Merge pull request #1326 from StochSS/develop

Release v2.4.7

__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.4.6'
+__version__ = '2.4.7'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

client/models/workflow-groups.js

@@ -22,5 +22,6 @@ var Collection = require('ampersand-collection');
 var WorkflowGroup = require('./workflow-group');
 
 module.exports = Collection.extend({
-  model: WorkflowGroup
+  model: WorkflowGroup,
+  comparator: "name"
 });

client/models/workflows.js

@@ -22,5 +22,6 @@ var Collection = require('ampersand-collection');
 var Workflow = require('./workflow');
 
 module.exports = Collection.extend({
-  model: Workflow
+  model: Workflow,
+  comparator: "name"
 });

client/pages/loading-page.js

@@ -70,12 +70,23 @@ let LoadingPage = PageView.extend({
           let yesBtn = document.querySelector("#uploadFileExistsModal .yes-modal-btn");
           let noBtn = document.querySelector("#uploadFileExistsModal .btn-secondary")
           yesBtn.addEventListener('click', function (e) {
+            modal.modal('hide');
             self.uploadFileFromLink(filePath, true);
           });
           noBtn.addEventListener('click', function (e) {
             window.location.href = self.homeLink;
           });
         }
+      },
+      error: function(err, response, body) {
+        if(document.querySelector("#errorModal")) {
+          document.querySelector("#errorModal").remove();
+        }
+        $(self.queryByHook("loading-spinner")).css("display", "none");
+        let modal = $(modals.errorHtml(body.Reason, body.Message)).modal();
+        modal.on('hidden.bs.modal', function (e) {
+          window.location.href = self.homeLink;
+        });
       }
     });
   },

client/pages/model-editor.js

@@ -260,11 +260,13 @@ let ModelEditor = PageView.extend({
       }else if(e.target.dataset.type === "notebook"){
         this.notebookWorkflow(e);
       }else if(!this.model.is_spatial) {
-        if(e.target.dataset.type === "ensemble") {
-          app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Ensemble Simulation");
-        }else if(e.target.dataset.type === "psweep") {
-          app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Parameter Sweep");
-        }
+        this.saveModel(() => {
+          if(e.target.dataset.type === "ensemble") {
+            app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Ensemble Simulation");
+          }else if(e.target.dataset.type === "psweep") {
+            app.newWorkflow(this, this.model.directory, this.model.is_spatial, "Parameter Sweep");
+          }
+        });
       }
     }
   },

client/settings-view/templates/simulationSettingsView.pug

@@ -24,7 +24,7 @@ div#simulation-settings.card
       | Consider the following when selecting an algorithm for your job.  If you would like StochSS to choose the algorithm, select <b>Choose for me</b>.
 
     ul.mb-0
-      li Algorithms <b>ODE</b> and <b>Hybrid ODE/SSA</b> work best to simulate models with a mode of <b>Concentration</b>.
+      li Algorithms <b>ODE</b>, <b>CLE</b>, and <b>Hybrid ODE/SSA</b> work best to simulate models with a mode of <b>Concentration</b>.
       li Algorithns <b>SSA</b>, <b>Tau Leaping</b>, and <b>Hybrid ODE/SSA</b> work best to simulate models with a mode of <b>Population</b>.
       li Algorithm <b>Hybrid ODE/SSA</b> is required if the model contains advanced components.
 
@@ -58,6 +58,14 @@ div#simulation-settings.card
 
             div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.ssa) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
+          div.col-sm-2
+
+            input.mr-2.inline(type="radio", name="simAlgorithm", data-hook="select-cle", data-name="CLE")
+
+            span.inline CLE
+
+            div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.cle) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
           div.col-sm-2
 
             input.mr-2.inline(type="radio", name="simAlgorithm", data-hook="select-tau-leaping", data-name="Tau-Leaping")
@@ -66,15 +74,15 @@ div#simulation-settings.card
 
             div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.tauLeaping) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
-          div.col-sm-3
+          div.col-sm-2
 
             input.mr-2.inline(type="radio", name="simAlgorithm", data-hook="select-hybrid-tau", data-name="Hybrid-Tau-Leaping")
 
             span.inline Hybrid ODE/SSA
 
             div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.hybrid) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
-          div.col-sm-3
+          div.col-sm-2
 
