void makeItemsItemSaveToDbEscaped(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)
/* Save makeItemsItem as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than makeItemsItemSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *description;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
description = sqlEscapeString(el->description);
dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,'%s',%u)",
tableName, el->bin, chrom, el->chromStart, el->chromEnd, name, el->score, strand, el->thickStart, el->thickEnd, el->itemRgb, description, el->id);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&description);
}
void cutterSaveToDbEscaped(struct sqlConnection *conn, struct cutter *el, char *tableName, int updateSize)
/* Save cutter as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than cutterSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *name, *seq, *scizsArray, *companiesArray, *refsArray;
name = sqlEscapeString(el->name);
seq = sqlEscapeString(el->seq);
scizsArray = sqlStringArrayToString(el->scizs, el->numSciz);
companiesArray = sqlCharArrayToString(el->companies, el->numCompanies);
refsArray = sqlUnsignedArrayToString(el->refs, el->numRefs);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,%d,%u,%u,%u,'%s',%u,'%s',%u,'%s')",
tableName, name, el->size , el->matchSize , seq, el->cut , el->overhang , el->palindromic , el->semicolon , el->numSciz , scizsArray , el->numCompanies , companiesArray , el->numRefs , refsArray );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&name);
freez(&seq);
freez(&scizsArray);
freez(&companiesArray);
freez(&refsArray);
}
void protVarLinkSaveToDbEscaped(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
/* Save protVarLink as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than protVarLinkSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *id, *attrType, *raKey, *acc, *displayVal;
id = sqlEscapeString(el->id);
attrType = sqlEscapeString(el->attrType);
raKey = sqlEscapeString(el->raKey);
acc = sqlEscapeString(el->acc);
displayVal = sqlEscapeString(el->displayVal);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')",
tableName, id, attrType, raKey, acc, displayVal);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&id);
freez(&attrType);
freez(&raKey);
freez(&acc);
freez(&displayVal);
}
void protVarSaveToDbEscaped(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
/* Save protVar as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than protVarSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *id, *name, *srcId, *baseChangeType, *location;
id = sqlEscapeString(el->id);
name = sqlEscapeString(el->name);
srcId = sqlEscapeString(el->srcId);
baseChangeType = sqlEscapeString(el->baseChangeType);
location = sqlEscapeString(el->location);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u)",
tableName, id, name, srcId, baseChangeType, location, el->coordinateAccuracy);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&id);
freez(&name);
freez(&srcId);
freez(&baseChangeType);
freez(&location);
}
void affyAtlasSaveToDbEscaped(struct sqlConnection *conn, struct affyAtlas *el, char *tableName, int updateSize)
/* Save affyAtlas as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than affyAtlasSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *annName, *probeSet, *detection, *tissue;
annName = sqlEscapeString(el->annName);
