Add project request & data upload forms

[eboileau]

Aims/objectives.

Project request form creates a template for creating projects. After project creation, users can upload dataset.

A clear and concise description of todo items.

Project request

At project creation, we define new selections; however these are not ultimately attached to a project, but to data records

• Free fields with validation: title, contact details, sources
• metadata:
  • RNA type: Dropdown. We need a predefined list with nomenclature
  • Modifications: MultiSelect. Modomics short name.
  • Methods: Dropdown. Methods. In the unlikely case of "new methods", contact maintainers.
  • Technology: Free input.
  • Organism: Dropdown. This is actually taxid. We may have to extend the initial import table.
  • CTO: Free input. How do we handle discrepancies that may arise due to typos, etc. hIPSC-CM vs. HiPSC-CM, ...
  • Assembly: Dropdown (dependent on organism). How to provide a list?

Upon submission, maintainers need to be notified by email. Are templates also sent as attachments, or simply written
somewhere on the server?

Dataset upload

All selections must already be available, there is no input except title.

• SMID selection as "DynamicDialog"? See above, this cannot be used to pre-fill selections. Projects can be created "independently", and metadata is attached to data records/dataset. This could e.g. allow to upload a dataset at a later time, w/o being restricted to the initial selection, provided the selection is already available in the DB. Can we simplify this?
• Select RNA type (Dropdown)
• Select modifications (MultiSelect dependent on RNA type)
• Select organism and cto (CascadeSelect dependent on modification_id)
• Select technology (CascadeSelect dependent on modification_id and organism_id )
• Select assembly (Dropdown dependent on taxid) - header check
• Title: Free input

We need to send feedback to the user during upload.

How do we handle upload of restricted data? i.e. data that is only accessible to the user? Do we want to do that in the end? Or maybe only for the other data formats (bedRMod always public)?

[eboileau]

Project request mostly completed. Remaining todos:

• date_published is currently nullable=False, but should really be nullable.
• I added SMTP_TO_ADDRESS to env variables, only locally now; this needs to be added to docker/app_container/files/entry_point.py, etc.
• Create DATA_SUB_PATH_SUB on app01.
• We need to add proper error handling in the FE if the POST request fails.
• Deal with RNA type in the BE (now hard coded in ProjectMetadata.vue)

[eboileau]

Dataset upload mostly done, we need to address:

• Styling, e.g. FileUpload preset, MultiSelect, no options missing for some components, etc.
• Deal with RNA type in the BE
• Do we need to handle upload errors? Probably not, but the display is not nice, see e.g. large file size. And what is a reasonable file size limit?
• We need to add proper error handling in the FE if the POST request fails. We need to handle all possible exceptions during dataset creation, and send meaningful info. Also we should send feedback during this process, before redirecting to home (e.g. annotating/liftover can take a few seconds/minutes, what is the newly created EUFID), etc.
• Clean dialog option (and also handling of it, if using for attachment - we need a single instance, what does this means?)
• Add the "Attach other file option" - this is a separate issue...