static
rc_t DB_Init(const SParam* p, DB_Handle* h)
{
rc_t rc;
if( (rc = VDBManagerMakeUpdate(&h->mgr, NULL)) != 0 ) {
LOGERR(klogErr, rc, "failed to create VDB Manager");
}
else if( (rc = VDBManagerMakeSchema(h->mgr, &h->schema)) != 0 ) {
LOGERR(klogErr, rc, "failed to create schema");
}
else if( (rc = VSchemaParseFile(h->schema, p->schema)) != 0 ) {
PLOGERR(klogErr, (klogErr, rc, "failed to parse schema file '$(schema)'", PLOG_S(schema), p->schema));
}
else if( (rc = VDBManagerCreateDB(h->mgr, &h->db, h->schema, "NCBI:align:db:alignment_evidence",
p->force ? kcmInit : kcmCreate, p->out)) != 0 ) {
PLOGERR(klogErr, (klogErr, rc, "failed to create database at '$(path)'", PLOG_S(path), p->out));
}
else if( (rc = ReferenceMgr_Make(&h->rmgr, h->db, h->mgr, (p->force_refw ? ewrefmgr_co_allREADs : 0),
p->refseqcfg, p->refseqpath, p->refseq_chunk, 350 * 1024 * 1024, 0)) != 0 ) {
LOGERR(klogErr, rc, "failed to create reference manager");
}
else if( (rc = CGWriterAlgn_Make(&h->walgn, &h->mappings, h->db, h->rmgr, p->min_mapq, p->single_mate, p->cluster_size)) != 0 ) {
LOGERR(klogErr, rc, "failed to create alignment writer");
}
else if( (rc = CGWriterSeq_Make(&h->wseq, &h->reads, h->db, (p->force_readw ? ewseq_co_SaveRead : 0) |
(p->no_spot_group ? 0 : ewseq_co_SpotGroup), p->qual_quant)) != 0 ) {
LOGERR(klogErr, rc, "failed to create sequence writer");
} else if( p->asm_path && (rc = CGWriterEvdInt_Make(&h->wev_int, &h->ev_int, h->db, h->rmgr, 0)) != 0 ) {
LOGERR(klogErr, rc, "failed to create evidence intervals writer");
} else if( p->asm_path && (rc = CGWriterEvdDnbs_Make(&h->wev_dnb, &h->ev_dnb, h->db, h->rmgr, 0)) != 0 ) {
LOGERR(klogErr, rc, "failed to create evidence dnbs writer");
} else {
const char** r = p->refFiles;
while( rc == 0 && *r != NULL ) {
if( (rc = ReferenceMgr_FastaPath(h->rmgr, *r++)) != 0 ) {
PLOGERR(klogInfo, (klogInfo, rc, "fasta file '$(file)'", "file=%s", r[-1]));
}
}
}
return rc;
}
rc_t KeyRingDatabaseSave ( struct KeyRingData* self, struct KDirectory* wd, const char* path )
{
rc_t rc;
VDBManager* vdbMgr;
rc = VDBManagerMakeUpdate( &vdbMgr, wd );
if (rc == 0)
{
VSchema* schema;
rc = VDBManagerMakeSchema(vdbMgr, &schema);
if (rc == 0)
{
rc = VSchemaParseText ( schema, "keyring_schema", schema_text, string_measure(schema_text, NULL) );
if (rc == 0)
{ /* create a database */
VDatabase* db;
rc = VDBManagerCreateDB(vdbMgr, & db, schema, "keyring:KEYRING", kcmCreate | kcmMD5, path);
if (rc == 0)
{
rc_t rc2;
rc = SaveProjects(&self->projects, db);
if (rc == 0)
rc = SaveObjects(&self->objects, db);
/*TODO: SaveKeys */
rc2 = VDatabaseRelease(db);
if (rc == 0)
rc = rc2;
}
}
VSchemaRelease(schema);
}
VDBManagerRelease(vdbMgr);
}
return rc;
}
static rc_t pacbio_load( context *ctx, ld_context *lctx,
bool cache_content, bool check_src_obj )
{
bool consensus_present = true;
rc_t rc1 = 0;
rc_t rc = KLoadProgressbar_Make( &lctx->xml_progress, 0 );
if ( rc != 0 )
LOGERR( klogErr, rc, "cannot create LoadProgressBar" );
if ( rc == 0 )
{
rc = VDBManagerMakeUpdate ( &lctx->vdb_mgr, lctx->wd );
if ( rc != 0 )
LOGERR( klogErr, rc, "cannot create vdb-update-manager" );
}
if ( rc == 0 )
rc = pacbio_load_schema( lctx, ctx->schema_name );
if ( rc == 0 )