probeSet = sqlEscapeString(el->probeSet);
detection = sqlEscapeString(el->detection);
tissue = sqlEscapeString(el->tissue);
dyStringPrintf(update, "insert into %s values ( '%s','%s',%f,'%s',%f,'%s')",
tableName, annName, probeSet, el->signal , detection, el->pval , tissue);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&annName);
freez(&probeSet);
freez(&detection);
freez(&tissue);
}
void taxonGeneticCodeSaveToDbEscaped(struct sqlConnection *conn, struct taxonGeneticCode *el, char *tableName, int updateSize)
/* Save taxonGeneticCode as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than taxonGeneticCodeSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *abbr, *name, *tranlsation, *starts, *comments;
abbr = sqlEscapeString(el->abbr);
name = sqlEscapeString(el->name);
tranlsation = sqlEscapeString(el->tranlsation);
starts = sqlEscapeString(el->starts);
comments = sqlEscapeString(el->comments);
dyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s','%s','%s')",
tableName, el->id , abbr, name, tranlsation, starts, comments);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&abbr);
freez(&name);
freez(&tranlsation);
freez(&starts);
freez(&comments);
}
void affy10KDetailsSaveToDbEscaped(struct sqlConnection *conn, struct affy10KDetails *el, char *tableName, int updateSize)
/* Save affy10KDetails as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than affy10KDetailsSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *affyId, *rsId, *tscId, *baseA, *baseB, *sequenceA, *sequenceB, *enzyme;
affyId = sqlEscapeString(el->affyId);
rsId = sqlEscapeString(el->rsId);
tscId = sqlEscapeString(el->tscId);
baseA = sqlEscapeString(el->baseA);
baseB = sqlEscapeString(el->baseB);
sequenceA = sqlEscapeString(el->sequenceA);
sequenceB = sqlEscapeString(el->sequenceB);
enzyme = sqlEscapeString(el->enzyme);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s','%s','%s','%s')",
tableName, affyId, rsId, tscId, baseA, baseB, sequenceA, sequenceB, enzyme);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&affyId);
freez(&rsId);
freez(&tscId);
freez(&baseA);
freez(&baseB);
freez(&sequenceA);
freez(&sequenceB);
freez(&enzyme);
}
struct edwScriptRegistry *edwScriptRegistryFromCgi()
/* Get script registery from cgi variables. Does authentication too. */
{
struct sqlConnection *conn = edwConnect();
char *user = sqlEscapeString(cgiString("user"));
char *password = sqlEscapeString(cgiString("password"));
char query[256];
sqlSafef(query, sizeof(query), "select * from edwScriptRegistry where name='%s'", user);
struct edwScriptRegistry *reg = edwScriptRegistryLoadByQuery(conn, query);
if (reg == NULL)
accessDenied();
char key[EDW_SID_SIZE];
edwMakeSid(password, key);
if (!sameString(reg->secretHash, key))
accessDenied();
sqlDisconnect(&conn);
return reg;
}
void sangerGeneToWBGeneIDSaveToDbEscaped(struct sqlConnection *conn, struct sangerGeneToWBGeneID *el, char *tableName, int updateSize)
/* Save sangerGeneToWBGeneID as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than sangerGeneToWBGeneIDSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *sangerGene, *WBGeneID;
sangerGene = sqlEscapeString(el->sangerGene);
WBGeneID = sqlEscapeString(el->WBGeneID);
dyStringPrintf(update, "insert into %s values ( '%s','%s')",
tableName, sangerGene, WBGeneID);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&sangerGene);
freez(&WBGeneID);
}
