080a160c7b9595d516c9c70e83689a09b60839d0 galt Mon Jun 3 12:16:53 2013 -0700 fix SQL Injection diff --git src/hg/hgc/peakClusters.c src/hg/hgc/peakClusters.c index 0ed1775..960acaa 100644 --- src/hg/hgc/peakClusters.c +++ src/hg/hgc/peakClusters.c @@ -109,34 +109,34 @@ webPrintLinkCellStart(); struct trackDb *tdb = hashFindVal(trackHash, table); if (tdb == NULL) printf("%s info n/a", table); else compositeMetadataToggle(database, tdb, "metadata", TRUE, FALSE); webPrintLinkCellEnd(); } static void queryInputTrackTable(struct dyString *query, char *inputTrackTable, struct slName *fieldList) /* Construct query in dyString to return contents of inputTrackTable ordered appropriately */ { struct dyString *fields = dyStringNew(0); struct slName *field; -dyStringPrintf(query, "select tableName "); +sqlDyStringPrintf(query, "select tableName "); for (field = fieldList; field != NULL; field = field->next) - dyStringPrintf(fields, ",%s", field->name); -dyStringPrintf(query, "%s from %s", fields->string, inputTrackTable); + sqlDyStringPrintfFrag(fields, ",%s", field->name); +sqlDyStringPrintf(query, "%-s from %s", fields->string, inputTrackTable); if (fieldList != NULL) // skip leading comma dyStringPrintf(query, " order by %s", fields->string+1); dyStringFree(&fields); } static void printPeakClusterTableHits(struct bed *cluster, struct sqlConnection *conn, char *inputTrackTable, struct slName *fieldList, char *vocab) /* Put out a lines in an html table that shows assayed sources that have hits in this * cluster, or if invert is set, that have misses. */ { char *vocabFile = NULL; struct hash *vocabHash = NULL; if (vocab) { @@ -208,38 +208,38 @@ static void printFactorSourceTableHits(struct bed *cluster, struct sqlConnection *conn, char *sourceTable, char *inputTrackTable, struct slName *fieldList, boolean invert, char *vocab) /* Put out a lines in an html table that shows assayed sources that have hits in this * cluster, or if invert is set, that have misses. */ { char *vocabFile = NULL; if (vocab) { vocabFile = cloneFirstWord(vocab); } /* Make the monster SQL query to get all assays*/ struct dyString *query = dyStringNew(0); -dyStringPrintf(query, "select %s.id,%s.name,%s.tableName", sourceTable, sourceTable, +sqlDyStringPrintf(query, "select %s.id,%s.name,%s.tableName", sourceTable, sourceTable, inputTrackTable); struct slName *field; for (field = fieldList; field != NULL; field = field->next) - dyStringPrintf(query, ",%s.%s", inputTrackTable, field->name); -dyStringPrintf(query, " from %s,%s ", inputTrackTable, sourceTable); -dyStringPrintf(query, " where %s.source = %s.description", inputTrackTable, sourceTable); -dyStringPrintf(query, " and factor='%s' order by %s.source", cluster->name, inputTrackTable); + sqlDyStringPrintf(query, ",%s.%s", inputTrackTable, field->name); +sqlDyStringPrintf(query, " from %s,%s ", inputTrackTable, sourceTable); +sqlDyStringPrintf(query, " where %s.source = %s.description", inputTrackTable, sourceTable); +sqlDyStringPrintf(query, " and factor='%s' order by %s.source", cluster->name, inputTrackTable); int displayNo = 0; int fieldCount = slCount(fieldList); struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) { int sourceId = sqlUnsigned(row[0]); double signal = cluster->expScores[sourceId]; boolean hit = (signal > 0); if (hit ^ invert) { printf("\n"); webPrintIntCell(++displayNo); if (!invert) @@ -292,52 +292,52 @@ } void doPeakClusters(struct trackDb *tdb, char *item) /* Display detailed info about a cluster of peaks from other tracks. */ { int start = cartInt(cart, "o"); char *table = tdb->table; int rowOffset = hOffsetPastBin(database, seqName, table); char query[256]; struct sqlResult *sr; char **row; struct bed *cluster = NULL; struct sqlConnection *conn = hAllocConn(database); cartWebStart(cart, database, "%s item details", tdb->shortLabel); -safef(query, sizeof(query), +sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) cluster = bedLoadN(row + rowOffset, 5); sqlFreeResult(&sr); if (cluster != NULL) { /* Get list of subgroups to display */ char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay"); if (inputTableFieldDisplay != NULL) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); char *vocab = trackDbSetting(tdb, "controlledVocabulary"); char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); /* Print out some information about the cluster overall. */ printf("Items in Cluster: %s of %d
