Example #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);
}
Example #2
0
struct bbiFile *fetchBbiForTrack(struct track *track)
/* Fetch bbiFile from track, opening it if it is not already open. */
{
struct bbiFile *bbi = track->bbiFile;
if (bbi == NULL)
    {
    char *fileName = NULL;
    if (track->parallelLoading) // do not use mysql during parallel fetch
	{
	fileName = cloneString(trackDbSetting(track->tdb, "bigDataUrl"));
	}
    else
	{
	struct sqlConnection *conn = NULL;
	if (!trackHubDatabase(database))
	    conn = hAllocConnTrack(database, track->tdb);
	fileName = bbiNameFromSettingOrTable(track->tdb, conn, track->table);
	hFreeConn(&conn);
	}
    
    #ifdef USE_GBIB_PWD
    #include "gbib.c"
    #endif

    bbi = track->bbiFile = bigBedFileOpen(fileName);
    }
return bbi;
}
Example #3
0
int bbExtraFieldIndex(struct trackDb *tdb, char* fieldName)
/* return the index of a given extra field from the bbInterval
 * 0 is the name-field of bigBed and is used as an error code 
 * as this is the default anyways */
{
if (fieldName==NULL)
    return 0;
// copied from hgc.c
// get .as file for track
struct sqlConnection *conn = NULL ;
if (!trackHubDatabase(database))
    conn = hAllocConnTrack(database, tdb);
struct asObject *as = asForTdb(conn, tdb);
hFreeConn(&conn);
if (as == NULL)
    return 0;

// search for field name, return index if found
struct asColumn *col = as->columnList;
int ix = 0;
for (;col != NULL;col=col->next, ix+=1)
    if (sameString(col->name, fieldName))
        return max(ix-3, 0); // never return a negative value
return 0;
}
Example #4
0
char *showTableField(struct trackDb *track, char *varName, boolean useJoiner)
/* Show table control and label. */
{
struct slName *name, *nameList = NULL;
char *selTable;

if (track == NULL)
    nameList = tablesForDb(findSelDb());
else
    nameList = cartTrackDbTablesForTrack(database, track, useJoiner);

/* Get currently selected table.  If it isn't in our list
 * then revert to first in list. */
selTable = cartUsualString(cart, varName, nameList->name);
if (!slNameInListUseCase(nameList, selTable))
    selTable = nameList->name;

/* Print out label and drop-down list. */
hPrintf("<B>table: </B>");
hPrintf("<SELECT NAME=\"%s\" %s>\n", varName, onChangeTable());
struct trackDb *selTdb = NULL;
for (name = nameList; name != NULL; name = name->next)
    {
    struct trackDb *tdb = NULL;
    if (track != NULL)
	tdb = findTdbForTable(database,track,name->name, ctLookupName);
    hPrintf("<OPTION VALUE=\"%s\"", name->name);
    // Disable options for related tables that are noGenome -- if a non-positional table
    // is selected then we output its entire contents.
    if (cartTrackDbIsNoGenome(database, name->name) &&
        (track == NULL || differentString(track->table, name->name)))
        hPrintf(" DISABLED"NO_GENOME_CLASS);
    else if (sameString(selTable, name->name))
        {
        hPrintf(" SELECTED");
        selTdb = tdb;
        }
    if (tdb != NULL)
	if ((curTrack == NULL) || differentWord(tdb->shortLabel, curTrack->shortLabel))
	    hPrintf(">%s (%s)\n", tdb->shortLabel, name->name);
	else
	    hPrintf(">%s\n", name->name);
    else
	hPrintf(">%s\n", name->name);
    }
hPrintf("</SELECT>\n");
if (!trackHubDatabase(database))
    {
    char *restrictDate = encodeRestrictionDateDisplay(database,selTdb);
    if (restrictDate)
	{
	hPrintf("<A HREF=\'%s\' TARGET=BLANK>restricted until:</A>&nbsp;%s",
		    ENCODE_DATA_RELEASE_POLICY, restrictDate);
	freeMem(restrictDate);
	}
    }
return selTable;
}
static void printGeneSuggestTrack(struct cartJson *cj, char *db)
/* Get the gene track used by hgSuggest for db (defaulting to cart db), or null if
 * there is none for this assembly. */
{
if (isEmpty(db))
    db = cartString(cj->cart, "db");
char *track = NULL;
if (! trackHubDatabase(db))
    track = assemblyGeneSuggestTrack(db);
jsonWriteString(cj->jw, "geneSuggestTrack", track);
}
Example #6
0
struct serverTable *findServer(char *db, boolean isTrans)
/* Return server for given database.  Db can either be
 * database name or description. */
{
if (trackHubDatabase(db))
    {
    struct serverTable *hubSt = trackHubServerTable(db, isTrans);
    if (hubSt != NULL)
	return hubSt;
    errAbort("Cannot get blat server parameters for track hub with database %s\n", db);
    }

static struct serverTable st;
struct sqlConnection *conn = hConnectCentral();
char query[256];
struct sqlResult *sr;
char **row;
char dbActualName[32];

/* If necessary convert database description to name. */
sqlSafef(query, sizeof(query), "select name from dbDb where name = '%s'", db);
if (!sqlExists(conn, query))
    {
    sqlSafef(query, sizeof(query), "select name from dbDb where description = '%s'", db);
    if (sqlQuickQuery(conn, query, dbActualName, sizeof(dbActualName)) != NULL)
        db = dbActualName;
    }

