static void getSubmittedFile(struct sqlConnection *conn, struct edwFile *bf,
char *submitDir, char *submitUrl, int submitId)
/* We know the submission, we know what the file is supposed to look like. Fetch it.
* If things go badly catch the error, attach it to the submission record, and then
* keep throwing. */
{
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
if (freeSpaceOnFileSystem(edwRootDir) < 2*bf->size)
errAbort("No space left in warehouse!!");
int hostId=0, submitDirId = 0;
int fd = edwOpenAndRecordInDir(conn, submitDir, bf->submitFileName, submitUrl,
&hostId, &submitDirId);
int fileId = edwFileFetch(conn, bf, fd, submitUrl, submitId, submitDirId, hostId);
close(fd);
edwAddQaJob(conn, fileId);
tellSubscribers(conn, submitDir, bf->submitFileName, fileId);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
handleSubmitError(conn, submitId, errCatch->message->string);
/* The handleSubmitError will keep on throwing. */
}
errCatchFree(&errCatch);
}
void edwFileResetTags(struct sqlConnection *conn, struct edwFile *ef, char *newTags)
/* Reset tags on file, strip out old validation and QA, schedule new validation and QA. */
/* Remove existing QA records and rerun QA agent on given file. */
{
long long fileId = ef->id;
/* Update database to let people know format revalidation is in progress. */
char query[4*1024];
sqlSafef(query, sizeof(query), "update edwFile set errorMessage = '%s' where id=%lld",
"Revalidation in progress.", fileId);
sqlUpdate(conn, query);
/* Update tags for file in edwFile table. */
sqlSafef(query, sizeof(query), "update edwFile set tags='%s' where id=%lld", newTags, fileId);
sqlUpdate(conn, query);
/* Get rid of records referring to file in other validation and qa tables. */
sqlSafef(query, sizeof(query), "delete from edwFastqFile where fileId=%lld", fileId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query),
"delete from edwQaPairSampleOverlap where elderFileId=%lld or youngerFileId=%lld",
fileId, fileId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query),
"delete from edwQaPairCorrelation where elderFileId=%lld or youngerFileId=%lld",
fileId, fileId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query), "delete from edwQaEnrich where fileId=%lld", fileId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query), "delete from edwQaContam where fileId=%lld", fileId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query), "delete from edwQaRepeat where fileId=%lld", fileId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query),
"delete from edwQaPairedEndFastq where fileId1=%lld or fileId2=%lld",
fileId, fileId);
sqlUpdate(conn, query);
/* schedule validator */
edwAddQaJob(conn, ef->id);
}
