814335cde61f999ae23626093306bdb6bf394f5e braney Sun Sep 20 07:00:39 2026 -0700 hgvs: cover a deprecated protein accession, and say what is not covered A protein accession that is no longer current resolves through ncbiRefSeqLinkHistorical, which is what lets a term from an old paper still find its position. Three such terms are added to the valid-terms list: NP_000054.2, which has three deprecated transcript versions behind it, and NP_055615.8, which has versions .8, .9 and .10. The other half of #38248 is NOT pinned, and the registry row says so rather than implying otherwise. That half picks the newest deprecated transcript by sorting on length first, so that .9 does not beat .10 as a string. I could not build a term that shows it: with the order by removed entirely, and again with a plain string sort, every term gives identical coordinates. The reason is in the data -- for the accessions with both a .9 and a .10, the versions differ only in where the UTR ends, so cdsStart, cdsEnd and exonCount are the same and a coding residue lands in the same place whichever version is chosen. Recorded as assertion-only, the honest level, with what was tried written down so the next person does not repeat it. refs #38248, refs #38391 diff --git src/utils/testRegistry/registry.tsv src/utils/testRegistry/registry.tsv index 243c9424cbc..cbd5dd08ae5 100644 --- src/utils/testRegistry/registry.tsv +++ src/utils/testRegistry/registry.tsv @@ -1,89 +1,89 @@ # registry.tsv - which unit test defends which Redmine ticket. refs #38391 # # A bug ticket has no way to say whether a test now defends its fix, and a test has no way # to say which bug it came from. This table answers both, and says which tickets are still # waiting for a test. It is hand written: nothing generates it, so adding the row is part # of writing the test. # # Unit tests only. The browser-page regression tests are the docent suite, refs #38252, # where the script is already named for its ticket. A ticket whose fix only changes what a # page says is that suite's job and is not in here at all. # # Seven tab separated columns, sorted by ticket then by test: # # ticket the Redmine number, digits only # release the version the fix ships in, digits only, from the ticket's Target version. # The table starts at v504. A fix on master with no target version yet takes # "-" until the ticket says. # test the file to open, as a path from kent/src, or "-" for a ticket that needs a # test and does not have one. A suite whose cases are make targets adds # ::target, e.g. tests/makefile::relPath # docent the browser test that watches the same ticket, from the docent suite in # hg/utils/docent/tests/regress, or "-" when there is none. Not a second copy # of that suite: it is here so "nothing is watching this ticket at all" is a # question the tool can answer, which is the question worth acting on. A # docent script does not make a unit test unnecessary where the why is # invisible; rm38309 cannot see a read past the end of an array, it asserts # something next to it. # why why this ticket needs a unit test rather than a browser test: # invisible the fix changes nothing on screen. No browser test can see # it, so a unit test is the only test there can be. # perf the fix is about speed or memory. The test has to catch # backsliding, so it measures work done -- queries, passes, # allocations, bytes -- and never wall-clock seconds. # library the fix is in library code that a browser reaches only # through a page, where much else can go wrong first. # evidence what has been seen, weakest first: unrecorded, assertion-only, sandbox-ab, # release-ab, caught-regression. "-" on a row with no test. The vocabulary is # proof.js's from the docent suite, minus the two levels that need a browser, # so the two tables can be read on one scale. Every row starts at unrecorded # and earns its way up by measurement, not by argument. # note what the test holds down. On a row with no test, what it would have to hold # down, which is the first thing the person who writes it needs. # # One ticket can have several rows and one test can defend several tickets; both happen # here already. A ticket cannot be both covered and waiting. # # `testRegistry check` reads every row and fails when one has rotted, so a test cannot be # renamed or deleted without coming here. # #ticket release test docent why evidence note 10138 504 hg/lib/tests/sessionDirTester.c rm10138.docent.yaml invisible sandbox-ab the session directory hash is 10 characters and the legacy 8 is a prefix of it 20824 504 hg/utils/netToBigNet/tests/makefile::simpleTest - library unrecorded a net converted to bigNet and back, byte compared 27988 504 hg/lib/tests/geoMirrorSelfTester.c - invisible sandbox-ab the host the visitor typed decides which gbNode row the server calls itself 36212 504 hg/lib/tests/bedItemRgbTester.c rm36212.docent.yaml library sandbox-ab an explicit itemRgb on beats the presence of a color setting, in the stanza and from a parent 37263 504 lib/tests/pathSimplifyTest.c - library unrecorded dot-dot collapsing, checked against the right answer rather than against the old one 37969 504 - rm37969.docent.yaml library - needs one: a quickLifted container must not hide the tracks inside it. BLOCKED: dumpTdbAndChildren is static in trackHub.c and its public caller needs a cart 37984 504 lib/tests/hmacTest.c - library sandbox-ab the pending social identity is signed with hmacMd5, not a plain md5 of salt plus fields 38086 504 - - invisible - needs one: a stale cart visibility variable must not hide a new BLAT result track. BLOCKED: checkGroup