int hubPublicAdd(char *table, char *url)
/* hubPublicAdd -- add url to hubPublic table */
{
struct errCatch *errCatch = errCatchNew();
boolean gotWarning = FALSE;
struct trackHub *tHub = NULL;
int dbCount = 0;
if (errCatchStart(errCatch))
tHub = trackHubOpen(url, "hub_1");
errCatchEnd(errCatch);
if (errCatch->gotError)
{
gotWarning = TRUE;
warn("%s", errCatch->message->string);
}
errCatchFree(&errCatch);
if (gotWarning)
return 1;
struct hashEl *hel;
struct hashCookie cookie = hashFirst(tHub->genomeHash);
struct dyString *dy = newDyString(1024);
while ((hel = hashNext(&cookie)) != NULL)
{
dbCount++;
dyStringPrintf(dy, "%s,", trackHubSkipHubName(hel->name));
}
printf("insert into %s (hubUrl,descriptionUrl,shortLabel,longLabel,registrationTime,dbCount,dbList) values (\"%s\",\"%s\", \"%s\", \"%s\", now(),%d, \"%s\");\n",
table, url, tHub->descriptionUrl, tHub->shortLabel, tHub->longLabel, dbCount, dy->string);
return 0;
}
int hubSettingsCheckInit(struct trackHub *hub, struct trackHubCheckOptions *options,
struct dyString *errors)
{
int retVal = 0;
if (hub->version != NULL && options->version == NULL)
options->version = hub->version;
struct trackHubSettingSpec *hubLevel = NULL;
int level = 0;
if (hub->version != NULL)
{
AllocVar(hubLevel);
if ((level = trackHubSettingLevel(hubLevel)) < 0)
{
dyStringPrintf(errors, "Unknown hub support level: %s. Defaulting to 'all'.\n",
hub->level);
retVal = 1;
}
else
options->level = hub->level;
}
verbose(2, "Checking hub '%s'", hub->longLabel);
if (options->level)
verbose(2, " for compliance to level '%s' (use -settings to view)", options->level);
verbose(2, "\n");
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
/* make hash of settings for this version, saving in options */
struct trackHubSettingSpec *setting, *settings =
trackHubSettingsForVersion(options->specHost, options->version);
options->settings = newHash(0);
options->suggest = NULL;
for (setting = settings; setting != NULL; setting = setting->next)
{
hashAdd(options->settings, setting->name, setting);
slNameAddHead(&options->suggest, setting->name);
}
/* TODO: ? also need to check settings not in this list (other tdb fields) */
// TODO: move extra file handling here (out of hubCheck)
if (options->extra != NULL)
{
struct hashCookie cookie = hashFirst(options->extra);
struct hashEl *hel;
while ((hel = hashNext(&cookie)) != NULL)
slNameAddHead(&options->suggest, hel->name);
}
slNameSort(&options->suggest);
verbose(3, "Suggest list has %d settings\n", slCount(options->suggest));
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
dyStringPrintf(errors, "%s", errCatch->message->string);
}
errCatchFree(&errCatch);
return retVal;
}
void cartJsonGetGroupedTrackDb(struct cartJson *cj, struct hash *paramHash)
/* Translate trackDb list (only a subset of the fields) into JSON array of track group objects;
* each group contains an array of track objects that may have subtracks. Send it in a wrapper
* object that includes the database from which it was taken; it's possible that by the time
* this reaches the client, the user might have switched to a new db. */
{
struct jsonWrite *jw = cj->jw;
struct trackDb *fullTrackList = NULL;
struct grp *fullGroupList = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
cartTrackDbInit(cj->cart, &fullTrackList, &fullGroupList, /* useAccessControl=*/TRUE);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
warn("%s", errCatch->message->string);
jsonWriteObjectStart(jw, "groupedTrackDb");
jsonWriteString(jw, "db", cartString(cj->cart, "db"));
jsonWriteListStart(jw, "groupedTrackDb");
jsonWriteListEnd(jw);
jsonWriteObjectEnd(jw);
return;
}
errCatchFree(&errCatch);
struct hash *groupedTrackRefList = hashTracksByGroup(fullTrackList);
// If the optional param 'fields' is given, hash the field names that should be returned.
