rc_t copy_table_meta ( const VTable *src_table, VTable *dst_table,
const char * excluded_nodes,
const bool show_meta, const bool schema_updated )
{
const KMetadata *src_meta;
rc_t rc;
if ( src_table == NULL || dst_table == NULL )
return RC( rcExe, rcNoTarg, rcCopying, rcParam, rcNull );
/* it is OK if excluded_nodes is NULL */
rc = VTableOpenMetadataRead ( src_table, & src_meta );
DISP_RC( rc, "copy_table_meta:VTableOpenMetadataRead() failed" );
if ( rc == 0 )
{
rc = copy_back_revisions ( src_meta, dst_table, show_meta );
if ( rc == 0 )
{
KMetadata *dst_meta;
rc = VTableOpenMetadataUpdate ( dst_table, & dst_meta );
DISP_RC( rc, "copy_table_meta:VTableOpenMetadataUpdate() failed" );
if ( rc == 0 )
{
if ( show_meta )
KOutMsg( "+++copy current metadata\n" );
rc = copy_stray_metadata ( src_meta, dst_meta, excluded_nodes,
show_meta );
if ( show_meta )
KOutMsg( "+++end of copy current metadata\n" );
/* enter a attribute "vdb-copy" under '/SOFTWARE/update'
*if the schema was updated ! */
if ( rc == 0 && schema_updated )
rc = enter_schema_update( dst_meta, show_meta );
/* enter a unconditional node under '/SOFTWARE/Copy'
<%TIMESTAMP%>
<Application date="%DATE%" name="vdb-copy" vers="%VERSION%"/>
</%TIMESTAMP%>
*/
if ( rc == 0 )
rc = enter_vdbcopy_node( dst_meta, show_meta );
KMetadataRelease ( dst_meta );
}
}
KMetadataRelease ( src_meta );
}
return rc;
}
static uint32_t get_child_count( KMDataNode *node )
{
uint32_t res = 0;
KNamelist *names;
rc_t rc = KMDataNodeListChild ( node, &names );
DISP_RC( rc, "get_child_count:KMDataNodeListChild() failed" );
if ( rc == 0 )
{
rc = KNamelistCount ( names, &res );
DISP_RC( rc, "get_child_count:KNamelistCount() failed" );
KNamelistRelease ( names );
}
return res;
}
static void setup_compress_context( const Args * args, p_compress_context ctx )
{
uint32_t count;
const char *value = NULL;
rc_t rc = ArgsParamCount( args, &count );
DISP_RC( rc, "ArgsParamCount() failed" );
if ( rc == 0 )
{
rc = ArgsParamValue( args, 0, &value );
DISP_RC( rc, "ArgsParamValue() failed" );
if ( rc == 0 )
ctx->src_file = string_dup_measure( value, NULL );
rc = ArgsParamValue( args, 1, &value );
DISP_RC( rc, "ArgsParamValue() failed" );
if ( rc == 0 )
ctx->dst_file = string_dup_measure( value, NULL );
}
value = get_str_option( args, OPTION_DIRECTION );
if ( value )
{
switch ( value[0] )
{
case 'c' :
case 'C' : ctx->direction = KC_COMPRESS; break;
case 'd' :
case 'D' : ctx->direction = KC_DECOMPRESS; break;
}
}
if ( ctx->direction == 0 )
ctx->direction = KC_DECOMPRESS;
value = get_str_option( args, OPTION_METHOD );
if ( value )
{
switch ( value[0] )
{
case 'g' :
case 'G' : ctx->method = KC_GZIP; break;
case 'b' :
case 'B' : ctx->method = KC_BZIP; break;
case 's' :
case 'S' : ctx->method = KC_SZIP; break;
}
}
if ( ctx->method == 0 )
ctx->method = KC_GZIP;
}
static rc_t CC scan_mod_dir(const KDirectory* dir,
uint32_t type, const char* name, void* data)
{
rc_t rc = 0;
const char ext[] = SHLX;
assert(data);
if (strlen(name) > strlen(ext) + 1 &&
name[strlen(name) - strlen(ext) - 1] == '.')
