From 3e32045f2c5a81a8d7b82c7d8c2252f44a5ca8e2 Mon Sep 17 00:00:00 2001 From: Andreas Hellander Date: Sat, 5 Sep 2020 12:16:45 +0200 Subject: [PATCH 01/29] Update README.md --- README.md | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 64a562708a..160b223de1 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,13 @@ -# StochSS: The Stochastic Simulation Service +# StochSS: Software as a service for simulation-driven investigations of stochastic biochemical models -StochSS is a platform for simulating biochemical systems supporting both continuous ODE and discrete stochastic simulations with [GillesPy2](https://github.com/GillesPy2/GillesPy2). +StochSS provides advanced tools for simulating and analyzing biochemical systems as Software as a Service. StochSS supports a wide range of model types ranging from continuous ODEs to discrete (spatial) stochastic simulations as well as advanced model analysis workflows. Try out StochSS here: https://app.stochss.org . -At the moment StochSS development on Windows is not supported. You can try using [Make for Windows](http://gnuwin32.sourceforge.net/packages/make.htm), but this is untested! +## Why use StochSS +StochSS provides both an easy-to-use UI for constructing biochemical models as well as intuitive UIs for the most common model analysis tools such as visualization of results, parameter sweeps and parameter inference. StochSS is built on top of Jupyter Hub, and this lets you seemlessly switch between UI representations and Notebooks exposing the full backend API. In this way a user can benefit from the best of graphical representations with a clear upgrade path to modeling as code. For this reason, StochSS is also uniquely suited for the computational biologist starting out with mathematical modeling of biochemical systems. + +StochSS is a sotware project involving several leading research groups in computational systems biology. We welcome collaborators to help expand the capabilities of StochSS. Read more about the project at www.stochss.org . + +*StochSS is intended to be used as Software as a Service. The instructions that follows help you set your own local development environment or deploy your own instance as SaaS. If you intend to mainly use StochSS for modeling, simulation and model analysis, consider using the hosted deployment at http://app.stochss.org which you can access without any installation. ## Requirements @@ -12,6 +17,8 @@ At the moment StochSS development on Windows is not supported. You can try using - [Docker Compose](https://docs.docker.com/compose/install/) (Only required if you want to run StochSS with [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#)) +*At the moment StochSS development on Windows is not supported. You can try using [Make for Windows](http://gnuwin32.sourceforge.net/packages/make.htm), but this is untested! + ## Quickstart - Build and run the stochss notebook server: `make` From 87a0ebfa762bd1b367db86f6b96f1f31c1b96e31 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Oct 2020 12:48:15 -0400 Subject: [PATCH 02/29] Fixed bug that was displaying the 'create new model in project using save as' warning for New Models that were not created in a project if the model had a '.' in it's name. Fixed bug that was preventing user from confirm that they wished to create a model in the required location of a project if the above warning is displayed. --- client/pages/file-browser.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index 965bac54cf..bab604d10e 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -724,15 +724,16 @@ let FileBrowser = PageView.extend({ } if(isModel) { let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl'; - let message = modelName.split(".")[0] !== input.value.trim() ? + let message = modelName !== input.value.trim() + ".mdl"? "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Your model will be saved directly in your project.

" : "" let modelPath = path.join(parentPath, modelName) + let queryString = "?path="+modelPath+"&message="+message; + let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString if(message){ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) {window.location.href = endpoint;}) }else{ - let queryString = "?path="+modelPath+"&message="+message; let existEP = path.join(app.getApiPath(), "model/exists")+queryString xhr({uri: existEP, json: true}, function (err, response, body) { if(body.exists) { @@ -740,7 +741,6 @@ let FileBrowser = PageView.extend({ let message = "A model already exists with that name" let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() }else{ - let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString window.location.href = endpoint } }) From 5bcbceb0207144f3dddff36bc402cbda52ccc75c Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Oct 2020 17:26:30 -0400 Subject: [PATCH 03/29] Fixed bug that was not checking for existing models when creating new models in a project using a path in the name. --- client/pages/file-browser.js | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index bab604d10e..576431c86c 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -729,12 +729,23 @@ let FileBrowser = PageView.extend({ let modelPath = path.join(parentPath, modelName) let queryString = "?path="+modelPath+"&message="+message; let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString + let existEP = path.join(app.getApiPath(), "model/exists")+queryString if(message){ let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); - yesBtn.addEventListener('click', function (e) {window.location.href = endpoint;}) + yesBtn.addEventListener('click', function (e) { + warningModal.modal('hide') + xhr({uri: existEP, json: true}, function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists" + let message = "A model already exists with that name" + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() + }else{ + window.location.href = endpoint + } + }) + }) }else{ - let existEP = path.join(app.getApiPath(), "model/exists")+queryString xhr({uri: existEP, json: true}, function (err, response, body) { if(body.exists) { let title = "Model Already Exists" From 8bd11d778bfcd69daee626e5fdfe154963427598 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Thu, 1 Oct 2020 17:29:13 -0400 Subject: [PATCH 04/29] Added a check to the add existing model function that makes sure the file being added is model file. --- stochss/handlers/project.py | 41 ++++++++++++++++++++++--------------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/stochss/handlers/project.py b/stochss/handlers/project.py index 161de6eccc..2dc2af1c4b 100644 --- a/stochss/handlers/project.py +++ b/stochss/handlers/project.py @@ -328,25 +328,32 @@ def get(self): mdl_path = os.path.join(user_dir, self.get_query_argument(name="mdlPath")) log.debug("Path to the project: %s", path) log.debug("Path to the model: %s", mdl_path) - try: - unique_path, changed = get_unique_file_name(mdl_path.split("/").pop(), path) - copyfile(mdl_path, unique_path) - resp = {"message": "The model {0} was successfully move into \ - {1}".format(mdl_path.split('/').pop(), path.split("/").pop())} - if changed: - resp['message'] += " as {0}".format(unique_path.split('/').pop()) - log.debug("Response message: %s", resp) - self.write(resp) - except IsADirectoryError as err: + if mdl_path.endswith('.mdl'): + try: + unique_path, changed = get_unique_file_name(mdl_path.split("/").pop(), path) + copyfile(mdl_path, unique_path) + resp = {"message": "The model {0} was successfully move into \ + {1}".format(mdl_path.split('/').pop(), path.split("/").pop())} + if changed: + resp['message'] += " as {0}".format(unique_path.split('/').pop()) + log.debug("Response message: %s", resp) + self.write(resp) + except IsADirectoryError as err: + self.set_status(406) + error = {"Reason":"Not A Model", + "Message":"Cannot move directories into StochSS Projects: {0}".format(err)} + log.error("Exception Information: %s", error) + self.write(error) + except FileNotFoundError as err: + self.set_status(404) + error = {"Reason":"Model Not Found", + "Message":"Could not find the model: {0}".format(err)} + log.error("Exception Information: %s", error) + self.write(error) + else: self.set_status(406) error = {"Reason":"Not A Model", - "Message":"Cannot move directories into StochSS Projects: {0}".format(err)} - log.error("Exception Information: %s", error) - self.write(error) - except FileNotFoundError as err: - self.set_status(404) - error = {"Reason":"Model Not Found", - "Message":"Could not find the model: {0}".format(err)} + "Message":"Cannot move non-model files into StochSS Projects"} log.error("Exception Information: %s", error) self.write(error) self.finish() From 2241655bba5c3dc34b4a19cdf3581ae220449231 Mon Sep 17 00:00:00 2001 From: Sean Matthew Date: Fri, 2 Oct 2020 10:23:42 -0400 Subject: [PATCH 05/29] Create CONTRIBUTING.md Resolves issue #931 on merge. --- CONTRIBUTING.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000000..3dc1057f0a --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,29 @@ +# CONTRIBUTING +By contributing to StochSS, you agree to the Code of Conduct and that the contents of this project are distributed under the [GNU GPL v3](/LICENSE). Please review both of these documents. If after reading you are interested in contributing, please follow these guidelines: + +## 1. Making Changes: +a) Create a fork from this repository ('https://github.com/StochSS/StochSS') +b) Create a new branch. +c) Please use a meaningful name, and include the issue # if applicable. +d) For bug fixes, branch from 'main' +e) For new features, branch from 'develop' +f) Be sure to document your code +g) Eliminate any commented-out or dead code. +h) If you are creating a new file, prepend the [COPYRIGHT](/COPYRIGHT) notice to the beginning of the file. +i) Create unit tests to cover changes. Unit tests should be placed in the [test](/stochss/tests) subdirectory. + +## 2. Submitting a Pull Request: +a) If changes are bug/hotfix, make a pull request to 'main'. +b) If other changes, or new features are being added, make a pull request to 'develop'. +c) Include a list of changes in the PR description. +d) Provide a usage guide/how-to for new features in the PR description. + +***Do NOT merge your own pull request. Once the request is submitted, the code must be reviewed and merged by someone else.*** + +## 3. Merging a Pull Request: +a) Verify correct merge destination ('main' for hotfix/bugs, 'develop' for features/changes). +b) Review code for logic, consistency, documentation, and commented-out or dead sections. +c) Verify that unit tests are provided for the new code, and that they accurately test the new feature/changes. +d) Check coverage by running [./run_tests.py](/stochss/tests/run_tests.py) from the project [test](/stochss/tests) subdirectory. +e) Make sure that all GitHub Actions resolve before merging the changes. +f) Merge! From 4b9877fc683f4067469a2f485f1348987163d896 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 11:41:46 -0400 Subject: [PATCH 06/29] Fixed bug that was atempting an ast.literal_eval on a parameter expression of type number. --- stochss/handlers/util/convert_to_sbml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stochss/handlers/util/convert_to_sbml.py b/stochss/handlers/util/convert_to_sbml.py index ecfa86f012..e8a557b279 100644 --- a/stochss/handlers/util/convert_to_sbml.py +++ b/stochss/handlers/util/convert_to_sbml.py @@ -101,7 +101,7 @@ def convert_parameters(sbml_model, parameters): param = sbml_model.createParameter() param.initDefaults() param.setId(parameter['name']) - param.setValue(ast.literal_eval(parameter['expression'])) + param.setValue(parameter['expression']) def convert_reactions(sbml_model, reactions): From 23c555989dd84fb9e0abb4a3beee16d4495ac198 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 12:51:33 -0400 Subject: [PATCH 07/29] Fixed bug with name new model files created from a sbml file. --- stochss/handlers/util/convert_sbml_to_model.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/stochss/handlers/util/convert_sbml_to_model.py b/stochss/handlers/util/convert_sbml_to_model.py index c0452fb5c2..39306826f5 100755 --- a/stochss/handlers/util/convert_sbml_to_model.py +++ b/stochss/handlers/util/convert_sbml_to_model.py @@ -2,7 +2,7 @@ import os import json -from .rename import get_unique_file_name +from .rename import get_unique_file_name, get_file_name from .stochss_errors import StochSSFileNotFoundError # from run_model import ModelFactory from gillespy2.sbml.SBMLimport import convert, __read_sbml_model, __get_math @@ -360,7 +360,7 @@ def convert_sbml_to_model(path, model_template): user_dir = "/home/jovyan" full_path = os.path.join(user_dir, path) - name = full_path.split('/').pop().split('.')[0] + name = get_file_name(full_path) template = json.loads(model_template) gillespy_model, sbml_errors = convert_to_gillespy_model(full_path) sbml_errors = list(map(lambda error: error[0], sbml_errors)) From c5fccac62330a05efff401d851a55aa75808b032 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 13:22:11 -0400 Subject: [PATCH 08/29] Removed 'Create Workflow Group' from the plus button in the Browse Files section of the project manager page. --- client/templates/includes/fileBrowserView.pug | 1 - 1 file changed, 1 deletion(-) diff --git a/client/templates/includes/fileBrowserView.pug b/client/templates/includes/fileBrowserView.pug index a0dbad0555..14e9de09be 100644 --- a/client/templates/includes/fileBrowserView.pug +++ b/client/templates/includes/fileBrowserView.pug @@ -29,7 +29,6 @@ div#browse-files.card.card-body ul.dropdown-menu(aria-labelledby="project-browse-files-add-btn") li.dropdown-item(id="new-directory" data-hook="new-directory") Create Directory - li.dropdown-item(id="browser-new-workflow-group" data-hook="browser-new-workflow-group") Create Workflow Group li.dropdown-item(id="browser-new-model" data-hook="browser-new-model") Create Model li.dropdown-divider li.dropdown-item(id="browser-existing-model" data-hook="browser-existing-model") Add Existing Model From 09ebeb156bdd35bec1cb78d5357a39bee1cc10e2 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 14:23:25 -0400 Subject: [PATCH 09/29] Added check to disable the ok button of the new model/directory modal on the project manager page. --- client/views/file-browser-view.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index a3181b61eb..f5016b1d76 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -773,12 +773,13 @@ module.exports = View.extend({ var endErrMsg = document.querySelector('#newModalModel #modelNameInputEndCharError') var charErrMsg = document.querySelector('#newModalModel #modelNameInputSpecCharError') let error = self.validateName(input.value) - okBtn.disabled = error !== "" + okBtn.disabled = error !== "" || input.value.trim() === "" charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" }); okBtn.addEventListener('click', function (e) { if (Boolean(input.value)) { + modal.modal('hide') var parentPath = self.parent.projectPath if(o && o.original && o.original._path !== "/"){ parentPath = o.original._path @@ -817,7 +818,6 @@ module.exports = View.extend({ let errorModal = $(modals.newDirectoryErrorHtml(body.Reason, body.Message)).modal() } }); - modal.modal('hide') } } }); From cf900ae0288de7ad5abf19042c75e10538bf85ab Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 14:38:12 -0400 Subject: [PATCH 10/29] Added check to ensure that a new model isn't using the same name as a model that already exists. --- client/views/file-browser-view.js | 30 +++++++++++++++++++++++++----- 1 file changed, 25 insertions(+), 5 deletions(-) diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index f5016b1d76..3b4860440e 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -786,17 +786,37 @@ module.exports = View.extend({ } if(isModel) { let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl'; - let message = modelName.split(".")[0] !== input.value.trim() ? + let message = modelName !== input.value.trim() + ".mdl"? "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Your model will be saved directly in your project.

