src/hg/lib/metaTbl.c 1.2
1.2 2010/03/18 23:36:05 tdreszer
Extended API for query and print functions
Index: src/hg/lib/metaTbl.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/metaTbl.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/lib/metaTbl.c 18 Mar 2010 01:48:26 -0000 1.1
+++ src/hg/lib/metaTbl.c 18 Mar 2010 23:36:05 -0000 1.2
@@ -211,11 +211,8 @@
}
/* -------------------------------- End autoSql Generated Code -------------------------------- */
-#define METATBL_DEFAULT_NAME "metaTbl"
-
-
enum metaObjType metaObjTypeStringToEnum(char *objType)
// Convert metadata objType string to enum
{
if(sameWord(objType,"table"))
@@ -257,9 +254,9 @@
}
}
struct metaObj *metadataLineParse(char *line)
-/* Parses a single formatted metadata line. */
+/* Parses a single formatted metadata line into metaObj for updates or queries. */
{
char *words[256]; // A lot!
int thisWord = 0;
struct metaObj *metaObj;
@@ -382,8 +379,112 @@
metaObj->objName, metaObjTypeEnumToString(metaObj->objType),metaObj->vars->var,metaVarTypeEnumToString(metaObj->vars->varType),metaObj->vars->val);
return metaObj;
}
+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 metaObj *metaObj = NULL;
+
+ if(obj == NULL)
+ errAbort("Need obj to create metaObj query object.\n");
+
+ AllocVar(metaObj);
+ metaObj->objName = cloneString(obj);
+ metaObj->objType = (type==NULL?otUnknown:metaObjTypeStringToEnum(type));
+
+ if(var != NULL)
+ {
+ struct metaVar * metaVar;
+ AllocVar(metaVar);
+
+ metaVar->var = cloneString(var);
+ metaVar->varType = (varType==NULL?vtUnknown:metaVarTypeStringToEnum(varType));
+ if(val != NULL)
+ metaVar->val = cloneString(val);
+ metaObj->vars = metaVar; // Only one
+ }
+return metaObj;
+}
+
+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));
+
+ 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);
+
+ // All words are expected to be var=val pairs!
+ for(thisWord=0;thisWord<count;thisWord++)
+ {
+ if(strchr(words[thisWord], '=') == NULL)
+ {
+ errAbort("Expected 'var=val' but found '%s'. This is not properly formatted metadata:\n\t%s\n",words[thisWord],line);
+ //metaObjsFree(&metaObj);
+ //return NULL;
+ }
+ AllocVar(rootVar);
+ char *var = cloneNextWordByDelimiter(&(words[thisWord]),'=');
+ char *val = cloneString(words[thisWord]);
+ struct metaByVar *oldVar = (struct metaByVar *)hashFindVal(varHash, var);
+ if(oldVar)
+ { // FIXME: Could build this for 'or' queries!
+ verbose(1, "The same variable appears twice: %s=%s and %s=%s. Ignoring second value.\n",
+ oldVar->var,oldVar->vals->val,var,val);
+ freeMem(var);
+ freeMem(val);
+ }
+ else
+ {
+ AllocVar(rootVar);
+ rootVar->var = var;
+ AllocVar(limbVal);
+ limbVal->val = val;
+ rootVar->vals = limbVal;
+ hashAdd(varHash, rootVar->var, rootVar);
+ slAddHead(&metaByVars,rootVar);
+ }
+ }
+ slReverse(&metaByVars);
+ verbose(2, "metaByVarsLineParse() first: %s=%s\n",metaByVars->var,metaByVars->vals->val);
+return metaByVars;
+}
+
+struct metaByVar*metaByVarCreate(char *var, char *varType,char *val)
+/* Creates a singular var=val pair struct for metadata queries. */
+{
+struct metaByVar *metaByVar = NULL;
+
+ if(var == NULL)
+ errAbort("Need variable to create metaByVar query object.\n");
+
+ AllocVar(metaByVar);
+ metaByVar->var = cloneString(var);
+ metaByVar->varType = (varType==NULL?vtUnknown:metaVarTypeStringToEnum(varType));
+
+ if(val != NULL)
+ {
+ struct metaLimbVal * limbVal;
+ AllocVar(limbVal);
+
+ limbVal->val = cloneString(val);
+ metaByVar->vals = limbVal; // Only one
+ }
+
+return metaByVar;
+}
+
struct metaObj *metaObjsLoadFromFormattedFile(char *fileName)
// Load all metaObjs from a file containing metadata formatted lines
{
struct metaObj *metaObjs = NULL;
@@ -448,13 +549,13 @@
return metaObjs;
}
-static struct metaRootVar *metaRootVarsLoadFromMemory(struct metaTbl **metaTblPtr,boolean buildHashes)
+static struct metaByVar *metaByVarsLoadFromMemory(struct metaTbl **metaTblPtr,boolean buildHashes)
// Load all metaVars from in memorys metaTbl struct, cannibalize strings. Expects sorted order.
