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);
}
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;
}
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;
}
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>");
}
}
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;
}
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);
}
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() */
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);
}
}
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;
}
}