/* Do a little join to get data to fit into the serverTable. */
sqlSafef(query, sizeof(query), "select dbDb.name,dbDb.description,blatServers.isTrans"
               ",blatServers.host,blatServers.port,dbDb.nibPath "
	       "from dbDb,blatServers where blatServers.isTrans = %d and "
	       "dbDb.name = '%s' and dbDb.name = blatServers.db", 
	       isTrans, db);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
    {
    errAbort("Can't find a server for %s database %s.  Click "
	     "<A HREF=\"/cgi-bin/hgBlat?%s&command=start&db=%s\">here</A> "
	     "to reset to default database.",
	     (isTrans ? "translated" : "DNA"), db,
	     cartSidUrlString(cart), hDefaultDb());
    }
st.db = cloneString(row[0]);
st.genome = cloneString(row[1]);
st.isTrans = atoi(row[2]);
st.host = cloneString(row[3]);
st.port = cloneString(row[4]);
st.nibDir = hReplaceGbdbSeqDir(row[5], st.db);

sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return &st;
}
Example #7
0
struct trackDb *hubCollectTracks( char *database,  struct grp **pGroupList)
/* Generate trackDb structures for all the tracks in attached hubs.  
 * Make grp structures for each hub. Returned group list is reversed. */
{
// return the cached copy if it exists
static struct trackDb *hubTrackDbs;
static struct grp *hubGroups;

if (hubTrackDbs != NULL)
    {
    if (pGroupList != NULL)
	*pGroupList = hubGroups;
    return hubTrackDbs;
    }

struct hubConnectStatus *hub, *hubList =  hubConnectGetHubs();
struct trackDb *tdbList = NULL;
for (hub = hubList; hub != NULL; hub = hub->next)
    {
    if (isEmpty(hub->errorMessage))
	{
        /* error catching in so it won't just abort  */
        struct errCatch *errCatch = errCatchNew();
        if (errCatchStart(errCatch))
	    {
	    struct trackDb *thisList = hubAddTracks(hub, database);
	    tdbList = slCat(tdbList, thisList);
	    }
        errCatchEnd(errCatch);
        if (errCatch->gotError)
	    {
	    warn("%s", errCatch->message->string);
	    hubUpdateStatus( errCatch->message->string, hub);
	    }
	else
	    {
	    if (!trackHubDatabase(database))
		{
		struct grp *grp = grpFromHub(hub);
		slAddHead(&hubGroups, grp);
		}
	    hubUpdateStatus(NULL, hub);
	    }

        errCatchFree(&errCatch);
	}
    }

hubTrackDbs = tdbList;
if (pGroupList != NULL)
    *pGroupList = hubGroups;
return tdbList;
}
Example #8
0
void printAllAssemblyListHtmlParm(char *db, struct dbDb *dbList,
                            char *dbCgi, bool allowInactive, char *javascript)
/* Prints to stdout the HTML to render a dropdown list containing the list
 * of assemblies for the current genome to choose from.  By default,
 * this includes only active assemblies with a database (with the
 * exception of the default assembly, which will be included even
 * if it isn't active).
 *  param db - The default assembly (the database name) to choose as selected.
 *             If NULL, no default selection.
 *  param allowInactive - if set, print all assemblies for this genome,
 *                        even if they're inactive or have no database
 */
{

char *assemblyList[128];
char *values[128];
int numAssemblies = 0;
struct dbDb *cur = NULL;
char *genome = hGenomeOrArchive(db);
char *selAssembly = NULL;

if (genome == NULL)
#ifdef LOWELAB
    genome = "Pyrococcus furiosus";
#else
    genome = "Human";
#endif
for (cur = dbList; cur != NULL; cur = cur->next)
    {
    /* Only for this genome */
    if (!sameWord(genome, cur->genome))
        continue;

    /* Save a pointer to the current assembly */
    if (sameWord(db, cur->name))
        selAssembly = cur->name;

    if (allowInactive ||
        ((cur->active || sameWord(cur->name, db))
                && (trackHubDatabase(db) || sqlDatabaseExists(cur->name))))
        {
        assemblyList[numAssemblies] = cur->description;
        values[numAssemblies] = cur->name;
        numAssemblies++;
	if (numAssemblies >= ArraySize(assemblyList))
	    internalErr();
        }