void polyGenotypeSaveToDbEscaped(struct sqlConnection *conn, struct polyGenotype *el, char *tableName, int updateSize)
/* Save polyGenotype as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than polyGenotypeSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *name, *ethnicGroup;
name = sqlEscapeString(el->name);
ethnicGroup = sqlEscapeString(el->ethnicGroup);
dyStringPrintf(update, "insert into %s values ( '%s','%s',%d,%d,%d,%d,%g,%g)",
tableName, name, ethnicGroup, el->plusPlus , el->plusMinus , el->minusMinus , el->sampleSize , el->alleleFrequency , el->unbiasedHeterozygosity );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&name);
freez(ðnicGroup);
}
void tfbsConsSaveToDbEscaped(struct sqlConnection *conn, struct tfbsCons *el, char *tableName, int updateSize)
/* Save tfbsCons as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than tfbsConsSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *species, *factor, *id;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
species = sqlEscapeString(el->species);
factor = sqlEscapeString(el->factor);
id = sqlEscapeString(el->id);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s')",
tableName, chrom, el->chromStart , el->chromEnd , name, el->score , strand, species, factor, id);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&species);
freez(&factor);
freez(&id);
}
void ggMrnaAliSaveToDbEscaped(struct sqlConnection *conn, struct ggMrnaAli *el, char *tableName, int updateSize)
/* Save ggMrnaAli as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than ggMrnaAliSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *tName, *strand, *qName;
tName = sqlEscapeString(el->tName);
strand = sqlEscapeString(el->strand);
qName = sqlEscapeString(el->qName);
dyStringPrintf(update, "insert into %s values ( '%s',%d,%d,'%s','%s',%d,%d,%u,%d,%d,%d,%d, NULL )",
tableName, tName, el->tStart , el->tEnd , strand, qName, el->qStart , el->qEnd , el->baseCount , el->orientation , el->hasIntrons , el->milliScore , el->blockCount );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&tName);
freez(&strand);
freez(&qName);
}
void affy10KSaveToDbEscaped(struct sqlConnection *conn, struct affy10K *el, char *tableName, int updateSize)
/* Save affy10K as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than affy10KSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom;
chrom = sqlEscapeString(el->chrom);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,%u)",
tableName, chrom, el->chromStart , el->chromEnd , el->affyId );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
}
static void
convert_query_term_to_sql( const GncSqlBackend* be, const gchar* fieldName, QofQueryTerm* pTerm, GString* sql )
{
QofQueryPredData* pPredData;
gboolean isInverted;
g_return_if_fail( pTerm != NULL );
g_return_if_fail( sql != NULL );
pPredData = qof_query_term_get_pred_data( pTerm );
isInverted = qof_query_term_is_inverted( pTerm );
if ( g_strcmp0( pPredData->type_name, QOF_TYPE_GUID ) == 0 )
{
query_guid_t guid_data = (query_guid_t)pPredData;
GList* guid_entry;
g_string_append( sql, "(" );
g_string_append( sql, fieldName );
switch ( guid_data->options )
{
case QOF_GUID_MATCH_ANY:
if ( isInverted ) g_string_append( sql, " NOT IN (" );
else g_string_append( sql, " IN (" );
break;
case QOF_GUID_MATCH_NONE:
if ( isInverted ) g_string_append( sql, " IN (" );
else g_string_append( sql, " NOT IN (" );
break;
