Index: src/hg/inc/mdb.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/mdb.h,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/inc/mdb.h	13 Apr 2010 19:49:20 -0000	1.1
+++ src/hg/inc/mdb.h	27 Apr 2010 22:33:22 -0000	1.2
@@ -1,293 +1,293 @@
 /* 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. */
 
 #ifndef MDB_H
 #define MDB_H
 
 #include "jksql.h"
 #define MDB_NUM_COLS 4
 
 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 *varType;	/* txt | binary */
     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. 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 mdbSaveToDbEscaped() */
 
 void mdbSaveToDbEscaped(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. Automatically
  * escapes all simple strings (not arrays of string) but may be slower than mdbSaveToDb().
  * For example automatically copies and converts:
  * "autosql's features include" --> "autosql\'s features include"
  * before inserting into 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 "trackDb.h"
 
-#define MDB_DEFAULT_NAME "mdb"
+#define MDB_DEFAULT_NAME "metaDb"
 
 // 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 object.
 //         Therefore, querying by var results in a (3 level) one to many to many structure.
 
 enum mdbVarType
 // metadata Variavble are only certain declared types
     {
     vtTxt     =0,  // Txt is default
     vtBinary  =1,  // Could support binary blobs
     vtUnknown =99  // Not determined.
     };
 
 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.
     enum mdbVarType varType; // txt | binary
     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.
     enum mdbVarType varType; // txt | binary
     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)
     };
 
 // -------------- Enum to Strings --------------
 enum mdbVarType mdbVarTypeStringToEnum(char *varType);
 // Convert metadata varType string to enum
 
 char *mdbVarTypeEnumToString(enum mdbVarType varType);
 // Convert metadata varType enum string
 
 // ------ 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 *varType,char *val);
 /* Creates a singular mdbObj query object based on obj and all other optional params. */
 
 struct mdbByVar *mdbByVarCreate(char *var, char *varType,char *val);
 /* Creates a singular var=val pair struct for 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
 
 
 // ------------------ 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 is 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.
 
 
 // ----------- Printing and Counting -----------
 void mdbObjPrint(struct mdbObj *mdbObjs,boolean raStyle);
 // prints objs and var=val pairs as formatted metadata lines or ra style
 
 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 -----------------
 char *mdbObjFindValue(struct mdbObj *mdbObj, char *var);
 // Finds the val associated with the var or retruns NULL
 
 boolean mdbObjContains(struct mdbObj *mdbObj, char *var, char *val);
 // Returns TRUE if object contains var, val or both
 
 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 mdbObjRemoveVars(struct mdbObj *mdbObjs, char *vars);
 // Prunes list of vars for an object, freeing the memory.  Doesn't touch DB.
 
 void mdbObjSwapVars(struct mdbObj *mdbObjs, char *vars,boolean deleteThis);
 // Replaces objs' vars with var=vap pairs provided, preparing for DB update.
 
 void mdbObjTransformToUpdate(struct mdbObj *mdbObjs, char *var, char *varType,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
 
 
 // --------------- Free at last ----------------
 void mdbObjsFree(struct mdbObj **mdbObjsPtr);
 // Frees one or more metadata objects and any contained mdbVars.  Will free any hashes as well.
 
 void mdbByVarsFree(struct mdbByVar **mdbByVarsPtr);
 // Frees one or more metadata vars and any contained vals and objs.  Will free any hashes as well.
 
 
 // ----------------- 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
 
 
 #endif /* MDB_H */
 