    }
cgiMakeDropListFull(dbCgi, assemblyList, values, numAssemblies,
                                selAssembly, javascript);
}
Example #9
0
static void writeFindPositionInfo(struct jsonWrite *jw, char *db, int taxId, char *hubUrl,
                                  char *position)
/* Write JSON for the info needed to populate the 'Find Position' section. */
{
char *genome = hGenome(db);
if (isEmpty(genome))
    {
    jsonWriteStringf(jw, "error", "No genome for db '%s'", db);
    }
else
    {
    jsonWriteString(jw, "db", db);
    jsonWriteNumber(jw, "taxId", taxId);
    jsonWriteString(jw, "genome", genome);
    struct slPair *dbOptions = NULL;
    char genomeLabel[PATH_LEN*4];
    if (isNotEmpty(hubUrl))
        {
        struct trackHub *hub = hubConnectGetHub(hubUrl);
        if (hub == NULL)
            {
            jsonWriteStringf(jw, "error", "Can't connect to hub at '%s'", hubUrl);
            return;
            }
        struct dbDb *dbDbList = trackHubGetDbDbs(hub->name);
        dbOptions = trackHubDbDbToValueLabel(dbDbList);
        safecpy(genomeLabel, sizeof(genomeLabel), hub->shortLabel);
        jsonWriteString(jw, "hubUrl", hubUrl);
        }
    else
        {
        dbOptions = hGetDbOptionsForGenome(genome);
        safecpy(genomeLabel, sizeof(genomeLabel), genome);
        }
    jsonWriteValueLabelList(jw, "dbOptions", dbOptions);
    jsonWriteString(jw, "genomeLabel", genomeLabel);
    jsonWriteString(jw, "position", position);
    char *suggestTrack = NULL;
    if (! trackHubDatabase(db))
        suggestTrack = assemblyGeneSuggestTrack(db);
    jsonWriteString(jw, "suggestTrack", suggestTrack);
    char *description = maybeGetDescriptionText(db);
    //#*** TODO: move jsonStringEscape inside jsonWriteString
    char *encoded = jsonStringEscape(description);
    jsonWriteString(jw, "description", encoded);
    listAssemblyHubs(jw);
    }
}
Example #10
0
void cartTrackDbInit(struct cart *cart, struct trackDb **retFullTrackList,
                     struct grp **retFullGroupList, boolean useAccessControl)
/* Get lists of all tracks and of groups that actually have tracks in them.
 * If useAccessControl, exclude tracks with 'tableBrowser off' nor tables listed
 * in the table tableAccessControl. */
{
char *db = cartString(cart, "db");
useAC = useAccessControl;
struct grp *hubGrpList = NULL;
struct trackDb *fullTrackList = getFullTrackList(cart, db, &hubGrpList);
boolean allTablesOk = hAllowAllTables() && !trackHubDatabase(db);
struct grp *fullGroupList = makeGroupList(db, fullTrackList, &hubGrpList, allTablesOk);
if (retFullTrackList != NULL)
    *retFullTrackList = fullTrackList;
if (retFullGroupList != NULL)
    *retFullGroupList = fullGroupList;
}
Example #11
0
static void getUiState(struct cartJson *cj, struct hash *paramHash)
/* Write out JSON for hgGateway.js's uiState object using current cart settings. */
{
char *db = cartUsualString(cj->cart, "db", hDefaultDb());
char *position = cartUsualString(cart, "position", hDefaultPos(db));
char *hubUrl = NULL;
if (trackHubDatabase(db))
    {
    struct trackHub *hub = hubConnectGetHubForDb(db);
    hubUrl = hub->url;
    }
writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position);
// If cart already has a pix setting, pass that along; otherwise the JS will
// set pix according to web browser window width.
int pix = cartUsualInt(cj->cart, "pix", 0);
if (pix)
    jsonWriteNumber(cj->jw, "pix", pix);
}
Example #12
0
void findClosestServer(char **pDb, char **pOrg)
/* If db doesn't have a blat server, look for the closest db (or org) that has one,
 * as hgPcr does. */
{
char *db = *pDb, *org = *pOrg;

if (trackHubDatabase(db) && (trackHubServerTable(db, FALSE) != NULL))
    {
    *pDb = db;
    *pOrg = hGenome(db);
    return;
    }

struct sqlConnection *conn = hConnectCentral();
char query[256];
sqlSafef(query, sizeof(query), "select db from blatServers where db = '%s'", db);
if (!sqlExists(conn, query))
    {
    sqlSafef(query, sizeof(query), "select blatServers.db from blatServers,dbDb "
	  "where blatServers.db = dbDb.name and dbDb.genome = '%s'", org);
    char *db = sqlQuickString(conn, query);
    if (db == NULL)
	{
	sqlSafef(query, sizeof(query), "select blatServers.db from blatServers,dbDb "
	      "where blatServers.db = dbDb.name order by dbDb.orderKey,dbDb.name desc");
	char *db = sqlQuickString(conn, query);
	if (db == NULL)
	    errAbort("central database tables blatServers and dbDb are disjoint/empty");
	else
	    {
	    *pDb = db;
	    *pOrg = hGenome(db);
	    }
	}
    else
	{
	*pDb = db;
	*pOrg = hGenome(db);
	}
    }
hDisconnectCentral(&conn);
}
Example #13
0
struct trackVersion *getTrackVersion(char *database, char *track)
// Get most recent trackVersion for given track in given database
{
boolean trackVersionExists = !trackHubDatabase(database) && hTableExists("hgFixed", "trackVersion");
struct trackVersion *trackVersion = NULL;
if (trackVersionExists)
    {
    char query[256];
    struct sqlConnection *conn = hAllocConn(database);

    sqlSafef(query, sizeof(query), "select * from hgFixed.trackVersion where db = '%s' AND name = '%s' order by ix DESC limit 1", database, track);
    struct sqlResult *sr = sqlGetResult(conn, query);
    char **row;
    if ((row = sqlNextRow(sr)) != NULL)
        trackVersion = trackVersionLoad(row);
    sqlFreeResult(&sr);
    hFreeConn(&conn);
    }
return trackVersion;
}
Example #14
0
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("&nbsp;&nbsp;&nbsp;&nbsp;<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);
}
Example #15
0
void showSchemaBam(char *table, struct trackDb *tdb)
/* Show schema on bam. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
    conn = hAllocConn(database);
char *fileName = bamFileName(table, conn, NULL);

struct asObject *as = bamAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf("&nbsp;&nbsp;&nbsp;&nbsp;<B>Primary Table:</B> %s<br>", table);
hPrintf("<B>BAM File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>SAM Format Specification</A> for  more details<BR>\n",
	"http://samtools.sourceforge.net/SAM1.pdf");

