/* mdb.h was originally generated by the autoSql program, which also * generated mdb.c and mdb.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef MDB_H #define MDB_H #include "jksql.h" #define MDB_NUM_COLS 3 struct mdb /* This contains metadata for a table, file or other predeclared object type. */ { struct mdb *next; /* Next in singly linked list. */ char *obj; /* Object name or ID. */ char *var; /* Metadata variable name. */ char *val; /* Metadata value. */ }; void mdbStaticLoad(char **row, struct mdb *ret); /* Load a row from mdb table into ret. The contents of ret will * be replaced at the next call to this function. */ struct mdb *mdbLoadByQuery(struct sqlConnection *conn, char *query); /* Load all mdb 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 mdbFreeList(). */ void mdbSaveToDb(struct sqlConnection *conn, struct mdb *el, char *tableName, int updateSize); /* Save mdb 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 mdb *mdbLoad(char **row); /* Load a mdb from row fetched with select * from mdb * from database. Dispose of this with mdbFree(). */ struct mdb *mdbLoadAll(char *fileName); /* Load all mdb from whitespace-separated file. * Dispose of this with mdbFreeList(). */ struct mdb *mdbLoadAllByChar(char *fileName, char chopper); /* Load all mdb from chopper separated file. * Dispose of this with mdbFreeList(). */ #define mdbLoadAllByTab(a) mdbLoadAllByChar(a, '\t'); /* Load all mdb from tab separated file. * Dispose of this with mdbFreeList(). */ struct mdb *mdbCommaIn(char **pS, struct mdb *ret); /* Create a mdb out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new mdb */ void mdbFree(struct mdb **pEl); /* Free a single dynamically allocated mdb such as created * with mdbLoad(). */ void mdbFreeList(struct mdb **pList); /* Free a list of dynamically allocated mdb's */ void mdbOutput(struct mdb *el, FILE *f, char sep, char lastSep); /* Print out mdb. Separate fields with sep. Follow last field with lastSep. */ #define mdbTabOut(el,f) mdbOutput(el,f,'\t','\n'); /* Print out mdb as a line in a tab-separated file. */ #define mdbCommaOut(el,f) mdbOutput(el,f,',',','); /* Print out mdb as a comma separated list including final comma. */ void mdbJsonOutput(struct mdb *el, FILE *f); /* Print out mdb in JSON format. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #include "cv.h" #include "trackDb.h" #define MDB_DEFAULT_NAME "metaDb" // The three mdb tuples #define MDB_OBJ "obj" #define MDB_VAR "var" #define MDB_VAL "val" // OBJECT TYPES #define MDB_OBJ_TYPE "objType" #define MDB_OBJ_TYPE_TABLE "table" #define MDB_OBJ_TYPE_FILE "file" #define MDB_OBJ_TYPE_COMPOSITE "composite" // WELL KNOWN MDB VARS #define MDB_VAR_PI CV_TERM_GRANT #define MDB_VAR_LAB CV_TERM_LAB #define MDB_VAR_COMPOSITE MDB_OBJ_TYPE_COMPOSITE #define MDB_VAR_ANTIBODY CV_TERM_ANTIBODY #define MDB_VAR_CELL CV_TERM_CELL #define MDB_VAR_DATATYPE CV_TERM_DATA_TYPE #define MDB_VAR_VIEW CV_TERM_VIEW #define MDB_VAR_CONTROL CV_TERM_CONTROL #define MDB_VAR_TREATMENT CV_TERM_TREATMENT #define MDB_VAR_TABLENAME "tableName" #define MDB_VAR_FILENAME "fileName" #define MDB_VAR_MD5SUM "md5sum" #define MDB_VAR_FILEINDEX "fileIndex" #define MDB_VAR_DCC_ACCESSION "dccAccession" #define MDB_VAR_PROJECT "project" #define MDB_VAR_REPLICATE "replicate" #define MDB_VAR_LAB_VERSION "labVersion" #define MDB_VAR_SOFTWARE_VERSION "softwareVersion" #define MDB_VAR_SUBMIT_VERSION "submittedDataVersion" // ENCODE Specific (at least for now) #define MDB_VAL_ENCODE_PROJECT "wgEncode" #define MDB_VAR_ENCODE_SUBID "subId" #define MDB_VAR_ENCODE_EDVS "expVars" #define MDB_VAR_ENCODE_EXP_ID "expId" #define MDB_VAR_ENCODE_DATE_UNRESTRICTED "dateUnrestricted" #define MDB_ENCODE_DATE_FORMAT "%F" #define MDB_VAL_ENCODE_EDV_NONE "None" // The mdb holds metadata primarily for tables. // Many types of objects could be supported, though currently files are the only other type. // It is easy to imagine using the current mdb to support hierarchical trees of metadata. // For example a composite type object called "myComposte" could have metadata that is valid for // all tables that have the var=composite val=myComposte metadata defined. // // There are 2 ways to