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/dbRIP.c src/hg/hgc/dbRIP.c index 8a90938..cbc819d 100644 --- src/hg/hgc/dbRIP.c +++ src/hg/hgc/dbRIP.c @@ -1,230 +1,231 @@ /* Handle details pages for dbRIP tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "hgc.h" #include "hui.h" #include "obscure.h" #include "cheapcgi.h" #include "htmshell.h" #include "dbRIP.h" #include "polyGenotype.h" static int sortEthnicGroup(const void *e1, const void *e2) /* used by slSort to sort the polyGenotype in order of ethnic group name */ { const struct polyGenotype *p1 = *((struct polyGenotype**)e1); const struct polyGenotype *p2 = *((struct polyGenotype**)e2); return(strcmp(p1->ethnicGroup, p2->ethnicGroup)); } static void polyTable(char *name) { struct sqlConnection *conn = hAllocConn(database); char query[256]; struct sqlResult *sr; char **row; struct polyGenotype *pgList = NULL; sqlSafef(query, sizeof query, "select * from polyGenotype where name = '%s'", name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct polyGenotype *pg; AllocVar(pg); pg = polyGenotypeLoad(row); slAddHead(&pgList, pg); } sqlFreeResult(&sr); hFreeConn(&conn); if (slCount(pgList) > 0) { struct polyGenotype *pg; int totalPlusPlus = 0; int totalPlusMinus = 0; int totalMinusMinus = 0; int totalSamples = 0; double alleleFrequency = 0.0; double unbiasedHeterozygosity = 0.0; int sampleSize = 0; int plusAlleles = 0; int minusAlleles = 0; slSort(&pgList,sortEthnicGroup); printf("<B>Polymorphism Frequencies and Genotypes:</B><BR>\n"); /* This surrounding table avoids the problem of the border lines of * the second table go missing. Something about the style sheet ... */ printf("<TABLE BGCOLOR=\"#FFFEE8\" CELLPADDING=0><TR><TD>\n"); printf("<TABLE BORDER=2 bgcolor=\"#e4cdf2\">\n"); printf("<TR bgcolor=\"#d2abf2\"><TH align=center>Ethnic Group</TH>"); printf("<TH align=center>Sample Size</TH>"); printf("<TH align=center>Allele Frequency</TH>"); printf("<TH align=center>+/+</TH>"); printf("<TH align=center>+/-</TH>"); printf("<TH align=center>-/-</TH>"); printf("<TH align=center>Unbiased Heterozygosity</TH>"); printf("</TR>\n"); for (pg = pgList; pg != NULL; pg = pg->next) { plusAlleles = (pg->plusPlus << 1) + pg->plusMinus; minusAlleles = (pg->minusMinus << 1) + pg->plusMinus; sampleSize = pg->plusPlus + pg->plusMinus + pg->minusMinus; if ((plusAlleles + minusAlleles) > 0) { alleleFrequency = (double)plusAlleles / (double)(plusAlleles + minusAlleles); } else alleleFrequency = 0.0; printf("<TR><TD align=left>%s</TD>", pg->ethnicGroup); printf("<TD align=center>%d</TD>", sampleSize); printf("<TD align=center>%.3f</TD>", alleleFrequency); printf("<TD align=center>%d</TD>", pg->plusPlus); printf("<TD align=center>%d</TD>", pg->plusMinus); printf("<TD align=center>%d</TD>", pg->minusMinus); /* adjust by 2N/(2N-1) for small sample heterozygosity calculation * http://www.genetics.org/cgi/content/abstract/89/3/583 * Masatoshi Nei (1978) */ if (sampleSize > 0) { unbiasedHeterozygosity=2*alleleFrequency*(1.0 - alleleFrequency); unbiasedHeterozygosity *= (double)(sampleSize << 1) / (double)((sampleSize << 1) - 1); } else unbiasedHeterozygosity=2*alleleFrequency*(1.0 - alleleFrequency); printf("<TD align=center>%.3f</TD>", unbiasedHeterozygosity); printf("</TR>\n"); totalSamples += sampleSize; totalPlusPlus += pg->plusPlus; totalMinusMinus += pg->minusMinus; totalPlusMinus += pg->plusMinus; } plusAlleles = (totalPlusPlus << 1) + totalPlusMinus; minusAlleles = (totalMinusMinus << 1) + totalPlusMinus; if ((plusAlleles + minusAlleles) > 0) { alleleFrequency = (double)plusAlleles / (double)(plusAlleles + minusAlleles); } else { alleleFrequency = 0.0; } printf("<TR><TH align=left>All Samples</TH>"); printf("<TH align=center>%d</TH>", totalSamples); printf("<TH align=center>%.3f</TH>", alleleFrequency); printf("<TH align=center>%d</TH>", totalPlusPlus); printf("<TH