rc_t vdi_repo( const Vector * v )
{
KConfig * cfg;
rc_t rc = KConfigMake( &cfg, NULL );
if ( rc == 0 )
{
const KRepositoryMgr * repomgr;
rc = KConfigMakeRepositoryMgrRead( cfg, &repomgr );
{
if ( VectorLength( v ) < 2 )
{
rc = vdi_repo_all( repomgr, true );
}
else
{
const String * which_repo = VectorGet( v, 1 );
if ( which_repo != NULL )
{
int32_t repo_id = index_of_match( which_repo, 4, "user", "site", "remote", "all" );
if ( repo_id < 0 || repo_id > 3 )
rc = KOutMsg( "unknow repository '%S'", which_repo );
else
rc = vdi_sub_repo( repomgr, v, which_repo, repo_id );
}
}
KRepositoryMgrRelease( repomgr );
}
KConfigRelease ( cfg );
}
return rc;
}
/* Make
*/
static
rc_t SRAMgrInitPath ( SRAMgr *mgr, const KDirectory *wd )
{
#if OLD_SRAPATH_MGR
/* try to make the path manager */
rc_t rc = SRAPathMake ( & mgr -> _pmgr, wd );
if ( GetRCState ( rc ) == rcNotFound && GetRCTarget ( rc ) == rcDylib )
{
/* we are operating outside of the archive */
assert ( mgr -> _pmgr == NULL );
rc = 0;
}
return rc;
#else
KConfig *kfg;
rc_t rc = KConfigMake ( & kfg, NULL );
if ( rc == 0 )
{
VFSManager *vfs;
rc = VFSManagerMake ( & vfs );
if ( rc == 0 )
{
rc = VFSManagerMakeResolver ( vfs, ( VResolver** ) & mgr -> _pmgr, kfg );
VFSManagerRelease ( vfs );
}
KConfigRelease ( kfg );
}
if ( rc != 0 )
mgr -> _pmgr = NULL;
return 0;
#endif
}
LIB_EXPORT rc_t CC ascp_locate(const char **ascp_bin, const char **private_file,
bool use_config, bool status)
{
static const char *bin = NULL;
static const char *key = NULL;
rc_t rc = 0;
KConfig *cfg = NULL;
bool found = false;
if (ascp_bin == NULL || private_file == NULL) {
return RC(rcNS, rcFile, rcCopying, rcParam, rcNull);
}
*ascp_bin = *private_file = NULL;
rc = returnAscp(bin, key, ascp_bin, private_file, &found);
if (rc != 0 || found) {
return rc;
}
rc = KConfigMake(&cfg, NULL);
if (rc != 0) {
return rc;
}
if (_KConfigAscpDisabled(cfg, status)) {
if (status) {
STSMSG(STS_INFO, ("Use of Aspera transfer is disabled "
"by the configuration, using HTTP transfer"));
}
}
else {
KDirectory *dir = NULL;
rc = _KConfigGetAscp(cfg, &bin, &key);
if (bin != NULL) {
assert(key && !rc);
RELEASE(KConfig, cfg);
rc = returnAscp(bin, key, ascp_bin, private_file, &found);
if (rc != 0 || found) {
return rc;
}
}
rc = KDirectoryNativeDir(&dir);
if (rc != 0) {
return rc;
}
while (ascp_path(&bin, &key)) {
if (_SystemHelp(bin, status)) {
if (_KDirectoryFileFound(dir, key, status)) {
break;
}
}
}
RELEASE(KDirectory, dir);
}
RELEASE(KConfig, cfg);
rc = returnAscp(bin, key, ascp_bin, private_file, &found);
if (rc != 0 || found) {
return rc;
}
else {
return RC(rcNS, rcFile, rcCopying, rcFile, rcNotFound);
}
}
DepFixture(const char *path)
: mgr(NULL)
, vmgr(NULL)
, resolver(NULL)
, siteless(false)
{
rc_t rc = 0;
KDirectory *wd = NULL;
if (KDirectoryNativeDir(&wd)) {
FAIL("failed to KDirectoryNativeDir");
}
const KDirectory *dir = NULL;
KConfig *cfg = NULL;
if (KDirectoryOpenDirRead(wd, &dir, false, path)) {
