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ebi-ait / dcp-ingest-central

Central point of access for the Ingestion Service of the HCA DCP
Apache License 2.0
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Archiving projects from HCA to SCEA #151

Open ami-day opened 3 years ago

ami-day commented 3 years ago

As a Wrangler I would like to use the hca-to-scea tool to submit datasets from HCA to SCEA

Acceptance criteria:

Given a UUID A project can be archived into SCEA without any manual steps.

Original wording from Ami

Integrate the hca-to-scea tools script into ingest prod.: ability to generate and edit the scea metadata files directly in ingest.

Currently the method to convert hca to datasets involves a semi-automated script (hca-to-scea tools) and multiple manual steps. It also requires editing to the protocol names and descriptions, and in many cases they need to be cut down to be more concise according to the scea guidelines. Sometimes multiple protocols need to be merged into 1 protocol or 1 protocol needs to be split into multiple protocols. The output files from the hca-to-scea tools script also often need to be manually tweaked. The goal here is to integrate the the hca-to-scea tool with ingest production: the ability to generate the required files in mage tab format directly from the browser and be able to edit the content of the files, including merging, adding, moving the protocols in the browser.

amnonkhen commented 3 years ago

@gabsie this requires a new screen added. Your input would be needed here when this gets close to be implemented.

yusra-haider commented 3 years ago

design discussion on backend: https://docs.google.com/document/d/1XIKpa7OZxkYtKZteovtT8tNBJh0INCuu1rZcuZphcN8/edit

gabsie commented 3 years ago

Hi, @amnonkhen - I will make a subtask for myself, but will also need some background. Is this for this sprint as well? Just asking?

Gabs

ami-day commented 2 years ago

Hi, @amnonkhen - I will make a subtask for myself, but will also need some background. Is this for this sprint as well? Just asking?

Gabs

@gabsie I'm going to look into this this sprint while i'm on development, once I've got somewhere, I'll set up a google meet with you to talk through. I'm going to use the integration of the geo-to-hca tool in ingest as a starting point for the design.

ami-day commented 2 years ago

creation of pypi package pull request: https://github.com/ebi-ait/hca-to-scea-tools/pull/78

ami-day commented 2 years ago

https://github.com/ebi-ait/ingest-ui/tree/dcp-222_ui_screen_run_scea_conversion

gabsie commented 2 years ago

@ami-day please add all your current tasks to this epic, as well as remove any that are currently outdated.

ami-day commented 1 year ago

Dataset tracking ticket in Operations board: https://github.com/ebi-ait/hca-ebi-wrangler-central/issues/866