void stopUpload(struct sqlConnection *conn)
/* Try and stop current upload. */
{
char *url = trimSpaces(cgiString("url"));
cgiMakeHiddenVar("url", url);
struct edwSubmit *sub = edwMostRecentSubmission(conn, url);
if (sub == NULL)
{
/* Submission hasn't happened yet - remove it from job queue. */
unsigned edwSubmitJobId = 0;
int posInQueue = edwSubmitPositionInQueue(conn, url, &edwSubmitJobId);
if (posInQueue >= 0)
{
char query[256];
sqlSafef(query, sizeof(query), "delete from edwSubmitJob where id=%u", edwSubmitJobId);
sqlUpdate(conn, query);
printf("Removed submission from %s from job queue\n", url);
}
}
else
{
char query[256];
sqlSafef(query, sizeof(query),
"update edwSubmit set errorMessage='Stopped by user.' where id=%u", sub->id);
sqlUpdate(conn, query);
}
monitorSubmission(conn);
}
void notOverlappingSelf(struct sqlConnection *conn, char *url)
/* Ensure we are only submission going on for this URL, allowing for time out
* and command line override. */
{
if (doNow) // Allow command line override
return;
/* Fetch most recent submission from this URL. */
struct edwSubmit *old = edwMostRecentSubmission(conn, url);
if (old == NULL)
return;
/* See if we have something in progress, meaning started but not ended. */
if (old->endUploadTime == 0 && isEmpty(old->errorMessage))
{
/* Check submission last alive time against our usual time out. */
long long maxStartTime = edwSubmitMaxStartTime(old, conn);
if (edwNow() - maxStartTime < edwSingleFileTimeout)
errAbort("Submission of %s already is in progress. Please come back in an hour", url);
}
edwSubmitFree(&old);
}
void edwScriptSubmitStatus()
/* edwScriptSubmitStatus - Programatically check status of submission.. */
{
/* Pause a second - prevent inadvertent harsh denial of service from scripts. */
sleep(2);
edwScriptRegistryFromCgi();
/* Get submission from url. */
struct sqlConnection *conn = edwConnect();
char query[512];
char *url = cgiString("url");
struct edwSubmit *sub = edwMostRecentSubmission(conn, url);
char *status = NULL;
if (sub == NULL)
{
int posInQueue = edwSubmitPositionInQueue(conn, url, NULL);
if (posInQueue == -1)
errAbort("%s has not been submitted", url);
else
status = "pending";
}
else
{
time_t endUploadTime = sub->endUploadTime;
if (!isEmpty(sub->errorMessage))
{
status = "error";
}
else if (endUploadTime == 0)
{
status = "uploading";
}
else
{
safef(query, sizeof(query),
"select count(*) from edwFile where submitId=%u and errorMessage != ''",
sub->id);
int errCount = sqlQuickNum(conn, query);
int newValid = edwSubmitCountNewValid(sub, conn);
if (newValid + errCount < sub->newFiles)
status = "validating";
else if (errCount > 0)
status = "error";
else
status = "success";
}
}
/* Construct JSON result */
struct dyString *dy = dyStringNew(0);
dyStringPrintf(dy, "{\n");
dyStringPrintf(dy, " \"status\": \"%s\"", status);
if (sameString(status, "error"))
{
dyStringPrintf(dy, ",\n");
dyStringPrintf(dy, " \"errors\": [\n");
int errCount = 0;
if (!isEmpty(sub->errorMessage))
{
addErrFile(dy, errCount, sub->url, sub->errorMessage);
++errCount;
}
safef(query, sizeof(query), "select * from edwFile where submitId=%u and errorMessage != ''",
sub->id);
struct edwFile *file, *fileList = edwFileLoadByQuery(conn, query);
for (file = fileList; file != NULL; file = file->next)
{
addErrFile(dy, errCount, file->submitFileName, file->errorMessage);
++errCount;
}
dyStringPrintf(dy, "\n ]\n");
dyStringPrintf(dy, "}\n");
}
else
{
dyStringPrintf(dy, "\n}\n");
}
/* Write out HTTP response */
printf("Content-Length: %d\r\n", dy->stringSize);
puts("Content-Type: application/json; charset=UTF-8\r");
puts("\r");
printf("%s", dy->string);
}
void monitorSubmission(struct sqlConnection *conn)
/* Write out information about submission. */
{
char *url = trimSpaces(cgiString("url"));
cgiMakeHiddenVar("url", url);
struct edwSubmit *sub = edwMostRecentSubmission(conn, url);
time_t startTime = 0, endTime = 0, endUploadTime = 0;
if (sub == NULL)
{
int posInQueue = edwSubmitPositionInQueue(conn, url, NULL);
if (posInQueue == 0)
printf("%s is first in the submission queue, but upload has not started<BR>\n", url);
else if (posInQueue > 0)
printf("%s is in submission queue with %d submissions ahead of it<BR>\n", url, posInQueue);
else
{
printf("%s status unknown.", url);
}
}
else
{
startTime = sub->startUploadTime;
endUploadTime = sub->endUploadTime;
endTime = (endUploadTime ? endUploadTime : edwNow());
int timeSpan = endTime - startTime;
long long thisUploadSize = sub->byteCount - sub->oldBytes;
long long curSize = 0; // Amount of current file we know we've transferred.
