Design of MorphoDepotAccession module

[muratmaga]

We need a module for people who want to create repositories that is accessible by MorphoDepot. The premise is, it should automate most, if not all, the tasks required for PI on the docs. Assuming all of this doable by gh cli, I envision an interface like this (also assuming that individual has already authenticated with GH).

• They start with a scene in which what will be the master volume (and the segmentation if there is one) is loaded.
• Display and confirm the segmentation object (if there is one) , if not create a blank one, ask them to enter at least one segment (I think this is a requirement).
• They choose a repository name
• Agree a license (Apache, CC-NC, etc)
• They enter the necessary metadata (both image and taxonomy) that will be used at topics. Collect the image metadata from image in the scene. I will make a minimum must list. Ideally this should be a dropdown list obtained somewhere on the cloud for consistent naming (i will look for a species list database, which probably provide a lot of other metadata as well). I would like to minimize typos and capitalization issues.
• Module create the color table/segmentation terminology (TBD)
• Creates the github repo under the user's account and pushes the contents that will go to GH (including an templated readme.MD file with metadata and specimen description, sets the necessary topic fields for findability)
• It uploads the image data to the S3 bucket we will create for MorphoDepot. The fixed url prefix would be: https://js2.jetstream-cloud.org:8001/swift/v1/MorphoDepot/. Then underneath it will create a folder based on the user's GH handle, and put the volume into this folder using the repository name. So if the user's github handle is amm554, and the chosen repository name for the data is zebrafishCT, then the master_volume should point out: https://js2.jetstream-cloud.org:8001/swift/v1/MorphoDepot/amm554/zebrafishCT.nrrd I think this convention provides unique URLs for all possible cases.
• Trigger an alert to morphodepot admins to review the data.

I think this is the minimum requirement for accessioning data.

[muratmaga]

This looks promising for making sure species data is correct. https://www.gbif.org/tools/species-lookup You upload a csv file with your name, and then displays the correct match with all the official taxonomy. Hopefully this can be automated from command line.

https://github.com/gbif/pygbif or this https://verifier.globalnames.org/

[muratmaga]

Object storage documentation from JS2: https://docs.jetstream-cloud.org/general/object/#trying-the-object-store-from-the-cli-using-swift