is static in customFactory.c and the path needs a cart 38126 504 lib/tests/htmlSanitizeTest.c rm38126.docent.yaml library unrecorded the allowlist that hub and custom track description HTML is filtered through 38184 504 - rm38184.docent.yaml invisible - needs one: db= resolving to the assembly already loaded must keep the session position. BLOCKED: needs a live cart, so hgcentral rows to read and write 38185 504 hg/hgSession/tests/backupParseTest.c rm38185.docent.yaml invisible unrecorded an empty pair in a session backup must not eat the variable in front of it 38185 504 lib/tests/cgiParseTest.c rm38185.docent.yaml invisible unrecorded an empty CGI pair must not abort the request 38198 504 - rm38198.docent.yaml library - needs one: a second lift has to update a track already in the hub. BLOCKED: readStanzas is static in trackHub.c and the public entry takes a cart and a trash file 38225 504 hg/lib/tests/mallocTopPadTester.c - perf sandbox-ab the hg.conf step size reaches the C library: the heap grows in one 16 MB jump, not the default one 38233 504 - - perf - needs one: RefSeq status is asked once per track, not once per gene; the test has to count the queries. BLOCKED: the change is in a static function in hgTracks/simpleTracks.c 38236 504 - rm38236.docent.yaml library - needs one: a quickLift chain with no aligned block in the window must not crash. BLOCKED: the change is in hgTracks/bigWigTrack.c -38248 504 - rm38248.docent.yaml library - needs one: a deprecated versioned NP_ accession has to resolve to RefSeq Historical. Reachable: hgHgvs is public, so this extends the existing hgvs test, and needs only reads +38248 504 hg/lib/tests/input/hgvs/validTerms.txt rm38248.docent.yaml library assertion-only a deprecated versioned NP_ accession still maps, through ncbiRefSeqLinkHistorical. The ticket's other half, taking the NEWEST deprecated transcript, is NOT pinned: with the order by removed and with a plain string sort, every term I could build gives identical coordinates, because the versions differ only in UTR ends 38249 504 hg/lib/tests/quickLiftTester.c rm38249.docent.yaml library unrecorded the target strand of a reverse complemented protein, found in the #38349 review 38253 504 - - perf - needs one: item coverage is built from feature runs, not one counter per base. BLOCKED: countOverlaps is static in hgTracks/simpleTracks.c and takes a struct track 38254 504 - - invisible - needs one: a composite subtrack's visibility has to settle before the parallel loaders start. BLOCKED: the change is in hgTracks.c, the file that holds main 38256 504 hg/utils/hubCheck/tests/makefile::relPath - library unrecorded a local hub given by a relative path: bigDataUrl resolved once, not twice 38260 504 hg/utils/hubCheck/tests/makefile::missingFile - library unrecorded hubCheck must say something about a bigDataUrl it cannot open 38268 504 hg/lib/tests/dataVersionPathTester.c rm38268.docent.yaml invisible sandbox-ab a hub track's dataVersion may name a file only under /gbdb, and only by a plain path 38272 504 - rm38272.docent.yaml invisible - needs one: a GenArk quickLift source assembly must not be looked for in MySQL. Reachable: asForDb is public; needs a genark accession and a tdb whose as can be built 38273 504 - - perf - needs one: a collection's hub file is copied when it is written, not on every session load; the test has to count the copies. BLOCKED: needs a cart and a trash file 38283 504 hg/lib/tests/hVarSubstHtmlTester.c rm38283.docent.yaml library sandbox-ab a hub description page may not use $hgsid, and a native one may use only the braced form 38285 504 hg/lib/tests/input/hgvs/validTerms.txt rm38285.docent.yaml library unrecorded bare codon numbers and ranges, with expected/hgvs/validTerms.txt beside it 38302 504 - rm38302.docent.yaml invisible - needs one: an activation token that is missing, empty or older than seven days is invalid. BLOCKED: the check is static in hgLogin.c and needs gbMembers rows 38303 504 hg/lib/tests/trashDirTester.c rm38303.docent.yaml invisible sandbox-ab a session file path spelled through a symlinked config directory, which broke 583 saved sessions 38309 504 - rm38309.docent.yaml invisible - needs one: exonFrames must not be read past the end on a transcript's last exon. BLOCKED: the change is inside drawing code in hgTracks/simpleTracks.c 38313 504 hg/lib/tests/snapshotTypeTester.c - library sandbox-ab the fast snapshotType reader agrees with raFromString, including on a longer tag that starts the same 38317 504 - - invisible - needs one: doKnownGene must not read an uninitialised stack refLink. BLOCKED: doKnownGene is static in hgc.c, 27000 lines and not linkable on its own 38318 504 hg/lib/tests/sessionDataTester.c - invisible unrecorded the returned path must be freeable through kent's own handler stack 38320 504 lib/tests/faSpeedReadTest.c - invisible unrecorded the buffer grower and its caller must agree on the size 38323 504 - - library - needs one: an api key made on one geo mirror has to work on all of them. BLOCKED: needs hubSpaceKeys rows in hgcentral, which means a test that writes 38328 504 hg/lib/tests/genarkLiftOverTester.c - invisible sandbox-ab the accession list is escaped where the values are, and a non-accession never reaches the query 38335 504 lib/tests/cgiParseTest.c rm38335.docent.yaml invisible unrecorded a pair with no =value must not lose the variable 38340 504 hg/hgSession/tests/backupParseTest.c - invisible unrecorded the same pair, read back out of a session backup 38340 504 lib/tests/cgiCookieTest.c - invisible unrecorded the same pair in a cookie header