{
rc = VSchemaParseFile ( lctx->schema, ctx->schema_name );
if ( rc != 0 )
PLOGERR( klogErr, ( klogErr, rc, "cannot to parse schema file '$(schema)'",
"schema=%s", ctx->schema_name ) );
}
if ( rc == 0 )
{
rc = MakeHDF5RootDir ( lctx->wd, &lctx->hdf5_dir, false, ctx->src_path );
if ( rc != 0 )
PLOGERR( klogErr, ( klogErr, rc, "cannot open hdf5-source-file '$(srcfile)'",
"srcfile=%s", ctx->src_path ) );
}
if ( rc == 0 )
{
KCreateMode cmode = kcmMD5 | kcmParents;
if ( ctx->force )
cmode |= kcmInit;
else
cmode |= kcmCreate;
rc = VDBManagerCreateDB( lctx->vdb_mgr, & lctx->database, lctx->schema,
PACBIO_SCHEMA_DB, cmode, ctx->dst_path );
if ( rc != 0 )
PLOGERR( klogErr, ( klogErr, rc, "cannot create output-database '$(dst)'",
"dst=%s", ctx->dst_path ) );
}
if ( rc == 0 && ctx_ld_sequence( ctx ) )
rc = load_seq( lctx, cache_content, check_src_obj );
if ( rc == 0 && ctx_ld_consensus( ctx ) )
{
rc1 = load_consensus( lctx, cache_content, check_src_obj );
if ( rc1 != 0 )
{
LOGMSG( klogWarn, "the consensus-group is missing" );
VDatabaseDropTable ( lctx->database, "CONSENSUS" );
consensus_present = false;
}
}
if ( rc == 0 )
{
if ( rc1 == 0 )
{
/* CONSENSUS exists, create a alias named SEQUENCE to CONSENSUS */
/* rc = pacbio_make_alias( lctx->database, "CONSENSUS", "SEQUENCE" ); */
}
else
{
/* CONSENSUS does not exist, create a alias named SEQUENCE to PULSE */
/* rc = pacbio_make_alias( lctx->database, "PULSE", "SEQUENCE" ); */
}
}
if ( rc == 0 && ctx_ld_passes( ctx )&& consensus_present )
{
rc1 = load_passes( lctx, cache_content, check_src_obj );
if ( rc1 != 0 )
LOGMSG( klogWarn, "the passes-table is missing" );
}
if ( rc == 0 && ctx_ld_metrics( ctx ) )
{
rc1 = load_metrics( lctx, cache_content, check_src_obj );
if ( rc1 != 0 )
LOGMSG( klogWarn, "the metrics-table is missing" );
}
return rc;
}
rc_t KMain ( int argc, char *argv [] )
{
VDBManager *vmgr;
rc_t rc = VDBManagerMakeUpdate ( & vmgr, NULL );
if ( rc != 0 )
LOGERR ( klogInt, rc, "failed to make update manager" );
else
{
VSchema *vschema;
rc = VDBManagerMakeSchema ( vmgr, & vschema );
if ( rc != 0 )
LOGERR ( klogInt, rc, "failed to make empty schema" );
else
{
const char *file = "align/align.vschema";
#if _DEBUGGING
VSchemaListSymtab ( vschema );
#endif
rc = VSchemaParseFile ( vschema, "align/align.vschema" );
#if _DEBUGGING
VSchemaListSymtab ( vschema );
#endif
if ( rc != 0 )
{
pLOGERR ( klogErr, rc, "failed to parse schema file '$(file)'"
, "file=%s"
, file );
}
else
{
VDatabase *vdb;
const char *path = "test-ac-db";
const char *typespec = "NCBI:align:db:alignment";
rc = VDBManagerCreateDB ( vmgr, & vdb, vschema, typespec, kcmInit, path );
if ( rc != 0 )
{
pLOGERR ( klogInt, rc, "failed to create '$(typespec)' db at '$(path)'"
, "typespec=%s,path=%s"
, typespec
, path
);
}
else
{
VTable *vtbl;
const char *member = "align";
path = member;
rc = VDatabaseCreateTable ( vdb, & vtbl, member, kcmInit, path );
if ( rc != 0 )
{
pLOGERR ( klogInt, rc, "failed to create '$(member)' table at '$(path)'"
, "member=%s,path=%s"
, member
, path
);
}
else
{
printf ( "done\n" );
VTableRelease ( vtbl );
}
VDatabaseRelease ( vdb );
}
}
VSchemaRelease ( vschema );
}
VDBManagerRelease ( vmgr );
}
return rc;
}
