static void get_meta_info( vdb_info_data * data, const KMetadata * meta )
{
const KMDataNode * node;
rc_t rc = KMetadataOpenNodeRead ( meta, &node, "schema" );
if ( rc == 0 )
{
size_t size;
rc = KMDataNodeReadAttr ( node, "name", data->schema_name, sizeof data->schema_name, &size );
if ( rc == 0 )
data->schema_name[ size ] = 0;
KMDataNodeRelease ( node );
}
rc = KMetadataOpenNodeRead ( meta, &node, "LOAD/timestamp" );
if ( rc == 0 )
{
rc = KMDataNodeReadAsU64 ( node, &data->ts.timestamp );
if ( rc == 0 )
{
KTime time_rec;
KTimeLocal ( &time_rec, data->ts.timestamp );
data->ts.year = time_rec.year;
data->ts.month = time_rec.month + 1;
data->ts.day = time_rec.day + 1;
data->ts.hour = time_rec.hour;
data->ts.minute= time_rec.minute;
}
KMDataNodeRelease ( node );
}
get_meta_event( meta, "SOFTWARE/formatter", &data->formatter );
get_meta_event( meta, "SOFTWARE/loader", &data->loader );
get_meta_event( meta, "SOFTWARE/update", &data->update );
}
static rc_t fill_timestring( char * s, size_t size )
{
KTime tr;
rc_t rc;
KTimeLocal ( &tr, KTimeStamp() );
/*
rc = string_printf ( s, size, NULL,
"%.04u-%.02u-%.02u %.02u:%.02u:%.02u",
tr.year, tr.month + 1, tr.day, tr.hour, tr.minute, tr.second );
*/
rc = string_printf ( s, size, NULL, "%lT", &tr );
DISP_RC( rc, "fill_timestring:string_printf( date/time ) failed" );
return rc;
}
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;
}
/* Dump
*/
static
void KThreadEventDump ( ctx_t ctx, KTime_t timestamp, const KFuncLoc * loc,
uint32_t lineno, xc_sev_t severity, xc_org_t origin, const void * xc_param,
const char * msg, const KThreadEvtNode * node )
{
const XCErr * xc = xc_param;
size_t pre_size, sz;
char pre [ 4096 ];
#if _DEBUGGING
const char *fname;
#endif
static const char * err_strings [ 3 ] [ 4 ] =
{
{ "NOTE", "WARNING", "SYSTEM ERROR", "FATAL SYSTEM ERROR" },
{ "NOTE", "WARNING", "INTERNAL ERROR", "FATAL INTERNAL ERROR" },
{ "NOTE", "WARNING", "USER ERROR", "FATAL USER ERROR" }
};
KTime tm;
KTimeLocal ( & tm, timestamp );
string_printf ( pre, sizeof pre, & pre_size
, "%04u-%02u-%02uT%02u:%02u:%02u "
, tm . year
, tm . month + 1
, tm . day
, tm . hour
, tm . minute
, tm . second
);
#if _DEBUGGING
string_printf ( & pre [ pre_size ], sizeof pre - pre_size, & sz
, "%.*s/%s/%s.%s:%u:"
, sizeof __FILE__ -
sizeof __mod__ -
sizeof __file__ -
sizeof __fext__ -
1
, __FILE__
, loc -> src -> mod
, loc -> src -> file
, loc -> src -> ext
, lineno
, loc -> func
);
pre_size += sz;
/* function name */
fname = loc -> func;
/* remove leading "Java_" from jni names */
if ( memcmp ( loc -> func, "Java_", sizeof "Java_" - 1 ) == 0 )
fname += sizeof "Java_" - 1;
/* print it into buffer */
string_printf ( & pre [ pre_size ], sizeof pre - pre_size, & sz
, "%s - "
, fname
);
/* convert jni names into Java fqn */
if ( fname != loc -> func )
{
size_t i;
for ( i = 0; i < sz; ++ i )
{
if ( pre [ pre_size + i ] == '_' )
pre [ pre_size + i ] = '.';
}
}
pre_size += sz;
#endif
string_printf ( & pre [ pre_size ], sizeof pre - pre_size, & sz
, "%s: "
, err_strings [ origin ] [ severity ]
);
pre_size += sz;
#if _DEBUGGING
string_printf ( & pre [ pre_size ], sizeof pre - pre_size, & sz
, "( %s ) "
, xc -> name
);
pre_size += sz;
#endif
string_printf ( & pre [ pre_size ], sizeof pre - pre_size, & sz
, "%s %s"
, extract_desc_xobj ( xc )
, extract_desc_xstate ( xc )
);
pre_size += sz;
if ( msg == NULL || msg [ 0 ] == 0 )
fprintf ( stderr, "%s.\n", pre );
else
fprintf ( stderr, "%s - %s.\n", pre, msg );
#if _DEBUGGING
if ( node != NULL )
{
fprintf ( stderr, "Stack Trace:\n" );
do
{
fprintf ( stderr
