categories appear all combined together about genometranslationcommons HOT 2 OPEN

This error log actually gives quite a typical stack trace that shows what happens inside ISA-Tab parsing: https://gist.github.com/drj11/23b3c9537ae250413a4034d5ad498ade

from genometranslationcommons.

Case notes: what is an attribute?

Please see refinery/data_set_manager/isa_tab_parser.py

Attribute instances are not created at many places in the code. In _parse_attribute https://github.com/refinery-platform/refinery-platform/blob/develop/refinery/data_set_manager/isa_tab_parser.py#L435-L442

In fact, Attribute is created it only one place.
It is created in _parse_attribute if the has_attribute flag is false by the time it is tested.

the has_attribute flag is set to True when either:

• header_components has length 1: and the node already has an attribute of that type
• header_components has length more than 1 (2?): and the node already has an attribute of that type and subtype;

However, _parse_attribute is not called unless the higher level code decides that the node is an attribute.
This is in _parse_node which calls is_attribute

from genometranslationcommons.