Commits for hiram

v498_preview to v498_preview2 (2026-04-27 to 2026-05-04) v498

2e1569df889bd13a340cf75a5c1182c798ab5955 Mon Apr 27 14:13:16 2026 -0700

• added quickLift file construction and getting to the end complete result refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 119, context: html, text, full: html, text

d9aaedf4614b86b3f4bd2aae4b44443019a14b45 Mon Apr 27 15:26:46 2026 -0700

• claude says it does not like the b in: set -beEu -o pipefail - so remove that and now have worked all the way to email notification to the user with all files present in appropriate locations refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 182, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 2, context: html, text, full: html, text

5be923c37e690d54b6d5c8e5835c3ebdb62f5f0c Mon Apr 27 16:00:13 2026 -0700

• correctly supply callback to autocomplete so it will indicate "No genomes found" when there is no match refs #31811
  • src/hg/js/liftRequest.js - lines changed 8, context: html, text, full: html, text

779b0a67557941da1d0402d9d6f2952ff54fb479 Mon Apr 27 16:48:42 2026 -0700

• add API assemblyRequest endpoint properly manage requests from the assemblySearch page system refs #31811
  • src/hg/hubApi/dataApi.h - lines changed 8, context: html, text, full: html, text
  • src/hg/hubApi/findGenome.c - lines changed 91, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 2, context: html, text, full: html, text
  • src/hg/js/assemblySearch.js - lines changed 19, context: html, text, full: html, text

49a0c84e41b604f646f25a3aa09fbb9a8e1177fa Tue Apr 28 11:28:49 2026 -0700

• try cluster running at 48Gb to avoid stoppage
  • src/hg/utils/automation/doTandemDup.pl - lines changed 4, context: html, text, full: html, text

a51a9e2eec975f01419e03107d70c74dfe5e0766 Tue Apr 28 14:35:28 2026 -0700

• different response messages for liftRequest vs. assembly request refs #31811
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 142, context: html, text, full: html, text

3eff31a9084b4a8a1587ba2fc43ab4e055e70979 Tue Apr 28 14:53:55 2026 -0700

• eliminate the HTTP_REFERER check and depend just on the userId cookie for security refs #31811
  • src/hg/hubApi/findGenome.c - lines changed 25, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 15, context: html, text, full: html, text

7a190b8ac6d95f66205385123542fc0c64a1469b Tue Apr 28 21:59:31 2026 -0700

• adding evaSnp8 contrib track refs #36957
  • src/hg/makeDb/trackDb/publicGenArk.txt - lines changed 1, context: html, text, full: html, text

41e8cd7271a59ef3d02db98d3064078444378fcb Wed Apr 29 14:24:47 2026 -0700

• beginning of the push script - to be continued refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 100, context: html, text, full: html, text

430bb5b5b7601fa51ed1872e5c7a55def547c450 Wed Apr 29 14:27:34 2026 -0700

• refactor the workflowMonitor to get json operations into galaxyState.py and finalizing state diagram refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/galaxyState.py - lines changed 107, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 242, context: html, text, full: html, text

d89c66b838902fda9dc142405b160305abc0d103 Wed Apr 29 16:18:52 2026 -0700

• this now only starts the alignment, the after alignment business has moved to other cron jobs refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 76, context: html, text, full: html, text

797000a8e6ef069d3e5a7b5034c0305f0ee97697 Wed Apr 29 16:20:51 2026 -0700

• enable the startup of the alignment refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 5, context: html, text, full: html, text

476ebb957aebb1a7f20ea71301e894c5422bd57e Wed Apr 29 21:41:01 2026 -0700

• subtle timing issue resolved and minor bugs fixed refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 3, context: html, text, full: html, text

1ad3e0a11b1650d330a3d69ae7cbea771d647bc0 Wed Apr 29 21:52:42 2026 -0700

• adding galaxy cleanup process to release history and workflow metadata refs #31811
  • src/hg/utils/otto/userRequests/galaxyCleanup.py - lines changed 78, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 10, context: html, text, full: html, text

5fed84fb663f977b33c69348c7990081a789b5dd Wed Apr 29 23:02:21 2026 -0700

• fixup printf in workflowMonitor.sh to make a clean successInvocationId.txt file and add business in ottoRequestPush.py to add status=6 setting to successful pushed file sets refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 128, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 1, context: html, text, full: html, text

cecf287ff26c79831fb222f8da03cd14546174e0 Wed Apr 29 23:02:43 2026 -0700

• expand process description in README refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 33, context: html, text, full: html, text

210c39cf46050fb9024471e07422aba588183dc8 Thu Apr 30 10:07:53 2026 -0700

• claude says to not use the -b bash setting refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 1, context: html, text, full: html, text

8dc26c657ea6c756d3ebf6bc38b525a940294400 Thu Apr 30 10:09:22 2026 -0700

• kegAlignLastz.sh should be with the other ottoRequest scripts refs #31811
  • src/hg/utils/otto/userRequests/kegAlignLastz.sh - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

d7fec1a55508e24c02bb2754c42baaad1d3c8394 Thu Apr 30 10:12:42 2026 -0700

• remove all the cruft from pairLastz.sh copy, not needed here refs #31811
  • src/hg/utils/otto/userRequests/kegAlignLastz.sh - lines changed 186, context: html, text, full: html, text

a4870c92799d2687ff7c6602663f5ec6e5599af2 Thu Apr 30 10:16:07 2026 -0700

• kegAlignLastz.sh has moved to this scripts directory refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 4, context: html, text, full: html, text

f1ab1958cec7cf4f14056692907e7518aa67273b Thu Apr 30 10:25:36 2026 -0700

• use flock to ensure only one instance of this script is ever running at one time refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 17, context: html, text, full: html, text

