/* encodeExp.h was originally generated by the autoSql program, which also * generated encodeExp.c and encodeExp.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef ENCODEEXP_H #define ENCODEEXP_H #include "jksql.h" #define ENCODEEXP_NUM_COLS 8 struct encodeExp /* ENCODE experiments */ { struct encodeExp *next; /* Next in singly linked list. */ unsigned ix; /* auto-increment ID */ char *organism; /* human or mouse */ char *lab; /* lab name from ENCODE cv.ra */ char *dataType; /* dataType from ENCODE cv.ra */ char *cellType; /* cellType from ENCODE cv.ra */ char *expVars; /* var=value list of experiment-defining variables. May be NULL if none. */ char *accession; /* wgEncodeE[H|M]00000N or NULL if proposed but not yet approved */ char *updateTime; /* auto-update timestamp */ }; void encodeExpStaticLoad(char **row, struct encodeExp *ret); /* Load a row from encodeExp table into ret. The contents of ret will * be replaced at the next call to this function. */ struct encodeExp *encodeExpLoadByQuery(struct sqlConnection *conn, char *query); /* Load all encodeExp 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 encodeExpFreeList(). */ void encodeExpSaveToDb(struct sqlConnection *conn, struct encodeExp *el, char *tableName, int updateSize); /* Save encodeExp 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. Strings are automatically escaped to allow insertion into the database. */ struct encodeExp *encodeExpLoad(char **row); /* Load a encodeExp from row fetched with select * from encodeExp * from database. Dispose of this with encodeExpFree(). */ struct encodeExp *encodeExpLoadAll(char *fileName); /* Load all encodeExp from whitespace-separated file. * Dispose of this with encodeExpFreeList(). */ struct encodeExp *encodeExpLoadAllByChar(char *fileName, char chopper); /* Load all encodeExp from chopper separated file. * Dispose of this with encodeExpFreeList(). */ #define encodeExpLoadAllByTab(a) encodeExpLoadAllByChar(a, '\t'); /* Load all encodeExp from tab separated file. * Dispose of this with encodeExpFreeList(). */ struct encodeExp *encodeExpCommaIn(char **pS, struct encodeExp *ret); /* Create a encodeExp out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new encodeExp */ void encodeExpFree(struct encodeExp **pEl); /* Free a single dynamically allocated encodeExp such as created * with encodeExpLoad(). */ void encodeExpFreeList(struct encodeExp **pList); /* Free a list of dynamically allocated encodeExp's */ void encodeExpOutput(struct encodeExp *el, FILE *f, char sep, char lastSep); /* Print out encodeExp. Separate fields with sep. Follow last field with lastSep. */ #define encodeExpTabOut(el,f) encodeExpOutput(el,f,'\t','\n'); /* Print out encodeExp as a line in a tab-separated file. */ #define encodeExpCommaOut(el,f) encodeExpOutput(el,f,',',','); /* Print out encodeExp as a comma separated list including final comma. */ void encodeExpJsonOutput(struct encodeExp *el, FILE *f); /* Print out encodeExp in JSON format. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #include "mdb.h" /* WARNING: When schema is changed, encodeExp.c will need changes as well */ #define ENCODE_EXP_FIELD_IX "ix" #define ENCODE_EXP_FIELD_ORGANISM "organism" #define ENCODE_EXP_FIELD_LAB "lab" #define ENCODE_EXP_FIELD_DATA_TYPE "dataType" #define ENCODE_EXP_FIELD_CELL_TYPE "cellType" #define ENCODE_EXP_FIELD_FACTORS "expVars" #define ENCODE_EXP_FIELD_ACCESSION "accession" #define ENCODE_EXP_FIELD_UPDATE_TIME "updateTime" #define ENCODE_EXP_ORGANISM_HUMAN "human" #define ENCODE_EXP_ORGANISM_MOUSE "mouse" #define ENCODE_EXP_NO_CELL "None" #define ENCODE_EXP_NO_VAR "None" #define ENCODE_EXP_TABLE "encodeExp" #define ENCODE_EXP_DATABASE "hgFixed" #define ENCODE_EXP_ACC_PREFIX "wgEncodeE" #define ENCODE_EXP_TABLE_LOCK "lock_encodeExp" #define ENCODE_EXP_IX_UNDEFINED 0 #define ENCODE_EXP_HISTORY_TABLE_SUFFIX "History" void encodeExpJson(struct dyString *json, struct encodeExp *el); /* Print out encodeExp in JSON format. Manually converted from autoSql which outputs * to file pointer. */ int encodeExpIdMax(struct sqlConnection *conn); /* Return largest ix value */ void encodeExpFieldIndex(char *fieldName); /* Get column number of named field in EncodeExp schema */ void encodeExpTableCreate(struct sqlConnection *conn, char *table); /* Create an encodeExp table and history */ void encodeExpTableDrop(struct sqlConnection *conn, char *tableName); /* Drop an encodeExp table and history */ void encodeExpTableRename(struct sqlConnection *conn, char *tableName, char *newTableName); /* Rename table and history table, updating triggers to match */ void encodeExpTableCopy(struct sqlConnection *conn, char *tableName, char *newTableName); /* Copy table and history table, updating triggers */ struct encodeExp *encodeExpLoadAllFromTable(struct sqlConnection *conn, char *table); /* Load all encodeExp in table */ struct