align=center>%d</TH>", totalPlusMinus); printf("<TH align=center>%d</TH>", totalMinusMinus); if (totalSamples > 0) { unbiasedHeterozygosity = 2 * alleleFrequency * (1.0 - alleleFrequency); unbiasedHeterozygosity *= (double)(totalSamples << 1)/(double)((totalSamples << 1) - 1); } else unbiasedHeterozygosity = 2 * alleleFrequency * (1.0 - alleleFrequency); printf("<TH align=center>%.3f</TH>", unbiasedHeterozygosity); printf("</TR>\n"); printf("</TABLE>\n"); printf("</TD></TR></TABLE>\n"); } else printf("<B>Polymorphism Frequencies and Genotypes:</B> NA<BR>\n"); } void dbRIP(struct trackDb *tdb, char *item, char *itemForUrl) /* Put up dbRIP track info */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; -char table[64]; +char table[HDB_MAX_TABLE_STRING]; boolean hasBin; struct dbRIP *loadItem; struct dyString *query = newDyString(512); char **row; boolean firstTime = TRUE; int start = cartInt(cart, "o"); int itemCount = 0; genericHeader(tdb, item); -hFindSplitTable(database, seqName, tdb->table, table, &hasBin); +if (!hFindSplitTable(database, seqName, tdb->table, table, sizeof table, &hasBin)) + errAbort("track %s not found", tdb->table); sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ", table, seqName); hAddBinToQuery(winStart, winEnd, query); sqlDyStringPrintf(query, "name = '%s' and chromStart = %d", item, start); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else htmlHorizontalLine(); ++itemCount; loadItem = dbRIPLoad(row+hasBin); printf("<B>Database ID:</B> %s<BR>\n", loadItem->name); printf("<B>Original ID:</B> %s<BR>\n", loadItem->originalId); printf("<B>Class:</B> %s<BR>\n", loadItem->polyClass); printf("<B>Family:</B> %s<BR>\n", loadItem->polyFamily); printf("<B>Subfamily:</B> %s<BR>\n", loadItem->polySubfamily); printf("<B>Associated Disease:</B> %s<BR>\n", loadItem->disease); printf("<B>Sequence of L1 insertion and 400bp flanking on each side:</B>"); printf("(<span style='color:blue;'>5' flanking-</span>"); // ' = ' printf("<span style='color:green;'><span style='text-decoration:underline;'>"); printf("TSD1</span>-</span><span style='color:red'>REPEAT SEQUENCE</span>"); printf("<span style='color:green;'>-<span style='text-decoration:underline;'>"); printf("TSD2</span>-</span><span style='color:blue;'>3' flanking</span>)<br>"); // ' = ' printf("(\"<span style='color:green; text-decoration:underline;'>nnnnn</span>\""); printf(" --> unknown TSD; \"<span style='color:red;'>NNNNNNNNNN</span>\" -->"); printf(" unknown Repeat Sequence):<BR>\n<PRE><span style='color:blue;'>%s", loadItem->polySeq); printf("</span></PRE><BR>\n"); printf("<B>Forward Primer:</B> %s<BR>\n", loadItem->forwardPrimer); printf("<B>Reverse Primer:</B> %s<BR>\n", loadItem->reversePrimer); if (loadItem->tm > 0.0) printf("<B>Annealing Temperature:</B> %.1f °C.<BR>\n", loadItem->tm); else printf("<B>Annealing Temperature:</B> NA<BR>\n"); if (loadItem->filledSize > 0) printf("<B>PCR Product Size (Filled):</B> %d bp.<BR>\n", loadItem->filledSize); else printf("<B>PCR Product Size (Filled):</B> NA<BR>\n"); if (loadItem->emptySize > 0) printf("<B>PCR Product Size (Empty):</B> %d bp.<BR>\n", loadItem->emptySize); else printf("<B>PCR Product Size (Empty):</B> NA<BR>\n"); printf("<B>Ascertaining Method:</B> %s<BR>\n", loadItem->ascertainingMethod); printf("<B>Insertion found in reference sequence:</B> %s<BR>\n", startsWith("UCSC",loadItem->polySource) ? "yes" : "no"); printf("<B>Remarks:</B> %s<BR>\n", loadItem->remarks); if (strlen(loadItem->genoRegion) > 0) printf("<B>Gene Context:</B> %s<BR>\n", loadItem->genoRegion); else printf("<B>Gene Context:</B> NA<BR>\n"); polyTable(loadItem->name); printPosOnChrom(loadItem->chrom, loadItem->chromStart, loadItem->chromEnd, loadItem->strand, TRUE, loadItem->name); printf("<HR>\n<B>Reference(s):</B> %s\n<HR>\n", loadItem->reference); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); }