aca9143822a9c12b16b33d479a5abb6495b6b4f0 braney Wed Aug 19 06:59:39 2026 -0700 lib, hgc, hgTables, hgHubConnect: share hubEncode, refs #38123 hgc.c and hgTables.c each had their own copy of hubEncode(). The two bodies were identical, so move the function to hubConnect.c next to isHubTrack() and let both CGIs call the one definition. Also use cgiEncode() rather than htmlEncode() for the db= value in the hgHubConnect assembly list. That value goes in a query string, so cgiEncode() is the right function there. Genome names are already limited to a safe character set, so this changes no output today. diff --git src/hg/hgc/bigBedClick.c src/hg/hgc/bigBedClick.c index 581afb8d859..88c809a5325 100644 --- src/hg/hgc/bigBedClick.c +++ src/hg/hgc/bigBedClick.c @@ -1,686 +1,687 @@ /* Handle details pages for wiggle tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "wiggle.h" #include "cart.h" #include "hgc.h" +#include "hubConnect.h" #include "hCommon.h" #include "hgColors.h" #include "bigBed.h" #include "hui.h" #include "subText.h" #include "web.h" #include "chromAlias.h" #include "quickLift.h" #include "hgConfig.h" #include "jsHelper.h" #include "jsonParse.h" #include "jsonWrite.h" static void bigGenePredLinks(char *track, char *item) /* output links to genePred driven sequence dumps */ { printf("<H3>Links to sequence:</H3>\n"); printf("<UL>\n"); puts("<LI>\n"); hgcAnchorSomewhere("htcTranslatedPredMRna", item, "translate", seqName); printf("Translated Protein</A> from genomic DNA\n"); puts("</LI>\n"); puts("<LI>\n"); hgcAnchorSomewhere("htcGeneMrna", item, track, seqName); printf("Predicted mRNA</A> \n"); puts("</LI>\n"); puts("<LI>\n"); hgcAnchorSomewhere("htcGeneInGenome", item, track, seqName); printf("Genomic Sequence</A> from assembly\n"); puts("</LI>\n"); printf("</UL>\n"); } void printMismatchString(char *a, char *b) /* given two strings of same length, print . for every match and for mismatches, the letter of b */ { int i = 0; while (TRUE) { if (a[i]=='\0' || b[i]=='\0') break; if (a[i]==b[i]) printf("."); else printf("%c", (b[i])); i++; } } static void extFieldMismatchCounts(char *val) /* crispr track: number of mismatches. A comma-sep string of integers */ { printf("<tr><td>Number of potential off-targets</td>\n"); printf("<td>\n"); char *words[255]; int wordCount = chopByChar(val, ',', words, ArraySize(words)); int i; printf("<table style='border-style: hidden'><tr>\n"); for (i=0; i<wordCount; i++) printf("<td style='border:1px solid #CCCCCC; font-weight: normal; width:auto'><b>%d mismatches:</b><br>%s off-targets</td>", i, words[i]); printf("</tr></table>\n"); } static void extFieldCrisprOfftargets(char *val, struct slPair *extraFields) /* crispr track: locations of off-targets. A |-separated string of coords, including strand and a score e.g. chr15;63615585-;71|chr16;8835640+;70 */ { if (NULL == val) { printf("<br><table class='bedExtraTbl'>\n"); printf("<tr><td>Potential Off-targets</td>\n"); printf("<td>No Off-targets found for this guide</td></tr>\n"); printf("</table>\n"); return; } printf("<tr><td>Potential Off-targets</td>\n"); printf("<td>\n"); char *coords[65536]; int coordCount = chopByChar(val, '|', coords, ArraySize(coords)); int i; struct subText *subList = NULL; slSafeAddHead(&subList, subTextNew("ig:", "intergenic ")); slSafeAddHead(&subList, subTextNew("ex:", "exon ")); slSafeAddHead(&subList, subTextNew("in:", "intron ")); slSafeAddHead(&subList, subTextNew("|", "-")); boolean hasDb = sqlDatabaseExists(database); boolean hasLocus = FALSE; struct sqlConnection *conn = NULL; if (hasDb) { conn = hAllocConn(database); hasLocus = sqlTableExists(conn, "locusName"); } if (coordCount==0) puts("Too many off-targets found to display or no off-targets. Please use the Crispor.org link at the top of the page to show all off-targets.