v494

Code changes:

• Added a species search bar to most CGIs and a slight reorganization of hgGateway: new species search bar instead of dropdowns on most cgis. The search bar uses the hubApi to find genomes, allowing connecting to genark assemblies without going through hgGateway or hgHubConnect first. Hide the species tree by default on hgGateway. Save the last 10 used assemblies to localStorage, display them on hgGateway, and set them as default selections in the search bar and the menu bar under 'Genomes' (#36535). Chris
• Search changes: special code to add item descriptions to MANE and HGNC search results, need a generic way to do this for bigBeds, fix some bugs with hgSearch as a result of the species selection changes (#34483). Chris
• Make users confirm they want to disconnect from a hub on hgTracks, as the button is right next to refresh and can/has been clicked accidentally (#36704). Chris
• Fixed assembly hub disconnect bug to also clear the db, org, and genome cart variables, otherwise going back to hgTracks from hgHubConnect results in viewing the genome for the first row of the defaultDb table (#37114). Chris
• 'GenArk archive' name changes to 'GenArk repository' (#37027). Hiram
• Add bold highlight to new genome search result menu (#34736). Hiram
• Adding hub email display to hub error output for public hubs (#36916). Max
• Hi-C tracks in arc mode previously included extra whitespace at the top, which became excessive when many arcs were hidden. The whitespace has been removed, and the height of these tracks is now just enough to accommodate the highest arc shown. (#36774). Jonathan
• Added HTML page for quickLift alignment differences (#36942). Braney
• Fixed an issue with the hubApi that caused a bad cache in trackDb (#37064). Brian
• Made a special case for the bigBed loader to only load a bed6 if asked to load a bed7 for backwards compatibility. Braney
• Updates to the faceted UI for composite tracks to support tracks that are on by default and to be more consistent when some subtracks have subsequently been hidden manually (e.g., via right click) (#36320). Jonathan
• The faceted UI for composites now imposes a limit on the number of subtracks that can be active at once for sanity reasons (the new limit of 1000 is still very high) (#36320). Jonathan
• When the faceted UI includes data type selectors, it is now possible to provide alternate labels for those checkboxes that don't match the internal names used for subtrack selection (#36320). Jonathan
• HubSpace changes: fixed a weird DataTables bug where we double-displayed rows when doing a hubUpload; documented on hgCustom that hubSpace exists; defaulted to the currently open hub name when selecting the upload button; and when viewing a hub's files (#36830). Chris
• Fix a Visible Tracks bug when calculating the tracks that are on (#37014). Chris
• Updated support for Multi-region exon mode knownGene processing. It now correctly handles the pseudoGenes checkbox in the track settings, all the trackSets including MANE, and also the comma-separated ID-list filtering (#37060). Galt
• Restoring static curl in build (#35988). Galt
• Adding XSS security fix to hub error printf (#36916). Max

Data changes:

• Continuous GenArk updates and liftOver file generation (#29545). Hiram