static struct hash *makeChromHashForTable(struct sqlConnection *conn, char *table)
/* Get a hash of all the chroms that are actually being used for the table.
* This is helpful for assemblies with huge numbers of chroms. */
{
char query[1024];
// Make sure that the table has a chrom field.
// a bbi table will NOT have a chrom field
int cIdx = sqlFieldIndex(conn, table, "chrom");
if (cIdx < 0)
return NULL;
sqlSafef(query, sizeof query, "select distinct chrom, 'dummyvalue' from %s", table);
struct hash *hash = sqlQuickHash(conn, query);
return hash;
}
void cdwReallyRemoveFiles(char *email, char *submitUrl, int fileCount, char *fileIds[])
/* cdwReallyRemoveFiles - Remove files from data warehouse. Generally you want to depricate them
* instead. */
{
/* First convert all fileIds to binary. Do this first so bad command lines get caught. */
long long ids[fileCount];
int i;
for (i = 0; i<fileCount; ++i)
ids[i] = sqlLongLong(fileIds[i]);
/* Get hash of all submissions by user from that URL. Hash is keyed by ascii version of
* submitId. */
struct sqlConnection *conn = cdwConnectReadWrite();
struct cdwUser *user = cdwMustGetUserFromEmail(conn, email);
char query[256];
sqlSafef(query, sizeof(query),
" select cdwSubmit.id,cdwSubmitDir.id from cdwSubmit,cdwSubmitDir "
" where cdwSubmit.submitDirId=cdwSubmitDir.id and userId=%d "
" and cdwSubmitDir.url='%s' ",
user->id, submitUrl);
struct hash *submitHash = sqlQuickHash(conn, query);
/* Make sure that files and submission really go together. */
for (i=0; i<fileCount; ++i)
{
long long fileId = ids[i];
char buf[64];
sqlSafef(query, sizeof(query), "select submitId from cdwFile where id=%lld", fileId);
char *result = sqlQuickQuery(conn, query, buf, sizeof(buf));
if (result == NULL)
errAbort("%lld is not a fileId in the warehouse", fileId);
if (hashLookup(submitHash, result) == NULL)
errAbort("File ID %lld does not belong to submission set based on %s", fileId, submitUrl);
}
/* OK - paranoid checking is done, now let's remove each file from the tables it is in. */
for (i=0; i<fileCount; ++i)
{
cdwReallyRemoveFile(conn, ids[i], really);
}
}
static struct hash* pubsLookupSequences(struct track *tg, struct sqlConnection* conn, char *articleId, bool getSnippet)
/* create a hash with a mapping annotId -> snippet or annotId -> shortSeq for an articleId*/
{
struct dyString *dy = dyStringNew(LARGEBUF);
char *sequenceTable = trackDbRequiredSetting(tg->tdb, "pubsSequenceTable");
// work around sql injection fix problem, suggested by galt
sqlDyStringPrintf(dy, "SELECT annotId, ");
if (getSnippet)
dyStringAppend(dy, "replace(replace(snippet, \"<B>\", \"\\n>>> \"), \"</B>\", \" <<<\\n\")" );
else
dyStringAppend(dy, "concat(substr(sequence,1,4),\"...\",substr(sequence,-4))" );
sqlDyStringPrintf(dy, " FROM %s WHERE articleId='%s' ", sequenceTable, articleId);
// end sql injection fix
struct hash *seqIdHash = sqlQuickHash(conn, dy->string);
//freeMem(sequenceTable); // trackDbRequiredSetting returns a value in a hash, so do not free
freeDyString(&dy);
return seqIdHash;
}
