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/gpcrParser/gpcrParser.c src/hg/gpcrParser/gpcrParser.c index bf5a882..b58e6ef 100644 --- src/hg/gpcrParser/gpcrParser.c +++ src/hg/gpcrParser/gpcrParser.c @@ -1,202 +1,202 @@ /** gpcrParser.c - Parses transmembrane cooridnates, outputs to xml file. */ /* Copyright (C) 2011 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "memalloc.h" #include "dystring.h" /** Method prototypes */ void catSeqFile(FILE* outfile, char* filename); void getTransFromFile(FILE* infile, char *path); FILE* createXMLFile(char* proteinID, char *path); void populateXMLFile(FILE *outfile, int tmNumber, char *proteinID, char *path); void addCoordinatesToXMLFile(FILE *outfile, int start, int end, char* mapTo, int count); void finishXMLFile(FILE *outfile, char *proteinID, int seqLength); void usage(char **argv); void usage(char **argv) { if(argv[1] == NULL) { errAbort( "gpcrParser - Create xml files for gpcr snakeplots.\n" "usage:\n gpcrParser TMHMMresult.htm [path]\n" " The first parameter is the html output from www.cbs.dtu.dk\n" " Path is the working directory holding the seq files needed to\n" " create the xml files. The xml files will be created in the path location.\n" " If no path location is entered, the seq files should be in your cwd\n" ); } } void catSeqFile(FILE* outfile, char* filename) /** Copies contents of one file to another file */ { FILE* infile; char* line = NULL; infile = mustOpen(filename, "r"); while( (line = readLine(infile)) != NULL ) { fprintf(outfile, "\t\t%s\n", line); freeMem(line); } carefulClose(&infile); } void finishXMLFile(FILE *outfile, char *proteinID, int seqLength) /** Add the closing lines to the file */ { fprintf(outfile, "\t\t\n</secondary-structure>\n\n\t</protein>\n\n\t<diagram>\n\n\t\t<colors>\n\n" "\t\t\t<define color=\"white\" red=\"255\" green=\"255\" blue=\"255\"/>\n\n" "\t\t\t<define color=\"red\" red=\"255\" green=\"0\" blue=\"0\"/>\n\n" "\t\t\t<color-scheme name=\"GPCRDB\">\n\n" "\t\t\t\t<residue-background color=\"white\"/>\n\n\t\t\t</color-scheme>\n\n" "\t\t\t<residue-color position=\"20\" color=\"white\"/>\n\n" "\t\t\t<residue-color position=\"21\" color=\"red\"/>\n\n" "\t\t</colors>\n\n\t\t<elipses>\n\n" "\t\t\t<exclude residueRange=\"1-%d\" />\n\n" "\t\t\t<include residueRange=\"1-1\"/>\n\n\t\t</elipses>\n\n" "\t\t<output>\n\n\t\t\t<image format=\"GIF\" filename=\"%s.gif\"/>\n\n" "\t\t\t<page template=\"H:\\dev\\crover\\nrdb\\sample-template.xsl\"" "filename=\"gpcr-rbdg-out.xml\" diagram-name=\"gpcr\"/>\n\n" "\t\t\t<image-map filename=\"%s.map\"/>\n\n\t\t</output>\n\n" "\t</diagram>\n\n</rbde-diagram>", seqLength-1, proteinID, proteinID ); } void addCoordinatesToXMLFile(FILE *outfile, int start, int end, char* mapTo, int count) /** Add each coordinate for the gpcr */ { fprintf(outfile, "\t\t\t"); if( sameString(mapTo, "TM") ) { fprintf(outfile, "<segment start=\"%d\" end=\"%d\" mapto=\"%s%d\" />\n", start, end, mapTo, count); } else { fprintf( outfile, "<segment start=\"%d\" end=\"%d\" mapto=\"%s\" />\n", start, end, mapTo ); } } void populateXMLFile(FILE *outfile, int tmNumber, char *proteinID, char *path) /** Adds the number of TM helices and sequence the the xml file */ { -struct dyString *filename = newDyString(128); +struct