e81403a315a24af601884b8a19e89bcecc92f267 galt Sat Dec 8 20:04:28 2018 -0800 Fixing hFindSplitTable and its use. Standard size, give real string size so no undetected overflows. Test result and abort if not found. Avoids SQL errors that otherwise will popup. Handles uninitialzed stack better for the output name. refs #22596. diff --git src/hg/hgc/wiggleClick.c src/hg/hgc/wiggleClick.c index 883d78e..423f322 100644 --- src/hg/hgc/wiggleClick.c +++ src/hg/hgc/wiggleClick.c @@ -1,280 +1,280 @@ /* Handle details pages for wiggle tracks. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "wiggle.h" #include "cart.h" #include "hgc.h" #include "hCommon.h" #include "hgColors.h" #include "obscure.h" #include "hmmstats.h" #include "customTrack.h" #include "bigWig.h" #include "hdb.h" void genericWiggleClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display details for Wiggle data tracks. * conn may be NULL for custom tracks when from file */ { char *chrom = cartString(cart, "c"); -char table[64]; -boolean hasBin; +char table[HDB_MAX_TABLE_STRING]; unsigned span = 0; struct wiggleDataStream *wds = wiggleDataStreamNew(); unsigned long long valuesMatched = 0; struct histoResult *histoGramResult; float *valuesArray = NULL; size_t valueCount = 0; struct customTrack *ct = NULL; boolean isCustom = FALSE; int operations = wigFetchStats; /* default operation */ if (startsWith("ct_", tdb->table)) { ct = lookupCt(tdb->table); if (!ct) { warn("<P>wiggleClick: can not find custom wiggle track '%s'</P>", tdb->table); return; } if (! ct->wiggle) { warn("<P>wiggleClick: called to do stats on a custom track that isn't wiggle data ?</P>"); return; } if (ct->dbTrack) { safef(table,ArraySize(table), "%s", ct->dbTableName); span = minSpan(conn, table, chrom, winStart, winEnd, cart, tdb); } else { safef(table,ArraySize(table), "%s", ct->wigFile); span = 0; /* cause all spans to be examined */ } isCustom = TRUE; } else { - hFindSplitTable(database, seqName, tdb->table, table, &hasBin); + if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, NULL)) + errAbort("track %s not found", tdb->table); /*span = spanInUse(conn, table, chrom, winStart, winEnd, cart);*/ span = minSpan(conn, table, chrom, winStart, winEnd, cart, tdb); } /* if for some reason we don't have a chrom and win positions, this * should be run in a loop that does one chrom at a time. In the * case of hgc, there seems to be a chrom and a position. */ wds->setSpanConstraint(wds, span); wds->setChromConstraint(wds, chrom); wds->setPositionConstraint(wds, winStart, winEnd); /* If our window is less than some number of points, we can do * the histogram too. */ #define MAX_WINDOW_ALLOW_STATS 100000001 #define MAX_WINDOW_ALLOW_STRING "100,000,000" if ((winEnd - winStart) < MAX_WINDOW_ALLOW_STATS) operations |= wigFetchAscii; /* We want to also fetch the actual data values so we can run a * histogram function on them. You can't fetch the data in the * form of the data array since the span information is then lost. * We have to do the ascii data list format, and prepare that to * send to the histogram function. */ if (isCustom) { if (ct->dbTrack) valuesMatched = wds->getData(wds, CUSTOM_TRASH, table, operations); else valuesMatched = wds->getData(wds, (char *)NULL, table, operations); } else valuesMatched = wds->getData(wds, database, table, operations); statsPreamble(wds, chrom, winStart, winEnd, span, valuesMatched, NULL); /* output statistics table * (+sort, +html output, +with header, +close table) */ wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE); if ((winEnd - winStart) < MAX_WINDOW_ALLOW_STATS) { char *words[16]; int wordCount = 0; char *dupe = cloneString(tdb->type); double minY, maxY, tDbMinY, tDbMaxY; float hMin, hMax, hRange; wordCount = chopLine(dupe, words); wigFetchMinMaxY(tdb, &minY, &maxY, &tDbMinY, &tDbMaxY, wordCount, words); hMin = min(minY,tDbMinY); hMax = max(maxY,tDbMaxY); hRange = hMax - hMin; /* convert the ascii data listings to one giant float array */ valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount); /* let's see if we really want to use the range from the track type * line, or the actual range in this data. If there is a good * actual range in the data, use that instead */ if (hRange > 0.0) { if (wds->stats->dataRange != 0) hRange = 0.0; } /* If we have