default:
PERR( "Unexpected GncGUID match type: %d\n", guid_data->options );
}
for ( guid_entry = guid_data->guids; guid_entry != NULL; guid_entry = guid_entry->next )
{
gchar guid_buf[GUID_ENCODING_LENGTH+1];
if ( guid_entry != guid_data->guids ) g_string_append( sql, "," );
(void)guid_to_string_buff( guid_entry->data, guid_buf );
g_string_append_printf( sql, "'%s'", guid_buf );
}
g_string_append( sql, "))" );
}
else if ( g_strcmp0( pPredData->type_name, QOF_TYPE_CHAR ) == 0 )
{
query_char_t char_data = (query_char_t)pPredData;
int i;
if ( isInverted )
{
g_string_append( sql, "NOT(" );
}
if ( char_data->options == QOF_CHAR_MATCH_NONE )
{
g_string_append( sql, "NOT " );
}
g_string_append( sql, "(" );
for ( i = 0; char_data->char_list[i] != '\0'; i++ )
{
if ( i != 0 )
{
g_string_append( sql, " OR " );
}
g_string_append( sql, fieldName );
g_string_append( sql, " = '" );
g_string_append_c( sql, char_data->char_list[i] );
g_string_append( sql, "'" );
}
g_string_append( sql, ") " );
if ( isInverted )
{
g_string_append( sql, ") " );
}
}
else if ( g_strcmp0( pPredData->type_name, QOF_TYPE_STRING ) == 0 )
{
query_string_t string_data = (query_string_t)pPredData;
sqlEscape* escape = sqlEscape_new();
if ( isInverted )
{
g_string_append( sql, "NOT(" );
}
if ( pPredData->how == QOF_COMPARE_NEQ )
{
g_string_append( sql, "NOT(" );
}
g_string_append( sql, fieldName );
if ( string_data->is_regex || string_data->options == QOF_STRING_MATCH_CASEINSENSITIVE )
{
PWARN( "String is_regex || option = QOF_STRING_MATCH_INSENSITIVE\n" );
}
// g_string_append( sql, " ~" );
// } else {
g_string_append( sql, " =" );
// }
// if( string_data->options == QOF_STRING_MATCH_CASEINSENSITIVE ) {
// g_string_append( sql, "*" );
// }
g_string_append( sql, "'" );
g_string_append( sql, sqlEscapeString( escape, string_data->matchstring ) );
g_string_append( sql, "'" );
if ( pPredData->how == QOF_COMPARE_NEQ )
{
g_string_append( sql, ")" );
}
if ( isInverted )
{
g_string_append( sql, ")" );
}
sqlEscape_destroy( escape );
}
else
{
g_string_append( sql, "(" );
g_string_append( sql, fieldName );
convert_query_comparison_to_sql( pPredData, isInverted, sql );
if ( strcmp( pPredData->type_name, QOF_TYPE_NUMERIC ) == 0 )
{
query_numeric_t pData = (query_numeric_t)pPredData;
double d = gnc_numeric_to_double( pData->amount );
g_string_append_printf( sql, "%f", d );
}
else if ( g_strcmp0( pPredData->type_name, QOF_TYPE_DATE ) == 0 )
{
query_date_t date_data = (query_date_t)pPredData;
gchar* datebuf;
datebuf = gnc_sql_convert_timespec_to_string( be, date_data->date );
g_string_append_printf( sql, "'%s'", datebuf );
}
else if ( strcmp( pPredData->type_name, QOF_TYPE_INT32 ) == 0 )
{
query_int32_t pData = (query_int32_t)pPredData;
g_string_append_printf( sql, "%d", pData->val );
}
else if ( strcmp( pPredData->type_name, QOF_TYPE_INT64 ) == 0 )
{
query_int64_t pData = (query_int64_t)pPredData;
g_string_append_printf( sql, "%" G_GINT64_FORMAT, pData->val );
}
else if ( strcmp( pPredData->type_name, QOF_TYPE_DOUBLE ) == 0 )
{
query_double_t pData = (query_double_t)pPredData;
g_string_append_printf( sql, "%f", pData->val );
}
else if ( strcmp( pPredData->type_name, QOF_TYPE_BOOLEAN ) == 0 )
{
query_boolean_t pData = (query_boolean_t)pPredData;
g_string_append_printf( sql, "%d", pData->val );
}
else
{
PERR( "Unknown query predicate type: %s\n", pPredData->type_name );
}
g_string_append( sql, ")" );
