void userSettingsLoadForm(struct userSettings *us)
/* Put up controls that let user name and save the current
 * set. */
{
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);

/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);
hPrintf("<H2>Load %s</H2>\n", us->formTitle);

hPrintf("<TABLE><TR><TD>\n");
hPrintf("<SELECT NAME=\"%s\" SIZE=%d>",
    us->nameVar, slCount(list));
printLabelList(us, list);
hPrintf("</SELECT>");
hPrintf("</TD><TD>");
cgiMakeButton(us->formVar, "load");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");
hPrintf("</TD></TR></TABLE>");

/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
Ejemplo n.º 2
0
static unsigned getLabelTypes(struct track *tg)
/* get set of labels to use */
{
unsigned labelSet = 0;

// label setting are on parent track
char prefix[128];
safef(prefix, sizeof(prefix), "%s.label", tg->tdb->track);
struct hashEl *labels = cartFindPrefix(cart, prefix);

if (labels == NULL)
    {
    // default to common name+accession and save this in cart so it makes sense in trackUi
    labelSet = useAcc;
    char setting[64];
    safef(setting, sizeof(setting), "%s.label.gene", tg->tdb->track);
    cartSetBoolean(cart, setting, TRUE);
    }
struct hashEl *label;
for (label = labels; label != NULL; label = label->next)
    {
    if (endsWith(label->name, ".orgCommon") && differentString(label->val, "0"))
        labelSet |= useOrgCommon;
    else if (endsWith(label->name, ".orgAbbrv") && differentString(label->val, "0"))
        labelSet |= useOrgAbbrv;
    else if (endsWith(label->name, ".db") && differentString(label->val, "0"))
        labelSet |= useOrgDb;
    else if (endsWith(label->name, ".gene") && differentString(label->val, "0"))
        labelSet |= useGene;
    else if (endsWith(label->name, ".acc") && differentString(label->val, "0"))
        labelSet |= useAcc;
    }
return labelSet;
}
Ejemplo n.º 3
0
void doPrintSelectedFields()
/* Actually produce selected field output as text stream. */
{
char *db = cartString(cart, hgtaDatabase);
char *table = cartString(cart, hgtaTable);
char *varPrefix = checkVarPrefix();
int varPrefixSize = strlen(varPrefix);
struct hashEl *varList = NULL, *var;
struct slName *fieldList = NULL, *field;

textOpen();

/* Gather together field list for primary and linked tables from cart. */
varList = cartFindPrefix(cart, varPrefix);
for (var = varList; var != NULL; var = var->next)
    {
    if (!sameString(var->val, "0"))
	{
	field = slNameNew(var->name + varPrefixSize);
	if (primaryOrLinked(field->name))
	    slAddHead(&fieldList, field);
	}
    }
if (fieldList == NULL)
    errAbort("Please go back and select at least one field");
slReverse(&fieldList);

/* Do output. */
tabOutSelectedFields(db, table, NULL, fieldList);

/* Clean up. */
slFreeList(&fieldList);
hashElFreeList(&varList);
}
boolean userSettingsAnySaved(struct userSettings *us)
/* Return TRUE if any user settings are saved. */
{
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
boolean any = (list != NULL);
slFreeList(&list);
return any;
}
Ejemplo n.º 5
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static void setCheckVarsForTable(char *dbTable, char *val)
/* Return list of check variables for this table. */
{
char prefix[128];
struct hashEl *varList, *var;
safef(prefix, sizeof(prefix), "%s%s.", checkVarPrefix(), dbTable);
varList = cartFindPrefix(cart, prefix);
for (var = varList; var != NULL; var = var->next)
    cartSetString(cart, var->name, val);
hashElFreeList(&varList);
}
void userSettingsCapturePrefix(struct userSettings *us, char *prefix)
/* Capture all variables that start with prefix. */
{
struct hashEl *el, *list = cartFindPrefix(us->cart, prefix);
for (el = list; el != NULL; el = el->next)
     {
    struct slName *n = slNameNew(el->name);
    slAddHead(&us->saveList, n);
    }
slFreeList(&list);
}
void userSettingsDropDown(struct userSettings *us)
/* Display list of available saved settings . */
{
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
if (list != NULL)
    {
    hPrintf("<SELECT NAME=\"%s\">\n", us->nameVar);
    slSort(&list, hashElCmp);
    printLabelList(us, list);
    slFreeList(&list);
    hPrintf("</SELECT>");
    }
}
Ejemplo n.º 8
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static struct dbTable *extraTableList(char *prefix)
/* Get list of tables (other than the primary table)
 * where we are displaying fields. */
{
struct hashEl *varList = NULL, *var;
int prefixSize = strlen(prefix);
struct dbTable *dtList = NULL, *dt;

