src/hg/lib/metaTbl.c 1.6
1.6 2010/03/25 21:53:43 tdreszer
Some adjustments recommened by Mark in code review
Index: src/hg/lib/metaTbl.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/metaTbl.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/hg/lib/metaTbl.c 24 Mar 2010 17:37:12 -0000 1.5
+++ src/hg/lib/metaTbl.c 25 Mar 2010 21:53:43 -0000 1.6
@@ -415,16 +415,17 @@
// ------ Loading files and parsing lines ------
struct metaObj *metadataLineParse(char *line)
/* Parses a single formatted metadata line into metaObj for updates or queries. */
{
-char *words[256]; // A lot!
int thisWord = 0;
struct metaObj *metaObj;
struct metaVar *metaVar;
char *cloneLine = cloneString(line);
// initial chop and determine if this looks like metadata
- int count = chopByWhiteRespectDoubleQuotes(cloneLine,words,ArraySize(words));
+ int count = chopByWhiteRespectDoubleQuotes(cloneLine,NULL,0);
+ char **words = needMem(sizeof(char *) * count);
+ count = chopByWhiteRespectDoubleQuotes(cloneLine,words,count);
if(count < 3 || words[thisWord] == NULL || differentWord(words[thisWord],"metadata"))
{
errAbort("This is not formatted metadata:\n\t%s\n",line);
}
@@ -487,8 +488,9 @@
hashAdd(metaObj->varHash, metaVar->var, metaVar); // pointer to struct to resolve type
slAddHead(&(metaObj->vars),metaVar);
}
}
+ freeMem(words);
// Special for old style ENCODE metadata
if(metaObj->objName == NULL)
{
@@ -565,18 +567,19 @@
struct metaByVar *metaByVarsLineParse(char *line)
/* Parses a line of "var1=val1 var2=val2 into a metaByVar object for queries. */
{
-char *words[256]; // A lot!
int thisWord = 0;
struct metaByVar *metaByVars = NULL;
struct metaByVar *rootVar = NULL;
struct metaLimbVal *limbVal = NULL;
char *cloneLine = cloneString(line);
struct hash* varHash; // There must not be multiple occurrances of the same var
// initial chop and determine if this looks like metadata
- int count = chopByWhiteRespectDoubleQuotes(cloneLine,words,ArraySize(words));
+ int count = chopByWhiteRespectDoubleQuotes(cloneLine,NULL,0);
+ char **words = needMem(sizeof(char *) * count);
+ count = chopByWhiteRespectDoubleQuotes(cloneLine,words,count);
verbose(3, "metaByVarsLineParse() word count:%d\n\t%s\n",count,line);
// Get objName and figure out if this is a delete line
varHash = hashNew(0);
@@ -611,8 +614,9 @@
hashAdd(varHash, rootVar->var, rootVar);
slAddHead(&metaByVars,rootVar);
}
}
+ freeMem(words);
slReverse(&metaByVars);
verbose(2, "metaByVarsLineParse() first: %s=%s\n",metaByVars->var,metaByVars->vals->val);
return metaByVars;
}
@@ -663,22 +667,19 @@
return metaObjs;
}
// -------------- Updating the DB --------------
-int metaObjsSetToDb(char * db,char *tableName,struct metaObj *metaObjs,boolean replace)
+int metaObjsSetToDb(struct sqlConnection *conn,char *tableName,struct metaObj *metaObjs,boolean replace)
// Adds or updates metadata obj/var pairs into the named table. Returns total rows affected
{
char query[8192];
struct metaObj *metaObj;
struct metaVar *metaVar;
int count = 0;
- if(db == NULL)
- db = METATBL_DEFAULT_DB;
if(tableName == NULL)
tableName = METATBL_DEFAULT_NAME;
-struct sqlConnection *conn = sqlConnect(db);
if(!sqlTableExists(conn,tableName))
errAbort("metaObjsSetToDb attempting to update non-existent table.\n");
for(metaObj = metaObjs;metaObj != NULL; metaObj = metaObj->next)
@@ -740,9 +741,9 @@
{
// Be sure to check for var existence first, then update
if (!replace)
{
- struct metaObj *objExists = metaObjQueryByObj(db,tableName,metaObj->objName,metaVar->var);
+ struct metaObj *objExists = metaObjQueryByObj(conn,tableName,metaObj->objName,metaVar->var);
if(objExists)
{
if(differentString(metaVar->val,objExists->vars->val)
|| metaVar->varType != objExists->vars->varType)
@@ -770,26 +771,26 @@
sqlUpdate(conn, query);
count++;
}
}
-sqlDisconnect(&conn);
return count;
}
// ------------------ Querys -------------------
-struct metaObj *metaObjQuery(char * db,char *table,struct metaObj *metaObj)
+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.
