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/makeDb/outside/hgFlyBase/hgFlyBase.c src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c index c1bdda8..6745f8f 100644 --- src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c +++ src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c @@ -1,620 +1,630 @@ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* hgFlyBase - Parse FlyBase genes.txt file and turn it into a couple of * tables. See http://flybase.org/.data/docs/refman/refman-B.html for a * description of these files. We don't try too hard to extract and * normalize every piece of data here, just the particularly valuable parts * we can't find elsewhere. In particular we want to get information on * wild-type function, phenotypes, and synonyms. * * Flybase records are separated by a line with a '#'. The fields * are line separated and each begin with a two character code that * defines the line type. Most fields start with '*' and a letter. * The first field is always '*a' and contains the gene symbol. * A particularly important and complex field is the '*E' field. * This describes a literature reference and data derived from it. * Subfields of the *E field start with % instead of * and are followed * by a single letter which means the same as when the field is * standalone. * * The '*A' field, indicating an allele, is also important and * constains subfields. This subfields start with '$'. If an * *A field has a $E subfield, the $E's sub-sub-fields start with * a '&'. * * From this we want to extract the following field types: * z - flybase ID * a - gene symbol * d - biological role of gene product * e - gene name * f - cellular compartment of which gene product is a component * i - synonyms (just for genes, not for alleles) * r - wild-type biological role * p - phenotypes of genes * A - allele with subfields * E - reference with subfields * F - function of gene product * * We'll make this into the following tables: * fbGene <flybase ID><gene symbol><gene name> * fbSynonym <flybase ID><synonom> (This includes gene symbol and name) * fbAllele <allele ID><flybase ID><allele name> * fbRef <reference ID><text> (These are not cleaned up from flybase) * fbRole <flybase ID><allele ID><reference ID><text> * The allele or reference ID's may be zero indicating * the annotation belongs the gene as a whole or flybase * respectively. * fbPhenotype <flybase ID><allele ID><reference ID><text> * fbGo <flybase ID><go ID><go aspect> * Note that we are ignoring the GO terms since we'll get them * from SwissProt, where the data is in a somewhat more regular * format. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dystring.h" #include "portable.h" #include "hdb.h" #include "hgRelate.h" char *tabDir = "."; boolean doLoad; char *geneTable = "bdgpGene"; boolean doTranscript = TRUE; void usage() /* Explain usage and exit. */ { errAbort( "hgFlyBase - Parse FlyBase genes.txt file and turn it into a couple of tables\n" "usage:\n" " hgFlyBase database genes.txt\n" "options:\n" " -geneTable=tbl - Use tbl instead of default %s\n" " -tab=dir - Output tab-separated files to directory.