{
char buf[PATH_MAX + 1];
rc = KDirectoryResolvePath
(dir, true, buf, sizeof buf, "%s/%s", data, name);
while (rc == 0) {
uint32_t type = KDirectoryPathType(dir, buf);
if (type & kptAlias) {
rc = KDirectoryResolveAlias
(dir, true, buf, sizeof buf, buf);
DISP_RC(rc, name);
}
else if (rc == 0) {
if (type == kptNotFound || type == kptBadPath) {
OUTMSG(("%s: %s\n", buf,
type == kptNotFound ? "not found" : "bad path"));
}
else { OUTMSG(("%s\n", buf)); }
break;
}
}
}
return rc;
}
static rc_t XmlMetaInit(rc_t rc, XmlMeta* meta,
const AppCtx* ctx, const char* xml)
{
const KFile* f = NULL;
const KXMLDoc* doc = NULL;
const KXMLNodeset* ns = NULL;
const KXMLNode* node = NULL;
const char path[] = "/Run";
memset(meta, 0, sizeof *meta);
if (rc) {
return rc;
}
if (rc == 0) {
rc = KDirectoryOpenFileRead(ctx->dir, &f, xml);
DISP_RC(rc, xml);
}
if (rc == 0) {
rc = KXMLMgrMakeDocRead(ctx->x_mgr, &doc, f);
DISP_RC(rc, xml);
}
if (rc == 0) {
rc = KXMLDocOpenNodesetRead(doc, &ns, path);
DISP_RC(rc, path);
}
if (rc == 0) {
rc = KXMLNodesetGetNodeRead(ns, &node, 0);
DISP_RC(rc, path);
}
if (rc == 0) {
rc = ParseSraMetaNode(node, path, NULL, &meta->root);
}
if (rc == 0 && !meta->root.found) {
meta->tr = calloc(1, sizeof *meta->tr);
if (meta->tr == NULL) {
rc = RC(rcExe, rcStorage, rcAllocating, rcMemory, rcExhausted);
}
else {
BSTreeInit(meta->tr);
rc = XmlMetaInitMembers(meta->tr, node);
}
}
RELEASE(KXMLNode, node);
RELEASE(KXMLNodeset, ns);
RELEASE(KXMLDoc, doc);
RELEASE(KFile, f);
return rc;
}
static void CC vdcd_reset_1_content( void *item, void *data )
{
rc_t rc;
p_col_def my_col_def = (p_col_def)item;
if ( my_col_def == NULL ) return;
rc = vds_clear( &(my_col_def->content) );
DISP_RC( rc, "dump_str_clear() failed" );
}
/*
* walks through the column-definitions and if a column
* has the to_copy-flag set, and it's name is in the
* given list of column-names the to copy-flag is cleared
* does not require an open cursor.
*/
rc_t col_defs_exclude_these_columns( col_defs* defs, const char * prefix, const char * column_names )
{
rc_t rc = 0;
const KNamelist *names;
if ( defs == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
/* it is OK if we have not column-names to exclude */
if ( column_names == NULL )
return 0;
if ( column_names[0] == 0 )
return 0;
rc = nlt_make_namelist_from_string( &names, column_names );
DISP_RC( rc, "col_defs_parse_string:nlt_make_namelist_from_string() failed" );
if ( rc == 0 )
{
uint32_t idx, len = VectorLength( &(defs->cols) );
size_t prefix_len = 0;
if ( prefix != 0 )
prefix_len = string_size( prefix ) + 2;
for ( idx = 0; idx < len; ++idx )
{
p_col_def col = (p_col_def) VectorGet ( &(defs->cols), idx );
if ( col != NULL )
{
if ( col->requested )
{
if ( nlt_is_name_in_namelist( names, col->name ) )
col->requested = false;
else
{
if ( prefix != NULL )
{
size_t len1 = string_size ( col->name ) + prefix_len;
char * s = malloc( len1 );
if ( s != NULL )
{
size_t num_writ;
rc_t rc1 = string_printf ( s, len1, &num_writ, "%s:%s", prefix, col->name );
if ( rc1 == 0 )
{
if ( nlt_is_name_in_namelist( names, s ) )
col->requested = false;
}
free( s );
}
}
}
}
}
}
KNamelistRelease( names );
}
return rc;
}
static rc_t copy_back_revisions ( const KMetadata *src_meta, VTable *dst_table,
const bool show_meta )
{
uint32_t max_revision, revision;
