038c31ecb2bd9e59311bb3009646ddc5374fa9d6 galt Fri Jul 13 23:06:35 2018 -0700 hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729 diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 33521b7..481bdec 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -590,30 +590,41 @@ } void hgcAnchor(char *group, char *item, char *other) /* Generate an anchor that calls click processing program with item * and other parameters. */ { hgcAnchorSomewhere(group, item, other, seqName); } void writeFramesetType() /* Write document type that shows a frame set, rather than regular HTML. */ { fputs("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Frameset//EN\">\n", stdout); } +void htmlFramesetStart(char *title) +/* Write DOCTYPE HTML and HEAD sections for framesets. */ +{ +/* Print start of HTML. */ +writeFramesetType(); +puts("<HTML>"); +char *meta = getCspMetaHeader(); +printf("<HEAD>\n%s<TITLE>%s</TITLE>\n</HEAD>\n\n", meta, title); +freeMem(meta); +} + boolean clipToChrom(int *pStart, int *pEnd) /* Clip start/end coordinates to fit in chromosome. */ { static int chromSize = -1; if (chromSize < 0) chromSize = hChromSize(database, seqName); if (*pStart < 0) *pStart = 0; if (*pEnd > chromSize) *pEnd = chromSize; return *pStart < *pEnd; } struct genbankCds getCds(struct sqlConnection *conn, char *acc) /* obtain and parse the CDS, errAbort if not found or invalid */ { @@ -7167,42 +7178,41 @@ if (isNotEmpty(cdsString)) genbankParseCds(cdsString, retCdsStart, retCdsEnd); } } } void htcBigPslAli(char *acc) /* Show alignment for accession in bigPsl file. */ { struct psl *psl; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); aliTable = cartString(cart, "aliTable"); if (isCustomTrack(aliTable)) { struct customTrack *ct = lookupCt(aliTable); tdb = ct->tdb; } else tdb = hashFindVal(trackHash, aliTable); -printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", acc, aliTable); +char title[1024]; +safef(title, sizeof title, "%s vs Genomic [%s]", acc, aliTable); +htmlFramesetStart(title); /* Get some environment vars. */ start = cartInt(cart, "l"); int end = cartInt(cart, "r"); char *chrom = cartString(cart, "c"); char *seq, *cdsString = NULL; struct lm *lm = lmInit(0); char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table); struct bbiFile *bbi = bigBedFileOpen(fileName); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; for (bb = bbList; bb != NULL; bb = bb->next) { @@ -7231,42 +7241,41 @@ struct dnaSeq *rnaSeq = newDnaSeq(seq, strlen(seq), acc); enum gfType type = gftRna; if (pslIsProtein(psl)) type = gftProt; showSomeAlignment(psl, rnaSeq, type, 0, rnaSeq->size, NULL, cdsStart, cdsEnd); } void htcBigPslAliInWindow(char *acc) /* Show alignment in window for accession in bigPsl file. */ { struct psl *partPsl, *wholePsl; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); aliTable = cartString(cart, "aliTable"); if (isCustomTrack(aliTable)) { struct customTrack *ct = lookupCt(aliTable); tdb = ct->tdb; } else tdb = hashFindVal(trackHash, aliTable); -printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", acc, aliTable); +char title[1024]; +safef(title, sizeof title, "%s vs Genomic [%s]", acc, aliTable); +htmlFramesetStart(title); /* Get some environment vars. */ start = cartInt(cart, "l"); int end = cartInt(cart, "r"); char *chrom = cartString(cart, "c"); char *seq, *cdsString = NULL; struct lm *lm = lmInit(0); char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table); struct bbiFile *bbi = bigBedFileOpen(fileName); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; for (bb = bbList; bb != NULL; bb = bb->next) { @@ -7320,35 +7329,34 @@ char table[64]; char accTmp[64]; struct sqlConnection *conn; struct sqlResult *sr; char **row; struct psl *psl; struct dnaSeq *rnaSeq; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; boolean hasBin; char accChopped[512] ; safef(accChopped, sizeof(accChopped), "%s",acc); chopSuffix(accChopped); -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); aliTable = cartString(cart, "aliTable"); -printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", accChopped, aliTable); +char