void fastq_stats_read(char *filename, struct fastq_stats *fqs)
/* read from a file */
{
struct lineFile *lf = lineFileOpen(filename, TRUE);
char *line;
char *words[FASTQ_MAX_LEN];
int numWords = 0;
int i, j;
if (!lineFileNext(lf, &line, NULL))
errAbort("bad file, total count section");
fqs->total_count = sqlUnsignedLong(line);
if (!lineFileNext(lf, &line, NULL))
errAbort("bad file, skipped count section");
fqs->all_b = sqlUnsignedLong(line);
if (!lineFileNext(lf, &line, NULL))
errAbort("bad file, skipped count section");
fqs->skipped_count = sqlUnsignedLong(line);
if (!lineFileNext(lf, &line, NULL))
errAbort("bad file, skipped count section");
fqs->kept_count = sqlUnsignedLong(line);
if (!lineFileNext(lf, &line, NULL))
errAbort("bad file, longest read section");
fqs->longest_read = sqlUnsigned(line);
numWords = lineFileChopTab(lf, words);
if (numWords != fqs->longest_read)
errAbort("bad file: original lengths section shoud have %u cols, has %d", fqs->longest_read, numWords);
for (i = 0; i < numWords; i++)
fqs->original_lengths[i] = sqlUnsignedLong(words[i]);
numWords = lineFileChopTab(lf, words);
if (numWords != fqs->longest_read)
errAbort("bad file: trimmed lengths section shoud have %u cols, has %d", fqs->longest_read, numWords);
for (i = 0; i < numWords; i++)
fqs->trimmed_lengths[i] = sqlUnsignedLong(words[i]);
for (i = 0; i <= FASTQ_SANGER_MAX_QUAL; i++)
{
numWords = lineFileChopTab(lf, words);
if (numWords != fqs->longest_read)
errAbort("bad file: before_quals section line %d shoud have %u cols, has %d", i+1, fqs->longest_read, numWords);
for (j = 0; j < numWords; j++)
fqs->before_quals[j][i] = sqlUnsignedLong(words[j]);
}
for (i = 0; i <= FASTQ_SANGER_MAX_QUAL; i++)
{
numWords = lineFileChopTab(lf, words);
if (numWords != fqs->longest_read)
errAbort("bad file: after_quals section line %d shoud have %u cols, has %d", i+1, fqs->longest_read, numWords);
for (j = 0; j < numWords; j++)
fqs->after_quals[j][i] = sqlUnsignedLong(words[j]);
}
lineFileClose(&lf);
}
struct galleryEntry *galLoad(char **row)
/* Load a session entry from a row. A row consists of:
* 0. gbMembers.realName
* 1. namedSessionDb.userName
* 2. gbMembers.idx
* 3. namedSessionDb.sessionName
* 4. namedSessionDb.useCount
* 5. namedSessionDb.settings
* 6. namedSessionDb.contents
* 7. namedSessionDb.firstUse */
{
char *dbIdx, *dbEnd;
struct galleryEntry *ret;
AllocVar(ret);
ret->realName = cloneString(row[0]);
ret->userName = cloneString(row[1]);
cgiDecodeFull(ret->userName, ret->userName, strlen(ret->userName));
ret->sessionName = cloneString(row[3]);
cgiDecodeFull(ret->sessionName, ret->sessionName, strlen(ret->sessionName));
ret->sessionUrl = dyStringCreate("hgS_doOtherUser=submit&hgS_otherUserName=%s&hgS_otherUserSessionName=%s", row[1], row[3]);
ret->imgPath = sessionThumbnailFilePath(row[2], row[3], row[7]);
if (fileExists(ret->imgPath))
ret->imgUri = sessionThumbnailFileUri(row[2], row[3], row[7]);
else
ret->imgUri = NULL;
ret->useCount = sqlUnsignedLong(row[4]);
ret->settings = cloneString(row[5]);
if (startsWith("db=", row[6]))
dbIdx = row[6] + 3;
else
dbIdx = strstr(row[6], "&db=") + 4;
if (dbIdx != NULL)
{
dbEnd = strchr(dbIdx, '&');
if (dbEnd != NULL)
ret->db = cloneStringZ(dbIdx, dbEnd-dbIdx);
else
ret->db = cloneString(dbIdx);
}
else
ret->db = cloneString("n/a");
ret->firstUse = cloneString(row[7]);
char *spacePt = strchr(ret->firstUse, ' ');
if (spacePt != NULL) *spacePt = '\0';
return ret;
}
void cdwJobCleanFailed(int submitId)
/* Check out the symlink to determine its type. */
{
struct sqlConnection *conn = sqlConnect("cdw");
struct dyString *query = dyStringNew(0);
sqlDyStringPrintf(query,
"select id, commandLine, startTime, endTime, returnCode, pid from cdwJob where submitId=%d "
"order by commandLine,CAST(returnCode AS unsigned)",
submitId);
// NOTE we need this CAST on returnCode since it can be -1. we want success 0 first.
// TODO DO we need to add any other conditions such as distinguishing
// between running, queued, and done?
/* Scan through result set finding redundant rows beyond success row. */
struct sqlResult *sr = sqlGetResult(conn, query->string);
char **row;
char *lastCommand = "";
boolean success = FALSE;
struct slInt *list = NULL;
struct slInt *e;
while ((row = sqlNextRow(sr)) != NULL)
{
unsigned int id = sqlUnsigned(row[0]);
char *commandLine = row[1];
unsigned long startTime = sqlUnsignedLong(row[2]);
unsigned long endTime = sqlUnsignedLong(row[3]);
int returnCode = sqlSigned(row[4]);
unsigned int pid = sqlUnsigned(row[5]);
verbose(2, "%u\t%s\t%lu\t%lu\t%d\t%u\t%u\n", id, commandLine, startTime, endTime, returnCode, pid, submitId);
if (sameString(lastCommand, commandLine))
{
if (success) // we already succeeded, the old failure is unwanted baggage.
{
e = slIntNew(id); // or add it to a list of rows whose ids should get removed
slAddHead(&list, e);
}
}
else
{
if (returnCode == 0)
success = TRUE;
else
success = FALSE;
}
// note fields pid and submitId are defined as signed integers in cdwJob table, probably should be unsigned.
lastCommand = cloneString(commandLine);
}
sqlFreeResult(&sr);
slReverse(&list);
for(e=list;e;e=e->next)
{
dyStringClear(query);
sqlDyStringPrintf(query, "delete from cdwJob where id=%u", (unsigned int) e->val);
//printf("%s\n", query->string);
sqlUpdate(conn, query->string);
}
/* Clean up and go home */
dyStringFree(&query);
sqlDisconnect(&conn);
}
