Merge branch 'develop' of github.com:stochss/stochss into develop

StochSS · Jul 19, 2021 · 4201e67 · 4201e67
2 parents 31241fe + ee50c8d
commit 4201e67
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diff --git a/COPYRIGHT b/COPYRIGHT
@@ -1,5 +1,5 @@
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/Makefile b/Makefile
@@ -114,7 +114,7 @@ build:  deps webpack
 		--build-arg JUPYTER_CONFIG_DIR=$(JUPYTER_CONFIG_DIR) \
 	  	-t $(DOCKER_STOCHSS_IMAGE):latest .
 
-test:   build
+test:   create_working_dir
 	docker run --rm \
 		--name $(DOCKER_STOCHSS_IMAGE) \
 		--env-file .env \
@@ -124,6 +124,8 @@ test:   build
 		$(DOCKER_STOCHSS_IMAGE):latest \
                 /stochss/stochss/tests/run_tests.py
 
+build_and_test: build test
+
 run:    create_working_dir
 	docker run --rm \
 		--name $(DOCKER_STOCHSS_IMAGE) \

diff --git a/client/app.js b/client/app.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/config.js b/client/config.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/graphics.js b/client/graphics.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/modals.js b/client/modals.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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
@@ -424,15 +424,26 @@ module.exports = {
 
         return templates.select(modalID, selectID, title, label, options)
     },
-    selectSpeciesHTML : (species) => {
-      let modalID = "speciesSelectModal";
-      let selectID = "speciesSelectList";
-      let title = "Preview Variable Selection";
-      let label = "Select a variable to preview: ";
+    selectPreviewTargetHTML : (species) => {
+      let modalID = "previewTargetSelectModal";
+      let selectID = "previewTargetSelectList";
+      let title = "Preview Target Selection";
+      let label = "Select a variable or property to preview: ";
       var options = species.map(function (name) {
         return `<option value="${name}">${name}</option>`
       });
-      options = options.join(" ");
+      options = `<optgroup label='Variables'>
+                     ${options.join(" ")}
+                 </optgroup>
+                 <optgroup label='Properties'>
+                     <option value='type'>Type</option>
+                     <option value='v[1]'>X Velocity</option>
+                     <option value='v[2]'>Y Velocity</option>
+                     <option value='v[3]'>Z Velocity</option>
+                     <option value='rho'>Density</option>
+                     <option value='mass'>Mass</option>
+                     <option value='nu'>Viscosity</option>
+                 </optgroup>`;
 
       return templates.select(modalID, selectID, title, label, options)
     },

diff --git a/client/views/view-domain-types.js → client/models/boundary-condition.js b/client/views/view-domain-types.js → client/models/boundary-condition.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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
@@ -16,11 +16,14 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-//views
-var View = require('ampersand-view');
-//templates
-var template = require('../templates/includes/domainTypesViewer.pug');
+//models
+var State = require('ampersand-state');
 
-module.exports = View.extend({
-  template: template,
+module.exports = State.extend({
+  props: {
+    compID: 'number',
+    name: 'string',
+    expression: 'string',
+    annotation: 'string'
+  }
 });
diff --git a/client/views/view-rules.js → client/models/boundary-conditions.js b/client/views/view-rules.js → client/models/boundary-conditions.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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
@@ -16,11 +16,20 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-//views
-var View = require('ampersand-view');
-//templates
-var template = require('../templates/includes/viewRules.pug');
+//collections
+var Collection = require('ampersand-collection');
+//models
+var BoundaryCondition = require('./boundary-condition');
 