rc_t rc = KMetadataMaxRevision ( src_meta, &max_revision );
DISP_RC( rc, "copy_back_revisions:KMetadataMaxRevision() failed" );
if ( rc != 0 ) return rc;
if ( max_revision == 0 ) return rc;
for ( revision = 1; revision <= max_revision && rc == 0; ++revision )
{
const KMetadata *src_rev_meta;
if ( show_meta )
KOutMsg( "+++copy metadata rev. #%u:\n", revision );
rc = KMetadataOpenRevision ( src_meta, &src_rev_meta, revision );
DISP_RC( rc, "copy_back_revisions:KMetadataOpenRevision() failed" );
if ( rc == 0 )
{
KMetadata *dst_meta;
rc = VTableOpenMetadataUpdate ( dst_table, & dst_meta );
DISP_RC( rc, "copy_table_meta:VTableOpenMetadataUpdate() failed" );
if ( rc == 0 )
{
rc = copy_stray_metadata ( src_rev_meta, dst_meta, NULL, show_meta );
if ( rc == 0 )
{
rc = KMetadataCommit ( dst_meta );
DISP_RC( rc, "copy_back_revisions:KMetadataCommit() failed" );
if ( rc == 0 )
{
rc = KMetadataFreeze ( dst_meta );
DISP_RC( rc, "copy_back_revisions:KMetadataFreeze() failed" );
}
}
KMetadataRelease ( dst_meta );
}
KMetadataRelease ( src_rev_meta );
}
}
return rc;
}
/** Init the static directory object */
static rc_t SpotIteratorInitDirectory(void) {
if (__SpotIteratorDirectory) {
return 0;
}
else {
rc_t rc = KDirectoryNativeDir(&__SpotIteratorDirectory);
DISP_RC(rc, "while calling KDirectoryNativeDir");
return rc;
}
}
bool vdcd_extract_from_table( col_defs* defs, const VTable *my_table )
{
bool col_defs_found = false;
KNamelist *names;
rc_t rc = VTableListCol( my_table, &names );
DISP_RC( rc, "VTableListCol() failed" );
if ( rc == 0 )
{
const VCursor *my_cursor;
rc = VTableCreateCursorRead( my_table, &my_cursor );
DISP_RC( rc, "VTableCreateCursorRead() failed" );
if ( rc == 0 )
{
uint32_t n;
uint32_t found = 0;
rc = KNamelistCount( names, &n );
DISP_RC( rc, "KNamelistCount() failed" );
if ( rc == 0 )
{
uint32_t i;
for ( i = 0; i < n && rc ==0; ++i )
{
const char *col_name;
rc = KNamelistGet( names, i, &col_name );
DISP_RC( rc, "KNamelistGet() failed" );
if ( rc == 0 )
{
p_col_def def = vdcd_append_col( defs, col_name );
rc = VCursorAddColumn( my_cursor, &(def->idx), def->name );
DISP_RC( rc, "VCursorAddColumn() failed" );
if ( rc == 0 )
{
rc = VCursorDatatype( my_cursor, def->idx,
&(def->type_decl), &(def->type_desc) );
DISP_RC( rc, "VCursorDatatype() failed" );
if ( rc == 0 )
{
found++;
}
}
}
}
col_defs_found = ( found > 0 );
}
rc = VCursorRelease( my_cursor );
DISP_RC( rc, "VCursorRelease() failed" );
}
rc = KNamelistRelease( names );
DISP_RC( rc, "KNamelistRelease() failed" );
}
return col_defs_found;
}
static rc_t AppCtxInit(rc_t rc, AppCtx* ctx) {
assert(ctx);
memset(ctx, 0 , sizeof *ctx);
if (rc) {
return rc;
}
if (rc == 0) {
rc = SRAMgrMakeUpdate(&ctx->s_mgr, NULL);
DISP_RC(rc, "while calling SRAMgrMakeUpdate");
}
if (rc == 0) {
rc = KXMLMgrMakeRead(&ctx->x_mgr);
DISP_RC(rc, "while calling KXMLMgrMakeRead");
}
if (rc == 0) {
rc = KDirectoryNativeDir(&ctx->dir);
DISP_RC(rc, "while calling KDirectoryNativeDir");
}
return rc;
}
static rc_t enter_version( KMDataNode *node, const char * key )
{
char buff[ 32 ];
rc_t rc;
rc = string_printf ( buff, sizeof( buff ), NULL, "%.3V", VDB_COPY_VERS );
assert ( rc == 0 );
rc = KMDataNodeWriteAttr ( node, key, buff );
DISP_RC( rc, "enter_version:KMDataNodeWriteAttr() failed" );
return rc;
}
