void hgLoadSqlTab(char *database, char *table, char *createFile,
int inCount, char *inNames[])
/* hgLoadSqlTab - Load table into database from SQL and text files. */
{
struct sqlConnection *conn = sqlConnect(database);
int loadOptions = 0;
int i=0;
boolean oldTable = optionExists("oldTable") || optionExists("append");
if (optionExists("warn"))
loadOptions |= SQL_TAB_FILE_WARN_ON_ERROR;
if (! optionExists("notOnServer"))
loadOptions |= SQL_TAB_FILE_ON_SERVER;
if (! oldTable)
{
struct dyString *dy = readAndReplaceTableName(createFile, table);
sqlRemakeTable(conn, table, dy->string);
dyStringFree(&dy);
}
verbose(1, "Scanning through %d files\n", inCount);
for (i=0; i < inCount; i++)
{
verbose(2, "Loading file %s into table %s\n", inNames[i], table);
if (sameString("stdin", inNames[i]))
sqlLoadTabFile(conn, "/dev/stdin", table,
(loadOptions & ~SQL_TAB_FILE_ON_SERVER));
else
sqlLoadTabFile(conn, inNames[i], table, loadOptions);
}
if (oldTable)
hgHistoryComment(conn, "Add contents of %d text file(s) to table %s.",
inCount, table);
else
hgHistoryComment(conn, "Load table %s directly from .sql and %d text file(s).",
table, inCount);
sqlDisconnect(&conn);
}
void loadPslTable(char *database, struct sqlConnection *conn, char *pslFile)
/* load one psl table */
{
char table[128];
char *tabFile;
boolean indirectLoad = FALSE;
verbose(1, "Processing %s\n", pslFile);
/* determine table name to use */
if (clTableName != NULL)
safef(table, sizeof(table), "%s", clTableName);
else
{
if (endsWith(pslFile, ".gz"))
{
char *stripGz;
stripGz = cloneString(pslFile);
chopSuffix(stripGz);
splitPath(stripGz, NULL, table, NULL);
freeMem(stripGz);
}
else
splitPath(pslFile, NULL, table, NULL);
}
setupTable(database, conn, table);
/* if a bin column is being added or if the input file is
* compressed, we must copy to an intermediate tab file */
indirectLoad = ((pslCreateOpts & PSL_WITH_BIN) != 0) || endsWith(pslFile, ".gz") || !noSort;
if (indirectLoad)
{
tabFile = "psl.tab";
if (pslCreateOpts & PSL_XA_FORMAT)
copyPslXaToTab(pslFile, tabFile);
else
copyPslToTab(pslFile, tabFile);
}
else
tabFile = pslFile;
sqlLoadTabFile(conn, tabFile, table, pslLoadOpts);
if (!noHistory)
hgHistoryComment(conn, "Add psl alignments to %s table", table);
if (indirectLoad && !keep)
unlink(tabFile);
}
void loadDatabase(char *database, char *tab, char *track)
/* Load database from tab file. */
{
struct sqlConnection *conn = sqlConnect(database);
struct dyString *dy = newDyString(1024);
/* First make table definition. */
if (sqlTable != NULL)
{
/* Read from file. */
char *sql, *s;
readInGulp(sqlTable, &sql, NULL);
/* Chop of end-of-statement semicolon if need be. */
s = strchr(sql, ';');
if (s != NULL) *s = 0;
sqlRemakeTable(conn, track, sql);
freez(&sql);
}
else if (!oldTable)
{
/* Create definition statement. */
verbose(1, "Creating table definition for %s\n", track);
sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track);
if (!noBin)
dyStringAppend(dy, " bin smallint unsigned not null,\n");
dyStringAppend(dy, " level int unsigned not null,\n");
dyStringAppend(dy, " tName varchar(255) not null,\n");
dyStringAppend(dy, " tStart int unsigned not null,\n");
dyStringAppend(dy, " tEnd int unsigned not null,\n");
dyStringAppend(dy, " strand char(1) not null,\n");
dyStringAppend(dy, " qName varchar(255) not null,\n");
