Changelog since 2024-10-17 the deployment to TEST: Sprint 7 changes for Isopod release

[edeutsch]

Please add your substantial commits since master was deployed to TEST on the date in the title by EDITING this post with a terse Changelog entry.

• Implement max_synonyms functionality for "synonyn lookup" /entity endpoint to fix problem of too many nodes overwhelming a browser #2367
• ARAX UI now by default uses format="slim" for synonym lookups, which suppresses the synonym concept graph, which was extremely resource intensive for drugs with many synonyms, but is user-settable via [Settings] #2367
• Replace NaN with None for /entity output
• TechnicalDebt: Removed deprecated RTXFeedback mechanism, including class and ancient references to it #2304
• DrugApprovalsKP added to KG2.10.2
• Modify the PathFinder service to ensure compatibility with TRAPI requests.
• Fixing issue with ARAX-expand not handling an exception in the case of a malformed response from a KP. #2455
• ARAX's Web browser user interface, on the Queries tab, in the color-coded status string on the right-hand side of each knowledge provider listed under each query edge, now has a new status code (Warning) and associated color (orange). This status code is currently used for two conditions: (1) indicating that one or more edges from a KP were dropped because they referenced nodes that do not exist in the KG returned by the KP; and (2) indicating that one or more edge attributes were dropped because their value field contained a floating-point value that is invalid to serialize in JSON (like infinity or nan). See #2467, #2469, and #2455.

ARAX UI Updates

PathFinder Support

• Add a simple interface for PathFinder queries
• Add support for new PathFinder TRAPI, with ability to add/remove path filters by clicking on a node name [ Only supports a single path (e.g. "p0") and a single aux graph per analysis ] [ Node bubbles are Alpha-sorted in each path summary ]
• Use Grid as the default layout for PathFinder results (some cleanup needed for certain cases)
• Add sidebar with filtering PF paths by nodes
• New pop-up window for filtering PF paths via a node "switchboard" -- allows to include/exclude
• Add PathFinder example JSON

Graph Display

• Remove Random ("R") graph layout option; replace with Grid ("G")
• Add controls to collapse/expand multiple edges between a pair of nodes When collapsed: edge thickness is (log) scaled to total number of edges (number in brackets) Uses cytoscape-expand-collapse.js plugin [ Disabled for Chromium browsers ]
• Decorate edges that have both a support graph [sg] and a qualifier [q]
• Replace node shapes with icons
• Update to Cytoscape 3.31.1

TRAPI

• Add support for multiple analyses / result
• Catch and report missing edge_id and aux_graph_id errors
• Update edge constraints property to attribute_constraints as per latest TRAPI

Misc

• Allow file drag into Response input (for viewing TRAPI)
• Add button for importing query_graph from JSON input into visual graph editor
• Capture new "Warning" Expand status; display with orange bubble
• Add "months" to text for long-running Queries in System Activity
• Add checkbox to show/suppress Concept Graph in Synonyms
• Add new user setting for max number of nodes to list in Synonyms [default=1000]
• Set default EXTernal API to plover/ci
• Tidy layout of Settings

[mohsenht]

Modify the PathFinder service to ensure compatibility with TRAPI requests.

[edeutsch]

Deployment to TEST request. closing this issue. Please put new changes in the next ChangeLog issue here:

https://github.com/RTXteam/RTX/issues/2515

[dkoslicki]

We good to close this @edeutsch ?

[edeutsch]

oh yes, I thought I had. closing!