char *fields = cartJsonOptionalParam(paramHash, "fields");
struct hash *fieldHash = hashFromCommaString(fields);
char *excludeTypes = cartJsonOptionalParam(paramHash, "excludeTypes");
struct hash *excludeTypesHash = hashFromCommaString(excludeTypes);
// Also check for optional parameter 'maxDepth':
int maxDepth = -1;
char *maxDepthStr = cartJsonOptionalParam(paramHash, "maxDepth");
if (isNotEmpty(maxDepthStr))
maxDepth = atoi(maxDepthStr);
jsonWriteObjectStart(jw, "groupedTrackDb");
jsonWriteString(jw, "db", cartString(cj->cart, "db"));
jsonWriteListStart(jw, "groupedTrackDb");
int nonEmptyGroupCount = 0;
struct grp *grp;
for (grp = fullGroupList; grp != NULL; grp = grp->next)
{
struct slRef *tdbRefList = hashFindVal(groupedTrackRefList, grp->name);
if (writeGroupedTrack(jw, grp->name, grp->label, fieldHash, excludeTypesHash,
maxDepth, tdbRefList))
{
nonEmptyGroupCount++;
}
}
if (nonEmptyGroupCount == 0)
{
// Catch-all for assembly hubs that don't declare groups for their tracks: add All Tracks
struct slRef *allTracks = sortedAllTracks(fullTrackList);
(void)writeGroupedTrack(jw, "allTracks", "All Tracks", fieldHash, excludeTypesHash,
maxDepth, allTracks);
}
jsonWriteListEnd(jw);
jsonWriteObjectEnd(jw);
}
int hubPublicCheck(char *table)
/* hubPublicCheck - checks that the labels in hubPublic match what is in the hub labels. */
{
struct sqlConnection *conn = hConnectCentral();
char query[512];
bool hasDescriptionUrl = sqlColumnExists(conn, table, "descriptionUrl");
if (hasDescriptionUrl)
sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList,descriptionUrl from %s",
table);
else
sqlSafef(query, sizeof(query), "select hubUrl, shortLabel,longLabel,dbList from %s",
table);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
int differences = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
char *url = row[0], *shortLabel = row[1], *longLabel = row[2], *dbList = row[3], *descriptionUrl = row[4];
struct errCatch *errCatch = errCatchNew();
boolean gotWarning = FALSE;
struct trackHub *tHub = NULL;
if (errCatchStart(errCatch))
tHub = trackHubOpen(url, "hub_1");
errCatchEnd(errCatch);
if (errCatch->gotError)
{
gotWarning = TRUE;
warn("%s", errCatch->message->string);
}
errCatchFree(&errCatch);
if (gotWarning)
{
continue;
}
if (!sameString(shortLabel, tHub->shortLabel))
{
differences++;
printf("update %s set shortLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->shortLabel, url);
}
if (!sameString(longLabel, tHub->longLabel))
{
differences++;
printf("update %s set longLabel=\"%s\" where hubUrl=\"%s\";\n",table, tHub->longLabel, url);
}
struct hashCookie cookie = hashFirst(tHub->genomeHash);
struct dyString *dy = newDyString(1024);
struct hashEl *hel;
while ((hel = hashNext(&cookie)) != NULL)
dyStringPrintf(dy, "%s,", trackHubSkipHubName(hel->name));
if (!sameString(dy->string, dbList))
{
differences++;
printf("update %s set dbList=\"%s\" where hubUrl=\"%s\";\n",table, dy->string, url);
}
if (hasDescriptionUrl && !isEmpty(tHub->descriptionUrl) && ((descriptionUrl == NULL) || !sameString(descriptionUrl, tHub->descriptionUrl)))
{
differences++;
printf("update %s set descriptionUrl=\"%s\" where hubUrl=\"%s\";\n",table, tHub->descriptionUrl, url);
}
trackHubClose(&tHub);
}
return differences;
}
void bamLoadItemsCore(struct track *tg, boolean isPaired)
/* Load BAM data into tg->items item list, unless zoomed out so far
* that the data would just end up in dense mode and be super-slow. */
{
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