             input.mr-2.inline(type="radio", name="simAlgorithm", data-hook="select-automatic", data-name="Automatic")
 

client/settings-view/views/simulation-settings-view.js

@@ -32,6 +32,7 @@ module.exports = View.extend({
   events: {
     'change [data-hook=select-ode]' : 'handleSelectSimulationAlgorithmClick',
     'change [data-hook=select-ssa]' : 'handleSelectSimulationAlgorithmClick',
+    'change [data-hook=select-cle]' : 'handleSelectSimulationAlgorithmClick',
     'change [data-hook=select-tau-leaping]' : 'handleSelectSimulationAlgorithmClick',
     'change [data-hook=select-hybrid-tau]' : 'handleSelectSimulationAlgorithmClick',
     'change [data-hook=select-automatic]' : 'handleSelectSimulationAlgorithmClick',
@@ -81,13 +82,14 @@ module.exports = View.extend({
     let isAutomatic = this.model.isAutomatic;
     let isODE = this.model.algorithm === "ODE";
     let isSSA = this.model.algorithm === "SSA";
+    let isCLE = this.model.algorithm === "CLE";
     let isLeaping = this.model.algorithm === "Tau-Leaping";
     let isHybrid = this.model.algorithm === "Hybrid-Tau-Leaping";
     $(this.queryByHook("relative-tolerance")).find('input').prop('disabled', !(isODE || isHybrid || isAutomatic));
     $(this.queryByHook("absolute-tolerance")).find('input').prop('disabled', !(isODE || isHybrid || isAutomatic));
-    $(this.queryByHook("trajectories")).find('input').prop('disabled', !(isSSA || isLeaping || isHybrid || isAutomatic));
-    $(this.queryByHook("seed")).find('input').prop('disabled', !(isSSA || isLeaping || isHybrid || isAutomatic));
-    $(this.queryByHook("tau-tolerance")).find('input').prop('disabled', !(isHybrid || isLeaping || isAutomatic));
+    $(this.queryByHook("trajectories")).find('input').prop('disabled', !(isSSA || isCLE || isLeaping || isHybrid || isAutomatic));
+    $(this.queryByHook("seed")).find('input').prop('disabled', !(isSSA || isCLE || isLeaping || isHybrid || isAutomatic));
+    $(this.queryByHook("tau-tolerance")).find('input').prop('disabled', !(isHybrid || isCLE || isLeaping || isAutomatic));
   },
   handleSelectSimulationAlgorithmClick: function (e) {
     let value = e.target.dataset.name;
@@ -128,7 +130,7 @@ module.exports = View.extend({
   updateValid: function (e) {},
   updateViewer: function () {
     $(this.queryByHook("view-algorithm")).html(this.algorithm);
-    let hideDeterministic = this.model.isAutomatic || this.model.algorithm === "SSA" || this.model.algorithm === "Tau-Leaping";
+    let hideDeterministic = this.model.isAutomatic || this.model.algorithm === "SSA" || this.model.algorithm === "CLE" || this.model.algorithm === "Tau-Leaping";
     let hideStochastic = this.model.isAutomatic || this.model.algorithm === "ODE" ;
     if(hideDeterministic) {
       $(this.queryByHook("view-deterministic-settings")).css("display", "none");

stochss/handlers/file_browser.py

@@ -685,10 +685,13 @@ async def get(self):
         log.debug(f"The command for the upload script: {cmd}")
         script = '/stochss/stochss/handlers/util/scripts/upload_remote_file.py'
         if cmd == "validate":
-            folder = StochSSFolder(path="")
-            resp = {'exists': folder.validate_upload_link(remote_path=path)}
-            log.debug(f"Response: {resp}")
-            self.write(resp)
+            try:
+                folder = StochSSFolder(path="")
+                resp = {'exists': folder.validate_upload_link(remote_path=path)}
+                log.debug(f"Response: {resp}")
+                self.write(resp)
+            except StochSSAPIError as err:
+                report_error(self, log, err)
         elif cmd is None:
             overwrite = self.get_query_argument(name='overwrite', default=False)
             outfile = f"{str(uuid.uuid4()).replace('-', '_')}.tmp"

stochss/handlers/util/ensemble_simulation.py

@@ -18,6 +18,7 @@
 
 
 import os
+import numpy
 import pickle
 import logging
 import traceback
@@ -88,7 +89,7 @@ def __update_timespan(self):
                 end = self.settings['timespanSettings']['endSim']
                 step_size = self.settings['timespanSettings']['timeStep']
                 self.g_model.timespan(
-                    TimeSpan.arange(t=end + step_size, increment=step_size)
+                    TimeSpan(numpy.arange(0, end + step_size, step_size))
                 )
 