{
// select obj,var,val where (var= [and val=]) or ([var= and] val=) order by obj,var
boolean buildHash = TRUE;
- struct dyString *dy = newDyString(4096);
- if(db == NULL)
- db = METATBL_DEFAULT_DB;
if(table == NULL)
table = METATBL_DEFAULT_NAME;
+ if(!sqlTableExists(conn,table))
+ return NULL;
+
+ struct dyString *dy = newDyString(4096);
dyStringPrintf(dy, "select objName,objType,var,varType,val from %s", table);
if(metaObj != NULL && metaObj->objName != NULL)
{
dyStringPrintf(dy, " where objName = '%s'", metaObj->objName);
@@ -816,45 +817,37 @@
}
dyStringPrintf(dy, " order by objName, var");
verbose(2, "Query: %s\n",dyStringContents(dy));
- struct sqlConnection *conn = sqlConnect(db);
- if(!sqlTableExists(conn,table))
- {
- dyStringFree(&dy);
- return NULL;
- }
-
struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
- sqlDisconnect(&conn);
verbose(2, "rows returned: %d\n",slCount(metaTbl));
return metaObjsLoadFromMemory(&metaTbl,buildHash);
}
-struct metaObj *metaObjQueryByObj(char * db,char *table,char *objName,char *varName)
+struct metaObj *metaObjQueryByObj(struct sqlConnection *conn,char *table,char *objName,char *varName)
// Query a single metadata object and optional var from a table (default metaTbl).
{
if(objName == NULL)
- return metaObjQuery(db,table,NULL);
+ return metaObjQuery(conn,table,NULL);
struct metaObj *queryObj = metaObjCreate(objName,NULL,varName,NULL,NULL);
-struct metaObj *resultObj = metaObjQuery(db,table,queryObj);
+struct metaObj *resultObj = metaObjQuery(conn,table,queryObj);
metaObjsFree(&queryObj);
return resultObj;
}
-struct metaByVar *metaByVarsQuery(char * db,char *table,struct metaByVar *metaByVars)
+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.
{
// select var,val,obj where (var= [and val in (val1,val2)]) or (var= [and val in (val1,val2)]) order by var,val,obj
- struct dyString *dy = newDyString(4096);
- if(db == NULL)
- db = METATBL_DEFAULT_DB;
if(table == NULL)
table = METATBL_DEFAULT_NAME;
+ if(!sqlTableExists(conn,table))
+ return NULL;
+ struct dyString *dy = newDyString(4096);
dyStringPrintf(dy, "select distinct objName,objType,var,varType,val from %s", table);
struct metaByVar *rootVar;
for(rootVar=metaByVars;rootVar!=NULL;rootVar=rootVar->next)
@@ -880,44 +873,37 @@
}
dyStringPrintf(dy, " order by var, val, objName");
verbose(2, "Query: %s\n",dyStringContents(dy));
- struct sqlConnection *conn = sqlConnect(db);
- if(!sqlTableExists(conn,table))
- {
- dyStringFree(&dy);
- return NULL;
- }
struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
- sqlDisconnect(&conn);
verbose(2, "rows returned: %d\n",slCount(metaTbl));
return metaByVarsLoadFromMemory(&metaTbl,TRUE);
}
-struct metaByVar *metaByVarQueryByVar(char * db,char *table,char *varName,char *val)
+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.