look at the metadata: By Obj: obj->[var=val] and By Var: var->[val->[obj]]. // By Obj: an object has many var/val pairs but only one val for each unique var. Querying by // object creates a single (2 level) one to many structure. // By Var: a variable has many possible values and each value may be defined for more than one obj // Therefore, querying by var results in a (3 level) one to many to many structure. struct mdbVar // The metadata var=val construct. This is contained by mdbObj { struct mdbVar* next; // Next in singly linked list of variables char *var; // Metadata variable name. char *val; // Metadata value. }; struct mdbObj // The standard container of a single object's metadata. // Also: when searching metadata obj->var->val this is the top struct. { struct mdbObj* next; // Next in singly linked list of objects char *obj; // Object name or ID boolean deleteThis; // Used when loading formatted file which may contain delete requests struct mdbVar* vars; // if NOT NULL: list of variables belonging to this object struct hash* varHash; // if NOT NULL: variables are also hashed! (var str to mdbVar struct) }; struct mdbLeafObj // When searching var->val->obj this is the bottom-level obj struct. { struct mdbLeafObj* next; // Next in singly linked list of variables char *obj; // Object name or ID }; struct mdbLimbVal // When searching var->val->obj this is the mid-level val->obj struct. { struct mdbLimbVal* next; // Next in singly linked list of variables char *val; // Metadata value. struct mdbLeafObj* objs; // if NOT NULL: list of Objects which have this variable struct hash* objHash; // if NOT NULL: hash of objects (val str to leafObj struct) }; struct mdbByVar // When searching metadata var->val->object this is the top struct { struct mdbByVar* next; // Next in singly linked list of variables char *var; // Metadata variable name. boolean notEqual; // For querying only struct mdbLimbVal* vals; // list of values associated with this var struct hash* valHash; // if NOT NULL: hash of vals (val str to limbVal struct) }; // -------------- Sort primitives -------------- int mdbObjCmp(const void *va, const void *vb); // Compare mdbObj to sort on obj name, case-insensitive. int mdbVarCmp(const void *va, const void *vb); // Compare mdbVar to sort on var name, case-insensitive. // ------ Parsing lines ------ struct mdbObj *metadataLineParse(char *line); /* Parses a single formatted metadata line into mdbObj for updates or queries. */ struct mdbByVar *mdbByVarsLineParse(char *line); /* Parses a line of "var1=val1 var2=val2 into a mdbByVar object for queries. */ // ------ Loading from args, hashes ------ struct mdbObj *mdbObjCreate(char *obj,char *var, char *val); /* Creates a singular mdbObj query object based on obj and all other optional params. */ struct mdbObj *mdbObjNew(char *obj,struct mdbVar *mdbVars); // Returns a new mdbObj with whatever was passed in. // An mdbObj requires and obj, so if one is not supplied it will be "[unknown]" struct mdbByVar *mdbByVarCreate(char *var, char *val); /* Creates a singular var=val pair struct for metadata queries. */ boolean mdbByVarAppend(struct mdbByVar *mdbByVars,char *var, char *val,boolean notEqual); /* Adds a another var to a list of mdbByVar pairs to be used in metadata queries. */ struct mdbObj *mdbObjsLoadFromHashes(struct hash *objsHash); // Load all mdbObjs from a file containing metadata formatted lines // ------ Loading from files ------ struct mdbObj *mdbObjsLoadFromFormattedFile(char *fileName,boolean *validated); // Load all mdbObjs from a file containing metadata formatted lines // If requested, will determine if a magic number at the end of the file matches contents struct mdbObj *mdbObjsLoadFromRAFile(char *fileName,boolean *validated); // Load all mdbObjs from a file containing RA formatted 'metaObjects' // If requested, will determine if a magic number at the end of the file matches contents // ------ Table name and creation ------ void mdbReCreate(struct sqlConnection *conn,char *tblName,boolean testOnly); // Creates ore Recreates the named mdb. char*mdbTableName(struct sqlConnection *conn,boolean mySandBox); // returns the mdb table name or NULL if conn