 

stochss/handlers/util/parameter_sweep.py

@@ -18,6 +18,7 @@
 
 import os
 import json
+import numpy
 import pickle
 import logging
 import traceback
@@ -120,7 +121,7 @@ def configure(self):
                 end = self.settings['timespanSettings']['endSim']
                 step_size = self.settings['timespanSettings']['timeStep']
                 self.g_model.timespan(
-                    TimeSpan.arange(t=end + step_size, increment=step_size)
+                    TimeSpan(numpy(0, end + step_size, step_size))
                 )
         kwargs = {"model":self.g_model, "settings":run_settings}
         parameters = []

stochss/handlers/util/stochss_folder.py

@@ -22,6 +22,7 @@
 import shutil
 import string
 import zipfile
+import tempfile
 import datetime
 import traceback
 
@@ -33,7 +34,7 @@
 from .stochss_model import StochSSModel
 from .stochss_sbml import StochSSSBMLModel
 from .stochss_errors import StochSSFileExistsError, StochSSFileNotFoundError, \
-                            StochSSPermissionsError
+                            StochSSPermissionsError, StochSSUnzipError
 
 
 class StochSSFolder(StochSSBase):
@@ -66,6 +67,38 @@ def __init__(self, path, new=False):
                 raise StochSSFileExistsError(message, traceback.format_exc()) from err
 
 
+    def __get_file_from_link(self, remote_path):
+        ext = remote_path.split('.').pop().split('?')[0]
+        if os.path.exists("/stochss/.proxies.txt"):
+            with open("/stochss/.proxies.txt", "r") as proxy_file:
+                proxy_ip = proxy_file.read().strip()
+                proxies = {
+                    "https": f"https://{proxy_ip}",
+                    "http": f"http://{proxy_ip}"
+                }
+        else:
+            proxies = None
+        response = requests.get(remote_path, allow_redirects=True, proxies=proxies)
+        body = response.content
+        if "download_presentation" in remote_path:
+            if ext in ("mdl", "smdl"):
+                file = f"{json.loads(body)['name']}.{ext}"
+            elif ext == "ipynb":
+                file = json.loads(body)['file']
+                body = json.dumps(json.loads(body)['notebook'])
+            elif ext == "job":
+                file = self.get_file(path=remote_path)
+        elif "?" in remote_path:
+            file = self.get_file(path=remote_path.split("?")[0])
+        else:
+            file = self.get_file(path=remote_path)
+        if response.status_code == 404:
+            message = f"Could not upload this file as {file} was not found."
+            if "?token=" in remote_path:
+                message += "  The token for this file may be out of date."
+            raise StochSSFileNotFoundError(message, traceback.format_exc())
+        return ext, file, body
+
     def __get_rmt_upld_path(self, file):
         if not file.endswith(".zip"):
             return file
@@ -150,18 +183,30 @@ def __get_presentation_notebook_name(cls, file_path):
         return name
 
 
-    @classmethod
-    def __overwrite(cls, path, ext):
-        if ext == "zip":
-            with zipfile.ZipFile(path, "r") as zip_file:
-                members = zip_file.namelist()
-                for name in members:
-                    if os.path.isdir(name):
-                        shutil.rmtree(name)
-                    elif os.path.exists(name):
-                        os.remove(name)
-        elif os.path.exists(path):
+    def __overwrite(self, path, ext, body):
+        if ext != "zip":
             os.remove(path)
+        else:
+            if os.path.exists(path):
+                os.remove(path)
+            file = self.get_file(path=path)
+            with tempfile.TemporaryDirectory() as tmp_dir:
+                ext_path = os.path.join(tmp_dir, file)
+                with open(ext_path, "wb") as zip_file:
+                    zip_file.write(body)
+                try:
+                    with zipfile.ZipFile(ext_path, 'r') as zip_file:
+                        members = set([name.split('/')[0] for name in zip_file.namelist()])
+                        for name in members:
+                            m_path = self.get_new_path(dst_path=name)
+                            if os.path.exists(m_path):
+                                if os.path.isdir(m_path):
+                                    shutil.rmtree(m_path)
+                                else:
+                                    os.remove(m_path)
+                except zipfile.BadZipFile as err:
+                    message = "File is not a zip file"
+                    raise StochSSFileNotFoundError(message, traceback.format_exc()) from err
 
