File Changes for chmalee

v495_preview2 to v495_base (2026-03-02 to 2026-03-09) v495

• src/hg/hgBlat/hgBlat.c
  • lines changed 3, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/hgConvert/hgConvert.c
  • lines changed 20, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 2, context: html, text, full: html, text
    58c24abcdc7e2fe836db993243c6ac15fce457b5 Wed Mar 4 15:20:15 2026 -0800
    Fix more universal species search bugs: hgConvert re-factor meant two hidden form variables were created for the hglft_toDb variable, so remove one of them; make organism comparison case insensitive so 'human' matches 'Human', as genark results are typically lower case; append hubUrl to hgGateway gotohgTracks form so any searched genark hub shows up as a connected hub on hgHubConnect, refs #36535, #36232
  • lines changed 8, context: html, text, full: html, text
    5247d2f093c036439e46930a40607d2a47a05f25 Thu Mar 5 11:34:12 2026 -0800
    For hgConvert only, filter the popular genomes list in the toDb section by what liftover chains we have available for the fromDb, refs #36232
  • lines changed 14, context: html, text, full: html, text
    c7221bad6eda31fe88c6f9880276d8f993ff876e Thu Mar 5 12:37:14 2026 -0800
    Disable recent/popular species list selection in the hgConvert toDb dropdown if there are no chains available to them. Leave them in the list but unselectable, refs #36232
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 28, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/hgPcr/hgPcr.c
  • lines changed 2, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/hgSearch/hgSearch.c
  • lines changed 31, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 1, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/htdocs/style/HGStyle.css
  • lines changed 17, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    9c7de0bd83bc6e1876dc0b8b7091127629a07bf0 Thu Mar 5 14:32:25 2026 -0800
    Fix array size bounds check for /getData/track endpoint to actually limit to 100 requested tracks
• src/hg/hubApi/getData.c
  • lines changed 8, context: html, text, full: html, text
    9c7de0bd83bc6e1876dc0b8b7091127629a07bf0 Thu Mar 5 14:32:25 2026 -0800
    Fix array size bounds check for /getData/track endpoint to actually limit to 100 requested tracks
• src/hg/inc/hgFind.h
  • lines changed 6, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/js/autocompleteCat.js
  • lines changed 9, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 6, context: html, text, full: html, text
    c7221bad6eda31fe88c6f9880276d8f993ff876e Thu Mar 5 12:37:14 2026 -0800
    Disable recent/popular species list selection in the hgConvert toDb dropdown if there are no chains available to them. Leave them in the list but unselectable, refs #36232
  • lines changed 3, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/js/hgGateway.js
  • lines changed 5, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 9, context: html, text, full: html, text
    58c24abcdc7e2fe836db993243c6ac15fce457b5 Wed Mar 4 15:20:15 2026 -0800
    Fix more universal species search bugs: hgConvert re-factor meant two hidden form variables were created for the hglft_toDb variable, so remove one of them; make organism comparison case insensitive so 'human' matches 'Human', as genark results are typically lower case; append hubUrl to hgGateway gotohgTracks form so any searched genark hub shows up as a connected hub on hgHubConnect, refs #36535, #36232
  • lines changed 9, context: html, text, full: html, text
    d84555710af610b002bd9492ca0702d622c00bc8 Thu Mar 5 11:07:17 2026 -0800
    Oops I overcorrected when fixing 3fb0b5d2a3d, which led to weird conditions where sometimes a genark hub would show up under 'Connected Hubs' depending on where you searched for the genark genome. When creating links to genarks, we only need the db= parameter, as fixUpDb in the cart code handles connecting to genarks transparently. So remove explicit hubUrl and genome parameters from genark links in the menu bar and in hgSearch ajax calls, refs #36535
  • lines changed 2, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/js/hgSearch.js
  • lines changed 17, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 4, context: html, text, full: html, text
    d84555710af610b002bd9492ca0702d622c00bc8 Thu Mar 5 11:07:17 2026 -0800
    Oops I overcorrected when fixing 3fb0b5d2a3d, which led to weird conditions where sometimes a genark hub would show up under 'Connected Hubs' depending on where you searched for the genark genome. When creating links to genarks, we only need the db= parameter, as fixUpDb in the cart code handles connecting to genarks transparently. So remove explicit hubUrl and genome parameters from genark links in the menu bar and in hgSearch ajax calls, refs #36535