-module.exports = View.extend({
-  template: template,
+module.exports = Collection.extend({
+  model: BoundaryCondition,
+  addNewBoundaryCondition: function (name, expression) {
+    let id = this.parent.getDefaultID();
+    let boundaryCondition = this.add({
+      compID: id,
+      name: name,
+      expression: expression,
+      annotation: ""
+    });
+  }
 });
diff --git a/client/models/creator.js b/client/models/creator.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/creators.js b/client/models/creators.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/domain-type.js b/client/models/domain-type.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/domain-types.js b/client/models/domain-types.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/domain.js b/client/models/domain.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/event-assignment.js b/client/models/event-assignment.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/event-assignments.js b/client/models/event-assignments.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/event.js b/client/models/event.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/events.js b/client/models/events.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/function-definition.js b/client/models/function-definition.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/function-definitions.js b/client/models/function-definitions.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/initial-condition.js b/client/models/initial-condition.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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
@@ -23,11 +23,12 @@ var Specie = require('./specie');
 module.exports = State.extend({
   props: {
     icType: 'string',
-    count: 'number',
+    annotation: 'string',
+    count: 'any',
     types: 'object',
-    x: 'number',
-    y: 'number',
-    z: 'number',
+    x: 'any',
+    y: 'any',
+    z: 'any',
   },
   children: {
     specie: Specie,

diff --git a/client/models/initial-conditions.js b/client/models/initial-conditions.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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
@@ -26,6 +26,7 @@ module.exports = Collection.extend({
   addInitialCondition: function (initialConditionType, types) {
     var initialCondition = new InitialCondition({
       icType: initialConditionType,
+      annotation: "",
       types: types,
       count: 0,
       x: 0,

diff --git a/client/models/job.js b/client/models/job.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/jobs.js b/client/models/jobs.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/me.js b/client/models/me.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/metadata.js b/client/models/metadata.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/model.js b/client/models/model.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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
@@ -16,6 +16,8 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
+let _ = require('underscore');
+//support files
 var app = require('../app');
 var path = require('path');
 //models
@@ -30,6 +32,7 @@ var Reactions = require('./reactions');
 var Rules = require('./rules');
 var Events = require('./events');
 var FunctionDefinitions = require('./function-definitions');
+var BoundaryConditions = require('./boundary-conditions');
 
 module.exports = Model.extend({
   url: function () {
@@ -49,7 +52,8 @@ module.exports = Model.extend({
     reactions: Reactions,
     rules: Rules,
     eventsCollection: Events,
-    functionDefinitions: FunctionDefinitions
+    functionDefinitions: FunctionDefinitions,
+    boundaryConditions: BoundaryConditions
   },
   children: {
     modelSettings: TimespanSettings,
@@ -91,12 +95,12 @@ module.exports = Model.extend({
     this.rules.on('add change remove', this.updateValid, this);
   },
   validateModel: function () {
-    if(!this.species.validateCollection()) return false;
+    if(!this.species.validateCollection(this.is_spatial)) return false;
     if(!this.parameters.validateCollection()) return false;
     if(!this.reactions.validateCollection()) return false;
     if(!this.eventsCollection.validateCollection()) return false;
     if(!this.rules.validateCollection()) return false;
-    if(this.reactions.length <= 0 && this.eventsCollection.length <= 0 && this.rules.length <= 0) {
+    if(!this.is_spatial && this.reactions.length <= 0 && this.eventsCollection.length <= 0 && this.rules.length <= 0) {
       this.error = {"type":"process"}
       return false;
     }
@@ -124,7 +128,10 @@ module.exports = Model.extend({
     return id;
   },
   autoSave: function () {
-    //TODO: implement auto save
+    let self = this;
+    setTimeout(function () {
+      app.postXHR(self.url(), self.toJSON(), { success: _.bind(self.autoSave, self) });
+    }, 120000);
   },
   //called when save button is clicked
   saveModel: function (cb=null) {

diff --git a/client/models/parameter-sweep-settings.js b/client/models/parameter-sweep-settings.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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

diff --git a/client/models/parameter.js b/client/models/parameter.js
@@ -1,6 +1,6 @@
 /*
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2020 StochSS developers.
+Copyright (C) 2019-2021 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