Release/v.1.0.0

.gitignore

@@ -1,4 +1,63 @@
-__pycache__
-.idea
-*.xml
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+src/__init__.pyc
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
 venv/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+
+# Translations
+*.mo
+*.pot
+
+# logging:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Mac an other
+**/.DS_Store
+.idea

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 UMCU Genetics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,114 @@
+<img src="https://i.imgur.com/zPP83aX.png" title="VUSualizer" alt="VUSualizer">
+
+# VUSualizer
+
+> A web interface that allows searching through Variant of Unknown Significance (VUS).
+
+Important dependencies: 
+- [Python 3.6.8 or higher](https://www.python.org/)
+  - [Flask](https://pypi.org/project/Flask/)
+  - [Flask-PyMongo](https://pypi.org/project/Flask-PyMongo/)
+  - [Flask-Login]()
+- [MongoDB](https://www.mongodb.com/)
+- [datatables.js](https://datatables.net/)
+- [alissa_interpret_client](https://github.com/UMCUGenetics/alissa_interpret_client)
+
+
+## Application Structure 
+```
+.
+|──────run.py - used to run the flask app, also doubles as .wsgi file
+|──────src/
+| |────__init__.py - creats the needed managers for Flask, Flask-PyMongo and Flask-Login
+| |────config.py - configuration for the whole app
+| |────datatable.py - class for querying MongoDB on the backend, returns data for datatables.js
+| |────forms.py - contains Flask-WTF forms
+| |────models.py - contains user model
+| |────static/ (.css .js .png)
+| |────templates/ (.html)
+| |────views/ (.py)
+| | |──main.py - manages handling for urls
+| | |──auth.py - manages handling for account-related urls, eg. /login, /logout, etc.
+|──────extra/ - importing data scripts and logging
+| |────import_data.py - loads new analyses from Alissa to import in MongoDB (VUSualizer)
+| |────config.py - configuration for the import data script
+| |────logging_config.yml - for logging files of the import data script
+```
+
+### [Datatables.js Server-side Processing](https://datatables.net/manual/server-side)
+Due to the amount of data, data needs to be filtered through the server.
+
+As of right now, two templates contain the client-sided datatables.js code:
+- base.html
+- all.html
+
+There are some "apis" that datatables.js interacts with. They are accessed through:
+- /_get_all_data
+- /_get_variant_data
+- /_get_gene_data
+- /_get_patient_data
+
+These urls are handled in main.py. The program then uses the DataTablesServer class from datatable.py to query the database and return the data back to datatables.js to create a browsable table. 
+
+
+## Installation
+
+1. Make a Python 3.6.8 venv in correct spot on server and install any requirements with pip:
+```
+$ python3 -m venv venv
+$ source ./venv/bin/activate
+$ pip install -r requirements.txt
+```
+If you receive a pip install error and it is due to the "mod_wsgi" package, this is not needed locally. use '#' before that package to prevent it from installing.
+2. Install MongoDB
+(Local MacOS example): https://docs.mongodb.com/manual/tutorial/install-mongodb-on-os-x/
+```
+$ brew tap mongodb/brew
+$ brew install [email protected]
+$ brew services start [email protected]
+```
+3. Configure the config.py (in src folder) and fill in a random string for the SECRET_KEY. The app will not work without a SECRET_KEY. A random string can be generated by using for example [String Generator](https://www.random.org/strings/) or any other string generator. Do not share this code with others, as this could potentially be used to generate fake cookies for logins. Changing it will result in users needing to login again, as the sessions are not valid anymore.
+(Optional) Configurate MONGO_URI in config.py if you're using different user details and/or database name
+4. Configure the config.py (in extra folder) for Alissa credentials and the location of the logging_config.yml file and VUSualizer app
+5. Load data into MongoDB with script in the "extra" folder.
+```
+$ (venv) python import_data.py
+```
+6. Add crontab to automatically check Alissa for new analyses (example shown below. every day on 3AM). This needs to be done with the admin user of the server. 
+```
+$ 0 3 * * * /path/to/VUSualizer/extra/import_data.py >> /path/to/VUSualizer/extra/cronlogs.log 2>&1
+```
+
+## Run for development
+Activate venv and then start the app
+```
+$ source ./venv/bin/activate
+$ python run.py
+```
+## Run for production (apache required)
+```
+$ mod_wsgi-express start-server run.py
+```
+
+## Run on local machine
+1. Configure the config.py (in extra folder) for VUSualizer location (required) and Alissa credentials (not required for running app)
+2. If development for import_data.py (not required for running app) --> 
+  - Change shebang python to ```#!/usr/bin/env python3``` or local equivalent
+  - Change filename parameter in logging_config.yml to correct local path
+3. Activate venv
+```
+$ source ./venv/bin/activate
+```
+4. Run run.py
+```
+$ python run.py
+```
+
+## Troubleshooting
+### Webpage does not load:
+1. Not connected to the UMCU server (either via VPN, on location (WiFi) or follow-me workspace)
+2. Service needs to be restarted:
+```
+$ sudo /bin/systemctl stop vusualizer-wsgi.service
+$ sudo /bin/systemctl start vusualizer-wsgi.service
+```

extra/config.py

@@ -0,0 +1,9 @@
+# Alissa settings
+alissa_base_uri = ''
+alissa_client_id = ''
+alissa_client_secret = ''
+alissa_username = ''
+alissa_password = ''
+mongodb_localhost = 'mongodb://localhost:27017/'
+logging_file = './logging_config.yml'
+vusualizer_path = './'