struct mdbObj *getMdbList(char *database)
/* Get list of metaDb objects for a database. */
{
struct sqlConnection *conn = sqlConnect(database);
struct mdbObj *list = mdbObjsQueryAll(conn, metaTable);
sqlDisconnect(&conn);
return list;
}
struct mdbObj *getMdbList(char *databases[], int databaseCount)
/* Get list of metaDb objects for database. */
{
struct mdbObj *mdbList = NULL;
int i;
for (i=0; i<databaseCount; ++i)
{
/* Grab list of all metaDb obj. */
char *database = databases[i];
struct sqlConnection *conn = sqlConnect(database);
struct mdbObj *oneList = mdbObjsQueryAll(conn, metaTable);
verbose(2, "%d objects in %s.%s\n", slCount(mdbList), database, metaTable);
mdbList = slCat(mdbList, oneList);
sqlDisconnect(&conn);
}
return mdbList;
}
void expFind(char *assembly, char *file)
/* Find experiments in metaDb and output .ra file */
{
verbose(1, "Finding experiments in %s:%s\n", assembly, mdb);
struct sqlConnection *connMeta;
struct mdbObj *meta = NULL, *metas = NULL;
struct encodeExp *exp = NULL, *exps = NULL;
struct hash *oldExps, *newExps;
char *key;
int expNum = 0;
FILE *f = mustOpen(file, "w");
/* create hash of keys for existing experiments so we can distinguish new ones */
oldExps = expKeyHashFromTable(connExp, table);
newExps = hashNew(0);
/* read mdb objects from database */
connMeta = sqlConnect(assembly);
metas = mdbObjsQueryAll(connMeta, mdb);
verbose(2, "Found %d objects\n", slCount(metas));
/* order so that oldest have lowest ids */
mdbObjsSortOnVars(&metas, "dateSubmitted lab dataType cell");
/* create new experiments */
while ((meta = slPopHead(&metas)) != NULL)
{
if (!mdbObjIsEncode(meta))
continue;
if (composite != NULL && !mdbObjInComposite(meta, composite))
continue;
exp = encodeExpFromMdb(connMeta,assembly,meta);
if (exp == NULL)
continue;
key = encodeExpKey(exp);
verbose(3, "key: %s\n", key);
if (hashLookup(newExps, key) == NULL &&
hashLookup(oldExps, key) == NULL)
{
verbose(2, "Found new experiment - Date: %s Experiment %d: %s\n",
mdbObjFindValue(meta, "dateSubmitted"), ++expNum, key);
/* save new experiment */
hashAdd(newExps, key, NULL);
slAddHead(&exps, exp);
}
/* Skip other metas belonging to the same exp by:
struct mdbVar *edvs = mdbObjFindEncodeEdvs(connMeta,meta); // Can't use encodeExpVars(exp) because of "None" issues
assert(edvs != NULL);
char *expVars = slPairListToString(edvs,FALSE); // don't bother with quoting since edvs should not have spaces
struct mdbObj *mdbExpObjs = mdbObjsFilterByVars(&metas,expVars,TRUE,TRUE);
freeMem(expVars);
mdbVarsFree(&edvs); // If you want to do this, then encodeExpFromMdb() above should be replaced with encodeExpFromMdbVars()
mdbObjFree(&mdbExpObjs);
// Filtering destroyed sort order // NOTE: Given the re-sort, this may not prove much more efficient
mdbObjsSortOnVars(&metas, "dateSubmitted lab dataType cell");
*/
}
/* write out experiments in .ra format */
slReverse(&exps);
while ((exp = slPopHead(&exps)) != NULL)
{
exp->organism = organism;
encodeExpToRaFile(exp, f);
}
carefulClose(&f);
sqlDisconnect(&connMeta);
}
