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/bioImage/bioImageLoad/bioImageLoad.c src/hg/bioImage/bioImageLoad/bioImageLoad.c index c2418a8..5a6e7a7 100644 --- src/hg/bioImage/bioImageLoad/bioImageLoad.c +++ src/hg/bioImage/bioImageLoad/bioImageLoad.c @@ -1,353 +1,355 @@ /* bioImageLoad - Load data into bioImage database. */ /* Copyright (C) 2013 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 "obscure.h" #include "ra.h" #include "jksql.h" #include "dystring.h" /* Variables you can override from command line. */ char *database = "bioImage"; boolean replace = FALSE; void usage() /* Explain usage and exit. */ { errAbort( "bioImageLoad - Load data into bioImage database\n" "usage:\n" " bioImageLoad setInfo.ra itemInfo.tab\n" "Please see bioImageLoad.doc for description of the .ra and .tab files\n" "Options:\n" " -database=%s - Specifically set database\n" " -replace - Replace image rather than complaining if it exists\n" , database ); } static struct optionSpec options[] = { {"database", OPTION_STRING,}, {"replace", OPTION_BOOLEAN,}, {NULL, 0}, }; struct hash *hashRowOffsets(char *line) /* Given a space-delimited line, create a hash keyed by the words in * line with values the position of the word (0 based) in line */ { struct hash *hash = hashNew(0); char *word; int wordIx = 0; while ((word = nextWord(&line)) != 0) { hashAdd(hash, word, intToPt(wordIx)); wordIx += 1; } return hash; } char *getVal(char *fieldName, struct hash *raHash, struct hash *rowHash, char **row, char *defaultVal) /* Return value in row if possible, else in ra, else in default. If no value and no default * return an error. */ { char *val = NULL; struct hashEl *hel = hashLookup(rowHash, fieldName); if (hel != NULL) { int rowIx = ptToInt(hel->val); val = row[rowIx]; } else { val = hashFindVal(raHash, fieldName); if (val == NULL) { if (defaultVal != NULL) val = defaultVal; else errAbort("Can't find value for field %s", fieldName); } } return val; } static char *requiredItemFields[] = {"fileName", "submitId"}; static char *requiredSetFields[] = {"contributor"}; static char *requiredFields[] = {"fullDir", "screenDir", "thumbDir", "taxon", "isEmbryo", "age", "bodyPart", "sliceType", "imageType", }; //static char *optionalFields[] = {"sectionSet", "sectionIx", "gene", "locusLink", "refSeq", "genbank", }; char *hashValOrDefault(struct hash *hash, char *key, char *defaultVal) /* Lookup key in hash and return value, or return default if it doesn't exist. */ { char *val = hashFindVal(hash, key); if (val == NULL) val = defaultVal; return val; } int findExactSubmissionId(struct sqlConnection *conn, char *contributors, char *publication, char *pubUrl, char *setUrl, char *itemUrl) /* Find ID of submissionSet that matches all parameters. Return 0 if none found. */ { char query[1024]; sqlSafef(query, sizeof(query), "select id from submissionSet " "where contributors = \"%s\" " "and publication = \"%s\" " "and pubUrl = '%s' and setUrl = '%s' and itemUrl = '%s'" , contributors, publication, pubUrl, setUrl, itemUrl); return sqlQuickNum(conn, query); } int findOrAddIdTable(struct sqlConnection *conn, char *table, char *field, char *value) /* Get ID associated with field.value in table. */ { char query[256]; int id; sqlSafef(query, sizeof(query), "select id from %s where %s = \"%s\"", table, field, value); id = sqlQuickNum(conn, query); if (id == 0) { sqlSafef(query, sizeof(query), "insert into %s values(default, \"%s\")", table, value); sqlUpdate(conn, query); id = sqlLastAutoId(conn); } return id; } int createSubmissionId(struct sqlConnection *conn, char *contributors, char *publication, char *pubUrl, char *setUrl, char *itemUrl) /* Add submission and contributors to database and return submission ID */ { struct slName *slNameListFromString(char *s, char delimiter); struct slName *contribList = NULL, *contrib; int