/* 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();

/* 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;
    }
hPrintf("</TR>\n");

/* Fetch sample rows. */
samfile_t *fh = bamOpen(fileName, NULL);
struct lm *lm = lmInit(0);
struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm);

/* Print sample lines. */
char *row[SAMALIGNMENT_NUM_COLS];
char numBuf[BAM_NUM_BUF_SIZE];
for (sam=samList; sam != NULL; sam = sam->next)
    {
    samAlignmentToRow(sam, numBuf, row);
    hPrintf("<TR>");
    for (colIx=0; colIx<colCount; ++colIx)
        {
        hPrintf("<TD>");
        xmlEscapeStringToFile(row[colIx], stdout);
        hPrintf("</TD>");
	}
    hPrintf("</TR>\n");
    }
hTableEnd();
printTrackHtml(tdb);

/* Clean up and go home. */
bamClose(&fh);
lmCleanup(&lm);
freeMem(fileName);
hFreeConn(&conn);
}
Example #16
0
void configMultiRegionPage()
/* Do multi-region config page after setting track visibility. If vis is -2, then visibility
 * is unchanged.  If -1 then set visibility to default, otherwise it should
 * be tvHide, tvDense, etc. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
int vis = -2;

configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);

hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
	cartUsualString(cart, "formMethod", "POST"));

webStartWrapperDetailedNoArgs(cart, database, "", "", FALSE, FALSE, FALSE, FALSE);

cartSaveSession(cart);


hPrintf("<BR>\n");

hTableStart();

virtModeType = cartUsualString(cart, "virtModeType", virtModeType);

hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "default", sameWord("default", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Exit multi-region mode");
hPrintf("</TD></TR>\n");

struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))  // no db conn for assembly hubs 
    conn = hAllocConn(database);

// Do we have a gene table for exonMostly?
findBestEMGeneTable(trackList);
if (emGeneTable)
    {
    hPrintf("<TR><TD>");
    cgiMakeRadioButton("virtModeType", "exonMostly", sameWord("exonMostly", virtModeType));
    hPrintf("</TD><TD>");
    hPrintf("Show exons using %s. &nbsp;&nbsp; Use padding of: ", emGeneTrack->shortLabel);
    hIntVar("emPadding", cartUsualInt(cart, "emPadding", emPadding), 3);
    hPrintf(" bases.");
    hPrintf("</TD></TR>\n");
    }

if (emGeneTable)
    {
    hPrintf("<TR><TD>");
    cgiMakeRadioButton("virtModeType", "geneMostly", sameWord("geneMostly", virtModeType));
    hPrintf("</TD><TD>");
    hPrintf("Show genes using %s. &nbsp;&nbsp; Use padding of: ", emGeneTrack->shortLabel);
    hIntVar("gmPadding", cartUsualInt(cart, "gmPadding", gmPadding), 3);
    hPrintf(" bases.");
    hPrintf("</TD></TR>\n");
    }

/* obsolete    
if (conn && sqlTableExists(conn,"knownCanonical"))
    {
    hPrintf("<TR><TD>");
    cgiMakeRadioButton("virtModeType", "kcGenes", sameWord("kcGenes", virtModeType));
    hPrintf("</TD><TD>");
    hPrintf("Show gene regions genome-wide.");
    hPrintf("</TD></TR>\n");
    }
*/

hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "customUrl", sameWord("customUrl", virtModeType));
hPrintf("</TD><TD>");
hPrintf("Enter Custom regions as BED, or a URL to them:<br>");
multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl);
struct dyString *dyMultiRegionsBedInput = dyStringNew(256);
if (strstr(multiRegionsBedUrl,"://"))
    {
    dyStringAppend(dyMultiRegionsBedInput, multiRegionsBedUrl);
    }
else
    {
    if (fileExists(multiRegionsBedUrl))
	{
	struct lineFile *lf = lineFileMayOpen(multiRegionsBedUrl, TRUE);
	char *line;
	int lineSize;
	while (lineFileNext(lf, &line, &lineSize))
	    {
	    dyStringPrintf(dyMultiRegionsBedInput, "%s\n", line);
	    }
	lineFileClose(&lf);
	}
    }
hPrintf("<TEXTAREA NAME='multiRegionsBedInput' ID='multiRegionsBedInput' rows='4' cols='58' style='white-space: pre;'>%s</TEXTAREA>",
    dyMultiRegionsBedInput->string);
hPrintf("</TD></TR>\n");


/* The AllChroms option will be released in future
if (emGeneTable && sqlTableExists(conn, emGeneTable))
    {
    hPrintf("<TR><TD>");
    cgiMakeRadioButton("virtModeType", "singleTrans", sameWord("singleTrans", virtModeType));
    hPrintf("</TD><TD>");
    hPrintf("Show only one transcript using an ID from %s : ", emGeneTrack->shortLabel);
    char *trans = cartUsualString(cart, "singleTransId", singleTransId);
    char sql[1024];
    sqlSafef(sql, sizeof sql, "select name from %s where name='%s'", emGeneTable, trans);
    char *result = sqlQuickString(conn, sql);
    if (!result)
	{
	sqlSafef(sql, sizeof sql, "select name from %s limit 1", emGeneTable);
	trans = sqlQuickString(conn, sql);
	}
    hTextVar("singleTransId", trans, 20);
    hPrintf("</TD></TR>\n");
    }
*/

