79672605ddcba54a4c42b0b87ac243fc5d86d810 angie Wed Jan 10 14:04:37 2018 -0800 Don't use (hgFixed.)trackVersion for NCBI RefSeq anymore -- tdb dataVersion is preferred now and included automatically by printDataVersion. refs #20108, #18997 note-141 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 087cdc0..2637959 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -4143,44 +4143,30 @@ * tracks... */ if (container == NULL && wordCount > 0) { type = words[0]; if (sameString(type, "maf") || sameString(type, "wigMaf") || sameString(type, "bigMaf") || sameString(type, "netAlign") || sameString(type, "encodePeak")) headerItem = NULL; else if (( sameString(type, "narrowPeak") || sameString(type, "broadPeak") || sameString(type, "gappedPeak") ) && headerItem && sameString(headerItem, ".") ) headerItem = NULL; } -// doNcbiRefSeq -if (sameWord(tdb->table, "ncbiRefSeqOther")) - { - struct dyString *dy = newDyString(1024); - dyStringPrintf(dy, "%s", item); - - struct trackVersion *trackVersion = getTrackVersion(database, "ncbiRefSeq"); - if ((trackVersion != NULL) && !isEmpty(trackVersion->version)) - dyStringPrintf(dy, " - Release %s", trackVersion->version); - - cartWebStart(cart, database, "%s (%s)", tdb->longLabel, dyStringCannibalize(&dy)); - headerItem = cloneString("ncbiRefSeqOther"); - } - /* Print header. */ genericHeader(tdb, headerItem); itemForUrl = getIdInUrl(tdb, item); if (itemForUrl != NULL && trackDbSetting(tdb, "url")) { printCustomUrl(tdb, itemForUrl, item == itemForUrl); printIframe(tdb, itemForUrl); } if (plus != NULL) { fputs(plus, stdout); } @@ -11822,38 +11808,31 @@ } htmlHorizontalLine(); return rl; } void doNcbiRefSeq(struct trackDb *tdb, char *itemName) /* Process click on a NCBI RefSeq gene. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; char query[256]; struct ncbiRefSeqLink *nrl; -struct dyString *dy = newDyString(1024); -dyStringPrintf(dy, "%s - %s ", tdb->longLabel, itemName); - -struct trackVersion *trackVersion = getTrackVersion(database, "ncbiRefSeq"); -if ((trackVersion != NULL) && !isEmpty(trackVersion->version)) - dyStringPrintf(dy, "- Release %s\n", trackVersion->version); - -cartWebStart(cart, database, "%s", dy->string); +cartWebStart(cart, database, "%s - %s ", tdb->longLabel, itemName); /* get refLink entry */ sqlSafef(query, sizeof(query), "select * from ncbiRefSeqLink where id = '%s'", itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find %s in ncbiRefSeqLink table.", itemName); nrl = ncbiRefSeqLinkLoad(row); sqlFreeResult(&sr); printf("<h2>RefSeq Gene %s</h2><br>\n", nrl->name); printf("<b>RefSeq:</b> <a href='"); printEntrezNucleotideUrl(stdout, nrl->id); printf("' target=_blank>%s</a>", nrl->id); printf(" <b>Status: </b>%s<br>\n", nrl->status); printf("<b>Description:</b> %s<br>\n", nrl->product); @@ -11929,35 +11908,30 @@ nrl->locusLinkId); printf("%s</a><br>\n", nrl->locusLinkId); } if (differentWord(nrl->name,"")) { printGeneCards(nrl->name); if (startsWith("hg", database)) { printf("<b>AceView:</b> "); printf("<a href = 'https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s' target=_blank>", nrl->name); printf("%s</a><br>\n", nrl->name); } } -if ((trackVersion != NULL) && !isEmpty(trackVersion->version)) - { - printf("<B>Annotation Release:</B> <A href='%s' TARGET=_blank> %s <BR></A>", trackVersion->comment, trackVersion->version); - } - htmlHorizontalLine(); if (differentWord("", nrl->description)) { printf("Summary of <b>%s</b><br>\n%s<br>\n", nrl->name, nrl->description); htmlHorizontalLine(); } static boolean hasSequence = TRUE; struct psl *pslList = getAlignments(conn, "ncbiRefSeqPsl", itemName); // if the itemName isn't found, it might be found as the nrl->mrnaAcc if (! pslList) pslList = getAlignments(conn, "ncbiRefSeqPsl", nrl->mrnaAcc); if (pslList) { char query[256];