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Add opt-in genome download feature #1149

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Description of proposed changes

When a corresponding FASTA file is placed in the same directory with auspice's
JSON file, for example a ncov_global.fasta is placed in the same directory with
ncov_global.json: the genome database handling functionality will kick in and
generate a file-based NeDB database at server startup time. A "Selected
Genomes (Fasta)" download button also then appears in side the "Download Data"
popup window. For dataset that doesn't have a corresponding FASTA file, this
functionality is inactive.

Related issue(s)

Fixes #1110

Testing

What steps should be taken to test the changes you've proposed?

  1. Apply this feature to the code base
  2. Installation again as normal.
  3. Place a FASTA file ncov_global.fasta to datasetDir (i.e. ./data) for testing with ncov_global.json. Start or restart asupice. Fasta record IDs inside the FASTA file and tree tip names should match for auspice to fetch the correct genome from the database.

If you added or changed behavior in the codebase, did you update the tests, or do you need help with this?

None.

Note:

Upgrading papaparse to newer version is not required for this feature to function properly, but I upgraded that in response to severe security warning by npm during installation process.

Thank you for contributing to Nextstrain!

Vang Le-Quy added 4 commits May 30, 2020 17:38
When a corresponding FASTA file is placed in the same directory with auspice's
JSON file, for example a ncov_global.fasta is placed in the same directory with
ncov_global.json: the genome database handling functionality will kick in and
generate a file-based NeDB database at server startup time. A "Selected
Genomes (Fasta)" download button also then appears in side the "Download Data"
popup window. For dataset that doesn't have a corresponding FASTA file, this
functionality is inactive.
@biocyberman biocyberman force-pushed the feature-download-genomes branch from 2b40b72 to 61e7d28 Compare May 30, 2020 18:17
@biocyberman
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@jameshadfield May be you or your teammates could check this out so we can merge or have feedback?
Thanks.

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Download subset of genome sequences for selected tree nodes
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