d033cea2063e9362949baf5b4d8b837597173a0d max Thu Sep 10 05:16:05 2026 -0700 Address the code review of the Sep 9 commits Faceted composite: text that comes from a hub - a metadata column's description, the name and title of a data type, and the values quoted back in the "could not load the metadata" row - is put on the page as text rather than as markup. The three places built their markup from template strings, so a value carrying angle brackets or a quote was read as HTML: the column description now goes through the shared htmlEncode() once where the header is parsed, and the other two build their elements as nodes. The error row reads better for it as well, since a value with brackets in it used to disappear from the message that was meant to show it. The saved UI state keys on the assembly as well as the metadata id. localStorage is per-origin, so two assemblies whose tracks share a name were sharing one entry, and a row order dragged on one came back on the other over a different set of samples. hgTrackUi passes the database down for it. State saved under the old key is dropped, which costs a facet selection or a page length. Imprinting: the five subtrack description pages link back to the container as hgTrackUi?db=$db&g=$parentTrack, without the hgsid. Native trackDb html is substituted by hgTrackDb as it loads the table, where there is no cart, so ${hgsid} came out empty and the link read 'hgsid=&g=...'. Matches what the Fiber-seq pages already do. The makeDoc note that described the old form is updated with the reason. UniProt otto: README.txt lists all eight things that reach runLog.txt. It had four, and was missing LOCKED, along with PREFLIGHT-FAIL, END and INTERRUPTED. refs #36210 refs #37599 refs #38300 diff --git src/hg/utils/otto/uniprot/README.txt src/hg/utils/otto/uniprot/README.txt index 1a89dc56e93..11a2dec2488 100644 --- src/hg/utils/otto/uniprot/README.txt +++ src/hg/utils/otto/uniprot/README.txt @@ -23,34 +23,40 @@ uniprotToTab needs the lxml XML parser. It is not in the python standard library and hgwdev has no system-wide copy, so it lives in a virtualenv in venv/. Build or rebuild it with: cd /hive/data/outside/otto/uniprot && ./makeVenv.sh Note that ~/.local is not enough: cron runs this as otto, which does not see anyone else's per-user python packages. Did it run? runLog.txt gets one line per run and is never truncated, so it is the history of the job: + PREFLIGHT-FAIL the venv or the parser was not usable, doUniprot never ran START a run began + END doUniprot returned, exit code on the line + LOCKED another doUniprot holds the lock file, this run did nothing NOCHANGE UniProt had no new release, nothing to do, no mail sent OK new release, tracks rebuilt FAIL the run died, exit code and log named on the line + INTERRUPTED a signal killed the run, the lock file was removed + +A normal month is START, END, then one of LOCKED, NOCHANGE, OK or FAIL. lastRun.log is the log of the most recent run and is overwritten every month. A failing run is kept as lastFail.log, and its last 25 lines are mailed to the MAILTO addresses in otto's crontab. A month without a new UniProt release sends no mail, so silence means "nothing to do", not "it worked". version.txt in each bigBed/ directory is what the trackDb dataVersion setting shows on the track description page. It is only rewritten when the release string changes, so its date on disk is the date the data last moved, not the date the pipeline last ran. Directories: fasta - current protein sequences and their sizes, named by taxon geneMaps/ - a mapping of the current protein sequences to the genome, one for each species and database.