boolean chromSeqFileExists(char *db, char *chrom)
/* Check whether chromInfo exists for a database, find the path of the */
/* sequence file for this chromosome and check if the file exists. */
{
char seqFile[512];
struct sqlConnection *conn = sqlConnect(db);
char query[256];
char *res = NULL;
boolean exists = FALSE;
/* if the database exists, check for the chromInfo file */
if (sqlDatabaseExists(db))
{
safef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom);
res = sqlQuickQuery(conn, query, seqFile, 512);
sqlDisconnect(&conn);
}
/* if there is not table or no information in the table or if the table */
/* exists but the file can not be opened return false, otherwise sequence */
/* file exists and return true */
if (res != NULL)
{
/* chromInfo table exists so check that sequence file can be opened */
FILE *f = fopen(seqFile, "rb");
if (f != NULL)
{
exists = TRUE;
fclose(f);
}
}
return exists;
}
boolean chromSeqFileExists(char *db, char *chrom)
/* Check whether chromInfo exists for a database, find the path of the */
/* sequence file for this chromosome and check if the file exists. */
{
char seqFile[512];
struct sqlConnection *conn = sqlConnect(db);
char query[256];
char *res = NULL;
boolean exists = FALSE;
/* if the database exists, check for the chromInfo file */
if (sqlDatabaseExists(db))
{
sqlSafef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom);
res = sqlQuickQuery(conn, query, seqFile, 512);
sqlDisconnect(&conn);
}
/* if there is not table or no information in the table or if the table */
/* exists but the file can not be opened return false, otherwise sequence */
/* file exists and return true */
if (res != NULL)
{
char *seqFile2 = hReplaceGbdb(seqFile);
exists = udcExists(seqFile2);
freeMem(seqFile2);
}
return exists;
}
void printAllAssemblyListHtmlParm(char *db, struct dbDb *dbList,
char *dbCgi, bool allowInactive, char *javascript)
/* Prints to stdout the HTML to render a dropdown list containing the list
* of assemblies for the current genome to choose from. By default,
* this includes only active assemblies with a database (with the
* exception of the default assembly, which will be included even
* if it isn't active).
* param db - The default assembly (the database name) to choose as selected.
* If NULL, no default selection.
* param allowInactive - if set, print all assemblies for this genome,
* even if they're inactive or have no database
*/
{
char *assemblyList[128];
char *values[128];
int numAssemblies = 0;
struct dbDb *cur = NULL;
char *genome = hGenomeOrArchive(db);
char *selAssembly = NULL;
if (genome == NULL)
#ifdef LOWELAB
genome = "Pyrococcus furiosus";
#else
genome = "Human";
#endif
for (cur = dbList; cur != NULL; cur = cur->next)
{
/* Only for this genome */
if (!sameWord(genome, cur->genome))
continue;
/* Save a pointer to the current assembly */
if (sameWord(db, cur->name))
selAssembly = cur->name;
if (allowInactive ||
((cur->active || sameWord(cur->name, db))
&& (trackHubDatabase(db) || sqlDatabaseExists(cur->name))))
{
assemblyList[numAssemblies] = cur->description;
values[numAssemblies] = cur->name;
numAssemblies++;
if (numAssemblies >= ArraySize(assemblyList))
internalErr();
}
}
cgiMakeDropListFull(dbCgi, assemblyList, values, numAssemblies,
selAssembly, javascript);
}
boolean checkDatabases(char *databases)
/* Check all databases in space delimited string exist. */
{
char *dupe = cloneString(databases);
char *s = dupe, *word;
boolean ok = TRUE;
while ((word = nextWord(&s)) != NULL)
{
if (!sqlDatabaseExists(word))
{
ok = FALSE;
break;
}
}
freeMem(dupe);
return ok;
}
static char *otherOrgPosition(struct otherOrg *otherOrg,
struct sqlConnection *conn, char *geneId)
/* Return position of gene ID in other organism or NULL if it doesn't exist;
* also make sure that the gene track is visible, and id highlighted, in
* hgTracks (the destination when this is used). */
{
char *id = otherOrgId(otherOrg, conn, geneId);
if (id != NULL)
{
if (otherOrg->db == NULL || otherOrg->geneTable == NULL
|| !sqlDatabaseExists(otherOrg->db))
return id;
else
return otherOrgPositionFromDb(otherOrg, id);
}
return NULL;
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
static void getItemLabel(struct sqlConnection *conn, char *transMapInfoTbl,
struct sqlConnection *geneConn, char *transMapGeneTbl,
unsigned labelSet,
struct linkedFeatures *lf)
/* get label for a transMap item */
{
struct transMapInfo *info = NULL;
struct transMapGene *gene = NULL;
boolean srcDbExists = FALSE;
if (labelSet & (useOrgCommon|useOrgAbbrv|useOrgDb|useGene))
{
info = transMapInfoQuery(conn, transMapInfoTbl, lf->name);
srcDbExists = sqlDatabaseExists(info->srcDb);
}
if ((labelSet & useGene) && (geneConn != NULL))
{
gene = transMapGeneQuery(geneConn, transMapGeneTbl,
info->srcDb, transMapIdToAcc(info->srcId));
}
struct dyString *label = dyStringNew(64);
if (labelSet & useOrgAbbrv && srcDbExists)
addToLabel(label, orgShortForDb(info->srcDb));
if (labelSet & useOrgCommon && srcDbExists)
addToLabel(label, hOrganism(info->srcDb));
if (labelSet & useOrgDb)
addToLabel(label, info->srcDb);
if (labelSet & useGene)
{
if ((gene != NULL) && (strlen(gene->geneName) > 0))
addToLabel(label, gene->geneName);
else
labelSet |= useAcc; // no gene, so force acc
}
if (labelSet & useAcc)
addToLabel(label, transMapIdToAcc(lf->name));
transMapInfoFree(&info);
transMapGeneFree(&gene);
lf->extra = dyStringCannibalize(&label);
}
static char *otherOrgProteinId(struct otherOrg *otherOrg, struct sqlConnection *conn,
char *geneId)
/* Return protein ID in other organism or NULL if it doesn't exist. */
{
char *otherId = otherOrgId(otherOrg, conn, geneId);
char *protId = NULL;
if (otherOrg->db != NULL && otherId != NULL && otherOrg->idToProtIdSql != NULL
&& sqlDatabaseExists(otherOrg->db))
{
struct sqlConnection *conn = hAllocConn(otherOrg->db);
char query[512];
safef(query, sizeof(query), otherOrg->idToProtIdSql, otherId);
protId = sqlQuickString(conn, query);
hFreeConn(&conn);
}
if (protId == NULL)
{
protId = otherId;
otherId = NULL;
}
freez(&otherId);
return protId;
}
static char *otherOrgExternalId(struct otherOrg *otherOrg, char *localId)
/* Convert other organism UCSC id to external database ID. */
{
char *otherId = NULL;
if (localId != NULL)
{
if (otherOrg->otherIdSql && sqlDatabaseExists(otherOrg->db))
{
struct sqlConnection *conn = hAllocConn(otherOrg->db);
char query[512];
safef(query, sizeof(query), otherOrg->otherIdSql, localId);
otherId = sqlQuickString(conn, query);
if (otherId == NULL && otherOrg->otherIdSql2 != NULL)
{
safef(query, sizeof(query), otherOrg->otherIdSql2, localId);
otherId = sqlQuickString(conn, query);
}
hFreeConn(&conn);
}
else
otherId = cloneString(localId);
}
return otherId;
}