, " %s/%s.%s:%s\n"
, node -> loc -> src -> mod
, node -> loc -> src -> file
, node -> loc -> src -> ext
, node -> loc -> func
);
node = node -> parent;
}
while ( node != NULL );
}
else if ( ctx != NULL )
{
fprintf ( stderr, "Stack Trace:\n" );
do
{
fprintf ( stderr
, " %s/%s.%s:%s\n"
, ctx -> loc -> src -> mod
, ctx -> loc -> src -> file
, ctx -> loc -> src -> ext
, ctx -> loc -> func
);
ctx = ctx -> caller;
}
while ( ctx != NULL );
}
#endif
}
static rc_t write_header( cg_dump_opts * opts, struct sg_lookup * lookup, lane * l )
{
char buffer[ 1024 ];
size_t num_writ_buf;
sg * entry = NULL;
rc_t rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#GENERATED_BY\t%s\n", UsageDefaultName );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate GENERATED_BY for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
if ( rc == 0 )
{
KTime now;
KTimeLocal ( &now, KTimeStamp () );
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#GENERATED_AT\t%lT\n", &now );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate GENERATED_AT for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#SOFTWARE_VERSION\t%.3V\n", KAppVersion() );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate SOFTWARE_VERSION for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#FORMAT_VERSION\t2.0\n" );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate FORMAT_VERSION for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#TYPE\tSAM_READS\n" );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate SAM_READS for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#SLIDE\t%.*s\n", ( l->name->len - 4 ), l->name->addr );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate SLIDE for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#LANE\t%.*s\n", 3, l->name->addr + ( ( l->name->len - 3 ) ) );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate LANE for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#BATCH_FILE_NUMBER\t%d\n", l->chunk );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate BATCH_FILE_NUMBER for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#LANE\t%S\n", l->name );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate LANE(2) for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
perform_sg_lookup( lookup, l->name, &entry );
if ( entry != NULL )
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#LIBRARY\t%S\n", &entry->lib );
else
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#LIBRARY\t%s\n", opts->lib ); /* opts->lib */
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate LIBRARY for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
if ( entry != NULL )
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#SAMPLE\t%S\n", &entry->sample );
else
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#SAMPLE\t%s\n", opts->sample ); /* opts->sample */
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate SAMPLE for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
if ( entry != NULL )
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#FIELD_SIZE\t%S\n", &entry->field_size );
else
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "#FIELD_SIZE\t460800\n" );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate FIELD_SIZE for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
if ( rc == 0 )
{
rc = string_printf ( buffer, sizeof buffer, &num_writ_buf, "\n>readOffset\tside\tbases\tscores\n" );
if ( rc != 0 )
{
(void)LOGERR( klogErr, rc, "cannot generate columns for header" );
}
else
rc = write_header_line( l, buffer, num_writ_buf );
}
return rc;
}
