Functions to add to next version

[dthoward96]

• check-submissions: Allow option to update a single submission instead of updating all submissions in log.
• other organism: Allow any organism to be used with the flag "other" .
  Other is currently added. It doesn't allow for GISAID submissions since it cannot be determined easily which epiCLI to use. The other option is a default generic submission template which will allow for any organism to be submitted to NCBI.
• gisaid: Create gisaid submission as a toggle option to be used with any organism. This will allow automated upload for NCBI but manual submission for gisaid when a CLI option doesn't exist.
  In order to support turning off GISAID submissions for other organisms, all epiCLI's have support added for them. This is to allow for any epiCLI to be connected to seqsender and used without issue. New epiCLI's can be easily added by its information to the internal metadata config file.
  • EpiArbo (Arbovirus)
  • EpiPox (Monkeypox)
• Table2asn submission validation.
  Table2asn submissions are made via email, this prevents seqsender from being able to validate a submission is correct before submitting it. Using the Table2asn validation file seqsender can now parse this file and detect issues which will then prevent submission and notify the user of what issues to correct.
• User config file validation.
  Config files are used to store user info and determine how seqsender processes their submissions. Current checks only validated that it loaded correctly as a yaml file. Now config files are checked against schema files which can determine if a user incorrectly filled out their submission file. If the user did incorrectly fill out their submission file it will now report an error message directing the user to the incorrect field and notifying them of what to change it to.

Adding these two features to this update as they are needed to resolve issues with incorporating Enteric BioSample attributes

• automatic biosample xml conversion to pandera schema
• pandera schema metadata validation

[dthoward96]

Version updates have been added. Currently bug fixing/documenting

• Submission Test
  • FLU
  • COVID
• Documentation