/* Build up list of tables to show by looking at
 * variables with right prefix in cart. */
varList = cartFindPrefix(cart, prefix);
for (var = varList; var != NULL; var = var->next)
    {
    if (cartBoolean(cart, var->name))
	{
	/* From variable name parse out database and table. */
	char *dbTab = cloneString(var->name + prefixSize);
	char *db = dbTab;
	char *table = strchr(db, '.');
	if (table == NULL)
	    internalErr();
	*table++ = 0;

	dt = dbTableNew(db, table);
	slAddHead(&dtList, dt);
	freez(&dbTab);
	}
    }
if (varList == NULL && curTrack != NULL)
    {
    char *defaultLinkedTables = trackDbSetting(curTrack, "defaultLinkedTables");
    if (defaultLinkedTables != NULL)
	{
	struct slName *t, *tables = slNameListFromString(defaultLinkedTables, ',');
	for (t = tables;  t != NULL;  t = t->next)
	    {
	    char varName[1024];
	    safef(varName, sizeof(varName), "%s%s.%s", prefix, database, t->name);
	    cartSetBoolean(cart, varName, TRUE);
	    dt = dbTableNew(database, t->name);
	    slAddHead(&dtList, dt);
	    }
	}
    }
slSort(&dtList, dbTableCmp);
return dtList;
}
Ejemplo n.º 9
0
void userSettingsSaveForm(struct userSettings *us)
/* Put up controls that let user name and save the current
 * set. */
{
char buf[1024];
struct hashEl *list = cartFindPrefix(us->cart, us->savePrefix);
safef(buf, sizeof(buf), "Save %s", us->formTitle);
makeTitle(buf, NULL);

/* Start form/save session/print title. */
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" NAME=\"usForm\" METHOD=GET>\n");
cartSaveSession(us->cart);

/* Put up controls that are always there. */
hPrintf("Please name this setup:\n");
cartMakeTextVar(us->cart, us->nameVar, "", 16);
hPrintf(" ");
cgiMakeButton(us->formVar, "save");
hPrintf(" ");
cgiMakeButton(us->formVar, "cancel");

/* Put up additional controls if have saved settings already. */
if (list != NULL)
    {
    struct dyString *js = newDyString(0);

    htmlHorizontalLine();
    slSort(&list, hashElCmp);
    hPrintf("Existing Setups:");
    dyStringPrintf(js, "document.usForm.%s.value=", us->nameVar);
    dyStringPrintf(js, "document.usForm.%s.options", us->listDisplayVar);
    dyStringPrintf(js, "[document.usForm.%s.selectedIndex].value;", us->listDisplayVar);

    hPrintf("<SELECT NAME=\"%s\" SIZE=%d onchange=\"%s\">",
    	us->listDisplayVar, slCount(list), js->string);
    printLabelList(us, list);
    hPrintf("</SELECT>\n");

    cgiMakeButton(us->formVar, "delete existing setup");
    }

/* Cleanup. */
hPrintf("</FORM>\n");
slFreeList(&list);
}
Ejemplo n.º 10
0
boolean checkWigDataFilter(char *db, char *table,
	char **constraint, double *ll, double *ul)
/*	check if filter exists, return its values, call with db="ct" for
 *	custom tracks	*/
{
char varPrefix[128];
struct hashEl *varList, *var;
char *pat = NULL;
char *cmp = NULL;
if (constraint != NULL)
    *constraint = NULL;	// Make sure return variable gets set to something at least.

