Added some documentation

fractalis/analytics/task.py

+"""This module provides AnalyticTask, which is a modification of a standard
+Celery task tailored to Fractalis."""
 import abc
 import json
 import re
 import logging
-import time
+from typing import List
 
 import pandas as pd
 from celery import Task
@@ -14,25 +16,45 @@ logger = logging.getLogger(__name__)
 
 
 class AnalyticTask(Task, metaclass=abc.ABCMeta):
-
+    """AnalyticTask is a tailored Celery Task that enforces a certain pattern
+    for all Fractalis analytic tasks and provides certain functionality like
+    the parsing of the arguments before submitting it to celery.
+    """
     @property
     @abc.abstractmethod
-    def name(self):
+    def name(self) -> str:
+        """The name of the task."""
         pass
 
     @staticmethod
-    def factory(task_name):
+    def factory(task_name: str) -> 'AnalyticTask':
+        """Initialize the correct task based on the given arguments.
+        :param task_name: The name of the task to initialize.
+        :return: An initialized child of this class.
+        """
         from . import TASK_REGISTRY
         for task in TASK_REGISTRY:
             if task.name == task_name:
                 return task()
 
     @abc.abstractmethod
-    def main(self):
+    def main(self) -> dict:
+        """Since we hijack run(), we need a new entry point for every task.
+        This method is called by our modified run method with all parsed 
+        arguments.
+        :return A dict containing the results of the task.
+        """
         pass
 
     @staticmethod
-    def prepare_args(data_tasks, args):
+    def prepare_args(data_tasks: List[str], args: dict) -> dict:
+        """Replace data task ids in the arguments with their associated 
+        data frame located on the file system.
+
+        :param data_tasks: We use this list to check access.
+        :param args: The arguments submitted to run()
+        :return: The new parsed arguments
+        """
         arguments = {}
         for arg in args:
             value = args[arg]
@@ -63,7 +85,13 @@ class AnalyticTask(Task, metaclass=abc.ABCMeta):
             arguments[arg] = value
         return arguments
 
-    def run(self, data_tasks, args):
+    def run(self, data_tasks: List[str], args: dict) -> str:
+        """This is called by the celery worker. This method calls other helper
+        methods to prepare and validate the in and output of a task.
+        :param data_tasks: List of data task ids from session to check access.
+        :param args: This is the dict of arguments submitted to the task.
+        :return: The result of the task.
+        """
         arguments = self.prepare_args(data_tasks, args)
         result = self.main(**arguments)
         try:

fractalis/data/etls/ada/handler_ada.py

@@ -7,7 +7,7 @@ from fractalis.data.etlhandler import ETLHandler
 
 class AdaHandler(ETLHandler):
     """This ETLHandler provides integration with ADA.
-    'Ada provides key infrastructure for secured integration, vizualization,
+    'Ada provides key infrastructure for secured integration, visualization,
     and analysis of anonymized clinical and experimental data stored in CSV
     and tranSMART format, or provided by RedCAP and Synapse apps.'
 

tests/test_session.py

+"""This module provides tests for the session interface of Fractalis."""
 from uuid import UUID
 from time import sleep
 
@@ -6,6 +7,7 @@ import flask
 from redis import StrictRedis
 
 
+# noinspection PyMissingOrEmptyDocstring,PyMissingTypeHints
 class TestSession(object):
 
     @pytest.fixture(scope='module')