static void printSampleRows(int sampleCount, struct sqlConnection *conn, char *table)
/* Put up sample values. */
{
char query[256];
struct sqlResult *sr;
char **row;
int i, columnCount = 0;
int itemRgbCol = -1;
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(database, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
/* Make table with header row containing name of fields. */
sqlSafef(query, sizeof(query), "describe %s", table);
sr = sqlGetResult(conn, query);
hTableStart();
hPrintf("<TR>");
while ((row = sqlNextRow(sr)) != NULL)
{
if (showItemRgb && sameWord(row[0],"reserved"))
{
hPrintf("<TH>itemRgb</TH>");
itemRgbCol = columnCount;
}
else
hPrintf("<TH>%s</TH>", row[0]);
++columnCount;
}
hPrintf("</TR>");
sqlFreeResult(&sr);
/* Get some sample fields. */
sqlSafef(query, sizeof(query), "select * from %s limit %d", table, sampleCount);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
hPrintf("<TR>");
for (i=0; i<columnCount; ++i)
{
if (showItemRgb && (i == itemRgbCol))
{
int rgb = atoi(row[i]);
hPrintf("<TD>%d,%d,%d</TD>", (rgb & 0xff0000) >> 16,
(rgb & 0xff00) >> 8, (rgb & 0xff));
}
else
{
if (row[i] == NULL)
{
hPrintf("<TD></TD>");
}
else
{
writeHtmlCell(row[i]);
}
}
}
void showSchemaBigBed(char *table, struct trackDb *tdb)
/* Show schema on bigBed. */
{
/* Figure out bigBed file name and open it. Get contents for first chromosome as an example. */
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bbiChromInfo *chromList = bbiChromList(bbi);
struct lm *lm = lmInit(0);
struct bigBedInterval *ivList = getNElements(bbi, chromList, lm, 10);
/* Get description of columns, making it up from BED records if need be. */
struct asObject *as = bigBedAsOrDefault(bbi);
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>Big Bed File:</B> %s", fileName);
if (bbi->version >= 2)
{
hPrintf("<BR><B>Item Count:</B> ");
printLongWithCommas(stdout, bigBedItemCount(bbi));
}
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (ivList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
if (ivList != NULL)
{
char *dupeRest = lmCloneString(lm, ivList->rest); /* Manage rest-stomping side-effect */
bigBedIntervalToRow(ivList, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
ivList->rest = dupeRest;
}
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
/* If more fields than descriptions put up minimally helpful info (at least has example). */
for ( ; colCount < bbi->fieldCount; ++colCount)
{
hPrintf("<TR><TD><TT>column%d</TT></TD>", colCount+1);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>n/a</TD></TR>\n");
}
hTableEnd();
if (ivList != NULL)
{
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
for (; colIx < colCount; ++colIx)
hPrintf("<TH>column%d</TH>", colIx+1);
hPrintf("</TR>\n");
/* Print sample lines. */
struct bigBedInterval *iv;
for (iv=ivList; iv != NULL; iv = iv->next)
{
bigBedIntervalToRow(iv, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
}
printTrackHtml(tdb);
/* Clean up and go home. */
lmCleanup(&lm);
bbiFileClose(&bbi);
freeMem(fileName);
hFreeConn(&conn);
}
void showSchemaVcf(char *table, struct trackDb *tdb, boolean isTabix)
/* Show schema on vcf. */
{
struct sqlConnection *conn = hAllocConn(database);
char *fileName = vcfFileName(tdb, conn, table, hDefaultChrom(database));
struct asObject *as = vcfAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>VCF File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>Variant Call Format specification</A> for more details<BR>\n",
"http://www.1000genomes.org/wiki/analysis/vcf4.0");
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
hTableEnd();
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Fetch sample rows. */
struct lineFile *lf = isTabix ? lineFileTabixMayOpen(fileName, TRUE) :
lineFileMayOpen(fileName, TRUE);
if (lf == NULL)
noWarnAbort();
char *row[VCF_MAX_SCHEMA_COLS];
int i;
for (i = 0; i < 10; i++)
{
int colCount = lineFileChop(lf, row);
int colIx;
if (i == 0)
{
// Print field names as column headers, using colCount to compute genotype span
hPrintf("<TR>");
for (colIx = 0, col = as->columnList; col != NULL && colIx < colCount;
colIx++, col = col->next)
{
if (sameString("genotypes", col->name) && colCount > colIx+1)
hPrintf("<TH colspan=%d>%s</TH>", colCount - colIx, col->name);
else
hPrintf("<TH>%s</TH>", col->name);
}
hPrintf("</TR>\n");
}
hPrintf("<TR>");
for (colIx=0; colIx < colCount; ++colIx)
{
if (colCount > VCFDATALINE_NUM_COLS && colIx == colCount - 1)
hPrintf("<TD>...</TD>");
else
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
printTrackHtml(tdb);
/* Clean up and go home. */
lineFileClose(&lf);
freeMem(fileName);
hFreeConn(&conn);
}
