int main(int argc, char *argv[])
/* Process command line. */
{
setlinebuf(stdout);
setlinebuf(stderr);
optionInit(&argc, argv, optionSpecs);
boolean drop = optionExists("drop");
gbVerbInit(optionInt("verbose", 0));
if (gbVerbose >= 5)
sqlMonitorEnable(JKSQL_TRACE);
if (drop)
{
if (argc != 2)
usage();
mgcDropTables(argv[1]);
}
else
{
if (argc != 3)
usage();
workDir = optionVal("workdir", "work/load/mgc");
gbMakeDirs(workDir);
allMgcTables = optionExists("allMgcTables");
mgcDbLoad(argv[1], argv[2]);
}
return 0;
}
void gbMakeFileDirs(char* path)
/* make all of the directories for a file */
{
char* last = strrchr(path, '/');
if (last != NULL)
{
*last = '\0';
gbMakeDirs(path);
*last = '/';
}
}
struct sqlDeleter* sqlDeleterNew(char* tmpDir, boolean verbEnabled)
/* create a new deleter object. If tmpdir is NULL, this will aways
* do direct deletes, rather than falling back to the join/copy on a
* large number of deleted. */
{
struct sqlDeleter* sd;
AllocVar(sd);
sd->lm = lmInit(32*1024);
sd->verbose = verbEnabled;
if (tmpDir != NULL)
{
strcpy(sd->tmpDir, tmpDir);
gbMakeDirs(tmpDir);
}
#ifdef COPY_TO_DELETE_HACK
sd->directMax = DIRECT_MAX;
#endif
return sd;
}
void databaseUpdate(struct gbSelect* select)
/* update the database from genbank state on disk */
{
struct sqlConnection *conn = hAllocConn(gDatabase);
struct gbStatusTbl* statusTbl;
boolean maxShrinkageExceeded;
char typePrefix[32], tmpDir[PATH_LEN];
gbVerbEnter(3, "update %s", gbSelectDesc(select));
/* Setup tmp dir for load, must be unique for each update due to
* initialLoad feature */
if (select->accPrefix != NULL)
safef(typePrefix, sizeof(typePrefix), "%s.%s", gbFmtSelect(select->type),
select->accPrefix);
else
safef(typePrefix, sizeof(typePrefix), "%s", gbFmtSelect(select->type));
safef(tmpDir, sizeof(tmpDir), "%s/%s/%s/%s",
gWorkDir, select->release->name, select->release->genome->database,
typePrefix);
if (!(gOptions.flags & DBLOAD_DRY_RUN))
gbMakeDirs(tmpDir);
/* Build list of entries that need processed. This also flags updates that
* have the change and new entries so we can limit the per-update processing.
*/
statusTbl = gbBuildState(conn, select, &gOptions, gMaxShrinkage, tmpDir,
gbVerbose, FALSE, &maxShrinkageExceeded);
if (maxShrinkageExceeded)
{
fprintf(stderr, "Warning: switching to dryRun mode due to maxShrinkage being exceeded\n");
gMaxShrinkageError = TRUE;
gOptions.flags |= DBLOAD_DRY_RUN;
}
if (gOptions.flags & DBLOAD_DRY_RUN)
{
gbVerbLeave(3, "dry run, skipping update %s", gbSelectDesc(select));
gbStatusTblFree(&statusTbl);
hFreeConn(&conn);
return;
}
checkForStop(); /* last safe place */
/* count global number of extFileChgs */
gExtFileChged += statusTbl->numExtChg;
/* first clean out old and changed */
deleteOutdated(conn, select, statusTbl, tmpDir);
/* meta data MUST be done first, it sets some gbStatus data */
processMetaData(conn, select, statusTbl, tmpDir);
processAligns(conn, select, statusTbl, tmpDir);
/* now it's safe to update the status table, delay commit for initialLoad */
if (gOptions.flags & DBLOAD_INITIAL)
slSafeAddHead(&gPendingStatusUpdates,
gbStatusTblUpdate(statusTbl, conn, FALSE));
else
gbStatusTblUpdate(statusTbl, conn, TRUE);
/* add this and partition to the loaded table, if not already there.
* set the extFile updated flag updates were done or this is the initial load */
updateLoadedTbl(select);
if (gOptions.flags & DBLOAD_INITIAL)
gbLoadedTblSetExtFileUpdated(gLoadedTbl, select);
if ((gOptions.flags & DBLOAD_INITIAL) == 0)
gbLoadedTblCommit(gLoadedTbl);
/* print before freeing memory */
gbVerbLeave(3, "update %s", gbSelectDesc(select));
gbStatusTblFree(&statusTbl);
hFreeConn(&conn);
}
