44ccfacbe3a3d4b300f80d48651c77837a4b571e galt Tue Apr 26 11:12:02 2022 -0700 SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix. diff --git src/hg/encode3/eap/eapAddStep/eapAddStep.c src/hg/encode3/eap/eapAddStep/eapAddStep.c index e719d36..34f0fe5 100644 --- src/hg/encode3/eap/eapAddStep/eapAddStep.c +++ src/hg/encode3/eap/eapAddStep/eapAddStep.c @@ -1,321 +1,321 @@ /* eapAddStep - Add a step to eapStep and related tables. This is just a small shortcut for doing it in SQL. You can only add steps defined in C code.. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dystring.h" #include "jksql.h" #include "eapDb.h" #include "eapLib.h" #include "intValTree.h" boolean clList = FALSE; void usage() /* Explain usage and exit. */ { errAbort( "eapAddStep - Add a step to eapStep and related tables. This is just a small shortcut for doing it in SQL. You can only add steps defined in C code.\n" "usage:\n" " eapAddStep stepName\n" "The step name can be a quoted pattern as well as in\n" " eapAddStep '*'\n" "to get them all.\n" "options:\n" " -list - Just list steps matching stepName pattern\n" ); } /* Command line validation table. */ static struct optionSpec options[] = { {"list", OPTION_BOOLEAN}, {NULL, 0}, }; struct stepInit /* Just stuff to help initialize a step */ { char *name; /* Name of step, should be same ase first software name */ int cpusRequested; /* # of cpus requested from job control system */ char *description; /* Sentence long description of step */ char *software; /* Comma separated list of software names. First one gives name to step. */ char *inputTypes; char *inputFormats; /* Comma separated list of input formats */ char *inputDescriptions; /* Comma separated list of input descriptions. */ char *outputTypes; char *outputFormats;/* Comma separated list of formats */ char *outputNamesInTempDir; /* Comma separated list of file names in temp dir */ char *outputDescriptions; /* Comma separated list of input descriptions. */ }; struct stepInit steps[] = { { "bwa_single_end", 2, // name and CPUs "Align single ended fastq with bwa to produce BAM sorted by genome position", // Description "eap_run_bwa_se,bwa,samtools", // software "reads", "fastq", // input names and formats "Reads in Sanger fastq format", // input description "alignments", "bam", "out.bam", // output names, formats, and file names "Alignments in BAM format sorted by genomic position including random pick of multi-aligners" }, { "bwa_paired_end", 2, "Align paired end fastqs with bwa to produce BAM sorted by genome position", // Description "eap_run_bwa_pe,bwa,samtools", "reads1,reads2", "fastq,fastq", "Forward direction reads in Sanger fastq format," // input description "Reverse direction reads in Sanger fastq format", "alignments", "bam", "out.bam", "Alignments in BAM format sorted by genomic position including random pick of multi-aligners" }, { "macs2_dnase_se", 1, "Call peaks and generate signal plot from a single ended DNAse bam file using Macs2", "eap_run_macs2_dnase_se,macs2,bedToBigBed,bedGraphToBigWig", "alignments", "bam", "Alignments of single end reads in bam format", "macs2_dnase_peaks,macs2_dnase_signal", "narrowPeak,bigWig", "out.narrowPeak.bigBed,out.bigWig", "Narrow peak calls from Macs2,Base-by-base signal graph from macs2" }, { "macs2_dnase_pe", 1, "Call peaks and generate signal plot from a paired end DNAse bam file using Macs2", "eap_run_macs2_dnase_pe,macs2,bedToBigBed,bedGraphToBigWig", "Alignments of paired end reads in bam format", "alignments", "bam", "macs2_dnase_peaks,macs2_dnase_signal", "narrowPeak,bigWig", "out.narrowPeak.bigBed,out.bigWig", "Narrow peak calls from Macs2,Base-by-base signal graph from macs2" }, { "hotspot", 1, "Call hotspots, peaks, and generate a signal plot from DNAse bam file using hotspot", "eap_run_hotspot,hotspot.py,edwBamFilter,starch,unstarch,hotspot,bedtools,eap_broadPeak_to_bigBed,eap_narrowPeak_to_bigBed,bedToBigBed,bedGraphToBigWig,bedmap,bedGraphPack", "alignments", "bam", "Alignments of reads with cuts on 5-prime ends in bam format", "hotspot_broad_peaks,hotspot_narrow_peaks,hotspot_signal", "broadPeak,narrowPeak,bigWig", "out.broadPeak.bigBed,out.narrowPeak.bigBed,out.bigWig", "Hotspot