}
}
void dbRIPSaveToDbEscaped(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)
/* Save dbRIP as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than dbRIPSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *originalId, *forwardPrimer, *reversePrimer, *polyClass, *polyFamily, *polySubfamily, *polySeq, *polySource, *reference, *ascertainingMethod, *remarks, *disease, *genoRegion;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
originalId = sqlEscapeString(el->originalId);
forwardPrimer = sqlEscapeString(el->forwardPrimer);
reversePrimer = sqlEscapeString(el->reversePrimer);
polyClass = sqlEscapeString(el->polyClass);
polyFamily = sqlEscapeString(el->polyFamily);
polySubfamily = sqlEscapeString(el->polySubfamily);
polySeq = sqlEscapeString(el->polySeq);
polySource = sqlEscapeString(el->polySource);
reference = sqlEscapeString(el->reference);
ascertainingMethod = sqlEscapeString(el->ascertainingMethod);
remarks = sqlEscapeString(el->remarks);
disease = sqlEscapeString(el->disease);
genoRegion = sqlEscapeString(el->genoRegion);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s',%g,%d,%d,'%s','%s')",
tableName, chrom, el->chromStart , el->chromEnd , name, el->score , strand, originalId, forwardPrimer, reversePrimer, polyClass, polyFamily, polySubfamily, polySeq, polySource, reference, ascertainingMethod, remarks, el->tm , el->filledSize , el->emptySize , disease, genoRegion);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&originalId);
freez(&forwardPrimer);
freez(&reversePrimer);
freez(&polyClass);
freez(&polyFamily);
freez(&polySubfamily);
freez(&polySeq);
freez(&polySource);
freez(&reference);
freez(&ascertainingMethod);
freez(&remarks);
freez(&disease);
freez(&genoRegion);
}
void tigrCmrGeneSaveToDbEscaped(struct sqlConnection *conn, struct tigrCmrGene *el, char *tableName, int updateSize)
/* Save tigrCmrGene as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than tigrCmrGeneSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *tigrCommon, *tigrGene, *tigrECN, *primLocus, *tigrMainRole, *tigrSubRole, *swissProt, *genbank, *goTerm;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
tigrCommon = sqlEscapeString(el->tigrCommon);
tigrGene = sqlEscapeString(el->tigrGene);
tigrECN = sqlEscapeString(el->tigrECN);
primLocus = sqlEscapeString(el->primLocus);
tigrMainRole = sqlEscapeString(el->tigrMainRole);
tigrSubRole = sqlEscapeString(el->tigrSubRole);
swissProt = sqlEscapeString(el->swissProt);
genbank = sqlEscapeString(el->genbank);
goTerm = sqlEscapeString(el->goTerm);
dyStringPrintf(update, "insert into %s values ( %d,'%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s',%u,%u,'%s','%s','%s','%s',%f,%f,%f,'%s')",
tableName, el->bin , chrom, el->chromStart , el->chromEnd , name, el->score , strand, tigrCommon, tigrGene, tigrECN, primLocus, el->tigrLength , el->tigrPepLength , tigrMainRole, tigrSubRole, swissProt, genbank, el->tigrMw , el->tigrPi , el->tigrGc , goTerm);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&tigrCommon);
freez(&tigrGene);
freez(&tigrECN);
freez(&primLocus);
freez(&tigrMainRole);
freez(&tigrSubRole);
freez(&swissProt);
freez(&genbank);
freez(&goTerm);
}
void genotypeSaveToDbEscaped(struct sqlConnection *conn, struct genotype *el, char *tableName, int updateSize)
