason, body.message)).modal();
+      }
+    });
+  },
   setupJstree: function () {
     var self = this;
     $.jstree.defaults.contextmenu.items = (o, cb) => {
@@ -1235,6 +1253,18 @@ let FileBrowser = PageView.extend({
           }
         }
       }
+      //Specific to zip archives
+      let extractAll = {
+        "extractAll" : {
+          "label" : "Extract All",
+          "_disabled" : false,
+          "separator_before" : false,
+          "separator_after" : false,
+          "action" : function (data) {
+            self.extractAll(o);
+          }
+        }
+      }
       if (o.type === 'root'){
         return folder
       }
@@ -1253,6 +1283,9 @@ let FileBrowser = PageView.extend({
       if (o.type === 'workflow') {
         return $.extend(open, workflow, common)
       }
+      if (o.text.endsWith(".zip")) {
+        return $.extend(open, extractAll, common)
+      }
       if (o.type === 'notebook' || o.type === "other") {
         return $.extend(open, common)
       }

client/styles/styles.css

@@ -1,3 +1,21 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2020 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
 body {
   min-width: 650px
 }

client/templates/includes/reactionsEditor.pug

@@ -35,6 +35,8 @@ div#reactions-editor.card.card-body
         tbody(data-hook="reaction-list")
 
       div.col-md-5.container-part(data-hook="reaction-details-container")
+
+    div(data-hook="massaction-message"): p.text-info To add a mass action reaction the model must have at least one parameter
 
     div(data-hook="process-component-error"): p.text-danger A model must have at least one reaction, event, or rule
 

client/views/file-browser-view.js

@@ -924,6 +924,24 @@ module.exports = View.extend({
       }
     });
   },
+  extractAll: function (o) {
+    let self = this;
+    let queryStr = "?path=" + o.original._path;
+    let endpoint = path.join(app.getApiPath(), "file/unzip") + queryStr;
+    app.getXHR(endpoint, {
+      success: function (err, response, body) {
+        let node = $('#models-jstree-view').jstree().get_node(o.parent);
+        if(node.type === "root"){
+          self.refreshJSTree();
+        }else{          
+          $('#models-jstree-view').jstree().refresh_node(node);
+        }
+      },
+      error: function (err, response, body) {
+        let modal = $(modals.newProjectModelErrorHtml(body.Reason, body.message)).modal();
+      }
+    });
+  },
   setupJstree: function () {
     var self = this;
     $.jstree.defaults.contextmenu.items = (o, cb) => {
@@ -1343,6 +1361,18 @@ module.exports = View.extend({
           }
         }
       }
+      //Specific to zip archives
+      let extractAll = {
+        "extractAll" : {
+          "label" : "Extract All",
+          "_disabled" : false,
+          "separator_before" : false,
+          "separator_after" : false,
+          "action" : function (data) {
+            self.extractAll(o);
+          }
+        }
+      }
       if (o.type === 'root'){
         return $.extend(refresh, project, commonFolder, downloadWCombine, {"Rename": common.Rename})
       }
@@ -1367,6 +1397,9 @@ module.exports = View.extend({
       if (o.type === 'workflow') {
         return $.extend(open, workflow, downloadWCombine, common)
       }
+      if (o.text.endsWith(".zip")) {
+        return $.extend(open, extractAll, download, common)
+      }
       if (o.type === 'notebook' || o.type === "other") {
         return $.extend(open, download, common)
       }

client/views/reactions-editor.js

@@ -133,9 +133,11 @@ module.exports = View.extend({
   },
   toggleReactionTypes: function (e, prev, curr) {
     if(curr && curr.add && this.collection.parent.parameters.length === 1){
+      $(this.queryByHook('massaction-message')).prop('hidden', true);
       $(this.queryByHook('add-reaction-full')).prop('hidden', false);
       $(this.queryByHook('add-reaction-partial')).prop('hidden', true);
     }else if(curr && !curr.add && this.collection.parent.parameters.length === 0){
+      $(this.queryByHook('massaction-message')).prop('hidden', false);
       $(this.queryByHook('add-reaction-full')).prop('hidden', true);
       $(this.queryByHook('add-reaction-partial')).prop('hidden', false);
     }

stochss/handlers/__init__.py

@@ -63,6 +63,7 @@ def get_page_handlers(route_start):
         (r"/stochss/api/file/download-zip\/?", DownloadZipFileAPIHandler),
         (r"/stochss/api/file/json-data\/?", JsonFileAPIHandler),
         (r"/stochss/api/file/duplicate\/?", DuplicateModelHandler),
+        (r"/stochss/api/file/unzip\/?", UnzipFileAPIHandler),
         (r"/stochss/api/directory/duplicate\/?", DuplicateDirectoryHandler),
         (r"/stochss/api/directory/create\/?", CreateDirectoryHandler),
         (r"/stochss/api/spatial/to-model\/?", ConvertToModelAPIHandler),

stochss/handlers/file_browser.py

@@ -674,3 +674,30 @@ async def get(self):
             log.debug("Response: %s", resp)
             self.write(resp)
         self.finish()
+
+
+class UnzipFileAPIHandler(APIHandler):
+    '''
+    ################################################################################################
+    Handler for unzipping zip archives.
+    ################################################################################################
+    '''
+
+    async def get(self):
+        '''
+        Unzip a zip archive.
+
+        Attributes
+        ----------
+        '''
+        self.set_header('Content-Type', 'application/json')
+        path = self.get_query_argument(name="path")
+        log.debug("The path to the zip archive: %s", path)
+        try:
+            file = StochSSFile(path=path)
+            resp = file.unzip(from_upload=False)
+            log.debug("Response Message: %s", resp)
+            self.write(resp)
+        except StochSSAPIError as err:
+            report_error(self, log, err)
+        self.finish()

stochss/handlers/util/ensemble_simulation.py

@@ -21,13 +21,14 @@
 import json
 import pickle
 import logging
+import traceback
 
 import numpy
 import plotly
-from gillespy2 import TauLeapingSolver, TauHybridSolver, SSACSolver, ODESolver
+from gillespy2 import TauHybridSolver
 
 from .stochss_job import StochSSJob
-from .stochss_errors import StochSSAPIError
+from .stochss_errors import StochSSAPIError, StochSSJobResultsError
 
 log = logging.getLogger("stochss")
 