int minAliQual = atoi(cartOrTdbString(cart, tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT));
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
int aliQualShadeMin = 0, aliQualShadeMax = 99, baseQualShadeMin = 0, baseQualShadeMax = 40;
parseIntRangeSetting(tg->tdb, "aliQualRange", &aliQualShadeMin, &aliQualShadeMax);
parseIntRangeSetting(tg->tdb, "baseQualRange", &baseQualShadeMin, &baseQualShadeMax);
struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag,
aliQualShadeMin, aliQualShadeMax, baseQualShadeMin, baseQualShadeMax};
char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
if (fileName == NULL)
{
if (tg->customPt)
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
fileName = bamFileNameFromTable(conn, tg->table, chromName);
hFreeConn(&conn);
}
}
char *fileName2 = hReplaceGbdb(fileName);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tg->tdb, "refUrl");
if (!isPaired)
bamFetchPlus(fileName2, posForBam, addBam, &btd, NULL, refUrl, cacheDir);
else
{
char *setting = trackDbSettingClosestToHomeOrDefault(tg->tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0)
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetchPlus(fileName2, posForBam, addBamPaired, &btd, NULL, refUrl, cacheDir);
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct linkedFeatures *lf = hel->val;
if (lf->start < winEnd && lf->end > winStart)
slAddHead(&(tg->items), lfsFromLf(lf));
}
}
freez(&fileName2);
if (tg->visibility != tvDense)
{
slReverse(&(tg->items));
if (isPaired)
slSort(&(tg->items), linkedFeaturesSeriesCmp);
else if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
slSort(&(tg->items), linkedFeaturesCmpOri);
else if (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_ALI_QUAL))
slSort(&(tg->items), linkedFeaturesCmpScore);
else
slSort(&(tg->items), linkedFeaturesCmpStart);
if (slCount(tg->items) > MAX_ITEMS_FOR_MAPBOX)
{
// flag drawItems to make a mapBox for the whole track
tg->customInt = 1;
tg->mapItem = dontMapItem;
}
}
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}
void edwSubmit(char *submitUrl, char *email)
/* edwSubmit - Submit URL with validated.txt to warehouse. */
{
/* Parse out url a little into submitDir and submitFile */
char *lastSlash = strrchr(submitUrl, '/');
if (lastSlash == NULL)
errAbort("%s is not a valid URL - it has no '/' in it.", submitUrl);
char *submitFile = lastSlash+1;
int submitDirSize = submitFile - submitUrl;
char submitDir[submitDirSize+1];
memcpy(submitDir, submitUrl, submitDirSize);
submitDir[submitDirSize] = 0; // Add trailing zero
/* Make sure user has access. */
struct sqlConnection *conn = edwConnectReadWrite();
struct edwUser *user = edwMustGetUserFromEmail(conn, email);
int userId = user->id;
/* See if we are already running on same submission. If so council patience and quit. */
notOverlappingSelf(conn, submitUrl);
/* Make a submit record. */
int submitId = makeNewEmptySubmitRecord(conn, submitUrl, userId);
/* The next errCatch block will fill these in if all goes well. */
struct submitFileRow *sfrList = NULL, *oldList = NULL, *newList = NULL;
int oldCount = 0;
long long oldBytes = 0, newBytes = 0, byteCount = 0;
/* Start catching errors from here and writing them in submitId. If we don't
* throw we'll end up having a list of all files in the submit in sfrList. */
struct errCatch *errCatch = errCatchNew();
char query[1024];
if (errCatchStart(errCatch))
{
/* Make sure they got a bit of space, enough for a reasonable submit file.
