src/hg/inc/metaTbl.h 1.7
1.7 2010/03/31 23:34:43 tdreszer
Tightening screws. Don't allow shared metaTbl update except from protected file.
Index: src/hg/inc/metaTbl.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/metaTbl.h,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/inc/metaTbl.h 30 Mar 2010 23:35:24 -0000 1.6
+++ src/hg/inc/metaTbl.h 31 Mar 2010 23:34:43 -0000 1.7
@@ -1,271 +1,296 @@
/* metaTbl.h was originally generated by the autoSql program, which also
* generated metaTbl.c and metaTbl.sql. This header links the database and
* the RAM representation of objects. */
#ifndef METATBL_H
#define METATBL_H
#include "jksql.h"
#define METATBL_NUM_COLS 5
struct metaTbl
/* This contains metadata for a table, file or other predeclared object type. */
{
struct metaTbl *next; // Next in singly linked list.
char *objName; // Object name or ID.
char *objType; // table | file
char *var; // Metadata variable name.
char *varType; // txt | binary
char *val; // Metadata value.
};
void metaTblStaticLoad(char **row, struct metaTbl *ret);
/* Load a row from metaTbl table into ret. The contents of ret will
* be replaced at the next call to this function. */
struct metaTbl *metaTblLoadByQuery(struct sqlConnection *conn, char *query);
/* Load all metaTbl 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 metaTblFreeList(). */
void metaTblSaveToDb(struct sqlConnection *conn, struct metaTbl *el, char *tableName, int updateSize);
/* Save metaTbl 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 metaTblSaveToDbEscaped() */
void metaTblSaveToDbEscaped(struct sqlConnection *conn, struct metaTbl *el, char *tableName, int updateSize);
/* Save metaTbl 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 metaTblSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
struct metaTbl *metaTblLoad(char **row);
/* Load a metaTbl from row fetched with select * from metaTbl
* from database. Dispose of this with metaTblFree(). */
struct metaTbl *metaTblLoadAll(char *fileName);
/* Load all metaTbl from whitespace-separated file.
* Dispose of this with metaTblFreeList(). */
struct metaTbl *metaTblLoadAllByChar(char *fileName, char chopper);
/* Load all metaTbl from chopper separated file.
* Dispose of this with metaTblFreeList(). */
#define metaTblLoadAllByTab(a) metaTblLoadAllByChar(a, '\t');
/* Load all metaTbl from tab separated file.
* Dispose of this with metaTblFreeList(). */
struct metaTbl *metaTblCommaIn(char **pS, struct metaTbl *ret);
/* Create a metaTbl out of a comma separated string.
* This will fill in ret if non-null, otherwise will
* return a new metaTbl */
void metaTblFree(struct metaTbl **pEl);
/* Free a single dynamically allocated metaTbl such as created
* with metaTblLoad(). */
void metaTblFreeList(struct metaTbl **pList);
/* Free a list of dynamically allocated metaTbl's */
void metaTblOutput(struct metaTbl *el, FILE *f, char sep, char lastSep);
/* Print out metaTbl. Separate fields with sep. Follow last field with lastSep. */
#define metaTblTabOut(el,f) metaTblOutput(el,f,'\t','\n');
/* Print out metaTbl as a line in a tab-separated file. */
#define metaTblCommaOut(el,f) metaTblOutput(el,f,',',',');
/* Print out metaTbl as a comma separated list including final comma. */
/* -------------------------------- End autoSql Generated Code -------------------------------- */
+#include "trackDb.h"
+
#define METATBL_DEFAULT_NAME "metaTbl"
// The metaTbl 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 metaTbl 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 metaObjType
// metadata Obects are only certain declared types
{
otUnknown=0, // Unknown type
otTable =1, // Table is default
otFile =2 // Files are also supported and used by ENCODE download only datasets.
