static void printCladeOrgDbTree(struct jsonWrite *jw)
/* Print out the tree of clades, organisms and dbs as JSON. Each node has value and label
* for menu options; clade nodes and org nodes also have children and default. */
{
jsonWriteListStart(jw, "cladeOrgDb");
struct slPair *clade, *cladeOptions = hGetCladeOptions();
struct dbDb *centralDbDbList = hDbDbList();
for (clade = cladeOptions; clade != NULL; clade = clade->next)
{
jsonWriteObjectStart(jw, NULL);
jsonWriteValueLabel(jw, clade->name, clade->val);
jsonWriteListStart(jw, "children");
struct slPair *org, *orgOptions = hGetGenomeOptionsForClade(clade->name);
for (org = orgOptions; org != NULL; org = org->next)
{
jsonWriteObjectStart(jw, NULL);
jsonWriteValueLabel(jw, org->name, org->val);
jsonWriteListStart(jw, "children");
struct dbDb *dbDb, *dbDbList;
if (isHubTrack(org->name))
dbDbList = trackHubGetDbDbs(clade->name);
else
dbDbList = centralDbDbList;
for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next)
{
if (sameString(org->name, dbDb->genome))
{
jsonWriteObjectStart(jw, NULL);
jsonWriteValueLabel(jw, dbDb->name, dbDb->description);
jsonWriteString(jw, "defaultPos", dbDb->defaultPos);
jsonWriteObjectEnd(jw);
}
}
jsonWriteListEnd(jw); // children (dbs)
jsonWriteString(jw, "default", trimSpaces(hDefaultDbForGenome(org->name)));
jsonWriteObjectEnd(jw); // org
}
jsonWriteListEnd(jw); // children (orgs)
jsonWriteString(jw, "default", trimSpaces(hDefaultGenomeForClade(clade->name)));
jsonWriteObjectEnd(jw); // clade
}
jsonWriteListEnd(jw);
}
void getDbGenomeClade(struct cart *cart, char **retDb, char **retGenome,
char **retClade, struct hash *oldVars)
/* Examine CGI and cart variables to determine which db, genome, or clade
* has been selected, and then adjust as necessary so that all three are
* consistent. Detect changes and reset db-specific cart variables.
* Save db, genome and clade in the cart so it will be consistent hereafter.
* The order of preference here is as follows:
* If we got a request that explicitly names the db, that takes
* highest priority, and we synch the organism to that db.
* If we get a cgi request for a specific organism then we use that
* organism to choose the DB. If just clade, go from there.
* In the cart only, we use the same order of preference.
* If someone requests an Genome we try to give them the same db as
* was in their cart, unless the Genome doesn't match.
*/
{
boolean gotClade = hGotClade();
*retDb = cgiOptionalString(dbCgiName);
*retGenome = cgiOptionalString(orgCgiName);
*retClade = cgiOptionalString(cladeCgiName);
/* phoneHome business */
phoneHome();
/* Was the database passed in as a cgi param?
* If so, it takes precedence and determines the genome. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
/* If no db was passed in as a cgi param then was the organism (a.k.a. genome)
* passed in as a cgi param?
* If so, the we use the proper database for that genome. */
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = getDbForGenome(*retGenome, cart);
*retGenome = hGenome(*retDb);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no cgi params passed in then we need to inspect the session */
else
{
*retDb = cartOptionalString(cart, dbCgiName);
*retGenome = cartOptionalString(cart, orgCgiName);
*retClade = cartOptionalString(cart, cladeCgiName);
/* If there was a db found in the session that determines everything. */
if (*retDb && hDbExists(*retDb))
{
*retGenome = hGenome(*retDb);
}
else if (*retGenome && !sameWord(*retGenome, "0"))
{
*retDb = hDefaultDbForGenome(*retGenome);
}
else if (*retClade && gotClade)
{
*retGenome = hDefaultGenomeForClade(*retClade);
*retDb = getDbForGenome(*retGenome, cart);
}
/* If no organism in the session then get the default db and organism. */
else
{
*retDb = hDefaultDb();
*retGenome = hGenome(*retDb);
}
}
*retDb = cloneString(*retDb);
*retGenome = cloneString(*retGenome);
*retClade = hClade(*retGenome);
/* Detect change of database and reset db-specific cart variables: */
if (oldVars)
{
char *oldDb = hashFindVal(oldVars, "db");
char *oldOrg = hashFindVal(oldVars, "org");
char *oldClade = hashFindVal(oldVars, "clade");
if ((!IS_CART_VAR_EMPTY(oldDb) && differentWord(oldDb, *retDb)) ||
(!IS_CART_VAR_EMPTY(oldOrg) && differentWord(oldOrg, *retGenome)) ||
(!IS_CART_VAR_EMPTY(oldClade) && differentWord(oldClade, *retClade)))
{
/* Change position to default -- unless it was passed in via CGI: */
if (cgiOptionalString("position") == NULL)
cartSetString(cart, "position", hDefaultPos(*retDb));
/* hgNear search term -- unless it was passed in via CGI: */
if (cgiOptionalString("near_search") == NULL)
cartRemove(cart, "near_search");
/* hgBlat results (hgUserPsl track): */
cartRemove(cart, "ss");
/* hgTables correlate: */
cartRemove(cart, "hgta_correlateTrack");
cartRemove(cart, "hgta_correlateTable");
cartRemove(cart, "hgta_correlateGroup");
cartRemove(cart, "hgta_correlateOp");
cartRemove(cart, "hgta_nextCorrelateTrack");
cartRemove(cart, "hgta_nextCorrelateTable");
cartRemove(cart, "hgta_nextCorrelateGroup");
cartRemove(cart, "hgta_nextCorrelateOp");
cartRemove(cart, "hgta_corrWinSize");
cartRemove(cart, "hgta_corrMaxLimitCount");
}
}
/* Save db, genome (as org) and clade in cart. */
cartSetString(cart, "db", *retDb);
cartSetString(cart, "org", *retGenome);
if (gotClade)
cartSetString(cart, "clade", *retClade);
}