if (isCustomTrack(table))
    db = "ct";

safef(varPrefix, sizeof(varPrefix), "%s%s.%s.", hgtaFilterVarPrefix, db, table);

varList = cartFindPrefix(cart, varPrefix);
if (varList == NULL)
    return FALSE;

/*	check varList, look for dataValue.pat and dataValue.cmp	*/

for (var = varList; var != NULL; var = var->next)
    {
    if (endsWith(var->name, ".pat"))
	{
	char *name;
	name = cloneString(var->name);
	tolowers(name);
	/*	make sure we are actually looking at datavalue	*/
	if (stringIn("datavalue", name) || stringIn("score", name))
	    {
	    pat = cloneString(var->val);
	    }
	freeMem(name);
	}
    if (endsWith(var->name, ".cmp"))
	{
	char *name;
	name = cloneString(var->name);
	tolowers(name);
	/*	make sure we are actually looking at datavalue	*/
	if (stringIn("datavalue", name) || stringIn("score", name))
	    {
	    cmp = cloneString(var->val);
	    tolowers(cmp);
	    if (stringIn("ignored", cmp))
		freez(&cmp);
	    }
	freeMem(name);
	}
    }

/*	Must get them both for this to work	*/
if (cmp && pat)
    {
    int wordCount = 0;
    char *words[2];
    char *dupe = cloneString(pat);

    wordCount = chopString(dupe, ", \t\n", words, ArraySize(words));
    switch (wordCount)
	{
	case 2: if (ul) *ul = sqlDouble(words[1]);
	case 1: if (ll) *ll = sqlDouble(words[0]);
		break;
	default:
	    warn("dataValue filter must be one or two numbers (two for 'in range').  "
		 "Please click the filter edit button and either set the comparison to 'ignored' "
		 "or set the dataValue threshold.");
	}
    if (sameWord(cmp,"in range") && (wordCount != 2))
	errAbort("'in range' dataValue filter must have two numbers input\n");

    if (constraint)
	*constraint = cmp;

    return TRUE;
    }
else
    return FALSE;
}	/*	static boolean checkWigDataFilter()	*/
Ejemplo n.º 11
0
char *filterClause(char *db, char *table, char *chrom, char *extraClause)
/* Get filter clause (something to put after 'where')
 * for table */
{
struct sqlConnection *conn = NULL;
char varPrefix[128];
int varPrefixSize, fieldNameSize;
struct hashEl *varList, *var;
struct dyString *dy = NULL;
boolean needAnd = FALSE;
char oldDb[128];
char dbTableBuf[256];
char explicitDb[128];
char splitTable[256];
char explicitDbTable[512];

/* Return just extraClause (which may be NULL) if no filter on us. */
if (! (anyFilter() && filteredOrLinked(db, table)))
    return cloneString(extraClause);
safef(oldDb, sizeof(oldDb), "%s", db);
dbOverrideFromTable(dbTableBuf, &db, &table);
if (!sameString(oldDb, db))
     safef(explicitDb, sizeof(explicitDb), "%s.", db);
else
     explicitDb[0] = 0;

/* Cope with split table and/or custom tracks. */
if (isCustomTrack(table))
    {
    conn = hAllocConn(CUSTOM_TRASH);
    struct customTrack *ct = ctLookupName(table);
    safef(explicitDbTable, sizeof(explicitDbTable), "%s", ct->dbTableName);
    }
else
    {
    conn = hAllocConn(db);
    safef(splitTable, sizeof(splitTable), "%s_%s", chrom, table);
    if (!sqlTableExists(conn, splitTable))
	safef(splitTable, sizeof(splitTable), "%s", table);
    safef(explicitDbTable, sizeof(explicitDbTable), "%s%s",
	  explicitDb, splitTable);
    }