};
enum metaVarType
// metadata Variavble are only certain declared types
{
vtUnknown=0, // Unknown type
vtTxt =1, // Txt is default
vtBinary =2 // Could support binary blobs
};
struct metaVar
// The metadata var=val construct. This is contained by metaObj
{
struct metaVar* next; // Next in singly linked list of variables
char *var; // Metadata variable name.
enum metaVarType varType; // txt | binary
char *val; // Metadata value.
};
struct metaObj
// The standard container of a single object's metadata.
// Also: when searching metadata obj->var->val this is the top struct.
{
struct metaObj* next; // Next in singly linked list of objects
- char *objName; // Object name or ID
+ char *obj; // Object name or ID
enum metaObjType objType; // table | file
boolean deleteThis; // Used when loading formatted file which may contain delete requests
struct metaVar* vars; // if NOT NULL: list of variables belonging to this object
struct hash* varHash; // if NOT NULL: variables are also hashed! (var str to metaVar struct)
};
struct metaLeafObj
// When searching var->val->obj this is the bottom-level obj struct.
{
struct metaLeafObj* next; // Next in singly linked list of variables
- char *objName; // Object name or ID
+ char *obj; // Object name or ID
enum metaObjType objType; // table | file
};
struct metaLimbVal
// When searching var->val->obj this is the mid-level val->obj struct.
{
struct metaLimbVal* next; // Next in singly linked list of variables
char *val; // Metadata value.
struct metaLeafObj* 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 metaByVar
// When searching metadata var->val->object this is the top struct
{
struct metaByVar* next; // Next in singly linked list of variables
char *var; // Metadata variable name.
enum metaVarType varType; // txt | binary
struct metaLimbVal* 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 metaObjType metaObjTypeStringToEnum(char *objType);
// Convert metadata objType string to enum
char *metaObjTypeEnumToString(enum metaObjType objType);
// Convert metadata objType enum string
enum metaVarType metaVarTypeStringToEnum(char *varType);
// Convert metadata varType string to enum
char *metaVarTypeEnumToString(enum metaVarType varType);
// Convert metadata varType enum string
-
-// ------ Loading files and parsing lines ------
+// ------ Parsing lines ------
struct metaObj *metadataLineParse(char *line);
/* Parses a single formatted metadata line into metaObj for updates or queries. */
-struct metaObj *metaObjCreate(char *obj,char *type,char *var, char *varType,char *val);
-/* Creates a singular metaObj query object based on obj and all other optional params. */
-
struct metaByVar *metaByVarsLineParse(char *line);
/* Parses a line of "var1=val1 var2=val2 into a metaByVar object for queries. */
+
+// ------ Loading from args, hashes and tdb ------
+struct metaObj *metaObjCreate(char *obj,char *type,char *var, char *varType,char *val);
+/* Creates a singular metaObj query object based on obj and all other optional params. */
+
struct metaByVar*metaByVarCreate(char *var, char *varType,char *val);
/* Creates a singular var=val pair struct for metadata queries. */
-struct metaObj *metaObjsLoadFromFormattedFile(char *fileName);
+struct metaObj *metaObjsLoadFromHashes(struct hash *objsHash);
// Load all metaObjs from a file containing metadata formatted lines
-struct metaObj *metaObjsLoadFromHashes(struct hash *objsHash);
+struct metaObj *metadataForTable(char *db,struct trackDb *tdb,char *table);
+// Returns the metadata for a table. Either tdb or table must be provided
+
+
+// ------ Loading from files ------
+struct metaObj *metaObjsLoadFromFormattedFile(char *fileName,boolean *validated);
// Load all metaObjs from a file containing metadata formatted lines
+// If requested, will determine if a magic number at the end of the file matches contents
-struct metaObj *metaObjsLoadFromRAFile(char *fileName);
+struct metaObj *metaObjsLoadFromRAFile(char *fileName,boolean *validated);
// Load all metaObjs 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 metaTblReCreate(struct sqlConnection *conn,char *tblName,boolean testOnly);
+// Creates ore Recreates the named metaTbl.