if (conn)
    {
    boolean altLocExists = sqlTableExists(conn, "altLocations");
    boolean fixLocExists = sqlTableExists(conn, "fixLocations");
    if (altLocExists || fixLocExists)
        {
        hPrintf("<TR><TD>");
        cgiMakeRadioButton("virtModeType", "singleAltHaplo",
                           sameWord("singleAltHaplo", virtModeType));
        hPrintf("</TD><TD>");
        hPrintf("Show one alternate haplotype");
        if (fixLocExists)
            hPrintf(" or fix patch");
        hPrintf(", placed on its chromosome, using ID: ");
        char *haplo = cartUsualString(cart, "singleAltHaploId", singleAltHaploId);
        char *foundHaplo = NULL;
        char sql[1024];
        if (altLocExists)
            {
            sqlSafef(sql, sizeof sql,
                     "select name from altLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
            foundHaplo = sqlQuickString(conn, sql);
            }
        if (!foundHaplo && fixLocExists)
            {
            sqlSafef(sql, sizeof sql,
                     "select name from fixLocations where name rlike '^%s(:[0-9-]+)?'", haplo);
            foundHaplo = sqlQuickString(conn, sql);
            }
        if (!foundHaplo)
            {
            if (altLocExists)
                sqlSafef(sql, sizeof sql, "select name from altLocations limit 1");
            else
                sqlSafef(sql, sizeof sql, "select name from fixLocations limit 1");
            haplo = sqlQuickString(conn, sql);
            chopSuffixAt(haplo, ':');
            }
        hTextVar("singleAltHaploId", haplo, 60);
        hPrintf("</TD></TR>\n");
        }
    }

/* disable demo for now
if (sameString(database,"hg19") || sameString(database, "hg38"))
    {
    hPrintf("<TR><TD>");
    cgiMakeRadioButton("virtModeType", "demo1", sameWord("demo1", virtModeType));
    hPrintf("</TD><TD>");
    hPrintf("demo1 two windows on two chroms (default pos on chr21, and same loc on chr22)");
    hPrintf("</TD></TR>\n");
    }
*/


/* Disabled for now 
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo2", sameWord("demo2", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo2 multiple "); 
hIntVar("demo2NumWindows", cartUsualInt(cart, "demo2NumWindows", demo2NumWindows), 3);
hPrintf(" windows on one chrom chr21 def posn, window size ");
hIntVar("demo2WindowSize", cartUsualInt(cart, "demo2WindowSize", demo2WindowSize), 3);
hPrintf(" and step size ");
hIntVar("demo2StepSize", cartUsualInt(cart, "demo2StepSize", demo2StepSize), 3);
hPrintf(" exon-like");
hPrintf("</TD></TR>\n");
*/

/* The AllChroms option will be released in future
if (conn)  // requires chromInfo from database. 
    { // TODO allow it to use assembly hubs via trackHubAllChromInfo() ?
    hPrintf("<TR><TD>");
    cgiMakeRadioButton("virtModeType", "allChroms", sameWord("allChroms", virtModeType));
    hPrintf("</TD><TD>");
    hPrintf("<br>Show all chromosomes.<br><span style='color:red'>Warning:</span> Turn off all tracks except bigBed, bigWig, and very sparse tracks.<br>Press Hide All to hide all tracks.");
    hPrintf("</TD></TR>\n");
    }
*/


/* Disabled for now 
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo4", sameWord("demo4", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo4 multiple (311) windows showing exons from TITIN gene uc031rqd.1.");
hPrintf("</TD></TR>\n");
*/

/* Disabled for now 
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo5", sameWord("demo5", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo5 alt locus on hg38. Shows alt chrom surrounded by regions of same size from reference genome.");
hPrintf("</TD></TR>\n");
*/

/* Disabled for now 
hPrintf("<TR><TD>");
cgiMakeRadioButton("virtModeType", "demo6", sameWord("demo6", virtModeType));
hPrintf("</TD><TD>");
hPrintf("demo6 shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2.");
hPrintf("</TD></TR>\n");
*/


hTableEnd();

hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>");
hCheckBox("emAltHighlight", cartUsualBoolean(cart, "emAltHighlight", FALSE));
hPrintf("</TD><TD>");
hPrintf("Highlight alternating regions in multi-region view");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");

hPrintf("<BR>\n");
hPrintf("<TABLE style=\"border:0px;width:650px \">\n");
hPrintf("<TR><TD>");
cgiMakeButton("topSubmit", "submit");
hPrintf("</TD><TD align=right>");
hPrintf("<A HREF=\"../goldenPath/help/multiRegionHelp.html\" target=_blank>Help</A>\n");
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");

hFreeConn(&conn);

cgiDown(0.9);

freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
Example #17
0
static struct grp *makeGroupList(char *db, struct trackDb *trackList, struct grp **pHubGrpList,
                                 boolean allTablesOk)
/* Get list of groups that actually have something in them. */
{
struct grp *groupsAll, *groupList = NULL, *group;
struct hash *groupsInTrackList = newHash(0);
struct hash *groupsInDatabase = newHash(0);
struct trackDb *track;

/* Stream through track list building up hash of active groups. */
for (track = trackList; track != NULL; track = track->next)
    {
    if (!hashLookup(groupsInTrackList,track->grp))
        hashAdd(groupsInTrackList, track->grp, NULL);
    }

