light cleanup & documentation

src/scripts/Alaska.py

@@ -1,10 +1,18 @@
+"""Contains the Alaska class.
+
+The Alaska class is inherited by all AlaskaX classes. The class contains
+all shared variables among the Alaska family.
 """
-Alaska.py
 
-Author: Joseph Min (kmin@caltech.edu)
+__author__ = 'Kyung Hoi (Joseph) Min'
+__copyright__ = 'Copyright 2017 WormLabCaltech'
+__credits__ = ['David Angeles', 'Raymond Lee', 'Juancarlos Chan']
+__license__ = "MIT"
+__version__ = "alpha"
+__maintainer__ = "Kyung Hoi (Joseph) Min"
+__email__ = "kmin@caltech.edu"
+__status__ = "alpha"
 
-This file contains the class Alaska, which is inherited by all Alaska scripts.
-"""
 import os
 import random
 import datetime as dt
@@ -95,23 +103,29 @@ class Alaska():
         'read_quant':           b'\x10', # perform read quantification
         'diff_exp':             b'\x11', # perform differential expression
         'do_all':               b'\x12', # perform qc, read quant, and diff exp
-        'proj_status':          b'\x13', # check project status
         'open_sleuth_server':   b'\x13',
+        'proj_status':          b'\x14', # check project status
         'test_copy_reads':      b'\x47',
         'test_set_vars':        b'\x48',
         'test_qc':              b'\x49',
         'test_read_quant':      b'\x50',
         'test_diff_exp':        b'\x51',
         'test_all':             b'\x52',
+        'get_status':           b'\x93',
         'save':                 b'\x94', # saves server state
         'load':                 b'\x95', # loads server state
         'log':                  b'\x96', # force log
-        'update_orgs':           b'\x97', # force organism update
+        'update_orgs':          b'\x97', # force organism update
         'start':                b'\x98', # start server
         'stop':                 b'\x99'  # stop server
     }
 
-    # Progress notes
+    # Server state.
+    SERVER_STATE = {
+        0: 'under maintenance',
+        1: 'active',
+    }
+
     # 0: This is a new project.
     # 1: raw reads fetched
     # 2: samples inferred.

src/scripts/AlaskaDocker.py

@@ -1,12 +1,20 @@
+"""Contains the AlaskaDocker class.
+
+The AlaskaDocker class is a wrapper around the Docker Python API, which is
+used to manage the spawning/monitoring/termination of Docker images and
+containers. All containers spawned by Alaska is spawned through an
+AlaskaDocker object.
 """
-AlaskaDocker.py
 
-Author: Joseph Min (kmin@caltech.edu)
+__author__ = 'Kyung Hoi (Joseph) Min'
+__copyright__ = 'Copyright 2017 WormLabCaltech'
+__credits__ = ['David Angeles', 'Raymond Lee', 'Juancarlos Chan']
+__license__ = "MIT"
+__version__ = "alpha"
+__maintainer__ = "Kyung Hoi (Joseph) Min"
+__email__ = "kmin@caltech.edu"
+__status__ = "alpha"
 
-This file contains the class AlaskaDocker, which deals with docker container
-spawning and output.
-Managed by AlaskaServer.
-"""
 import docker
 from Alaska import Alaska
 from threading import Thread
@@ -44,7 +52,7 @@ def out_listener(self):
         Listens container output and records.
         """
         for l in self.hook():
-            l = l.decode(self.ENCODING).strip()
+            l = l.decode(Alaska.ENCODING).strip()
             self.output += l
 
         self.running = False

src/scripts/AlaskaJob.py

@@ -1,11 +1,22 @@
+"""Contains the AlaskaJob class.
+
+Computationally-intense processes are managed by creating AlaskaJob objects.
+The AlaskaJob class serves as an intermediary between the AlaskaServer and
+AlaskaDocker. Specifically, this class provides abstractions that simplify
+spawning containers, reading their output and terminating them. Quality
+control, read alignment and differential expression analysis are done by using
+this class.
 """
-AlaskaJob.py
 
-Author: Joseph Min (kmin@caltech.edu)
+__author__ = 'Kyung Hoi (Joseph) Min'
+__copyright__ = 'Copyright 2017 WormLabCaltech'
+__credits__ = ['David Angeles', 'Raymond Lee', 'Juancarlos Chan']
+__license__ = "MIT"
+__version__ = "alpha"
+__maintainer__ = "Kyung Hoi (Joseph) Min"
+__email__ = "kmin@caltech.edu"
+__status__ = "alpha"
 
-This file contains the class AlaskaJob, which contains job information.
-Managed by Alaskaserver.
-"""
 import io
 import contextlib as cl
 import json
@@ -64,7 +75,7 @@ def save(self, folder=None):
         Saves job information to JSON.
         """
         if folder is None: # if folder not given, save to project root
-            path = self.JOBS_DIR
+            path = Alaska.JOBS_DIR
         else:
             path = folder
 
@@ -76,7 +87,7 @@ def load(self, folder=None, proj=None):
         Load job from JSON.
         """
         if folder is None:
-            path = self.JOBS_DIR
+            path = Alaska.JOBS_DIR
         else:
             path = folder
 

src/scripts/AlaskaOrganism.py

@@ -1,13 +1,18 @@
-"""
-AlaskaOrganism.py
-
-Author: Joseph Min (kmin@caltech.edu)
+"""Contains the AlaskaOrganism class.
 
-Contains AlaskaOrganism class.
-AlaskaOrganism is an object that contains information of each organism.
-(Including all available reference sequences.)
+Contains all necessary information about a model organism. This class holds
+multiple AlaskaReference objects, one for each reference version.
 """
 
+__author__ = 'Kyung Hoi (Joseph) Min'
+__copyright__ = 'Copyright 2017 WormLabCaltech'
+__credits__ = ['David Angeles', 'Raymond Lee', 'Juancarlos Chan']
+__license__ = "MIT"
+__version__ = "alpha"
+__maintainer__ = "Kyung Hoi (Joseph) Min"
+__email__ = "kmin@caltech.edu"
+__status__ = "alpha"
+
 import os
 import json
 from Alaska import Alaska
@@ -28,7 +33,7 @@ def __init__(self, genus, species):
         self.full = '{}_{}'.format(genus, species)
         self.short = '{}_{}'.format(genus[0].lower(), species)
         self.refs = {}
-        self.path = '{}/{}/{}'.format(self.ORGS_DIR, genus, species)
+        self.path = '{}/{}/{}'.format(Alaska.ORGS_DIR, genus, species)
 
     def add_new_ref(self, version, cds, bed):
         """
@@ -42,7 +47,7 @@ def save(self, folder=None):
         Saves organism data to JSON.
         """
         if folder is None:
-            path = self.ORGS_DIR
+            path = Alaska.ORGS_DIR
         else:
             path = folder
 
@@ -56,7 +61,7 @@ def load(self, folder=None):
         Loads organism from JSON.
         """
         if folder is None:
-            path = self.ORGS_DIR
+            path = Alaska.ORGS_DIR
         else:
             path = folder