supplied but the table doesn't exist // -------------- Updating the DB -------------- int mdbObjsSetToDb(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObjs, boolean replace,boolean testOnly); // Adds or updates metadata obj/var pairs into the named table. Returns total rows affected int mdbObjsLoadToDb(struct sqlConnection *conn,char *tableName,struct mdbObj *mdbObjs, boolean testOnly); // Adds mdb Objs with minimal error checking // ------------------ Querys ------------------- struct mdbObj *mdbObjQuery(struct sqlConnection *conn,char *table,struct mdbObj *mdbObj); // Query the metadata table by obj and optional vars and vals in mdbObj struct. // If mdbObj NULL query all. Returns new mdbObj struct fully populated and sorted in obj,var order. #define mdbObjsQueryAll(conn,table) mdbObjQuery((conn),(table),NULL) struct mdbObj *mdbObjQueryByObj(struct sqlConnection *conn,char *table,char *obj,char *var); // Query a single metadata object and optional var from a table (default mdb). struct mdbByVar *mdbByVarsQuery(struct sqlConnection *conn,char *table,struct mdbByVar *mdbByVars); // Query the metadata table by one or more var=val pairs to find the distinct set of objs // that satisfy ANY conditions. // Returns new mdbByVar struct fully populated and sorted in var,val,obj order. #define mdbByVarsQueryAll(conn,table) mdbByVarsQuery((conn),(table),NULL) struct mdbByVar *mdbByVarQueryByVar(struct sqlConnection *conn,char *table,char *varName,char *val); // Query a single metadata variable and optional val from a table (default mdb) // for searching val->obj. struct mdbObj *mdbObjsQueryByVars(struct sqlConnection *conn,char *table, struct mdbByVar *mdbByVars); // Query the metadata table by one or more var=val pairs to find the distinct set of objs // that satisfy ALL conditions. // Returns new mdbObj struct fully populated and sorted in obj,var order. struct mdbObj *mdbObjsQueryByVarValString(struct sqlConnection *conn,char *tableName,char *varVals); // returns mdbObjs matching varVals in form of: // [var1=val1 var2=val2a,val2b var3=v%3 var4="val 4" var5!=val5 var6=] // var2=val2a,val2b: matches asny of comma separated list // var3=v%3 : matches '%' and '?' wild cards. // var4="val 4" : matches simple double quoted strings. // var5!=val5 : matches not equal. // var6= : matches that var exists (same as var6=%). var6!= also works. #define mdbObjsQueryByVarVals(conn,varVals) mdbObjsQueryByVarValString((conn),NULL,(varVals)) struct mdbObj *mdbObjsQueryByVarPairs(struct sqlConnection *conn,char *tableName, struct slPair *varValPairs); // returns mdbObjs matching varValPairs provided. // The != logic of mdbObjsQueryByVarValString() is not possible, but other cases are supported: // as val may be NULL, a comma delimited list, double quoted string, containing wilds: % and ? #define mdbObjsQueryByVarValPairs(conn,varValPairs) \ mdbObjsQueryByVarPairs((conn),NULL,(varValPairs)) struct mdbObj *mdbObjQueryCompositeObj(struct sqlConnection *conn,char *tableName, struct mdbObj *mdbObj); // returns NULL or the composite mdbObj associated with the object passed in. #define mdbObjQueryComposite(conn,mdbObj) mdbObjQueryCompositeObj((conn),NULL,(mdbObj)) // ----------- Printing and Counting ----------- void mdbObjPrint(struct mdbObj *mdbObjs,boolean raStyle); // prints objs and var=val pairs as formatted metadata lines or ra style void mdbObjPrintToFile(struct mdbObj *mdbObjs,boolean raStyle, char *file); // prints (to file) objs and var=val pairs as formatted metadata lines or ra style void mdbObjPrintToStream(struct mdbObj *mdbObjs,boolean raStyle, FILE *outF); // prints (to stream) objs and var=val pairs as formatted metadata lines or ra style int mdbObjPrintToTabFile(struct mdbObj *mdbObjs, char *file); // prints all objs as tab delimited obj var val into file for SQL LOAD DATA. Returns count. void mdbObjPrintOrderedToStream(FILE *outF,struct mdbObj **mdbObjs,char *order, char *separator, boolean header); // prints mdbObjs as a table, but only the vars listed in comma delimited order. // Examples of separator: " " "\t\t" or "", in which case this is an HTML table. // mdbObjs list will be reordered. Sort fails when vars are