[cmdline] Pre-commit cleanup

beat/cmdline/algorithms.py

@@ -34,26 +34,24 @@
 ###################################################################################
 
 
-import click
 import logging
 import os
-import simplejson as json
 
+import click
+import simplejson as json
 
+from beat.backend.python.algorithm import Storage as AlgorithmStorage
 from beat.core import algorithm
-from beat.core.execution import DockerExecutor
-from beat.core.dock import Host
 from beat.core import hash
-from beat.backend.python.algorithm import Storage as AlgorithmStorage
+from beat.core.dock import Host
+from beat.core.execution import DockerExecutor
 
-from . import common
 from . import commands
-
-from .decorators import raise_on_error
+from . import common
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
-
+from .decorators import raise_on_error
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/cache.py

@@ -34,20 +34,20 @@
 ###################################################################################
 
 
-import os
-import click
 import fnmatch
 import logging
+import os
 
+import click
 import simplejson
 
-from beat.core.data import CachedDataSource, load_data_index
+from beat.core.data import CachedDataSource
+from beat.core.data import load_data_index
 from beat.core.utils import NumpyJSONEncoder
 
 from . import common
-from .decorators import raise_on_error
 from .click_helper import AliasedGroup
-
+from .decorators import raise_on_error
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/commands.py

@@ -33,13 +33,13 @@
 #                                                                                 #
 ###################################################################################
 
-import click
 import types
 
-from .scripts import main_cli
-from .decorators import raise_on_error
+import click
 
 from . import common
+from .decorators import raise_on_error
+from .scripts import main_cli
 
 
 def copy_func(f, name=None):

beat/cmdline/common.py

@@ -36,29 +36,29 @@
 
 """Utility functions that are useful to all sub-commands"""
 
-import os
-import glob
-import fnmatch
-import difflib
 import collections
-
+import difflib
+import fnmatch
+import glob
 import logging
+import os
+
+from enum import Enum
+from enum import unique
 
+import simplejson
 import six
 import termcolor
-import simplejson
-
-from enum import Enum, unique
 
-from beat.core import dataformat
+from beat.core import algorithm
 from beat.core import database
+from beat.core import dataformat
+from beat.core import experiment
 from beat.core import library
 from beat.core import plotter
 from beat.core import plotterparameter
 from beat.core import protocoltemplate
-from beat.core import algorithm
 from beat.core import toolchain
-from beat.core import experiment
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/config.py

@@ -37,91 +37,85 @@
 """Configuration manipulation and display"""
 
 
-import os
-import sys
 import copy
-import logging
 import getpass
+import logging
+import os
+import sys
+
 import click
 import simplejson
 
-from .decorators import verbosity_option
 from .click_helper import AliasedGroup
-
+from .decorators import verbosity_option
 
 logger = logging.getLogger(__name__)
 
-
+#  Default values for the command-line utility
 DEFAULTS = {
-    'platform': 'https://www.beat-eu.org/platform/',
-    'user': getpass.getuser(),
-    'token': None,
-    'prefix': os.path.realpath(os.path.join(os.curdir, 'prefix')),
-    'cache': 'cache',
-    'editor': None,
-    }
-"""Default values for the command-line utility"""
+    "platform": "https://www.beat-eu.org/platform/",
+    "user": getpass.getuser(),
+    "token": None,
+    "prefix": os.path.realpath(os.path.join(os.curdir, "prefix")),
+    "cache": "cache",
+    "editor": None,
+}
 
 
+#  Documentation for the configuration parameters
 DOC = {
-    'platform': 'Web address of the BEAT platform',
-    'user': 'User name for operations that create, delete or edit objects',
-    'token': 'Secret key of the user on the BEAT platform',
-    'prefix': 'Directory containing BEAT objects',
-    'cache': 'Directory to use for data caching (relative to prefix)',
-    'editor': 'Editor to be used to edit local files',
-    }
-"""Documentation for configuration parameters"""
+    "platform": "Web address of the BEAT platform",
+    "user": "User name for operations that create, delete or edit objects",
+    "token": "Secret key of the user on the BEAT platform",
+    "prefix": "Directory containing BEAT objects",
+    "cache": "Directory to use for data caching (relative to prefix)",
+    "editor": "Editor to be used to edit local files",
+}
 
 
 class Configuration(object):
-    '''Keeps track of configuration elements'''
+    """Keeps track of configuration elements"""
 