/* Get list of filter variables for this table. */
safef(varPrefix, sizeof(varPrefix), "%s%s.%s.", hgtaFilterVarPrefix, db, table);
varPrefixSize = strlen(varPrefix);
varList = cartFindPrefix(cart, varPrefix);
if (varList == NULL)
    {
    hFreeConn(&conn);
    return cloneString(extraClause);
    }

/* Create filter clause string, stepping through vars. */
dy = dyStringNew(0);
for (var = varList; var != NULL; var = var->next)
    {
    /* Parse variable name into field and type. */
    char field[64], *s, *type;
    s = var->name + varPrefixSize;
    type = strchr(s, '.');
    if (type == NULL)
        internalErr();
    fieldNameSize = type - s;
    if (fieldNameSize >= sizeof(field))
        internalErr();
    memcpy(field, s, fieldNameSize);
    field[fieldNameSize] = 0;
    sqlCkId(field);
    type += 1;
    /* rawLogic and rawQuery are handled below;
     * filterMaxOutputVar is not really a filter variable and is handled
     * in wiggle.c. */
    if (startsWith("raw", type) || sameString(filterMaxOutputVar, type))
	continue;
    /*	Any other variables that are missing a name:
     *		<varPrefix>..<type>
     *	are illegal
     */
    if (fieldNameSize < 1)
	{
	warn("Missing name in cart variable: %s\n", var->name);
	continue;
	}
    if (sameString(type, filterDdVar))
        {
	char *patVar = filterPatternVarName(db, table, field);
	struct slName *patList = cartOptionalSlNameList(cart, patVar);
	normalizePatList(&patList);
	if (slCount(patList) > 0)
	    {
	    char *ddVal = cartString(cart, var->name);
	    boolean neg = sameString(ddVal, ddOpMenu[1]);
	    char *fieldType = getSqlType(conn, explicitDbTable, field);
	    boolean needOr = FALSE;
	    if (needAnd) dyStringAppend(dy, " and ");
	    needAnd = TRUE;
	    if (neg) dyStringAppend(dy, "not ");
	    boolean composite = (slCount(patList) > 1);
	    if (composite || neg) dyStringAppendC(dy, '(');
	    struct slName *pat;
	    for (pat = patList;  pat != NULL;  pat = pat->next)
		{
		char *sqlPat = sqlLikeFromWild(pat->name);
		if (needOr)
		    dyStringAppend(dy, " OR ");
		needOr = TRUE;
		if (isSqlSetType(fieldType))
		    {
		    sqlDyStringPrintfFrag(dy, "FIND_IN_SET('%s', %s.%s)>0 ",
				   sqlPat, explicitDbTable , field);
		    }
		else
		    {
		    sqlDyStringPrintfFrag(dy, "%s.%s ", explicitDbTable, field);
		    if (sqlWildcardIn(sqlPat))
			dyStringAppend(dy, "like ");
		    else
			dyStringAppend(dy, "= ");
		    sqlDyStringPrintf(dy, "'%s'", sqlPat);
		    }
		freez(&sqlPat);
		}
	    if (composite || neg) dyStringAppendC(dy, ')');
	    }
	}
    else if (sameString(type, filterCmpVar))
        {
	char *patVar = filterPatternVarName(db, table, field);
	char *pat = trimSpaces(cartOptionalString(cart, patVar));
	char *cmpVal = cartString(cart, var->name);
	if (cmpReal(pat, cmpVal))
	    {
	    if (needAnd) dyStringAppend(dy, " and ");
	    needAnd = TRUE;
	    if (sameString(cmpVal, "in range"))
	        {
		char *words[2];
		int wordCount;
		char *dupe = cloneString(pat);