dyStringAppend(dy, " qStart int unsigned not null,\n");
dyStringAppend(dy, " qEnd int unsigned not null,\n");
dyStringAppend(dy, " chainId int unsigned not null,\n");
dyStringAppend(dy, " ali int unsigned not null,\n");
dyStringAppend(dy, " score double not null,\n");
dyStringAppend(dy, " qOver int not null, \n");
dyStringAppend(dy, " qFar int not null, \n");
dyStringAppend(dy, " qDup int not null, \n");
dyStringAppend(dy, " type varchar(255) not null,\n");
dyStringAppend(dy, " tN int not null, \n");
dyStringAppend(dy, " qN int not null, \n");
dyStringAppend(dy, " tR int not null, \n");
dyStringAppend(dy, " qR int not null, \n");
dyStringAppend(dy, " tNewR int not null, \n");
dyStringAppend(dy, " qNewR int not null, \n");
dyStringAppend(dy, " tOldR int not null, \n");
dyStringAppend(dy, " qOldR int not null, \n");
dyStringAppend(dy, " tTrf int not null, \n");
dyStringAppend(dy, " qTrf int not null, \n");
dyStringAppend(dy, "#Indices\n");
if (!noBin)
dyStringAppend(dy, " INDEX(tName(16),bin),\n");
dyStringAppend(dy, " INDEX(tName(16),tStart)\n");
dyStringAppend(dy, ")\n");
sqlRemakeTable(conn, track, dy->string);
}
dyStringClear(dy);
sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track);
verbose(1, "Loading %s into %s\n", track, database);
sqlUpdate(conn, dy->string);
/* add a comment to the history table and finish up connection */
hgHistoryComment(conn, "Loaded net table %s", track);
sqlDisconnect(&conn);
}
static void loadDatabase(char *database, char *track, int bedSize, struct bedStub *bedList)
/* Load database from bedList. */
{
struct sqlConnection *conn;
struct dyString *dy = newDyString(1024);
char *tab = (char *)NULL;
int loadOptions = (optionExists("onServer") ? SQL_TAB_FILE_ON_SERVER : 0);
if ( ! noLoad )
conn = sqlConnect(database);
if ((char *)NULL != tmpDir)
tab = cloneString(rTempName(tmpDir,"loadBed",".tab"));
else
tab = cloneString("bed.tab");
if (bedDetail && sqlTable == NULL)
errAbort("bedDetail format requires sqlTable option");
if (bedDetail && !strictTab)
errAbort("bedDetail format must be tab separated");
if (bedDetail && !noBin)
noBin = TRUE;
/* First make table definition. */
if (sqlTable != NULL && !oldTable)
{
/* Read from file. */
char *sql, *s;
readInGulp(sqlTable, &sql, NULL);
/* Chop off end-of-statement semicolon if need be. */
s = strchr(sql, ';');
if (s != NULL) *s = 0;
if ( !noLoad )
{
if (renameSqlTable)
{
char *pos = stringIn("CREATE TABLE ", sql);
if (pos == NULL)
errAbort("Can't find CREATE TABLE in %s\n", sqlTable);
char *oldSql = cloneString(sql);
nextWord(&pos); nextWord(&pos);
char *tableName = nextWord(&pos);
sql = replaceChars(oldSql, tableName, track);
}
verbose(1, "Creating table definition for %s\n", track);
sqlRemakeTable(conn, track, sql);
if (!noBin)
addBinToEmptyTable(conn, track);
adjustSqlTableColumns(conn, track, bedSize);
}
freez(&sql);
}
else if (!oldTable)
{
int minLength;
if (noLoad)
minLength=6;
else if (maxChromNameLength)
minLength = maxChromNameLength;
else
minLength = hGetMinIndexLength(database);
verbose(2, "INDEX chrom length: %d\n", minLength);
/* Create definition statement. */
verbose(1, "Creating table definition for %s\n", track);
dyStringPrintf(dy, "CREATE TABLE %s (\n", track);
if (!noBin)
dyStringAppend(dy, " bin smallint unsigned not null,\n");