FAIL("failed to KDirectoryOpenDirRead()");
}
if (KConfigMake(&cfg, dir)) {
FAIL("failed to KConfigMake()");
}
RELEASE(KDirectory, dir);
if (VFSManagerMakeFromKfg(&vmgr, cfg)) {
FAIL("failed to VFSManagerMakeFromKfg()");
}
if (VFSManagerGetResolver(vmgr, &resolver)) {
FAIL("failed to VFSManagerGetResolver");
}
String *result = NULL;
rc = KConfigReadString(cfg, "repository/site/main/tracearc/root",
&result);
if (rc != 0) {
if (rc == SILENT_RC(rcKFG, rcNode, rcOpening, rcPath, rcNotFound)) {
rc = 0;
siteless = true;
}
else {
FAIL(
"failed to KConfigReadString(repository/site/main/tracearc/root)");
}
}
else {
assert(result);
KPathType t = KDirectoryPathType(wd, result->addr);
if (t != kptDir) {
siteless = true;
}
}
RELEASE(String, result);
RELEASE(KConfig, cfg);
if (VDBManagerMakeReadWithVFSManager(&mgr, NULL, vmgr)) {
FAIL("failed to VDBManagerMakeReadWithVFSManager()");
}
RELEASE(KDirectory, wd);
}
CKConfig::CKConfig(void)
{
KConfig* cfg;
if ( rc_t rc = KConfigMake(&cfg, 0) ) {
*x_InitPtr() = 0;
NCBI_THROW2(CSraException, eInitFailed,
"Cannot create KConfig", rc);
}
*x_InitPtr() = cfg;
}
LIB_EXPORT rc_t CC ascp_locate(const char **ascp_bin, const char **private_file,
bool use_config, bool status)
{
rc_t rc = 0;
KConfig *cfg = NULL;
if (ascp_bin == NULL || private_file == NULL) {
return RC(rcNS, rcFile, rcCopying, rcParam, rcNull);
}
*ascp_bin = *private_file = NULL;
rc = KConfigMake(&cfg, NULL);
if (rc != 0) {
return rc;
}
if (_KConfigAscpDisabled(cfg, status)) {
if (status) {
STSMSG(STS_INFO, ("Use of Aspera transfer is disabled "
"by the configuration, using HTTP transfer"));
}
}
else {
KDirectory *dir = NULL;
const char *bin = NULL;
const char *key = NULL;
rc = _KConfigGetAscp(cfg, ascp_bin, private_file);
if (*ascp_bin != NULL) {
assert(*private_file && !rc);
RELEASE(KConfig, cfg);
return 0;
}
rc = KDirectoryNativeDir(&dir);
if (rc != 0) {
return rc;
}
while (ascp_path(&bin, &key)) {
if (_SystemHelp(bin, status)) {
if (_KDirectoryFileFound(dir, key, status)) {
*ascp_bin = string_dup_measure(bin, NULL);
*private_file = string_dup_measure(key, NULL);
if (*ascp_bin == NULL || *private_file == NULL) {
free((void*)*ascp_bin);
free((void*)*private_file);
*ascp_bin = *private_file = NULL;
return RC(rcNS,
rcStorage, rcAllocating, rcMemory, rcExhausted);
}
break;
}
}
}
RELEASE(KDirectory, dir);
}
RELEASE(KConfig, cfg);
return rc;
}
rc_t CC KMain(int argc, char* argv[]) {
rc_t rc = 0;
Params prm;
KConfig* cfg = NULL;
if (rc == 0)
{ rc = ParamsConstruct(argc, argv, &prm); }
if (rc == 0) {
rc = KConfigMake(&cfg, NULL);
DISP_RC(rc, "while calling KConfigMake");
}
if (rc == 0) {
if (prm.modeSetNode)
{ rc = SetNode(cfg, &prm); }
if (prm.modeShowCfg)
{ rc = ShowConfig(cfg, &prm); }
if (prm.modeShowFiles) {
rc_t rc3 = ShowFiles(cfg, &prm);
if (rc3 != 0 && rc == 0)
{ rc = rc3; }
}
if (prm.modeShowModules) {
rc_t rc3 = ShowModules(cfg, &prm);
if (rc3 != 0 && rc == 0)
{ rc = rc3; }
}
if (prm.modeShowLoadPath) {
const char* path = NULL;