{
-struct metaRootVar *rootVars = NULL;
-struct metaRootVar *rootVar = NULL;
+struct metaByVar *rootVars = NULL;
+struct metaByVar *rootVar = NULL;
struct metaLimbVal *limbVal = NULL;
struct metaLeafObj *leafObj;
struct metaTbl *thisRow;
while((thisRow = slPopHead(metaTblPtr)) != NULL)
@@ -587,9 +688,9 @@
{
// Be sure to check for var existence first, then update
if (!replace)
{
- struct metaObj *objExists = metaObjVarLoadFromTbl(conn,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)
@@ -620,73 +721,215 @@
}
return count;
}
-struct metaObj *metaObjsLoadAllFromTbl(struct sqlConnection *conn,char *tableName)
-// Load all metaObjs from a table (default metaTbl). Will build varHash.
+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.
+// Retruns 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(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);
+
+ struct metaVar *metaVar;
+ for(metaVar=metaObj->vars;metaVar!=NULL;metaVar=metaVar->next)
+ {
+ if(metaVar==metaObj->vars)
+ dyStringPrintf(dy, " and (");
+ else
+ dyStringPrintf(dy, " or ");
+ if(metaVar->var != NULL && metaVar->val != NULL)
+ dyStringPrintf(dy, "(var = '%s' and val = '%s')", metaVar->var, sqlEscapeString(metaVar->val));
+ else if(metaVar->var != NULL)
+ dyStringPrintf(dy, "var = '%s'", metaVar->var);
+ else if(metaVar->val != NULL)
+ dyStringPrintf(dy, "val = '%s'", sqlEscapeString(metaVar->val));
+ else
+ errAbort("metaObjQuery has empty metaVar struct.\n");
+ buildHash = FALSE; // too few variables
+ }
+ if(metaObj->vars != NULL)
+ dyStringPrintf(dy, ")");
+ }
+ dyStringPrintf(dy, " order by objName, var");
+
+ struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
+ return metaObjsLoadFromMemory(&metaTbl,buildHash);
+}
+
+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).
{
- char query[256];
- if(tableName == NULL)
- tableName = METATBL_DEFAULT_NAME;
- safef(query, sizeof(query),
- "select objName,objType,var,varType,val from %s order by objName, var",
- tableName);
- struct metaTbl *metaTbl = metaTblLoadByQuery(conn, query);
- return metaObjsLoadFromMemory(&metaTbl,TRUE);
+if(objName == NULL)
+ return metaObjQuery(conn,table,NULL);
+
+struct metaObj *queryObj = metaObjCreate(objName,NULL,varName,NULL,NULL);
+struct metaObj *resultObj = metaObjQuery(conn,table,queryObj);
+metaObjsFree(&queryObj);
+return resultObj;
}
-struct metaObj *metaObjLoadFromTbl(struct sqlConnection *conn,char *tableName,char *objName)
-// Load a metaObj from a table (default metaTbl). Will build varHash.
+struct metaByVar *metaByVarsQuery(struct sqlConnection *conn,char *table,struct metaByVar *metaByVars)
+// Query the metadata table by vars and vals in metaByVar struct. If metaByVar is NULL query all.
+// Retruns new metaByVar struct fully populated and sorted in var,val,obj order.