" : "" let modelPath = path.join(parentPath, modelName) - let endpoint = path.join(app.getBasePath(), app.routePrefix, 'models/edit')+"?path="+modelPath+"&message="+message; + let queryString = "?path="+modelPath+"&message="+message; + let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString + let existEP = path.join(app.getApiPath(), "model/exists")+queryString if(message){ - modal.modal('hide') let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); - yesBtn.addEventListener('click', function (e) {window.location.href = endpoint;}) + yesBtn.addEventListener('click', function (e) { + warningModal.modal('hide') + xhr({uri: existEP, json: true}, function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists" + let message = "A model already exists with that name" + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() + }else{ + window.location.href = endpoint + } + }) + }) }else{ - window.location.href = endpoint; + xhr({uri: existEP, json: true}, function (err, response, body) { + if(body.exists) { + let title = "Model Already Exists" + let message = "A model already exists with that name" + let errorModel = $(modals.newProjectOrWorkflowGroupErrorHtml(title, message)).modal() + }else{ + window.location.href = endpoint + } + }) } }else{ let dirName = input.value.trim(); From dc02b7d656314679dce5c9e0750f6a2146b7afde Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 15:13:52 -0400 Subject: [PATCH 11/29] Fixed the model save as check in the project manager page. --- client/views/file-browser-view.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index 3b4860440e..42b000fb6e 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -785,7 +785,7 @@ module.exports = View.extend({ parentPath = o.original._path } if(isModel) { - let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl'; + let modelName = !o || (o && o.type === "root") ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl'; let message = modelName !== input.value.trim() + ".mdl"? "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Your model will be saved directly in your project.

" : "" let modelPath = path.join(parentPath, modelName) From b61a327552490325f496bef1a4304206e9d90c2e Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Mon, 5 Oct 2020 16:17:33 -0400 Subject: [PATCH 12/29] Added error catch for upload improperly formatted zip archives. Updated the file and text input validation functions. --- client/views/file-browser-view.js | 37 +++++++++++++++++++++++++------ 1 file changed, 30 insertions(+), 7 deletions(-) diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index 42b000fb6e..4b2153f4a1 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -233,19 +233,40 @@ module.exports = View.extend({ let uploadBtn = document.querySelector('#uploadFileModal .upload-modal-btn'); let fileInput = document.querySelector('#uploadFileModal #fileForUpload'); let input = document.querySelector('#uploadFileModal #fileNameInput'); + let fileCharErrMsg = document.querySelector('#uploadFileModal #fileSpecCharError') + let nameEndErrMsg = document.querySelector('#uploadFileModal #fileNameInputEndCharError') + let nameCharErrMsg = document.querySelector('#uploadFileModal #fileNameInputSpecCharError') + let nameUsageMsg = document.querySelector('#uploadFileModal #fileNameUsageMessage') fileInput.addEventListener('change', function (e) { - if(fileInput.files.length){ + let fileErr = !fileInput.files.length ? "" : self.validateName(fileInput.files[0].name) + let nameErr = self.validateName(input.value) + if(!fileInput.files.length) { + uploadBtn.disabled = true + fileCharErrMsg.style.display = 'none' + }else if(fileErr === "" || (Boolean(input.value) && nameErr === "")){ uploadBtn.disabled = false + fileCharErrMsg.style.display = 'none' }else{ uploadBtn.disabled = true + fileCharErrMsg.style.display = 'block' } }) input.addEventListener("input", function (e) { - var endErrMsg = document.querySelector('#uploadFileModal #fileNameInputEndCharError') - var charErrMsg = document.querySelector('#uploadFileModal #fileNameInputSpecCharError') - let error = self.validateName(input.value) - charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" - endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" + let fileErr = !fileInput.files.length ? "" : self.validateName(fileInput.files[0].name) + let nameErr = self.validateName(input.value) + if(!fileInput.files.length) { + uploadBtn.disabled = true + fileCharErrMsg.style.display = 'none' + }else if(fileErr === "" || (Boolean(input.value) && nameErr === "")){ + uploadBtn.disabled = false + fileCharErrMsg.style.display = 'none' + }else{ + uploadBtn.disabled = true + fileCharErrMsg.style.display = 'block' + } + nameCharErrMsg.style.display = nameErr === "both" || nameErr === "special" ? "block" : "none" + nameEndErrMsg.style.display = nameErr === "both" || nameErr === "forward" ? "block" : "none" + nameUsageMsg.style.display = nameErr !== "" ? "block" : "none" }); uploadBtn.addEventListener('click', function (e) { let file = fileInput.files[0] @@ -278,6 +299,8 @@ module.exports = View.extend({ if(resp.errors.length > 0){ let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal(); } + }else{ + let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal() } } req.send(formData) @@ -661,7 +684,7 @@ module.exports = View.extend({ var endErrMsg = document.querySelector('#newProjectModelModal #modelPathInputEndCharError') var charErrMsg = document.querySelector('#newProjectModelModal #modelPathInputSpecCharError') let error = self.validateName(input.value) - okBtn.disabled = error !== "" + okBtn.disabled = error !== "" || input.value.trim() === "" charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" }); From 359a855dd668b3c5d04d0fa84beb7b98e56787c8 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Oct 2020 10:52:16 -0400 Subject: [PATCH 13/29] Updated the warning message that displays when a user attempts to use the save as feature when creating a new model in a project from the file browser page. Changed the upload file button data hooks to make them unique from the project managers upload buttons. Updated the upload file event listener to use the new datahook. Removed un-needed document event listener that closed modal backdrops(fixed bug that was caused by multiple buttons with the same datahook and separate event listeners). Fixed bug that was using the user's home directory for the upload dst when uploading files to a project from the browse files section. Added checks that remove all directories from the options upload input box if the target file is a model or could be converted to a model. Added function to display save as warning message to the user if the user is attempting to use the save as feature when uploading models to a project. Added check that will refresh the models section of the project manager if a model was uploaded. Refactored the 'handleUploadModelClick' function to call the 'uploadFile' function of the file-browser-view in order to remove duplicate code. --- client/pages/file-browser.js | 2 +- client/pages/project-manager.js | 48 +----------- client/templates/includes/fileBrowserView.pug | 6 +- client/views/file-browser-view.js | 78 +++++++++++-------- 4 files changed, 52 insertions(+), 82 deletions(-) diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index 576431c86c..fb6c1fe3a5 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -725,7 +725,7 @@ let FileBrowser = PageView.extend({ if(isModel) { let modelName = o && o.type === "project" ? input.value.trim().split("/").pop() + '.mdl' : input.value.trim() + '.mdl'; let message = modelName !== input.value.trim() + ".mdl"? - "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Your model will be saved directly in your project.

" : "" + "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Do you wish to save your model directly in your project?

" : "" let modelPath = path.join(parentPath, modelName) let queryString = "?path="+modelPath+"&message="+message; let endpoint = path.join(app.getBasePath(), "stochss/models/edit")+queryString diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js index e7c3a2da1a..bef03bcca7 100644 --- a/client/pages/project-manager.js +++ b/client/pages/project-manager.js @@ -247,54 +247,8 @@ let ProjectManager = PageView.extend({ }); }, handleUploadModelClick: function (e) { - let self = this let type = e.target.dataset.type - if(document.querySelector('#uploadFileModal')) { - document.querySelector('#uploadFileModal').remove() - } - let modal = $(modals.uploadFileHtml(type)).modal(); - let uploadBtn = document.querySelector('#uploadFileModal .upload-modal-btn'); - let fileInput = document.querySelector('#uploadFileModal #fileForUpload'); - let input = document.querySelector('#uploadFileModal #fileNameInput'); - fileInput.addEventListener('change', function (e) { - if(fileInput.files.length){ - uploadBtn.disabled = false - }else{ - uploadBtn.disabled = true - } - }) - input.addEventListener("input", function (e) { - var endErrMsg = document.querySelector('#uploadFileModal #fileNameInputEndCharError') - var charErrMsg = document.querySelector('#uploadFileModal #fileNameInputSpecCharError') - let error = self.validateName(input.value) - charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none" - endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none" - }); - uploadBtn.addEventListener('click', function (e) { - let file = fileInput.files[0] - var fileinfo = {"type":type,"name":"","path":self.projectPath} - if(Boolean(input.value) && self.validateName(input.value) === ""){ - fileinfo.name = input.value - } - let formData = new FormData() - formData.append("datafile", file) - formData.append("fileinfo", JSON.stringify(fileinfo)) - let endpoint = path.join(app.getApiPath(), 'file/upload'); - let req = new XMLHttpRequest(); - req.open("POST", endpoint) - req.onload = function (e) { - var resp = JSON.parse(req.response) - if(req.status < 400) { - if(resp.errors.length > 0){ - let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal(); - }else{ - self.update("model-editor") - } - } - } - req.send(formData) - modal.modal('hide') - }) + this.projectFileBrowser.uploadFile(undefined, type) }, addNewModel: function (isSpatial) { let self = this diff --git a/client/templates/includes/fileBrowserView.pug b/client/templates/includes/fileBrowserView.pug index 14e9de09be..d6e2783076 100644 --- a/client/templates/includes/fileBrowserView.pug +++ b/client/templates/includes/fileBrowserView.pug @@ -33,9 +33,9 @@ div#browse-files.card.card-body li.dropdown-divider li.dropdown-item(id="browser-existing-model" data-hook="browser-existing-model") Add Existing Model li.dropdown-divider - li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="model") Upload StochSS Model - li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="sbml") Upload SBML Model - li.dropdown-item(id="upload-file-btn" data-hook="upload-file-btn", data-type="file") Upload File + li.dropdown-item(id="upload-file-btn-bf" data-hook="upload-file-btn-bf", data-type="model") Upload StochSS Model + li.dropdown-item(id="upload-file-btn-bf" data-hook="upload-file-btn-bf", data-type="sbml") Upload SBML Model + li.dropdown-item(id="upload-file-btn-bf" data-hook="upload-file-btn-bf", data-type="file") Upload File button.btn.btn-primary.box-shadow(id="options-for-node" data-hook="options-for-node" disabled) Actions diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index 4b2153f4a1..57f583876e 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -21,7 +21,7 @@ module.exports = View.extend({ 'click [data-hook=browser-new-workflow-group]' : 'handleCreateWorkflowGroupClick', 'click [data-hook=browser-new-model]' : 'handleCreateModelClick', 'click [data-hook=browser-existing-model]' : 'handleAddExistingModelClick', - 'click [data-hook=upload-file-btn]' : 'handleUploadFileClick', + 'click [data-hook=upload-file-btn-bf]' : 'handleUploadFileClick', 'click [data-hook=file-browser-help]' : function () { let modal = $(modals.operationInfoModalHtml('file-browser')).modal(); }, @@ -124,7 +124,6 @@ module.exports = View.extend({ xhr({uri: endpoint}, function(err, response, body) { if(response.statusCode < 400) { node.original._path = path.join(newDir, file) - console.log((oldPath.includes('trash/') || newDir.endsWith('trash'))) self.updateParent(node.type, (oldPath.includes('trash/') || newDir.endsWith('trash'))) }else{ body = JSON.parse(body) @@ -162,13 +161,6 @@ module.exports = View.extend({ var self = this; this.nodeForContextMenu = ""; this.jstreeIsLoaded = false - // Remove all backdrop on close - $(document).on('hide.bs.modal', '.modal', function (e) { - if($(".modal-backdrop").length > 1) { - $(".modal-backdrop").remove(); - } - e.target.remove() - }); window.addEventListener('pageshow', function (e) { var navType = window.performance.navigation.type if(navType === 2){ @@ -270,42 +262,66 @@ module.exports = View.extend({ }); uploadBtn.addEventListener('click', function (e) { let file = fileInput.files[0] - var fileinfo = {"type":type,"name":"","path":"/"} + var fileinfo = {"type":type,"name":"","path":self.parent.projectPath} if(o && o.original){ fileinfo.path = o.original._path } if(Boolean(input.value) && self.validateName(input.value) === ""){ - fileinfo.name = input.value.trim() + let name = input.value.trim() + if(file.name.endsWith(".mdl") || (type === "model" && file.name.endsWith(".json"))){ + fileinfo.name = name.split('/').pop() + }else if(file.name.endsWith(".sbml") || (type === "sbml" && file.name.endsWith(".xml"))){ + fileinfo.name = name.split('/').pop() + }else{ + fileinfo.name = name + } } let formData = new FormData() formData.append("datafile", file) formData.append("fileinfo", JSON.stringify(fileinfo)) let endpoint = path.join(app.getApiPath(), 'file/upload'); - let req = new XMLHttpRequest(); - req.open("POST", endpoint) - req.onload = function (e) { - var resp = JSON.parse(req.response) - if(req.status < 400) { - if(o){ - var node = $('#models-jstree-view').jstree().get_node(o.parent); - if(node.type === "root" || node.type === "#"){ - self.refreshJSTree(); - }else{ - $('#models-jstree-view').jstree().refresh_node(node); - } - }else{ + if(Boolean(input.value) && fileinfo.name !== input.value.trim()){ + let message = "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Do you wish to save your model directly in your project?