rc_t rc3 = KConfigGetLoadPath(cfg, &path);
if (rc3 == 0) {
if (path != NULL && path[0])
{ OUTMSG(("%s\n", path)); }
}
else if (rc == 0)
{ rc = rc3; }
}
}
if (prm.modeShowEnv)
{ ShowEnv(&prm); }
RELEASE(KConfig, cfg);
if (rc == 0 && prm.modeCreate)
{ rc = CreateConfig(argv[0]); }
ParamsDestruct(&prm);
return rc;
}
LIB_EXPORT rc_t CC aspera_options(AscpOptions *opt) {
KConfig *cfg = NULL;
rc_t rc = 0;
if (opt == NULL) {
return RC(rcNS, rcFile, rcVisiting, rcParam, rcNull);
}
memset(opt, 0, sizeof *opt);
rc = KConfigMake(&cfg, NULL);
if (rc == 0) {
rc = _KConfigGetAscpRate(cfg, &opt->target_rate);
opt->disabled = _KConfigAscpDisabled(cfg, false);
}
RELEASE(KConfig, cfg);
return rc;
}
LIB_EXPORT rc_t CC RefSeqMgr_Make( const RefSeqMgr** cself, const VDBManager* vmgr,
uint32_t reader_options, size_t cache, uint32_t keep_open_num )
{
rc_t rc = 0;
RefSeqMgr* obj = NULL;
if ( cself == NULL || vmgr == NULL )
{
rc = RC( rcAlign, rcIndex, rcConstructing, rcParam, rcNull );
}
else
{
obj = calloc( 1, sizeof( *obj ) );
if ( obj == NULL )
{
rc = RC( rcAlign, rcIndex, rcConstructing, rcMemory, rcExhausted );
}
else
{
rc = KConfigMake( &obj->kfg, NULL );
if ( rc == 0 )
{
rc = VDBManagerAddRef( vmgr );
if ( rc == 0 )
{
obj->vmgr = vmgr;
obj->cache = cache;
obj->num_open_max = keep_open_num;
obj->reader_options = reader_options;
}
}
}
}
if ( rc == 0 )
{
*cself = obj;
/* ALIGN_DBG( "max_open: %u", obj->num_open_max ); */
}
else
{
RefSeqMgr_Release( obj );
ALIGN_DBGERR( rc );
}
return rc;
}
LIB_EXPORT rc_t CC KNSManagerMake ( KNSManager **mgrp )
{
KConfig* kfg;
rc_t rc = KConfigMake(&kfg, NULL);
if ( rc == 0 )
{
rc_t rc2;
rc = KNSManagerMakeConfig ( mgrp, kfg );
if ( rc == 0 )
KNSManagerLoadAWS ( *mgrp );
rc2 = KConfigRelease ( kfg );
if ( rc == 0 )
{
rc = rc2;
}
}
return rc;
}
/*)) Loading config. BTW, resource is a name of file or URL
((*/
LIB_EXPORT
rc_t CC
XFS_LoadConfig_ZHR (
const char * Resource,
const struct KConfig ** Config
)
{
rc_t RCt;
const struct KFile * File;
struct KConfig * TmpConfig;
RCt = 0;
TmpConfig = NULL;
File = NULL;
if ( Resource == NULL || Config == NULL ) {
return XFS_RC ( rcNull );
}
* Config = NULL;
/* Trying to open resource as file */
RCt = XFS_OpenResourceRead_MHR ( Resource, & File );
if ( RCt == 0 ) {
RCt = KConfigMake (
& TmpConfig,
NULL /* We need new clear config each time */
);
if ( RCt == 0 ) {
RCt = KConfigLoadFile ( TmpConfig, Resource, File );
if ( RCt == 0 ) {
* Config = TmpConfig;
}
else {
KConfigRelease ( TmpConfig );
}
}
KFileRelease ( File );
}
return RCt;
} /* XFS_LoadConfig_ZHR () */
static rc_t check_if_schema_exists( KDirectory * dir, const char * schema_name )
{
KConfig * cfg;
rc_t rc = KConfigMake ( &cfg, NULL );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "check_if_schema_exists:KConfigMake() failed" );
}
else
{
const KConfigNode *node;
rc = KConfigOpenNodeRead ( cfg, &node, "vdb/schema/paths" );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "check_if_schema_exists:KConfigOpenNodeRead( 'vdb/schema/paths' ) failed" );
