src/hg/lib/metaTbl.c 1.4
1.4 2010/03/19 21:22:59 tdreszer
Added support routines for hgTrackUi using metaTbl
Index: src/hg/lib/metaTbl.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/metaTbl.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/lib/metaTbl.c 19 Mar 2010 17:34:33 -0000 1.3
+++ src/hg/lib/metaTbl.c 19 Mar 2010 21:22:59 -0000 1.4
@@ -213,8 +213,39 @@
/* -------------------------------- End autoSql Generated Code -------------------------------- */
// ------- (static) convert from autoSql -------
+static void metaVarFree(struct metaVar **metaVarPtr)
+// Frees a single metaVar struct
+{
+ freeMem((*metaVarPtr)->val);
+ freeMem((*metaVarPtr)->var);
+ freez(metaVarPtr);
+}
+
+static void metaLeafObjFree(struct metaLeafObj **leafObjPtr)
+// Frees a single metaVar struct
+{
+ freeMem((*leafObjPtr)->objName);
+ freez(leafObjPtr);
+}
+
+static void metaLimbValFree(struct metaLimbVal **limbValPtr)
+// Frees a single metaVar struct
+{
+struct metaLimbVal *limbVal = *limbValPtr;
+
+ // Free hash first (shared memory)
+ hashFree(&(limbVal->objHash));
+
+ struct metaLeafObj *leafObj = NULL;
+ while((leafObj = slPopHead(&(limbVal->objs))) != NULL)
+ metaLeafObjFree(&leafObj);
+
+ freeMem(limbVal->val);
+ freez(limbValPtr);
+}
+
static struct metaObj *metaObjsLoadFromMemory(struct metaTbl **metaTblPtr,boolean buildHashes)
// Load all metaObjs from in memory metaTbl struct, cannibalize strings. Expects sorted order.
{
struct metaObj *metaObj = NULL;
@@ -252,9 +283,13 @@
freeMem(thisRow);
}
-slReverse(&metaObjs);
+// Finish very last object
+if(metaObjs && metaObjs->vars)
+ slReverse(&(metaObjs->vars));
+if(metaObjs)
+ slReverse(&metaObjs);
return metaObjs;
}
@@ -271,10 +306,12 @@
// Start at root
if (rootVar == NULL || differentString(thisRow->var,rootVar->var) )
{
// Finish last var before starting next!
- if(rootVar != NULL)
- slReverse(&(rootVar->vals));
+ if(rootVars && rootVars->vals && rootVars->vals->objs)
+ slReverse(&(rootVars->vals->objs));
+ if(rootVars && rootVars->vals)
+ slReverse(&(rootVars->vals));
// Start new var
AllocVar(rootVar);
limbVal = NULL; // Very important!
rootVar->var = thisRow->var;
@@ -293,9 +330,9 @@
// Continue with limb
if (limbVal == NULL || differentString(thisRow->val,limbVal->val) )
{
// Finish last val before starting next!
- if(limbVal != NULL)
+ if(limbVal != NULL && limbVal->objs != NULL)
slReverse(&(limbVal->objs));
// Start new val
AllocVar(limbVal);
limbVal->val = thisRow->val; // FIXME: binary?
@@ -320,9 +357,15 @@
freeMem(thisRow);
}
-slReverse(&rootVars);
+// Finish very last object
+if(rootVars && rootVars->vals && rootVars->vals->objs)
+ slReverse(&(rootVars->vals->objs));
+if(rootVars && rootVars->vals)
+ slReverse(&(rootVars->vals));
+if(rootVars && rootVars->vals)
+ slReverse(&rootVars);
return rootVars;
}
@@ -436,11 +479,9 @@
if(oldVar)
{
verbose(1, "The same variable appears twice: %s=%s and %s=%s. Ignoring second value.\n",
oldVar->var,oldVar->val,metaVar->var,metaVar->val);
- freeMem(metaVar->var);
- freeMem(metaVar->val);
- freeMem(metaVar);
+ metaVarFree(&metaVar);
}
else
{
hashAdd(metaObj->varHash, metaVar->var, metaVar); // pointer to struct to resolve type
@@ -622,19 +663,23 @@
return metaObjs;
}
// -------------- Updating the DB --------------
-int metaObjsSetToDb(struct sqlConnection *conn,char *tableName,struct metaObj *metaObjs,boolean replace)
+int metaObjsSetToDb(char * db,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);
+
for(metaObj = metaObjs;metaObj != NULL; metaObj = metaObj->next)
{
// Handle delete requests first
if(metaObj->deleteThis)
@@ -693,9 +738,9 @@
{
// Be sure to check for var existence first, then update
if (!replace)
{
- struct metaObj *objExists = metaObjQueryByObj(conn,tableName,metaObj->objName,metaVar->var);