+
+char*metaTblName(struct sqlConnection *conn,boolean mySandBox);
+// returns the metaTbl name or NULL if conn supplied but the table doesn't exist
// -------------- Updating the DB --------------
int metaObjsSetToDb(struct sqlConnection *conn,char *tableName,struct metaObj *metaObjs,boolean replace,boolean testOnly);
// Adds or updates metadata obj/var pairs into the named table. Returns total rows affected
// ------------------ Querys -------------------
struct metaObj *metaObjQuery(struct sqlConnection *conn,char *table,struct metaObj *metaObj);
// Query the metadata table by obj and optional vars and vals in metaObj struct. If metaObj is NULL query all.
// Returns new metaObj struct fully populated and sorted in obj,var order.
#define metaObjsQueryAll(conn,table) metaObjQuery((conn),(table),NULL)
-struct metaObj *metaObjQueryByObj(struct sqlConnection *conn,char *table,char *objName,char *varName);
+struct metaObj *metaObjQueryByObj(struct sqlConnection *conn,char *table,char *obj,char *var);
// Query a single metadata object and optional var from a table (default metaTbl).
struct metaByVar *metaByVarsQuery(struct sqlConnection *conn,char *table,struct metaByVar *metaByVars);
// Query the metadata table by one or more var=val pairs to find the distinct set of objs that satisfy ANY conditions.
// Returns new metaByVar struct fully populated and sorted in var,val,obj order.
#define metaByVarsQueryAll(conn,table) metaByVarsQuery((conn),(table),NULL)
struct metaByVar *metaByVarQueryByVar(struct sqlConnection *conn,char *table,char *varName,char *val);
// Query a single metadata variable and optional val from a table (default metaTbl) for searching val->obj.
struct metaObj *metaObjsQueryByVars(struct sqlConnection *conn,char *table,struct metaByVar *metaByVars);
// Query the metadata table by one or more var=val pairs to find the distinct set of objs that satisfy ALL conditions.
// Returns new metaObj struct fully populated and sorted in obj,var order.
// ----------- Printing and Counting -----------
void metaObjPrint(struct metaObj *metaObjs,boolean raStyle);
// prints objs and var=val pairs as formatted metadata lines or ra style
void metaByVarPrint(struct metaByVar *metaByVars,boolean raStyle);
// prints var=val pairs and objs that go with them single lines or ra style
int metaObjCount(struct metaObj *metaObjs, boolean objs);
// returns the count of vars belonging to this obj or objs;
int metaByVarCount(struct metaByVar *metaByVars,boolean vars, boolean vals);
// returns the count of objs belonging to this set of vars;
// ----------------- Utilities -----------------
+char *metadataFindValue(struct metaObj *metaObj, char *var);
+// Finds the val associated with the var or retruns NULL
+
boolean metaObjContains(struct metaObj *metaObj, char *var, char *val);
// Returns TRUE if object contains var, val or both
boolean metaByVarContains(struct metaByVar *metaByVar, char *val, char *obj);
// Returns TRUE if var contains val, obj or both
void metaObjReorderVars(struct metaObj *metaObjs, char *vars,boolean back);
// Reorders vars list based upon list of vars "cell antibody treatment". Send to front or back.
void metaObjRemoveVars(struct metaObj *metaObjs, char *vars);
// Prunes list of vars for an object, freeing the memory. Doesn't touch DB.
void metaObjTransformToUpdate(struct metaObj *metaObjs, char *var, char *varType,char *val,boolean deleteThis);
/* Turns one or more metaObjs into the stucture needed to add/update or delete. */
+int metaObjCRC(struct metaObj *metaObjs);
+// returns a summ of all individual CRC values of all metObj strings
+
// --------------- Free at last ----------------
void metaObjsFree(struct metaObj **metaObjsPtr);
// Frees one or more metadata objects and any contained metaVars. Will free any hashes as well.
void metaByVarsFree(struct metaByVar **metaByVarsPtr);
// Frees one or more metadata vars and any contained vals and objs. Will free any hashes as well.
#endif /* METATBL_H */