missing in objs. char *mdbObjVarValPairsAsLine(struct mdbObj *mdbObj,boolean objTypeExclude,boolean cvLabels); // returns NULL or a line for a single mdbObj as "var1=val1; var2=val2 ...". Must be freed. void mdbByVarPrint(struct mdbByVar *mdbByVars,boolean raStyle); // prints var=val pairs and objs that go with them single lines or ra style int mdbObjCount(struct mdbObj *mdbObjs, boolean objs); // returns the count of vars belonging to this obj or objs; int mdbByVarCount(struct mdbByVar *mdbByVars,boolean vars, boolean vals); // returns the count of objs belonging to this set of vars; // ----------------- Utilities ----------------- struct hash *mdbObjsHash(struct mdbObj *mdbObjs); // Returns a hash object for this set of mdbObjs, keyed on the obj. // WARNING: any changes to the members of the mdbObjs list may lead to invalid pointers in the hash struct mdbObj *mdbObjLookUp(struct hash *mdbObjsHash, char *obj); // Returns an mdbObj from the objsHash // WARNING: any changes to the members of the mdbObjs list used to make the mdbObjsHash // may lead to invalid pointers in the hash void mdbObjsHashFree(struct hash **pMdbObjsHash); // Frees an mdbObjs hash. struct mdbVar *mdbObjFind(struct mdbObj *mdbObj, char *var); // Finds the val associated with the var or retruns NULL char *mdbObjFindValue(struct mdbObj *mdbObj, char *var); // Finds the val associated with the var or retruns NULL struct slName *mdbObjsFindAllVals(struct mdbObj *mdbObjs, char *var, char *emptyToken); // Returns a list of all vals in mdbObjs for a requested var // Will add empty only if there is atleast one empty val and at least one val found boolean mdbObjContains(struct mdbObj *mdbObj, char *var, char *val); // Returns TRUE if object contains var, val or both boolean mdbObjsContainAltleastOneMatchingVar(struct mdbObj *mdbObjs, char *var, char *val); // Returns TRUE if any object in set contains var #define mdbObjsContainAtleastOne(mdbObjs, var) \ mdbObjsContainAltleastOneMatchingVar((mdbObjs),(var),NULL) struct mdbObj *mdbObjsCommonVars(struct mdbObj *mdbObjs); // Returns a new mdbObj with all vars that are contained in every obj passed in. // Note that the returnd mdbObj has a meaningles obj name and vals. boolean mdbByVarContains(struct mdbByVar *mdbByVar, char *val, char *obj); // Returns TRUE if var contains val, obj or both void mdbObjReorderVars(struct mdbObj *mdbObjs, char *vars,boolean back); // Reorders vars list based upon list of vars "cell antibody treatment". Send to front or back. void mdbObjReorderByCv(struct mdbObj *mdbObjs, boolean includeHidden); // Reorders vars list based upon cv.ra typeOfTerms priority void mdbObjsSortOnVars(struct mdbObj **mdbObjs, char *vars); // Sorts on var,val pairs vars lists: fwd case-sensitive. // Assumes all objs' vars are in identical order. // Optionally give list of vars "cell antibody treatment" to sort on // (bringing to front of vars lists). void mdbObjsSortOnVarPairs(struct mdbObj **mdbObjs,struct slPair *varValPairs); // Sorts on var,val pairs vars lists: fwd case-sensitive. // Assumes all objs' vars are in identical order. // This method will use mdbObjsSortOnVars() void mdbObjsSortOnCv(struct mdbObj **mdbObjs, boolean includeHidden); // Puts obj->vars in order based upon cv.ra typeOfTerms priority, // then case-sensitively sorts all objs in list based upon that var order. boolean mdbObjRemoveOneVar(struct mdbObj *mdbObj, char *var, char *val); // returns TRUE if var (and optional val) are found and surgically removed from one mdbObj void mdbObjRemoveVars(struct mdbObj *mdbObjs, char *vars); // Prunes list of vars for an object, freeing the memory. Doesn't touch DB. void mdbObjRemoveHiddenVars(struct mdbObj *mdbObjs); // Prunes list of vars for mdb objs that have been declared as hidden in cv.ra typeOfTerms boolean mdbObjsHasCommonVar(struct mdbObj *mdbList, char *var, boolean missingOk); // Returns TRUE if all mbObjs passed in have the var with the same value char *mdbRemoveCommonVar(struct mdbObj *mdbList, char *var); // Removes var from set of mdbObjs but only if all that hav it have a commmon val // Returns the val if removed, else NULL boolean mdbObjSetVar(struct mdbObj *mdbObj, char *var,char *val); // Sets the string value to a single var in an obj, preparing for DB update. // returns TRUE if updated, FALSE if added boolean mdbObjSetVarInt(struct mdbObj *mdbObj, char *var,int val); // Sets an integer value to a single var in an obj, preparing for DB update. // returns TRUE if updated, FALSE if added void mdbObjSwapVars(struct mdbObj *mdbObjs, char *vars,boolean deleteThis); // Replaces objs' vars with var=vap pairs provided, preparing for DB update. struct mdbObj *mdbObjsFilter(struct mdbObj **pMdbObjs, char *var, char *val,boolean returnMatches); // Filters mdb objects to only those that include/exclude vars. Optionally checks val too. // Returns matched or unmatched items objects as requested, maintaining sort order struct mdbObj *mdbObjsFilterByVars(struct mdbObj **pMdbObjs,char *vars, boolean noneEqualsNotFound,boolean returnMatches); // Filters mdb objects to only those that include/exclude var=val pairs // (e.g. "var1=val1 var2 var3!=val3 var4=None"). // Supports != ("var!=" means var not found). // Optionally supports var=None equal to var is not found // Returns matched or unmatched items objects as requested. // Multiple passes means sort order is destroyed. struct mdbObj *mdbObjsFilterTablesOrFiles(struct mdbObj **pMdbObjs,boolean table, boolean files); // Filters mdb objects to only those that have associated tables or files. // Returns removed non-table/file objects // Note: Since table/file objects overlap, there are 3 possibilites: tables, files, table && files struct mdbObj *mdbObjIntersection(struct mdbObj **a, struct mdbObj *b); // return objs removed from pA while making an intersection of two mdbObj lists. // List b is untouched but pA will contain the resulting intersection void mdbObjTransformToUpdate(struct mdbObj *mdbObjs, char *var, char *val,boolean deleteThis); // Turns one or more mdbObjs into the stucture needed to add/update or delete. struct mdbObj *mdbObjClone(const struct mdbObj *mdbObj); // Clones a single mdbObj, including hash and maintining order struct slName *mdbObjToSlName(struct mdbObj *mdbObjs); // Creates slNames list of mdbObjs->obj. mdbObjs remains untouched int mdbVarCmp(const void *va, const void *vb); /* Compare to sort on label. */ // ----------------- Validation and specialty APIs ----------------- boolean mdbObjIsComposite(struct mdbObj *mdbObj); // returns TRUE if this is a valid composite object boolean mdbObjIsCompositeMember(struct mdbObj *mdbObj); // returns TRUE if this is valid member of a composite. DOES not confirm that composite obj exists int mdbObjsValidate(struct mdbObj *mdbObjs, boolean full); // Validates vars and vals against cv.ra. Returns count of errors found. // Full considers vars not defined in cv as invalids struct slName *mdbObjFindCompositeNamedEncodeEdvs(struct sqlConnection *conn, char *tableName,struct mdbObj *mdbObj); // returns NULL or the Experiment Defining Variable names for this composite #define mdbObjFindCompositeEncodeEdvs(conn,mdbObj) \ mdbObjFindCompositeNamedEncodeEdvs((conn),NULL,(mdbObj)) struct mdbVar *mdbObjFindEncodeEdvPairs(struct sqlConnection *conn,char *tableName, struct mdbObj *mdbObj,boolean includeNone); // returns NULL or the Experiment Defining Variables and values for this composite member object // If includeNone, then defined variables not found in obj will be included as {var}="None". #define mdbObjFindEncodeEdvs(conn,mdbObj,includeNone) \ mdbObjFindEncodeEdvPairs((conn),NULL,(mdbObj),(includeNone)) struct mdbObj *mdbObjsEncodeExperimentify(struct sqlConnection *conn,char *db,char *tableName, char *expTable,struct mdbObj **pMdbObjs,int warn, boolean createExpIfNecessary,boolean updateAccession); // Organizes objects into experiments and validates experiment IDs. // Will add/update the ids in the structures. // If warn=1, then prints to stdout all the experiments/obs with missing or wrong expIds; // warn=2, then print line for each obj with expId or warning. // createExpIfNecessary means add expId to encodeExp table. updateAccession too if necessary. // Returns a new set of mdbObjs that is what can (and should) // be used to update the mdb via mdbObjsSetToDb(). boolean mdbObjIsEncode(struct