wire e2e gene set loading prototype

server/common/annotations/annotations.py

@@ -8,7 +8,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar
 
 
 class Annotations(metaclass=ABCMeta):
-    """ baseclass for annotations, including ontologies"""
+    """ baseclass for annotations, including ontologies and gene sets"""
 
     """ our default ontology is the PURL for the Cell Ontology.
     See http://www.obofoundry.org/ontology/cl.html """
@@ -64,6 +64,16 @@ class Annotations(metaclass=ABCMeta):
         """Write the labels (df) to a persistent storage such that it can later be read"""
         pass
 
+    @abstractmethod
+    def read_genesets(self, data_adaptor):
+        """Return the genesets as a list of list, ie, [['gsname', ['gene1', 'gene2']], ...] """
+        pass
+
+    @abstractmethod
+    def write_genesets(self, gs, data_adaptor):
+        """Write the genesets (gs) to a persistent storage such that it can later be read"""
+        pass
+
     @abstractmethod
     def update_parameters(self, parameters, data_adaptor):
         """Update configuration parameters that describe information about the annotations feature"""