* We do this here just because we can make error message more informative. */
long long diskFreeSpace = freeSpaceOnFileSystem(edwRootDir);
if (diskFreeSpace < 4*1024*1024)
errAbort("No space left in warehouse!");
/* Open remote submission file. This is most likely where we will fail. */
int hostId=0, submitDirId = 0;
long long startUploadTime = edwNow();
int remoteFd = edwOpenAndRecordInDir(conn, submitDir, submitFile, submitUrl,
&hostId, &submitDirId);
/* Copy to local temp file. */
char tempSubmitFile[PATH_LEN];
fetchFdToTempFile(remoteFd, tempSubmitFile);
mustCloseFd(&remoteFd);
long long endUploadTime = edwNow();
/* Calculate MD5 sum, and see if we already have such a file. */
char *md5 = md5HexForFile(tempSubmitFile);
int fileId = findFileGivenMd5AndSubmitDir(conn, md5, submitDirId);
/* If we already have it, then delete temp file, otherwise put file in file table. */
char submitLocalPath[PATH_LEN];
if (fileId != 0)
{
remove(tempSubmitFile);
char submitRelativePath[PATH_LEN];
sqlSafef(query, sizeof(query), "select edwFileName from edwFile where id=%d", fileId);
sqlNeedQuickQuery(conn, query, submitRelativePath, sizeof(submitRelativePath));
safef(submitLocalPath, sizeof(submitLocalPath), "%s%s", edwRootDir, submitRelativePath);
}
else
{
/* Looks like it's the first time we've seen this submission file, so
* save the file itself. We'll get to the records inside the file in a bit. */
fileId = makeNewEmptyFileRecord(conn, submitId, submitDirId, submitFile, 0);
/* Get file/path names for submission file inside warehouse. */
char edwFile[PATH_LEN];
edwMakeFileNameAndPath(fileId, submitFile, edwFile, submitLocalPath);
/* Move file to final resting place and get update time and size from local file system. */
mustRename(tempSubmitFile, submitLocalPath);
time_t updateTime = fileModTime(submitLocalPath);
off_t size = fileSize(submitLocalPath);
/* Update file table which now should be complete including updateTime. */
sqlSafef(query, sizeof(query),
"update edwFile set "
" updateTime=%lld, size=%lld, md5='%s', edwFileName='%s',"
" startUploadTime=%lld, endUploadTime=%lld"
" where id=%u\n",
(long long)updateTime, (long long)size, md5, edwFile,
startUploadTime, endUploadTime, fileId);
sqlUpdate(conn, query);
}
/* By now there is a submit file on the local file system. We parse it out. */
edwParseSubmitFile(conn, submitLocalPath, submitUrl, &sfrList);
/* Save our progress so far to submit table. */
sqlSafef(query, sizeof(query),
"update edwSubmit"
" set submitFileId=%lld, submitDirId=%lld, fileCount=%d where id=%d",
(long long)fileId, (long long)submitDirId, slCount(sfrList), submitId);
sqlUpdate(conn, query);
/* Weed out files we already have. */
struct submitFileRow *sfr, *sfrNext;
for (sfr = sfrList; sfr != NULL; sfr = sfrNext)
{
sfrNext = sfr->next;
struct edwFile *bf = sfr->file;
long long fileId;
if ((fileId = edwGotFile(conn, submitDir, bf->submitFileName, bf->md5, bf->size)) >= 0)
{
++oldCount;
oldBytes += bf->size;
sfr->md5MatchFileId = fileId;
slAddHead(&oldList, sfr);
}
else
slAddHead(&newList, sfr);
byteCount += bf->size;
}
sfrList = NULL;
slReverse(&newList);
slReverse(&oldList);
/* Update database with oldFile count. */
sqlSafef(query, sizeof(query),
"update edwSubmit set oldFiles=%d,oldBytes=%lld,byteCount=%lld where id=%u",
oldCount, oldBytes, byteCount, submitId);
sqlUpdate(conn, query);
/* Deal with old files. This may throw an error. We do it before downloading new
* files since we want to fail fast if we are going to fail. */
int updateCount = handleOldFileTags(conn, oldList, doUpdate);
sqlSafef(query, sizeof(query),
"update edwSubmit set metaChangeCount=%d where id=%u", updateCount, submitId);
sqlUpdate(conn, query);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
handleSubmitError(conn, submitId, errCatch->message->string);
/* The handleSubmitError will keep on throwing. */
}
errCatchFree(&errCatch);
/* Go through list attempting to load the files if we don't already have them. */
struct submitFileRow *sfr;
for (sfr = newList; sfr != NULL; sfr = sfr->next)
{
if (edwSubmitShouldStop(conn, submitId))
break;
struct edwFile *bf = sfr->file;
int submitUrlSize = strlen(submitDir) + strlen(bf->submitFileName) + 1;
char submitUrl[submitUrlSize];
safef(submitUrl, submitUrlSize, "%s%s", submitDir, bf->submitFileName);
if (edwGotFile(conn, submitDir, bf->submitFileName, bf->md5, bf->size)<0)
{
/* We can't get a ID for this file. There's two possible reasons -
* either somebody is in the middle of fetching it or nobody's started.
* If somebody is in the middle of fetching it, assume they died
* if they took more than an hour, and start up another fetch.