/* Save genotype as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than genotypeSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *rsId, *SNPalleles, *chrom, *strand, *assembly, *center, *protLSID, *assayLSID, *panelLSID, *NA06985, *NA06991, *NA06993, *NA06993_dup, *NA06994, *NA07000, *NA07019, *NA07022, *NA07029, *NA07034, *NA07048, *NA07055, *NA07056, *NA07345, *NA07348, *NA07357, *NA10830, *NA10831, *NA10835, *NA10838, *NA10839, *NA10846, *NA10847, *NA10851, *NA10854, *NA10855, *NA10856, *NA10857, *NA10859, *NA10860, *NA10861, *NA10863, *NA11829, *NA11830, *NA11831, *NA11832, *NA11839, *NA11840, *NA11881, *NA11882, *NA11992, *NA11993, *NA11993_dup, *NA11994, *NA11995, *NA12003, *NA12003_dup, *NA12004, *NA12005, *NA12006, *NA12043, *NA12044, *NA12056, *NA12057, *NA12144, *NA12145, *NA12146, *NA12154, *NA12155, *NA12156, *NA12156_dup, *NA12234, *NA12236, *NA12239, *NA12248, *NA12248_dup, *NA12249, *NA12264, *NA12707, *NA12716, *NA12717, *NA12740, *NA12750, *NA12751, *NA12752, *NA12753, *NA12760, *NA12761, *NA12762, *NA12763, *NA12801, *NA12802, *NA12812, *NA12813, *NA12814, *NA12815, *NA12864, *NA12865, *NA12872, *NA12873, *NA12874, *NA12875, *NA12878, *NA12891, *NA12892;
rsId = sqlEscapeString(el->rsId);
SNPalleles = sqlEscapeString(el->SNPalleles);
chrom = sqlEscapeString(el->chrom);
strand = sqlEscapeString(el->strand);
assembly = sqlEscapeString(el->assembly);
center = sqlEscapeString(el->center);
protLSID = sqlEscapeString(el->protLSID);
assayLSID = sqlEscapeString(el->assayLSID);
panelLSID = sqlEscapeString(el->panelLSID);
NA06985 = sqlEscapeString(el->NA06985);
NA06991 = sqlEscapeString(el->NA06991);
NA06993 = sqlEscapeString(el->NA06993);
NA06993_dup = sqlEscapeString(el->NA06993_dup);
NA06994 = sqlEscapeString(el->NA06994);
NA07000 = sqlEscapeString(el->NA07000);
NA07019 = sqlEscapeString(el->NA07019);
NA07022 = sqlEscapeString(el->NA07022);
NA07029 = sqlEscapeString(el->NA07029);
NA07034 = sqlEscapeString(el->NA07034);
NA07048 = sqlEscapeString(el->NA07048);
NA07055 = sqlEscapeString(el->NA07055);
NA07056 = sqlEscapeString(el->NA07056);
NA07345 = sqlEscapeString(el->NA07345);
NA07348 = sqlEscapeString(el->NA07348);
NA07357 = sqlEscapeString(el->NA07357);
NA10830 = sqlEscapeString(el->NA10830);
NA10831 = sqlEscapeString(el->NA10831);
NA10835 = sqlEscapeString(el->NA10835);
NA10838 = sqlEscapeString(el->NA10838);
NA10839 = sqlEscapeString(el->NA10839);
NA10846 = sqlEscapeString(el->NA10846);
NA10847 = sqlEscapeString(el->NA10847);
NA10851 = sqlEscapeString(el->NA10851);
NA10854 = sqlEscapeString(el->NA10854);
NA10855 = sqlEscapeString(el->NA10855);
NA10856 = sqlEscapeString(el->NA10856);
NA10857 = sqlEscapeString(el->NA10857);
NA10859 = sqlEscapeString(el->NA10859);
NA10860 = sqlEscapeString(el->NA10860);
NA10861 = sqlEscapeString(el->NA10861);
NA10863 = sqlEscapeString(el->NA10863);
NA11829 = sqlEscapeString(el->NA11829);
NA11830 = sqlEscapeString(el->NA11830);
NA11831 = sqlEscapeString(el->NA11831);
NA11832 = sqlEscapeString(el->NA11832);
NA11839 = sqlEscapeString(el->NA11839);
NA11840 = sqlEscapeString(el->NA11840);
NA11881 = sqlEscapeString(el->NA11881);
NA11882 = sqlEscapeString(el->NA11882);
NA11992 = sqlEscapeString(el->NA11992);
NA11993 = sqlEscapeString(el->NA11993);
NA11993_dup = sqlEscapeString(el->NA11993_dup);
NA11994 = sqlEscapeString(el->NA11994);
NA11995 = sqlEscapeString(el->NA11995);
NA12003 = sqlEscapeString(el->NA12003);
NA12003_dup = sqlEscapeString(el->NA12003_dup);
