示例#1
0
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);
}
示例#2
0
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;
}
示例#3
0
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);
    }
}
示例#4
0
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;
}
示例#5
0
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;
}
示例#6
0
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:&nbsp\n");
    name = filterFieldVarName(db, rootTable, "_", filterMaxOutputVar);
    cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
		cartUsualString(cart, name, maxOutMenu[0]));
    hPrintf("&nbsp;lines</TD></TR></TABLE>\n");
    }

freez(&table);
hFreeConn(&conn);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
示例#7
0
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:&nbsp\n");
    name = filterFieldVarName("ct", table, "_", filterMaxOutputVar);
    cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
		cartUsualString(cart, name, maxOutMenu[0]));
    hPrintf("&nbsp;lines</TD></TR></TABLE>\n");
    }

hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}