void saveExpsTable(struct expRecord *records)
/* Create the Exps table. */
{
struct expRecord *cur;
struct sqlConnection *conn = sqlConnect(database);
char expTableName[100];
safef(expTableName, sizeof(expTableName), "%sExps", table);
expRecordCreateTable(conn, expTableName);
for (cur = records; cur != NULL; cur = cur->next)
expRecordSaveToDb(conn, cur, expTableName, 2048);
sqlDisconnect(&conn);
}
int lineToExpTable(char *line, char *table)
/* Create expression format table from line. */
{
FILE *f = hgCreateTabFile(tabDir, table);
int count = lineToExp(line, f);
if (doLoad)
{
struct sqlConnection *conn = sqlConnect(database);
expRecordCreateTable(conn, table);
hgLoadTabFile(conn, tabDir, table, &f);
hgRemoveTabFile(tabDir, table);
sqlDisconnect(&conn);
}
return count;
}
void makeNewExpTable(char *oldTable, struct maMedSpec *medList, char *newTable)
/* Create new expTable in hgFixed that is very similar
* to oldExpTable, but with rows defined by medList. */
{
struct maMedSpec *med;
struct expRecord *oldExp, newExp;
struct sqlConnection *conn = sqlConnect("hgFixed");
FILE *f = hgCreateTabFile(tabDir, newTable);
char query[256], **row;
struct sqlResult *sr;
int curId = 0;
for (med = medList; med != NULL; med = med->next)
{
/* Load expression record from old table of first
* thing in median. */
sqlSafef(query, sizeof(query),
"select * from %s where id = %d", oldTable, med->ids[0]);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
errAbort("Can't find id %d in %s\n", med->ids[0], oldTable);
oldExp = expRecordLoad(row);
sqlFreeResult(&sr);
if (oldExp->numExtras < 3)
errAbort("Can only deal with old tables with 3 extras or more");
/* Create new expression record, mostly just a shallow copy of old. */
newExp = *oldExp;
newExp.id = curId;
++curId;
newExp.name = newExp.description = med->name;
newExp.extras[2] = med->group;
/* Save new one, free old one. */
expRecordTabOut(&newExp, f);
expRecordFree(&oldExp);
}
if (doLoad)
{
expRecordCreateTable(conn, newTable);
hgLoadTabFile(conn, tabDir, newTable, &f);
hgRemoveTabFile(tabDir, newTable);
}
sqlDisconnect(&conn);
}
struct hash *makeExpsTable(char *database, char *expTable, char *expFile,
int *expCount)
/* Open experiment file and use it to create experiment table.
Use optional fields if present, otherwise defaults.
Return a hash of expId's, keyed by name */
{
struct lineFile *lf = lineFileOpen(expFile, TRUE);
FILE *f = hgCreateTabFile(tabDir, expTable);
int expId = 0;
char *words[6];
int wordCt;
struct hash *expHash = newHash(0);
while ((wordCt = lineFileChopNext(lf, words, ArraySize(words))))
{
char *name = words[0];
hashAddInt(expHash, name, expId);
fprintf(f, "%d\t%s\t", expId++, name);
fprintf(f, "%s\t", wordCt > 1 ? words[1] : name);
fprintf(f, "%s\t", wordCt > 2 ? words[2] : expUrl);
fprintf(f, "%s\t", wordCt > 3 ? words[3] : expRef);
fprintf(f, "%s\t", wordCt > 4 ? words[4] : expCredit);
fprintf(f, "0\n"); /* extras */
}
if (expId <= 0)
errAbort("No experiments in %s", lf->fileName);
verbose(2, "%d experiments\n", expId);
if (doLoad)
{
struct sqlConnection *conn = sqlConnect(database);
expRecordCreateTable(conn, expTable);
hgLoadTabFile(conn, tabDir, expTable, &f);
sqlDisconnect(&conn);
}
lineFileClose(&lf);
if (expCount)
*expCount = expId;
return expHash;
}
