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);
}
static rc_t resolve_accession( VFSManager * vfs_mgr, const char * accession, const String ** path )
{
VResolver * resolver;
rc_t rc = VFSManagerGetResolver( vfs_mgr, &resolver );
if ( rc == 0 )
{
const VPath * vpath;
rc = VPathMakeSysPath( ( VPath** )&vpath, accession );
if ( rc == 0 )
{
const VPath * rpath;
rc = VResolverLocal( resolver, vpath, &rpath );
if ( GetRCState( rc ) == rcNotFound )
rc = VResolverRemote( resolver, vpath, &rpath, NULL );
if ( rc == 0 )
{
const String * s;
rc = VPathMakeString( rpath, &s );
if ( rc == 0 )
{
rc = StringCopy ( path, s );
free ((void*)s);
}
VPathRelease ( rpath );
}
VPathRelease ( vpath );
}
VResolverRelease( resolver );
}
return rc;
}
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);
}
string CVResolver::Resolve(const string& acc_or_path) const
{
if ( !CVPath::IsPlainAccession(acc_or_path) ) {
// already a path
return acc_or_path;
}
CVPath acc(m_Mgr, acc_or_path, CVPath::eAcc);
const VPath* path;
rc_t rc = VResolverLocal(*this, acc, &path);
if ( rc ) {
rc = VResolverRemote(*this, eProtocolNone, acc, &path);
}
if ( rc ) {
if ( CDirEntry(acc_or_path).Exists() ) {
// local file
return acc_or_path;
}
NCBI_THROW2_FMT(CSraException, eNotFound,
"Cannot find acc path: "<<acc_or_path, rc);
}
return CVPath(path).ToString();
}
/* ResolveTablePath
* takes either an accession or path
* substitutes any arguments
* resolves via SRAPath mgr if present
*/
rc_t ResolveTablePath ( const SRAMgr *mgr,
char *path, size_t psize, const char *spec, va_list args )
{
#if OLD_SRAPATH_MGR
int len;
char tblpath [ 4096 ];
const SRAPath *pmgr = mgr -> _pmgr;
/* if no path manager or if the spec string has embedded path separators,
then this can't be an accession - just print it out */
if ( mgr -> _pmgr == NULL || strchr( spec, '/' ) != NULL )
{
len = vsnprintf ( path, psize, spec, args );
if ( len < 0 || ( size_t ) len >= psize )
return RC ( rcSRA, rcTable, rcOpening, rcPath, rcExcessive );
return 0;
}
/* create a copy - not likely to be too large */
len = vsnprintf ( tblpath, sizeof tblpath, spec, args );
if ( len < 0 || ( size_t ) len >= sizeof tblpath )
return RC ( rcSRA, rcTable, rcOpening, rcPath, rcExcessive );
/* test if the path exists in current directory, i.e. with assumed dot */
if ( ! SRAPathTest ( pmgr, tblpath ) )
{
rc_t rc = SRAPathFind ( pmgr, tblpath, path, psize );
if ( rc == 0 )
return 0;
}
/* use the path given */
if ( ( size_t ) len >= psize )
return RC ( rcSRA, rcTable, rcOpening, rcBuffer, rcInsufficient );
strcpy ( path, tblpath );
return 0;
#else
VFSManager *vfs;
rc_t rc = VFSManagerMake ( & vfs );
if ( rc == 0 )
{
VPath *accession;
const VPath *tblpath = NULL;
rc = VFSManagerVMakePath ( vfs, & accession, spec, args );
if ( rc == 0 )
{
rc = VResolverLocal ( ( const VResolver* ) mgr -> _pmgr, accession, & tblpath );
if ( rc == 0 )
{
size_t size;
rc = VPathReadPath ( tblpath, path, psize, & size );
VPathRelease ( tblpath );
}
VPathRelease ( accession );
}
VFSManagerRelease ( vfs );
}
return rc;
#endif
}