" + let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() + let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); + yesBtn.addEventListener('click', function (e) { + warningModal.modal('hide') + self.openUploadRequest(endpoint, formData, o) + }) + }else{ + self.openUploadRequest(endpoint, formData, o) + } + modal.modal('hide') + }) + }, + openUploadRequest: function (endpoint, formData, o) { + let self = this + let req = new XMLHttpRequest(); + req.open("POST", endpoint) + req.onload = function (e) { + var resp = JSON.parse(req.response) + if(req.status < 400) { + if(o){ + var node = $('#models-jstree-view').jstree().get_node(o.parent); + if(node.type === "root" || node.type === "#"){ self.refreshJSTree(); - } - if(resp.errors.length > 0){ - let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal(); + }else{ + $('#models-jstree-view').jstree().refresh_node(node); } }else{ - let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal() + self.refreshJSTree(); } + if(resp.file.endsWith(".mdl") || resp.file.endsWith(".sbml")) { + self.parent.update("file-browser") + } + if(resp.errors.length > 0){ + let errorModal = $(modals.uploadFileErrorsHtml(file.name, type, resp.message, resp.errors)).modal(); + } + }else{ + let zipErrorModal = $(modals.projectExportErrorHtml(resp.Reason, resp.Message)).modal() } - req.send(formData) - modal.modal('hide') - }) + } + req.send(formData) }, deleteFile: function (o) { var fileType = o.type From 164496b8f7e9549e23fdb5a01a164223d5ba260f Mon Sep 17 00:00:00 2001 From: seanebum Date: Tue, 6 Oct 2020 11:18:32 -0400 Subject: [PATCH 14/29] minor updates to README --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 160b223de1..5ef58c0739 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,9 @@ StochSS provides advanced tools for simulating and analyzing biochemical systems ## Why use StochSS StochSS provides both an easy-to-use UI for constructing biochemical models as well as intuitive UIs for the most common model analysis tools such as visualization of results, parameter sweeps and parameter inference. StochSS is built on top of Jupyter Hub, and this lets you seemlessly switch between UI representations and Notebooks exposing the full backend API. In this way a user can benefit from the best of graphical representations with a clear upgrade path to modeling as code. For this reason, StochSS is also uniquely suited for the computational biologist starting out with mathematical modeling of biochemical systems. -StochSS is a sotware project involving several leading research groups in computational systems biology. We welcome collaborators to help expand the capabilities of StochSS. Read more about the project at www.stochss.org . +StochSS is a software project involving several leading research groups in computational systems biology. We welcome collaborators to help expand the capabilities of StochSS. Read more about the project at www.stochss.org . -*StochSS is intended to be used as Software as a Service. The instructions that follows help you set your own local development environment or deploy your own instance as SaaS. If you intend to mainly use StochSS for modeling, simulation and model analysis, consider using the hosted deployment at http://app.stochss.org which you can access without any installation. +StochSS is intended to be used as Software as a Service. The following instructions can help you set up your own local development environment or deploy your own instance as SaaS. If you intend to mainly use StochSS for modeling, simulation and model analysis, consider using [StochSS Live!](https://live.stochss.org) ## Requirements @@ -17,7 +17,7 @@ StochSS is a sotware project involving several leading research groups in comput - [Docker Compose](https://docs.docker.com/compose/install/) (Only required if you want to run StochSS with [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#)) -*At the moment StochSS development on Windows is not supported. You can try using [Make for Windows](http://gnuwin32.sourceforge.net/packages/make.htm), but this is untested! +At the moment StochSS development on Windows is not supported. You can try using [Make for Windows](http://gnuwin32.sourceforge.net/packages/make.htm), but this is untested! ## Quickstart From 214e3d89deafd2d51bc23839539654f3905b50cd Mon Sep 17 00:00:00 2001 From: seanebum Date: Tue, 6 Oct 2020 11:21:00 -0400 Subject: [PATCH 15/29] removed space before period and made stochss.org a link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5ef58c0739..27d98f5305 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ StochSS provides advanced tools for simulating and analyzing biochemical systems ## Why use StochSS StochSS provides both an easy-to-use UI for constructing biochemical models as well as intuitive UIs for the most common model analysis tools such as visualization of results, parameter sweeps and parameter inference. StochSS is built on top of Jupyter Hub, and this lets you seemlessly switch between UI representations and Notebooks exposing the full backend API. In this way a user can benefit from the best of graphical representations with a clear upgrade path to modeling as code. For this reason, StochSS is also uniquely suited for the computational biologist starting out with mathematical modeling of biochemical systems. -StochSS is a software project involving several leading research groups in computational systems biology. We welcome collaborators to help expand the capabilities of StochSS. Read more about the project at www.stochss.org . +StochSS is a software project involving several leading research groups in computational systems biology. We welcome collaborators to help expand the capabilities of StochSS. Read more about the project at [www.stochss.org](http://www.stochss.org). StochSS is intended to be used as Software as a Service. The following instructions can help you set up your own local development environment or deploy your own instance as SaaS. If you intend to mainly use StochSS for modeling, simulation and model analysis, consider using [StochSS Live!](https://live.stochss.org) From bf5ca2071ebeb27172095a47c22af5029bbb93bf Mon Sep 17 00:00:00 2001 From: seanebum Date: Tue, 6 Oct 2020 11:53:46 -0400 Subject: [PATCH 16/29] made updates to installation instructions for StochSS local deployments --- README.md | 40 ++++++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 27d98f5305..5bfc56dcc7 100644 --- a/README.md +++ b/README.md @@ -1,34 +1,34 @@ # StochSS: Software as a service for simulation-driven investigations of stochastic biochemical models -StochSS provides advanced tools for simulating and analyzing biochemical systems as Software as a Service. StochSS supports a wide range of model types ranging from continuous ODEs to discrete (spatial) stochastic simulations as well as advanced model analysis workflows. Try out StochSS here: https://app.stochss.org . - +StochSS provides advanced tools for simulating and analyzing biochemical systems as Software as a Service. StochSS supports a wide range of model types ranging from continuous ODEs to discrete (spatial) stochastic simulations as well as advanced model analysis workflows. + +**Try out [StochSS Live!](https://live.stochss.org)** + ## Why use StochSS StochSS provides both an easy-to-use UI for constructing biochemical models as well as intuitive UIs for the most common model analysis tools such as visualization of results, parameter sweeps and parameter inference. StochSS is built on top of Jupyter Hub, and this lets you seemlessly switch between UI representations and Notebooks exposing the full backend API. In this way a user can benefit from the best of graphical representations with a clear upgrade path to modeling as code. For this reason, StochSS is also uniquely suited for the computational biologist starting out with mathematical modeling of biochemical systems. StochSS is a software project involving several leading research groups in computational systems biology. We welcome collaborators to help expand the capabilities of StochSS. Read more about the project at [www.stochss.org](http://www.stochss.org). -StochSS is intended to be used as Software as a Service. The following instructions can help you set up your own local development environment or deploy your own instance as SaaS. If you intend to mainly use StochSS for modeling, simulation and model analysis, consider using [StochSS Live!](https://live.stochss.org) +StochSS is intended to be used as Software as a Service via [StochSS Live!](https://live.stochss.org). The following instructions can help you set up your own local development environment or deploy your own instance as SaaS. -## Requirements +## Deploying your own Single-User StochSS Instance +### Requirements - [Nodejs](https://nodejs.org/) - [Docker Desktop](https://www.docker.com/products/docker-desktop) (Windows and Mac) or [Docker Engine](https://docs.docker.com/install/) (Linux, Mac, and Windows) -- [Docker Compose](https://docs.docker.com/compose/install/) (Only required if you want to run StochSS with [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#)) - At the moment StochSS development on Windows is not supported. You can try using [Make for Windows](http://gnuwin32.sourceforge.net/packages/make.htm), but this is untested! -## Quickstart +### Quickstart - Build and run the stochss notebook server: `make` - Once your terminal calms down you'll see a link to your server that looks something like this: `127.0.0.1:8888/?token=X8dSfd...` - - Navigate to that link and get started! -## Setup +### Setup - Build the docker container: `make build`. @@ -38,27 +38,31 @@ At the moment StochSS development on Windows is not supported. You can try using - Upon changing backend code in stochss/handlers you can update a running StochSS notebook server with `make update`. -### Add a python dependency +#### Add a python dependency Use requirements.txt to add Python dependencies that will be installed into the StochSS docker container. -## JupyterHub +## Deploying Multi-User StochSS -JupyterHub is a multi-user system for spawning Jupyter notebook servers. We use JupyterHub to serve the StochSS home page and spawn StochSS notebook servers. +- StochSS uses [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#) as the basis for the multi-user deployment. See their documentation for more details on configuring the JupyterHub environment. + +### Requirements -### Setup +In addition to the single-user requirements, you will need [Docker Compose](https://docs.docker.com/compose/install/). + +#### Setup -- [Optional] To set admins for JupyterHub, make a file called `userlist` in the `jupyterhub/` directory. On each line of this file place a username followed by the word 'admin'. For example: `myuser admin`. If using Google OAuth, the uesrname will be a gmail address. Navigate to `/hub/admin` to use the JupyterHub admin interface. +- [Optional] To set admins for JupyterHub, make a file called `userlist` in the `jupyterhub/` directory. On each line of this file place a username followed by the word 'admin'. For example: `myuser admin`. If using Google OAuth, the uesername will be a gmail address. Navigate to `/hub/admin` to use the JupyterHub admin interface. - [Optional] By default multi-user StochSS is set up to allocate 2 logical cpus per user, reserving 2 logical cpus for the hub container and underlying OS. You can define a list of "power users" that are excluded from resource limitations by adding a text file called `.power_users` (note the leading period) to the `jupyterhub/` directory with one username/email address on each line of the file. -### Run Locally +#### Run Locally - To run JupyterHub locally run `make hub` and go to 127.0.0.1:8888. -### Setup Staging Server +#### Set Up A Staging Server -To setup the staging environment you'll need the correct Google OAuth setup in `jupyterhub/secrets/.oauth.staging.env`. Do not wrap these environment variables in quotes! +To set up the staging environment you'll need to [set up Google OAuth](https://developers.google.com/identity/protocols/oauth2) for your instance. Once you're set up, you'll need to put your OAuth credentials in `jupyterhub/secrets/.oauth.staging.env`. Do not wrap these environment variables in quotes! Example oauth file: @@ -76,7 +80,7 @@ make build_hub make run_hub_staging ``` -### Setup Production Server +#### Set Up A Production Server Similar to staging, except you'll need the correct Google OAuth credentials set in `jupyterhub/secrets/.oauth.prod.env`. From 2d336d79b4b0d9953470c96fc8527edc19e0c727 Mon Sep 17 00:00:00 2001 From: seanebum Date: Tue, 6 Oct 2020 11:59:02 -0400 Subject: [PATCH 17/29] fixed headers/lists --- README.md | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 5bfc56dcc7..e8d16cb7a1 100644 --- a/README.md +++ b/README.md @@ -44,23 +44,21 @@ Use requirements.txt to add Python dependencies that will be installed into the ## Deploying Multi-User StochSS -- StochSS uses [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#) as the basis for the multi-user deployment. See their documentation for more details on configuring the JupyterHub environment. +StochSS uses [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#) as the basis for the multi-user deployment. See their documentation for more details on configuring the JupyterHub environment. -### Requirements +### Setup -In addition to the single-user requirements, you will need [Docker Compose](https://docs.docker.com/compose/install/). - -#### Setup +- In addition to the single-user requirements, you will need [Docker Compose](https://docs.docker.com/compose/install/). - [Optional] To set admins for JupyterHub, make a file called `userlist` in the `jupyterhub/` directory. On each line of this file place a username followed by the word 'admin'. For example: `myuser admin`. If using Google OAuth, the uesername will be a gmail address. Navigate