diff --git a/src/cbPyLib/cellbrowser/cellbrowser.py b/src/cbPyLib/cellbrowser/cellbrowser.py index ab1ffbd..b7167d1 100755 --- a/src/cbPyLib/cellbrowser/cellbrowser.py +++ b/src/cbPyLib/cellbrowser/cellbrowser.py @@ -165,6 +165,7 @@ def sendDebugToFile(fname): logger.setLevel(logging.DEBUG) #By default, logs all messages # log to console + consLevel = logging.INFO ch = logging.StreamHandler() #StreamHandler logs to console ch.setLevel(consLevel) ch_format = logging.Formatter('%(asctime)s - %(message)s') @@ -5509,6 +5510,14 @@ def fixupName(inConfFname, inConf): relPath = relpath(dirname(abspath(inConfFname)), dataRoot) else: + if not "name" in inConf: + errAbort("Not running in data hierarchy mode. " + "The config file %s needs at least the setting 'name' to a short string, e.g. 'cortex-dev'. " + "If you set a dataRoot directory in your ~/.cellbrowser file or via the CBDATAROOT variable, then the input datasets " + "are assumed to be under one single directory and their subdirectory name is the datasetname. " + "See https://cellbrowser.readthedocs.io/en/master/collections.html " + "Otherwise, as now, they can be spread out over the entire filesystem but then the directory name cannot be used to " + "derive the cell browser dataset name. Instead, a 'name' setting must be present in every cellbrowser.conf file." % inConfName) relPath = inConf["name"] dsName = inConf["name"]