\n"); else { printf("<table style='border-collapse:collapse; font-size:12px; table-layout:fixed'>\n"); printf("<tr>\n" "<th style='width:26em'>Mismatched nucleotides</th>\n" "<th style='width:9em'>CFD Score</th>\n"); if (hasLocus) printf("<th style='width:40em'>Locus</th>\n"); printf("<th style='width:30em'>Position</th></tr>\n"); } boolean collapsed = FALSE; for (i=0; i<coordCount; i++) { if (i>10) { collapsed = TRUE; printf("<tr class='crisprLinkHidden' style='display:none'>\n"); } else printf("<tr>\n"); // parse single coordinate string // chr15;63615585-;71 = chrom;startPosStrand;scoreAsInt char *parts[3]; chopByChar(coords[i], ';', parts, 3); char* chrom = parts[0]; char* posStrand = parts[1]; char* scoreStr = parts[2]; // get score and strand char strand = *(posStrand+strlen(posStrand)-1); int pos = atol(posStrand); int scoreInt = atoi(scoreStr); float score = (float)scoreInt/1000; // get the DNA sequence - this is slow! twoBit currently does not cache // if the input is not sorted and this list is sorted by off-target score (CFD) struct dnaSeq *seq = hDnaFromSeq(database, chrom, pos, pos+23, dnaUpper); if (strand=='-') reverseComplement(seq->dna, seq->size); char *guideSeq = (char*)slPairFindVal(extraFields, "guideSeq"); // PAM = the last three chars of the off-target int seqLen = strlen(seq->dna); char *pam = seq->dna+(seqLen-3); // print sequence + PAM printf("<td><tt>"); printMismatchString(guideSeq, seq->dna); printf(" %s", pam); printf("</tt></td>\n"); // print score of off-target printf("<td>%0.3f</td>", score); // print name of this locus if (hasLocus) { struct sqlResult *sr = hRangeQuery(conn, "locusName", chrom, pos, pos+23, NULL, 0); char **row; row = sqlNextRow(sr); if (row != NULL) { char *desc = row[4]; char *descLong = subTextString(subList, desc); printf("<td>%s</td>", descLong); freeMem(descLong); } sqlFreeResult(&sr); } // print link to location printf("<td><a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d (%c)</a></td>\n", hgTracksPathAndSettings(), database, chrom, pos+1, pos+23, chrom, pos+1, strand); printf("</tr>\n"); } if (hasDb) hFreeConn(&conn); printf("<tr>\n"); if (coordCount!=0) printf("</table>\n"); if (collapsed) { printf("<p><a id='crisprShowAllLink' href='#'>" "Show all %d off-targets...</a>\n", coordCount); jsOnEventById("click", "crisprShowAllLink", "crisprShowAll(); return false;"); // inline .js is bad style but why pollute our global .js files for such a rare // case? Maybe we should have a generic "collapsible" class, like bootstrap? jsInline( "function crisprShowAll() {\n" " $('#crisprShowAllLink').hide();\n" " $('.crisprLinkHidden').show();\n" " return false;\n" "}\n" ); } } static void detailsTabPrintSpecial(char *name, char *val, struct slPair *extraFields) /* some extra fields require special printing code, they all start with '_' */ { if (sameWord(name, "_mismatchCounts")) extFieldMismatchCounts(val); else if (sameWord(name, "_crisprOfftargets")) extFieldCrisprOfftargets(val, extraFields); } static int seekAndPrintTable(struct trackDb *tdb, char *detailsUrl, off_t offset, struct slPair *extraFields) /* seek to 0 at url, get headers, then seek to offset, read tab-sep fields and output * (extraFields are needed for some special field handlers). Return the number of fields * successfully printed. */ { int printCount = 0; // open