encodeExp *encodeExpFromMdb(struct sqlConnection *conn,char *db, struct mdbObj *mdb); /* Create an encodeExp from an ENCODE metaDb object */ struct encodeExp *encodeExpFromMdbVars(char *db, struct mdbVar *vars); // Creates and returns an encodeExp struct from mdbVars, but does not .touch the table // Only Experiment Defining Variables should be in the list. struct encodeExp *encodeExpFromRa(struct hash *ra); /* Load an encodeExp from a Ra hash */ struct hash *encodeExpToRaFile(struct encodeExp *exp, FILE *f); /* Create a Ra hash from an encodeExp. Print to file if non NULL */ struct hash *encodeExpToRa(struct encodeExp *exp); /* Create a Ra hash from an encodeExp */ boolean encodeExpSame(struct encodeExp *exp, struct encodeExp *exp2); /* Return TRUE if two experiments are the same */ struct encodeExp *encodeExpGetByIdFromTable(struct sqlConnection *conn, char *tableName, int id); /* Return experiment specified by id from named table */ struct encodeExp *encodeExpGetById(struct sqlConnection *conn, int id); /* Return experiment specified by id from default table */ void encodeExpAdd(struct sqlConnection *conn, char *tableName, struct encodeExp *exp); /* Add encodeExp as a new row to the table specified by tableName. Update accession using index assigned with autoincrement */ void encodeExpRemove(struct sqlConnection *conn, char *tableName, struct encodeExp *exp, char *why); /* Delete row containing experiment from encodeExp. * WARNING: This is a management function, not for regular use. Accession must * not be present. In general, experiments should be reviewed before adding to table * rather than added and removed if problematic. */ char *encodeExpAddAccession(struct sqlConnection *conn, char *tableName, int id); /* Add accession field to an existing "temp" experiment. This is done * after experiment is determined to be valid. * Return the accession. */ int encodeExpIdOffset(); /* Length of prefix preceding experiment ID in the accession. * Prefix is defined string + 1 for org character */ void encodeExpSetAccession(struct encodeExp *exp, char *tableName); // Adds accession field to an existing experiment, updating the table. void encodeExpRemoveAccession(struct sqlConnection *conn, char *tableName, int id); /* Revoke an experiment by removing the accession. */ boolean encodeExpIsAccessioned(struct encodeExp *exp); /* Determine if experiment has an accession (not unaccessioned or deaccessioned) */ char *encodeExpKey(struct encodeExp *exp); /* Create a hash key from an encodeExp */ char *encodeExpVars(struct encodeExp *exp); // Create a string of all experiment defining vars and vals as "lab=UW dataType=ChipSeq ..." // WARNING: May be missing var=None if the var was added after composite had exps. struct encodeExp *encodeExpGetFromTable(char *organism, char *lab, char *dataType, char *cell, struct slPair *varPairs, char *table); /* Return experiments matching args in named experiment table. * Organism, Lab and DataType must be non-null */ struct encodeExp *encodeExpGet(char *organism, char *lab, char *dataType, char *cell, struct slPair *varPairs); /* Return experiments matching args in default experiment table. * Organism, Lab and DataType must be non-null */ struct encodeExp *encodeExpGetByMdbVarsFromTable(char *db, struct mdbVar *vars, char *table); /* Return experiments by looking up mdb var list from the named experiment table */ struct encodeExp *encodeExpGetByMdbVars(char *db, struct mdbVar *vars); /* Return experiments by looking up mdb var list from the default experiment table */ struct encodeExp *encodeExpGetOrCreateByMdbVarsFromTable(char *db, struct mdbVar *vars, char *table); // Return experiment looked up or created from the mdb var list from the named experiment table. #define encodeExpGetOrCreateByMdbVars(db,vars) \ encodeExpGetOrCreateByMdbVarsFromTable((db),(vars),ENCODE_EXP_TABLE) int encodeExpExists(char *db, struct mdbVar *vars); /* Return TRUE if at least one experiment exists for these vars */ char *encodeGetExpAccessionByMdbVars(char *db, struct mdbVar *vars); /* Return accession of (first) experiment matching vars, or NULL if not found */ void encodeExpUpdate(struct sqlConnection *conn, char *tableName, int id, char *var, char *newVal, char *oldVal); /* Update field in encodeExp or var in expVars, identified by id with value. * If oldVal is non-NULL, verify it matches experiment, as a safety check. * Abort if experiment is accessioned (must deaccession first) */ struct encodeExp *encodeExpGetByAccession(struct sqlConnection *conn, char *accession); /* Return experiment specified by accession from default table */ char *encodeExpGetVar(struct encodeExp *exp, char *varName); /* Return value of an expVar, or NULL if not found */ char *encodeExpGetField(struct encodeExp *exp, char *var); /* Return value of a field, whether part of schema or an expVar */ #endif /* ENCODEEXP_H */