int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2 && !optionExists("settings"))
usage();
struct trackHubCheckOptions *checkOptions = NULL;
AllocVar(checkOptions);
checkOptions->specHost = (optionExists("test") ? "genome-test.soe.ucsc.edu" : "genome.ucsc.edu");
checkOptions->specHost = optionVal("specHost", checkOptions->specHost);
checkOptions->printMeta = optionExists("printMeta");
checkOptions->checkFiles = !optionExists("noTracks");
checkOptions->checkSettings = optionExists("checkSettings");
struct trackHubSettingSpec *setting = NULL;
AllocVar(setting);
setting->level = optionVal("level", "all");
if (trackHubSettingLevel(setting) < 0)
{
fprintf(stderr, "ERROR: Unrecognized support level %s\n\n", setting->level);
usage();
}
checkOptions->level = setting->level;
char *version = NULL;
if (optionExists("version"))
version = optionVal("version", NULL);
checkOptions->version = version;
char *extraFile = optionVal("extra", NULL);
if (extraFile != NULL)
addExtras(extraFile, checkOptions);
cacheTime = optionInt("cacheTime", cacheTime);
udcSetCacheTimeout(cacheTime);
// UDC cache dir: first check for hg.conf setting, then override with command line option if given.
setUdcCacheDir();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
knetUdcInstall(); // make the htslib library use udc
if (optionExists("settings"))
{
showSettings(checkOptions);
return 0;
}
struct dyString *errors = newDyString(1024);
if (trackHubCheck(argv[1], checkOptions, errors))
{
// uniquify and count errors
struct slName *errs = slNameListFromString(errors->string, '\n');
slUniqify(&errs, slNameCmp, slNameFree);
int errCount = slCount(errs);
printf("Found %d problem%s:\n", errCount, errCount == 1 ? "" : "s");
printf("%s\n", slNameListToString(errs, '\n'));
return 1;
}
return 0;
}
struct slPair *mdbSelectPairs(struct cart *cart, struct slPair *mdbVars)
// Returns the current mdb vars and vals in the table of drop down selects
{
// figure out how many metadata selects are visible.
int numMetadataSelects = 0;
struct slPair *mdbSelectPairs = NULL;
if (mdbVars == NULL)
return 0;
// Get the current number of rows in the table of mdb selects
for (;;)
{
char buf[256];
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
char *str = cartOptionalString(cart, buf);
if (isEmpty(str))
break;
else
numMetadataSelects++;
}
// Requesting to add or delete any?
int delSearchSelect = cartUsualInt(cart, TRACK_SEARCH_DEL_ROW, 0); // 1-based row to delete
int addSearchSelect = cartUsualInt(cart, TRACK_SEARCH_ADD_ROW, 0); // 1-based row to insert after
if (delSearchSelect)
numMetadataSelects--;
if (addSearchSelect)
numMetadataSelects++;
if (numMetadataSelects)
{
int ix;
char buf[256];
for (ix = 0; ix < numMetadataSelects; ix++)
{
int offset; // used to handle additions/deletions
if (addSearchSelect > 0 && ix >= addSearchSelect)
offset = 0; // do nothing to offset (i.e. copy data from previous row)
else if (delSearchSelect > 0 && ix + 1 >= delSearchSelect)
offset = 2;
else
offset = 1;
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, ix + offset);
char *var = cartOptionalString(cart, buf);
char *val = NULL;
// We need to make sure var is valid in this assembly; if it isn't, reset it to "cell".
if (slPairFindVal(mdbVars,var) == NULL)
var = "cell";
else
{
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, ix + offset);
enum cvSearchable searchBy = cvSearchMethod(var);
if (searchBy == cvSearchByMultiSelect)
{
// Multi-selects as comma delimited list of values
struct slName *vals = cartOptionalSlNameList(cart,buf);
if (vals)
{
val = slNameListToString(vals,','); // A comma delimited list of values
slNameFreeList(&vals);
}
}
else if (searchBy == cvSearchBySingleSelect
|| searchBy == cvSearchByFreeText
|| searchBy == cvSearchByWildList)
val = cloneString(cartUsualString(cart, buf,ANYLABEL));
//else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
// {
// // TO BE IMPLEMENTED
// }
if (val != NULL && sameString(val, ANYLABEL))
val = NULL;
}
slPairAdd(&mdbSelectPairs,var,val); // val already cloned
}
if (delSearchSelect > 0)
{
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
}
}
else
{
// create defaults
slPairAdd(&mdbSelectPairs,"cell", NULL);
slPairAdd(&mdbSelectPairs,"antibody",NULL);
}
slReverse(&mdbSelectPairs);
return mdbSelectPairs;
}