static void showTableFieldsDb(char *db, char *rootTable, boolean withGetButton)
/* Put up a little html table with a check box, name, and hopefully
* a description for each field in SQL rootTable. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(db);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
struct asObject *asObj = asForTable(conn, rootTable);
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(tdb); /* should we expect itemRgb instead of "reserved" */
struct slName *fieldList;
if (isBigBed(database, rootTable, curTrack, ctLookupName))
fieldList = bigBedGetFields(rootTable, conn);
else if (isBamTable(rootTable))
fieldList = bamGetFields();
else if (isVcfTable(rootTable, NULL))
fieldList = vcfGetFields();
else
{
char *table = chromTable(conn, rootTable);
fieldList = sqlListFields(conn, table);
freez(&table);
}
showTableFieldsOnList(db, rootTable, asObj, fieldList, showItemRgb, withGetButton);
hFreeConn(&conn);
}
struct bed *getFilteredBeds(struct sqlConnection *conn,
char *table, struct region *region, struct lm *lm, int *retFieldCount)
/* Get list of beds on single region that pass filtering. */
{
boolean isTabix = FALSE;
/* region may be part of a list, and the routines we call work on lists of
* regions. Temporarily force region->next to NULL and restore at end. */
struct region *oldNext = region->next;
struct bed *bedList = NULL;
region->next = NULL;
if (isBigBed(database, table, curTrack, ctLookupName))
bedList = bigBedGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount);
else if (isBamTable(table))
bedList = bamGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount);
else if (isVcfTable(table, &isTabix))
bedList = vcfGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount,
isTabix);
else if (isCustomTrack(table))
bedList = customTrackGetFilteredBeds(database, table, region, lm, retFieldCount);
else if (sameWord(table, WIKI_TRACK_TABLE))
bedList = wikiTrackGetFilteredBeds(table, region, lm, retFieldCount);
else
bedList = dbGetFilteredBedsOnRegions(conn, database, database, table, table, region, lm,
retFieldCount);
region->next = oldNext;
return bedList;
}
static struct slName *getExamples(char *db, struct sqlConnection *conn,
char *table, char *field, int count)
/* Return a list of several example values of table.field. */
{
boolean isTabix = FALSE;
if (isBamTable(table))
{
assert(sameString(field, "qName"));
return randomBamIds(table, conn, count);
}
else if (isBigBed(db, table, curTrack, ctLookupName))
{
assert(sameString(field, "name"));
return randomBigBedIds(table, conn, count);
}
else if (isVcfTable(table, &isTabix))
{
assert(sameString(field, "id"));
return randomVcfIds(table, conn, count, isTabix);
}
else
{
char fullTable[HDB_MAX_TABLE_STRING];
char *c = strchr(table, '.');
if (c || ! hFindSplitTable(database, NULL, table, fullTable, NULL))
safecpy(fullTable, sizeof(fullTable), table);
return sqlRandomSampleConn(conn, fullTable, field, count);
}
}
boolean canIntersect(char *db, char *table)
/* Return true if table exists and is positional. */
{
if (isCustomTrack(table) && ctLookupName(table) != NULL)
return TRUE;
if (isBamTable(table))
return TRUE;
if (isBigWigTable(table))
return TRUE;
if (isBigBed(database, table, curTrack, ctLookupName))
return TRUE;
if (isVcfTable(table, NULL))
return TRUE;
if (isHubTrack(table))
return TRUE;
if (sameWord(table, WIKI_TRACK_TABLE))
return TRUE;
if (hTableOrSplitExists(db, table))
return isPositional(db, table);
return FALSE;
}
static struct hash *getAllPossibleIds(struct sqlConnection *conn,
struct lm *lm, char *idField, char *extraWhere)
/* If curTable is a custom track or bigFile, return NULL. Otherwise,
* make a hash of all identifiers in curTable (and alias tables if specified)
* so that we can check the validity of pasted/uploaded identifiers. */
{
if (isCustomTrack(curTable) || isBamTable(curTable) || isVcfTable(curTable, NULL) ||
isBigBed(database, curTable, curTrack, ctLookupName))
return NULL;
struct hash *matchHash = hashNew(20);
struct slName *tableList;
char *xrefTable = NULL, *xrefIdField = NULL, *aliasField = NULL;
struct sqlConnection *alternateConn = conn;
if (sameWord(curTable, WIKI_TRACK_TABLE))
alternateConn = wikiConnect();
if (sameWord(curTable, WIKI_TRACK_TABLE))
tableList = slNameNew(WIKI_TRACK_TABLE);
else if (strchr(curTable, '.'))
