Add user-generated annotations tests to the server (#1164)

* Add user-generated annotations tests to the server

Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969

* Auto-format python code

* @skip_if: passing lambdas > than property strings

* Respond to feedback from @bkmartinjr

server/common/annotations.py

@@ -42,7 +42,7 @@ class Annotations(metaclass=ABCMeta):
             raise OntologyLoadFailure(f"Unable to find OBO ontology path: {path}") from e
 
         except SyntaxError as e:
-            msg = ''.join(traceback.format_exception_only(SyntaxError, e))
+            msg = "".join(traceback.format_exception_only(SyntaxError, e))
             raise OntologyLoadFailure(msg) from e
 
         except Exception as e:

server/common/app_config.py

@@ -13,16 +13,12 @@ class AppFeature(object):
             setattr(self, k, v)
 
     def todict(self):
-        d = dict(
-            available=self.available,
-            method=self.method,
-            path=self.path)
+        d = dict(available=self.available, method=self.method, path=self.path)
         d.update(self.extra)
         return d
 
 
 class AppConfig(object):
-
     def __init__(self, **kw):
         super().__init__()
 
@@ -47,10 +43,20 @@ class AppConfig(object):
         # parameters
         self.diffexp_may_be_slow = False
 
-        inputs = ["datapath", "dataroot", "title", "about", "scripts", "layout",
-                  "max_category_items", "diffexp_lfc_cutoff",
-                  "obs_names", "var_names",
-                  "anndata_backed", "disable_diffexp"]
+        inputs = [
+            "datapath",
+            "dataroot",
+            "title",
+            "about",
+            "scripts",
+            "layout",
+            "max_category_items",
+            "diffexp_lfc_cutoff",
+            "obs_names",
+            "var_names",
+            "anndata_backed",
+            "disable_diffexp",
+        ]
 
         self.update(inputs, kw)
 
@@ -80,9 +86,7 @@ class AppConfig(object):
         title = self.get_title(data_adaptor)
         about = self.get_about(data_adaptor)
 
-        display_names = dict(
-            engine=data_adaptor.get_name(),
-            dataset=title)
+        display_names = dict(engine=data_adaptor.get_name(), dataset=title)
 
         # library_versions
         library_versions = {}
@@ -90,7 +94,7 @@ class AppConfig(object):
         library_versions["cellxgene"] = cellxgene_version
 
         # links
-        links = {"about-dataset" : about}
+        links = {"about-dataset": about}
 
         # parameters
         parameters = {

server/common/data_locator.py

@@ -84,7 +84,7 @@ class DataLocator:
         # and clean it up when done.  If the path has a suffix/extension,
         # do our best to create a file with the same.
         ext = os.path.splitext(self.path)
-        suffix = None if ext[1] == '' else ext[1]
+        suffix = None if ext[1] == "" else ext[1]
         with self.open() as src, tempfile.NamedTemporaryFile(prefix="cellxgene_", suffix=suffix, delete=False) as tmp:
             tmp.write(src.read())
             tmp.close()

server/common/errors.py

@@ -2,6 +2,7 @@ class FilterError(Exception):
     """
     Raised when filter is malformed
     """
+
     pass
 
 
@@ -9,6 +10,7 @@ class JSONEncodingValueError(Exception):
     """
     Raised when data cannot be encoded into json
     """
+
     pass
 
 
@@ -16,6 +18,7 @@ class MimeTypeError(Exception):
     """
     Raised when incompatible MIME type selected
     """
+
     pass
 
 
@@ -23,6 +26,7 @@ class PrepareError(Exception):
     """
     Raised when data is misprepared
     """
+
     pass
 
 
@@ -30,6 +34,7 @@ class DatasetAccessError(Exception):
     """
     Raised when file loaded into a DataAdaptor is misformatted
     """
+
     pass
 
 
@@ -37,6 +42,7 @@ class DisabledFeatureError(Exception):
     """
     Raised when an attempt to use a disabled feature occurs
     """
+
     pass
 
 
@@ -44,6 +50,7 @@ class AnnotationsError(Exception):
     """
     Raised when an attempt to use the annotations feature fails
     """
+
     pass
 
 
@@ -51,4 +58,5 @@ class OntologyLoadFailure(Exception):
     """
     Raised when reading the ontology file fails
     """
+
     pass

server/common/rest.py

@@ -29,9 +29,7 @@ def schema_get_helper(data_adaptor, annotations):
 
 def schema_get(data_adaptor, annotations):
     schema = schema_get_helper(data_adaptor, annotations)
-    return make_response(
-        jsonify({"schema": schema}), HTTPStatus.OK
-    )
+    return make_response(jsonify({"schema": schema}), HTTPStatus.OK)
 
 
 def config_get(app_config, data_adaptor, annotations):

server/common/utils.py

@@ -92,20 +92,18 @@ def jsonify_numpy(data):
 def dtype_to_schema(dtype):
     schema = {}
     if dtype == np.float32:
-        schema['type'] = 'float32'
+        schema["type"] = "float32"
     elif dtype == np.int32:
-        schema['type'] = 'int32'
+        schema["type"] = "int32"
     elif dtype == np.bool_:
-        schema['type'] = 'boolean'
+        schema["type"] = "boolean"
     elif dtype == np.str:
-        schema['type'] = 'string'
+        schema["type"] = "string"
     elif dtype == "category":
         schema["type"] = "categorical"
         schema["categories"] = dtype.categories.tolist()
     else:
-        raise TypeError(
-            f"Annotations of type {dtype} are unsupported."
-        )
+        raise TypeError(f"Annotations of type {dtype} are unsupported.")
     return schema