/* Scan through group table, putting in ones where we have data. */
groupsAll = hLoadGrps(db);
for (group = slPopHead(&groupsAll); group != NULL; group = slPopHead(&groupsAll))
    {
    if (hashLookup(groupsInTrackList, group->name))
	{
	slAddTail(&groupList, group);
	hashAdd(groupsInDatabase, group->name, group);
	}
    else
        grpFree(&group);
    }

/* if we have custom tracks, we want to add the track hubs
 * after that group */
struct grp *addAfter = NULL;
if ((groupList != NULL) && sameString(groupList->name, "user"))
    addAfter = groupList;

/* Add in groups from hubs. */
for (group = slPopHead(pHubGrpList); group != NULL; group = slPopHead(pHubGrpList))
    {
    // if the group isn't represented in any track, don't add it to list
    if (!hashLookup(groupsInTrackList,group->name))
	continue;
    /* check to see if we're inserting hubs rather than
     * adding them to the front of the list */
    struct grp *newGrp = grpDup(group);
    if (addAfter != NULL)
	{
	newGrp->next = addAfter->next;
	addAfter->next = newGrp;
	}
    else
	slAddHead(&groupList, newGrp);
    hashAdd(groupsInDatabase, newGrp->name, newGrp);
    }

/* Do some error checking for tracks with group names that are
 * not in database.  Just warn about them. */
if (!trackHubDatabase(db))
    for (track = trackList; track != NULL; track = track->next)
    {
    if (!hashLookup(groupsInDatabase, track->grp))
         warn("Track %s has group %s, which isn't in grp table",
	 	track->table, track->grp);
    }

/* Create dummy group for all tracks. */
AllocVar(group);
group->name = cloneString("allTracks");
group->label = cloneString("All Tracks");
slAddTail(&groupList, group);

/* Create another dummy group for all tables. */
if (allTablesOk)
    {
    AllocVar(group);
    group->name = cloneString("allTables");
    group->label = cloneString("All Tables");
    slAddTail(&groupList, group);
    }

hashFree(&groupsInTrackList);
hashFree(&groupsInDatabase);
return groupList;
}
Example #18
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");
}
Example #19
0
void showMainControlTable(struct sqlConnection *conn)
/* Put up table with main controls for main page. */
{
struct grp *selGroup;
boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
        isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE;
boolean gotClade = hGotClade();
struct hTableInfo *hti = NULL;

hPrintf("<TABLE BORDER=0>\n");

/* Print clade, genome and assembly line. */
    {
    if (gotClade)
        {
        hPrintf("<TR><TD><B>clade:</B>\n");
        printCladeListHtml(hGenome(database), onChangeClade());
        nbSpaces(3);
        hPrintf("<B>genome:</B>\n");
        printGenomeListForCladeHtml(database, onChangeOrg());
        }
    else
        {
        hPrintf("<TR><TD><B>genome:</B>\n");
        printGenomeListHtml(database, onChangeOrg());
        }
    nbSpaces(3);
    hPrintf("<B>assembly:</B>\n");
    printAssemblyListHtml(database, onChangeDb());
    hPrintf("</TD></TR>\n");
    }

/* Print group and track line. */
    {
    hPrintf("<TR><TD>");
    selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
    nbSpaces(3);
    curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
    nbSpaces(3);
    boolean hasCustomTracks = FALSE;
    struct trackDb *t;
    for (t = fullTrackList;  t != NULL;  t = t->next)
        {
        if (isCustomTrack(t->table))
            {
            hasCustomTracks = TRUE;
            break;
            }
        }
    hOnClickButton("document.customTrackForm.submit();return false;",
                   hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);

    hPrintf(" ");
    if (hubConnectTableExists())
	hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");

    hPrintf("</TD></TR>\n");
    }

/* Print table line. */
    {
    hPrintf("<TR><TD>");
    curTable = showTableField(curTrack, hgtaTable, TRUE);
    if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL))  /* In same database */
        {
        hti = getHti(database, curTable, conn);
        isPositional = htiIsPositional(hti);
        }
    isLongTabix = isLongTabixTable( curTable);
    isBam = isBamTable( curTable);
    isVcf = isVcfTable(curTable, NULL);
    isWig = isWiggle(database, curTable);
    if (isBigWigTable(curTable))
        {
        isPositional = TRUE;
        isWig = TRUE;
        }
    isHalSnake = isHalTable( curTable);
    isMaf = isMafTable(database, curTrack, curTable);
    isBedGr = isBedGraph(curTable);
    isArray = isMicroarray(curTrack, curTable);
    struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
    isPal = isPalCompatible(conn, tdb, curTable);
    nbSpaces(1);
    if (isCustomTrack(curTable))
        {
        isChromGraphCt = isChromGraph(tdb);
        }
    cgiMakeButton(hgtaDoSchema, "describe table schema");
    hPrintf("</TD></TR>\n");
    }

if (curTrack == NULL)
    {
    struct trackDb *tdb = hTrackDbForTrack(database, curTable);
    struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb);
    if (cTdb)
        curTrack = cTdb;
    else
        curTrack = tdb;
    isMaf = isMafTable(database, curTrack, curTable);
    }

/* Region line */
{
char *regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
char *range = cartUsualString(cart, hgtaRange, "");
if (isPositional)
    {
    boolean doEncode = FALSE; 

    if (!trackHubDatabase(database))
	doEncode = sqlTableExists(conn, "encodeRegions");

    hPrintf("<TR><TD><B>region:</B>\n");