mdbObj *mdbObj); // Returns TRUE if MDB object is an ENCODE object (project=wgEncode) boolean mdbObjEncodeIsUnrestricted(struct mdbObj *mdb); // Return true if this object is still within data restriction time period boolean mdbObjInComposite(struct mdbObj *mdb, char *composite); // Returns TRUE if metaDb object is in specified composite. // If composite is NULL, always return true // FIXME: KATE Why return true if composite not defined??? // -- Requested by Kate? -- //struct encodeExp *encodeExps(char *composite,char *expTable); //struct mdbObjs *mdbObjsForDefinedExpId(int expId); // Returns the mdb objects belonging to a single encode experiment defined in the encodExp table // --------------- Free at last ---------------- void mdbObjsFree(struct mdbObj **mdbObjsPtr); // Frees one or more metadata objects and any contained mdbVars. Will free any hashes as well. #define mdbObjFree(mdbObjPtr) mdbObjsFree(mdbObjPtr) void mdbVarsFree(struct mdbVar **mdbVarsPtr); // Frees one or more metadata vars and any val as well #define mdbVarFree(mdbVarPtr) mdbVarsFree(mdbVarPtr) void mdbByVarsFree(struct mdbByVar **mdbByVarsPtr); // Frees one or more metadata vars and any contained vals and objs. Will free any hashes as well. #define mdbByVarFree(mdbByVarPtr) mdbByVarsFree(mdbByVarPtr) // ----------------- CGI specific routines for use with tdb ----------------- const struct mdbObj *metadataForTable(char *db,struct trackDb *tdb,char *table); // Returns the metadata for a table. NEVER FREE THIS STRUCT! // This is the main routine for CGIs to access metadata const char *metadataFindValue(struct trackDb *tdb, char *var); // Finds the val associated with the var or retruns NULL #define MDB_VAL_STD_TRUNCATION 64 struct mdbObj *mdbObjSearch(struct sqlConnection *conn, char *var, char *val, char *op, int limit); // Search the metaDb table for objs by var and val. // Can restrict by op "is", "like", "in" and accept (non-zero) limited string size // Search is via mysql, so it's case-insensitive. Return is sorted on obj. struct mdbObj *mdbObjRepeatedSearch(struct sqlConnection *conn,struct slPair *varValPairs, boolean tables,boolean files); // Search the metaDb table for objs by var,val pairs. Uses mdbCvSearchMethod() if available. // This method will use mdbObjsQueryByVars() struct slName *mdbObjNameSearch(struct sqlConnection *conn, char *var, char *val, char *op, int limit, boolean tables, boolean files); // Search the metaDb table for objs by var and val. // Can restrict by op "is" or "like" and accept (non-zero) limited string size // Search is via mysql, so it's case-insensitive. Return is sorted on obj. struct slName *mdbValSearch(struct sqlConnection *conn, char *var, int limit, boolean hasTableName, boolean hasFileName); // Search the metaDb table for vals by var. // Can impose (non-zero) limit on returned string size of val // Search is via mysql, so it's case-insensitive. Return is sorted on val. // Searchable vars are only for table or file objects. // Further restrict to vars associated with tableName, fileName or both. struct slPair *mdbValLabelSearch(struct sqlConnection *conn, char *var, int limit, boolean tags, boolean hasTableName, boolean hasFileName); // Search the metaDb table for vals by var and returns val (as pair->name) // and controlled vocabulary (cv) label (if it exists) (as pair->val). // Can impose (non-zero) limit on returned string size of name. // Searchable vars are only for table or file objects. // Further restrict to vars associated with tableName, fileName or both. // Return is case insensitive sorted on label (cv label or else val). // If requested, return cv tag instead of mdb val. #define mdbPairVal(pair) (pair)->name #define mdbPairLabel(pair) (pair)->val struct slPair *mdbVarsSearchable(struct sqlConnection *conn, boolean hasTableName, boolean hasFileName); // returns a white list of mdb vars that actually exist in the current DB. // Searchable vars are only for table or file objects. // Further restrict to vars associated with tableName, fileName or both. struct mdbObj *metadataForTableFromTdb(struct trackDb *tdb); // Returns the metadata for a table from a tdb setting. #endif /* MDB_H */