FIXTURE_TEST_CASE(Test1LocalDep, EmptyFixture) {
rc_t rc = 0;
const char SRR413283[] = "SRR413283";
VPath* acc = NULL;
REQUIRE_RC(VFSManagerMakePath(vmgr, &acc, SRR413283));
const VPath *local = NULL;
REQUIRE_RC_FAIL(VResolverLocal(resolver, acc, &local));
RELEASE(VPath, acc);
const VDatabase *db = NULL;
REQUIRE_RC(VDBManagerOpenDBRead(mgr, &db, NULL, SRR413283));
const VDBDependencies *dep = NULL;
// missing
REQUIRE_RC(VDatabaseListDependencies(db, &dep, true));
uint32_t count = 1;
REQUIRE_RC(VDBDependenciesCount(dep, &count));
CHECK_EQUAL(count, (uint32_t)0);
RELEASE(VDBDependencies, dep);
REQUIRE_RC(VDatabaseListDependencies(db, &dep, false));
REQUIRE_RC(VDBDependenciesCount(dep, &count));
CHECK_EQUAL(count, (uint32_t)1);
RELEASE(VDBDependencies, dep);
RELEASE(VDatabase, db);
RELEASE(VPath, local);
}
FIXTURE_TEST_CASE(TestManyNoDep, EmptyFixture) {
rc_t rc = 0;
const char SRR543323[] = "SRR543323";
VPath* acc = NULL;
REQUIRE_RC(VFSManagerMakePath(vmgr, &acc, SRR543323));
const VPath *local = NULL;
REQUIRE_RC_FAIL(VResolverLocal(resolver, acc, &local));
RELEASE(VPath, acc);
struct VSchema *schema;
REQUIRE_RC(VDBManagerMakeSRASchema(mgr, &schema));
const VDatabase *db = NULL;
REQUIRE_RC(VDBManagerOpenDBRead(mgr, &db, schema, SRR543323));
REQUIRE_RC(VSchemaRelease(schema));
const VDBDependencies *dep = NULL;
// missing
REQUIRE_RC(VDatabaseListDependencies(db, &dep, true));
uint32_t count = 1;
REQUIRE_RC(VDBDependenciesCount(dep, &count));
CHECK_EQUAL(count, (uint32_t)21);
RELEASE(VDBDependencies, dep);
REQUIRE_RC(VDatabaseListDependencies(db, &dep, false));
REQUIRE_RC(VDBDependenciesCount(dep, &count));
CHECK_EQUAL(count, (uint32_t)21);
RELEASE(VDBDependencies, dep);
RELEASE(VDatabase, db);
RELEASE(VPath, local);
}
FIXTURE_TEST_CASE(Test1YesDep, RefseqFixture) {
if (siteless) {
TEST_MESSAGE("Test skipped because site repository does not exist");
return;
}
rc_t rc = 0;
const VDatabase *db = NULL;
const char SRR619505[] = "SRR619505";
REQUIRE_RC(VDBManagerOpenDBRead(mgr, &db, NULL, SRR619505));
RELEASE(VDatabase, db);
VPath* acc = NULL;
REQUIRE_RC(VFSManagerMakePath(vmgr, &acc, SRR619505));
const VPath *local = NULL;
REQUIRE_RC(VResolverLocal(resolver, acc, &local));
RELEASE(VPath, acc);
const String *s = NULL;
REQUIRE_RC(VPathMakeString(local, &s));
REQUIRE(s && s->addr);
REQUIRE_RC(VDBManagerOpenDBRead(mgr, &db, NULL, s->addr));
const VDBDependencies *dep = NULL;
// missing
REQUIRE_RC(VDatabaseListDependencies(db, &dep, true));
uint32_t count = 1;
REQUIRE_RC(VDBDependenciesCount(dep, &count));
CHECK_EQUAL(count, (uint32_t)0);
RELEASE(VDBDependencies, dep);
REQUIRE_RC(VDatabaseListDependencies(db, &dep, false));
REQUIRE_RC(VDBDependenciesCount(dep, &count));
CHECK_EQUAL(count, (uint32_t)1);
RELEASE(VDBDependencies, dep);
RELEASE(VDatabase, db);
free(const_cast<String*>(s));
RELEASE(VPath, local);
}
static rc_t ReportDepend(const ReportFuncs *f,
uint32_t indent, const VDatabase* db)
{
rc_t rc = 0;
const VDBDependencies* dep = NULL;
const char tag[] = "Dependencies";
assert(db);
reportOpen(indent, tag, 0);
rc = VDatabaseListDependencies(db, &dep, false);
if (rc != 0) {
reportError(indent + 1, rc, "VDatabaseListDependencies");
}
else {
uint32_t count = 0;
rc = VDBDependenciesCount(dep, &count);
if (rc != 0) {
reportError(indent + 1, rc, "VDBDependenciesCount");
}
else {
uint32_t missing = 0;
const char tag[] = "List";
rc = VDBDependenciesReportDepend1(dep, f,
count, indent + 2, false, &missing);
if (rc == 0) {
reportOpen(indent + 1, tag, 2, "count", 'd', count,
"missing", 'd', missing);
}
else {
reportOpen(indent + 1, tag, 1, "count", 'd', count);
}
rc = VDBDependenciesReportDepend1(dep, f,
count, indent + 2, true, &missing);
reportClose(indent + 1, tag);
}
}
reportClose(indent, tag);
RELEASE(VDBDependencies, dep);
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;
}