    /* If regionType not allowed force it to "genome". */
    if ((sameString(regionType, hgtaRegionTypeUserRegions) &&
	 userRegionsFileName() == NULL) ||
	(sameString(regionType, hgtaRegionTypeEncode) && !doEncode))
	regionType = hgtaRegionTypeGenome;
    // Is "genome" is not allowed because of tdb 'tableBrowser noGenome'?
    boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) ||
                             (curTable && cartTrackDbIsNoGenome(database, curTable)));
    // If "genome" is selected but not allowed, force it to "range":
    if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome)
        regionType = hgtaRegionTypeRange;
    jsTrackingVar("regionType", regionType);
    if (disableGenome)
        {
        makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED");
        hPrintf("&nbsp;<span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
                "&nbsp;");
        }
    else
        {
        makeRegionButton(hgtaRegionTypeGenome, regionType);
        hPrintf("&nbsp;genome&nbsp;");
        }
    if (doEncode)
        {
	makeRegionButton(hgtaRegionTypeEncode, regionType);
	hPrintf("&nbsp;ENCODE Pilot regions&nbsp;");
	}
    makeRegionButton(hgtaRegionTypeRange, regionType);
    hPrintf("&nbsp;position&nbsp;");
    hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
    	hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
    cgiMakeButton(hgtaDoLookupPosition, "lookup");
    hPrintf("&nbsp;");
    if (userRegionsFileName() != NULL)
	{
	makeRegionButton(hgtaRegionTypeUserRegions, regionType);
	hPrintf("&nbsp;defined regions&nbsp;");
	cgiMakeButton(hgtaDoSetUserRegions, "change");
	hPrintf("&nbsp;");
	cgiMakeButton(hgtaDoClearUserRegions, "clear");
	}
    else
	cgiMakeButton(hgtaDoSetUserRegions, "define regions");
    hPrintf("</TD></TR>\n");
    }
else
    {
    /* Need to put at least stubs of cgi variables in for JavaScript to work. */
    jsTrackingVar("regionType", regionType);
    cgiMakeHiddenVar(hgtaRange, range);
    cgiMakeHiddenVar(hgtaRegionType, regionType);
    }

/* Select identifiers line (if applicable). */
if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL)
    {
    hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n");
    cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
    hPrintf(" ");
    cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
    if (identifierFileName() != NULL)
        {
	hPrintf("&nbsp;");
	cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
	}
    hPrintf("</TD></TR>\n");
    }
}

/* microarray options */
/*   button for option page here (median/log-ratio, etc)  */

/* Filter line. */
{
hPrintf("<TR><TD><B>filter:</B>\n");
if (anyFilter())
    {
    cgiMakeButton(hgtaDoFilterPage, "edit");
    hPrintf(" ");
    cgiMakeButton(hgtaDoClearFilter, "clear");
    if (isWig || isBedGr)
	wigShowFilter(conn);
    }
else
    {
    cgiMakeButton(hgtaDoFilterPage, "create");
    }
hPrintf("</TD></TR>\n");
}

/* Composite track subtrack merge line. */
boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix);
if (canSubtrackMerge)
    {
    hPrintf("<TR><TD><B>subtrack merge:</B>\n");
    if (anySubtrackMerge(database, curTable))
	{
	cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
	hPrintf(" ");
	cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
	}
    else
	{
	cgiMakeButton(hgtaDoSubtrackMergePage, "create");
	}
    hPrintf("</TD></TR>\n");
    }

/* Intersection line. */
if (isPositional)
    {
    if (anyIntersection())
        {
	hPrintf("<TR><TD><B>intersection with %s:</B>\n",
		cartString(cart, hgtaIntersectTable));
	cgiMakeButton(hgtaDoIntersectPage, "edit");
	hPrintf(" ");
	cgiMakeButton(hgtaDoClearIntersect, "clear");
        hPrintf("</TD></TR>\n");
	}
    else if (canIntersect(database, curTable))
        {
	hPrintf("<TR><TD><B>intersection:</B>\n");
	cgiMakeButton(hgtaDoIntersectPage, "create");
        hPrintf("</TD></TR>\n");
	}
    }

/* Correlation line. */
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (correlateTrackTableOK(tdb, curTable))
    {
    char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
    hPrintf("<TR><TD><B>correlation:</B>\n");
    if (differentWord(table2, "none") && strlen(table2) && ! isNoGenomeDisabled(database, table2))
        {
        struct grp *groupList = fullGroupList;
        struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup);
        struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack);
        if (tdbIsComposite(tdb2))
            {
	    struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks);
	    struct slRef *tdbRef;
	    for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
                {
		struct trackDb *subTdb = tdbRef->val;
                if (sameString(table2, subTdb->table))
                    {
                    tdb2 = subTdb;
                    break;
                    }
                }
	    slFreeList(&tdbRefList);
            }
        cgiMakeButton(hgtaDoCorrelatePage, "calculate");
        cgiMakeButton(hgtaDoClearCorrelate, "clear");
        if (tdb2 && tdb2->shortLabel)
            hPrintf("&nbsp;(with:&nbsp;&nbsp;%s)", tdb2->shortLabel);

#ifdef NOT_YET
        /* debugging 	dbg	vvvvv	*/
        if (curTrack && curTrack->type)		/*	dbg	*/
            {
            hPrintf("<BR>&nbsp;(debug:&nbsp;'%s',&nbsp;'%s(%s)')",
                    curTrack->type, tdb2->type, table2);
            }
        /* debugging 	debug	^^^^^	*/
#endif