* So here we fetch unless somebody else is fetching recently. */
if (edwGettingFile(conn, submitDir, bf->submitFileName) < 0)
{
verbose(1, "Fetching %s\n", bf->submitFileName);
getSubmittedFile(conn, bf, submitDir, submitUrl, submitId);
newBytes += bf->size;
sqlSafef(query, sizeof(query),
"update edwSubmit set newFiles=newFiles+1,newBytes=%lld where id=%d",
newBytes, submitId);
sqlUpdate(conn, query);
}
}
else
{
verbose(2, "Already got %s\n", bf->submitFileName);
sqlSafef(query, sizeof(query), "update edwSubmit set oldFiles=oldFiles+1 where id=%d",
submitId);
sqlUpdate(conn, query);
}
if (sfr->replacesFile != 0)
{
/* What happens when the replacement doesn't validate? */
verbose(2, "Replacing %s with %s\n", sfr->replaces, bf->submitFileName);
sqlSafef(query, sizeof(query),
"update edwFile set replacedBy=%u, deprecated='%s' where id=%u",
bf->id, sfr->replaceReason, sfr->replacesFile);
sqlUpdate(conn, query);
}
}
/* If we made it here, update submit endUploadTime */
sqlSafef(query, sizeof(query),
"update edwSubmit set endUploadTime=%lld where id=%d",
edwNow(), submitId);
sqlUpdate(conn, query);
/* Get a real submission record and then set things up so mail user when all done. */
struct edwSubmit *submit = edwSubmitFromId(conn, submitId);
sqlDisconnect(&conn); // We'll be waiting a while so free connection
waitForValidationAndSendEmail(submit, email);
}
int edwFileFetch(struct sqlConnection *conn, struct edwFile *ef, int fd,
char *submitFileName, unsigned submitId, unsigned submitDirId, unsigned hostId)
/* Fetch file and if successful update a bunch of the fields in ef with the result.
* Returns fileId. */
{
ef->id = makeNewEmptyFileRecord(conn, submitId, submitDirId, ef->submitFileName, ef->size);
/* Update edwSubmit with file in transit info */
char query[256];
sqlSafef(query, sizeof(query), "update edwSubmit set fileIdInTransit=%lld where id=%u",
(long long)ef->id, submitId);
sqlUpdate(conn, query);
sqlSafef(query, sizeof(query), "select paraFetchStreams from edwHost where id=%u", hostId);
int paraFetchStreams = sqlQuickNum(conn, query);
struct paraFetchInterruptContext interruptContext = {.conn=conn, .submitId=submitId};
/* Wrap getting the file, the actual data transfer, with an error catcher that
* will remove partly uploaded files. Perhaps some day we'll attempt to rescue
* ones that are just truncated by downloading the rest, but not now. */
struct errCatch *errCatch = errCatchNew();
char tempName[PATH_LEN] = "";
char edwFile[PATH_LEN] = "", edwPath[PATH_LEN];
if (errCatchStart(errCatch))
{
/* Now make temp file name and open temp file in an atomic operation */
char *tempDir = edwTempDir();
safef(tempName, PATH_LEN, "%sedwSubmitXXXXXX", tempDir);
int localFd = mustMkstemp(tempName);
/* Update file name in database with temp file name so web app can track us. */
char query[PATH_LEN+128];
sqlSafef(query, sizeof(query),
"update edwFile set edwFileName='%s' where id=%lld",
tempName + strlen(edwRootDir), (long long)ef->id);
sqlUpdate(conn, query);
/* Do actual upload tracking how long it takes. */
ef->startUploadTime = edwNow();
mustCloseFd(&localFd);
if (!parallelFetchInterruptable(submitFileName, tempName, paraFetchStreams, 4, FALSE, FALSE,
paraFetchInterruptFunction, &interruptContext))
{
if (interruptContext.isInterrupted)
errAbort("Submission stopped by user.");
else
errAbort("parallel fetch of %s failed", submitFileName);
}
ef->endUploadTime = edwNow();
/* Rename file both in file system and (via ef) database. */
edwMakeFileNameAndPath(ef->id, submitFileName, edwFile, edwPath);
mustRename(tempName, edwPath);
if (endsWith(edwPath, ".gz") && !encode3IsGzipped(edwPath))
errAbort("%s has .gz suffix, but is not gzipped", submitFileName);
ef->edwFileName = cloneString(edwFile);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
/* Attempt to remove any partial file. */
if (tempName[0] != 0)
{
verbose(1, "Removing partial %s\n", tempName);
parallelFetchRemovePartial(tempName);
remove(tempName);
}
handleSubmitError(conn, submitId, errCatch->message->string); // Throws further