/* Print title letting them know if upload is done or in progress. */
printf("<B>Submission by %s is ", userEmail);
if (!isEmpty(sub->errorMessage))
{
if (endUploadTime == 0)
printf("having problems...");
else
printf("stopped by uploader request.");
}
else if (endUploadTime != 0)
{
printf("uploaded.");
}
else
printf("in progress...");
printf("</B><BR>\n");
/* Print URL and how far along we are at the file level. */
if (!isEmpty(sub->errorMessage))
{
printf("<B>error:</B> %s<BR>\n", sub->errorMessage);
cgiMakeButton("getUrl", "try submission again");
printf("<BR>");
}
printf("<B>url:</B> %s<BR>\n", sub->url);
printf("<B>files count:</B> %d<BR>\n", sub->fileCount);
if (sub->oldFiles > 0)
printf("<B>files already in warehouse:</B> %u<BR>\n", sub->oldFiles);
if (sub->metaChangeCount > 0)
printf("<B>old files with new tags in this submission</B> %d<BR>", sub->metaChangeCount);
if (sub->oldFiles != sub->fileCount)
{
printf("<B>files transferred:</B> %u<BR>\n", sub->newFiles);
printf("<B>files remaining:</B> %u<BR>\n", sub->fileCount - sub->oldFiles - sub->newFiles);
}
/* Report validation status */
printf("<B>new files validated:</B> %u of %u<BR>\n", edwSubmitCountNewValid(sub, conn),
sub->newFiles);
/* Print error message, and in case of error skip file-in-transfer info. */
if (isEmpty(sub->errorMessage))
{
/* If possible print information about file en route */
if (endUploadTime == 0)
{
struct edwFile *ef = edwFileInProgress(conn, sub->id);
if (ef != NULL)
{
char path[PATH_LEN];
safef(path, sizeof(path), "%s%s", edwRootDir, ef->edwFileName);
if (ef->endUploadTime > 0)
curSize = ef->size;
else
curSize = paraFetchedSoFar(path);
printf("<B>file in route:</B> %s", ef->submitFileName);
printf(" (%d%% transferred)<BR>\n", (int)(100.0 * curSize / ef->size));
}
}
}
/* Report bytes transferred */
long long transferredThisTime = curSize + sub->newBytes;
printf("<B>total bytes transferred:</B> ");
long long totalTransferred = transferredThisTime + sub->oldBytes;
printLongWithCommas(stdout, totalTransferred);
printf(" of ");
printLongWithCommas(stdout, sub->byteCount);
if (sub->byteCount != 0)
printf(" (%d%%)<BR>\n", (int)(100.0 * totalTransferred / sub->byteCount));
else
printf("<BR>\n");
/* Report transfer speed if possible */
if (isEmpty(sub->errorMessage))
{
if (timeSpan > 0)
{
printf("<B>transfer speed:</B> ");
printLongWithCommas(stdout, (curSize + sub->newBytes)/timeSpan);
printf(" bytes/sec<BR>\n");
}
/* Report start time and duration */
printf("<B>submission started:</B> %s<BR>\n", ctime(&startTime));
struct dyString *duration = edwFormatDuration(timeSpan);
/* Try and give them an ETA if we aren't finished */
if (endUploadTime == 0 && timeSpan > 0)
{
printf("<B>time so far:</B> %s<BR>\n", duration->string);
double bytesPerSecond = (double)transferredThisTime/timeSpan;
long long bytesRemaining = thisUploadSize - curSize - sub->newBytes;
if (bytesPerSecond > 0)
{
long long estimatedFinish = bytesRemaining/bytesPerSecond;
struct dyString *eta = edwFormatDuration(estimatedFinish);
printf("<B>estimated finish in:</B> %s<BR>\n", eta->string);
}
}
else
{
printf("<B>submission time:</B> %s<BR>\n", duration->string);
cgiMakeButton("getUrl", "submit another data set");
}
}
}
cgiMakeButton("monitor", "refresh status");
if (endUploadTime == 0 && isEmpty(sub->errorMessage))
cgiMakeButton(stopButtonName, "stop upload");
printf(" <input type=\"button\" value=\"browse submissions\" "
"onclick=\"window.location.href='edwWebBrowse';\">\n");
edwPrintLogOutButton();
}