		wordCount = chopString(dupe, ", \t\n", words, ArraySize(words));
		if (wordCount < 2)	/* Fake short input */
		    words[1] = "2000000000";
		if (strchr(pat, '.')) /* Assume floating point */
		    {
		    double a = atof(words[0]), b = atof(words[1]);
		    sqlDyStringPrintfFrag(dy, "%s.%s >= %f && %s.%s <= %f",
		    	explicitDbTable, field, a, explicitDbTable, field, b);
		    }
		else
		    {
		    int a = atoi(words[0]), b = atoi(words[1]);
		    sqlDyStringPrintfFrag(dy, "%s.%s >= %d && %s.%s <= %d",
		    	explicitDbTable, field, a, explicitDbTable, field, b);
		    }
		freez(&dupe);
		}
	    else
	        {
		// cmpVal has been checked already above in cmpReal for legal values.
		sqlDyStringPrintfFrag(dy, "%s.%s %-s ", explicitDbTable, field, cmpVal);
		if (strchr(pat, '.'))	/* Assume floating point. */
		    dyStringPrintf(dy, "%f", atof(pat));
		else
		    dyStringPrintf(dy, "%d", atoi(pat));
		}
	    }
	}
    }
/* Handle rawQuery if any */
    {
    char *varName;
    char *logic, *query;
    varName = filterFieldVarName(db, table, "", filterRawLogicVar);
    logic = cartUsualString(cart, varName, logOpMenu[0]);
    varName = filterFieldVarName(db, table, "", filterRawQueryVar);
    query = trimSpaces(cartOptionalString(cart, varName));
    if (query != NULL && query[0] != 0)
        {
	if (needAnd) dyStringPrintf(dy, " %s ", logic);
	sqlSanityCheckWhere(query, dy);
	}
    }

/* Clean up and return */
hFreeConn(&conn);
hashElFreeList(&varList);
if (dy->stringSize == 0)
    {
    dyStringFree(&dy);
    return cloneString(extraClause);
    }
else
    {
    if (isNotEmpty(extraClause))
	dyStringPrintf(dy, " and %s", extraClause);
    return dyStringCannibalize(&dy);
    }
}
Ejemplo n.º 12
0
struct joinerDtf *filteringTables()
/* Get list of tables we're filtering on as joinerDtf list (with
 * the field entry NULL). */
{
if (!anyFilter())
    return NULL;
else
    {
    struct joinerDtf *dtfList = NULL, *dtf;
    struct hashEl *varList, *var;
    struct hash *uniqHash = hashNew(0);
    int prefixSize = strlen(hgtaFilterVarPrefix);
    varList = cartFindPrefix(cart, hgtaFilterVarPrefix);
    for (var = varList; var != NULL; var = var->next)
        {
	char *dupe = cloneString(var->name + prefixSize);
	char *parts[5];
	int partCount;
	char dbTable[256];
	char *db, *table, *field, *type;
	partCount = chopByChar(dupe, '.', parts, ArraySize(parts));
	if (partCount != 4)
	    {
	    warn("Part count != expected 4 line %d of %s", __LINE__, __FILE__);
	    continue;
	    }
	db = parts[0];
	table = parts[1];
	field = parts[2];
	type = parts[3];
	safef(dbTable, sizeof(dbTable), "%s.%s", db, table);
	if (! filteredOrLinked(db, table))
	    continue;
	if (!hashLookup(uniqHash, dbTable))
	    {
	    boolean gotFilter = FALSE;

	    if (sameString(type, filterPatternVar))
	        {
		char *pat = trimSpaces(var->val);
		gotFilter = wildReal(pat);
		}
	    else if (sameString(type, filterCmpVar))
	        {
		char *patVar = filterPatternVarName(db, table, field);
		char *pat = trimSpaces(cartOptionalString(cart, patVar));
		gotFilter = cmpReal(pat, var->val);
		}
	    else if (sameString(type, filterRawQueryVar))
	        {
		char *pat = trimSpaces(var->val);
		gotFilter = (pat != NULL && pat[0] != 0);
		}
	    if (gotFilter)
		{
		hashAdd(uniqHash, dbTable, NULL);
		AllocVar(dtf);
		dtf->database = cloneString(db);
		dtf->table = cloneString(table);
		slAddHead(&dtfList, dtf);
		}
	    }
	freeMem(dupe);
	}
    hashFree(&uniqHash);
    return dtfList;
    }
}