TSV Input file, schema updates, marker gene flexibility, aesthetic changes

Updates mostly aimed at increasing the responsiveness of ElasticSearch query resolving, plus an effort at abstracting away from MSK Spectrum specific tools.

We're also deeming this our official version 1 of Mira!

1. Input files now assume tsv/mtx/json files in one directory.
   This should be easier to read into memory and MUCH faster to load. In addition, the loader no longer assumes any connection to an outside database - just give it the directory path with all the relevant files and it's good to go!

2. Elasticsearch schema changes
   We've now nested gene records inside their respective cell records, eliminating the need to do join-like queries when we add filters. This makes the graphQL resolvers much simpler, and queries should now return data to the front end faster.

3. Marker gene flexibility
   You can now specify different marker genes for each dashboard loaded. At this point, we still assume that each dashboard has exactly one marker gene table, but we're aiming to have this as an optional table in the future. There are still some bugs to work out, so for now we've removed the counts from the CellAssign table.

4. Aesthetic changes
   Quite a number of aesthetic changes, including replacing the dropdown of dashboard type with a tabbed view. We've also changed the font and several of the theme colours :)

Binned UMAP plot + Cumulative gene expression prototype

UMAP plot is now binned, with coloring done based on majority (categorical), average (numerical), or density (subset). To add additional support, we removed the third UMAP plot and replaced it with two histogram plots.

Additional changes:

• Schema changes on both Elasticsearch and GraphQL end to support binned UMAP plots
• Removal of cell type subsetting interaction in CellAssign table

We also introduce prototype dashboards. The first is a cumulative gene expression dashboard, which features 2 UMAP plots (one for genes expression, one is a "normal" UMAP), and a text box area to enter a comma separated list of genes you want to see the cumulative expression of.

Support for revised cell schema

• Index for cells is now dashboard_cells, merges redim and sample cells indices
• UI fixes for metadata table
• Bug fixes for query sizes in rho table and scatterplot
• Revamp of loading CLI

Patient Dashboards

Support for patient level dashboards!

Added

• Coloring on site, surgery, treatment for non-sample dashboards

Changed

• Metadata table support for merged dashboards
• Metadata table aesthetic changes
• CLI for loader
• Loading support for patient dashboards
  • bulk loading by type
  • memory improvements for gene matrix
  • merged metadata and dashboard entry together
• Bug fixes

Base

• .env files for base URLs to enable quicker setup of instances
• Spectrum header update
• Sample selection with QC metrics
• Three UMAP hexbin density plots with overlaid scatterplot (via highlighting)
• CellAssign table
• Loader pulls from rdata, not JSON
• Loader pulls metadata from Google Sheets