submissionSetId; char query[1024]; sqlSafef(query, sizeof(query), "insert into submissionSet " "values(default, \"%s\", \"%s\", '%s', '%s', '%s')", contributors, publication, pubUrl, setUrl, itemUrl); sqlUpdate(conn, query); submissionSetId = sqlLastAutoId(conn); contribList = slNameListFromComma(contributors); for (contrib = contribList; contrib != NULL; contrib = contrib->next) { int contribId = findOrAddIdTable(conn, "contributor", "name", skipLeadingSpaces(contrib->name)); sqlSafef(query, sizeof(query), "insert into submissionContributor values(%d, %d)", submissionSetId, contribId); sqlUpdate(conn, query); } slFreeList(&contribList); return submissionSetId; } int saveSubmissionSet(struct sqlConnection *conn, struct hash *raHash) /* Create submissionSet, submissionContributor, and contributor records. */ { char *contributor = hashMustFindVal(raHash, "contributor"); char *publication = hashValOrDefault(raHash, "publication", ""); char *pubUrl = hashValOrDefault(raHash, "pubUrl", ""); char *setUrl = hashValOrDefault(raHash, "setUrl", ""); char *itemUrl = hashValOrDefault(raHash, "itemUrl", ""); int submissionId = findExactSubmissionId(conn, contributor, publication, pubUrl, setUrl, itemUrl); if (submissionId != 0) return submissionId; else return createSubmissionId(conn, contributor, publication, pubUrl, setUrl, itemUrl); } int cachedId(struct sqlConnection *conn, char *tableName, char *fieldName, struct hash *cache, char *raFieldName, struct hash *raHash, struct hash *rowHash, char **row) /* Get value for named field, and see if it exists in table. If so * return associated id, otherwise create new table entry and return * that id. */ { char *value = getVal(raFieldName, raHash, rowHash, row, ""); if (value[0] == 0) return 0; return findOrAddIdTable(conn, tableName, fieldName, value); } void bioImageLoad(char *setRaFile, char *itemTabFile) /* bioImageLoad - Load data into bioImage database. */ { struct hash *raHash = raReadSingle(setRaFile); struct hash *rowHash; struct lineFile *lf = lineFileOpen(itemTabFile, TRUE); char *line, *words[256]; struct sqlConnection *conn = sqlConnect(database); int rowSize; int submissionSetId; struct hash *fullDirHash = newHash(0); struct hash *screenDirHash = newHash(0); struct hash *thumbDirHash = newHash(0); struct hash *treatmentHash = newHash(0); struct hash *bodyPartHash = newHash(0); struct hash *sliceTypeHash = newHash(0); struct hash *imageTypeHash = newHash(0); struct hash *sectionSetHash = newHash(0); struct dyString *dy = dyStringNew(0); /* Read first line of tab file, and from it get all the field names. */ if (!lineFileNext(lf, &line, NULL)) errAbort("%s appears to be empty", lf->fileName); if (line[0] != '#') errAbort("First line of %s needs to start with #, and then contain field names", lf->fileName); rowHash = hashRowOffsets(line+1); rowSize = rowHash->elCount; if (rowSize >= ArraySize(words)) errAbort("Too many fields in %s", lf->fileName); /* Check that have all required fields */ { char *fieldName; int i; for (i=0; i<ArraySize(requiredSetFields); ++i) { fieldName = requiredSetFields[i]; if (!hashLookup(raHash, fieldName)) errAbort("Field %s is not in %s", fieldName, setRaFile); } for (i=0; i<ArraySize(requiredItemFields); ++i) { fieldName = requiredItemFields[i]; if (!hashLookup(rowHash, fieldName)) errAbort("Field %s is not in %s", fieldName, itemTabFile); } for (i=0; i<ArraySize(requiredFields); ++i) { fieldName = requiredFields[i]; if (!hashLookup(rowHash, fieldName) && !hashLookup(raHash, fieldName)) errAbort("Field %s is not in %s or %s", fieldName, setRaFile, itemTabFile); } } /* Create/find submission record. */ submissionSetId = saveSubmissionSet(conn, raHash); /* Process rest of tab file. */ while (lineFileNextRowTab(lf, words, rowSize)) { int fullDir = cachedId(conn, "location", "name", fullDirHash, "fullDir", raHash, rowHash, words); int