Commits for lrnassar

v470_base to v471_preview (2024-08-26 to 2024-09-02) v471

886ae501407aadc5b12c409cfaddc901b658fb76 Mon Aug 26 17:38:01 2024 -0700

• Tweaking runtime of GeCC otto to be at the start of the day, no RM.
  • src/hg/utils/otto/otto.crontab - lines changed 1, context: html, text, full: html, text

e587dcbf8a830c0c391309cb48bad26b186331b8 Mon Aug 26 17:40:31 2024 -0700

• Adding a new function that checks the current running otto crontab vs. the one committed to git.
  • src/hg/utils/otto/ottoCompareGitVsHiveFiles.py - lines changed 30, context: html, text, full: html, text

a76e089c36bb0ffb0877804fa4ae1c6eca75cbba Tue Aug 27 16:28:48 2024 -0700

• Adding an extra line that informs users they can remove specific highlights via right click. Refs #34353
  • src/hg/js/hgTracks.js - lines changed 1, context: html, text, full: html, text

77c1fd0753c5b43a3c10baa351ed40962be704cb Tue Aug 27 16:53:48 2024 -0700

• Small change to generateUsageStats.py was to improve how it splits character lines. Before if counts were high, e.g. track:1034, it would slice out last 2 numbers but keep the :10. For the assemblyStatsCron various changes were made as documented in the RM ticket. This script is a fairly big mess, and has a lot of room for improvement via functions, better commentings, not using bash to write out, and general optimizations like parsing files mutltiple times. However, it is only used internally for general exploratory overviews and thus it has not warranted a proper restructuring and cleaning. The primary motivation here was to add up counts from track usage across all hubs instead of only reporting the highest one. Refs #34266
  • src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/assemblyStatsCron.py - lines changed 183, context: html, text, full: html, text

2aea926850613e4fcef435265d32564573fdb613 Wed Aug 28 11:23:21 2024 -0700

• Adding the runTrimLogs.sh script made by ChrisL to the tree, this has been running for a few years now. It processes the raw error logs into a better format that can be ingested by the various stats scripts such as the monthly usage reports. Primarily it makes sure that any error log lines belonging to a single cart does not span multiple lines. The second script is a small addition to check if the error logs are no longer updating. This has come up various times over the years, most recently botht he asia and euro logs had not updated since May, roughly 4.5 months old. No RM.
  • src/utils/qa/checkErrorLogsAreUpToDate.py - lines changed 26, context: html, text, full: html, text
  • src/utils/qa/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/runTrimLogs.sh - lines changed 222, context: html, text, full: html, text

87435ae48fec925550b10151ef921ef36d75bb67 Wed Aug 28 12:46:28 2024 -0700

• Removing this from this dir as it already exists in ~/kent/src/hg/logCrawl/trimLogs/.
  • src/utils/qa/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/runTrimLogs.sh - lines changed 222, context: html, text, full: html, text

ab18d0d8e378370ecc459e1b3ec8f5d72996296f Wed Aug 28 13:54:21 2024 -0700

• Fixing up the run function which began to fail when wget'ing the hgRender image. The arguments going into subprocess were getting mangled. No RM, image comparison cron issue.
  • src/utils/qa/imageComp.py - lines changed 45, context: html, text, full: html, text

7312dbe29eb58ff58fb753cbbd66f48a399a823c Thu Aug 29 17:01:56 2024 -0700

• Announcement for downloading all track data in current region, refs #31817
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 25, context: html, text, full: html, text
  • src/hg/htdocs/images/downloadCurrentRegion.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/indexNews.html - lines changed 12, context: html, text, full: html, text

cab1b236636738fdd2743f6b59798b136e4ead86 Thu Aug 29 18:15:34 2024 -0700

• Adding ChrisL's wording clarifying the use of curly brackets when field names overlap, refs #34363
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 4, context: html, text, full: html, text

bbd23e87bdbc50a9ee58c32982ff7987cb943af6 Tue Sep 3 08:58:25 2024 -0700

• Removing these tracks from internal trackDb since they are to be released only as public hubs refs #34352
  • src/hg/makeDb/trackDb/human/enigma.html - lines changed 145, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.enigmaTracks.ra - lines changed 70, context: html, text, full: html, text