dyStringAppend(dy, " chrom varchar(255) not null,\n");
dyStringAppend(dy, " chromStart int unsigned not null,\n");
dyStringAppend(dy, " chromEnd int unsigned not null,\n");
if (bedSize >= 4)
maybeBedGraph(4, dy, " name varchar(255) not null,\n");
if (bedSize >= 5)
{
if (allowNegativeScores)
maybeBedGraph(5, dy, " score int not null,\n");
else
maybeBedGraph(5, dy, " score int unsigned not null,\n");
}
if (bedSize >= 6)
maybeBedGraph(6, dy, " strand char(1) not null,\n");
if (bedSize >= 7)
maybeBedGraph(7, dy, " thickStart int unsigned not null,\n");
if (bedSize >= 8)
maybeBedGraph(8, dy, " thickEnd int unsigned not null,\n");
/* As of 2004-11-22 the reserved field is used as itemRgb in code */
if (bedSize >= 9)
maybeBedGraph(9, dy, " reserved int unsigned not null,\n");
if (bedSize >= 10)
maybeBedGraph(10, dy, " blockCount int unsigned not null,\n");
if (bedSize >= 11)
maybeBedGraph(11, dy, " blockSizes longblob not null,\n");
if (bedSize >= 12)
maybeBedGraph(12, dy, " chromStarts longblob not null,\n");
if (bedSize >= 13)
maybeBedGraph(13, dy, " expCount int unsigned not null,\n");
if (bedSize >= 14)
maybeBedGraph(14, dy, " expIds longblob not null,\n");
if (bedSize >= 15)
maybeBedGraph(15, dy, " expScores longblob not null,\n");
dyStringAppend(dy, "#Indices\n");
if (nameIx && (bedSize >= 4) && (0 == bedGraph))
dyStringAppend(dy, " INDEX(name(16)),\n");
if (noBin)
{
dyStringPrintf(dy, " INDEX(chrom(%d),chromStart)\n", minLength);
}
else
{
dyStringPrintf(dy, " INDEX(chrom(%d),bin)\n", minLength);
}
dyStringAppend(dy, ")\n");
if (noLoad)
verbose(2,"%s", dy->string);
else
sqlRemakeTable(conn, track, dy->string);
}
verbose(1, "Saving %s\n", tab);
writeBedTab(tab, bedList, bedSize);
if ( ! noLoad )
{
verbose(1, "Loading %s\n", database);
if (customTrackLoader)
sqlLoadTabFile(conn, tab, track, loadOptions|SQL_TAB_FILE_WARN_ON_WARN);
else
sqlLoadTabFile(conn, tab, track, loadOptions);
if (! noHistory)
{
char comment[256];
/* add a comment to the history table and finish up connection */
safef(comment, sizeof(comment),
"Add %d element(s) from bed list to %s table",
slCount(bedList), track);
hgHistoryComment(conn, comment);
}
if(fillInScoreColumn != NULL)
{
char query[500];
char buf[500];
struct sqlResult *sr;
safef(query, sizeof(query), "select sum(score) from %s", track);
if(sqlQuickQuery(conn, query, buf, sizeof(buf)))
{
unsigned sum = sqlUnsigned(buf);
if (!sum)
{
safef(query, sizeof(query), "select min(%s), max(%s) from %s", fillInScoreColumn, fillInScoreColumn, track);
if ((sr = sqlGetResult(conn, query)) != NULL)
{
char **row = sqlNextRow(sr);
if(row != NULL)
{
float min = sqlFloat(row[0]);
float max = sqlFloat(row[1]);
if ( !(max == -1 && min == -1)) // if score is -1 then ignore, as if it werent present
{
if (max == min || sameString(row[0],row[1])) // this will lead to 'inf' score value in SQL update causing an error
errAbort("Could not set score in table %s max(%s)=min(%s)=%s\n", track, fillInScoreColumn, fillInScoreColumn, row[0]);
sqlFreeResult(&sr);
// Calculate a, b s/t f(x) = ax + b maps min-max => minScore-1000
float a = (1000-minScore) / (max - min);
float b = 1000 - ((1000-minScore) * max) / (max - min);
safef(query, sizeof(query), "update %s set score = round((%f * %s) + %f)", track, a, fillInScoreColumn, b);