}
else
{
char buffer[ 1024 ];
size_t num_read;
rc = KConfigNodeRead ( node, 0, buffer, sizeof buffer, &num_read, NULL );
if ( rc != 0 )
{
LOGERR( klogErr, rc, "check_if_schema_exists:KConfigNodeRead() failed" );
}
else
{
uint32_t path_type;
buffer[ num_read ] = 0;
path_type = KDirectoryPathType ( dir, "%s/%s", buffer, schema_name );
if ( ( path_type & kptFile ) == 0 )
{
rc = RC( rcExe, rcFile, rcConstructing, rcParam, rcInvalid );
}
}
KConfigNodeRelease ( node );
}
KConfigRelease ( cfg );
}
return rc;
}
LIB_EXPORT rc_t CC aspera_get(
const char *ascp_bin, const char *private_file, const char *aSrc,
const char *dest, AscpOptions *opt)
{
char path[PATH_MAX] = "";
AscpOptions dummy;
bool status = false;
int64_t prev = -1;
int attempt = 0;
KDirectory *dir = NULL;
TQuitting *quitting = NULL;
const char *src = aSrc;
rc_t rc = KDirectoryNativeDir(&dir);
if (rc != 0) {
return rc;
}
if (ascp_bin == NULL || private_file == NULL ||
src == NULL || dest == NULL)
{
return RC(rcNS, rcFile, rcCopying, rcParam, rcNull);
}
if (opt == NULL) {
memset(&dummy, 0, sizeof dummy);
opt = &dummy;
}
if (opt->ascp_options == NULL && opt->target_rate[0] == '\0') {
KConfig *cfg = NULL;
rc_t rc = KConfigMake(&cfg, NULL);
DISP_RC(rc, "cannot KConfigMake");
if (rc == 0) {
rc = _KConfigGetAscpRate(cfg,
opt->target_rate, sizeof opt->target_rate);
DISP_RC(rc, "cannot get aspera max rate");
}
RELEASE(KConfig, cfg);
}
sStatus = status = opt->status;
quitting = opt->quitting;
{
/* remove trailing #... or ?... from src path:
it could come from Revolver */
size_t s = string_size(aSrc);
const char *n = string_chr(aSrc, s, '#');
const char *q = string_chr(aSrc, s, '?');
if (q != NULL && (n == NULL || q < n)) {
n = q;
}
if (n != NULL) {
if (n - aSrc + 1 > sizeof path) {
return RC(rcNS, rcFile, rcCopying, rcBuffer, rcInsufficient);
}
else {
#if _DEBUGGING
size_t s =
#endif
string_copy(path, sizeof path, aSrc, n - aSrc);
assert(s <= sizeof path);
src = path;
}
}
}
while (true) {
rc = run_ascp(ascp_bin, private_file, src, dest, opt);
if (rc == 0) {
if (status) {
STSMSG(STS_DBG, ("ascp finished with success"));
}
break;
}
else if (rc == SILENT_RC(rcExe,
rcProcess, rcExecuting, rcMemory, rcExhausted))
{
if (status) {
STSMSG(STS_DBG, ("ascp failed: %R", rc));
}
break;
}
else {
rc_t rc2 = 0;
uint64_t size = 0;
if (quitting != NULL) {
rc2 = quitting();
if (rc2 != 0) {
break;
}
}
if (status) {
STSMSG(STS_DBG, ("ascp failed: %R", rc));
}
rc2 = KDirectoryFileSize(dir, &size, "%s", dest);
if (rc2 ==
SILENT_RC(rcFS, rcDirectory, rcAccessing, rcPath, rcNotFound))
{
if (prev < 0) {
if (status) {
STSMSG(0, ("fasp download failed. "
"File not found. Retrying..."));
}
prev = 0;
}
else {
if (status) {
STSMSG(0, ("fasp download failed. File not found."));
}
break;
}
}
else if (rc2 != 0 || (int64_t)size < prev) {
if (status) {
STSMSG(0, ("fasp download failed. KDirectoryFileSize "
"after ascp run: rc = %ld, size = %ld", rc, size));
