File Changes for chmalee

v497_base to v498_preview (2026-04-20 to 2026-04-27) v498

• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 50, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 1, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 4, context: html, text, full: html, text
    4f03efa12fa7a52cad6b78f24d295ff5d80405c0 Thu Apr 23 12:14:00 2026 -0700
    Try to make it more obvious that clicking the 'view' button next to a track file in hubspace connects the whole hub. Add a banner above the table indicating this and with a link that connects the entire hub, refs Max/Baihe email
• src/hg/htdocs/style/hgMyData.css
  • lines changed 8, context: html, text, full: html, text
    d40ace87860e49440a8ffcd09a4a68a682ad07ec Thu Apr 23 12:57:12 2026 -0700
    add nowrap rules to more settings in the hubSpace data table to prevent row heights from growing when a filename is too long for the current window size and forces an adjustment by Data Tables. adjust columns when the window size grows dynamically. this should ensure the view in buttons are always the same size regardless of screen width or table content, refs Max/Baihe email
• src/hg/inc/hubSpace.h
  • lines changed 2, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/trackHub.h
  • lines changed 5, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/userdata.h
  • lines changed 31, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    ae1db8bd101ae572e4382748dc4b19b176449fa0 Thu Apr 23 09:22:05 2026 -0700
    Fix hubSpace quota calculation to use quotax(1024x1024x1024) rather than quotax10^9, refs #37425
• src/hg/js/hgMyData.js
  • lines changed 455, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 36, context: html, text, full: html, text
    0db69910b2561b37d888bdff69895117eea55175 Thu Apr 23 12:00:09 2026 -0700
    Make file names in hubSpace links to view/download the files. Add a copy icon next to each file that copies the url for easy linking to hub.txts, refs Max/Baihe email
  • lines changed 34, context: html, text, full: html, text
    4f03efa12fa7a52cad6b78f24d295ff5d80405c0 Thu Apr 23 12:14:00 2026 -0700
    Try to make it more obvious that clicking the 'view' button next to a track file in hubspace connects the whole hub. Add a banner above the table indicating this and with a link that connects the entire hub, refs Max/Baihe email
  • lines changed 24, context: html, text, full: html, text
    d40ace87860e49440a8ffcd09a4a68a682ad07ec Thu Apr 23 12:57:12 2026 -0700
    add nowrap rules to more settings in the hubSpace data table to prevent row heights from growing when a filename is too long for the current window size and forces an adjustment by Data Tables. adjust columns when the window size grows dynamically. this should ensure the view in buttons are always the same size regardless of screen width or table content, refs Max/Baihe email
• src/hg/js/hgTracks.js
  • lines changed 13, context: html, text, full: html, text
    d5580b384522b44b2d374446d33304a1adf2e13a Mon Apr 20 14:05:06 2026 -0700
    hgTracks: wrap setInHistory calls in try/catch, refs #37367
• src/hg/lib/hubSpace.as
  • lines changed 1, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubSpace.c
  • lines changed 33, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubSpace.sql
  • lines changed 1, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubSpaceQuotas.c
  • lines changed 3, context: html, text, full: html, text
    ae1db8bd101ae572e4382748dc4b19b176449fa0 Thu Apr 23 09:22:05 2026 -0700
    Fix hubSpace quota calculation to use quotax(1024x1024x1024) rather than quotax10^9, refs #37425
• src/hg/lib/trackHub.c
  • lines changed 19, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/userdata.c
  • lines changed 295, context: html, text, full: html, text
    404d5bb6d8c0418d5f06535ef470e36c35d2a237 Thu Apr 16 15:57:56 2026 -0700
    Add assembly hub support to hubSpace. Users can upload a .2bit to create an assembly hub, optionally alongside their own *.hub.txt (prefix names like araTha1.hub.txt are recognized) and sibling track files. Uploads run in parallel; hub.txt mutations are serialized per-hub via flock so arrival order does not matter. - hubSpace table gains a hubType column ('trackHub' or 'assemblyHub'); ON DUPLICATE KEY UPDATE excludes it so a re-upload cannot revert an upgraded hub. - writeHubText can now emit an assembly stanza derived from the 2bit; upgradeHubTxtForAssembly promotes an existing plain hub.txt in place when a 2bit arrives after tracks. - pre-finish decides synthesize vs upgrade vs leave-alone from server state (existing rows, hub.txt on disk) plus a single client flag (batchHasHubTxt); client-supplied hubType is no longer trusted. - Client UI adds 2bit as a file type, locks the genome field when the hub is authoritative (drilled-in or batch hub.txt), defaults new uploads to an existing assembly hub at top level, and routes hgTracks URLs through 'genome=' vs 'db=' by hubType. - Fix pre-existing nested-path bug in hubPathFromParentDir (*firstSlash = 0). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    90668959b76ef7d792bac3cbc4eb509a58c6c317 Thu Apr 23 11:25:38 2026 -0700
    Adding mergeSpannedItems to gnomad CNV and structural variants tracks on hg38, refs Max email