title[1024]; +safef(title, sizeof title, "%s vs Genomic [%s]", accChopped, aliTable); +htmlFramesetStart(title); /* Get some environment vars. */ start = cartInt(cart, "o"); conn = hAllocConn(database); getCdsStartAndStop(conn, accChopped, aliTable, &cdsStart, &cdsEnd); /* Look up alignments in database */ hFindSplitTable(database, seqName, aliTable, table, &hasBin); sqlSafef(query, sizeof query, "select * from %s where qName like '%s%%' and tName=\"%s\" and tStart=%d", table, acc, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", acc, start); psl = pslLoad(row+hasBin); @@ -7410,35 +7418,33 @@ char **row; struct psl *wholePsl, *partPsl; struct dnaSeq *rnaSeq; char *aliTable; int start; unsigned int cdsStart = 0, cdsEnd = 0; boolean hasBin; char accChopped[512] ; safef(accChopped, sizeof(accChopped), "%s",acc); chopSuffix(accChopped); /* Get some environment vars. */ aliTable = cartString(cart, "aliTable"); start = cartInt(cart, "o"); -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", - accChopped, aliTable); +char title[1024]; +safef(title, sizeof title, "%s vs Genomic [%s]", accChopped, aliTable); +htmlFramesetStart(title); conn = hAllocConn(database); getCdsStartAndStop(conn, accChopped, aliTable, &cdsStart, &cdsEnd); if (startsWith("user", aliTable)) { char *pslName, *faName, *qName; struct lineFile *lf; bioSeq *oSeqList = NULL, *oSeq = NULL; struct psl *psl; int start; enum gfType tt, qt; boolean isProt; char *ss = cartOptionalString(cart, "ss"); @@ -7575,34 +7581,34 @@ chainFree(&chain); psl = pslTrimToTargetRange(fatPsl, winStart, winEnd); pslFree(&fatPsl); if (sameWord(otherDb, "seq")) { qSeq = hExtSeqPart(database, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s", psl->qName); } else { qSeq = loadGenomePart(otherDb, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s.%s", otherOrg, psl->qName); } -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>%s %s vs %s %s </TITLE>\n</HEAD>\n\n", +char title[1024]; +safef(title, sizeof title, "%s %s vs %s %s ", (otherOrg == NULL ? "" : otherOrg), psl->qName, org, psl->tName ); +htmlFramesetStart(title); showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, 0, 0); } void htcChainTransAli(char *item) /* Draw detailed alignment representation of a chain with translated protein */ { struct chain *chain; struct psl *fatPsl, *psl = NULL; int id = atoi(item); char *track = cartString(cart, "o"); char *type = trackTypeInfo(track); char *typeWords[2]; char *otherDb = NULL, *org = NULL, *otherOrg = NULL; struct dnaSeq *qSeq = NULL; char name[128]; @@ -7632,53 +7638,52 @@ chainFree(&chain); psl = pslTrimToTargetRange(fatPsl, winStart, winEnd); pslFree(&fatPsl); if (sameWord(otherDb, "seq")) { qSeq = hExtSeq(database, psl->qName); safef(name, sizeof name, "%s", psl->qName); } else { qSeq = loadGenomePart(otherDb, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s.%s", otherOrg, psl->qName); } -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>%s %s vs %s %s </TITLE>\n</HEAD>\n\n", +char title[1024]; +safef(title, sizeof title, "%s %s vs %s %s ", (otherOrg == NULL ? "" : otherOrg), psl->qName, org, psl->tName ); +htmlFramesetStart(title); /*showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, 0, 0); */ showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, cdsStart, cdsEnd); } void htcUserAli(char *fileNames) /* Show alignment for accession. */ { char *pslName, *faName, *qName; struct lineFile *lf; bioSeq *oSeqList = NULL, *oSeq = NULL; struct psl *psl; int start; enum gfType tt, qt; boolean isProt; -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>User Sequence vs Genomic</TITLE>\n</HEAD>\n\n"); +char title[1024]; +safef(title, sizeof title, "User Sequence vs Genomic"); +htmlFramesetStart(title); start = cartInt(cart, "o"); parseSs(fileNames, &pslName, &faName, &qName); pslxFileOpen(pslName, &qt, &tt, &lf); isProt = (qt == gftProt); while ((psl = pslNext(lf)) != NULL) { if (sameString(psl->tName, seqName) && psl->tStart == start && sameString(psl->qName, qName)) break; pslFree(&psl); } lineFileClose(&lf); if (psl == NULL) errAbort("Couldn't find alignment at %s:%d", seqName, start); oSeqList = faReadAllSeq(faName, !isProt); @@ -7695,34 +7700,33 @@ /* Show protein to translated dna alignment for accession. */ { struct psl *psl; int start; enum gfType qt = gftProt; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *seq = NULL; char query[256], **row; char fullTable[64]; boolean hasBin; char buffer[256]; int addp = 0; char *pred = NULL; -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>Protein Sequence vs Genomic</TITLE>\n</HEAD>\n\n"); +char title[1024]; +safef(title, sizeof title, "Protein Sequence vs Genomic"); +htmlFramesetStart(title); addp = cartUsualInt(cart, "addp",0); pred = cartUsualString(cart, "pred",NULL); start = cartInt(cart, "o"); hFindSplitTable(database, seqName, table, fullTable, &hasBin); sqlSafef(query, sizeof query, "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", fullTable, readName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", readName, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); if ((addp == 1) || (pred != NULL)) { char *ptr; @@ -7760,34 +7764,33 @@ showSomeAlignment(psl, seq, qt, 0, seq->size, NULL, 0, 0); } void htcBlatXeno(char *readName, char *table) /* Show alignment for accession. */ { struct psl *psl; int start; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); struct dnaSeq *seq; char query[256], **row; char fullTable[64]; boolean hasBin; -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>Sequence %s</TITLE>\n</HEAD>\n\n", readName); +char title[1024]; +safef(title, sizeof title, "Sequence %s", readName); +htmlFramesetStart(title); start = cartInt(cart, "o"); hFindSplitTable(database, seqName, table, fullTable, &hasBin); sqlSafef(query, sizeof query, "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", fullTable, readName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", readName, start); psl = pslLoad(row+hasBin); sqlFreeResult(&sr); hFreeConn(&conn); seq = hExtSeq(database, readName); showSomeAlignment(psl, seq, gftDnaX, 0, seq->size, NULL, 0, 0); } @@ -8108,34 +8111,34 @@ void htcIlluminaProbesAlign(char *item) /* If the click came from "show alignment" on the Illumina */ /* probes details page, show the standard alignment page. */ { struct psl *psl; struct dnaSeq *seq; struct sqlResult *sr; struct sqlConnection *conn = hAllocConn(database); char query[256], **row; int start; char *pslTable = cgiUsualString("pslTable", "illuminaProbesAlign"); char *seqTable = cgiUsualString("seqTable", "illuminaProbesSeq"); char *probeName = item; char *probeString; int rowOffset = hOffsetPastBin(database, seqName, pslTable); -/* Print start of HTML. */ -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>Sequence %s</TITLE>\n</HEAD>\n\n", probeName); + +char title[1024]; +safef(title, sizeof title, "Sequence %s", probeName); +htmlFramesetStart(title); start = cartInt(cart, "o"); /* get psl */ sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tName = '%s' and tStart=%d", pslTable, probeName, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) == NULL) errAbort("Couldn't find alignment for %s at %d", probeName, start); psl = pslLoad(row+rowOffset); sqlFreeResult(&sr); sqlSafef(query, sizeof(query), "select seq from %s where id = '%s'", seqTable, probeName); probeString = sqlNeedQuickString(conn, query); seq = newDnaSeq(probeString, strlen(probeString), probeName); hFreeConn(&conn); showSomeAlignment(psl, seq, gftDna, 0, seq->size, probeName, 0, 0); pslFree(&psl); @@ -14223,33 +14226,33 @@ /* In hg10 tables, psl->qName can be org.chrom. Strip it down to just * the chrom: */ qChrom = psl->qName; if ((ptr = strchr(qChrom, '.')) != NULL) qChrom = ptr+1; /* Make sure that otherOrg's chrom size matches psl's qSize */ if (hChromSize(database, qChrom) != psl->qSize) errAbort("Alignment's query size for %s is %d, but the size of %s in database %s is %d. Incorrect database in trackDb.type?", qChrom, psl->qSize, qChrom, otherDb, hChromSize(otherDb, qChrom)); psl = pslTrimToTargetRange(psl, winStart, winEnd); qSeq = loadGenomePart(otherDb, qChrom, psl->qStart, psl->qEnd); snprintf(name, sizeof(name), "%s.