0aa99b19411f52674c57d49c8b41c2706c78bf29 Thu Apr 30 10:44:15 2026 -0700

• add URL path names to the final email notice refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 35, context: html, text, full: html, text

dbf1f3970c63ee81e66dca929395aa575a536a26 Thu Apr 30 11:52:20 2026 -0700

• eliminate duplicate code section and protect all net tracks with file exist test refs #31811
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 32, context: html, text, full: html, text

e8d1fff44e0f7ecd4629cfcc2ac671d6af78d8ae Thu Apr 30 12:54:54 2026 -0700

• add an ottoRequest table interactive CGI viewer and verify lift.over URL links for email are valid refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 214, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 22, context: html, text, full: html, text

c62810dcb9b6b76fd427ce776219fb5eb02357dd Thu Apr 30 13:18:29 2026 -0700

• set the table to class sortable to allow column header sort function refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 4, context: html, text, full: html, text

3976a8ec6b27464bd64e93916821dbcb52cd7671 Thu Apr 30 23:01:52 2026 -0700

• this actually might be working all the way through now refs #31811
  • src/hg/utils/otto/userRequests/kegAlignLastz.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 30, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 1, context: html, text, full: html, text

4e6a1fde309912e1c07c1b24e91e0ca1bea0e07c Thu Apr 30 23:19:34 2026 -0700

• readjust ottoRequest to run every 7 minutes refs #31811
  • src/hg/utils/otto/otto.crontab - lines changed 2, context: html, text, full: html, text

3a85cb72b4b01663b80635ce8c7196100627d188 Thu Apr 30 23:49:28 2026 -0700

• cron jobs expose PATH issues refs #31811
  • src/hg/utils/otto/userRequests/kegAlignLastz.sh - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 10, context: html, text, full: html, text

a5fca314f31035baabe4d29cd6ff1d40ccddef0d Thu Apr 30 23:59:37 2026 -0700

• do not need the stderr status information messages refs #31811
  • src/hg/utils/otto/userRequests/galaxyState.py - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 1, context: html, text, full: html, text

36e424927ba8b56ebb84e78ad311c4bfde7c0246 Fri May 1 10:49:53 2026 -0700

• no need for the stderr output and all kent commands use full /cluster/bin/ path names to avoid cron job problems refs #31811
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 4, context: html, text, full: html, text

24891487d4c04f503b44631ea97773e8a2071b56 Fri May 1 12:39:24 2026 -0700

• explicit path names to allow these scripts to work on cron jobs refs #31811
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 1, context: html, text, full: html, text

e1625b2bf30df1d1f9385bc79fc2cbd45a05d511 Fri May 1 12:41:32 2026 -0700

• explicit path names to allow these scripts to work on cron jobs refs #31811
  • src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 1, context: html, text, full: html, text

b17a43e2a64efaca2ee008e7e466764fea60407a Fri May 1 12:44:21 2026 -0700

• explicit path names to allow function on cron jobs refs #31811
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 3, context: html, text, full: html, text

bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700

• explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
  • src/hg/utils/automation/asmHubAllGaps.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubAugustusGene.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubCpG.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubEnsGene.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubNcbiGene.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubNcbiRefSeq.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubSimpleRepeat.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTanDups.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubWindowMasker.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubXenoRefGene.pl - lines changed 1, context: html, text, full: html, text

717d052c4047454ff8bece9b57a5d7f54c4f0154 Fri May 1 13:23:12 2026 -0700

• one more explicit path name for cron safety refs #31811
  • src/hg/utils/automation/AsmHub.pm - lines changed 1, context: html, text, full: html, text

974a36818d9920f331467faf1668e602c2c0e1fe Fri May 1 13:39:41 2026 -0700

• add correct path to hgsql refs #31811
  • src/hg/utils/automation/addQuickLift.py - lines changed 1, context: html, text, full: html, text

4b4338b902614b327f6921ed1255415508250510 Fri May 1 13:53:01 2026 -0700

• do not need to see the stderr informational outputs refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 5, context: html, text, full: html, text

211c215c654c363993a9d480cbda679de0bbd7e9 Fri May 1 13:59:15 2026 -0700

• eliminating stderr information to avoid cron job noise refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/galaxyCleanup.py - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 5, context: html, text, full: html, text

70b873ace3ffca0850aa635f7fc43c71cc7b09d5 Fri May 1 14:50:19 2026 -0700

• further silent the cron outputs and add a status indicator to the watch.cgi page refs #31811
  • src/hg/utils/otto/userRequests/galaxyStatus.py - lines changed 52, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 57, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 43, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 2, context: html, text, full: html, text

dca6b246ce843e81430fbcda629c2478876b16fb Fri May 1 15:45:20 2026 -0700

• silence in the back there refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 1, context: html, text, full: html, text

aeaebac6e25be25c1205747abf248fd7092ebdb3 Sat May 2 14:53:35 2026 -0700

• add a reset button and outlinks to browsers refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 12, context: html, text, full: html, text

55fcac8a40acd4e41d0bcdff1c878f7214a58d6d Sun May 3 13:20:45 2026 -0700

• should be cron quiet now on no error conditions refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 9, context: html, text, full: html, text