tableList = slNameNew(curTable);
else
tableList = hSplitTableNames(database, curTable);
if (idField != NULL)
addPrimaryIdsToHash(alternateConn, matchHash, idField, tableList, lm, extraWhere);
getXrefInfo(alternateConn, &xrefTable, &xrefIdField, &aliasField);
if (xrefTable != NULL)
{
addXrefIdsToHash(alternateConn, matchHash, idField,
xrefTable, xrefIdField, aliasField, lm, extraWhere);
}
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
return matchHash;
}
static void filterControlsForTableDb(char *db, char *rootTable)
/* Put up filter controls for a single database table. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(db))
conn = hAllocConn(db);
char *table = chromTable(conn, rootTable);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
boolean isSmallWig = isWiggle(db, table);
boolean isBigWig = tdb ? tdbIsBigWig(tdb) : isBigWigTable(table);
boolean isWig = isSmallWig || isBigWig;
boolean isBedGr = tdb ? tdbIsBedGraph(tdb) : isBedGraph(rootTable);
boolean isBb = tdb ? tdbIsBigBed(tdb) : isBigBed(database, table, curTrack, ctLookupName);
boolean isBam = tdb ? tdbIsBam(tdb) : isBamTable(rootTable);
boolean isVcf = tdb ? tdbIsVcf(tdb) : isVcfTable(rootTable, NULL);
int bedGraphColumn = 5; /* default score column */
if (isBedGr)
{
int wordCount;
char *words[8];
char *typeLine = cloneString(tdb->type);
wordCount = chopLine(typeLine,words);
if (wordCount > 1)
bedGraphColumn = sqlUnsigned(words[1]);
freez(&typeLine);
}
if (isWig)
{
hPrintf("<TABLE BORDER=0>\n");
if ((tdb != NULL) && (tdb->type != NULL))
{
double min, max;
wiggleMinMax(tdb,&min,&max);
numericFilterWithLimits(db, rootTable, filterDataValueVar,filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g:%g]) "
"</TD></TR></TABLE>\n", min, max);
}
else
{
numericFilter(db, rootTable, filterDataValueVar,filterDataValueVar, "");
hPrintf("</TABLE>\n");
}
}
else
{
struct sqlFieldType *ftList;
if (isBb)
ftList = bigBedListFieldsAndTypes(tdb, conn);
else if (isBam)
ftList = bamListFieldsAndTypes();
else if (isVcf)
ftList = vcfListFieldsAndTypes();
else
ftList = sqlListFieldsAndTypes(conn, table);
printSqlFieldListAsControlTable(ftList, db, rootTable, tdb, isBedGr);
}
/* Printf free-form query row. */
if (!(isWig||isBedGr||isBam||isVcf))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD>\n");
name = filterFieldVarName(db, rootTable, "", filterRawLogicVar);
cgiMakeDropList(name, logOpMenu, logOpMenuSize,
cartUsualString(cart, name, logOpMenu[0]));
hPrintf(" Free-form query: ");
name = filterFieldVarName(db, rootTable, "", filterRawQueryVar);
char *val = cartUsualString(cart, name, "");
// escape double quotes to avoid HTML parse trouble in the text input.
val = htmlEncodeText(val, FALSE);
cgiMakeTextVar(name, val, 50);
hPrintf("</TD></TR></TABLE>\n");
}
if (isWig||isBedGr||isBam||isVcf)
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName(db, rootTable, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
freez(&table);
hFreeConn(&conn);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
static void filterControlsForTableCt(char *db, char *table)
/* Put up filter controls for a custom track. */
{
struct customTrack *ct = ctLookupName(table);
char *type = ct->dbTrackType;
puts("<TABLE BORDER=0>");
if (type != NULL && startsWithWord("maf", type))
{
stringFilterOption(db, table, "chrom", " AND ");
integerFilter(db, table, "chromStart", "chromStart", " AND ");
integerFilter(db, table, "chromEnd", "chromEnd", " AND ");
}
else if (type != NULL && (startsWithWord("makeItems", type) || sameWord("bedDetail", type) || sameWord("pgSnp", type)))
{
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlFieldType *ftList = sqlListFieldsAndTypes(conn, ct->dbTableName);
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
hFreeConn(&conn);
}
else if (ct->wiggle || isBigWigTable(table))
{
if ((ct->tdb != NULL) && (ct->tdb != NULL))
{
double min, max;
wiggleMinMax(ct->tdb,&min,&max);
numericFilterWithLimits("ct", table, filterDataValueVar, filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g,%g]) "
"</TD></TR>\n", min, max);
}
else
{
numericFilter("ct", table, filterDataValueVar, filterDataValueVar,"");
}
}
else if (isBigBed(db, table, curTrack, ctLookupName))
{
struct sqlFieldType *ftList = bigBedListFieldsAndTypes(ct->tdb, NULL);
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
}
else if (isBamTable(table))
{
struct sqlFieldType *ftList = bamListFieldsAndTypes();
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
}
else if (isVcfTable(table, NULL))
{
struct sqlFieldType *ftList = vcfListFieldsAndTypes();
printSqlFieldListAsControlTable(ftList, db, table, ct->tdb, FALSE);
}
else
{
if (ct->fieldCount >= 3)
{
stringFilterOption(db, table, "chrom", " AND ");
integerFilter(db, table, "chromStart", "chromStart", " AND ");
integerFilter(db, table, "chromEnd", "chromEnd", " AND ");
}
if (ct->fieldCount >= 4)
{
stringFilterOption(db, table, "name", " AND ");
}
if (ct->fieldCount >= 5)
{
numericFilter(db, table, "score", "score", " AND ");
}
if (ct->fieldCount >= 6)
{
stringFilterOption(db, table, "strand", " AND ");
}
if (ct->fieldCount >= 8)
{
integerFilter(db, table, "thickStart", "thickStart", " AND ");
integerFilter(db, table, "thickEnd", "thickEnd", " AND ");
}
if (ct->fieldCount >= 12)
{
integerFilter(db, table, "blockCount", "blockCount", " AND ");
}
/* These are not bed fields, just extra constraints that we offer: */
if (ct->fieldCount >= 3)
{
integerFilter(db, table, "chromLength", "(chromEnd - chromStart)",
(ct->fieldCount >= 8) ? " AND " : "");
}
if (ct->fieldCount >= 8)
{
integerFilter( db, table, "thickLength", "(thickEnd - thickStart)", " AND ");
eqFilterOption(db, table, "compareStarts","chromStart","thickStart", " AND ");
eqFilterOption(db, table, "compareEnds", "chromEnd", "thickEnd", "");
}
}
puts("</TABLE>");
if (ct->wiggle || isBigWigTable(table) || isBamTable(table) || isVcfTable(table, NULL))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName("ct", table, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}