\n" " -noLoad - If true don't load database and don't clean up tab files\n" , geneTable ); } static struct optionSpec options[] = { {"tab", OPTION_STRING}, {"noLoad", OPTION_BOOLEAN}, {"geneTable", OPTION_STRING}, {NULL, 0}, }; char *ungreekTable[] = { "agr", "alpha", "bgr", "beta", "dgr", "delta", "egr", "epsilon", "eegr", "eta", "ggr", "gamma", "igr", "iota", "ohgr", "omega", "thgr", "theta", "zgr", "zeta", }; char *hideTagTable[] = { "up", "/up", "down", "/down", }; char *spelledGreek(char *abbr) /* Convert from 'agr;' to 'alpha' or return NULL */ { int i; for (i=0; i<ArraySize(ungreekTable); i += 2) if (sameWord(ungreekTable[i], abbr)) return ungreekTable[i+1]; return NULL; } char *ungreek(char *s) /* Get rid of greek characters and unwanted tags. */ { -struct dyString *dy = newDyString(0); +struct dyString *dy = dyStringNew(0); char *result; char c; while ((c = *s++) != 0) { boolean special = FALSE; if (c == '&') { char *e = strchr(s, ';'); if (e != NULL) { int size = e - s; if (size <= 4) { char abbr[5]; char *english; memcpy(abbr, s, size); abbr[size] = 0; english = spelledGreek(abbr); if (english != NULL) { dyStringAppend(dy, english); special = TRUE; s = e+1; if (s[0] == '\'') ++s; } } } } else if (c == '<') { char *e = strchr(s, '>'); if (e != NULL) { int size = e - s; if (size < 8) { int i; char tag[8]; memcpy(tag, s, size); tag[size] = 0; for (i=0; i<ArraySize(hideTagTable); ++i) { if (sameWord(tag, hideTagTable[i])) { special = TRUE; s = e+1; break; } } } } } if (!special) dyStringAppendC(dy, c); } result = cloneString(dy->string); dyStringFree(&dy); return result; } struct dyString *suckSameLines(struct lineFile *lf, char *line) /* Suck up lines concatenating as long as they begin with the same * first two characters as initial line. */ { struct dyString *dy = dyStringNew(0); char c1 = line[0], c2 = line[1]; dyStringAppend(dy, line+3); while (lineFileNext(lf, &line, NULL)) { if (line[0] != c1 || line[1] != c2) { lineFileReuse(lf); break; } dyStringAppend(dy, line+2); } return dy; } struct ref /* Keep track of reference. */ { int id; /* Reference ID. */ }; void remakeTables(struct sqlConnection *conn) /* Remake all our tables. */ { -sqlRemakeTable(conn, "fbGene", +char query[1024]; +sqlSafef(query, sizeof query, "#Links FlyBase IDs, gene symbols and gene names\n" -NOSQLINJ "CREATE TABLE fbGene (\n" +"CREATE TABLE fbGene (\n" " geneId varchar(255) not null, # FlyBase ID\n" " geneSym varchar(255) not null, # Short gene symbol\n" " geneName varchar(255) not null, # Gene name - up to a couple of words\n" " #Indices\n" " PRIMARY KEY(geneId(11)),\n" " INDEX(geneSym(8)),\n" " INDEX(geneName(12))\n" ")\n"); +sqlRemakeTable(conn, "fbGene", query); -sqlRemakeTable(conn, "fbTranscript", +sqlSafef(query, sizeof query, "#Links FlyBase gene IDs and BDGP transcripts\n" -NOSQLINJ "CREATE TABLE fbTranscript (\n" +"CREATE TABLE fbTranscript (\n" " geneId varchar(255) not null, # FlyBase ID\n" " transcriptId varchar(255) not null, # BDGP Transcript ID\n" " #Indices\n" " PRIMARY KEY(transcriptId(11)),\n" " INDEX(transcriptId(11))\n" ")\n"); +sqlRemakeTable(conn, "fbTranscript", query); -sqlRemakeTable(conn, "fbSynonym", +sqlSafef(query, sizeof query, "#Links all the names we call a gene to it's flybase ID\n" -NOSQLINJ "CREATE TABLE fbSynonym (\n" +"CREATE TABLE fbSynonym (\n" " geneId varchar(255) not null, # FlyBase ID\n" " name varchar(255) not null, # A name (synonym or real\n" " #Indices\n" " INDEX(geneId(11)),\n" " INDEX(name(12))\n" ")\n"); +sqlRemakeTable(conn, "fbSynonym", query); -sqlRemakeTable(conn, "fbAllele", +sqlSafef(query, sizeof query, "#The alleles of a gene\n" -NOSQLINJ "CREATE TABLE fbAllele (\n" +"CREATE TABLE fbAllele (\n" " id int not null, # Allele ID\n" " geneId varchar(255) not null, # Flybase ID of gene\n" " name varchar(255) not null, # Allele name\n" " #Indices\n" " PRIMARY