{
- char query[256];
- if(tableName == NULL)
- tableName = METATBL_DEFAULT_NAME;
- safef(query, sizeof(query),
- "select objName,objType,var,varType,val from %s where objName = '%s' order by var",
- tableName,objName);
- struct metaTbl *metaTbl = metaTblLoadByQuery(conn, query);
- return metaObjsLoadFromMemory(&metaTbl,TRUE);
+// 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(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)
+ {
+ if(rootVar==metaByVars)
+ dyStringPrintf(dy, " where ");
+ else
+ dyStringPrintf(dy, " or ");
+ dyStringPrintf(dy, "(var = '%s'", rootVar->var);
+
+ struct metaLimbVal *limbVal;
+ for(limbVal=rootVar->vals;limbVal!=NULL;limbVal=limbVal->next)
+ {
+ if(limbVal==rootVar->vals)
+ dyStringPrintf(dy, " and val in (");
+ else
+ dyStringPrintf(dy, ",");
+ dyStringPrintf(dy, "'%s'", sqlEscapeString(limbVal->val));
+ }
+ if(rootVar->vals != NULL)
+ dyStringPrintf(dy, ")");
+ dyStringPrintf(dy, ")");
+ }
+ dyStringPrintf(dy, " order by var, val, objName");
+
+ struct metaTbl *metaTbl = metaTblLoadByQuery(conn, dyStringCannibalize(&dy));
+ return metaByVarsLoadFromMemory(&metaTbl,TRUE);
}
-struct metaObj *metaObjVarLoadFromTbl(struct sqlConnection *conn,char *tableName,char *objName,char *varName)
-// Load a single metadata obj/var pair from a table (default metaTbl). No objHash build
+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.
{
- char query[256];
- if(tableName == NULL)
- tableName = METATBL_DEFAULT_NAME;
- safef(query, sizeof(query),
- "select objName,objType,var,varType,val from %s where objName = '%s' and var = '%s'",
- tableName,objName,varName);
- struct metaTbl *metaTbl = metaTblLoadByQuery(conn, query);
- return metaObjsLoadFromMemory(&metaTbl,FALSE); // No need for has with one var!
+if(varName == NULL)
+ return metaByVarsQuery(conn,table,NULL);
+
+struct metaByVar *queryVar = metaByVarCreate(varName,NULL,val);
+struct metaByVar *resultVar = metaByVarsQuery(conn,table,queryVar);
+metaByVarsFree(&queryVar);
+return resultVar;
}
-struct metaRootVar *metaRootVarsLoadAllFromTbl(struct sqlConnection *conn,char *tableName)
-// Load all metaVars from a table (default metaTbl) for searching var->val->obj. Will build objHash.
+void metaObjPrint(struct metaObj *metaObjs,boolean printLong)
+// prints objs and var=val pairs as formatted metadata lines or long view
{
- char query[256];
- if(tableName == NULL)
- tableName = METATBL_DEFAULT_NAME;
- safef(query, sizeof(query),
- "select objName,objType,var,varType,val from %s order by var, val, objName",
- tableName);
- struct metaTbl *metaTbl = metaTblLoadByQuery(conn, query);
- return metaRootVarsLoadFromMemory(&metaTbl,TRUE);
+struct metaObj *metaObj = NULL;
+for(metaObj=metaObjs;metaObj!=NULL;metaObj=metaObj->next)
+ {
+ if(metaObj->objName == NULL)
+ continue;
+
+ printf("metadata %s %s%s",metaObj->objName,
+ metaObjTypeEnumToString(metaObj->objType),(printLong?"\n\t":" "));
+
+ struct metaVar *metaVar = NULL;
+ for(metaVar=metaObj->vars;metaVar!=NULL;metaVar=metaVar->next)
+ {
+ if(metaVar->var != NULL && metaVar->val != NULL)
+ {
+ printf("%s=",metaVar->var);
+ if(metaVar->varType == vtBinary)
+ printf("binary%s",(printLong?"\n\t":" "));
+ else
+ printf("%s%s",metaVar->val,(printLong?"\n\t":" "));
+ }
+ }
+ printf("\n");
+ }
}
-struct metaRootVar *metaRootVarLoadFromTbl(struct sqlConnection *conn,char *tableName,char *varName)