to `/hub/admin` to use the JupyterHub admin interface. - [Optional] By default multi-user StochSS is set up to allocate 2 logical cpus per user, reserving 2 logical cpus for the hub container and underlying OS. You can define a list of "power users" that are excluded from resource limitations by adding a text file called `.power_users` (note the leading period) to the `jupyterhub/` directory with one username/email address on each line of the file. -#### Run Locally +### Run Locally -- To run JupyterHub locally run `make hub` and go to 127.0.0.1:8888. +To run JupyterHub locally run `make hub` and go to 127.0.0.1:8888. -#### Set Up A Staging Server +### Set Up A Staging Server To set up the staging environment you'll need to [set up Google OAuth](https://developers.google.com/identity/protocols/oauth2) for your instance. Once you're set up, you'll need to put your OAuth credentials in `jupyterhub/secrets/.oauth.staging.env`. Do not wrap these environment variables in quotes! @@ -80,7 +78,7 @@ make build_hub make run_hub_staging ``` -#### Set Up A Production Server +### Set Up A Production Server Similar to staging, except you'll need the correct Google OAuth credentials set in `jupyterhub/secrets/.oauth.prod.env`. From 8502f8e599112b29b13d2e5f7aac9c14db757571 Mon Sep 17 00:00:00 2001 From: seanebum Date: Tue, 6 Oct 2020 12:08:28 -0400 Subject: [PATCH 18/29] added code of conduct file --- CODE_OF_CONDUCT.md | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 CODE_OF_CONDUCT.md diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000000..4cb837e82f --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,44 @@ +Contributor Covenant Code of Conduct +==================================== + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project contributors are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project contributors have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project contributors. + +## Enforcement + +If a contributor engages in harassing behaviour, the project organizers may take any action they deem appropriate, including warning the offender or expelling them from online forums, online project resources, face-to-face meetings, or any other project-related activity or resource. + +If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact a member of the project team immediately. Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. + +## Attribution + +Portions of this Code of Conduct were adapted from Electron's [Contributor Covenant Code of Conduct](https://github.com/electron/electron/blob/master/CODE_OF_CONDUCT.md), which itself was adapted from the [Contributor Covenant](http://contributor-covenant.org/version/1/4), version 1.4. From b1385eb111c2ddcc0ff8d688168b6df6f548883f Mon Sep 17 00:00:00 2001 From: Matthew Geiger Date: Tue, 6 Oct 2020 12:22:11 -0400 Subject: [PATCH 19/29] Update CONTRIBUTING.md --- CONTRIBUTING.md | 44 ++++++++++++++++---------------------------- 1 file changed, 16 insertions(+), 28 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3dc1057f0a..02530f2162 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,29 +1,17 @@ # CONTRIBUTING -By contributing to StochSS, you agree to the Code of Conduct and that the contents of this project are distributed under the [GNU GPL v3](/LICENSE). Please review both of these documents. If after reading you are interested in contributing, please follow these guidelines: - -## 1. Making Changes: -a) Create a fork from this repository ('https://github.com/StochSS/StochSS') -b) Create a new branch. -c) Please use a meaningful name, and include the issue # if applicable. -d) For bug fixes, branch from 'main' -e) For new features, branch from 'develop' -f) Be sure to document your code -g) Eliminate any commented-out or dead code. -h) If you are creating a new file, prepend the [COPYRIGHT](/COPYRIGHT) notice to the beginning of the file. -i) Create unit tests to cover changes. Unit tests should be placed in the [test](/stochss/tests) subdirectory. - -## 2. Submitting a Pull Request: -a) If changes are bug/hotfix, make a pull request to 'main'. -b) If other changes, or new features are being added, make a pull request to 'develop'. -c) Include a list of changes in the PR description. -d) Provide a usage guide/how-to for new features in the PR description. - -***Do NOT merge your own pull request. Once the request is submitted, the code must be reviewed and merged by someone else.*** - -## 3. Merging a Pull Request: -a) Verify correct merge destination ('main' for hotfix/bugs, 'develop' for features/changes). -b) Review code for logic, consistency, documentation, and commented-out or dead sections. -c) Verify that unit tests are provided for the new code, and that they accurately test the new feature/changes. -d) Check coverage by running [./run_tests.py](/stochss/tests/run_tests.py) from the project [test](/stochss/tests) subdirectory. -e) Make sure that all GitHub Actions resolve before merging the changes. -f) Merge! +By contributing to StochSS, you agree to the [Code of Conduct](/CODE_OF_CONDUCT.md) and the conditions of the [GNU GPL v3](/LICENSE). Please review both of these documents before contributing. + +## Making Changes +1. Fork [the project repository]('https://github.com/StochSS/StochSS') +2. Create a new branch from the 'develop' branch. Use a meaningful name and include an issue number if applicable. +3. Add your changes. Be sure to document your code and remove any dead code. +4. Add the [COPYRIGHT](/COPYRIGHT) notice to the beginning of any new files you create. +5. Create unit tests to cover changes. Unit tests should be placed in the [test](/stochss/tests) subdirectory. + +## Submitting a Pull Request +1. Make a pull request to 'develop'. +2. Include a list of changes in the PR description. +3. Link relevant issues to the pull request. +4. Add labels relevant to any changes made. +5. Provide a clear description of any new features in the PR description. +6. Add any relevant StochSS team members as reviewers. From b9e5dec4044b752375d42cffa5a8ce6ae461051b Mon Sep 17 00:00:00 2001 From: Matthew Geiger Date: Tue, 6 Oct 2020 12:23:31 -0400 Subject: [PATCH 20/29] Update CONTRIBUTING.md --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 02530f2162..5cc500aece 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,7 +2,7 @@ By contributing to StochSS, you agree to the [Code of Conduct](/CODE_OF_CONDUCT.md) and the conditions of the [GNU GPL v3](/LICENSE). Please review both of these documents before contributing. ## Making Changes -1. Fork [the project repository]('https://github.com/StochSS/StochSS') +1. Fork [the project repository](https://github.com/StochSS/StochSS). 2. Create a new branch from the 'develop' branch. Use a meaningful name and include an issue number if applicable. 3. Add your changes. Be sure to document your code and remove any dead code. 4. Add the [COPYRIGHT](/COPYRIGHT) notice to the beginning of any new files you create. From 6a4cbf6b9e530e035b74eb30f27f0f018f6dd133 Mon Sep 17 00:00:00 2001 From: Matthew Geiger Date: Tue, 6 Oct 2020 12:26:45 -0400 Subject: [PATCH 21/29] Update CONTRIBUTING.md --- CONTRIBUTING.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 5cc500aece..964a4d0a5b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,9 +4,10 @@ By contributing to StochSS, you agree to the [Code of Conduct](/CODE_OF_CONDUCT. ## Making Changes 1. Fork [the project repository](https://github.com/StochSS/StochSS). 2. Create a new branch from the 'develop' branch. Use a meaningful name and include an issue number if applicable. -3. Add your changes. Be sure to document your code and remove any dead code. +3. Add new changes to your branch. Be sure to document your code and remove any dead code. 4. Add the [COPYRIGHT](/COPYRIGHT) notice to the beginning of any new files you create. 5. Create unit tests to cover changes. Unit tests should be placed in the [test](/stochss/tests) subdirectory. +6. Use [pylint](https://pylint.org) to validate any new Python code to ensure [PEP 8](https://www.python.org/dev/peps/pep-0008/) compliance. ## Submitting a Pull Request 1. Make a pull request to 'develop'. From ec132992ea07a2424ec696597245d2703a365d60 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Oct 2020 13:48:33 -0400 Subject: [PATCH 22/29] Added Copyrights to js page files and support files. --- client/app.js | 18 ++++++++++++++++++ client/config.js | 18 ++++++++++++++++++ client/graphics.js | 18 ++++++++++++++++++ client/modals.js | 18 ++++++++++++++++++ client/page-help.js | 18 ++++++++++++++++++ client/pages/base.js | 18 ++++++++++++++++++ client/pages/file-browser.js | 18 ++++++++++++++++++ client/pages/home.js | 18 ++++++++++++++++++ client/pages/model-editor.js | 18 ++++++++++++++++++ client/pages/page.js | 18 ++++++++++++++++++ client/pages/project-browser.js | 18 ++++++++++++++++++ client/pages/project-manager.js | 18 ++++++++++++++++++ client/pages/quickstart.js | 18 ++++++++++++++++++ client/pages/users-home.js | 18 ++++++++++++++++++ client/pages/workflow-manager.js | 18 ++++++++++++++++++ client/pages/workflow-selection.js | 18 ++++++++++++++++++ client/reaction-types.js | 18 ++++++++++++++++++ client/tooltips.js | 18 ++++++++++++++++++ 18 files changed, 324 insertions(+) diff --git a/client/app.js b/client/app.js index 4af2ff06fd..1ad5139789 100644 --- a/client/app.js +++ b/client/app.js @@ -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 . +*/ + //var config = require('./config.js')(process.env.NODE_ENV); let path = require('path'); diff --git a/client/config.js b/client/config.js index db2b39cb0f..8fb86111be 100644 --- a/client/config.js +++ b/client/config.js @@ -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 . +*/ + let path = require('path'); diff --git a/client/graphics.js b/client/graphics.js index 79c0088164..3f0299ce16 100644 --- a/client/graphics.js +++ b/client/graphics.js @@ -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 . +*/ + module.exports = { logo: ` diff --git a/client/modals.js b/client/modals.js index c42582d132..e638d8a486 100644 --- a/client/modals.js +++ b/client/modals.js @@ -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 . +*/ + let help = require('./page-help') let templates = { diff --git a/client/page-help.js b/client/page-help.js index 4cc733a6cb..a5a42fa3c5 100644 --- a/client/page-help.js +++ b/client/page-help.js @@ -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 . +*/ + module.exports = { 'file-browser' : `

Open/Edit a File: Double-click on a file or right-click on a file and click Open/Edit. diff --git a/client/pages/base.js b/client/pages/base.js index 10ba8a5957..4e295992ed 100644 --- a/client/pages/base.js +++ b/client/pages/base.js @@ -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 . +*/ + var View = require('ampersand-view'); module.exports = View.extend({ diff --git a/client/pages/file-browser.js b/client/pages/file-browser.js index fb6c1fe3a5..3c4aa50d6d 100644 --- a/client/pages/file-browser.js +++ b/client/pages/file-browser.js @@ -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 . +*/ + let jstree = require('jstree'); let path = require('path'); let xhr = require('xhr'); diff --git a/client/pages/home.js b/client/pages/home.js index 733bd149fb..4b1b4121f4 100644 --- a/client/pages/home.js +++ b/client/pages/home.js @@ -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 . +*/ + let $ = require('jquery'); let PageView = require('./base'); let graphics = require('../graphics'); diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js index 28e018607b..adaa8fde29 100644 --- a/client/pages/model-editor.js +++ b/client/pages/model-editor.js @@ -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 . +*/ + var _ = require('underscore'); var $ = require('jquery'); let path = require('path'); diff --git a/client/pages/page.js b/client/pages/page.js index 958c24aa25..3e434457ef 100644 --- a/client/pages/page.js +++ b/client/pages/page.js @@ -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 . +*/ + let PageView = require('./base'); let MainView = require('../views/main'); //var templates = require('../templates'); diff --git a/client/pages/project-browser.js b/client/pages/project-browser.js index 4178d8578b..051fc554c8 100644 --- a/client/pages/project-browser.js +++ b/client/pages/project-browser.js @@ -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 . +*/ + let $ = require('jquery'); let path = require('path'); let xhr = require('xhr'); diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js index bef03bcca7..cdff7f2f21 100644 --- a/client/pages/project-manager.js +++ b/client/pages/project-manager.js @@ -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 . +*/ + var $ = require('jquery'); var xhr = require('xhr'); var path = require('path'); diff --git a/client/pages/quickstart.js b/client/pages/quickstart.js index 549c2484bc..bf64e271f7 100644 --- a/client/pages/quickstart.js +++ b/client/pages/quickstart.js @@ -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 . +*/ + // views var PageView = require('./base'); // templates diff --git a/client/pages/users-home.js b/client/pages/users-home.js index 1d4747bddc..52d08b29af 100644 --- a/client/pages/users-home.js +++ b/client/pages/users-home.js @@ -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 . +*/ + let $ = require('jquery'); let xhr = require('xhr'); let path = require('path'); diff --git a/client/pages/workflow-manager.js b/client/pages/workflow-manager.js index facee01c89..868f16d7b0 100644 --- a/client/pages/workflow-manager.js +++ b/client/pages/workflow-manager.js @@ -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 . +*/ + var _ = require('underscore'); var $ = require('jquery'); var path = require('path'); diff --git a/client/pages/workflow-selection.js b/client/pages/workflow-selection.js index 014e88840e..0254d31ee8 100644 --- a/client/pages/workflow-selection.js +++ b/client/pages/workflow-selection.js @@ -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 . +*/ + var $ = require('jquery'); var xhr = require('xhr'); var path = require('path'); diff --git a/client/reaction-types.js b/client/reaction-types.js index b8fb1e83d8..503db760d3 100644 --- a/client/reaction-types.js +++ b/client/reaction-types.js @@ -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 . +*/ + module.exports = { creation: { reactants: [], diff --git a/client/tooltips.js b/client/tooltips.js index 43f6be5762..213ca5763e 100644 --- a/client/tooltips.js +++ b/client/tooltips.js @@ -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 . +*/ + module.exports = { speciesEditor: { name: "Names for species, parameters, reactions, events, and rules must be unique.", From 1cebfb2ce87accee1dfb01f6b62574d09b051f7d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Oct 2020 13:50:59 -0400 Subject: [PATCH 23/29] Added Copyrights to js model files. --- client/models/creator.js | 18 ++++++++++++++++++ client/models/event-assignment.js | 18 ++++++++++++++++++ client/models/event-assignments.js | 18 ++++++++++++++++++ client/models/event.js | 18 ++++++++++++++++++ client/models/events.js | 18 ++++++++++++++++++ client/models/function-definition.js | 18 ++++++++++++++++++ client/models/function-definitions.js | 18 ++++++++++++++++++ client/models/initial-condition.js | 18 ++++++++++++++++++ client/models/initial-conditions.js | 18 ++++++++++++++++++ client/models/me.js | 18 ++++++++++++++++++ client/models/mesh-settings.js | 18 ++++++++++++++++++ client/models/model-settings.js | 18 ++++++++++++++++++ client/models/model.js | 18 ++++++++++++++++++ client/models/models.js | 18 ++++++++++++++++++ client/models/parameter-sweep-settings.js | 18 ++++++++++++++++++ client/models/parameter.js | 18 ++++++++++++++++++ client/models/parameters.js | 18 ++++++++++++++++++ client/models/plots.js | 18 ++++++++++++++++++ client/models/project.js | 18 ++++++++++++++++++ client/models/reaction.js | 18 ++++++++++++++++++ client/models/reactions.js | 18 ++++++++++++++++++ client/models/results-settings.js | 18 ++++++++++++++++++ client/models/rule.js | 18 ++++++++++++++++++ client/models/rules.js | 18 ++++++++++++++++++ client/models/settings.js | 18 ++++++++++++++++++ client/models/simulation-settings.js | 18 ++++++++++++++++++ client/models/specie.js | 18 ++++++++++++++++++ client/models/species.js | 18 ++++++++++++++++++ client/models/ssa-settings.js | 18 ++++++++++++++++++ client/models/stoich-specie.js | 18 ++++++++++++++++++ client/models/stoich-species.js | 18 ++++++++++++++++++ client/models/subdomain.js | 18 ++++++++++++++++++ client/models/subdomains.js | 18 ++++++++++++++++++ client/models/workflow-group.js | 18 ++++++++++++++++++ client/models/workflow-groups.js | 18 ++++++++++++++++++ client/models/workflow.js | 18 ++++++++++++++++++ client/models/workflows.js | 18 ++++++++++++++++++ 37 files changed, 666 insertions(+) diff --git a/client/models/creator.js b/client/models/creator.js index 48b899cf16..103eec1764 100644 --- a/client/models/creator.js +++ b/client/models/creator.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/event-assignment.js b/client/models/event-assignment.js index c2c6c57cb9..ba196aa514 100644 --- a/client/models/event-assignment.js +++ b/client/models/event-assignment.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/event-assignments.js b/client/models/event-assignments.js index e7ee1bac52..bbfd272226 100644 --- a/client/models/event-assignments.js +++ b/client/models/event-assignments.js @@ -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 . +*/ + //models var EventAssignment = require('./event-assignment'); //collections diff --git a/client/models/event.js b/client/models/event.js index db75d71540..0a248a8f8d 100644 --- a/client/models/event.js +++ b/client/models/event.js @@ -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 . +*/ + //models var State = require('ampersand-state'); //collections diff --git a/client/models/events.js b/client/models/events.js index 78e46352c8..f839e3e824 100644 --- a/client/models/events.js +++ b/client/models/events.js @@ -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 . +*/ + var _ = require('underscore'); //models var Event = require('./event'); diff --git a/client/models/function-definition.js b/client/models/function-definition.js index 799595bd97..eef7d7caae 100644 --- a/client/models/function-definition.js +++ b/client/models/function-definition.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/function-definitions.js b/client/models/function-definitions.js index 9ae5a68cf7..4dab2ad8bc 100644 --- a/client/models/function-definitions.js +++ b/client/models/function-definitions.js @@ -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 . +*/ + //collections var Collection = require('ampersand-collection'); //models diff --git a/client/models/initial-condition.js b/client/models/initial-condition.js index 733aeb2242..05f14d727d 100644 --- a/client/models/initial-condition.js +++ b/client/models/initial-condition.js @@ -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 . +*/ + // Models var State = require('ampersand-state'); var Specie = require('./specie'); diff --git a/client/models/initial-conditions.js b/client/models/initial-conditions.js index e9f7d5bf41..c2ea49696c 100644 --- a/client/models/initial-conditions.js +++ b/client/models/initial-conditions.js @@ -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 . +*/ + // Collections var Collection = require('ampersand-collection'); //Models diff --git a/client/models/me.js b/client/models/me.js index 4202a3aa41..5fdbe15e6c 100644 --- a/client/models/me.js +++ b/client/models/me.js @@ -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 . +*/ + var path = require('path'); var app = require('ampersand-app'); var Model = require('ampersand-model'); diff --git a/client/models/mesh-settings.js b/client/models/mesh-settings.js index 0e1d4a37f7..94c4ae2c4f 100644 --- a/client/models/mesh-settings.js +++ b/client/models/mesh-settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); var Subdomains = require('./subdomains'); diff --git a/client/models/model-settings.js b/client/models/model-settings.js index 115e045b26..f77fb8d42f 100644 --- a/client/models/model-settings.js +++ b/client/models/model-settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/model.js b/client/models/model.js index afa1640508..9c5d9e102e 100644 --- a/client/models/model.js +++ b/client/models/model.js @@ -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 . +*/ + var app = require('../app'); var path = require('path'); var xhr = require('xhr'); diff --git a/client/models/models.js b/client/models/models.js index 2fe24c9801..d35fba09e9 100644 --- a/client/models/models.js +++ b/client/models/models.js @@ -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 . +*/ + var app = require('ampersand-app'); var RestCollection = require('ampersand-rest-collection'); var Model = require('./model'); diff --git a/client/models/parameter-sweep-settings.js b/client/models/parameter-sweep-settings.js index 7db84b69da..f4a5609836 100644 --- a/client/models/parameter-sweep-settings.js +++ b/client/models/parameter-sweep-settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); var Parameter = require('./parameter'); diff --git a/client/models/parameter.js b/client/models/parameter.js index 1db4e83019..9efeb349ec 100644 --- a/client/models/parameter.js +++ b/client/models/parameter.js @@ -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 . +*/ + var _ = require('underscore'); //models var State = require('ampersand-state'); diff --git a/client/models/parameters.js b/client/models/parameters.js index c8e48ac625..a17ed642f8 100644 --- a/client/models/parameters.js +++ b/client/models/parameters.js @@ -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 . +*/ + var _ = require('underscore'); //models var Parameter = require('./parameter'); diff --git a/client/models/plots.js b/client/models/plots.js index 3f7e990f71..bd6a22cbaf 100644 --- a/client/models/plots.js +++ b/client/models/plots.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/project.js b/client/models/project.js index 329adc2757..568ae61861 100644 --- a/client/models/project.js +++ b/client/models/project.js @@ -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 . +*/ + var path = require('path'); //Support Files var app = require('../app.js'); diff --git a/client/models/reaction.js b/client/models/reaction.js index 69ea0443c1..6a0ab05867 100644 --- a/client/models/reaction.js +++ b/client/models/reaction.js @@ -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 . +*/ + var _ = require('underscore'); //models var State = require('ampersand-state'); diff --git a/client/models/reactions.js b/client/models/reactions.js index bfe38e252c..03383330e5 100644 --- a/client/models/reactions.js +++ b/client/models/reactions.js @@ -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 . +*/ + var _ = require('underscore'); var Events = require('ampersand-events'); //models diff --git a/client/models/results-settings.js b/client/models/results-settings.js index 557a4cbfbf..ffae215597 100644 --- a/client/models/results-settings.js +++ b/client/models/results-settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/rule.js b/client/models/rule.js index ce77fb4931..449a13c62c 100644 --- a/client/models/rule.js +++ b/client/models/rule.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/rules.js b/client/models/rules.js index 6a9ceb501c..7ebc5dc512 100644 --- a/client/models/rules.js +++ b/client/models/rules.js @@ -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 . +*/ + var _ = require('underscore'); //models var Rule = require('./rule'); diff --git a/client/models/settings.js b/client/models/settings.js index e6d831dbe2..7b80a1271c 100644 --- a/client/models/settings.js +++ b/client/models/settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); var SimulationSettings = require('./simulation-settings'); diff --git a/client/models/simulation-settings.js b/client/models/simulation-settings.js index bcdf480ee8..92a36fd970 100644 --- a/client/models/simulation-settings.js +++ b/client/models/simulation-settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/specie.js b/client/models/specie.js index 8b8ab17118..2af85c351f 100644 --- a/client/models/specie.js +++ b/client/models/specie.js @@ -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 . +*/ + var _ = require('underscore'); //models var State = require('ampersand-state'); diff --git a/client/models/species.js b/client/models/species.js index 355fbb8652..a6b249216e 100644 --- a/client/models/species.js +++ b/client/models/species.js @@ -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 . +*/ + var _ = require('underscore'); //models var Specie = require('./specie'); diff --git a/client/models/ssa-settings.js b/client/models/ssa-settings.js index e3c6ff496a..79b4f7ff0b 100644 --- a/client/models/ssa-settings.js +++ b/client/models/ssa-settings.js @@ -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 . +*/ + //models var State = require('ampersand-state'); diff --git a/client/models/stoich-specie.js b/client/models/stoich-specie.js index 050452f92f..a11311f9f5 100644 --- a/client/models/stoich-specie.js +++ b/client/models/stoich-specie.js @@ -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 . +*/ + var _ = require('underscore'); //models var State = require('ampersand-state'); diff --git a/client/models/stoich-species.js b/client/models/stoich-species.js index 3c1ed48fa8..53d398197f 100644 --- a/client/models/stoich-species.js +++ b/client/models/stoich-species.js @@ -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 . +*/ + var _ = require('underscore'); //models var StoichSpecie = require('./stoich-specie'); diff --git a/client/models/subdomain.js b/client/models/subdomain.js index 090c6b430a..e65ca8a550 100644 --- a/client/models/subdomain.js +++ b/client/models/subdomain.js @@ -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 . +*/ + //model var State = require('ampersand-state'); diff --git a/client/models/subdomains.js b/client/models/subdomains.js index fd5b97d4a8..a1fe7dfc6e 100644 --- a/client/models/subdomains.js +++ b/client/models/subdomains.js @@ -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 . +*/ + //models var Subdomain = require('./subdomain'); //collections diff --git a/client/models/workflow-group.js b/client/models/workflow-group.js index ce59a2cf68..689b7e6262 100644 --- a/client/models/workflow-group.js +++ b/client/models/workflow-group.js @@ -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 . +*/ + //collections var WorkflowCollection = require('./workflows'); //models diff --git a/client/models/workflow-groups.js b/client/models/workflow-groups.js index 134e8e561c..c8a1e49d2f 100644 --- a/client/models/workflow-groups.js +++ b/client/models/workflow-groups.js @@ -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 . +*/ + //collections var Collection = require('ampersand-collection'); //models diff --git a/client/models/workflow.js b/client/models/workflow.js index b3c8749d06..c847ce18b8 100644 --- a/client/models/workflow.js +++ b/client/models/workflow.js @@ -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 . +*/ + //collections //models var State = require('ampersand-state'); diff --git a/client/models/workflows.js b/client/models/workflows.js index d6aa302d5d..1073cd8037 100644 --- a/client/models/workflows.js +++ b/client/models/workflows.js @@ -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 . +*/ + //collections var Collection = require('ampersand-collection'); //models From 4bd039f1834fb654f6e53fcd8638e2292261ab71 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Tue, 6 Oct 2020 13:56:26 -0400 Subject: [PATCH 24/29] Added Copyright blocks to js view files. --- client/views/creator-listing.js | 18 ++++++++++++++++++ client/views/edit-advanced-specie.js | 18 ++++++++++++++++++ client/views/edit-custom-stoich-specie.js | 18 ++++++++++++++++++ client/views/edit-event-assignment.js | 18 ++++++++++++++++++ client/views/edit-function-definition.js | 18 ++++++++++++++++++ client/views/edit-initial-condition.js | 18 ++++++++++++++++++ client/views/edit-model-view.js | 18 ++++++++++++++++++ client/views/edit-models-view.js | 18 ++++++++++++++++++ client/views/edit-parameter.js | 18 ++++++++++++++++++ client/views/edit-place-details.js | 18 ++++++++++++++++++ client/views/edit-project.js | 18 ++++++++++++++++++ client/views/edit-rule.js | 18 ++++++++++++++++++ client/views/edit-scatter-details.js | 18 ++++++++++++++++++ client/views/edit-spatial-specie.js | 18 ++++++++++++++++++ client/views/edit-specie.js | 18 ++++++++++++++++++ client/views/edit-stoich-specie.js | 18 ++++++++++++++++++ client/views/edit-workflow-group-view.js | 18 ++++++++++++++++++ client/views/edit-workflow-groups-view.js | 18 ++++++++++++++++++ client/views/edit-workflow-view.js | 18 ++++++++++++++++++ client/views/edit-workflows-view.js | 18 ++++++++++++++++++ client/views/event-assignments-editor.js | 18 ++++++++++++++++++ client/views/event-assignments-viewer.js | 18 ++++++++++++++++++ client/views/event-details.js | 18 ++++++++++++++++++ client/views/event-listings.js | 18 ++++++++++++++++++ client/views/events-editor.js | 18 ++++++++++++++++++ client/views/events-viewer.js | 18 ++++++++++++++++++ client/views/file-browser-view.js | 18 ++++++++++++++++++ client/views/hybrid-settings.js | 18 ++++++++++++++++++ client/views/initial-conditions-editor.js | 18 ++++++++++++++++++ client/views/input.js | 18 ++++++++++++++++++ client/views/main.js | 18 ++++++++++++++++++ client/views/mesh-editor.js | 18 ++++++++++++++++++ client/views/meta-data.js | 18 ++++++++++++++++++ client/views/model-settings-viewer.js | 18 ++++++++++++++++++ client/views/model-settings.js | 18 ++++++++++++++++++ client/views/model-state-buttons.js | 18 ++++++++++++++++++ client/views/model-viewer.js | 18 ++++++++++++++++++ client/views/models-viewer.js | 18 ++++++++++++++++++ .../views/parameter-sweep-settings-viewer.js | 18 ++++++++++++++++++ client/views/parameter-sweep-settings.js | 18 ++++++++++++++++++ client/views/parameters-editor.js | 18 ++++++++++++++++++ client/views/parameters-viewer.js | 18 ++++++++++++++++++ client/views/plots-view.js | 18 ++++++++++++++++++ client/views/project-viewer.js | 18 ++++++++++++++++++ client/views/reactant-product.js | 18 ++++++++++++++++++ client/views/reaction-details.js | 18 ++++++++++++++++++ client/views/reaction-listing.js | 18 ++++++++++++++++++ client/views/reaction-subdomains.js | 18 ++++++++++++++++++ client/views/reactions-editor.js | 18 ++++++++++++++++++ client/views/reactions-viewer.js | 18 ++++++++++++++++++ client/views/rules-editor.js | 18 ++++++++++++++++++ client/views/rules-viewer.js | 18 ++++++++++++++++++ client/views/sbml-component-editor.js | 18 ++++++++++++++++++ client/views/simulation-settings-viewer.js | 18 ++++++++++++++++++ client/views/simulation-settings.js | 18 ++++++++++++++++++ client/views/species-editor.js | 18 ++++++++++++++++++ client/views/species-viewer.js | 18 ++++++++++++++++++ client/views/subdomain.js | 18 ++++++++++++++++++ client/views/tests.js | 18 ++++++++++++++++++ client/views/view-event-assignments.js | 18 ++++++++++++++++++ client/views/view-events.js | 18 ++++++++++++++++++ client/views/view-parameter.js | 18 ++++++++++++++++++ client/views/view-reactions.js | 18 ++++++++++++++++++ client/views/view-rules.js | 18 ++++++++++++++++++ client/views/view-specie.js | 18 ++++++++++++++++++ client/views/workflow-editor.js | 18 ++++++++++++++++++ client/views/workflow-group-viewer.js | 18 ++++++++++++++++++ client/views/workflow-groups-viewer.js | 18 ++++++++++++++++++ client/views/workflow-info.js | 18 ++++++++++++++++++ client/views/workflow-results.js | 18 ++++++++++++++++++ client/views/workflow-state-buttons.js | 18 ++++++++++++++++++ client/views/workflow-status.js | 18 ++++++++++++++++++ client/views/workflow-viewer.js | 18 ++++++++++++++++++ client/views/workflows-viewer.js | 18 ++++++++++++++++++ 74 files changed, 1332 insertions(+) diff --git a/client/views/creator-listing.js b/client/views/creator-listing.js index 720102e158..b46fd6bfb4 100644 --- a/client/views/creator-listing.js +++ b/client/views/creator-listing.js @@ -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 . +*/ + //views var View = require('ampersand-view'); //templates diff --git a/client/views/edit-advanced-specie.js b/client/views/edit-advanced-specie.js index 6fcefbcbb4..881b88334a 100644 --- a/client/views/edit-advanced-specie.js +++ b/client/views/edit-advanced-specie.js @@ -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 . +*/ + var tests = require('./tests'); var $ = require('jquery'); //views diff --git a/client/views/edit-custom-stoich-specie.js b/client/views/edit-custom-stoich-specie.js index 828c1caee8..5db31730e7 100644 --- a/client/views/edit-custom-stoich-specie.js +++ b/client/views/edit-custom-stoich-specie.js @@ -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 . +*/ + var $ = require('jquery'); //views var SelectView = require('ampersand-select-view'); diff --git a/client/views/edit-event-assignment.js b/client/views/edit-event-assignment.js index 0540c8eef8..d8122af303 100644 --- a/client/views/edit-event-assignment.js +++ b/client/views/edit-event-assignment.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/edit-function-definition.js b/client/views/edit-function-definition.js index 484a0e9570..61a3261b45 100644 --- a/client/views/edit-function-definition.js +++ b/client/views/edit-function-definition.js @@ -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 . +*/ + var $ = require('jquery'); //support files var modals = require('../modals'); diff --git a/client/views/edit-initial-condition.js b/client/views/edit-initial-condition.js index 798348255c..5a68fa96e0 100644 --- a/client/views/edit-initial-condition.js +++ b/client/views/edit-initial-condition.js @@ -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 . +*/ + //views var View = require('ampersand-view'); var SelectView = require('ampersand-select-view'); diff --git a/client/views/edit-model-view.js b/client/views/edit-model-view.js index cdcca8ec82..f79988227f 100644 --- a/client/views/edit-model-view.js +++ b/client/views/edit-model-view.js @@ -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 . +*/ + var $ = require('jquery'); var _ = require('underscore'); var xhr = require('xhr'); diff --git a/client/views/edit-models-view.js b/client/views/edit-models-view.js index f7e43e941a..3d4543b771 100644 --- a/client/views/edit-models-view.js +++ b/client/views/edit-models-view.js @@ -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 . +*/ + let $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/edit-parameter.js b/client/views/edit-parameter.js index 5775acebd0..8552f49075 100644 --- a/client/views/edit-parameter.js +++ b/client/views/edit-parameter.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/edit-place-details.js b/client/views/edit-place-details.js index 969c7f1e0b..0542db0dd9 100644 --- a/client/views/edit-place-details.js +++ b/client/views/edit-place-details.js @@ -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 . +*/ + var tests = require('./tests'); //views var View = require('ampersand-view'); diff --git a/client/views/edit-project.js b/client/views/edit-project.js index beae9ec95e..ad12151381 100644 --- a/client/views/edit-project.js +++ b/client/views/edit-project.js @@ -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 . +*/ + let $ = require('jquery'); let xhr = require('xhr'); let path = require('path'); diff --git a/client/views/edit-rule.js b/client/views/edit-rule.js index d6f4aa1b9a..8c8a7fd6bf 100644 --- a/client/views/edit-rule.js +++ b/client/views/edit-rule.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/edit-scatter-details.js b/client/views/edit-scatter-details.js index 2067dc7b58..9b8bd830ed 100644 --- a/client/views/edit-scatter-details.js +++ b/client/views/edit-scatter-details.js @@ -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 . +*/ + var tests = require('./tests'); //views var View = require('ampersand-view'); diff --git a/client/views/edit-spatial-specie.js b/client/views/edit-spatial-specie.js index 36a3636ae1..5638d63bb7 100644 --- a/client/views/edit-spatial-specie.js +++ b/client/views/edit-spatial-specie.js @@ -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 . +*/ + var tests = require('./tests'); var _ = require('underscore'); //views diff --git a/client/views/edit-specie.js b/client/views/edit-specie.js index d641c56d09..29f57e049d 100644 --- a/client/views/edit-specie.js +++ b/client/views/edit-specie.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/edit-stoich-specie.js b/client/views/edit-stoich-specie.js index 6b3ca40928..162806b2e6 100644 --- a/client/views/edit-stoich-specie.js +++ b/client/views/edit-stoich-specie.js @@ -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 . +*/ + var $ = require('jquery'); //views var SelectView = require('ampersand-select-view'); diff --git a/client/views/edit-workflow-group-view.js b/client/views/edit-workflow-group-view.js index a9545e50d8..4651bfface 100644 --- a/client/views/edit-workflow-group-view.js +++ b/client/views/edit-workflow-group-view.js @@ -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 . +*/ + var $ = require('jquery'); var xhr = require('xhr'); var path = require('path'); diff --git a/client/views/edit-workflow-groups-view.js b/client/views/edit-workflow-groups-view.js index 89109e2c92..e902f7d876 100644 --- a/client/views/edit-workflow-groups-view.js +++ b/client/views/edit-workflow-groups-view.js @@ -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 . +*/ + //views var View = require('ampersand-view'); var EditWorkflowGroupView = require('./edit-workflow-group-view'); diff --git a/client/views/edit-workflow-view.js b/client/views/edit-workflow-view.js index e4f15df186..ffe317a78c 100644 --- a/client/views/edit-workflow-view.js +++ b/client/views/edit-workflow-view.js @@ -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 . +*/ + var $ = require('jquery'); var _ = require('underscore'); var xhr = require('xhr'); diff --git a/client/views/edit-workflows-view.js b/client/views/edit-workflows-view.js index a7bae109c4..c28d9038f1 100644 --- a/client/views/edit-workflows-view.js +++ b/client/views/edit-workflows-view.js @@ -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 . +*/ + var $ = require('jquery'); var xhr = require('xhr'); var path = require('path'); diff --git a/client/views/event-assignments-editor.js b/client/views/event-assignments-editor.js index 552566702c..917820a137 100644 --- a/client/views/event-assignments-editor.js +++ b/client/views/event-assignments-editor.js @@ -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 . +*/ + //views var View = require('ampersand-view'); var EditEventAssignment = require('./edit-event-assignment'); diff --git a/client/views/event-assignments-viewer.js b/client/views/event-assignments-viewer.js index aa14af9a32..ee3551a067 100644 --- a/client/views/event-assignments-viewer.js +++ b/client/views/event-assignments-viewer.js @@ -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 . +*/ + //views var View = require('ampersand-view'); var ViewAssignments = require('./view-event-assignments'); diff --git a/client/views/event-details.js b/client/views/event-details.js index c435f0017b..00f2b5a580 100644 --- a/client/views/event-details.js +++ b/client/views/event-details.js @@ -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 . +*/ + var $ = require('jquery'); var tests = require('./tests'); //views diff --git a/client/views/event-listings.js b/client/views/event-listings.js index 9bd75fcc1a..2f248816f7 100644 --- a/client/views/event-listings.js +++ b/client/views/event-listings.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/events-editor.js b/client/views/events-editor.js index ad1e47c55e..cf368cfc29 100644 --- a/client/views/events-editor.js +++ b/client/views/events-editor.js @@ -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 . +*/ + var ViewSwitcher = require('ampersand-view-switcher'); var $ = require('jquery'); //support files diff --git a/client/views/events-viewer.js b/client/views/events-viewer.js index 544e7bfe0e..7a5a93cd3a 100644 --- a/client/views/events-viewer.js +++ b/client/views/events-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index 57f583876e..7c1fdbab93 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -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 . +*/ + let jstree = require('jstree'); let path = require('path'); let xhr = require('xhr'); diff --git a/client/views/hybrid-settings.js b/client/views/hybrid-settings.js index 5d2965306b..da2b1434b6 100644 --- a/client/views/hybrid-settings.js +++ b/client/views/hybrid-settings.js @@ -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 . +*/ + var tests = require('./tests'); //views var View = require('ampersand-view'); diff --git a/client/views/initial-conditions-editor.js b/client/views/initial-conditions-editor.js index f5845d4866..f8a3a60b19 100644 --- a/client/views/initial-conditions-editor.js +++ b/client/views/initial-conditions-editor.