dyString *filename = dyStringNew(128); if(path == NULL) dyStringPrintf(filename, "%s.seq", proteinID); else dyStringPrintf(filename, "%s%s.seq", path, proteinID); fprintf(outfile, "%d\" id-prefix=\"TM\" nterm-id=\"N-term\" cterm-id=\"C-term\" direction=\"down\" />\n\n" "\t</diagram-layout>\n\n\t<protein>\n\n\t\t<name>%s</name>\n\n\t\t<residue-codes>\n\n", tmNumber, proteinID ); catSeqFile(outfile, filename->string); fprintf(outfile, "\n\n\t\t</residue-codes>\n\n\t\t<secondary-structure>\n\n"); -freeDyString(&filename); +dyStringFree(&filename); } FILE* createXMLFile(char* proteinID, char *path) { FILE* outfile; -struct dyString *filename = newDyString(128); +struct dyString *filename = dyStringNew(128); if(path == NULL) dyStringPrintf(filename, "%s.xml", proteinID); else dyStringPrintf(filename, "%s%s.xml", path, proteinID); outfile = mustOpen(filename->string, "w"); fprintf(outfile, "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n\n" "<rbde-diagram xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"" " xsi:noNamespaceSchemaLocation=\"H:\\dev\\crover\\xml\\xsd\\residue-based-diagram.xsd\">\n\n" "\t<diagram-layout>\n\n\t\t<tm-bundle tm-number=\"" ); -freeDyString(&filename); +dyStringFree(&filename); return outfile; } void getTransFromFile(FILE* infile, char *path) { FILE* outfile = NULL; int start, end, tmNumber, count, seqLength; char *line, *token; -struct dyString *proteinID = newDyString(24); +struct dyString *proteinID = dyStringNew(24); start = end = tmNumber = count = seqLength = 0; while( ( line = readLine(infile) ) != NULL ) { /*grab the protein ID after each <PRE> tag*/ while( (token = nextWord(&line)) != NULL ) { if( sameString(token,"<PRE>#")) { /*create a new xml file*/ token = nextWord(&line); dyStringAppend(proteinID, token); token = lastWordInLine(line); seqLength = atoi(token); } if( sameString(token,"predicted") ) { /*grab the number of transmembrane helices*/ token = lastWordInLine(line); tmNumber = atoi(token); if(tmNumber > 0) { outfile = createXMLFile(proteinID->string, path); populateXMLFile(outfile, tmNumber, proteinID->string, path); } } if( sameString(token,"</PRE>") ) { /*close the xml file*/ carefulClose(&outfile); dyStringClear(proteinID); count = 0; } if( sameString(token,"TMhelix") ) { if( (token = nextWord(&line)) != NULL ) { /*get the start*/ start = atoi(token); if( (token = nextWord(&line)) != NULL ) end = atoi(token); } if( count == 0) addCoordinatesToXMLFile(outfile, 1, start-1, "N-term", count); count++; addCoordinatesToXMLFile(outfile, start, end, "TM", count); if( count == tmNumber && outfile != NULL ) { addCoordinatesToXMLFile(outfile,end+1,seqLength,"C-term",count); finishXMLFile(outfile, proteinID->string, seqLength); } } } /*end inner while*/ } /*end outer while*/ freeMem(line); - freeDyString(&proteinID); + dyStringFree(&proteinID); } int main(int argc, char** argv) { FILE *infile; -struct dyString *path = newDyString(128); +struct dyString *path = dyStringNew(128); usage(argv); if(argv[2] != NULL) { dyStringAppend(path, argv[2]); if(!endsWith(path->string, "/")) dyStringAppend(path, "/"); } infile = mustOpen(argv[1], "r"); getTransFromFile(infile, path->string); carefulClose(&infile); -freeDyString(&path); +dyStringFree(&path); return 0; }