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-0700 hgvs: cover a deprecated protein accession, and say what is not covered A protein accession that is no longer current resolves through ncbiRefSeqLinkHistorical, which is what lets a term from an old paper still find its position.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 @@ -52,31 +52,31 @@ 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