calls,Peak calls from hotspot,Base-by-base signal graph from hotspot" }, { "macs2_chip_se", 1, "Generate peaks and signal for single ended ChIP-seq BAM files from IP and control using Macs2", "eap_run_macs2_chip_se,macs2,bedToBigBed,bedGraphToBigWig", "chipBam,controlBam", "bam,bam", "Alignments of single end reads from IP,Alignments of single end reads from control", "macs2_chip_peaks,macs2_chip_signal", "narrowPeak,bigWig", "out.narrowPeak.bigBed,out.bigWig", "Narrow peak calls from Macs2,Base-by-base signal graph from macs2" }, { "macs2_chip_pe", 1, "Generate peaks and signal for paired end ChIP-seq BAM files from IP and control using Macs2", "eap_run_macs2_chip_pe,macs2,bedToBigBed,bedGraphToBigWig", "chipBam,controlBam", "bam,bam", "Alignments of paired end reads from IP,Alignments of paired end reads from control", "macs2_chip_peaks,macs2_chip_signal", "narrowPeak,bigWig", "out.narrowPeak.bigBed,out.bigWig", "Narrow peak calls from Macs2,Base-by-base signal graph from macs2" }, { "spp_chip_se", 1, "Generate peaks single end ChIP-seq BAM files from IP and control using SPP", "eap_run_spp_chip_se,Rscript,bedToBigBed", "chipBam,controlBam", "bam,bam", "Alignments of single end reads from IP,Alignments of single end reads from control", "spp_chip_peaks", "narrowPeak", "out.narrowPeak.bigBed", "Narrow peak calls from SPP" }, { "sum_bigWig", 1, "Add together signals from multiple bigWigs producing a bigWig for the sum", "eap_pool_big_wig,bigWigMerge,bedGraphPack,bedGraphToBigWig", "signal", "bigWig", "List of bigWig files", "pooled_signal", "bigWig", "out.bigWig", "Sum of inputs signals" }, { "replicated_hotspot", 1, "Pool together two replicates and run hotspot on them", "eap_pool_hotspot,eap_run_hotspot,edwBamFilter,hotspot.py,starch,unstarch,hotspot,bedtools,eap_broadPeak_to_bigBed,eap_narrowPeak_to_bigBed,bedToBigBed,bedGraphToBigWig,bedmap,bedGraphPack", "alignments", "bam", "Alignments in bam format", "hotspot_broad_peaks,hotspot_narrow_peaks,hotspot_signal", "broadPeak,narrowPeak,bigWig", "out.broadPeak.bigBed,out.narrowPeak.bigBed,out.bigWig", "Hotspot calls,Peak calls from hotspot,Base-by-base signal graph from hotspot" }, { "phantom_peak_stats", 1, "Run the phantom peaks stats tools to calculate RSC and NSC among other things.", "eap_run_phantom_peak_spp,Rscript", "alignments", "bam", "Alignments from some sort of peaky data set in BAM format", "", "", "", "", }, { "dnase_stats", 1, "Subsample bam file to 5M mapped reads, run hotspot, and collect a bunch of statistics.", "eap_dnase_stats,edwBamStats,bigBedToBed,edwBamFilter,bigWigAverageOverBed,eap_run_phantom_peak_spp,Rscript,eap_run_hotspot,hotspot.py,starch,unstarch,hotspot,bedtools,eap_broadPeak_to_bigBed,eap_narrowPeak_to_bigBed,bedToBigBed,bedGraphToBigWig,bedmap,bedGraphPack", "alignments", "bam", "Alignments from a DNAse hypersensitivity assay in BAM format", "", "", "", "", }, }; int commaSepCount(char *s) /* Count number of comma-separated items assuming there can be a terminal non-separating comma * or not. */ { if (isEmpty(s)) return 0; int commaCount = countChars(s, ','); int sepCount = commaCount; char lastC = lastChar(s); if (lastC == ',') --sepCount; return sepCount + 1; } void initStep(struct sqlConnection *conn, struct stepInit *init) /* Create step based on initializer */ { /* Do a little validation on while counting up inputs and outputs */ int inCount = commaSepCount(init->inputTypes); int matchCount = commaSepCount(init->inputFormats); if (inCount != matchCount) errAbort("inputTypes has %d elements but inputFormats has %d in step %s", inCount, matchCount, init->name); matchCount = commaSepCount(init->inputDescriptions); if (inCount != matchCount) errAbort("inputTypes has %d elements but inputDescriptions has %d in step %s", inCount, matchCount, init->name); int outCount = commaSepCount(init->outputTypes); matchCount = commaSepCount(init->outputFormats); if (outCount != matchCount) errAbort("outputTypes has %d elements but outputFormats has %d in step %s", outCount, matchCount, init->name); matchCount = commaSepCount(init->outputNamesInTempDir); if (outCount != matchCount) errAbort("outputTypes has %d elements but outputNamesInTempDir has %d in step %s", outCount, matchCount, init->name); matchCount = commaSepCount(init->outputDescriptions); if (outCount != matchCount) errAbort("outputTypes has %d elements but outputDescriptions has %d in step %s", outCount, matchCount, init->name); struct dyString *query = dyStringNew(0); -dyStringPrintf(query, "select count(*) from eapStep where name='%s'", init->name); +sqlDyStringPrintf(query, "select count(*) from eapStep where name='%s'", init->name); int existingCount = sqlQuickNum(conn, query->string); if (existingCount > 0) { warn("%s already exists in eapStep", init->name); dyStringFree(&query); return; } /* Parse out software part and make sure that all pieces are there. */ char **softwareArray; int softwareCount; sqlStringDynamicArray(init->software, &softwareArray, &softwareCount); unsigned softwareIds[softwareCount]; int i; for (i=0; i<softwareCount; ++i) { char *name = softwareArray[i]; dyStringClear(query); - dyStringPrintf(query, "select id from eapSoftware where name='%s'", name); + sqlDyStringPrintf(query, "select id from eapSoftware where name='%s'", name); unsigned softwareId = sqlQuickNum(conn, query->string); if (softwareId == 0) errAbort("Software %s doesn't exist by that name in eapSoftware", name); softwareIds[i] = softwareId; } /* Make step record. */ dyStringClear(query); -dyStringAppend(query, +sqlDyStringPrintf(query, "insert eapStep (name,cpusRequested,description," " inCount,inputTypes,inputFormats,inputDescriptions," " outCount,outputNamesInTempDir,outputTypes,outputFormats,outputDescriptions)" " values ("); -dyStringPrintf(query, "'%s',", init->name); -dyStringPrintf(query, "%d,", init->cpusRequested); -dyStringPrintf(query, "\"%s\",", init->description); -dyStringPrintf(query, "%d,", inCount); -dyStringPrintf(query, "'%s',", init->inputTypes); -dyStringPrintf(query, "'%s',", init->inputFormats); -dyStringPrintf(query, "\"%s\",", init->inputDescriptions); -dyStringPrintf(query, "%d,", outCount); -dyStringPrintf(query, "'%s',", init->outputNamesInTempDir); -dyStringPrintf(query, "'%s',", init->outputTypes); -dyStringPrintf(query, "'%s',", init->outputFormats); -dyStringPrintf(query, "\"%s\"", init->outputDescriptions); -dyStringPrintf(query, ")"); +sqlDyStringPrintf(query, "'%s',", init->name); +sqlDyStringPrintf(query, "%d,", init->cpusRequested); +sqlDyStringPrintf(query, "\"%s\",", init->description); +sqlDyStringPrintf(query, "%d,", inCount); +sqlDyStringPrintf(query, "'%s',", init->inputTypes); +sqlDyStringPrintf(query, "'%s',", init->inputFormats); +sqlDyStringPrintf(query, "\"%s\",", init->inputDescriptions); +sqlDyStringPrintf(query, "%d,", outCount); +sqlDyStringPrintf(query, "'%s',", init->outputNamesInTempDir); +sqlDyStringPrintf(query, "'%s',", init->outputTypes); +sqlDyStringPrintf(query, "'%s',", init->outputFormats); +sqlDyStringPrintf(query, "\"%s\"", init->outputDescriptions); +sqlDyStringPrintf(query, ")"); sqlUpdate(conn, query->string); /* Make software/step associations. */ for (i=0; i<softwareCount; ++i) { dyStringClear(query); - dyStringPrintf(query, "insert eapStepSoftware (step,software) values ('%s','%s')", + sqlDyStringPrintf(query, "insert eapStepSoftware (step,software) values ('%s','%s')", init->name, softwareArray[i]); sqlUpdate(conn, query->string); } /* Force step version stuff to be made right away */ eapCurrentStepVersion(conn, init->name); /* Clean up. */ dyStringFree(&query); freez(&softwareArray[0]); freez(&softwareArray); } void eapAddStep(char *pattern) /* eapAddStep - Add a step to eapStep and related tables. This is just a small shortcut for doing * it in SQL. You can only add steps defined in C code.. */ { struct sqlConnection *conn = eapConnectReadWrite(); int i; for (i=0; i<ArraySize(steps); ++i) { struct stepInit *init = &steps[i]; if (wildMatch(pattern, init->name)) { if (clList) puts(init->name); else initStep(conn, init); } } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 2) usage(); clList = optionExists("list"); eapAddStep(argv[1]); return 0; }