NA12004 = sqlEscapeString(el->NA12004);
NA12005 = sqlEscapeString(el->NA12005);
NA12006 = sqlEscapeString(el->NA12006);
NA12043 = sqlEscapeString(el->NA12043);
NA12044 = sqlEscapeString(el->NA12044);
NA12056 = sqlEscapeString(el->NA12056);
NA12057 = sqlEscapeString(el->NA12057);
NA12144 = sqlEscapeString(el->NA12144);
NA12145 = sqlEscapeString(el->NA12145);
NA12146 = sqlEscapeString(el->NA12146);
NA12154 = sqlEscapeString(el->NA12154);
NA12155 = sqlEscapeString(el->NA12155);
NA12156 = sqlEscapeString(el->NA12156);
NA12156_dup = sqlEscapeString(el->NA12156_dup);
NA12234 = sqlEscapeString(el->NA12234);
NA12236 = sqlEscapeString(el->NA12236);
NA12239 = sqlEscapeString(el->NA12239);
NA12248 = sqlEscapeString(el->NA12248);
NA12248_dup = sqlEscapeString(el->NA12248_dup);
NA12249 = sqlEscapeString(el->NA12249);
NA12264 = sqlEscapeString(el->NA12264);
NA12707 = sqlEscapeString(el->NA12707);
NA12716 = sqlEscapeString(el->NA12716);
NA12717 = sqlEscapeString(el->NA12717);
NA12740 = sqlEscapeString(el->NA12740);
NA12750 = sqlEscapeString(el->NA12750);
NA12751 = sqlEscapeString(el->NA12751);
NA12752 = sqlEscapeString(el->NA12752);
NA12753 = sqlEscapeString(el->NA12753);
NA12760 = sqlEscapeString(el->NA12760);
NA12761 = sqlEscapeString(el->NA12761);
NA12762 = sqlEscapeString(el->NA12762);
NA12763 = sqlEscapeString(el->NA12763);
NA12801 = sqlEscapeString(el->NA12801);
NA12802 = sqlEscapeString(el->NA12802);
NA12812 = sqlEscapeString(el->NA12812);
NA12813 = sqlEscapeString(el->NA12813);
NA12814 = sqlEscapeString(el->NA12814);
NA12815 = sqlEscapeString(el->NA12815);
NA12864 = sqlEscapeString(el->NA12864);
NA12865 = sqlEscapeString(el->NA12865);
NA12872 = sqlEscapeString(el->NA12872);
NA12873 = sqlEscapeString(el->NA12873);
NA12874 = sqlEscapeString(el->NA12874);
NA12875 = sqlEscapeString(el->NA12875);
NA12878 = sqlEscapeString(el->NA12878);
NA12891 = sqlEscapeString(el->NA12891);
NA12892 = sqlEscapeString(el->NA12892);
dyStringPrintf(update, "insert into %s values ( '%s','%s','%s',%d,'%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s')",
tableName, rsId, SNPalleles, chrom, el->chromStart , strand, assembly, center, protLSID, assayLSID, panelLSID, NA06985, NA06991, NA06993, NA06993_dup, NA06994, NA07000, NA07019, NA07022, NA07029, NA07034, NA07048, NA07055, NA07056, NA07345, NA07348, NA07357, NA10830, NA10831, NA10835, NA10838, NA10839, NA10846, NA10847, NA10851, NA10854, NA10855, NA10856, NA10857, NA10859, NA10860, NA10861, NA10863, NA11829, NA11830, NA11831, NA11832, NA11839, NA11840, NA11881, NA11882, NA11992, NA11993, NA11993_dup, NA11994, NA11995, NA12003, NA12003_dup, NA12004, NA12005, NA12006, NA12043, NA12044, NA12056, NA12057, NA12144, NA12145, NA12146, NA12154, NA12155, NA12156, NA12156_dup, NA12234, NA12236, NA12239, NA12248, NA12248_dup, NA12249, NA12264, NA12707, NA12716, NA12717, NA12740, NA12750, NA12751, NA12752, NA12753, NA12760, NA12761, NA12762, NA12763, NA12801, NA12802, NA12812, NA12813, NA12814, NA12815, NA12864, NA12865, NA12872, NA12873, NA12874, NA12875, NA12878, NA12891, NA12892);
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&rsId);
freez(&SNPalleles);
freez(&chrom);
freez(&strand);
freez(&assembly);
freez(¢er);
freez(&protLSID);
freez(&assayLSID);
freez(&panelLSID);
freez(&NA06985);
freez(&NA06991);
freez(&NA06993);
freez(&NA06993_dup);
freez(&NA06994);
freez(&NA07000);
freez(&NA07019);
freez(&NA07022);
freez(&NA07029);