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    83054537b0ec9ce3e74c6c20fc907c560406f836 Wed Mar 4 15:45:03 2026 -0800
    Fix typo found in code review, refs #37187
  • lines changed 9, context: html, text, full: html, text
    9db87ad5938d116af4d1e73f3e92cc29392df83c Thu Mar 5 14:58:24 2026 -0800
    Limit current tracks download feature to 100 tracks so we don't timeout out hubApi requests, refs #36858
• src/hg/js/react/lib/SpeciesSearch.jsx
  • lines changed 25, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
• src/hg/js/utils.js
  • lines changed 59, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 14, context: html, text, full: html, text
    d84555710af610b002bd9492ca0702d622c00bc8 Thu Mar 5 11:07:17 2026 -0800
    Oops I overcorrected when fixing 3fb0b5d2a3d, which led to weird conditions where sometimes a genark hub would show up under 'Connected Hubs' depending on where you searched for the genark genome. When creating links to genarks, we only need the db= parameter, as fixUpDb in the cart code handles connecting to genarks transparently. So remove explicit hubUrl and genome parameters from genark links in the menu bar and in hgSearch ajax calls, refs #36535
  • lines changed 9, context: html, text, full: html, text
    c7221bad6eda31fe88c6f9880276d8f993ff876e Thu Mar 5 12:37:14 2026 -0800
    Disable recent/popular species list selection in the hgConvert toDb dropdown if there are no chains available to them. Leave them in the list but unselectable, refs #36232
  • lines changed 16, context: html, text, full: html, text
    4fc775d4d4ce03a5e1236a5ce1e266b5a0a5e68e Fri Mar 6 11:13:42 2026 -0800
    database name in menubar links needs to include the hubUrl and hub_id when making a link to a non-genark assembly hub, refs #36535
  • lines changed 10, context: html, text, full: html, text
    24db314b5051da133465b7d5e0944aeba4bf25a0 Fri Mar 6 11:58:12 2026 -0800
    Make better labels when printing recent genomes to the menu bar. Don't print the default hg38/hg19/mm10/mm39/hs1 since they are already there by default, refs #36535
  • lines changed 9, context: html, text, full: html, text
    754cf0e3c480484878009aa5ce6dd815f1126d0c Fri Mar 6 15:02:34 2026 -0800
    most public assembly hubs do not have blat/pcr servers available, so when a public hub has been selected from the 'recents' dropdown in the search bar on those cgis, submit their form so the backend can print a message to page telling the user we don't have blat/pcr availabel for those assemblies, refs #36535
• src/hg/lib/hgFind.c
  • lines changed 190, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/lib/web.c
  • lines changed 28, context: html, text, full: html, text
    16eee40c920d259c10ee345472708d0cc0cc3393 Tue Mar 3 11:25:23 2026 -0800
    Adds an hg.conf defined 'popular' species list to the new search bar as a 'default' list of results upon focus of the search bar. Combines with 'recents' list. Add a chevron next to the search bar so users know the autocomplete has some default options, refs #36232
  • lines changed 36, context: html, text, full: html, text
    a029a389a46082c6ab69d5053d5c17912dd72bf6 Thu Mar 5 12:18:56 2026 -0800
    Make menubar assembly link clicks add to recents list, refs #36535
  • lines changed 1, context: html, text, full: html, text
    397351b825b3ea9a7fb6ac7a2f64359166c9ba32 Thu Mar 5 12:25:51 2026 -0800
    Oops forgot the usual trackHubDatabase check, refs #36535
  • lines changed 10, context: html, text, full: html, text
    4fc775d4d4ce03a5e1236a5ce1e266b5a0a5e68e Fri Mar 6 11:13:42 2026 -0800
    database name in menubar links needs to include the hubUrl and hub_id when making a link to a non-genark assembly hub, refs #36535
  • lines changed 3, context: html, text, full: html, text
    24db314b5051da133465b7d5e0944aeba4bf25a0 Fri Mar 6 11:58:12 2026 -0800
    Make better labels when printing recent genomes to the menu bar. Don't print the default hg38/hg19/mm10/mm39/hs1 since they are already there by default, refs #36535
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 15, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/utils/hubCheck/tests/expected/genomesConfigErrors.output.txt
  • lines changed 2, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126
• src/hg/utils/hubCheck/tests/input/misconfigGenomes.txt
  • lines changed 1, context: html, text, full: html, text
    049e50b2293ce5e9102eef9177a7cb88b49d7a10 Wed Mar 4 14:14:03 2026 -0800
    Move chromosome:start-end parsing into it's own function in hgFind so we can call just that code from elsewhere. Add a defaultPosition check for assembly hub into hubCheck that verifies the requested chromosome exists for that assembly. Do not warn if the range is too large since we actually silently accept that anyways and clamp to the chromosome ends. refs #37126