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/input.js b/client/views/input.js index e52ea6d14c..89ef1cac9a 100644 --- a/client/views/input.js +++ b/client/views/input.js @@ -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 . +*/ + var AmpersandInputView = require('ampersand-input-view'); module.exports = AmpersandInputView.extend({ diff --git a/client/views/main.js b/client/views/main.js index 77cdebe121..0c87eac712 100644 --- a/client/views/main.js +++ b/client/views/main.js @@ -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 . +*/ + var _ = require('underscore'); var $ = require('jquery'); //var setFavicon = require('favicon-setter'); diff --git a/client/views/mesh-editor.js b/client/views/mesh-editor.js index 426bca1ef2..113d190796 100644 --- a/client/views/mesh-editor.js +++ b/client/views/mesh-editor.js @@ -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 . +*/ + var app = require('ampersand-app'); var $ = require('jquery'); var tests = require('./tests'); diff --git a/client/views/meta-data.js b/client/views/meta-data.js index ba9c723e33..f82c8987db 100644 --- a/client/views/meta-data.js +++ b/client/views/meta-data.js @@ -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 . +*/ + var $ = require('jquery'); var path = require('path'); var xhr = require('xhr'); diff --git a/client/views/model-settings-viewer.js b/client/views/model-settings-viewer.js index 330e602d33..976636e339 100644 --- a/client/views/model-settings-viewer.js +++ b/client/views/model-settings-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/model-settings.js b/client/views/model-settings.js index bc4d5e2356..426d8d6247 100644 --- a/client/views/model-settings.js +++ b/client/views/model-settings.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/model-state-buttons.js b/client/views/model-state-buttons.js index a79707c4df..5a5d16418c 100644 --- a/client/views/model-state-buttons.js +++ b/client/views/model-state-buttons.js @@ -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 . +*/ + var xhr = require('xhr'); var path = require('path'); var Plotly = require('../lib/plotly'); diff --git a/client/views/model-viewer.js b/client/views/model-viewer.js index 81a008ef56..8ee7390ed9 100644 --- a/client/views/model-viewer.js +++ b/client/views/model-viewer.js @@ -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 . +*/ + var path = require('path'); var $ = require('jquery'); //views diff --git a/client/views/models-viewer.js b/client/views/models-viewer.js index fcc2c3c7c5..6efca88b22 100644 --- a/client/views/models-viewer.js +++ b/client/views/models-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/parameter-sweep-settings-viewer.js b/client/views/parameter-sweep-settings-viewer.js index c11db2c59e..ae33389d35 100644 --- a/client/views/parameter-sweep-settings-viewer.js +++ b/client/views/parameter-sweep-settings-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/parameter-sweep-settings.js b/client/views/parameter-sweep-settings.js index 94bf1e7376..5c1dae9451 100644 --- a/client/views/parameter-sweep-settings.js +++ b/client/views/parameter-sweep-settings.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/parameters-editor.js b/client/views/parameters-editor.js index cb4aa760ab..1c2c235483 100644 --- a/client/views/parameters-editor.js +++ b/client/views/parameters-editor.js @@ -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 . +*/ + var $ = require('jquery'); //support files var Tooltips = require('../tooltips'); diff --git a/client/views/parameters-viewer.js b/client/views/parameters-viewer.js index 9c09acb76c..fdba80e330 100644 --- a/client/views/parameters-viewer.js +++ b/client/views/parameters-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/plots-view.js b/client/views/plots-view.js index 22c871a093..ec55f6429a 100644 --- a/client/views/plots-view.js +++ b/client/views/plots-view.js @@ -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 . +*/ + var $ = require('jquery'); var path = require('path'); var xhr = require('xhr'); diff --git a/client/views/project-viewer.js b/client/views/project-viewer.js index d9f4d476d0..a9cb97d923 100644 --- a/client/views/project-viewer.js +++ b/client/views/project-viewer.js @@ -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 . +*/ + var path = require('path'); var $ = require('jquery'); //Views diff --git a/client/views/reactant-product.js b/client/views/reactant-product.js index 1056a86876..b663d4c17d 100644 --- a/client/views/reactant-product.js +++ b/client/views/reactant-product.js @@ -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 . +*/ + var $ = require('jquery'); //models var StoichSpecie = require('../models/stoich-specie'); diff --git a/client/views/reaction-details.js b/client/views/reaction-details.js index bd26e34b37..433629fcbb 100644 --- a/client/views/reaction-details.js +++ b/client/views/reaction-details.js @@ -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 . +*/ + var _ = require('underscore'); var $ = require('jquery'); var katex = require('katex'); diff --git a/client/views/reaction-listing.js b/client/views/reaction-listing.js index 24f110abc9..864c24a43d 100644 --- a/client/views/reaction-listing.js +++ b/client/views/reaction-listing.js @@ -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 . +*/ + var $ = require('jquery'); var katex = require('katex'); //support files diff --git a/client/views/reaction-subdomains.js b/client/views/reaction-subdomains.js index 6a872107d0..52100487be 100644 --- a/client/views/reaction-subdomains.js +++ b/client/views/reaction-subdomains.js @@ -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 . +*/ + //views var View = require('ampersand-view'); var SubdomainsView = require('./subdomain'); diff --git a/client/views/reactions-editor.js b/client/views/reactions-editor.js index ae53fa0f00..30788e85a3 100644 --- a/client/views/reactions-editor.js +++ b/client/views/reactions-editor.js @@ -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 . +*/ + var ViewSwitcher = require('ampersand-view-switcher'); var katex = require('katex'); var _ = require('underscore'); diff --git a/client/views/reactions-viewer.js b/client/views/reactions-viewer.js index 1c9aef5414..ef411c0334 100644 --- a/client/views/reactions-viewer.js +++ b/client/views/reactions-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/rules-editor.js b/client/views/rules-editor.js index 22e9400fd0..a7933eae4b 100644 --- a/client/views/rules-editor.js +++ b/client/views/rules-editor.js @@ -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 . +*/ + var $ = require('jquery'); //support files var Tooltips = require('../tooltips'); diff --git a/client/views/rules-viewer.js b/client/views/rules-viewer.js index 4d980e4db8..4cb6770732 100644 --- a/client/views/rules-viewer.js +++ b/client/views/rules-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/sbml-component-editor.js b/client/views/sbml-component-editor.js index 577a065692..75e5324e50 100644 --- a/client/views/sbml-component-editor.js +++ b/client/views/sbml-component-editor.js @@ -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 . +*/ + var $ = require('jquery'); //support files var Tooltips = require('../tooltips'); diff --git a/client/views/simulation-settings-viewer.js b/client/views/simulation-settings-viewer.js index 900e993ab1..e8b8de5145 100644 --- a/client/views/simulation-settings-viewer.js +++ b/client/views/simulation-settings-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/simulation-settings.js b/client/views/simulation-settings.js index 6ddff6c62c..3513730619 100644 --- a/client/views/simulation-settings.js +++ b/client/views/simulation-settings.js @@ -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 . +*/ + var $ = require('jquery'); //support files var tests = require('./tests'); diff --git a/client/views/species-editor.js b/client/views/species-editor.js index 989bef7f8f..436c2f4e69 100644 --- a/client/views/species-editor.js +++ b/client/views/species-editor.js @@ -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 . +*/ + var $ = require('jquery'); //support files var modals = require('../modals'); diff --git a/client/views/species-viewer.js b/client/views/species-viewer.js index d4a9ae0b9e..8e876191cd 100644 --- a/client/views/species-viewer.js +++ b/client/views/species-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/subdomain.js b/client/views/subdomain.js index 3a8b81bf09..7b2751ed00 100644 --- a/client/views/subdomain.js +++ b/client/views/subdomain.js @@ -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 . +*/ + var _ = require('underscore'); var $ = require('jquery'); //views diff --git a/client/views/tests.js b/client/views/tests.js index d6d276d138..057fcf283a 100644 --- a/client/views/tests.js +++ b/client/views/tests.js @@ -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 . +*/ + module.exports = { nameTests: [ function (text) { diff --git a/client/views/view-event-assignments.js b/client/views/view-event-assignments.js index 198018fec7..709bab1ce8 100644 --- a/client/views/view-event-assignments.js +++ b/client/views/view-event-assignments.js @@ -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 . +*/ + //views var View = require('ampersand-view'); //templates diff --git a/client/views/view-events.js b/client/views/view-events.js index d1b8a53ca6..437417b836 100644 --- a/client/views/view-events.js +++ b/client/views/view-events.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/view-parameter.js b/client/views/view-parameter.js index a6d2d21324..a5ba33c0a4 100644 --- a/client/views/view-parameter.js +++ b/client/views/view-parameter.js @@ -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 . +*/ + //views var View = require('ampersand-view'); //templates diff --git a/client/views/view-reactions.js b/client/views/view-reactions.js index 0a24116766..750a351d30 100644 --- a/client/views/view-reactions.js +++ b/client/views/view-reactions.js @@ -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 . +*/ + var katex = require('katex'); //views var View = require('ampersand-view'); diff --git a/client/views/view-rules.js b/client/views/view-rules.js index b426da2813..c4939f45d4 100644 --- a/client/views/view-rules.js +++ b/client/views/view-rules.js @@ -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 . +*/ + //views var View = require('ampersand-view'); //templates diff --git a/client/views/view-specie.js b/client/views/view-specie.js index 358905b291..667dad970e 100644 --- a/client/views/view-specie.js +++ b/client/views/view-specie.js @@ -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 . +*/ + //views var View = require('ampersand-view'); //templates diff --git a/client/views/workflow-editor.js b/client/views/workflow-editor.js index b2f48b6305..02c3674d81 100644 --- a/client/views/workflow-editor.js +++ b/client/views/workflow-editor.js @@ -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 . +*/ + var _ = require('underscore'); var $ = require('jquery'); //models diff --git a/client/views/workflow-group-viewer.js b/client/views/workflow-group-viewer.js index f9400435dd..ea4a93b18e 100644 --- a/client/views/workflow-group-viewer.js +++ b/client/views/workflow-group-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/workflow-groups-viewer.js b/client/views/workflow-groups-viewer.js index cd7dcd3c05..2367d81633 100644 --- a/client/views/workflow-groups-viewer.js +++ b/client/views/workflow-groups-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/workflow-info.js b/client/views/workflow-info.js index 371be73647..1ac37fb9ca 100644 --- a/client/views/workflow-info.js +++ b/client/views/workflow-info.js @@ -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 . +*/ + var $ = require('jquery'); var path = require('path'); var xhr = require('xhr'); diff --git a/client/views/workflow-results.js b/client/views/workflow-results.js index 510163d19a..10d1dd312b 100644 --- a/client/views/workflow-results.js +++ b/client/views/workflow-results.js @@ -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 . +*/ + var $ = require('jquery'); var path = require('path'); var xhr = require('xhr'); diff --git a/client/views/workflow-state-buttons.js b/client/views/workflow-state-buttons.js index 2c6e45c38f..5a30586beb 100644 --- a/client/views/workflow-state-buttons.js +++ b/client/views/workflow-state-buttons.js @@ -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 . +*/ + var $ = require('jquery'); var xhr = require('xhr'); var path = require('path'); diff --git a/client/views/workflow-status.js b/client/views/workflow-status.js index 6e33fe9ac2..bc963fd4dc 100644 --- a/client/views/workflow-status.js +++ b/client/views/workflow-status.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); diff --git a/client/views/workflow-viewer.js b/client/views/workflow-viewer.js index 098ab91df8..13feb24f33 100644 --- a/client/views/workflow-viewer.js +++ b/client/views/workflow-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //collection var Collection = require('ampersand-collection'); diff --git a/client/views/workflows-viewer.js b/client/views/workflows-viewer.js index 1c8a10f229..d540abf6ad 100644 --- a/client/views/workflows-viewer.js +++ b/client/views/workflows-viewer.js @@ -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 . +*/ + var $ = require('jquery'); //views var View = require('ampersand-view'); From e4f56fb84fb83702e574ef5a7be2127a7533dac6 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Oct 2020 11:34:27 -0400 Subject: [PATCH 25/29] Added name validity check to test for save as when uploading files on the project manager. --- client/views/file-browser-view.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/client/views/file-browser-view.js b/client/views/file-browser-view.js index 7c1fdbab93..eb55fa789b 100644 --- a/client/views/file-browser-view.js +++ b/client/views/file-browser-view.js @@ -298,21 +298,21 @@ module.exports = View.extend({ formData.append("datafile", file) formData.append("fileinfo", JSON.stringify(fileinfo)) let endpoint = path.join(app.getApiPath(), 'file/upload'); - if(Boolean(input.value) && fileinfo.name !== input.value.trim()){ + if(Boolean(input.value) && self.validateName(input.value) === "" && fileinfo.name !== input.value.trim()){ let message = "Warning: Models are saved directly in StochSS Projects and cannot be saved to the "+input.value.trim().split("/")[0]+" directory in the project.

Do you wish to save your model directly in your project?