KEY(id),\n" " INDEX(geneId(11))\n" ")\n"); +sqlRemakeTable(conn, "fbAllele", query); -sqlRemakeTable(conn, "fbRef", +sqlSafef(query, sizeof query, "#A literature or sometimes database reference\n" -NOSQLINJ "CREATE TABLE fbRef (\n" +"CREATE TABLE fbRef (\n" " id int not null, # Reference ID\n" " text longblob not null, # Usually begins with flybase ref ID, but not always\n" " #Indices\n" " PRIMARY KEY(id)\n" ")\n"); +sqlRemakeTable(conn, "fbRef", query); -sqlRemakeTable(conn, "fbRole", +sqlSafef(query, sizeof query, "#Role of gene in wildType\n" -NOSQLINJ "CREATE TABLE fbRole (\n" +"CREATE TABLE fbRole (\n" " geneId varchar(255) not null, # Flybase Gene ID\n" " fbAllele int not null, # ID in fbAllele table or 0 if not allele-specific\n" " fbRef int not null, # ID in fbRef table\n" " text longblob not null, # Descriptive text\n" " #Indices\n" " INDEX(geneId(11))\n" ")\n"); +sqlRemakeTable(conn, "fbRole", query); -sqlRemakeTable(conn, "fbPhenotype", +sqlSafef(query, sizeof query, "#Observed phenotype in mutant. Sometimes contains gene function info\n" -NOSQLINJ "CREATE TABLE fbPhenotype (\n" +"CREATE TABLE fbPhenotype (\n" " geneId varchar(255) not null, # Flybase Gene ID\n" " fbAllele int not null, # ID in fbAllele table or 0 if not allele-specific\n" " fbRef int not null, # ID in fbRef table\n" " text longblob not null, # Descriptive text\n" " #Indices\n" " INDEX(geneId(11))\n" ")\n"); +sqlRemakeTable(conn, "fbPhenotype", query); -sqlRemakeTable(conn, "fbGo", +sqlSafef(query, sizeof query, "#Links FlyBase gene IDs and GO IDs/aspects\n" -NOSQLINJ "CREATE TABLE fbGo (\n" +"CREATE TABLE fbGo (\n" " geneId varchar(255) not null, # FlyBase ID\n" " goId varchar(255) not null, # GO ID\n" " aspect varchar(255) not null, # P (process), F (function) or C (cellular component)" " #Indices\n" " INDEX(geneId(11)),\n" " INDEX(goId(10))\n" ")\n"); +sqlRemakeTable(conn, "fbGo", query); -sqlRemakeTable(conn, "fbUniProt", +sqlSafef(query, sizeof query, "#Links FlyBase gene IDs and UniProt IDs/aspects\n" -NOSQLINJ "CREATE TABLE fbUniProt (\n" +"CREATE TABLE fbUniProt (\n" " geneId varchar(255) not null, # FlyBase ID\n" " uniProtId varchar(255) not null, # UniProt ID\n" " #Indices\n" " INDEX(geneId(11)),\n" " INDEX(uniProtId(6))\n" ")\n"); +sqlRemakeTable(conn, "fbUniProt", query); } struct geneAlt /* Gene and list of isoforms. */ { struct geneAlt *next; char *fbName; /* Flybase gene name. */ char *bdgpName; /* BDGP Gene name. */ struct slName *isoformList; /* List of BDGP isoforms. */ }; void getAllSplices(char *database, FILE *f) /* Write out table linking flybase genes with BDGP transcripts -- * unfortunately bdgpGeneInfo lacks -R* transcript/isoform identifiers, * so strip those off of bdgpGene.name. * This is not necessary with flyBaseGene/flyBase2004Xref where -R*'s * are preserved. */ { struct sqlConnection *conn = sqlConnect(database); struct sqlResult *sr; char query[256], **row; struct geneAlt *altList = NULL, *alt; struct hash *bdgpHash = newHash(16); /* Keyed by bdgp gene id. */ struct slName *n; /* First build up list of all genes with flybase and bdgp ids. */ sqlSafef(query, sizeof(query), "select bdgpName,flyBaseId from bdgpGeneInfo"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(alt); alt->bdgpName = cloneString(row[0]); alt->fbName = cloneString(row[1]); slAddHead(&altList, alt); hashAdd(bdgpHash, alt->bdgpName, alt); } sqlFreeResult(&sr); slReverse(&altList); /* Now associate splicing variants. */ sqlSafef(query, sizeof(query), "select name from %s", geneTable); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *s = row[0]; char *e = rStringIn("-R", s); int size = e ? (e - s) : strlen(s); char bdgpGene[16]; if (size >= sizeof(bdgpGene)) errAbort("'%s' too big", s); memcpy(bdgpGene, s, size); bdgpGene[size] = 0; alt = hashMustFindVal(bdgpHash, bdgpGene); n = slNameNew(s); slAddTail(&alt->isoformList, n); } sqlFreeResult(&sr); sqlDisconnect(&conn); for (alt = altList; alt != NULL; alt = alt->next) { for (n = alt->isoformList; n != NULL; n = n->next) fprintf(f, "%s\t%s\n", alt->fbName, n->name); } freeHash(&bdgpHash); } void hgFlyBase(char *database, char *genesFile) /* hgFlyBase - Parse FlyBase genes.txt file and turn it into a couple of * tables. */ { char *tGene = "fbGene"; char *tSynonym = "fbSynonym"; char *tAllele = "fbAllele"; char *tRef = "fbRef"; char *tRole = "fbRole"; char *tPhenotype = "fbPhenotype"; char *tTranscript = "fbTranscript"; char *tGo = "fbGo"; char *tUniProt = "fbUniProt"; FILE *fGene = hgCreateTabFile(tabDir, tGene); FILE *fSynonym = hgCreateTabFile(tabDir, tSynonym); FILE *fAllele = hgCreateTabFile(tabDir, tAllele); FILE *fRef = hgCreateTabFile(tabDir, tRef); FILE *fRole = hgCreateTabFile(tabDir, tRole); FILE *fPhenotype = hgCreateTabFile(tabDir, tPhenotype); FILE *fTranscript = NULL; FILE *fGo = hgCreateTabFile(tabDir, tGo); FILE *fUniProt = hgCreateTabFile(tabDir, tUniProt); struct lineFile *lf = lineFileOpen(genesFile, TRUE); struct hash *refHash = newHash(19); int nextRefId = 0; int nextAlleleId = 0; char *line, sub, type, *rest, *s; char *geneSym = NULL, *geneName = NULL, *geneId = NULL; int recordCount = 0; struct slName *synList = NULL, *syn; int curAllele = 0, curRef = 0; struct ref *ref = NULL; struct sqlConnection *conn; struct hash *goUniqHash = newHash(18); /* Make table from flybase genes to BGDP transcripts. */ if (doTranscript) { fTranscript = hgCreateTabFile(tabDir, tTranscript); getAllSplices(database, fTranscript); } /* Make dummy reference for flybase itself. */ fprintf(fRef, "0\tFlyBase\n"); /* Loop through parsing and writing tab files. */ while (lineFileNext(lf, &line, NULL)) { sub = line[0]; if (sub == '#') { /* End of record. */ ++recordCount; if (geneId == NULL) errAbort("Record without *z line ending line %d of %s", lf->lineIx, lf->fileName); /* Write out synonyms. */ s = naForNull(geneSym); geneSym = ungreek(s); freeMem(s); s = naForNull(geneName); geneName = ungreek(s); if (! sameString(s, "n/a")) freeMem(s); if (geneSym != NULL && !sameString(geneSym, "n/a")) slNameStore(&synList, geneSym); if (geneName != NULL && !sameString(geneName, "n/a")) slNameStore(&synList, geneName); for (syn = synList; syn != NULL; syn = syn->next) { s = ungreek(syn->name); fprintf(fSynonym, "%s\t%s\n", geneId, s); freeMem(s); } /* Write out gene record. */ fprintf(fGene, "%s\t%s\t%s\n", geneId, geneSym, geneName); /* Clean up. */ freez(&geneSym); freez(&geneName); freez(&geneId); slFreeList(&synList); ref = NULL; curRef = curAllele = 0; continue; } else if (sub == 0) errAbort("blank line %d of %s, not allowed in gene.txt", lf->lineIx, lf->fileName); else if (isalnum(sub)) errAbort("line %d of %s begins with %c, not allowed", lf->lineIx, lf->fileName, sub); type = line[1]; rest = trimSpaces(line+2); if (sub == '*' && type == 'a') geneSym = cloneString(rest); else if (sub == '*' && type == 'e') geneName = cloneString(rest); else if (sub == '*' && type == 'z') { geneId = cloneString(rest); if (!startsWith("FBgn", geneId)) errAbort("Bad FlyBase gene ID %s line %d of %s", geneId, lf->lineIx, lf->fileName); } else if (type == 'i' && (sub == '*' || sub == '$')) { if (strlen(rest) > 2) /* Avoid short useless ones. */ slNameStore(&synList, rest); } else if (sub == '*' && type == 'A') { if (geneId == NULL) errAbort("Allele before geneId line %d of %s", lf->lineIx, lf->fileName); curAllele = ++nextAlleleId; fprintf(fAllele, "%d\t%s\t%s\n", curAllele, geneId, rest); if (!sameString(rest, "classical") && !sameString(rest, "in vitro") && !sameString(rest, "wild-type") ) { slNameStore(&synList, rest); } } else if (sub == '*' && type == 'm') { if (geneId == NULL) errAbort("*m protein ID before geneId line %d of %s", lf->lineIx, lf->fileName); if (startsWith("UniProt", rest)) { char *ptr = strchr(rest, ':'); if (ptr != NULL) ptr++; else errAbort("Trouble parsing UniProt ID %s like %d of %s", rest, lf->lineIx, lf->fileName); fprintf(fUniProt, "%s\t%s\n", geneId, ptr); } } else if (type == 'E') { ref = hashFindVal(refHash, rest); if (ref == NULL) { AllocVar(ref); ref->id = ++nextRefId; hashAdd(refHash, rest, ref); subChar(rest, '\t', ' '); fprintf(fRef, "%d\t%s\n", ref->id, rest); } curRef = ref->id; } else if ((type == 'k' || type == 'r' || type == 'p') && sub != '@') { FILE *f = (type == 'r' ? fRole : fPhenotype); struct dyString *dy = suckSameLines(lf, line); subChar(dy->string, '\t', ' '); if (geneId == NULL) errAbort("Expecting *z in record before line %d of %s", lf->lineIx, lf->fileName); fprintf(f, "%s\t%d\t%d\t%s\n", geneId, curAllele, curRef, dy->string); dyStringFree(&dy); } else if (type == 'd' || type == 'f' || type == 'F') { FILE *f = fGo; char aspect = (type == 'd') ? 'P' : (type == 'f') ? 'C' : 'F'; char *goId = rest; char *p = strstr(goId, " ; "); char assoc[128]; if (p == NULL) continue; else goId = firstWordInLine(p + 3); safef(assoc, sizeof(assoc), "%s.%s", geneId, goId); if (hashLookup(goUniqHash, assoc) == NULL) { hashAddInt(goUniqHash, assoc, 1); fprintf(f, "%s\t%s\t%c\n", geneId, goId, aspect); } } } printf("Processed %d records in %d lines\n", recordCount, lf->lineIx); lineFileClose(&lf); conn = sqlConnect(database); remakeTables(conn); if (doLoad) { printf("Loading %s\n", tGene); hgLoadTabFile(conn, tabDir, tGene, &fGene); if (doTranscript) { printf("Loading %s\n", tTranscript); hgLoadTabFile(conn, tabDir, tTranscript, &fTranscript); } printf("Loading %s\n", tSynonym); hgLoadTabFile(conn, tabDir, tSynonym, &fSynonym); printf("Loading %s\n", tAllele); hgLoadTabFile(conn, tabDir, tAllele, &fAllele); printf("Loading %s\n", tRef); hgLoadTabFile(conn, tabDir, tRef, &fRef); printf("Loading %s\n", tRole); hgLoadTabFile(conn, tabDir, tRole, &fRole); printf("Loading %s\n", tPhenotype); hgLoadTabFile(conn, tabDir, tPhenotype, &fPhenotype); printf("Loading %s\n", tGo); hgLoadTabFile(conn, tabDir, tGo, &fGo); printf("Loading %s\n", tUniProt); hgLoadTabFile(conn, tabDir, tUniProt, &fUniProt); hgRemoveTabFile(tabDir, tGene); if (doTranscript) hgRemoveTabFile(tabDir, tTranscript); hgRemoveTabFile(tabDir, tSynonym); hgRemoveTabFile(tabDir, tAllele); hgRemoveTabFile(tabDir, tRef); hgRemoveTabFile(tabDir, tRole); hgRemoveTabFile(tabDir, tPhenotype); hgRemoveTabFile(tabDir, tGo); hgRemoveTabFile(tabDir, tUniProt); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); doLoad = !optionExists("noLoad"); if (optionExists("tab")) { tabDir = optionVal("tab", tabDir); makeDir(tabDir); } geneTable = optionVal("geneTable", geneTable); doTranscript = sameString(geneTable, "bdgpGene"); hgFlyBase(argv[1], argv[2]); return 0; }