assert(FALSE); // We never get here
}
errCatchFree(&errCatch);
/* Now we got the file. We'll go ahead and save the file name and stuff. */
sqlSafef(query, sizeof(query),
"update edwFile set"
" edwFileName='%s', startUploadTime=%lld, endUploadTime=%lld"
" where id = %d"
, ef->edwFileName, ef->startUploadTime, ef->endUploadTime, ef->id);
sqlUpdate(conn, query);
/* Wrap the validations in an error catcher that will save error to file table in database */
errCatch = errCatchNew();
boolean success = FALSE;
if (errCatchStart(errCatch))
{
/* Check MD5 sum here. */
unsigned char md5bin[16];
md5ForFile(edwPath, md5bin);
char md5[33];
hexBinaryString(md5bin, sizeof(md5bin), md5, sizeof(md5));
if (!sameWord(md5, ef->md5))
errAbort("%s has md5 mismatch: %s != %s. File may be corrupted in upload, or file may have "
"been changed since validateManifest was run. Please check that md5 of file "
"before upload is really %s. If it is then try submitting again, otherwise "
"rerun validateManifest and then try submitting again. \n",
ef->submitFileName, ef->md5, md5, ef->md5);
/* Finish updating a bunch more of edwFile record. Note there is a requirement in
* the validFile section that ef->updateTime be updated last. A nonzero ef->updateTime
* is used as a sign of record complete. */
struct dyString *dy = dyStringNew(0); /* Includes tag so query may be long */
sqlDyStringPrintf(dy, "update edwFile set md5='%s',size=%lld,updateTime=%lld",
md5, ef->size, ef->updateTime);
dyStringAppend(dy, ", tags='");
dyStringAppend(dy, ef->tags);
dyStringPrintf(dy, "' where id=%d", ef->id);
sqlUpdate(conn, dy->string);
dyStringFree(&dy);
/* Update edwSubmit so file no longer shown as in transit */
sqlSafef(query, sizeof(query), "update edwSubmit set fileIdInTransit=0 where id=%u", submitId);
sqlUpdate(conn, query);
success = TRUE;
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
handleFileError(conn, submitId, ef->id, errCatch->message->string);
}
return ef->id;
}
void autoUpgradeTableAddSessionKey(struct sqlConnection *conn, char *tableName)
/* Try to upgrade the table by adding sessionKey field
* in a safe way handling success failures and retries
* with multiple CGIs running. */
{
boolean testAgain = checkAutoUpgradeTableResultTimeIsOld(tableName);
if (testAgain)
{
// Get the advisory lock for this table
// This prevents multiple CGI processes from trying to upgrade simultaneously
char lockName[256];
safef(lockName, sizeof lockName, "AUTO_UPGRADE_%s", tableName);
sqlGetLock(conn, lockName);
// Make sure that the table has not been already upgraded by some earlier process.
// We do not want to upgrade more than once.
if (sqlFieldIndex(conn, tableName, "sessionKey") == -1)
{
char result[4096];
// Put a catch around the table upgrade attempt,
// both to allow us to continue if it fails,
// and to catch the error message and save it in the results file
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
char query[256];
sqlSafef(query, sizeof query, "alter table %s add column sessionKey varchar(255) NOT NULL default ''", tableName);
sqlUpdate(conn, query);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
safef(result, sizeof result, "AUTOUPGRADE FAILED\n%s", errCatch->message->string);
}
else
{
safef(result, sizeof result, "OK\n");
}
errCatchFree(&errCatch);
writeAutoUpgradeTableResult(tableName, result);
}
// Release the advisory lock for this table
sqlReleaseLock(conn, lockName);
}
else
{ // in the interests of speed, just use the old result
char *oldResult = readAutoUpgradeTableResult(tableName);
if (oldResult)
{
if (startsWith("AUTOUPGRADE FAILED", oldResult))
{
// cannot do this here since it is too early and the warn handler does not work right
// it ends up writing html and javascript before the cookie and response header have even been finished.
// warn("%s", oldResult);
// instead, save the error message for access later from select places like hgGateway
if (!dyUpgradeError)
dyUpgradeError = dyStringNew(256);
else
dyStringPrintf(dyUpgradeError,"\n");
dyStringPrintf(dyUpgradeError,"%s", oldResult);
}
}
}
}