a valid range, use a specified 20 bin histogram * NOTE: pass 21 as binCount to get a 20 bin histogram */ if (hRange > 0.0) histoGramResult = histoGram(valuesArray, valueCount, (hRange/20.0), (unsigned) 21, hMin, hMin, hMax, (struct histoResult *)NULL); else histoGramResult = histoGram(valuesArray, valueCount, NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit, (float) (wds->stats->lowerLimit + wds->stats->dataRange), (struct histoResult *)NULL); /* histoGram() may return NULL if it doesn't work, that's OK, the * print out will indicate no results (TRUE == html output) */ printHistoGram(histoGramResult, TRUE); freeHistoGram(&histoGramResult); freeMem(valuesArray); } else { printf("<P>(viewing windows of fewer than %s bases will also" " display a histogram)</P>\n", MAX_WINDOW_ALLOW_STRING); } wiggleDataStreamFree(&wds); } void bbiIntervalStatsReport(struct bbiInterval *bbList, char *table, char *chrom, bits32 start, bits32 end) /* Write out little statistical report in HTML */ { /* Loop through list and calculate some stats. */ bits64 iCount = 0; bits64 iTotalSize = 0; bits32 biggestSize = 0, smallestSize = BIGNUM; struct bbiInterval *bb; double sum = 0.0, sumSquares = 0.0; double minVal = bbList->val, maxVal = bbList->val; for (bb = bbList; bb != NULL; bb = bb->next) { iCount += 1; bits32 size = bb->end - bb->start; iTotalSize += size; if (biggestSize < size) biggestSize = size; if (smallestSize > size) smallestSize = size; double val = bb->val; sum += val; sumSquares += val * val; if (minVal > val) minVal = val; if (maxVal < val) maxVal = val; } char num1Buf[64], num2Buf[64]; /* big enough for 2^64 (and then some) */ sprintLongWithCommas(num1Buf, iCount); sprintLongWithCommas(num2Buf, iTotalSize); bits32 winSize = end-start; printf("<B>Statistics on:</B> %s <B>items covering</B> %s bases (%4.2f%% coverage)<BR>\n", num1Buf, num2Buf, 100.0*iTotalSize/winSize); printf("<B>Average item spans</B> %4.2f <B>bases.</B> ", (double)iTotalSize/iCount); if (biggestSize != smallestSize) { sprintLongWithCommas(num1Buf, smallestSize); sprintLongWithCommas(num2Buf, biggestSize); printf("<B>Minimum span</B> %s <B>maximum span</B> %s", num1Buf, num2Buf); } printf("<BR>\n"); printf("<B>Average value</B> %g <B>min</B> %g <B>max</B> %g <B> standard deviation </B> %g<BR>\n", sum/iCount, minVal, maxVal, calcStdFromSums(sum, sumSquares, iCount)); } static void bigWigClick(struct trackDb *tdb, char *fileName) /* Display details for BigWig data tracks. */ { char *chrom = cartString(cart, "c"); /* Open BigWig file and get interval list. */ struct bbiFile *bbi = NULL; struct lm *lm = lmInit(0); struct bbiInterval *bbList = NULL; char *maxWinToQuery = trackDbSettingClosestToHome(tdb, "maxWindowToQuery"); unsigned maxWTQ = 0; if (isNotEmpty(maxWinToQuery)) maxWTQ = sqlUnsigned(maxWinToQuery); if ((maxWinToQuery == NULL) || (maxWTQ > winEnd-winStart)) { bbi = bigWigFileOpen(fileName); bbList = bigWigIntervalQuery(bbi, chrom, winStart, winEnd, lm); } char num1Buf[64], num2Buf[64]; /* big enough for 2^64 (and then some) */ sprintLongWithCommas(num1Buf, BASE_1(winStart)); sprintLongWithCommas(num2Buf, winEnd); printf("<B>Position: </B> %s:%s-%s<BR>\n", chrom, num1Buf, num2Buf ); sprintLongWithCommas(num1Buf, winEnd-winStart); printf("<B>Total Bases in view: </B> %s <BR>\n", num1Buf); if (bbList != NULL) { bbiIntervalStatsReport(bbList, tdb->table, chrom, winStart, winEnd); } else if ((bbi == NULL) && (maxWTQ <= winEnd-winStart)) { sprintLongWithCommas(num1Buf, maxWTQ); printf("<P>Zoom in to a view less than %s bases to see data summary.</P>",num1Buf); } else { printf("<P>No data overlapping current position.</P>"); } lmCleanup(&lm); bbiFileClose(&bbi); } void genericBigWigClick(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display details for BigWig built in tracks. */ { char *fileName = trackDbSetting(tdb, "bigDataUrl"); if (fileName == NULL) { char query[256]; sqlSafef(query, sizeof(query), "select fileName from %s", tdb->table); fileName = sqlQuickString(conn, query); if (fileName == NULL) errAbort("Missing fileName in %s table", tdb->table); } bigWigClick(tdb, hReplaceGbdb(fileName)); // tiny memory leak } void bigWigCustomClick(struct trackDb *tdb) /* Display details for BigWig custom tracks. */ { bigWigClick(tdb, trackDbSetting(tdb, "bigDataUrl")); }