+ struct metaObj *objExists = metaObjQueryByObj(db,tableName,metaObj->objName,metaVar->var);
if(objExists)
{
if(differentString(metaVar->val,objExists->vars->val)
|| metaVar->varType != objExists->vars->varType)
@@ -723,21 +768,26 @@
sqlUpdate(conn, query);
count++;
}
}
+sqlDisconnect(&conn);
return count;
}
// ------------------ Querys -------------------
-struct metaObj *metaObjQuery(struct sqlConnection *conn,char *table,struct metaObj *metaObj)
+struct metaObj *metaObjQuery(char * db,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;
+
dyStringPrintf(dy, "select objName,objType,var,varType,val from %s", table);
if(metaObj != NULL && metaObj->objName != NULL)
{
dyStringPrintf(dy, " where objName = '%s'", metaObj->objName);
@@ -764,33 +814,39 @@
}
dyStringPrintf(dy, " order by objName, var");
verbose(2, "Query: %s\n",dyStringContents(dy));
+ struct sqlConnection *conn = sqlConnect(db);
struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
+ sqlDisconnect(&conn);
verbose(2, "rows returned: %d\n",slCount(metaTbl));
return metaObjsLoadFromMemory(&metaTbl,buildHash);
}
-struct metaObj *metaObjQueryByObj(struct sqlConnection *conn,char *table,char *objName,char *varName)
+struct metaObj *metaObjQueryByObj(char * db,char *table,char *objName,char *varName)
// Query a single metadata object and optional var from a table (default metaTbl).
{
if(objName == NULL)
- return metaObjQuery(conn,table,NULL);
+ return metaObjQuery(db,table,NULL);
struct metaObj *queryObj = metaObjCreate(objName,NULL,varName,NULL,NULL);
-struct metaObj *resultObj = metaObjQuery(conn,table,queryObj);
+struct metaObj *resultObj = metaObjQuery(db,table,queryObj);
metaObjsFree(&queryObj);
return resultObj;
}
-struct metaByVar *metaByVarsQuery(struct sqlConnection *conn,char *table,struct metaByVar *metaByVars)
+struct metaByVar *metaByVarsQuery(char * db,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;
+
dyStringPrintf(dy, "select distinct objName,objType,var,varType,val from %s", table);
struct metaByVar *rootVar;
for(rootVar=metaByVars;rootVar!=NULL;rootVar=rootVar->next)
@@ -816,33 +872,39 @@
}
dyStringPrintf(dy, " order by var, val, objName");
verbose(2, "Query: %s\n",dyStringContents(dy));
+ struct sqlConnection *conn = sqlConnect(db);
struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
+ sqlDisconnect(&conn);
verbose(2, "rows returned: %d\n",slCount(metaTbl));
return metaByVarsLoadFromMemory(&metaTbl,TRUE);
}
-struct metaByVar *metaByVarQueryByVar(struct sqlConnection *conn,char *table,char *varName,char *val)
+struct metaByVar *metaByVarQueryByVar(char * db,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(conn,table,NULL);
+ return metaByVarsQuery(db,table,NULL);
struct metaByVar *queryVar = metaByVarCreate(varName,NULL,val);
-struct metaByVar *resultVar = metaByVarsQuery(conn,table,queryVar);
+struct metaByVar *resultVar = metaByVarsQuery(db,table,queryVar);
metaByVarsFree(&queryVar);
return resultVar;
}
-struct metaObj *metaObjsQueryByVars(struct sqlConnection *conn,char *table,struct metaByVar *metaByVars)
+struct metaObj *metaObjsQueryByVars(char * db,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;
+
dyStringPrintf(dy, "select distinct objName,objType,var,varType,val from %s", table);
struct metaByVar *rootVar;
for(rootVar=metaByVars;rootVar!=NULL;rootVar=rootVar->next)
@@ -868,9 +930,11 @@
}
dyStringPrintf(dy, " order by objName, var");
verbose(2, "Query: %s\n",dyStringContents(dy));
+ struct sqlConnection *conn = sqlConnect(db);
struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
+ sqlDisconnect(&conn);
verbose(2, "rows returned: %d\n",slCount(metaTbl));
return metaObjsLoadFromMemory(&metaTbl,TRUE);
}
@@ -995,8 +1059,124 @@
}
return count;
}
+// ----------------- Utilities -----------------
+boolean metaObjContains(struct metaObj *metaObj, char *var, char *val)
