genesets route for local server (#2079)

* first cut at GET /genesets route

* update existing tests to match code changes

* more GET /genesets and initial tests

* add missing test fixture

* geneset validation accepts OTA format

* genesets route: better error handling, more tests

* lint

local_server/common/annotations/annotations.py

@@ -3,19 +3,34 @@ from abc import ABCMeta, abstractmethod
 import fastobo
 import fsspec
 
-from local_server.common.errors import OntologyLoadFailure
+from local_server.common.errors import OntologyLoadFailure, DisabledFeatureError
 from local_server.common.utils.type_conversion_utils import get_schema_type_hint_of_array
 
 
 class Annotations(metaclass=ABCMeta):
-    """ baseclass for annotations, including ontologies"""
+    """ baseclass for annotations, including ontologies and genesets"""
 
     """ our default ontology is the PURL for the Cell Ontology.
     See http://www.obofoundry.org/ontology/cl.html """
     DefaultOnotology = "http://purl.obolibrary.org/obo/cl.obo"
 
-    def __init__(self):
+    def __init__(self, config={}):
         self.ontology_data = None
+        self.config = config
+
+    def user_annotations_enabled(self):
+        return self.config.get("user-annotations", False)
+
+    def genesets_save_enabled(self):
+        return self.config.get("genesets-save", False)
+
+    def check_user_annotations_enabled(self):
+        if not self.user_annotations_enabled():
+            raise DisabledFeatureError("User annotations are disabled.")
+
+    def check_genesets_save_enabled(self):
+        if not self.genesets_save_enabled():
+            raise DisabledFeatureError("User genesets save is disabled.")
 
     def load_ontology(self, path):
         """Load and parse ontologies - currently support OBO files only."""
@@ -64,7 +79,66 @@ 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 from persistent storage """
+        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"""
         pass
+
+    Genesets_Header = [
+        "geneset_name",
+        "geneset_description",
+        "gene_symbol",
+        "gene_description",
+    ]
+
+    @staticmethod
+    def genesets_to_csv(genesets):
+        """
+        Convert the internal genesets format (returned by read_geneset) into
+        the simple Tidy CSV.
+        """
+        from io import StringIO
+        import csv
+
+        if type(genesets) == dict:
+            genesets = genesets.values()
+
+        with StringIO() as sio:
+            writer = csv.writer(sio, dialect='excel')
+            writer.writerow(Annotations.Genesets_Header)
+            for geneset in genesets:
+                # genes may be empty, in which case we skip the geneset entirely
+                genes = geneset["genes"]
+                if not genes:
+                    writer.writerow([geneset["geneset_name"], geneset.get("geneset_description", ""), "", ""])
+                else:
+                    writer.writerows(
+                        [
+                            [
+                                geneset["geneset_name"],
+                                geneset.get("geneset_description", ""),
+                                gene["gene_symbol"],
+                                gene.get("gene_description", ""),
+                            ]
+                            for gene in genes
+                        ]
+                    )
+            return sio.getvalue()
+
+    @staticmethod
+    def genesets_to_response(genesets):
+        """
+        Convert the internal genesets format (returned by read_geneset) into
+        the dict expected by the JSON REST API
+        """
+        return list(genesets.values())