Refactor repository

[bedroesb]

Main differences are:

• Simpler structure reflecting the latest decisions, including the creation of a Python library that can be used by a data broker platform of choice. (this could ARC, Galaxy or a webapp to be made)
• Highlighting the difference between the Data broker - Data broker platform - MARS-CLI
• Introduction of the MARS-CLI backbone based on code written by Marcos (biosamples_external_references.py) (Thanks @kdp-cloud )
• Taking out old links and files from BioHackathon
• Hosting the repository services in one folder called repository-services including isajson-biosamples and isajson-ena. Accompanied with a docker compose and a README to set them up
• README explaining some components of MARS
  • ISA-JSON as metadata carrier
  • Data broker platform
  • MARS-CLI
  • ISA-JSON support by repositories
• Test data bundled together in the test-data folder
• Description of the stakeholders updated and moved to a separate file
• Taking out the code for the JS webapp, since currently not compatible with the Python Library route we decided to take. Can be brought back in if possible.
• New diagram

PREVIEW the repo structure here

[bedroesb]

@apriltuesday I agree. I think it would make sense that the webapp from @xiaoranzhou would be part of an implementation example of MARS using ARC. We could improve on the implementation in the Data Broker platform section of the README.

[xiaoranzhou]

Hi, I have just created a pull request to the BioHackathon 27 repo by using the following code. https://github.com/xiaoranzhou/mars/tree/27-web Yesterday DataPLANT had a meeting and we are going to integrate the web app into our PlantDataHub. More developments are needed for a production ready tool.

[floradanna]

@xiaoranzhou it is great to hear that PlantDataHub will use the web app. It would be nice if the web app would use the python library we are making for MARS. If you need any help in making use of the MARS python library let us know.

In Belgium, we plan to deploy the MARS-CLI in Galaxy Belgium (as Galaxy tool).

I would suggest to keep the code of each deployment of MARS separated in a different repository.

[xiaoranzhou]

@xiaoranzhou it is great to hear that PlantDataHub will use the web app. It would be nice if the web app would use the python library we are making for MARS. If you need any help in making use of the MARS python library let us know.

In Belgium, we plan to deploy the MARS-CLI in Galaxy Belgium (as Galaxy tool).

I would suggest to keep the code of each deployment of MARS separated in a different repository.

Yes, we plan to use the CLI for sure. I am also participating the development and testing. So there won't be any problem. Should we use the same MARS-CLI or have some adaptation of each implementation? If DataPLANT is have own implementation, it should be also listed in the MARS project.

[bedroesb]

hello @xiaoranzhou. I think it would be the most beneficial if it is the same code we are using for the same functions. Otherwise when for example the ISA-JSON improves/changes in shape, we have to update a lot more code. In your implementation it might be nice to have a flask/fastapi instance that makes use of the MARS-CLI as a python library, where you could communicate with.

Sorry if I understand things wrongly!

[xiaoranzhou]

hello @xiaoranzhou. I think it would be the most beneficial if it is the same code we are using for the same functions. Otherwise when for example the ISA-JSON improves/changes in shape, we have to update a lot more code. In your implementation it might be nice to have a flask/fastapi instance that makes use of the MARS-CLI as a python library, where you could communicate with.

Sorry if I understand things wrongly!

• Same code: yes, I agree.
• Implementation: DataPLANT also use CLI tools and would like to do it in the CI/CD of GitLab. I think it will work for any CLI tools.

[bedroesb]

@xiaoranzhou that sounds great! It needs for sure to be clear from this repo which types of implementations and solutions exist.