Merge pull request #20 from phyloviz/monolith-transition

Monolith transition

.gitattributes

@@ -0,0 +1,5 @@
+*.yml filter=ignorelines
+
+# to delete lines commented with # gitignore in yaml files
+# git config --global filter.ignorelines.clean "sed '/^# gitignore/d'"
+# git config --global filter.ignorelines.smudge cat

README.md

@@ -48,8 +48,10 @@ at the forefront of biomedical research.
 Discover the power and versatility of the PHYLOViZ Web Platform, and unlock new insights into phylogenetic data
 analysis, by visiting the [PHYLOViZ Web Platform](https://web.phyloviz.net/) website.
 
-To see a demo of the PHYLOViZ Web Platform in action, check out this [video](https://www.youtube.com/watch?v=761A27KgHIY). 
-It provides an overview of the platform's features and showcases its capabilities for phylogenetic analysis and visualization.
+To see a demo of the PHYLOViZ Web Platform in action, check out
+this [video](https://www.youtube.com/watch?v=761A27KgHIY).
+It provides an overview of the platform's features and showcases its capabilities for phylogenetic analysis and
+visualization.
 
 ---
 

docker-compose.yml

@@ -74,60 +74,25 @@ services:
     depends_on:
       - tool_registry
 
-  administration:
+  core:
     build:
-      context: ./src/backend/microservices/administration
+      context: ./src/backend/core
       dockerfile: Dockerfile
     ports:
       - '8088:8088'
     network_mode: host
     depends_on:
       - mongodb
-      - cache
-
-  compute:
-    build:
-      context: ./src/backend/microservices/compute
-      dockerfile: Dockerfile
-    ports:
-      - '8086:8086'
-    network_mode: host
-    depends_on:
-      - mongodb
-      - cache
-
-  file-transfer:
-    build:
-      context: ./src/backend/microservices/file-transfer
-      dockerfile: Dockerfile
-    ports:
-      - '8089:8089'
-    network_mode: host
-    depends_on:
-      - mongodb
-      - cache
 
   gateway:
     build:
-      context: ./src/backend/microservices/gateway
+      context: ./src/backend/gateway
       dockerfile: Dockerfile
     ports:
       - '8083:8083'
     network_mode: host
     depends_on:
       - mongodb
-      - cache
-
-  visualization:
-    build:
-      context: ./src/backend/microservices/visualization
-      dockerfile: Dockerfile
-    ports:
-      - '8085:8085'
-    network_mode: host
-    depends_on:
-      - mongodb
-      - cache
 
 volumes:
   keycloak_db_data:

docs/CONTRIBUTING.md

@@ -1,6 +1,8 @@
 # Contributing to PHYLOViZ Web Platform
 
-Thank you for your interest in contributing to the PHYLOViZ Web Platform! We welcome contributions from the community to help improve and enhance the platform's functionality. This guide will provide you with an overview of the contribution process.
+Thank you for your interest in contributing to the PHYLOViZ Web Platform! We welcome contributions from the community to
+help improve and enhance the platform's functionality. This guide will provide you with an overview of the contribution
+process.
 
 ## Table of Contents
 
@@ -16,8 +18,10 @@ Thank you for your interest in contributing to the PHYLOViZ Web Platform! We wel
 Before you start contributing to the PHYLOViZ Web Platform, please take a moment to review the following guidelines:
 
 1. Familiarize yourself with the project by exploring the documentation, codebase, and existing issues.
-2. If you plan to work on a new feature or significant changes, it's recommended to discuss it with the project maintainers beforehand to ensure it aligns with the project's goals and roadmap.
-3. Make sure to follow the coding style and conventions used in the project. Adhering to consistent code formatting will make the review process smoother.
+2. If you plan to work on a new feature or significant changes, it's recommended to discuss it with the project
+   maintainers beforehand to ensure it aligns with the project's goals and roadmap.
+3. Make sure to follow the coding style and conventions used in the project. Adhering to consistent code formatting will
+   make the review process smoother.
 4. Test your changes thoroughly to ensure they don't introduce any regressions or issues.
 5. Document your code updates and any new features or changes you introduce.
 6. Respect the existing contributors and maintain a positive and inclusive attitude towards other community members.
@@ -37,7 +41,8 @@ To contribute to the PHYLOViZ Web Platform, follow these steps:
 