int changed = sqlUpdateRows(conn, query, NULL);
verbose(2, "update query: %s; changed: %d\n", query, changed);
}
else
{
sqlFreeResult(&sr);
verbose(2, "score not updated; all values for column %s are -1\n", fillInScoreColumn);
}
}
}
}
}
}
sqlDisconnect(&conn);
/* if temp dir specified, unlink file to make it disappear */
if ((char *)NULL != tmpDir)
unlink(tab);
}
else
verbose(1, "No load option selected, see file: %s\n", tab);
} /* static void loadDatabase() */
void dbTrash(char *db)
/* dbTrash - drop tables from a database older than specified N hours. */
{
char query[256];
struct sqlResult *sr;
char **row;
int updateTimeIx;
int createTimeIx;
int dataLengthIx;
int indexLengthIx;
int nameIx;
int timeIxUsed;
unsigned long long totalSize = 0;
// expiredTableNames: table exists and is in metaInfo and subject to age limits
struct slName *expiredTableNames = NULL;
struct slName *lostTables = NULL; // tables existing but not in metaInfo
unsigned long long lostTableCount = 0;
struct hash *expiredHash = newHash(10); // as determined by metaInfo
struct hash *notExpiredHash = newHash(10);
struct sqlConnection *conn = sqlConnect(db);
if (extFileCheck)
checkExtFile(conn);
time_t ageSeconds = (time_t)(ageHours * 3600); /* age in seconds */
sqlSafef(query,sizeof(query),"select name,UNIX_TIMESTAMP(lastUse) from %s WHERE "
"lastUse < DATE_SUB(NOW(), INTERVAL %ld SECOND);", CT_META_INFO,ageSeconds);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
hashAddInt(expiredHash, row[0], sqlSigned(row[1]));
sqlFreeResult(&sr);
sqlSafef(query,sizeof(query),"select name,UNIX_TIMESTAMP(lastUse) from %s WHERE "
"lastUse >= DATE_SUB(NOW(), INTERVAL %ld SECOND);",CT_META_INFO,ageSeconds);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
hashAddInt(notExpiredHash, row[0], sqlSigned(row[1]));
sqlFreeResult(&sr);
if (tableStatus) // show table status is very expensive, use only when asked
{
/* run through the table status business to get table size information */
sqlSafef(query,sizeof(query),"show table status");
STATUS_INIT;
while ((row = sqlNextRow(sr)) != NULL)
{
/* if not doing history too, and this is the history table, next row */
if ((!historyToo) && (sameWord(row[nameIx],"history")))
continue;
/* also skip the metaInfo table */
if ((!historyToo) && (sameWord(row[nameIx],CT_META_INFO)))
continue;
/* don't delete the extFile table */
if (sameWord(row[nameIx],CT_EXTFILE))
continue;
SCAN_STATUS;
if (hashLookup(expiredHash,row[nameIx]))
{
slNameAddHead(&expiredTableNames, row[nameIx]);
verbose(3,"%s %ld drop %s\n",row[timeIxUsed], (unsigned long)timep,
row[nameIx]);
/* If sizes are non-NULL, add them up */
if ( ((char *)NULL != row[dataLengthIx]) &&
((char *)NULL != row[indexLengthIx]) )
totalSize += sqlLongLong(row[dataLengthIx])
+ sqlLongLong(row[indexLengthIx]);
hashRemove(expiredHash, row[nameIx]);
}
else
{
if (hashLookup(notExpiredHash,row[nameIx]))
verbose(3,"%s %ld OK %s\n",row[timeIxUsed], (unsigned long)timep,
row[nameIx]);
else
{ /* table exists, but not in metaInfo, is it old enough ? */
if (timep < dropTime)
{
slNameAddHead(&expiredTableNames, row[nameIx]);
verbose(2,"%s %ld dropt %s lost table\n",
row[timeIxUsed], (unsigned long)timep, row[nameIx]);
/* If sizes are non-NULL, add them up */
if ( ((char *)NULL != row[dataLengthIx]) &&
((char *)NULL != row[indexLengthIx]) )
