080a160c7b9595d516c9c70e83689a09b60839d0 galt Mon Jun 3 12:16:53 2013 -0700 fix SQL Injection diff --git src/hg/inc/rnaHybridization.h src/hg/inc/rnaHybridization.h index 30e53ef..47315d8 100644 --- src/hg/inc/rnaHybridization.h +++ src/hg/inc/rnaHybridization.h @@ -1,109 +1,98 @@ /* rnaHybridization.h was originally generated by the autoSql program, which also * generated rnaHybridization.c and rnaHybridization.sql. This header links the database and * the RAM representation of objects. */ #ifndef RNAHYBRIDIZATION_H #define RNAHYBRIDIZATION_H #ifndef JKSQL_H #include "jksql.h" #endif #define RNAHYBRIDIZATION_NUM_COLS 20 struct rnaHybridization /* perfect hybridizations on RNA level */ { struct rnaHybridization *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position in chromosome for pattern region */ unsigned chromEnd; /* End position in chromosome for pattern region */ char *name; /* match name */ unsigned dummy; /* dummy field to align with bed 6 structure */ char strand[2]; /* strand for pattern region */ char *chromTarget; /* Reference sequence chromosome for target region */ unsigned chromStartTarget; /* Start position in chromosome for target region */ unsigned chromEndTarget; /* End position in chromosome for target region */ char strandTarget[2]; /* strand for target region */ char *refSeqTarget; /* refSeq gene name for target or empty */ char *aorfTarget; /* AORF gene name for target or empty */ char *igenicsTarget; /* intergenics name for target or empty */ char *trnaTarget; /* */ char *JGITarget; /* */ char *patternSeq; /* Sequence of pattern region 5'-3' */ char *targetSeq; /* Sequence of target region 3'-5' */ float gcContent; /* GC content ranging from 0 to 1 */ unsigned matchLength; /* Length of hybridization site */ unsigned targetAnnotation; /* 1 if target is annotated on same strand, zero otherwise */ }; void rnaHybridizationStaticLoad(char **row, struct rnaHybridization *ret); /* Load a row from rnaHybridization table into ret. The contents of ret will * be replaced at the next call to this function. */ struct rnaHybridization *rnaHybridizationLoad(char **row); /* Load a rnaHybridization from row fetched with select * from rnaHybridization * from database. Dispose of this with rnaHybridizationFree(). */ struct rnaHybridization *rnaHybridizationLoadAll(char *fileName); /* Load all rnaHybridization from whitespace-separated file. * Dispose of this with rnaHybridizationFreeList(). */ struct rnaHybridization *rnaHybridizationLoadAllByChar(char *fileName, char chopper); /* Load all rnaHybridization from chopper separated file. * Dispose of this with rnaHybridizationFreeList(). */ #define rnaHybridizationLoadAllByTab(a) rnaHybridizationLoadAllByChar(a, '\t'); /* Load all rnaHybridization from tab separated file. * Dispose of this with rnaHybridizationFreeList(). */ struct rnaHybridization *rnaHybridizationLoadByQuery(struct sqlConnection *conn, char *query); /* Load all rnaHybridization from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with rnaHybridizationFreeList(). */ void rnaHybridizationSaveToDb(struct sqlConnection *conn, struct rnaHybridization *el, char *tableName, int updateSize); /* Save rnaHybridization as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are - * inserted as NULL. Note that strings must be escaped to allow insertion into the database. - * For example "autosql's features include" --> "autosql\'s features include" - * If worried about this use rnaHybridizationSaveToDbEscaped() */ - -void rnaHybridizationSaveToDbEscaped(struct sqlConnection *conn, struct rnaHybridization *el, char *tableName, int updateSize); -/* Save rnaHybridization as a row to the table specified by tableName. - * As blob fields may be arbitrary size updateSize specifies the approx size. - * of a string that would contain the entire query. Automatically - * escapes all simple strings (not arrays of string) but may be slower than rnaHybridizationSaveToDb(). - * For example automatically copies and converts: - * "autosql's features include" --> "autosql\'s features include" - * before inserting into database. */ + * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ struct rnaHybridization *rnaHybridizationCommaIn(char **pS, struct rnaHybridization *ret); /* Create a rnaHybridization out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new rnaHybridization */ void rnaHybridizationFree(struct rnaHybridization **pEl); /* Free a single dynamically allocated rnaHybridization such as created * with rnaHybridizationLoad(). */ void rnaHybridizationFreeList(struct rnaHybridization **pList); /* Free a list of dynamically allocated rnaHybridization's */ void rnaHybridizationOutput(struct rnaHybridization *el, FILE *f, char sep, char lastSep); /* Print out rnaHybridization. Separate fields with sep. Follow last field with lastSep. */ #define rnaHybridizationTabOut(el,f) rnaHybridizationOutput(el,f,'\t','\n'); /* Print out rnaHybridization as a line in a tab-separated file. */ #define rnaHybridizationCommaOut(el,f) rnaHybridizationOutput(el,f,',',','); /* Print out rnaHybridization as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* RNAHYBRIDIZATION_H */