IDType SyntenyRegionAdaptor_store(SyntenyRegionAdaptor *sra, IDType clusterId, SyntenyRegion *region) {
IDType regionId = 0;
StatementHandle *sth;
char qStr[1024];
if (!region) {
fprintf(stderr, "Error: region is not a SyntenyRegion\n");
} else {
sprintf(qStr, "insert into synteny_region (synteny_cluster_id,dnafrag_id,seq_start,seq_end)"
" VALUES (" IDFMTSTR ", " IDFMTSTR ", %d, %d)",
clusterId,
SyntenyRegion_getDNAFragId(region),
SyntenyRegion_getSeqStart(region),
SyntenyRegion_getSeqEnd(region));
sth = sra->prepare((BaseAdaptor *)sra, qStr, strlen(qStr));
sth->execute(sth);
regionId = sth->getInsertId(sth);
SyntenyRegion_setDbID(region, regionId);
SyntenyRegion_setAdaptor(region, sra);
}
return regionId;
}
// This method was a mess - tidied and rearranged
IDType IntronSupportingEvidenceAdaptor_store(IntronSupportingEvidenceAdaptor *isea, IntronSupportingEvidence *sf) {
if (sf == NULL) {
fprintf(stderr,"sf is NULL in IntronSupportingEvidenceAdaptor_store\n");
exit(1);
}
Class_assertType(CLASS_INTRONSUPPORTINGEVIDENCE, sf->objectType);
DBAdaptor *db = isea->dba;
AnalysisAdaptor *analysisAdaptor = DBAdaptor_getAnalysisAdaptor(db);
if (IntronSupportingEvidence_isStored(sf, db)) {
fprintf(stderr,"ISE already stored\n");
return IntronSupportingEvidence_getDbID(sf);
}
Analysis *analysis = IntronSupportingEvidence_getAnalysis(sf);
if (!Analysis_isStored(analysis, db)) {
AnalysisAdaptor_store(analysisAdaptor, analysis);
}
IDType analysisId = Analysis_getDbID(analysis);
// Think the above is equivalent to this horror
//my $analysis_id = $analysis->is_stored($db) ? $analysis->dbID() : $db->get_AnalysisAdaptor()->store($analysis);
/* No transfer (see GeneAdaptor for why)
my $seq_region_id;
($sf, $seq_region_id) = $self->_pre_store($sf);
*/
IDType seqRegionId = BaseFeatureAdaptor_preStore((BaseFeatureAdaptor *)isea, (SeqFeature*)sf);
char qStr[1024];
sprintf(qStr, "INSERT IGNORE INTO intron_supporting_evidence "
"(analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name, score, score_type, is_splice_canonical) "
"VALUES ("IDFMTSTR","IDFMTSTR",%ld,%ld,%d,'%s',%f,'%s',%d)",
analysisId,
seqRegionId,
IntronSupportingEvidence_getSeqRegionStart((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionEnd((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionStrand((SeqFeature*)sf),
IntronSupportingEvidence_getHitName(sf),
IntronSupportingEvidence_getScore(sf),
IntronSupportingEvidence_getScoreType(sf),
IntronSupportingEvidence_getIsSpliceCanonical(sf));
StatementHandle *sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
IDType sfId = sth->getInsertId(sth);
sth->finish(sth);
if (!sfId) {
sprintf(qStr,"SELECT intron_supporting_evidence_id "
"FROM intron_supporting_evidence "
"WHERE analysis_id = "IDFMTSTR
" AND seq_region_id = "IDFMTSTR
" AND seq_region_start = %ld"
" AND seq_region_end = %ld"
" AND seq_region_strand = %d"
" AND hit_name = '%s'",
analysisId,
seqRegionId,
IntronSupportingEvidence_getSeqRegionStart((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionEnd((SeqFeature*)sf),
IntronSupportingEvidence_getSeqRegionStrand((SeqFeature*)sf),
IntronSupportingEvidence_getHitName(sf));
sth = isea->prepare((BaseAdaptor *)isea,qStr,strlen(qStr));
sth->execute(sth);
if (sth->numRows(sth) > 0) {
ResultRow *row = sth->fetchRow(sth);
sfId = row->getLongLongAt(row, 0);
}
sth->finish(sth);
}
IntronSupportingEvidence_setAdaptor((SeqFeature*)sf, (BaseAdaptor*)isea);
IntronSupportingEvidence_setDbID(sf, sfId);
return IntronSupportingEvidence_getDbID(sf);
}
IDType DBEntryAdaptor_store(DBEntryAdaptor *dbea, DBEntry *exObj,
IDType ensObject, char *ensType, int ignoreRelease) {
fprintf(stderr,"DBEntryAdaptor_store does not implement ignoreRelease functionality yet\n");
