move common code into server, update tests and makefile (#2425)

* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests

server/common/annotations/annotations.py

@@ -0,0 +1,90 @@
+from abc import ABCMeta, abstractmethod
+
+from server.common.errors import DisabledFeatureError
+from server.common.utils.type_conversion_utils import get_schema_type_hint_of_array
+from server.common.genesets import write_gene_sets_tidycsv
+
+
+class Annotations(metaclass=ABCMeta):
+    """baseclass for annotations and gene sets"""
+
+    def __init__(self, config={}):
+        self.config = config
+
+    def user_annotations_enabled(self):
+        return self.config.get("user-annotations", False)
+
+    def gene_sets_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_gene_sets_save_enabled(self):
+        if not self.gene_sets_save_enabled():
+            raise DisabledFeatureError("User gene sets save is disabled.")
+
+    def get_schema(self, data_adaptor):
+        schema = []
+        labels = self.read_labels(data_adaptor)
+        if labels is not None and not labels.empty:
+            for col in labels.columns:
+                col_schema = dict(name=col, writable=True)
+                col_schema.update(get_schema_type_hint_of_array(labels[col]))
+                schema.append(col_schema)
+
+        return schema
+
+    @abstractmethod
+    def set_collection(self, name):
+        """set or create a new annotation collection"""
+        pass
+
+    @abstractmethod
+    def read_labels(self, data_adaptor):
+        """Return the labels as a pandas.DataFrame"""
+        pass
+
+    @abstractmethod
+    def write_labels(self, df, data_adaptor):
+        """Write the labels (df) to a persistent storage such that it can later be read"""
+        pass
+
+    @abstractmethod
+    def read_gene_sets(self, data_adaptor):
+        """Return the gene sets from persistent storage"""
+        pass
+
+    @abstractmethod
+    def write_gene_sets(self, gs, data_adaptor):
+        """Write the gene sets (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
+
+    @staticmethod
+    def gene_sets_to_csv(genesets):
+        """
+        Convert the internal gene sets format (returned by read_gene_set) into
+        the simple Tidy CSV.
+        """
+        from io import StringIO
+
+        if isinstance(genesets, dict):
+            genesets = genesets.values()
+
+        with StringIO() as sio:
+            write_gene_sets_tidycsv(sio, genesets)
+            return sio.getvalue()
+
+    @staticmethod
+    def gene_sets_to_response(genesets):
+        """
+        Convert the internal gene sets format (returned by read_gene_set) into
+        the dict expected by the JSON REST API
+        """
+        return list(genesets.values())