freez(&NA07034);
freez(&NA07048);
freez(&NA07055);
freez(&NA07056);
freez(&NA07345);
freez(&NA07348);
freez(&NA07357);
freez(&NA10830);
freez(&NA10831);
freez(&NA10835);
freez(&NA10838);
freez(&NA10839);
freez(&NA10846);
freez(&NA10847);
freez(&NA10851);
freez(&NA10854);
freez(&NA10855);
freez(&NA10856);
freez(&NA10857);
freez(&NA10859);
freez(&NA10860);
freez(&NA10861);
freez(&NA10863);
freez(&NA11829);
freez(&NA11830);
freez(&NA11831);
freez(&NA11832);
freez(&NA11839);
freez(&NA11840);
freez(&NA11881);
freez(&NA11882);
freez(&NA11992);
freez(&NA11993);
freez(&NA11993_dup);
freez(&NA11994);
freez(&NA11995);
freez(&NA12003);
freez(&NA12003_dup);
freez(&NA12004);
freez(&NA12005);
freez(&NA12006);
freez(&NA12043);
freez(&NA12044);
freez(&NA12056);
freez(&NA12057);
freez(&NA12144);
freez(&NA12145);
freez(&NA12146);
freez(&NA12154);
freez(&NA12155);
freez(&NA12156);
freez(&NA12156_dup);
freez(&NA12234);
freez(&NA12236);
freez(&NA12239);
freez(&NA12248);
freez(&NA12248_dup);
freez(&NA12249);
freez(&NA12264);
freez(&NA12707);
freez(&NA12716);
freez(&NA12717);
freez(&NA12740);
freez(&NA12750);
freez(&NA12751);
freez(&NA12752);
freez(&NA12753);
freez(&NA12760);
freez(&NA12761);
freez(&NA12762);
freez(&NA12763);
freez(&NA12801);
freez(&NA12802);
freez(&NA12812);
freez(&NA12813);
freez(&NA12814);
freez(&NA12815);
freez(&NA12864);
freez(&NA12865);
freez(&NA12872);
freez(&NA12873);
freez(&NA12874);
freez(&NA12875);
freez(&NA12878);
freez(&NA12891);
freez(&NA12892);
}
void hapmapPrimateAllelesSaveToDbEscaped(struct sqlConnection *conn, struct hapmapPrimateAlleles *el, char *tableName, int updateSize)
/* Save hapmapPrimateAlleles as a row to the table specified by tableName.
* As blob fields may be arbitrary size updateSize specifies the approx size.
* of a string that would contain the entire query. Automatically
* escapes all simple strings (not arrays of string) but may be slower than hapmapPrimateAllelesSaveToDb().
* For example automatically copies and converts:
* "autosql's features include" --> "autosql\'s features include"
* before inserting into database. */
{
struct dyString *update = newDyString(updateSize);
char *chrom, *name, *strand, *refAllele, *otherAllele, *chimpChrom, *chimpStrand, *chimpAllele, *rhesusChrom, *rhesusStrand, *rhesusAllele;
chrom = sqlEscapeString(el->chrom);
name = sqlEscapeString(el->name);
strand = sqlEscapeString(el->strand);
refAllele = sqlEscapeString(el->refAllele);
otherAllele = sqlEscapeString(el->otherAllele);
chimpChrom = sqlEscapeString(el->chimpChrom);
chimpStrand = sqlEscapeString(el->chimpStrand);
chimpAllele = sqlEscapeString(el->chimpAllele);
rhesusChrom = sqlEscapeString(el->rhesusChrom);
rhesusStrand = sqlEscapeString(el->rhesusStrand);
rhesusAllele = sqlEscapeString(el->rhesusAllele);
dyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s',%u,'%s','%s',%u,'%s',%u,'%s','%s',%u)",
tableName, chrom, el->chromStart , el->chromEnd , name, el->score , strand, refAllele, otherAllele, chimpChrom, el->chimpPos , chimpStrand, chimpAllele, el->chimpQual , rhesusChrom, el->rhesusPos , rhesusStrand, rhesusAllele, el->rhesusQual );
sqlUpdate(conn, update->string);
freeDyString(&update);
freez(&chrom);
freez(&name);
freez(&strand);
freez(&refAllele);
freez(&otherAllele);
freez(&chimpChrom);
freez(&chimpStrand);
freez(&chimpAllele);
freez(&rhesusChrom);
freez(&rhesusStrand);
freez(&rhesusAllele);
}