static rc_t enter_time( KMDataNode *node, const char * key )
{
char timestring[ 160 ];
rc_t rc = fill_timestring( timestring, sizeof timestring );
if ( rc == 0 )
{
rc = KMDataNodeWriteAttr ( node, key, timestring );
DISP_RC( rc, "enter_time:KMDataNodeWriteAttr( timestring ) failed" );
}
return rc;
}
static rc_t ShowModDir(const KDirectory* native, char* path) {
rc_t rc = 0;
const KDirectory* dir = NULL;
assert(native && path);
rc = KDirectoryOpenDirRead(native, &dir, false, path);
DISP_RC(rc, path);
if (rc == 0) {
rc = KDirectoryVVisit(dir, false, scan_mod_dir, path, ".", NULL);
}
return rc;
}
/*
* calls VTableListReadableColumns to get a list of all column-names of the table
* creates a temporary read-cursor to test and get the column-type
* walks the KNamelist with the available column-names
* tries to add every one of them to the temp. cursor
* if the column can be added to the cursor, it is appended
* to the column-definition list
*/
rc_t col_defs_extract_from_table( col_defs* defs, const VTable *table )
{
KNamelist *names;
rc_t rc;
if ( defs == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcSelf, rcNull );
if ( table == NULL )
return RC( rcExe, rcNoTarg, rcResolving, rcParam, rcNull );
rc = VTableListReadableColumns( table, &names );
DISP_RC( rc, "col_defs_extract_from_table:VTableListReadableColumns() failed" );
if ( rc == 0 )
{
const VCursor *cursor;
rc = VTableCreateCursorRead( table, &cursor );
DISP_RC( rc, "col_defs_extract_from_table:VTableCreateCursorRead() failed" );
if ( rc == 0 )
{
uint32_t count;
rc = KNamelistCount( names, &count );
DISP_RC( rc, "col_defs_extract_from_table:KNamelistCount() failed" );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *name;
rc = KNamelistGet( names, idx, &name );
DISP_RC( rc, "col_defs_extract_from_table:KNamelistGet() failed" );
if ( rc == 0 )
{
uint32_t temp_idx;
rc_t rc1 = VCursorAddColumn( cursor, &temp_idx, "%s", name );
DISP_RC( rc1, "col_defs_extract_from_table:VCursorAddColumn() failed" );
if ( rc1 == 0 )
{
rc = col_defs_append_col( defs, name );
DISP_RC( rc, "col_defs_extract_from_table:col_defs_append_col() failed" );
}
}
}
}
rc = VCursorRelease( cursor );
DISP_RC( rc, "col_defs_extract_from_table:VCursorRelease() failed" );
}
rc = KNamelistRelease( names );
DISP_RC( rc, "col_defs_extract_from_table:KNamelistRelease() failed" );
}
return rc;
}
static rc_t vdb_fastq_database( const p_dump_context ctx,
const VDBManager *mgr,
fastq_ctx * fctx )
{
const VDatabase * db;
VSchema *schema = NULL;
rc_t rc;
vdh_parse_schema( mgr, &schema, &(ctx->schema_list) );
rc = VDBManagerOpenDBRead( mgr, &db, schema, ctx->path );
DISP_RC( rc, "VDBManagerOpenDBRead() failed" );
if ( rc == 0 )
{
bool table_defined = ( ctx->table != NULL );
if ( !table_defined )
table_defined = vdh_take_this_table_from_db( ctx, db, "SEQUENCE" );
if ( table_defined )
{
const VTable * tbl;
rc = VDatabaseOpenTableRead( db, &tbl, ctx->table );
DISP_RC( rc, "VDatabaseOpenTableRead() failed" );
if ( rc == 0 )
{
rc = vdb_fastq_tbl( ctx, tbl, fctx );
VTableRelease( tbl );
}
}
else
{
LOGMSG( klogInfo, "opened as vdb-database, but no table found/defined" );
ctx->usage_requested = true;
}
VDatabaseRelease( db );
}
VSchemaRelease( schema );
return rc;
}
static rc_t bam_header(const VDatabase* db) {
rc_t rc = 0;
const char path[] = "BAM_HEADER";