}
break;
}
else if ((int64_t)size > prev) {
if (status) {
STSMSG(STS_INFO, (" fasp download failed. %ld bytes "
"received so far. Retrying...", size));
}
attempt = 0;
prev = size;
}
else {
if (attempt++ > 3) {
break;
}
if (status) {
STSMSG(STS_INFO, (" fasp download failed. %ld bytes "
"received so far. Retrying %d...", size, attempt));
}
}
}
}
RELEASE(KDirectory, dir);
return rc;
}
LIB_EXPORT rc_t CC aspera_get(
const char *ascp_bin, const char *private_file, const char *src,
const char *dest, AscpOptions *opt)
{
AscpOptions dummy;
bool status = false;
uint64_t prev = 0;
int attempt = 0;
KDirectory *dir = NULL;
TQuitting *quitting = NULL;
rc_t rc = KDirectoryNativeDir(&dir);
if (rc != 0) {
return rc;
}
if (ascp_bin == NULL || private_file == NULL ||
src == NULL || dest == NULL)
{
return RC(rcNS, rcFile, rcCopying, rcParam, rcNull);
}
if (opt == NULL) {
memset(&dummy, 0, sizeof dummy);
opt = &dummy;
}
if (opt->target_rate == NULL) {
KConfig *cfg = NULL;
rc_t rc = KConfigMake(&cfg, NULL);
DISP_RC(rc, "cannot KConfigMake");
if (rc == 0) {
rc = _KConfigGetAscpRate(cfg, &opt->target_rate);
DISP_RC(rc, "cannot get aspera max rate");
}
RELEASE(KConfig, cfg);
}
sStatus = status = opt->status;
quitting = opt->quitting;
while (true) {
rc = run_ascp(ascp_bin, private_file, src, dest, opt);
if (rc == 0) {
if (status) {
STSMSG(STS_DBG, ("ascp finished with success"));
}
break;
}
else if (rc == SILENT_RC(rcExe,
rcProcess, rcExecuting, rcMemory, rcExhausted))
{
if (status) {
STSMSG(STS_DBG, ("ascp failed: %R", rc));
}
break;
}
else {
rc_t rc = 0;
uint64_t size = 0;
if (quitting != NULL) {
rc = quitting();
if (rc != 0) {
break;
}
}
if (status) {
STSMSG(STS_DBG, ("ascp failed: %R", rc));
}
rc = KDirectoryFileSize(dir, &size, dest);
if (rc != 0 || size < prev) {
if (status) {
STSMSG(0, ("KDirectoryFileSize after ascp run: "
"rc = %ld, size = %ld", rc, size));
}
break;
}
else if (size > prev) {
if (status) {
STSMSG(STS_INFO, (" fasp download failed. %ld bytes "
"received so far. Retrying...", size));
}
attempt = 0;
prev = size;
} else {
if (attempt++ > 3) {
break;
}
if (status) {
STSMSG(STS_INFO, (" fasp download failed. %ld bytes "
"received so far. Retrying %d...", size, attempt));
}
}
}
}
RELEASE(KDirectory, dir);
return rc;
}
static rc_t get_cache_path_from_repo_mgr( tool_options * options )
{
KConfig * cfg;
rc_t rc = KConfigMake ( &cfg, NULL );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KConfigMake() failed in $(func)", "func=%s", __func__ ) );
}
else
{
const KRepositoryMgr *repo_mgr;
rc = KConfigMakeRepositoryMgrRead ( cfg, &repo_mgr );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KConfigMakeRepositoryMgrRead() failed in $(func)", "func=%s", __func__ ) );
}
else
{
KRepositoryVector repos;
VectorInit ( &repos, 0, 5 );
rc = KRepositoryMgrUserRepositories ( repo_mgr, &repos );
if ( rc != 0 )
{
rc = 0; /* we do not have a user-repository, but that is OK, the caller will display the lack of it ... */
}