@@ -59,36 +60,57 @@ def __init__(self, path, preview=False):
 
 
     def __get_run_settings(self):
-        solver_map = {"SSA":SSACSolver, "Tau-Leaping":TauLeapingSolver,
-                      "ODE":ODESolver, "Hybrid-Tau-Leaping":TauHybridSolver}
+        solver_map = {"ODE":self.g_model.get_best_solver_algo("ODE"),
+                      "SSA":self.g_model.get_best_solver_algo("SSA"),
+                      "Tau-Leaping":self.g_model.get_best_solver_algo("Tau-Leaping"),
+                      "Hybrid-Tau-Leaping":TauHybridSolver}
         run_settings = self.get_run_settings(settings=self.settings, solver_map=solver_map)
-        if run_settings['solver'].name == "SSACSolver":
+        instance_solvers = ["SSACSolver", "TauLeapingCSolver", "ODECSolver"]
+        if run_settings['solver'].name in instance_solvers :
             run_settings['solver'] = run_settings['solver'](model=self.g_model)
         return run_settings
 
 
+    def __store_csv_results(self, results):
+        try:
+            results.to_csv(path="results", nametag="results_csv", stamp=self.get_time_stamp())
+        except Exception as err:
+            log.error("Error storing csv results: %s\n%s",
+                      str(err), traceback.format_exc())
+
+
     @classmethod
-    def __plot_results(cls, results):
-        plots = {"trajectories":results.plotplotly(return_plotly_figure=True)}
-        if len(results) > 1:
-            plots['stddevran'] = results.plotplotly_std_dev_range(return_plotly_figure=True)
-            std_res = results.stddev_ensemble()
-            plots['stddev'] = std_res.plotplotly(return_plotly_figure=True)
-            avg_res = results.average_ensemble()
-            plots['avg'] = avg_res.plotplotly(return_plotly_figure=True)
-        for _, plot in plots.items():
-            plot["config"] = {"responsive":True}
-        with open('results/plots.json', 'w') as plots_file:
-            json.dump(plots, plots_file, cls=plotly.utils.PlotlyJSONEncoder,
-                      indent=4, sort_keys=True)
-
-
-    def __store_results(self, results):
-        if not 'results' in os.listdir():
-            os.mkdir('results')
-        with open('results/results.p', 'wb') as results_file:
-            pickle.dump(results, results_file)
-        results.to_csv(path="results", nametag="results_csv", stamp=self.get_time_stamp())
+    def __store_pickled_results(cls, results):
+        try:
+            with open('results/results.p', 'wb') as results_file:
+                pickle.dump(results, results_file)
+        except Exception as err:
+            message = f"Error storing pickled results: {err}\n{traceback.format_exc()}"
+            log.error(message)
+            return message
+        return False
+
+
+    @classmethod
+    def __store_result_plots(cls, results):
+        try:
+            plots = {"trajectories":results.plotplotly(return_plotly_figure=True)}
+            if len(results) > 1:
+                plots['stddevran'] = results.plotplotly_std_dev_range(return_plotly_figure=True)
+                std_res = results.stddev_ensemble()
+                plots['stddev'] = std_res.plotplotly(return_plotly_figure=True)
+                avg_res = results.average_ensemble()
+                plots['avg'] = avg_res.plotplotly(return_plotly_figure=True)
+            for _, plot in plots.items():
+                plot["config"] = {"responsive":True}
+            with open('results/plots.json', 'w') as plots_file:
+                json.dump(plots, plots_file, cls=plotly.utils.PlotlyJSONEncoder,
+                          indent=4, sort_keys=True)
+        except Exception as err:
+            message = f"Error storing result plots: {err}\n{traceback.format_exc()}"
+            log.error(message)
+            return message
+        return False
 
 
     def __update_timespan(self):
@@ -126,7 +148,7 @@ def run(self, preview=False, verbose=True):
             log.info("Running the ensemble simulation")
         if self.settings['simulationSettings']['isAutomatic']:
             self.__update_timespan()
-            is_ode = self.g_model.get_best_solver().name == "ODESolver"
+            is_ode = self.g_model.get_best_solver().name in ["ODESolver", "ODECSolver"]
             results = self.g_model.run(number_of_trajectories=1 if is_ode else 100)
         else:
             kwargs = self.__get_run_settings()
@@ -135,8 +157,15 @@ def run(self, preview=False, verbose=True):
         if verbose:
             log.info("The ensemble simulation has completed")
             log.info("Storing the results as pickle and csv")
-        self.__store_results(results=results)
+        if not 'results' in os.listdir():
+            os.mkdir('results')
+        self.__store_csv_results(results=results)
+        pkl_err = self.__store_pickled_results(results=results)
         if verbose:
             log.info("Storing the polts of the results")
-        self.__plot_results(results=results)
+        plt_err = self.__store_result_plots(results=results)
+        if pkl_err and plt_err:
+            message = "An unexpected error occured with the result object"
+            trace = f"{pkl_err}\n{plt_err}"
+            raise StochSSJobResultsError(message, trace)
         return None