const KMetadata* meta = NULL;
const KMDataNode* node = NULL;
char* buffer = NULL;
assert(db);
if (rc == 0) {
rc = VDatabaseOpenMetadataRead(db, &meta);
DISP_RC(rc, "while calling VDatabaseOpenMetadataRead");
}
if (rc == 0) {
rc = KMetadataOpenNodeRead(meta, &node, "%s", path);
if (GetRCState(rc) == rcNotFound)
{ rc = 0; }
else {
DISP_RC2(rc, path, "while calling KMetadataOpenNodeRead");
if (rc == 0) {
int i = 0;
size_t bsize = 0;
size_t size = 1024;
for (i = 0; i < 2; ++i) {
free(buffer);
bsize = size + 1;
buffer = malloc(bsize);
if (buffer == NULL) {
rc = RC(rcExe, rcStorage, rcAllocating,
rcMemory, rcExhausted);
}
else {
rc = KMDataNodeReadCString(node, buffer, bsize, &size);
if (rc == 0) {
break;
}
else if (i == 0
&& GetRCObject(rc) == (enum RCObject)rcBuffer
&& GetRCState (rc) == rcInsufficient)
{
rc = 0;
}
}
DISP_RC2(rc, path, "while calling KMDataNodeReadCString");
}
}
}
}
if (rc == 0 && buffer)
{ OUTMSG(("BAM_HEADER: {\n%s}\n\n", buffer)); }
DESTRUCT(KMDataNode, node);
DESTRUCT(KMetadata, meta);
free(buffer);
return rc;
}
static rc_t enter_date_name_vers( KMDataNode *node )
{
rc_t rc = enter_time( node, "run" );
DISP_RC( rc, "enter_date_name_vers:enter_time() failed" );
if ( rc == 0 )
{
rc = KMDataNodeWriteAttr ( node, "tool", "vdb-copy" );
DISP_RC( rc, "enter_date_name_vers:KMDataNodeWriteAttr(tool=vdb-copy) failed" );
if ( rc == 0 )
{
rc = enter_version ( node, "vers" );
DISP_RC( rc, "enter_date_name_vers:enter_version() failed" );
if ( rc == 0 )
{
rc = KMDataNodeWriteAttr ( node, "build", __DATE__ );
DISP_RC( rc, "enter_date_name_vers:KMDataNodeWriteAttr(build=_DATE_) failed" );
}
}
}
return rc;
}
static rc_t XmlMetaInitMembers(BSTree* tr, const KXMLNode* node) {
rc_t rc = 0;
const char path[] = "Member";
uint32_t count = 0;
uint32_t idx = 0;
const KXMLNodeset *members = NULL;
if (rc == 0) {
rc = KXMLNodeOpenNodesetRead(node, &members, path);
DISP_RC(rc, path);
}
if (rc == 0) {
rc = KXMLNodesetCount(members, &count);
DISP_RC(rc, path);
}
for (idx = 0; idx < count && rc == 0; ++idx) {
const KXMLNode *node = NULL;
char member_name[256] = "";
if (rc == 0) {
rc = KXMLNodesetGetNodeRead(members, &node, idx);
DISP_RC(rc, path);
}
if (rc == 0) {
size_t size = 0;
rc = KXMLNodeReadAttrCString(node, "member_name",
member_name, sizeof member_name, &size);
if (rc) {
if (GetRCState(rc) == rcInsufficient) {
member_name[sizeof member_name - 1] = '\0';
rc = 0;
}
}
}
if (rc == 0) {
rc = XmlMetaInitMemser(tr, node, path, member_name);
}
RELEASE(KXMLNode, node);
}
RELEASE(KXMLNodeset, members);
return rc;
}
static rc_t copy_metadata_root ( const KMDataNode *src_root, KMDataNode *dst_root,
const char * excluded_nodes,
const bool show_meta )
{
KNamelist *names;
const KNamelist *excluded_names = NULL;
uint32_t i, count;
rc_t rc = KMDataNodeListChild ( src_root, & names );
DISP_RC( rc, "copy_metadata_root:KMDataNodeListChild() failed" );
if ( rc != 0 ) return rc;
if ( excluded_nodes != NULL )
{
rc = nlt_make_namelist_from_string( &excluded_names, excluded_nodes );
DISP_RC( rc, "copy_metadata_root:nlt_make_namelist_from_string() failed" );
if ( rc != 0 ) return rc;
}
rc = KNamelistCount ( names, & count );
for ( i = 0; rc == 0 && i < count; ++ i )
{
const char *node_path;
rc = KNamelistGet ( names, i, & node_path );
