static rc_t VDBDependenciesReportDepend1(const VDBDependencies *self,
const ReportFuncs *f,
uint32_t count, uint32_t indent, bool toreport, uint32_t *missing)
{
KDirectory *dir = NULL;
rc_t rc = 0;
uint32_t i = ~0;
assert(missing);
*missing = 0;
for (i = 0; i < count; ++i) {
bool isMissing = false;
bool local = false;
const char* seq_id = "";
const char* path = NULL;
rc = VDBDependenciesSeqId(self, &seq_id, i);
if (rc != 0 && toreport)
reportErrorStrInt(indent, rc, "VDBDependenciesSeqId",
"origin", "VDatabaseListDependencies", "idx", i);
if (rc == 0) {
rc = VDBDependenciesLocal(self, &local, i);
if (rc != 0 && toreport) {
reportErrorStrInt(indent, rc,
"VDBDependenciesLocal",
"origin", "VDatabaseListDependencies", "idx", i);
}
}
if (rc == 0) {
rc = VDBDependenciesPath(self, &path, i);
if (rc != 0 && toreport) {
reportErrorStrInt(indent, rc, "VDBDependenciesPath",
"origin", "VDatabaseListDependencies", "idx", i);
}
}
if (rc == 0) {
if (!local && (path == NULL || path[0] == '\0')) {
isMissing = true;
++*missing;
}
if (toreport) {
bool reported = false;
if (!isMissing && !local) {
rc_t rc = 0;
bool readable = false;
uint64_t size = ~0;
KTime_t date = 0;
bool ready = false;
if (dir == NULL)
{ rc = KDirectoryNativeDir(&dir); }
assert(!local && path && path[0]);
if (dir != NULL) {
rc = KDirectoryFileSize(dir, &size, "%s", path);
if (rc == 0)
{ rc = KDirectoryDate(dir, &date, "%s", path); }
if (rc == 0) {
const KFile* f = NULL;
rc = KDirectoryOpenFileRead(dir, &f, "%s", path);
if (rc == 0) {
char buffer[1024];
size_t num_read = 0;
size_t bsize =
size > sizeof buffer ? sizeof buffer : size;
rc = KFileReadAll(f,
0, buffer, bsize, &num_read);
if (rc == 0 && num_read != bsize) {
rc = RC(rcVDB, rcFile, rcReading,
rcBuffer, rcExcessive);
}
if (rc == 0)
{ readable = true; }
}
KFileRelease(f);
}
if (rc == 0)
{ ready = true; }
}
if (ready) {
KTime kt;
memset(&kt, 0, sizeof kt);
KTimeLocal(&kt, date);
report(indent, "Dependency", 7,
"index", 'd', i,
"seq_id", 's', seq_id,
"local", 's', local ? "true" : "false",
"path", 's', path,
"size", 'u', size,
"date", 'T', &kt,
"readable", 's', readable ? "true" : "false");
reported = true;
}
else {
report(indent, "Dependency", 5,
"index", 'd', i,
"seq_id", 's', seq_id,
"local", 's', local ? "true" : "false",
"path", 's', path,
"error", 'R', rc);
reported = true;
}
}
if (!reported) {
report(indent, "Dependency", 4,
"index", 'd', i,
"seq_id", 's', seq_id,
"local", 's', local ? "true" : "false",
"path", 's', path == NULL ? "" : path);
}
}
}
if (rc != 0 && !toreport)
{ break; }
}
RELEASE(KDirectory, dir);
return rc;
}
static rc_t align_info(const Params* prm) {
rc_t rc = 0;
const VDatabase* db = NULL;
const VDBManager* mgr = NULL;
const KDBManager *kmgr = NULL;
VSchema* schema = NULL;
bool is_db = false;
if (prm == NULL)
{ return RC(rcExe, rcQuery, rcExecuting, rcParam, rcNull); }
if (rc == 0) {
rc = VDBManagerMakeRead(&mgr, NULL);
DISP_RC(rc, "while calling VDBManagerMakeRead");
}
if (rc == 0) {
rc = VDBManagerOpenKDBManagerRead(mgr, &kmgr);
DISP_RC(rc, "while calling VDBManagerOpenKDBManagerRead");
}
if (rc == 0) {
rc = VDBManagerMakeSRASchema(mgr, &schema);
DISP_RC(rc, "while calling VDBManagerMakeSRASchema");
}
if (rc == 0) {
/* const char path[] = "/panfs/pan1/trace_work/scratch/XXX000013"; */
rc = VDBManagerOpenDBRead(mgr, &db, schema, prm->dbPath);
if (rc == 0) {
is_db = true;
}
else if (rc == SILENT_RC(rcDB, rcMgr, rcOpening, rcDatabase, rcIncorrect)) {
PLOGMSG(klogWarn, (klogWarn,
"'$(path)' is not a database", "path=%s", prm->dbPath));
rc = 0;
}
else {
PLOGERR(klogErr,
(klogErr, rc, "$(path)", "path=%s", prm->dbPath));
}
}
if (is_db) {
if (rc == 0) {
if (prm->paramRef) {
const VDBDependencies* dep = NULL;
uint32_t count = 0;
int i = 0;
rc = VDatabaseListDependencies(db, &dep, false);
DISP_RC2(rc, prm->dbPath,
"while calling VDatabaseListDependencies");
if (rc == 0) {
rc = VDBDependenciesCount(dep, &count);
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesCount");
}
for (i = 0; i < count && rc == 0; ++i) {
bool circular = false;
const char* name = NULL;
const char* path = NULL;
const char* remote = NULL;
bool local = false;
const char* seqId = NULL;
rc = VDBDependenciesCircular(dep, &circular, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesCircular");
break;
}
rc = VDBDependenciesName(dep, &name, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesName");
break;
}
rc = VDBDependenciesPath(dep, &path, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesPath");
break;
}
rc = VDBDependenciesLocal(dep, &local, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesLocal");
break;
}
rc = VDBDependenciesSeqId(dep, &seqId, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesSeqId");
break;
}
rc = VDBDependenciesPathRemote(dep, &remote, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesRemote");
break;
}
OUTMSG(("%s,%s,%s,%s", seqId, name,
(circular ? "true" : "false"),
(local ? "local" : "remote")));
if (path && path[0]) {
OUTMSG((":%s", path));
}
else if (remote && remote[0]) {
OUTMSG(("::%s", remote));
}
OUTMSG(("\n"));
}
DESTRUCT(VDBDependencies, dep);
}
if (prm->paramBamHeader) {
rc_t rc3 = bam_header(db);
if (rc3 != 0 && rc == 0)
{ rc = rc3; }
}
if (prm->paramQuality) {
rc_t rc3 = qual_stats(prm, db);
if (rc3 != 0 && rc == 0)
{ rc = rc3; }
}
}
}
DESTRUCT(VSchema, schema);
DESTRUCT(KDBManager, kmgr);
DESTRUCT(VDBManager, mgr);
DESTRUCT(VDatabase, db);
return rc;
}