config refactor (#1854)

* split out config

* add tests for base and app config, refactor client config out of app config

* refactor default config retrieval

* create config test class and helper functions

* move default_config into server to fix import issue

server/test/fixtures/database/__init__.py

@@ -29,34 +29,26 @@ class TestDatabase:
 
     def _create_test_user(self):
         user = CellxGeneUser(id="test_user_id")
-        user2 = CellxGeneUser(id='1234')
+        user2 = CellxGeneUser(id="1234")
         self.db.session.add(user)
         self.db.session.add(user2)
         self.db.session.commit()
 
     def _create_test_dataset(self):
-        dataset = CellxGeneDataset(
-            name="test_dataset",
-        )
+        dataset = CellxGeneDataset(name="test_dataset",)
         self.db.session.add(dataset)
         self.db.session.commit()
 
     def _create_test_annotation(self):
-        dataset = self.db.query([CellxGeneDataset],
-                                [CellxGeneDataset.name == "test_dataset"],
-                                )[0]
-        annotation = Annotation(
-            tiledb_uri="tiledb_uri",
-            user_id="test_user_id",
-            dataset_id=str(dataset.id)
-        )
+        dataset = self.db.query([CellxGeneDataset], [CellxGeneDataset.name == "test_dataset"],)[0]
+        annotation = Annotation(tiledb_uri="tiledb_uri", user_id="test_user_id", dataset_id=str(dataset.id))
         self.db.session.add(annotation)
         self.db.session.commit()
 
     @staticmethod
     def get_random_string():
         letters = string.ascii_lowercase
-        return ''.join(random.choice(letters) for i in range(12))
+        return "".join(random.choice(letters) for i in range(12))
 
     def _create_test_users(self, user_count: int = 10):
         users = []
@@ -80,10 +72,8 @@ class TestDatabase:
         for i in range(annotation_count):
             dataset = self.order_by_random(CellxGeneDataset)
             user = self.order_by_random(CellxGeneUser)
-            annotations.append(Annotation(
-                tiledb_uri=self.get_random_string(),
-                user_id=user.id,
-                dataset_id=str(dataset.id)
-            ))
+            annotations.append(
+                Annotation(tiledb_uri=self.get_random_string(), user_id=user.id, dataset_id=str(dataset.id))
+            )
         self.db.session.add_all(annotations)
         self.db.session.commit()

server/test/fixtures/dataset_config_outline.py

@@ -0,0 +1,37 @@
+f"""
+dataset:
+  app:
+    scripts: {scripts} #list of strs (filenames) or dicts containing keys
+    inline_scripts: {inline_scripts} #list of strs (filenames)
+
+    about_legal_tos: {about_legal_tos}
+    about_legal_privacy: {about_legal_privacy}
+
+    authentication_enable: {authentication_enable}
+
+  presentation:
+    max_categories: {max_categories}
+    custom_colors: {custom_colors}
+
+  user_annotations:
+    enable: {enable_users_annotations}
+    type: {annotation_type}
+    hosted_tiledb_array:
+      db_uri: {db_uri}
+      hosted_file_directory: {hosted_file_directory}
+    local_file_csv:
+      directory: {local_file_csv_directory}
+      file: {local_file_csv_file}
+    ontology:
+      enable: {ontology_enabled}
+      obo_location: {obo_location}
+
+  embeddings:
+    names: {embedding_names}
+    enable_reembedding: {enable_reembedding}
+
+  diffexp:
+    enable: {enable_difexp}
+    lfc_cutoff: {lfc_cutoff}
+    top_n: {top_n}
+"""

server/test/fixtures/server_config_outline.py

@@ -0,0 +1,62 @@
+f"""server:
+  app:
+    verbose: {verbose}
+    debug: {debug}
+    host: {host}
+    port: {port}
+    open_browser: {open_browser}
+    force_https: {force_https}
+    flask_secret_key: {flask_secret_key}
+    generate_cache_control_headers: {generate_cache_control_headers}
+    server_timing_headers: {server_timing_headers}
+    csp_directives: {csp_directives}
+    api_base_url: {api_base_url}
+    web_base_url: {web_base_url}
+  authentication:
+    type: {auth_type}
+    params_oauth:
+      oauth_api_base_url: {oauth_api_base_url}
+      client_id: {client_id}
+      client_secret: {client_secret}
+      jwt_decode_options: {jwt_decode_options}
+      session_cookie:  {session_cookie}
+      cookie:  {cookie}
+
+  multi_dataset:
+    dataroot: {dataroot}
+    index: {index}
+    allowed_matrix_types: {allowed_matrix_types}
+    matrix_cache:
+      max_datasets: {max_cached_datasets}
+      timelimit_s: {timelimit_s}
+
+  single_dataset:
+    datapath: {dataset_datapath}
+    obs_names: {obs_names}
+    var_names: {var_names}
+    about: {about}
+    title: {title}
+
+  diffexp:
+    alg_cxg: # number of threads to use is computed from: min(max_workers, cpu_multipler * cpu_count)
+      max_workers: {diffexp_max_workers}
+      cpu_multiplier: {cpu_multiplier}
+      target_workunit: {target_workunit}  # The target number of matrix elements that are evaluated in one thread.
+
+  data_locator:
+    s3:
+      region_name: {data_locater_region_name}
+
+  adaptor:
+    cxg_adaptor:
+      tiledb_ctx:
+        sm.tile_cache_size:  {cxg_tile_cache_size}
+        sm.num_reader_threads:  {cxg_num_reader_threads}
+
+    anndata_adaptor:
+      backed: {anndata_backed}
+
+  limits:
+    column_request_max: {column_request_max}
+    diffexp_cellcount_max: {diffexp_cellcount_max}
+"""