+// Returns TRUE if object contains var, val or both
+{
+if (metaObj != NULL)
+ {
+ struct metaVar *metaVar;
+ for(metaVar=metaObj->vars;metaVar!=NULL;metaVar=metaVar->next)
+ {
+ if(differentStringNullOk(var,metaVar->var) != 0)
+ continue;
+ if(differentStringNullOk(val,metaVar->val) != 0)
+ continue;
+ return TRUE;
+ }
+ }
+return FALSE;
+}
+
+boolean metaByVarContains(struct metaByVar *metaByVar, char *val, char *obj)
+// Returns TRUE if var contains val, obj or both
+{
+if (metaByVar != NULL)
+ {
+ struct metaLimbVal *limbVal;
+ for(limbVal=metaByVar->vals;limbVal!=NULL;limbVal=limbVal->next)
+ {
+ if(differentStringNullOk(val,limbVal->val) != 0)
+ continue;
+
+ struct metaLeafObj *leafObj;
+ for(leafObj=limbVal->objs;leafObj!=NULL;leafObj=leafObj->next)
+ {
+ if(differentStringNullOk(obj,leafObj->objName) != 0)
+ continue;
+ return TRUE;
+ }
+ }
+ }
+return FALSE;
+}
+
+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 *cloneLine = cloneString(vars);
+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 *metaVar = NULL;
+ while((metaVar = slPopHead(&(metaObj->vars))) != NULL)
+ {
+ ix = stringArrayIx(metaVar->var,words,count);
+ if(ix < 0)
+ slAddHead(&orderedVars,metaVar);
+ else
+ varsToReorder[ix] = metaVar;
+ }
+
+ if(back) // add to front of backward list
+ {
+ for( ix=0; ix<count; ix++ )
+ {
+ if(varsToReorder[ix] != NULL)
+ slAddHead(&orderedVars,varsToReorder[ix]);
+ }
+ }
+ slReverse(&orderedVars);
+
+ if(!back) // Add to front of forward list
+ {
+ for( ix=count-1; ix>=0; ix-- )
+ {
+ if(varsToReorder[ix] != NULL)
+ slAddHead(&orderedVars,varsToReorder[ix]);
+ }
+ }
+
+ metaObj->vars = orderedVars;
+ }
+}
+
+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 *cloneLine = cloneString(vars);
+int count = chopLine(cloneLine,words);
+
+struct metaObj *metaObj = NULL;
+for( metaObj=metaObjs; metaObj!=NULL; metaObj=metaObj->next )
+ {
+ int ix;
+ struct metaVar *keepTheseVars = NULL;
+
+ struct metaVar *metaVar = NULL;
+ while((metaVar = slPopHead(&(metaObj->vars))) != NULL)
+ {
+ ix = stringArrayIx(metaVar->var,words,count);
+ if(ix < 0)
+ slAddHead(&keepTheseVars,metaVar);
+ }
+
+ slReverse(&keepTheseVars);
+ metaObj->vars = keepTheseVars;
+ }
+}
// --------------- Free at last ----------------
void metaObjsFree(struct metaObj **metaObjsPtr)
// Frees one or more metadata objects and any contained metaVars. Will free any hashes as well.
@@ -1008,23 +1188,16 @@
struct metaObj *metaObj = NULL;
while((metaObj = slPopHead(metaObjsPtr)) != NULL)
{
// Free hash first (shared memory)
- if(metaObj->varHash != NULL)
hashFree(&(metaObj->varHash));
// free all leaves
struct metaVar *metaVar = NULL;
while((metaVar = slPopHead(&(metaObj->vars))) != NULL)
- {
- if(metaVar->val)
- freeMem(metaVar->val);
- if(metaVar->var)
- freeMem(metaVar->var);
- freeMem(metaVar);
- }
+ metaVarFree(&metaVar);
+
// The rest of root
- if(metaObj->objName)
freeMem(metaObj->objName);
freeMem(metaObj);
}
freez(metaObjsPtr);
@@ -1040,32 +1213,15 @@
struct metaByVar *rootVar = NULL;
while((rootVar = slPopHead(metaByVarsPtr)) != NULL)
{
// Free hash first (shared memory)
- if(rootVar->valHash != NULL)
hashFree(&(rootVar->valHash));
// free all limbs
struct metaLimbVal *limbVal = NULL;
while((limbVal = slPopHead(&(rootVar->vals))) != NULL)
- {
- // Free hash first (shared memory)
- if(limbVal->objHash != NULL)
- hashFree(&(limbVal->objHash));
+ metaLimbValFree(&limbVal);
- // free all leaves
- struct metaLeafObj *leafObj = NULL;
- while((leafObj = slPopHead(&(limbVal->objs))) != NULL)
- {
- if(leafObj->objName != NULL)
- freeMem(leafObj->objName);
- freeMem(leafObj);
- }
- // The rest of limb
- if(limbVal->val)
- freeMem(limbVal->val);
- freeMem(limbVal);
- }
// The rest of root
if(rootVar->var)
freeMem(rootVar->var);
freeMem(rootVar);