\n", cluster->name, - sqlRowCount(conn, inputTrackTable)); + sqlRowCount(conn, sqlCheckTableName(inputTrackTable))); printf("Cluster Score (out of 1000): %d
\n", cluster->score); printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); /* In a new section put up list of hits. */ webNewSection("List of Items in Cluster"); webPrintLinkTableStart(); printClusterTableHeader(fieldList, FALSE, FALSE, TRUE); printPeakClusterTableHits(cluster, conn, inputTrackTable, fieldList, vocab); } else errAbort("Missing required trackDb setting %s for track %s", "inputTableFieldDisplay", tdb->track); webPrintLinkTableEnd(); } printf("", hgcPathAndSettings(), @@ -350,55 +350,55 @@ hFreeConn(&conn); } void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start) /* Display detailed info about a cluster of peaks from other tracks. */ { int rowOffset = hOffsetPastBin(database, seqName, tdb->table); char **row; struct sqlResult *sr; char query[256]; char *motifTable = NULL; #ifdef TXCLUSTER_MOTIFS_TABLE motifTable = TXCLUSTER_MOTIFS_TABLE; #endif -safef(query, sizeof(query), +sqlSafef(query, sizeof(query), "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d", tdb->table, item, seqName, start); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); struct bed *cluster = NULL; if (row != NULL) cluster = bedLoadN(row + rowOffset, 15); sqlFreeResult(&sr); if (cluster != NULL) { char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); struct dnaMotif *motif = NULL; struct dnaSeq **seqs = NULL; struct bed6FloatScore *hits = NULL; if(motifTable != NULL && sqlTableExists(conn, motifTable)) { struct sqlResult *sr; int rowOffset; char where[256]; motif = loadDnaMotif(item, "transRegCodeMotif"); - safef(where, sizeof(where), "name = '%s'", item); + sqlSafefFrag(where, sizeof(where), "name = '%s'", item); sr = hRangeQuery(conn, "wgEncodeRegTfbsClusteredMotifs", cluster->chrom, cluster->chromStart, cluster->chromEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { struct bed6FloatScore *hit = NULL; AllocVar(hit); hit->chromStart = sqlUnsigned(row[rowOffset + 1]); hit->chromEnd = sqlUnsigned(row[rowOffset + 2]); hit->score = sqlFloat(row[rowOffset + 4]); hit->strand[0] = row[rowOffset + 5][0]; slAddHead(&hits, hit); } sqlFreeResult(&sr); } @@ -409,61 +409,61 @@ char *file = cloneFirstWord(vocab); factorLink = controlledVocabLink(file, "term", factorLink, factorLink, factorLink, ""); } printf("Factor: %s
\n", factorLink); printf("Cluster Score (out of 1000): %d
\n", cluster->score); if(motif != NULL && hits != NULL) { struct bed6FloatScore *hit = NULL; int i; seqs = needMem(sizeof(struct dnaSeq *) * slCount(hits)); for (hit = hits, i = 0; hit != NULL; hit = hit->next, i++) { char query[256]; float maxScore = -1; - safef(query, sizeof(query), + sqlSafef(query, sizeof(query), "select max(score) from %s where name = '%s'", "wgEncodeRegTfbsClusteredMotifs", item); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if(!isEmpty(row[0])) { maxScore = sqlFloat(row[0]); } } sqlFreeResult(&sr); struct dnaSeq *seq = hDnaFromSeq(database, seqName, hit->chromStart, hit->chromEnd, dnaLower); if(hit->strand[0] == '-') reverseComplement(seq->dna, seq->size); seqs[i] = seq; printf("Motif Score #%d: %.2f (max: %.2f)
\n", i + 1, hit->score, maxScore); } } printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL); if(seqs != NULL) { motifMultipleHitsSection(seqs, slCount(hits), motif); } /* Get list of tracks we'll look through for input. */ char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable"); - safef(query, sizeof(query), + sqlSafef(query, sizeof(query), "select tableName from %s where factor='%s' order by source", inputTrackTable, cluster->name); /* Next do the lists of hits and misses. We have the hits from the non-zero signals in * cluster->expScores. We need to figure out the sources actually assayed though * some other way. We'll do this by one of two techniques. */ char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay"); if (inputTableFieldDisplay != NULL) { struct slName *fieldList = stringToSlNames(inputTableFieldDisplay); char *vocab = trackDbSetting(tdb, "controlledVocabulary"); /* In a new section put up list of hits. */ webNewSection("List of %s Items in Cluster", cluster->name); webPrintLinkTableStart();