totalSize += sqlLongLong(row[dataLengthIx])
+ sqlLongLong(row[indexLengthIx]);
}
else
verbose(3,"%s %ld OKt %s\n",row[timeIxUsed],
(unsigned long)timep, row[nameIx]);
}
}
}
sqlFreeResult(&sr);
}
else
{ // simple 'show tables' is more efficient than 'show table status'
sqlSafef(query,sizeof(query),"show tables");
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
if (hashLookup(expiredHash,row[0]))
{
slNameAddHead(&expiredTableNames, row[0]);
time_t lastUse = (time_t)hashIntVal(expiredHash,row[0]);
struct tm *lastUseTm = localtime(&lastUse);
verbose(3,"%4d-%02d-%02d %02d:%02d:%02d %ld drop %s\n",
lastUseTm->tm_year+1900, lastUseTm->tm_mon+1,
lastUseTm->tm_mday, lastUseTm->tm_hour, lastUseTm->tm_min,
lastUseTm->tm_sec, (unsigned long)lastUse,row[0]);
hashRemove(expiredHash, row[0]);
}
else if (hashLookup(notExpiredHash,row[0]))
{
time_t lastUse = (time_t)hashIntVal(notExpiredHash,row[0]);
struct tm *lastUseTm = localtime(&lastUse);
verbose(3,"%4d-%02d-%02d %02d:%02d:%02d %ld OK %s\n",
lastUseTm->tm_year+1900, lastUseTm->tm_mon+1,
lastUseTm->tm_mday, lastUseTm->tm_hour, lastUseTm->tm_min,
lastUseTm->tm_sec, (unsigned long)lastUse,row[0]);
}
else
{
struct slName *el = slNameNew(row[0]);
slAddHead(&lostTables, el);
}
}
sqlFreeResult(&sr);
lostTableCount = slCount(lostTables);
// If tables exist, but not in metaInfo, check their age to expire them.
// It turns out even this show table status is slow too, so, only
// run thru it if asked to eliminate lost tables. It is better to
// do this operation with the stand-alone perl script on the customTrash
// database machine.
if (delLostTable && lostTables)
{
struct slName *el;
for (el = lostTables; el != NULL; el = el->next)
{
if (sameWord(el->name,"history"))
continue;
if (sameWord(el->name,CT_META_INFO))
continue;
if (sameWord(el->name,CT_EXTFILE))
continue;
boolean oneTableOnly = FALSE; // protect against multiple tables
/* get table time information to see if it is expired */
sqlSafef(query,sizeof(query),"show table status like '%s'", el->name);
STATUS_INIT;
while ((row = sqlNextRow(sr)) != NULL)
{
if (oneTableOnly)
errAbort("ERROR: query: '%s' returned more than one table "
"name\n", query);
else
oneTableOnly = TRUE;
if (differentWord(row[nameIx], el->name))
errAbort("ERROR: query: '%s' did not return table name '%s' != '%s'\n", query, el->name, row[nameIx]);
SCAN_STATUS;
if (timep < dropTime)
{
slNameAddHead(&expiredTableNames, row[nameIx]);
verbose(2,"%s %ld dropt %s lost table\n",
row[timeIxUsed], (unsigned long)timep, row[nameIx]);
}
else
verbose(3,"%s %ld OKt %s\n",
row[timeIxUsed], (unsigned long)timep, row[nameIx]);
}
sqlFreeResult(&sr);
}
}
}
/* perhaps the table was already dropped, but not from the metaInfo */
struct hashEl *elList = hashElListHash(expiredHash);
struct hashEl *el;
for (el = elList; el != NULL; el = el->next)
{
verbose(2,"%s exists in %s only\n", el->name, CT_META_INFO);
if (drop)
ctTouchLastUse(conn, el->name, FALSE); /* removes metaInfo row */
}
if (drop)
{
char comment[256];
if (expiredTableNames)
{
struct slName *el;
int droppedCount = 0;
/* customTrash DB user permissions do not have permissions to
* drop tables. Must use standard special user that has all
* permissions. If we are not using the standard user at this
* point, then switch to it.