" let warningModal = $(modals.newProjectModelWarningHtml(message)).modal() let yesBtn = document.querySelector('#newProjectModelWarningModal .yes-modal-btn'); yesBtn.addEventListener('click', function (e) { warningModal.modal('hide') - self.openUploadRequest(endpoint, formData, o) + self.openUploadRequest(endpoint, formData, file, type, o) }) }else{ - self.openUploadRequest(endpoint, formData, o) + self.openUploadRequest(endpoint, formData, file, type, o) } modal.modal('hide') }) }, - openUploadRequest: function (endpoint, formData, o) { + openUploadRequest: function (endpoint, formData, file, type, o) { let self = this let req = new XMLHttpRequest(); req.open("POST", endpoint) From bae2e6bf153fa4a63d34b837c6872bd20e39029d Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Oct 2020 11:49:15 -0400 Subject: [PATCH 26/29] Added copyright block to the handler files. --- stochss/handlers/__init__.py | 18 ++++++++++++++++++ stochss/handlers/file_browser.py | 18 ++++++++++++++++++ stochss/handlers/log.py | 18 ++++++++++++++++++ stochss/handlers/models.py | 18 ++++++++++++++++++ stochss/handlers/pages.py | 18 ++++++++++++++++++ stochss/handlers/project.py | 18 ++++++++++++++++++ stochss/handlers/workflows.py | 18 ++++++++++++++++++ 7 files changed, 126 insertions(+) diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py index cc05296c64..a63245929f 100644 --- a/stochss/handlers/__init__.py +++ b/stochss/handlers/__init__.py @@ -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 . +''' + import logging from notebook.utils import url_path_join diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py index 2766136a32..39a00b7d1d 100644 --- a/stochss/handlers/file_browser.py +++ b/stochss/handlers/file_browser.py @@ -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 . +''' + ''' APIHandler documentation: https://github.com/jupyter/notebook/blob/master/notebook/base/handlers.py#L583 diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py index 1742c8040e..795f7f09eb 100644 --- a/stochss/handlers/log.py +++ b/stochss/handlers/log.py @@ -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 . +''' + import logging from tornado.log import LogFormatter diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py index 4b53cad825..913e43d778 100644 --- a/stochss/handlers/models.py +++ b/stochss/handlers/models.py @@ -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 . +''' + ''' Use BaseHandler for page requests since the base API handler has some logic that prevents diff --git a/stochss/handlers/pages.py b/stochss/handlers/pages.py index ae6302c0df..f5df99782d 100644 --- a/stochss/handlers/pages.py +++ b/stochss/handlers/pages.py @@ -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 . +''' + import os import logging from tornado import web diff --git a/stochss/handlers/project.py b/stochss/handlers/project.py index 2dc2af1c4b..bd2ec2881d 100644 --- a/stochss/handlers/project.py +++ b/stochss/handlers/project.py @@ -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 . +''' + ''' Use BaseHandler for page requests since the base API handler has some logic that prevents diff --git a/stochss/handlers/workflows.py b/stochss/handlers/workflows.py index e57852e37b..a4fe0e46f2 100644 --- a/stochss/handlers/workflows.py +++ b/stochss/handlers/workflows.py @@ -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 . +''' + ''' Use BaseHandler for page requests since the base API handler has some logic that prevents From f1df49bec2fbe220f3adf2684d4d6b5773186059 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Oct 2020 12:04:46 -0400 Subject: [PATCH 27/29] Added copyright block to the script files. --- .../handlers/util/convert_sbml_to_model.py | 18 ++++++++++++++++++ .../convert_to_1d_param_sweep_notebook.py | 19 +++++++++++++++++++ .../convert_to_2d_param_sweep_notebook.py | 19 +++++++++++++++++++ stochss/handlers/util/convert_to_combine.py | 18 ++++++++++++++++++ .../convert_to_model_inference_notebook.py | 19 +++++++++++++++++++ stochss/handlers/util/convert_to_notebook.py | 19 +++++++++++++++++++ stochss/handlers/util/convert_to_sbml.py | 18 ++++++++++++++++++ stochss/handlers/util/convert_to_sciope_me.py | 19 +++++++++++++++++++ stochss/handlers/util/convert_to_smdl_mdl.py | 18 ++++++++++++++++++ stochss/handlers/util/duplicate.py | 18 ++++++++++++++++++ .../handlers/util/generate_notebook_cells.py | 19 +++++++++++++++++++ stochss/handlers/util/generate_zip_file.py | 18 ++++++++++++++++++ stochss/handlers/util/ls.py | 18 ++++++++++++++++++ stochss/handlers/util/parameter_sweep.py | 17 +++++++++++++++++ stochss/handlers/util/plot_results.py | 17 +++++++++++++++++ stochss/handlers/util/rename.py | 18 ++++++++++++++++++ stochss/handlers/util/run_model.py | 18 ++++++++++++++++++ stochss/handlers/util/run_workflow.py | 17 +++++++++++++++++ stochss/handlers/util/stochss_errors.py | 18 ++++++++++++++++++ stochss/handlers/util/upload_file.py | 18 ++++++++++++++++++ stochss/handlers/util/workflow_status.py | 18 ++++++++++++++++++ 21 files changed, 381 insertions(+) diff --git a/stochss/handlers/util/convert_sbml_to_model.py b/stochss/handlers/util/convert_sbml_to_model.py index 39306826f5..6a2bff31a6 100755 --- a/stochss/handlers/util/convert_sbml_to_model.py +++ b/stochss/handlers/util/convert_sbml_to_model.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import json from .rename import get_unique_file_name, get_file_name diff --git a/stochss/handlers/util/convert_to_1d_param_sweep_notebook.py b/stochss/handlers/util/convert_to_1d_param_sweep_notebook.py index bd95110266..20792d8f6d 100644 --- a/stochss/handlers/util/convert_to_1d_param_sweep_notebook.py +++ b/stochss/handlers/util/convert_to_1d_param_sweep_notebook.py @@ -1,4 +1,23 @@ #!/usr/bin/env python3 + +''' +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 . +''' + import json import nbformat import traceback diff --git a/stochss/handlers/util/convert_to_2d_param_sweep_notebook.py b/stochss/handlers/util/convert_to_2d_param_sweep_notebook.py index 89f2345a73..ffdb49d100 100644 --- a/stochss/handlers/util/convert_to_2d_param_sweep_notebook.py +++ b/stochss/handlers/util/convert_to_2d_param_sweep_notebook.py @@ -1,4 +1,23 @@ #!/usr/bin/env python3 + +''' +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 . +''' + import json import nbformat import traceback diff --git a/stochss/handlers/util/convert_to_combine.py b/stochss/handlers/util/convert_to_combine.py index 8d0ba5ca98..bc10e90f01 100644 --- a/stochss/handlers/util/convert_to_combine.py +++ b/stochss/handlers/util/convert_to_combine.py @@ -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 . +''' + import os import json import tempfile diff --git a/stochss/handlers/util/convert_to_model_inference_notebook.py b/stochss/handlers/util/convert_to_model_inference_notebook.py index e56200e7c7..fad1cae026 100644 --- a/stochss/handlers/util/convert_to_model_inference_notebook.py +++ b/stochss/handlers/util/convert_to_model_inference_notebook.py @@ -1,4 +1,23 @@ #!/usr/bin/env python3 + +''' +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 . +''' + import json from os import path from json.decoder import JSONDecodeError diff --git a/stochss/handlers/util/convert_to_notebook.py b/stochss/handlers/util/convert_to_notebook.py index 18f6daa039..993504e28b 100644 --- a/stochss/handlers/util/convert_to_notebook.py +++ b/stochss/handlers/util/convert_to_notebook.py @@ -1,4 +1,23 @@ #!/usr/bin/env python3 + +''' +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 . +''' + import json import nbformat import traceback diff --git a/stochss/handlers/util/convert_to_sbml.py b/stochss/handlers/util/convert_to_sbml.py index e8a557b279..68b74cadee 100644 --- a/stochss/handlers/util/convert_to_sbml.py +++ b/stochss/handlers/util/convert_to_sbml.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import ast import json diff --git a/stochss/handlers/util/convert_to_sciope_me.py b/stochss/handlers/util/convert_to_sciope_me.py index e6c89154b2..9e82e25819 100644 --- a/stochss/handlers/util/convert_to_sciope_me.py +++ b/stochss/handlers/util/convert_to_sciope_me.py @@ -1,4 +1,23 @@ #!/usr/bin/env python3 + +''' +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 . +''' + import json import nbformat import traceback diff --git a/stochss/handlers/util/convert_to_smdl_mdl.py b/stochss/handlers/util/convert_to_smdl_mdl.py index 214e03151f..1ad245ea0f 100644 --- a/stochss/handlers/util/convert_to_smdl_mdl.py +++ b/stochss/handlers/util/convert_to_smdl_mdl.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import json import traceback diff --git a/stochss/handlers/util/duplicate.py b/stochss/handlers/util/duplicate.py index 1ed0b388f2..6af27cf692 100644 --- a/stochss/handlers/util/duplicate.py +++ b/stochss/handlers/util/duplicate.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import traceback from os import path diff --git a/stochss/handlers/util/generate_notebook_cells.py b/stochss/handlers/util/generate_notebook_cells.py index d8dcdb8d1b..bace32ab2f 100644 --- a/stochss/handlers/util/generate_notebook_cells.py +++ b/stochss/handlers/util/generate_notebook_cells.py @@ -1,4 +1,23 @@ #!/usr/bin/env python3 + +''' +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 . +''' + import json diff --git a/stochss/handlers/util/generate_zip_file.py b/stochss/handlers/util/generate_zip_file.py index 9320a2948d..bb71cb7acd 100644 --- a/stochss/handlers/util/generate_zip_file.py +++ b/stochss/handlers/util/generate_zip_file.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import shutil import traceback diff --git a/stochss/handlers/util/ls.py b/stochss/handlers/util/ls.py index ce92cea9af..1c50767066 100644 --- a/stochss/handlers/util/ls.py +++ b/stochss/handlers/util/ls.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import json import traceback diff --git a/stochss/handlers/util/parameter_sweep.py b/stochss/handlers/util/parameter_sweep.py index 1676f2dce2..3871019a7d 100755 --- a/stochss/handlers/util/parameter_sweep.py +++ b/stochss/handlers/util/parameter_sweep.py @@ -1,5 +1,22 @@ #!/usr/bin/env python3 +''' +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 . +''' import os import copy diff --git a/stochss/handlers/util/plot_results.py b/stochss/handlers/util/plot_results.py index bd19f8986f..1aa2e62757 100755 --- a/stochss/handlers/util/plot_results.py +++ b/stochss/handlers/util/plot_results.py @@ -1,5 +1,22 @@ #!/usr/bin/env python3 +''' +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 . +''' import os import json diff --git a/stochss/handlers/util/rename.py b/stochss/handlers/util/rename.py index 3e6003ec25..819ab8ec09 100644 --- a/stochss/handlers/util/rename.py +++ b/stochss/handlers/util/rename.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import json import shutil diff --git a/stochss/handlers/util/run_model.py b/stochss/handlers/util/run_model.py index 74d3aea88f..bdc2994b35 100755 --- a/stochss/handlers/util/run_model.py +++ b/stochss/handlers/util/run_model.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import sys import json diff --git a/stochss/handlers/util/run_workflow.py b/stochss/handlers/util/run_workflow.py index cc0071ac2a..45ca764a1b 100755 --- a/stochss/handlers/util/run_workflow.py +++ b/stochss/handlers/util/run_workflow.py @@ -1,5 +1,22 @@ #!/usr/bin/env python3 +''' +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 . +''' import os import sys diff --git a/stochss/handlers/util/stochss_errors.py b/stochss/handlers/util/stochss_errors.py index 00bc72084d..0fe189a577 100644 --- a/stochss/handlers/util/stochss_errors.py +++ b/stochss/handlers/util/stochss_errors.py @@ -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 . +''' + class StochSSAPIError(Exception): def __init__(self, status_code, reason, msg, trace): diff --git a/stochss/handlers/util/upload_file.py b/stochss/handlers/util/upload_file.py index e1c28e86bc..68261a5d84 100755 --- a/stochss/handlers/util/upload_file.py +++ b/stochss/handlers/util/upload_file.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os import json import zipfile diff --git a/stochss/handlers/util/workflow_status.py b/stochss/handlers/util/workflow_status.py index 1f2e9b6fce..af7224715f 100644 --- a/stochss/handlers/util/workflow_status.py +++ b/stochss/handlers/util/workflow_status.py @@ -1,5 +1,23 @@ #!/usr/bin/env python3 +''' +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 . +''' + import os From 25dafdaeb58d51e7b198ddcb72b281aeb6a2b628 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Oct 2020 13:38:24 -0400 Subject: [PATCH 28/29] Added backwards compatible functionality for setting sbml param values. --- stochss/handlers/util/convert_to_sbml.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/stochss/handlers/util/convert_to_sbml.py b/stochss/handlers/util/convert_to_sbml.py index 68b74cadee..e395ddd453 100644 --- a/stochss/handlers/util/convert_to_sbml.py +++ b/stochss/handlers/util/convert_to_sbml.py @@ -119,7 +119,10 @@ def convert_parameters(sbml_model, parameters): param = sbml_model.createParameter() param.initDefaults() param.setId(parameter['name']) - param.setValue(parameter['expression']) + if isinstance(parameter['name'], str): + param.setValue(ast.literal_eval(parameter['expression'])) + else: + param.setValue(parameter['expression']) def convert_reactions(sbml_model, reactions): From a7349c4fb278e3bca55c85c4db85294717540a75 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 7 Oct 2020 13:54:18 -0400 Subject: [PATCH 29/29] Added backwards compatible functionality for setting sbml param values take 2. --- stochss/handlers/util/convert_to_sbml.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/stochss/handlers/util/convert_to_sbml.py b/stochss/handlers/util/convert_to_sbml.py index e395ddd453..2b9e8e9fad 100644 --- a/stochss/handlers/util/convert_to_sbml.py +++ b/stochss/handlers/util/convert_to_sbml.py @@ -119,9 +119,9 @@ def convert_parameters(sbml_model, parameters): param = sbml_model.createParameter() param.initDefaults() param.setId(parameter['name']) - if isinstance(parameter['name'], str): + try: param.setValue(ast.literal_eval(parameter['expression'])) - else: + except ValueError: param.setValue(parameter['expression'])