Commits for braney

v442_base to v443_preview (2023-01-09 to 2023-01-17) v443

1f99db8cf7ec62a0a6e8a4418ce2ad8441a4c1f8 Sat Dec 31 14:25:56 2022 -0800

• the script actually sends the mail now.
  • src/hg/utils/otto/knownGene/genIspcrMail.sh - lines changed 2, context: html, text, full: html, text

12c80e276f91d0920d4c39e76870745a69e19b4d Mon Jan 9 16:47:40 2023 -0800

• add support for curated hubs to hubApi
  • src/hg/hubApi/apiUtils.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 33, context: html, text, full: html, text

427fef992306654becd9988cbd95cc8e98d34156 Mon Jan 9 16:50:30 2023 -0800

• oops, forgot an include file
  • src/hg/inc/hubConnect.h - lines changed 3, context: html, text, full: html, text

088c1ae0aed4212f6939ac991cb6fe7d1393acda Tue Jan 10 10:18:49 2023 -0800

• revert a change I made to recognize bad db's instead of defaulting to the cart or hg38, but this broke undecorated specification of "genome", which is handled through the cart. Oops.
  • src/hg/lib/web.c - lines changed 6, context: html, text, full: html, text

0f2021c604acf2101f3481e94e768940aa0358f6 Tue Jan 10 16:07:00 2023 -0800

• make sure connection to hgCentral is closed even if the asmAlias table doesn't exist
  • src/hg/lib/asmAlias.c - lines changed 3, context: html, text, full: html, text

b02d20dede590203b6ecca10be473e7e22179a51 Thu Jan 12 13:12:53 2023 -0800

• deal with some weird edge cases in hub that Hiram's hub illicit. Don't read a single trackDb.txt file more than once even if it's referenced from mulitple hubs. Also, only the first time a genome is defined does it get to populate its own groups. Subsequent examples get put into their own group, just like a normal track hub does.
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hubApi/apiUtils.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 2, context: html, text, full: html, text

72a519115340ddb42712b0e0b8d29f093be28400 Thu Jan 12 13:33:54 2023 -0800

• add transcript rank to knownGene format GENCODE
  • src/hg/lib/gencodeBGP.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/knownAttrs.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildCore.sh - lines changed 4, context: html, text, full: html, text

b7e9664a721ac8e117840473859dcd25ae412842 Fri Jan 13 13:42:04 2023 -0800

• oops, missed a place
  • src/hg/utils/hubCrawl/hubCrawl.c - lines changed 2, context: html, text, full: html, text