*/
if (sameWord(db,CUSTOM_TRASH))
{
sqlDisconnect(&conn);
conn = sqlConnect(db);
}
for (el = expiredTableNames; el != NULL; el = el->next)
{
verbose(2,"# drop %s\n", el->name);
sqlDropTable(conn, el->name);
ctTouchLastUse(conn, el->name, FALSE); /* removes metaInfo row */
++droppedCount;
}
/* add a comment to the history table and finish up connection */
if (tableStatus)
safef(comment, sizeof(comment), "Dropped %d tables with "
"total size %llu, %llu lost tables",
droppedCount, totalSize, lostTableCount);
else
safef(comment, sizeof(comment),
"Dropped %d tables, no size info, %llu lost tables",
droppedCount, lostTableCount);
verbose(2,"# %s\n", comment);
hgHistoryComment(conn, "%s", comment);
}
else
{
safef(comment, sizeof(comment),
"Dropped no tables, none expired, %llu lost tables",
lostTableCount);
verbose(2,"# %s\n", comment);
}
}
else
{
char comment[256];
if (expiredTableNames)
{
int droppedCount = slCount(expiredTableNames);
if (tableStatus)
safef(comment, sizeof(comment), "Would have dropped %d tables with "
"total size %llu, %llu lost tables",
droppedCount, totalSize, lostTableCount);
else
safef(comment, sizeof(comment),
"Would have dropped %d tables, no size info, %llu lost tables",
droppedCount, lostTableCount);
verbose(2,"# %s\n", comment);
}
else
{
safef(comment, sizeof(comment),
"Would have dropped no tables, none expired, %llu lost tables",
lostTableCount);
verbose(2,"# %s\n", comment);
}
}
sqlDisconnect(&conn);
}
void dbTrash(char *db)
/* dbTrash - drop tables from a database older than specified N hours. */
{
char query[256];
struct sqlResult *sr;
char **row;
int updateTimeIx;
int createTimeIx;
int dataLengthIx;
int indexLengthIx;
int nameIx;
int timeIxUsed;
unsigned long long totalSize = 0;
struct slName *tableNames = NULL; /* subject to age limits */
struct hash *expiredHash = newHash(10);
struct hash *notExpiredHash = newHash(10);
struct sqlConnection *conn = sqlConnect(db);
if (extFileCheck)
checkExtFile(conn);
time_t ageSeconds = (time_t)(ageHours * 3600); /* age in seconds */
safef(query,sizeof(query),"select name from %s WHERE "
"lastUse < DATE_SUB(NOW(), INTERVAL %ld SECOND);", CT_META_INFO,ageSeconds);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
hashAddInt(expiredHash, row[0], 1);
sqlFreeResult(&sr);
safef(query,sizeof(query),"select name from %s WHERE "
"lastUse >= DATE_SUB(NOW(), INTERVAL %ld SECOND);",CT_META_INFO,ageSeconds);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
hashAddInt(notExpiredHash, row[0], 1);
sqlFreeResult(&sr);
/* run through the table status business to get table size information */
safef(query,sizeof(query),"show table status");
sr = sqlGetResult(conn, query);
nameIx = sqlFieldColumn(sr, "Name");
createTimeIx = sqlFieldColumn(sr, "Create_time");
updateTimeIx = sqlFieldColumn(sr, "Update_time");
dataLengthIx = sqlFieldColumn(sr, "Data_length");
indexLengthIx = sqlFieldColumn(sr, "Index_length");
while ((row = sqlNextRow(sr)) != NULL)
{
struct tm tm;
time_t timep = 0;
/* if not doing history too, and this is the history table, next row */
if ((!historyToo) && (sameWord(row[nameIx],"history")))
continue;
/* also skip the metaInfo table */