 ## Submitting a Contribution
 
-Once you have made your changes and pushed them to your forked repository, you can submit your contribution by following these steps:
+Once you have made your changes and pushed them to your forked repository, you can submit your contribution by following
+these steps:
 
 1. Navigate to the original repository on GitHub.
 2. Locate the "Pull Requests" tab.
@@ -49,36 +54,46 @@ Once you have made your changes and pushed them to your forked repository, you c
 
 ## Code Review Process
 
-After submitting a pull request, the project maintainers will review your code and provide feedback. Here's what you can expect during the review process:
+After submitting a pull request, the project maintainers will review your code and provide feedback. Here's what you can
+expect during the review process:
 
 1. The maintainers will review your code for adherence to coding standards, functionality, and any potential issues.
-2. They may request changes or improvements to your code. Please address these requests promptly and make the necessary updates.
-3. Once your code meets the project's requirements and standards, it will be approved and merged into the main repository.
-4. If there are any conflicts or issues during the review process, maintain an open and collaborative mindset to resolve them.
+2. They may request changes or improvements to your code. Please address these requests promptly and make the necessary
+   updates.
+3. Once your code meets the project's requirements and standards, it will be approved and merged into the main
+   repository.
+4. If there are any conflicts or issues during the review process, maintain an open and collaborative mindset to resolve
+   them.
 
 ## Community Guidelines
 
 To ensure a positive and inclusive community environment, we kindly request that you adhere to the following guidelines:
 
-1. Treat all community members with respect and courtesy. Avoid any form of harassment, discrimination, or offensive behavior.
+1. Treat all community members with respect and courtesy. Avoid any form of harassment, discrimination, or offensive
+   behavior.
 2. Be considerate of others' opinions and perspectives, even if they differ from your own.
 3. Provide constructive feedback and suggestions to help improve the project.
 4. Help others in the community by sharing your knowledge and expertise.
 5. Avoid spamming, advertising, or promoting unrelated content within the community channels.
-6. If you encounter any issues or have concerns about the project or community, reach out to the project maintainers privately.
+6. If you encounter any issues or have concerns about the project or community, reach out to the project maintainers
+   privately.
 
 ## Contact Information
 
-If you have any questions, concerns, or need assistance, you can reach out to the authors of the PHYLOViZ Web Platform through the following emails:
+If you have any questions, concerns, or need assistance, you can reach out to the authors of the PHYLOViZ Web Platform
+through the following emails:
 
 - André Jesus: [[email protected]](mailto:[email protected])
 - André Páscoa: [[email protected]](mailto:[email protected])
 - Nyckollas Brandão: [[email protected]](mailto:[email protected])
 
-Please feel free to contact any of the authors if you have any inquiries related to the PHYLOViZ Web Platform. They will be happy to assist you.
+Please feel free to contact any of the authors if you have any inquiries related to the PHYLOViZ Web Platform. They will
+be happy to assist you.
 
-If you encounter any bugs, have feature requests, or would like to report any issues, please visit the [Issues](https://github.com/phyloviz/phyloviz-web-platform/issues) section 
-on GitHub and create a new issue. 
+If you encounter any bugs, have feature requests, or would like to report any issues, please visit
+the [Issues](https://github.com/phyloviz/phyloviz-web-platform/issues) section
+on GitHub and create a new issue.
 Your feedback and contributions are valuable to us, and we appreciate your help in improving the platform.
 
-We appreciate your interest and contribution to the PHYLOViZ Web Platform. Thank you for helping us improve the platform and make it even better for the community!
+We appreciate your interest and contribution to the PHYLOViZ Web Platform. Thank you for helping us improve the platform
+and make it even better for the community!