        }
    else
        cgiMakeButton(hgtaDoCorrelatePage, "create");

    hPrintf("</TD></TR>\n");
    }

/* Print output type line. */
showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);

/* Print output destination line. */
    {
    char *compressType =
	cartUsualString(cart, hgtaCompressType, textOutCompressNone);
    char *fileName = cartUsualString(cart, hgtaOutFileName, "");
    hPrintf("<TR><TD>\n");
    hPrintf("<B>output file:</B>&nbsp;");
    cgiMakeTextVar(hgtaOutFileName, fileName, 29);
    hPrintf("&nbsp;(leave blank to keep output in browser)</TD></TR>\n");
    hPrintf("<TR><TD>\n");
    hPrintf("<B>file type returned:&nbsp;</B>");
    cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
	sameWord(textOutCompressNone, compressType));
    hPrintf("&nbsp;plain text&nbsp&nbsp");
    cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
	sameWord(textOutCompressGzip, compressType));
    hPrintf("&nbsp;gzip compressed");
    hPrintf("</TD></TR>\n");
    }

hPrintf("</TABLE>\n");


/* Submit buttons. */
    {
    hPrintf("<BR>\n");
    if (isWig || isBam || isVcf || isLongTabix)
	{
	char *name;
	extern char *maxOutMenu[];
	char *maxOutput = maxOutMenu[0];

	if (isCustomTrack(curTable))
	    name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
	else
	    name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar);

	maxOutput = cartUsualString(cart, name, maxOutMenu[0]);

	if (isWig)
	    hPrintf(
		"<I>Note: to return more than %s lines, change the filter setting"
		" (above). The entire data set may be available for download as"
		" a very large file that contains the original data values (not"
		" compressed into the wiggle format) -- see the Downloads page."
		"</I><BR>", maxOutput);
	else if (isBam || isVcf || isLongTabix)
	    hPrintf(
		"<I>Note: to return more than %s lines, change the filter setting"
		" (above). Please consider downloading the entire data from our Download pages."
		"</I><BR>", maxOutput);
	}
    else if (anySubtrackMerge(database, curTable) || anyIntersection())
	{
	hPrintf("<I>Note: The all fields and selected fields output formats "
		"are not available when a%s has been specified.</I><BR>",
		canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
	}
    cgiMakeButton(hgtaDoTopSubmit, "get output");
    hPrintf(" ");
    if (isPositional || isWig)
	{
	cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
	hPrintf(" ");
	}

#ifdef SOMETIMES
    hPrintf(" ");
    cgiMakeButton(hgtaDoTest, "test");
#endif /* SOMETIMES */
    }
hPrintf("<P>"
	"To reset <B>all</B> user cart settings (including custom tracks), \n"
	"<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
	getScriptName());

}
Example #20
0
static void showLinkedTables(struct joiner *joiner, struct dbTable *inList,
	char *varPrefix, char *buttonName, char *buttonText)
/* Print section with list of linked tables and check boxes to turn them
 * on. */
{
struct dbTable *outList = NULL, *out, *in;
char dtName[256];
struct hash *uniqHash = newHash(0);
struct hash *inHash = newHash(8);

/* Build up list of tables we link to in outList. */
for (in = inList; in != NULL; in = in->next)
    {
    struct sqlConnection *conn = NULL;
    if (!trackHubDatabase(database))
	conn = hAllocConn(in->db);
    struct joinerPair *jpList, *jp;

    /* Keep track of tables in inList. */
    safef(dtName, sizeof(dtName), "%s.%s", inList->db, inList->table);
    hashAdd(inHash, dtName, NULL);

    /* First table in input is not allowed in output. */
    if (in == inList)
        hashAdd(uniqHash, dtName, NULL);

    /* Scan through joining information and add tables,
     * avoiding duplicate additions. */
    jpList = joinerRelate(joiner, in->db, in->table);
    for (jp = jpList; jp != NULL; jp = jp->next)
        {
	safef(dtName, sizeof(dtName), "%s.%s",
		jp->b->database, jp->b->table);
	if (!hashLookup(uniqHash, dtName) &&
	   !cartTrackDbIsAccessDenied(jp->b->database, jp->b->table))
	    {
	    hashAdd(uniqHash, dtName, NULL);
	    out = dbTableNew(jp->b->database, jp->b->table);
	    slAddHead(&outList, out);
	    }
	}
    joinerPairFreeList(&jpList);
    hFreeConn(&conn);
    }
slSort(&outList, dbTableCmp);

/* Print html. */
if (outList != NULL)
    {
    webNewSection("Linked Tables");
    hTableStart();
    for (out = outList; out != NULL; out = out->next)
	{
	struct sqlConnection *conn = hAllocConn(out->db);
	struct asObject *asObj = asForTable(conn, out->table);
	char *var = dbTableVar(varPrefix, out->db, out->table);
	hPrintf("<TR>");
	hPrintf("<TD>");
	cgiMakeCheckBox(var, varOn(var));
	hPrintf("</TD>");
	hPrintf("<TD>%s</TD>", out->db);
	hPrintf("<TD>%s</TD>", out->table);
	hPrintf("<TD>");
	if (asObj != NULL)
	    hPrintf("%s", asObj->comment);
	else
	    hPrintf("&nbsp;");
	hPrintf("</TD>");
	hPrintf("</TR>");
	hFreeConn(&conn);
	}
    hTableEnd();
    hPrintf("<BR>");

    cgiMakeButton(buttonName, buttonText);
    }
}