What's left

Must User Stories

US01 Share a dataset

Epic epic

US01:01 Standard ingestion format

• Document the specification of the vcf format needed for loading data to the Genome Browser (which fields are needed)

US01:02 Add dataset

• Script for loading dataset metadata to database - done?
  • (GUI for defining metadata? (Should) )
• Scripts or checklists (procedures) for setting up genome browser instances for new datasets (?)
  • This may refer to documentation of deployment of the browser (using Ansible). Or it may, more likely, refer to loading new datasets in a previously deployed browser, and making it available publicly. This is in part documented in the link below (the data loading bit, and how to write the settings.json file to point to the correct database/collection), but it also is connected to deployment as the portal must be made aware of the new dataset/dataset version.
• Scripts or checklists (procedures) for loading vcf data to genome browser instance - #432
  • This is documented in a text file at https://github.com/NBISweden/swefreq-browser/blob/develop/docs/README-loading_data.txt
• Other?

US01:03 Clear interface

• User account UI (upload credentials etc) - #444
• Search field for datasets
• Pagination for dataset listing

US02 Describe dataset

Done-ish

US02:01 Metadata editing

• (Metadata editing interface (GUI or script) (Could) )

US02:05 Request access to individual data

• Separate database field (and GUI rendering) for specified instructions and contact details - #437

US06 Browse datasets

• Demonstrate setting up Genome browser for second dataset - #431
• Browser integration - #362
• More?

US07 Beacon access

Push to separate project?

US07:02 ELIXIR Beacon

• Deploy and integrate ELIXIR Beacon reference implementation for all datasets

US14 Bioschema markup of datasets

• Add bioschema Dataset metadata to dataset pages, generated from available metadata - #435
• Add bioschema DataCatalog metadata to site front page - #436

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Should User Stories

US07:01 Query same variant in several datasets

• Put a pan-beacon, over all datasets

US08 Dataset statistics

US08:01 Rudimentary statistics

• Add view for dataset admins to show who has downloaded a dataset

US10 Server monitoring

• Make current server monitoring implementation available, visible and documented for future Resource support personnel

US13 SweFreq Maintenance Strategy

• Write Roadmap and Operation procedures documents