A modular and easily extendable system for repeatable workflows
Task management systems are crucial tools in modern organizations, by simplifying the coordination of teams and their work. Those tools were developed mainly for task scheduling, assignment, follow-up, and accountability. On the other hand, scientific workflow systems also appeared to help putting together a set of computational processes through the pipeline of inputs and outputs from each, creating in the end a more complex processing workflow. However, there is sometimes a lack of solutions that combine both manually operated tasks with automatic processes, in the same workflow system.
TASKA is a web-based platform that incorporates some of the best functionalities of both systems, addressing the collaborative needs of a task manager with well-structured computational pipelines. The system is currently being used by EMIF (European Medical Information Framework) for the coordination of clinical studies.
A demo installation of TASKA is available online at https://bioinformatics.ua.pt/taska. Please use the following credentials to login:
User: demo
Password: demo
Tech
TASKA uses a number of open source projects to work properly, such as:
* [ReactJS] - HTML enhanced for web apps! * [NPM] - The frontend package manager * [Django] - Web framework python-based * [Django Rest Framework] - Toolkit for building Web APIs in Django projects * [PostgreSQL] - The object-relational database management system * [Docker] - The computer program that performs operating-system-level virtualization * [Make] - Utility for building and maintaining groups of programs
Installation
Taska requires Docker, Docker-compose and Make to run.
Install Docker
* Full instructions at https://docs.docker.com/install/
Install docker-compose
* Full instructions at https://docs.docker.com/compose/install/
Edit docker-compose.yml with deploy specific details. The varibles that should be configured are the following:
11 - POSTGRES_USER= user used in the postgreSQL. This user should match wih the user used in row 23
12 - POSTGRES_PASS= password used in the postgreSQL. This password should match wih the user used in row 23
...
10 - "xxxx:8000" change the xxxx for the port to access the container
...
25 - DOCKER_POSTGRES_USER= user used in the postgreSQL.
26 - DOCKER_POSTGRES_PASS= password used in the postgreSQL.
27 - DOCKER_POSTGRES_DB= database name
28 - DOCKER_POSTGRES_HOST= host name, default is the container defined in the docker-compose file
29 - DOCKER_POSTGRES_PORT= db container port
...
30 - DOCKER_SECRET=place_your_secret_here # secret salted used on passwords
# The following 5 rows are related with the settings to the email system
31 - EMAIL_USE_TLS=
32 - EMAIL_HOST=
33 - EMAIL_PORT=
34 - EMAIL_HOST_USER=
35 - EMAIL_HOST_PASSWORD=
36 - EMAIL_URL= #System url that will be added in some email templates
37 - DEFAULT_FROM_EMAIL= # the from address in the emails
...
42 - PUBLIC_IP= # the associated domain must be specified, to prevent fake HTTP Host headers
...
45 - BASE_DIR=/taska # if the page wont run on root but on a subdirectory instead it must be specified here
...
48 - RAVEN_URL= # raven url for error loggingAfter the costumization of the docker-compose file, it is only necessary perform the following commands to have the installation running. (This process can take a few minutes)
$ make
$ make runScientific contributions
-
J. Almeida, R. Ribeiro, and J. L. Oliveira, “A modular workflow management framework”, in Proceedings of the 11th International Conference on Health Informatics (HealthInf 2018), 2018.
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J. R. Almeida, T. M. Godinho, L. Bastião Silva, C. Costa, and J. L. Oliveira, “Services orchestration and workflow management in distributed medical imaging environments”, in Computer-Based Medical Systems (CBMS), 2018 IEEE 31th International Symposium on, IEEE, 2018.
Core Team
- University of Aveiro, Dept. Electronics, Telecommunications and Informatics (DETI / IEETA), Aveiro, Portugal
↩ - BMD Software, Aveiro, Portugal
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