screenDir = cachedId(conn, "location", "name", screenDirHash, "screenDir", raHash, rowHash, words); int thumbDir = cachedId(conn, "location", "name", thumbDirHash, "thumbDir", raHash, rowHash, words); int bodyPart = cachedId(conn, "bodyPart", "name", bodyPartHash, "bodyPart", raHash, rowHash, words); int sliceType = cachedId(conn, "sliceType", "name", sliceTypeHash, "sliceType", raHash, rowHash, words); int imageType = cachedId(conn, "imageType", "name", imageTypeHash, "imageType", raHash, rowHash, words); int treatment = cachedId(conn, "treatment", "conditions", treatmentHash, "treatment", raHash, rowHash, words); char *fileName = getVal("fileName", raHash, rowHash, words, NULL); char *submitId = getVal("submitId", raHash, rowHash, words, NULL); char *taxon = getVal("taxon", raHash, rowHash, words, NULL); char *isEmbryo = getVal("isEmbryo", raHash, rowHash, words, NULL); char *age = getVal("age", raHash, rowHash, words, NULL); char *sectionSet = getVal("sectionSet", raHash, rowHash, words, ""); char *sectionIx = getVal("sectionIx", raHash, rowHash, words, "0"); char *gene = getVal("gene", raHash, rowHash, words, ""); char *locusLink = getVal("locusLink", raHash, rowHash, words, ""); char *refSeq = getVal("refSeq", raHash, rowHash, words, ""); char *genbank = getVal("genbank", raHash, rowHash, words, ""); char *priority = getVal("priority", raHash, rowHash, words, "200"); int sectionId = 0; int oldId; // char *xzy = getVal("xzy", raHash, rowHash, words, xzy); if (sectionSet[0] != 0 && !sameString(sectionSet, "0")) { struct hashEl *hel = hashLookup(sectionSetHash, sectionSet); if (hel != NULL) sectionId = ptToInt(hel->val); else { - sqlUpdate(conn, NOSQLINJ "insert into sectionSet values(default)"); + dyStringClear(dy); + sqlDyStringPrintf(dy, "insert into sectionSet values(default)"); + sqlUpdate(conn, dy->string); sectionId = sqlLastAutoId(conn); hashAdd(sectionSetHash, sectionSet, intToPt(sectionId)); } } dyStringClear(dy); sqlDyStringPrintf(dy, "select id from image "); sqlDyStringPrintf(dy, "where fileName = '%s' ", fileName); sqlDyStringPrintf(dy, "and fullLocation = %d", fullDir); oldId = sqlQuickNum(conn, dy->string); if (oldId != 0) { if (replace) { dyStringClear(dy); sqlDyStringPrintf(dy, "delete from image where id = %d", oldId); sqlUpdate(conn, dy->string); } else errAbort("%s is already in database line %d of %s", fileName, lf->lineIx, lf->fileName); } dyStringClear(dy); sqlDyStringPrintf(dy, "insert into image set\n"); sqlDyStringPrintf(dy, " id = default,\n"); sqlDyStringPrintf(dy, " fileName = '%s',\n", fileName); sqlDyStringPrintf(dy, " fullLocation = %d,\n", fullDir); sqlDyStringPrintf(dy, " screenLocation = %d,\n", screenDir); sqlDyStringPrintf(dy, " thumbLocation = %d,\n", thumbDir); sqlDyStringPrintf(dy, " submissionSet = %d,\n", submissionSetId); sqlDyStringPrintf(dy, " sectionSet = %d,\n", sectionId); sqlDyStringPrintf(dy, " sectionIx = '%s',\n", sectionIx); sqlDyStringPrintf(dy, " submitId = '%s',\n", submitId); sqlDyStringPrintf(dy, " gene = '%s',\n", gene); sqlDyStringPrintf(dy, " locusLink = '%s',\n", locusLink); sqlDyStringPrintf(dy, " refSeq = '%s',\n", refSeq); sqlDyStringPrintf(dy, " genbank = '%s',\n", genbank); sqlDyStringPrintf(dy, " priority = '%s',\n", priority); sqlDyStringPrintf(dy, " taxon = '%s',\n", taxon); sqlDyStringPrintf(dy, " isEmbryo = '%s',\n", isEmbryo); sqlDyStringPrintf(dy, " age = '%s',\n", age); sqlDyStringPrintf(dy, " bodyPart = %d,\n", bodyPart); sqlDyStringPrintf(dy, " sliceType = %d,\n", sliceType); sqlDyStringPrintf(dy, " imageType = %d,\n", imageType); sqlDyStringPrintf(dy, " treatment = %d\n", treatment); sqlUpdate(conn, dy->string); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); database = optionVal("database", database); replace = optionExists("replace"); bioImageLoad(argv[1], argv[2]); return 0; }