if ((!historyToo) && (sameWord(row[nameIx],CT_META_INFO)))
continue;
/* don't delete the extFile table */
if (sameWord(row[nameIx],CT_EXTFILE))
continue;
/* Update_time is sometimes NULL on MySQL 5
* so if it fails, then check the Create_time
*/
timeIxUsed = updateTimeIx;
if ((row[updateTimeIx] != NULL) &&
(sscanf(row[updateTimeIx], "%4d-%2d-%2d %2d:%2d:%2d",
&(tm.tm_year), &(tm.tm_mon), &(tm.tm_mday),
&(tm.tm_hour), &(tm.tm_min), &(tm.tm_sec)) != 6) )
{
timeIxUsed = createTimeIx;
if (sscanf(row[createTimeIx], "%4d-%2d-%2d %2d:%2d:%2d",
&(tm.tm_year), &(tm.tm_mon), &(tm.tm_mday),
&(tm.tm_hour), &(tm.tm_min), &(tm.tm_sec)) != 6)
{
verbose(2,"%s %s %s\n",
row[createTimeIx],row[updateTimeIx],row[nameIx]);
errAbort("could not parse date %s or %s on table %s\n",
row[createTimeIx], row[updateTimeIx], row[nameIx]);
}
}
tm.tm_year -= 1900;
tm.tm_mon -= 1;
tm.tm_isdst = -1; /* do not know timezone, figure it out */
timep = mktime(&tm);
if (hashLookup(expiredHash,row[nameIx]))
{
slNameAddHead(&tableNames, row[nameIx]);
verbose(3,"%s %ld drop %s\n",row[timeIxUsed], (unsigned long)timep,
row[nameIx]);
/* If sizes are non-NULL, add them up */
if ( ((char *)NULL != row[dataLengthIx]) &&
((char *)NULL != row[indexLengthIx]) )
totalSize += sqlLongLong(row[dataLengthIx])
+ sqlLongLong(row[indexLengthIx]);
hashRemove(expiredHash, row[nameIx]);
}
else
{
if (hashLookup(notExpiredHash,row[nameIx]))
verbose(3,"%s %ld OK %s\n",row[timeIxUsed], (unsigned long)timep,
row[nameIx]);
else
{ /* table exists, but not in metaInfo, is it old enough ? */
if (timep < dropTime)
{
slNameAddHead(&tableNames, row[nameIx]);
verbose(2,"%s %ld dropt %s\n",
row[timeIxUsed], (unsigned long)timep, row[nameIx]);
/* If sizes are non-NULL, add them up */
if ( ((char *)NULL != row[dataLengthIx]) &&
((char *)NULL != row[indexLengthIx]) )
totalSize += sqlLongLong(row[dataLengthIx])
+ sqlLongLong(row[indexLengthIx]);
}
else
verbose(3,"%s %ld OKt %s\n",row[timeIxUsed],
(unsigned long)timep, row[nameIx]);
}
}
}
sqlFreeResult(&sr);
/* perhaps the table was already dropped, but not from the metaInfo */
struct hashEl *elList = hashElListHash(expiredHash);
struct hashEl *el;
for (el = elList; el != NULL; el = el->next)
{
verbose(2,"%s exists in %s only\n", el->name, CT_META_INFO);
if (drop)
ctTouchLastUse(conn, el->name, FALSE); /* removes metaInfo row */
}
if (drop)
{
if (tableNames)
{
char comment[256];
struct slName *el;
int droppedCount = 0;
/* customTrash DB user permissions do not have permissions to
* drop tables. Must use standard special user that has all
* permissions. If we are not using the standard user at this
* point, then switch to it.
*/
if (sameWord(db,CUSTOM_TRASH))
{
sqlDisconnect(&conn);
conn = sqlConnect(db);
}
for (el = tableNames; el != NULL; el = el->next)
{
verbose(2,"# drop %s\n", el->name);
sqlDropTable(conn, el->name);
ctTouchLastUse(conn, el->name, FALSE); /* removes metaInfo row */
++droppedCount;
}
/* add a comment to the history table and finish up connection */
safef(comment, sizeof(comment),
"Dropped %d tables with total size %llu", droppedCount, totalSize);
verbose(2,"# %s\n", comment);
hgHistoryComment(conn, comment);
}
}
sqlDisconnect(&conn);
}