DISP_RC( rc, "copy_metadata_root:KNamelistGet() failed" );
if ( rc == 0 )
{
bool is_excluded = false;
if ( excluded_names != NULL )
is_excluded = nlt_is_name_in_namelist( excluded_names, node_path );
if ( !is_excluded )
rc = copy_metadata_child ( src_root, dst_root, node_path, show_meta );
}
}
if ( excluded_names != NULL )
KNamelistRelease( excluded_names );
KNamelistRelease ( names );
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;
}
static
rc_t privReadStdinLine(char* buf, size_t bsize, bool destroy)
{
rc_t rc = 0;
static const KFile* std_in = NULL;
static uint64_t pos = 0;
size_t num_read = 0;
if (destroy) {
RELEASE(KFile, std_in);
pos = 0;
return rc;
}
if (std_in == NULL) {
rc = KFileMakeStdIn(&std_in);
if (rc != 0) {
DISP_RC(rc, "KFileMakeStdIn");
return rc;
}
}
rc = KFileRead(std_in, pos, buf, bsize, &num_read);
DISP_RC(rc, "KFileRead");
pos += num_read;
if (num_read) {
bool done = false;
buf[num_read] = '\0';
while (num_read > 0 && !done) {
switch (buf[num_read - 1]) {
case '\n':
case '\r':
buf[--num_read] = '\0';
break;
default:
done = true;
break;
}
}
}
return rc;
}
static rc_t copy_metadata_data ( const KMDataNode *snode, KMDataNode *dnode )
{
char buffer [ 1024 ];
size_t total, bytes, remaining;
/* copy node data unless already set */
rc_t rc = KMDataNodeRead ( dnode, 0, buffer, 0, & bytes, & total );
DISP_RC( rc, "copy_metadata_child:KMDataNodeRead(dst) failed" );
if ( rc == 0 && total == 0 )
do
{
rc = KMDataNodeRead ( snode, total, buffer, sizeof buffer, & bytes, & remaining );
DISP_RC( rc, "copy_metadata_child:KMDataNodeRead(src) failed" );
if ( rc == 0 )
{
rc = KMDataNodeAppend ( dnode, buffer, bytes );
DISP_RC( rc, "copy_metadata_child:KMDataNodeAppend(dst) failed" );
if ( rc != 0 ) break;
}
total += bytes;
} while ( remaining != 0 );
return rc;
}
static rc_t vdb_prepare_cursor( const p_dump_context ctx, const VTable * tbl, fastq_ctx * fctx )
{
rc_t rc;
/* first we try to open READ/QUALITY/NAME */
rc = VTableCreateCachedCursorRead( tbl, &fctx->cursor, ctx->cur_cache_size );
DISP_RC( rc, "VTableCreateCursorRead( 1st ) failed" );
if ( rc == 0 )
{
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_read, "(INSDC:dna:text)READ" );
if ( rc == 0 && ctx->format == df_fastq )
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_qual, "(INSDC:quality:text:phred_33)QUALITY" );
else
fctx->idx_qual = INVALID_COLUMN;
if ( rc == 0 )
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_name, "(ascii)NAME" );
if ( rc == 0 )
rc = VCursorOpen ( fctx->cursor );
if ( rc != 0 )
{
VCursorRelease( fctx->cursor );
rc = VTableCreateCachedCursorRead( tbl, &fctx->cursor, ctx->cur_cache_size );
DISP_RC( rc, "VTableCreateCursorRead( 2nd ) failed" );
if ( rc == 0 )
{
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_read, "(INSDC:dna:text)READ" );
if ( rc == 0 && ctx->format == df_fastq )
rc = VCursorAddColumn( fctx->cursor, &fctx->idx_qual, "(INSDC:quality:text:phred_33)QUALITY" );
else
fctx->idx_qual = INVALID_COLUMN;
if ( rc == 0 )
rc = VCursorOpen ( fctx->cursor );
fctx->idx_name = INVALID_COLUMN;
}
}
}
return rc;
}
static rc_t SetNode(KConfig* cfg, const Params* prm) {
rc_t rc = 0;
KConfigNode* node = NULL;
char* name = NULL;
char* val = NULL;
assert(cfg && prm && prm->setValue);
name = strdup(prm->setValue);
if (name == NULL)