 
     def __upload_file(self, file, body, new_name=None):
@@ -529,38 +574,13 @@ def upload_from_link(self, remote_path, overwrite=False):
         overwrite : bool
             Overwrite the existing files.
         '''
-        ext = remote_path.split('.').pop()
-        if os.path.exists("/stochss/.proxies.txt"):
-            with open("/stochss/.proxies.txt", "r") as proxy_file:
-                proxy_ip = proxy_file.read().strip()
-                proxies = {
-                    "https": f"https://{proxy_ip}",
-                    "http": f"http://{proxy_ip}"
-                }
-        else:
-            proxies = None
-        body = requests.get(remote_path, allow_redirects=True, proxies=proxies).content
-        if "download_presentation" in remote_path:
-            if ext in ("mdl", "smdl"):
-                file = f"{json.loads(body)['name']}.{ext}"
-            elif ext == "ipynb":
-                file = json.loads(body)['file']
-                body = json.dumps(json.loads(body)['notebook'])
-        else:
-            file = self.get_file(path=remote_path)
-        if "404: Not Found" in body.decode():
-            message = f"Could not upload this file as {file} was not found."
-            if "?token=" in file:
-                message += "  The token for this file may be out of date."
-            return {"message": message, "reason":"File Not Found"}
-        if "?token=" in file:
-            file = file.split("?token=")[0]
+        ext, file, body = self.__get_file_from_link(remote_path)
         path = self.get_new_path(dst_path=file)
-        if os.path.exists(path):
-            if not overwrite:
-                message = f"Could not upload this file as {file} already exists"
-                return {"message":message, "reason":"File Already Exists"}
-            self.__overwrite(path=path, ext=ext)
+        if overwrite:
+            self.__overwrite(path=path, ext=ext, body=body)
+        elif os.path.exists(path):
+            message = f"Could not upload this file as {file} already exists"
+            return {"message":message, "reason":"File Already Exists"}
         try:
             file_types = {"mdl":"model", "smdl":"model", "sbml":"sbml"}
             file_type = file_types[ext] if ext in file_types.keys() else "file"
@@ -581,25 +601,22 @@ def validate_upload_link(self, remote_path):
         remote_path : str
             Path to the remote file
         '''
-        ext = remote_path.split('.').pop()
-        body = requests.get(remote_path, allow_redirects=True).content
-        if "download_presentation" in remote_path:
-            if ext in ("mdl", "smdl"):
-                file = f"{json.loads(body)['name']}.{ext}"
-            elif ext == "ipynb":
-                file = json.loads(body)['file']
-                body = json.dumps(json.loads(body)['notebook'])
-            elif ext == "job":
-                file = self.get_file(path=remote_path)
-        else:
-            file = self.get_file(path=remote_path)
-        if "?token=" in file:
-            file = file.split("?token=")[0]
+        ext, file, body = self.__get_file_from_link(remote_path)
         path = self.get_new_path(dst_path=file)
-        if ext == "zip":
-            with zipfile.ZipFile(path, "r") as zip_file:
-                members = zip_file.namelist()
-                for name in members:
-                    if os.path.exists(name):
-                        return True
-        return os.path.exists(path)
+        exists = os.path.exists(path)
+        if ext != "zip" or exists:
+            return exists
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            ext_path = os.path.join(tmp_dir, file)
+            with open(ext_path, "wb") as zip_file:
+                zip_file.write(body)
+            try:
+                with zipfile.ZipFile(ext_path, 'r') as zip_file:
+                    members = set([name.split('/')[0] for name in zip_file.namelist()])
+                    for name in members:
+                        if os.path.exists(self.get_new_path(dst_path=name)):
+                            return True
+            except zipfile.BadZipFile as err:
+                message = "File is not a zip file"
+                raise StochSSFileNotFoundError(message, traceback.format_exc()) from err
+        return False