the URL and get the first line char *headerLine = readOneLineMaybeBgzip(detailsUrl, 0, 0); if (headerLine == NULL) { printf("Error: Could not open the URL referenced in detailsUrls, %s", detailsUrl); return printCount; } boolean skipEmptyFields = trackDbSettingOn(tdb, "skipEmptyFields"); // get the headers char *headers[1024]; int headerCount = chopTabs(headerLine, headers); // clone the headers int i; for (i=0; i<headerCount; i++) headers[i] = cloneString(headers[i]); // read a line char *detailsLine = readOneLineMaybeBgzip(detailsUrl, offset, 0);; if (!detailsLine || isEmpty(detailsLine)) return printCount; char *fields[1024]; int fieldCount = chopTabs(detailsLine, fields); if (fieldCount!=headerCount) { printf("Error encountered when reading %s:<br>", detailsUrl); printf("The header line of the tab-sep file has a different number of fields compared "); printf("with the line pointed to by offset %lld in the bigBed file.<br>", (long long int)offset); printf("Number of headers: %d", headerCount); printf("Number of fields at offset: %d", fieldCount); return printCount; } struct slName *tblFieldNames = NULL; struct hash *fieldsToEmbeddedTbl = hashNew(0); struct embeddedTbl *tblList = NULL; getExtraTableFields(tdb, &tblFieldNames, &tblList, fieldsToEmbeddedTbl); // print the table for all external extra fields printf("<br><table class='bedExtraTbl'>\n"); fieldCount = min(fieldCount, headerCount); struct embeddedTbl *userTbl = NULL; struct dyString *tableLabelsDy = dyStringNew(0); dyStringPrintf(tableLabelsDy, "var _jsonHgcLabels = ["); for (i=0; i<fieldCount; i++) { char *name = headers[i]; char *val = fields[i]; // skip this field if it's empty and "skipEmptyFields" option is set if (skipEmptyFields && isEmpty(val)) continue; // skip an optional '#' on the first field name if (i == 0 && startsWith("#", name)) name = skipBeyondDelimit(name, '#'); if (startsWith("_", name) && !(startsWith("_json", name)) && !(startsWith("json", name))) detailsTabPrintSpecial(name, val, extraFields); else if (slNameInList(tblFieldNames, name)) { userTbl = (struct embeddedTbl *)hashFindVal(fieldsToEmbeddedTbl, name); userTbl->encodedTbl = val; printEmbeddedTable(tdb, userTbl, tableLabelsDy); } else { // the field name and value come from the hub's bigBed when this is a hub track printFieldLabelWithId(hubEncode(tdb, name), hubEncode(tdb, name)); printf("<td>%s</td></tr>\n", hubEncode(tdb, val)); } printCount++; } printf("</table>\n"); dyStringPrintf(tableLabelsDy, "];\n"); jsInline(dyStringCannibalize(&tableLabelsDy)); return printCount; } struct slPair *parseDetailsTablUrls(struct trackDb *tdb) /* Parse detailsUrls setting string into an slPair list of {offset column name, fileOrUrl} */ { char *detailsUrlsStr = trackDbSetting(tdb, "detailsUrls"); if (!detailsUrlsStr) detailsUrlsStr = trackDbSetting(tdb, "detailsTabUrls"); if (!detailsUrlsStr) return NULL; struct slPair *detailsUrls = slPairListFromString(detailsUrlsStr, TRUE); if (!detailsUrls) { printf("Problem when parsing trackDb setting detailsUrls<br>\n"); printf("Expected: a space-separated key=val list, like 'fieldName1=URL1 fieldName2=URL2'<br>\n"); printf("But got: '%s'<br>", detailsUrlsStr); return NULL; } struct slPair *pair; for (pair = detailsUrls; pair != NULL; pair = pair->next) pair->val = hReplaceGbdb(replaceChars(pair->val, "$db", database)); return detailsUrls; } static int printAllExternalExtraFields(struct trackDb *tdb, struct slPair *extraFields) /* handle the "detailsUrls" trackDb setting: * For each field, print a separate html table with all field names and values * from the external tab-sep file. Return the number of fields we successfully printed */ { int printCount = 0; struct slPair *detailsUrls = parseDetailsTablUrls(tdb), *pair; for (pair = detailsUrls; pair != NULL; pair = pair->next) { char *fieldName = pair->name; char *detailsUrl = pair->val; // get extra bigBed field (=the offset) and seek to it void *p = slPairFindVal(extraFields, fieldName); if (p==NULL) { printf("Error when parsing trackDb detailsUrls statement:<br>\n"); printf("Cannot find extra bigBed field with name %s\n", fieldName); return 0; } char *offsetStr = (char*)p; if (offsetStr==NULL || sameWord(offsetStr, "0")) { /* need to show the empty off-targets for crispr tracks */ if (startsWith("crispr", tdb->track)) extFieldCrisprOfftargets(NULL, NULL); // empty or "0" value in bigBed means that the lookup should not be performed continue; } off_t offset = atoll(offsetStr); printCount += seekAndPrintTable(tdb, detailsUrl, offset, extraFields); } slPairFreeValsAndList(&detailsUrls); return printCount; } static struct hash *detailsScriptGroupByPlotType(struct trackDb *tdb) /* Parse detailsScript.<plotType>.<fieldName> trackDb settings and return a hash * of plotType -> slPair list (fieldName -> jsonConfig). Returns NULL if no settings found. * See also hgc.c detailsScriptFieldNames() which parses the same settings for field skipping. */ { struct slName *settings = trackDbLocalSettingsWildMatch(tdb, DETAILS_SCRIPT_PREFIX); if (settings == NULL) return NULL; struct hash *plotTypeHash = hashNew(0); struct slName *setting; for (setting = settings; setting != NULL; setting = setting->next) { // Parse "detailsScript.<plotType>.<fieldName>" char *key = cloneString(setting->name); char *dot1 = strchr(key, '.'); if (dot1 == NULL) continue; dot1++; char *dot2 = strchr(dot1, '.'); if (dot2 == NULL) continue; *dot2 = '\0'; char *plotType = dot1; if (!isSymbolString(plotType)) // plotTypes must be simple strings - no XSS injection from hub continue; char *fieldName = dot2 + 1; char *jsonConfig = trackDbSetting(tdb, setting->name); struct slPair *entry; AllocVar(entry); entry->name = cloneString(fieldName); entry->val = cloneString(jsonConfig); struct slPair *existing = hashFindVal(plotTypeHash, plotType); slAddTail(&existing, entry); if (hashLookup(plotTypeHash, plotType) == NULL) hashAdd(plotTypeHash, plotType, entry); else hashReplace(plotTypeHash, plotType, existing); } slFreeList(&settings); return plotTypeHash; } static void bigBedClick(char *fileName, struct trackDb *tdb, char *item, int start, int end, int bedSize) /* Handle click in generic bigBed track. */ { char *chrom = cartString(cart, "c"); /* Open BigWig file and get interval list. */ struct bbiFile *bbi = bigBedFileOpenAlias(fileName, chromAliasFindAliases); struct lm *lm = lmInit(0); int ivStart = start, ivEnd = end; char *itemForUrl = item; if (start == end) { // item is an insertion; expand the search range from 0 bases to 2 so we catch it: ivStart = max(0, start-1); ivEnd++; } char *quickLiftFile = cloneString(trackDbSetting(tdb, "quickLiftUrl")); struct hash *chainHash = NULL; struct bigBedInterval *bbList = NULL; if (quickLiftFile) bbList = quickLiftGetIntervals(quickLiftFile, bbi, chrom, ivStart, ivEnd, &chainHash); else bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm); /* Get bedSize if it's not already defined. */ boolean bigBedOnePath = cfgOptionBooleanDefault("bigBedOnePath", TRUE); if (bigBedOnePath && (bedSize == 0)) bedSize = bbi->definedFieldCount; char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL); int minScore = 0; if (scoreFilter) minScore = atoi(scoreFilter); /* Find particular item in list - matching start, and item if possible. */ boolean found = FALSE; boolean firstTime = TRUE; struct bigBedInterval *bb; for (bb = bbList; bb != NULL; bb = bb->next) { if (bedSize > 3) { char *name = cloneFirstWordByDelimiterNoSkip(bb->rest, '\t'); boolean match = (isEmpty(name) && isEmpty(item)) || sameOk(name, item); freez(&name); if (!match) continue; } int seq1Seq2Fields = 0; // check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign) boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2"); if (seq1Seq2 && bedSize == 6) seq1Seq2Fields = 2; char *fields[bedSize+seq1Seq2Fields]; char startBuf[16], endBuf[16]; char *rest = cloneString(bb->rest); char *restFields[256]; int restCount = 0; int restBedFields = 0; char **extraFields = NULL; int extraFieldCount = 0; struct slPair *extraFieldPairs = NULL; if (isNotEmpty(rest)) { restCount = chopTabs(rest, restFields); restBedFields = bedSize - 3; if (restCount > restBedFields) { extraFields = (restFields + restBedFields); extraFieldCount = restCount - restBedFields; extraFieldPairs = getExtraFields(tdb, extraFields, extraFieldCount); } } int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, bedSize+seq1Seq2Fields); if (bbFieldCount != bedSize+seq1Seq2Fields) { errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)", bedSize, fileName, bbFieldCount); } struct bed *bed = NULL; if (quickLiftFile) { if ((bed = quickLiftIntervalsToBed(bbi, chainHash, bb)) == NULL) continue; } else { bed = bedLoadN(fields, bedSize); } if ((bed == NULL) || (bedSize >= 6 && scoreFilter && bed->score < minScore)) continue; if (!(bed->chromStart == start && bed->chromEnd == end)) continue; found = TRUE; if (firstTime) { printf("<BR>\n"); firstTime = FALSE; } // if there are extra fields, load them up because we may want to use them in URL: itemForUrl = getIdInUrl(tdb, item); printCustomUrlWithFields(tdb, bed->name, bed->name, item == itemForUrl, extraFieldPairs); if (itemForUrl) printIframe(tdb, itemForUrl); bedPrintPos(bed, bedSize, tdb); // display seq1 and seq2 if (seq1Seq2 && bedSize+seq1Seq2Fields == 8) printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>" "<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]); else if (restCount > 0) { if (restCount > restBedFields) { int printCount = extraFieldsPrint(tdb, NULL, extraFields, extraFieldCount); printCount += printAllExternalExtraFields(tdb, extraFieldPairs); if (printCount == 0) { int i; char label[20]; safef(label, sizeof(label), "nonBedFieldsLabel"); printf("<B>%s </B>", trackDbSettingOrDefault(tdb, label, "Non-BED fields:")); for (i = restBedFields; i < restCount; i++) printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]); printf("<BR>\n"); } } if (sameString(tdb->type, "bigGenePred")) bigGenePredLinks(tdb->track, item); if (startsWith("hprcDeletions", tdb->track) || startsWith("hprcInserts", tdb->track) || startsWith("hprcArr", tdb->track)) { // the source field, which is the first item after the itemRgb will // have all the other chains // TODO: make this controlled by a trackDb setting char *oChainList[2048]; int i, numChains = chopCommas(cloneString(restFields[6]), oChainList); char *oChain = NULL; struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "var chainVis = {"); for (i = 0; i < numChains; i++) { oChain = oChainList[i]; char *cartVar = catTwoStrings("chainHprc", oChain); char *chainVis = cartOptionalString(cart, cartVar); if (chainVis == NULL) { cartVar = catTwoStrings(cartVar, "_sel"); chainVis = cartOptionalString(cart, cartVar); // TODO: this is not getting the vis right, because _sel is not the // same as a visibility } dyStringPrintf(ds, "\"%s\": \"%s\", ", oChain, chainVis != NULL ? hStringFromTv(hTvFromString(chainVis)) : "Hide"); } dyStringPrintf(ds, "};\n"); jsInline(dyStringCannibalize(&ds)); } } if (isCustomTrack(tdb->track)) { time_t timep = bbiUpdateTime(bbi); printBbiUpdateTime(&timep); } char *motifPwmTable = trackDbSetting(tdb, "motifPwmTable"); if (motifPwmTable) { struct dnaSeq *seq = hDnaFromSeq(database, bed->chrom, bed->chromStart, bed->chromEnd, dnaLower); if (bed->strand[0] == '-') reverseComplement(seq->dna, seq->size); struct dnaMotif *motif = loadDnaMotif(bed->name, motifPwmTable); motifHitSection(seq, motif); } // detailsScript.*: load JS visualization scripts and export field data as JSON // see also hgc.c detailsScriptFieldNames() which parses the same settings to skip fields struct hash *plotTypeHash = detailsScriptGroupByPlotType(tdb); if (plotTypeHash) { // Build the bedDetails JSON object using jsonWrite struct jsonWrite *jw = jsonWriteNew(); jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "track", tdb->track); jsonWriteString(jw, "chrom", chrom); jsonWriteNumber(jw, "start", bed->chromStart); jsonWriteNumber(jw, "end", bed->chromEnd); jsonWriteObjectStart(jw, "scripts"); struct hashEl *hel, *helList = hashElListHash(plotTypeHash); for (hel = helList; hel != NULL; hel = hel->next) { struct slPair *fieldList = hel->val; jsonWriteListStart(jw, hel->name); struct slPair *fp; for (fp = fieldList; fp != NULL; fp = fp->next) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "field", fp->name); // Look up field value from bigBed extra fields char *fv = ""; if (extraFieldPairs) { char *found = slPairFindVal(extraFieldPairs, fp->name); if (found) fv = found; } jsonWriteString(jw, "value", fv); // Parse trackDb JSON config and merge its keys into this object char *jsonConfig = fp->val; if (isNotEmpty(jsonConfig)) { struct jsonElement *configEl = jsonParse(jsonConfig); struct hash *configHash = jsonObjectVal(configEl, "detailsScript config"); struct hashEl *cel, *celList = hashElListHash(configHash); for (cel = celList; cel != NULL; cel = cel->next) jsonWriteJsonElement(jw, cel->name, cel->val); hashElFreeList(&celList); } jsonWriteObjectEnd(jw); } jsonWriteListEnd(jw); } jsonWriteObjectEnd(jw); // scripts jsonWriteObjectEnd(jw); // root // Emit as inline JavaScript struct dyString *ds = dyStringNew(1024); dyStringPrintf(ds, "var bedDetails = %s;\n", jw->dy->string); // Dynamically import and call each plot type's module for (hel = helList; hel != NULL; hel = hel->next) dyStringPrintf(ds, "$(document).ready(function() {\n" " import('../js/hgc.%s.js').then(function(mod) { mod.%s(bedDetails); });\n" "});\n", hel->name, hel->name); jsInline(dyStringCannibalize(&ds)); jsonWriteFree(&jw); hashElFreeList(&helList); hashFree(&plotTypeHash); } } if (!found) { printf("No item %s starting at %d\n", emptyForNull(item), start); } lmCleanup(&lm); bbiFileClose(&bbi); } void genericBigBedClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end, int bedSize) /* Handle click in generic bigBed track. */ { char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table); bigBedClick(fileName, tdb, item, start, end, bedSize); } void bigBedCustomClick(struct trackDb *tdb) /* Display details for BigWig custom tracks. */ { char *fileName = trackDbSetting(tdb, "bigDataUrl"); char *item = cartOptionalString(cart, "i"); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); bigBedClick(fileName, tdb, item, start, end, 0); }