%s", otherOrg, qChrom); -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>%s %dk</TITLE>\n</HEAD>\n\n", name, psl->qStart/1000); +char title[1024]; +safef(title, sizeof title, "%s %dk", name, psl->qStart/1000); +htmlFramesetStart(title); showSomeAlignment(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, 0, 0); } void doAlignCompGeno(struct trackDb *tdb, char *itemName, char *otherGenome) /* Handle click on blat or blastz track in a generic fashion */ /* otherGenome is the text to display for genome name on details page */ { char query[256]; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row; int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); char *chrom = cartString(cart, "c"); struct psl *pslList = NULL, *psl; @@ -20303,31 +20306,31 @@ printPos(gc->chrom, gc->chromStart, gc->chromEnd, NULL, FALSE, NULL); printf("<B>GC Percentage:</B> %3.1f%%<BR>\n", ((float)gc->gcPpt)/10); gcPercentFree(&gc); } printTrackHtml(tdb); sqlFreeResult(&sr); hFreeConn(&conn); } void chuckHtmlStart(char *title) /* Prints the header appropriate for the title * passed in. Links html to chucks stylesheet for * easier maintaince */ { -printf("<HTML>\n<HEAD>\n"); +printf("<HTML>\n<HEAD>\n%s", getCspMetaHeader()); // FIXME blueStyle should not be absolute to genome-test and should be called by: // webIncludeResourceFile("blueStyle.css"); printf("<LINK REL=STYLESHEET TYPE=\"text/css\" href=\"http://genome-test.cse.ucsc.edu/style/blueStyle.css\" title=\"Chuck Style\">\n"); printf("<title>%s</title>\n</head><body bgcolor=\"#f3f3ff\">",title); } void chuckHtmlContactInfo() /* Writes out Chuck's email so people bother Chuck instead of Jim */ { puts("<br><br><span style='font-size:x-small;'><i>If you have comments and/or suggestions please email " "<a href=\"mailto:sugnet@cse.ucsc.edu\">sugnet@cse.ucsc.edu</a>.</span>\n"); } void abbr(char *s, char *fluff) @@ -22645,31 +22648,31 @@ char query[100]; struct dnaSeq *winDna; struct bed *bedList = NULL, *oneBed; int s, e; if (!c || !l || !r) errAbort("Bad Range"); s = atoi(l); e = atoi(r); winDna = hDnaFromSeq(database, c, s, e, dnaUpper); if (sameString(getBed, "all")) sqlSafef(query, sizeof(query), "select * from cutters"); else sqlSafef(query, sizeof(query), "select * from cutters where name=\'%s\'", getBed); cut = cutterLoadByQuery(conn, query); bedList = matchEnzymes(cut, winDna, s); -puts("<HTML>\n<HEAD><TITLE>Enzyme Output</TITLE></HEAD>\n<BODY><PRE><TT>"); +printf("<HTML>\n<HEAD>\n%s<TITLE>Enzyme Output</TITLE></HEAD>\n<BODY><PRE><TT>", getCspMetaHeader()); for (oneBed = bedList; oneBed != NULL; oneBed = oneBed->next) { freeMem(oneBed->chrom); oneBed->chrom = cloneString(c); bedTabOutN(oneBed, 6, stdout); } puts("</TT></PRE>\n"); cartFooter(); bedFreeList(&bedList); cutterFreeList(&cut); hFreeConn(&conn); exit(0); } static void doCutters(char *item) @@ -23080,33 +23083,34 @@ "tName = '%s' AND tStart = %d " "AND tEnd = %d", pslTable, chrom, start, end); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if(row != NULL) { psl = pslLoad(row+hasBin); } else { errAbort("No alignment infomation\n"); } qSeq = loadGenomePart(db, psl->qName, psl->qStart, psl->qEnd); safef(name, sizeof name, "%s in %s(%d-%d)", item,psl->qName, psl->qStart, psl->qEnd); -writeFramesetType(); -puts("<HTML>"); -printf("<HEAD>\n<TITLE>%s %dk</TITLE>\n</HEAD>\n\n", name, psl->qStart/1000); + +char title[1024]; +safef(title, sizeof title, "%s %dk", name, psl->qStart/1000); +htmlFramesetStart(title); showSomeAlignment2(psl, qSeq, gftDnaX, psl->qStart, psl->qEnd, name, item, "", psl->qStart, psl->qEnd); } void doPutaFrag(struct trackDb *tdb, char *item) /* display the potential pseudo and coding track */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row, table[256], query[256], *parts[6]; struct putaInfo *info = NULL; int start = cartInt(cart, "o"), end = cartInt(cart, "t"); char *db = cgiString("db"); char *name = cartString(cart, "i"), *chr = cartString(cart, "c"); char pslTable[256]; char otherString[256];