{
if(varName == NULL)
- return metaByVarsQuery(db,table,NULL);
+ return metaByVarsQuery(conn,table,NULL);
struct metaByVar *queryVar = metaByVarCreate(varName,NULL,val);
-struct metaByVar *resultVar = metaByVarsQuery(db,table,queryVar);
+struct metaByVar *resultVar = metaByVarsQuery(conn,table,queryVar);
metaByVarsFree(&queryVar);
return resultVar;
}
-struct metaObj *metaObjsQueryByVars(char * db,char *table,struct metaByVar *metaByVars)
+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.
{
// select var,val,obj where (var= [and val in (val1,val2)]) or (var= [and val in (val1,val2)]) order by var,val,obj
- struct dyString *dy = newDyString(4096);
- if(db == NULL)
- db = METATBL_DEFAULT_DB;
if(table == NULL)
table = METATBL_DEFAULT_NAME;
+ if(!sqlTableExists(conn,table))
+ return NULL;
+ struct dyString *dy = newDyString(4096);
dyStringPrintf(dy, "select distinct objName,objType,var,varType,val from %s", table);
struct metaByVar *rootVar;
for(rootVar=metaByVars;rootVar!=NULL;rootVar=rootVar->next)
@@ -943,16 +929,9 @@
}
dyStringPrintf(dy, " order by objName, var");
verbose(2, "Query: %s\n",dyStringContents(dy));
- struct sqlConnection *conn = sqlConnect(db);
- if(!sqlTableExists(conn,table))
- {
- dyStringFree(&dy);
- return NULL;
- }
struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
- sqlDisconnect(&conn);
verbose(2, "rows returned: %d\n",slCount(metaTbl));
return metaObjsLoadFromMemory(&metaTbl,TRUE);
}
@@ -1119,20 +1098,21 @@
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.
{
-char *words[48];
+//char *words[48];
char *cloneLine = cloneString(vars);
-int count = chopLine(cloneLine,words);
+int count = chopByWhite(cloneLine,NULL,0);
+char **words = needMem(sizeof(char *) * count);
+count = chopByWhite(cloneLine,words,count);
+//int count = chopLine(cloneLine,words);
struct metaObj *metaObj = NULL;
for( metaObj=metaObjs; metaObj!=NULL; metaObj=metaObj->next )
{
int ix;
struct metaVar *orderedVars = NULL;
- struct metaVar *varsToReorder[48];
- for( ix=0; ix<count; ix++ )
- varsToReorder[ix] = NULL; // Be certain
+ struct metaVar **varsToReorder = needMem(sizeof(struct metaVar *) * count);
struct metaVar *metaVar = NULL;
while((metaVar = slPopHead(&(metaObj->vars))) != NULL)
{
@@ -1162,17 +1142,22 @@
}
}
metaObj->vars = orderedVars;
+ freeMem(varsToReorder);
}
+ freeMem(words);
}
void metaObjRemoveVars(struct metaObj *metaObjs, char *vars)
// Prunes list of vars for an object, freeing the memory. Doesn't touch DB.
{
-char *words[48];
+//char *words[48];
char *cloneLine = cloneString(vars);
-int count = chopLine(cloneLine,words);
+int count = chopByWhite(cloneLine,NULL,0);
+char **words = needMem(sizeof(char *) * count);
+count = chopByWhite(cloneLine,words,count);
+//int count = chopLine(cloneLine,words);
struct metaObj *metaObj = NULL;
for( metaObj=metaObjs; metaObj!=NULL; metaObj=metaObj->next )
{
@@ -1189,8 +1174,9 @@
slReverse(&keepTheseVars);
metaObj->vars = keepTheseVars;
}
+ freeMem(words);
}
// --------------- Free at last ----------------
void metaObjsFree(struct metaObj **metaObjsPtr)