char qStr[512];
StatementHandle *sth;
ResultRow *row;
IDType dbRef;
IDType dbX;
//
// Check for the existance of the external_db, throw if it does not exist
//
sprintf(qStr,
"SELECT external_db_id"
" FROM external_db"
" WHERE db_name = '%s'"
" AND db_release = %s",
DBEntry_getDbName(exObj),
DBEntry_getRelease(exObj));
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
row = sth->fetchRow(sth);
if( row == NULL ) {
sth->finish(sth);
fprintf(stderr,"Error: external_db [%s] release [%s] does not exist\n",
DBEntry_getDbName(exObj), DBEntry_getRelease(exObj));
exit(1);
}
dbRef = row->getLongLongAt(row,0);
sth->finish(sth);
//
// Check for the existance of the external reference, add it if not present
//
sprintf(qStr,
"SELECT xref_id"
" FROM xref"
" WHERE external_db_id = " IDFMTSTR
" AND dbprimary_acc = '%s'"
" AND version = %s",
dbRef,
DBEntry_getPrimaryId(exObj),
DBEntry_getVersion(exObj));
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
row = sth->fetchRow(sth);
if (row != NULL) {
dbX = row->getLongLongAt(row,0);
sth->finish(sth);
} else {
//
// store the new xref
//
// First finish the old sth
sth->finish(sth);
// NIY Handling NULL values
sprintf(qStr,
"INSERT ignore INTO xref"
" SET dbprimary_acc = '%s',"
" display_label = '%s',"
" version = %s,"
" description = '%s',"
" external_db_id = " IDFMTSTR,
DBEntry_getPrimaryId(exObj),
DBEntry_getDisplayId(exObj),
DBEntry_getVersion(exObj),
DBEntry_getDescription(exObj),
dbRef
);
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
dbX = sth->getInsertId(sth);
sth->finish(sth);
//
// store the synonyms for the new xref
//
if (DBEntry_getAllSynonyms(exObj)) {
StatementHandle *checkSth;
StatementHandle *storeSth;
int i;
Vector *synonyms;
sprintf(qStr,
"SELECT xref_id, synonym"
" FROM external_synonym"
" WHERE xref_id = %" IDFMTSTR
" AND synonym = '%%s'");
checkSth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sprintf(qStr,
"INSERT ignore INTO external_synonym"
" SET xref_id = %" IDFMTSTR ", synonym = '%%s'");
storeSth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
synonyms = DBEntry_getAllSynonyms(exObj);
for (i=0;i<Vector_getNumElement(synonyms); i++) {
char *syn = Vector_getElementAt(synonyms,i);
checkSth->execute(checkSth, dbX, syn);
row = checkSth->fetchRow(checkSth);
if (!row) {
storeSth->execute(storeSth, dbX, syn);
}
}
checkSth->finish(checkSth);
storeSth->finish(storeSth);
}
}
//
// check if the object mapping was already stored
//
sprintf(qStr,
"SELECT xref_id"
" FROM object_xref"
" WHERE xref_id = " IDFMTSTR
" AND ensembl_object_type = '%s'"
" AND ensembl_id = " IDFMTSTR,
dbX, ensType, ensObject);
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
row = sth->fetchRow(sth);
// NOTE row will be invalid after this call but will still
// indicate whether something was found
sth->finish(sth);
if (!row) {
IDType Xidt;
//
// Store the reference to the internal ensembl object
//
sprintf(qStr,
"INSERT ignore INTO object_xref"
" SET xref_id = " IDFMTSTR ","
" ensembl_object_type = '%s',"
" ensembl_id = " IDFMTSTR,
dbX, ensType, ensObject);
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
DBEntry_setDbID(exObj, dbX);
DBEntry_setAdaptor(exObj, (BaseAdaptor *)dbea);
Xidt = sth->getInsertId(sth);
//
// If this is an IdentityXref need to store in that table too
//
if (DBEntry_getIdentityXref(exObj)) {
IdentityXref *idx = DBEntry_getIdentityXref(exObj);
sprintf(qStr,
"INSERT ignore INTO identity_xref"
" SET object_xref_id = " IDFMTSTR ","
" query_identity = %f,"
" target_identity = %f",
Xidt,
IdentityXref_getQueryIdentity(idx),
IdentityXref_getTargetIdentity(idx));
sth = dbea->prepare((BaseAdaptor *)dbea,qStr,strlen(qStr));
sth->execute(sth);
sth->finish(sth);
}
}
return dbX;
}
