v2.2.8.0

geppetto-vfb v2.2.8.0

This release completes the migration of Virtual Fly Brain's report queries onto the
VFBquery backend and makes every term in a report table directly clickable. It also
brings a set of browsing, navigation and query-feedback improvements, and ships the
updated Java query processor (uk.ac.vfb.geppetto v2.2.4.18).

Released from master. Supersedes v2.2.7.2.

Highlights

Reports are now served by the VFBquery backend. All remaining report queries —
connectivity (upstream/downstream class, neuron-to-neuron and neuron-to-region),
expression, dataset and template queries — have been migrated from the legacy
multi-step query chains to the VFBquery service behind v3-cached. Results are
consistent, cached, and faster to load.

Every term in a report is a link. Report tables now render names, types,
templates, developmental stages and imaging techniques as clickable links that open
the corresponding term. Opening a term from a result link now closes the query
window automatically, the same way the gross-anatomy tags already behaved.
Non-VFB identifiers and external URLs are shown as plain text rather than broken
links, so an unexpected value can never produce a misleading link.

Clearer feedback while a query runs. Launching a query now shows an immediate,
reassuring notice across every entry point, and the slow-query warning has been
reworded to be less alarming.

What's new and improved

Queries

• Added the Anatomy Expressed In query (AnatomyExpressedIn), replacing the
  previous ExpressionOverlapsHere entry point. (#1680, #1681)
• Migrated connectivity queries to VFBquery: upstream class connectivity (#1673)
  and the second batch — downstream class, neuron-to-neuron and neuron-to-region
  connectivity (#1674).
• Expressed in results are now a list of individually clickable chips. (#1682)
• Fixed class-connectivity chains to include the focus term itself. (#1670)
• Routed expression-pattern-fragment queries through the instance-side processor. (#1671)

Report links

• New per-cell term-link rendering parses [label](id) markdown and turns each
  cell value into a link. (#1686, #1687)
• Template, developmental stage and imaging-technique columns are now linked;
  non-VFB ids render as plain text. (#1687)
• Self-referential VFB URLs are resolved back to short-form identifiers so the link
  opens the term in place. (#1687)
• Opening a term from a result link hides the query window. (#1687)

Browsing and navigation

• Template ROI Browser rewired to the VFBquery endpoint. (#1678, #1679)
• Tree Browser scrolls the selected node into view within the virtualised list,
  so the active selection is always visible on remount. (#1688)
• Fixed numeric sorting in result tables.

Messaging

• Immediate query-loading feedback across all entry points. (#1683, #1684)
• Softer wording for the slow-query warning. (#1685)

Backend shipped with this release

• uk.ac.vfb.geppetto query processor: v2.2.4.18
• org.geppetto.datasources: VFBv2.3.5

Docker images

Pushing the v2.2.8.0 tag builds and publishes:

• virtualflybrain/geppetto-vfb:v2.2.8.0-local.wss
• virtualflybrain/geppetto-vfb:v2.2.8.0-remote

Full changelog

Merged pull requests since v2.2.7.2 (#1670–#1690): connectivity self-inclusion fix
(#1670), epFrag instance-side routing (#1671), uk.ac.vfb.geppetto bump (#1672),
upstream-class connectivity migration (#1673), connectivity batch 2 (#1674),
Template ROI Browser rewire (#1678, #1679), Anatomy Expressed In (#1680, #1681),
Expressed-in chip list (#1682), query-loading feedback (#1683, #1684), softer
query warning (#1685), markdown link component (#1686, #1687), Tree Browser
scroll-into-view (#1688), and lint follow-up (#1689).

Full diff: v2.2.7.2...v2.2.8.0