-// Load a metaVar from a table (default metaTbl) for searching val->obj. Will build objHash
+void metaByVarPrint(struct metaByVar *metaByVars,boolean printLong)
+// prints var=val pairs and objs that go with them single lines or long view
{
- char query[256];
- if(tableName == NULL)
- tableName = METATBL_DEFAULT_NAME;
- safef(query, sizeof(query),
- "select objName,objType,var,val from %s where var = '%s' order by val, objName",
- tableName,varName);
- struct metaTbl *metaTbl = metaTblLoadByQuery(conn, query);
- return metaRootVarsLoadFromMemory(&metaTbl,TRUE);
+struct metaByVar *rootVar = NULL;
+for(rootVar=metaByVars;rootVar!=NULL;rootVar=rootVar->next)
+ {
+ if(rootVar->var == NULL)
+ continue;
+ struct metaLimbVal *limbVal = NULL;
+ for(limbVal=rootVar->vals;limbVal!=NULL;limbVal=limbVal->next)
+ {
+ if(limbVal->val == NULL)
+ continue;
+
+ printf("metaVariable %s=",rootVar->var);
+ if(rootVar->varType == vtBinary)
+ printf("binary%s",(printLong?"\n\t":" "));
+ else
+ printf("%s%s",limbVal->val,(printLong?"\n\t":" "));
+
+ struct metaLeafObj *leafObj = NULL;
+ for(leafObj=limbVal->objs;leafObj!=NULL;leafObj=leafObj->next)
+ {
+ if(leafObj->objName != NULL)
+ printf("%s%s",leafObj->objName,(printLong?"\n\t":" "));
+ }
+ }
+ printf("\n");
+ }
+}
+
+
+int metaObjCount(struct metaObj *metaObjs)
+// returns the count of vars belonging to this obj or objs;
+{
+int count = 0;
+struct metaObj *metaObj = NULL;
+for(metaObj=metaObjs;metaObj!=NULL;metaObj=metaObj->next)
+ {
+ if(metaObj->objName == NULL)
+ continue;
+ struct metaVar *metaVar = NULL;
+ for(metaVar=metaObj->vars;metaVar!=NULL;metaVar=metaVar->next)
+ {
+ if(metaVar->var != NULL && metaVar->val != NULL)
+ count++;
+ }
+ }
+return count;
+}
+
+int metaByVarCount(struct metaByVar *metaByVars)
+// returns the count of objs belonging to this set of vars;
+{
+int count = 0;
+struct metaByVar *rootVar = NULL;
+for(rootVar=metaByVars;rootVar!=NULL;rootVar=rootVar->next)
+ {
+ if(rootVar->var == NULL)
+ continue;
+ struct metaLimbVal *limbVal = NULL;
+ for(limbVal=rootVar->vals;limbVal!=NULL;limbVal=limbVal->next)
+ {
+ if(limbVal->val == NULL)
+ continue;
+ struct metaLeafObj *leafObj = NULL;
+ for(leafObj=limbVal->objs;leafObj!=NULL;leafObj=leafObj->next)
+ {
+ if(leafObj->objName != NULL)
+ count++;
+ }
+ }
+ }
+return count;
}
+
void metaObjsFree(struct metaObj **metaObjsPtr)
// Frees one or more metadata objects and any contained metaVars. Will free any hashes as well.
{
@@ -718,16 +961,16 @@
freez(metaObjsPtr);
}
}
-void metaRootVarsFree(struct metaRootVar **metaRootVarsPtr)
+void metaByVarsFree(struct metaByVar **metaByVarsPtr)
// Frees one or more metadata vars and any contained vals and objs. Will free any hashes as well.
{
-if(metaRootVarsPtr != NULL && *metaRootVarsPtr != NULL)
+if(metaByVarsPtr != NULL && *metaByVarsPtr != NULL)
{
// free all roots
- struct metaRootVar *rootVar = NULL;
- while((rootVar = slPopHead(metaRootVarsPtr)) != NULL)
+ struct metaByVar *rootVar = NULL;
+ while((rootVar = slPopHead(metaByVarsPtr)) != NULL)
{
// Free hash first (shared memory)
if(rootVar->valHash != NULL)
hashFree(&(rootVar->valHash));
@@ -757,9 +1000,9 @@
if(rootVar->var)
freeMem(rootVar->var);
freeMem(rootVar);
}
- freez(metaRootVarsPtr);
+ freez(metaByVarsPtr);
}
}
// TODO: Print formatted metadata lines!