else
{
uint32_t idx;
for ( idx = 0; idx < VectorLength( &repos ) && rc == 0; ++idx )
{
const KRepository *repo = VectorGet( &repos, idx );
if ( repo != 0 )
{
char path[ 4096 ];
rc = KRepositoryRoot ( repo, path, sizeof path, NULL );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KRepositoryRoot( for repo # $(idx) ) failed in $(func)", "idx=%u,func=%s", idx, __func__ ) );
}
else
{
bool add = true;
if ( options->user_repo_name != NULL )
{
char name[ 1024 ];
rc = KRepositoryName ( repo, name, sizeof name, NULL );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KRepositoryName( for repo # $(idx) ) failed in $(func)", "idx=%u,func=%s", idx, __func__ ) );
}
else
add = string_cmp_1( options->user_repo_name, name );
}
if ( add )
{
rc = add_tool_options_path( options, path );
if ( options->detailed )
KOutMsg( "source: %s\n", path );
}
}
}
}
{
rc_t rc2 = KRepositoryVectorWhack ( &repos );
if ( rc2 != 0 )
{
PLOGERR( klogErr, ( klogErr, rc2,
"KRepositoryVectorWhack() failed in $(func)", "func=%s", __func__ ) );
}
}
}
{
rc_t rc2 = KRepositoryMgrRelease ( repo_mgr );
if ( rc2 != 0 )
{
PLOGERR( klogErr, ( klogErr, rc2,
"KRepositoryMgrRelease() failed in $(func)", "func=%s", __func__ ) );
}
}
}
{
rc_t rc2 = KConfigRelease ( cfg );
if ( rc2 != 0 )
{
PLOGERR( klogErr, ( klogErr, rc2,
"KConfigRelease() failed in $(func)", "func=%s", __func__ ) );
}
}
}
return rc;
}
static rc_t perform( tool_options * options, Args * args )
{
visit_ctx octx;
rc_t rc2, rc = KDirectoryNativeDir( &octx.dir );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KDirectoryNativeDir() failed in $(func)", "func=%s", __func__ ) );
}
else
{
rc = KConfigMake ( &octx.cfg, NULL );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KConfigMake() failed in $(func)", "func=%s", __func__ ) );
}
else
{
rc = KConfigMakeRepositoryMgrRead ( octx.cfg, &octx.repo_mgr );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"KConfigMakeRepositoryMgrRead() failed in $(func)", "func=%s", __func__ ) );
}
else
{
octx.options = options;
octx.data = NULL;
switch( options->main_function )
{
case tf_report : rc = perform_report( &octx ); break;
case tf_rreport : rc = perform_rreport( &octx ); break;
case tf_unlock : rc = perform_unlock( &octx ); break;
case tf_clear : rc = perform_clear( &octx ); break;
case tf_enable : rc = perform_set_disable( &octx, false ); break;
case tf_disable : rc = perform_set_disable( &octx, true ); break;
case tf_unknown : rc = Usage( args ); break;
}
rc2 = KRepositoryMgrRelease ( octx.repo_mgr );
if ( rc2 != 0 )
{
PLOGERR( klogErr, ( klogErr, rc2,
"KRepositoryMgrRelease() failed in $(func)", "func=%s", __func__ ) );
}
}
rc2 = KConfigRelease ( octx.cfg );
if ( rc2 != 0 )
{
PLOGERR( klogErr, ( klogErr, rc2,
"KConfigRelease() failed in $(func)", "func=%s", __func__ ) );
}
}
rc2 = KDirectoryRelease( octx.dir );
if ( rc2 != 0 )
{
PLOGERR( klogErr, ( klogErr, rc2,
"KDirectoryRelease() failed in $(func)", "func=%s", __func__ ) );
}
}
return rc;
}