{ return RC(rcExe, rcStorage, rcAllocating, rcMemory, rcExhausted); }
val = strchr(name, '=');
if (val == NULL || *(val + 1) == '\0') {
rc_t rc = RC(rcExe, rcArgv, rcParsing, rcParam, rcInvalid);
LOGERR(klogErr, rc, "Bad " OPTION_SET " value");
}
if (rc == 0) {
*(val++) = '\0';
rc = KConfigOpenNodeUpdate(cfg, &node, name);
if (rc != 0) {
PLOGERR(klogErr, (klogErr, rc,
"Cannot open node '$(name)' for update", "name=%s", name));
}
}
if (rc == 0) {
assert(val);
rc = KConfigNodeWrite(node, val, strlen(val));
if (rc != 0) {
PLOGERR(klogErr, (klogErr, rc,
"Cannot write value '$(val) to node '$(name)'",
"val=%s,name=%s", val, name));
}
}
if (rc == 0) {
rc = KConfigCommit(cfg);
DISP_RC(rc, "while calling KConfigCommit");
}
free(name);
name = NULL;
RELEASE(KConfigNode, node);
return rc;
}
/********************************************************************
helper function to display the version of the vdb-manager
********************************************************************/
rc_t vdh_show_manager_version( const VDBManager *my_manager )
{
uint32_t version;
rc_t rc = VDBManagerVersion( my_manager, &version );
DISP_RC( rc, "VDBManagerVersion() failed" );
if ( rc == 0 )
{
PLOGMSG ( klogInfo, ( klogInfo, "manager-version = $(maj).$(min).$(rel)",
"vers=0x%X,maj=%u,min=%u,rel=%u",
version,
version >> 24,
( version >> 16 ) & 0xFF,
version & 0xFFFF ));
}
static rc_t copy_stray_metadata ( const KMetadata *src_meta, KMetadata *dst_meta,
const char * excluded_nodes,
const bool show_meta )
{
/* open root node */
const KMDataNode *src_root;
rc_t rc = KMetadataOpenNodeRead ( src_meta, & src_root, NULL );
DISP_RC( rc, "copy_stray_metadata:KMetadataOpenNodeRead() failed" );
if ( rc == 0 )
{
KMDataNode *dst_root;
rc = KMetadataOpenNodeUpdate ( dst_meta, & dst_root, NULL );
DISP_RC( rc, "copy_stray_metadata:KMetadataOpenNodeUpdate() failed" );
if ( rc == 0 )
{
/* treat the root node in a special way */
rc = copy_metadata_root ( src_root, dst_root, excluded_nodes, show_meta );
KMDataNodeRelease ( dst_root );
}
KMDataNodeRelease ( src_root );
}
return rc;
}
static rc_t enter_schema_update( KMetadata *dst_meta, const bool show_meta )
{
rc_t rc;
KMDataNode *sw_node;
if ( show_meta )
KOutMsg( "--- entering schema-update\n" );
rc = KMetadataOpenNodeUpdate ( dst_meta, &sw_node, "SOFTWARE" );
DISP_RC( rc, "enter_schema_update:KMetadataOpenNodeUpdate('SOFTWARE') failed" );
if ( rc == 0 )
{
KMDataNode *update_node;
rc = KMDataNodeOpenNodeUpdate ( sw_node, &update_node, "update" );
DISP_RC( rc, "enter_schema_update:KMDataNodeOpenNodeUpdate('update') failed" );
if ( rc == 0 )
{
rc = enter_date_name_vers( update_node );
KMDataNodeRelease ( update_node );
}
KMDataNodeRelease ( sw_node );
}
return rc;
}
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 init_ictx( struct ictx * ictx, const dump_context * ctx, const Args * args )
{
rc_t rc = KFileMakeStdIn ( &( ictx->std_in ) );
DISP_RC( rc, "KFileMakeStdIn() failed" );
if ( rc == 0 )
{
ictx->ctx = ctx;
ictx->args = args;
VectorInit( &ictx->history, 0, 10 );
ictx->interactive = ( KFileType ( ictx->std_in ) == kfdCharDev );
ictx->done = false;
CONST_STRING( &(ictx->PROMPT), "\nvdb $" );
StringInit( &(ictx->SInputLine), &( ictx->inputline[0] ), sizeof( ictx->inputline ), 0 );
rc = vdp_init_ctx( &ictx->vsctx, args );
}
return rc;
}