     def __init__(self, args):
 
         self.files = [
-            os.path.expanduser('~/.beatrc'),
-            os.path.realpath('./.beatrc'),
+            os.path.expanduser("~/.beatrc"),
+            os.path.realpath("./.beatrc"),
         ]
 
         self.__data = copy.deepcopy(DEFAULTS)
         for k in self.files:
             if os.path.exists(k):
-                with open(k, 'rt') as f: tmp = simplejson.load(f)
+                with open(k, "rt") as f:
+                    tmp = simplejson.load(f)
                 self.__data.update(tmp)
                 logger.info("Loaded configuration file `%s'", k)
 
         for key in DEFAULTS:
-            self.__data[key] = args.get('--%s' % key) or self.__data[key]
-
+            self.__data[key] = args.get("--%s" % key) or self.__data[key]
 
     @property
     def path(self):
-        '''The directory for the prefix'''
-
-        return self.__data['prefix']
+        """The directory for the prefix"""
 
+        return self.__data["prefix"]
 
     @property
     def cache(self):
-        '''The directory for the cache'''
-
-        if os.path.isabs(self.__data['cache']):
-            return self.__data['cache']
-        return os.path.join(self.__data['prefix'], self.__data['cache'])
+        """The directory for the cache"""
 
+        if os.path.isabs(self.__data["cache"]):
+            return self.__data["cache"]
+        return os.path.join(self.__data["prefix"], self.__data["cache"])
 
     @property
     def database_paths(self):
-        '''A dict of paths for databases'''
-
-        return dict(
-            (k, self.__data[k]) for k in self.__data if self.is_database_key(k)
-        )
+        """A dict of paths for databases"""
 
+        return dict((k, self.__data[k]) for k in self.__data if self.is_database_key(k))
 
     def set(self, key, value, local=False):
-        '''Sets or resets a field in the configuration'''
+        """Sets or resets a field in the configuration"""
 
         if not self._is_valid_key(key):
             logger.error("Don't know about parameter `%s'", key)
@@ -134,9 +128,8 @@ class Configuration(object):
 
         self.save(local)
 
-
     def save(self, local=False):
-        '''Saves contents to configuration file
+        """Saves contents to configuration file
 
         Parameters:
 
@@ -144,39 +137,34 @@ class Configuration(object):
                 if set to ``True``, then save
                 configuration values to local configuration file (typically
                 ``.beatrc``)
-        '''
+        """
 
         path = self.files[0]
         if local:
             path = self.files[1]
 
         flags = os.O_WRONLY | os.O_CREAT | os.O_TRUNC
-        with os.fdopen(os.open(path, flags, 0o600), 'wt') as f:
-            f.write(simplejson.dumps(
-                self.__data, sort_keys=True, indent=4,
-                separators=(',', ': ')
-            ))
-
+        with os.fdopen(os.open(path, flags, 0o600), "wt") as f:
+            f.write(
+                simplejson.dumps(
+                    self.__data, sort_keys=True, indent=4, separators=(",", ": ")
+                )
+            )
 
     def _is_valid_key(self, key):
         return key in DEFAULTS or self.is_database_key(key)
 
-
     def is_database_key(self, key):
-        return key.startswith('database/')
-
+        return key.startswith("database/")
 
     def __str__(self):
         return simplejson.dumps(
-            self.__data, sort_keys=True,
-            indent=4, separators=(',', ': ')
+            self.__data, sort_keys=True, indent=4, separators=(",", ": ")
         )
 
-
     def as_dict(self):
         return copy.copy(self.__data)
 
-
     def __getattr__(self, key):
         return self.__data[key]
 
@@ -188,6 +176,7 @@ def config(ctx):
     """The manager for beat cmdline configuration."""
     pass
 
+
 @config.command()
 @click.pass_context
 def show(ctx):
@@ -195,11 +184,11 @@ def show(ctx):
 
     Lists the configuration after resolving defaults and saved variables
     """
-    click.echo(ctx.meta['config'])
+    click.echo(ctx.meta["config"])
 
 
 @config.command()
-@click.argument('key')
+@click.argument("key")
 @click.pass_context
 def get(ctx, key):
     """Prints out the contents of a single field.
@@ -221,19 +210,22 @@ def get(ctx, key):
     -----
     * If the key is not found.
     """
-    value = getattr(ctx.meta['config'], key)
+    value = getattr(ctx.meta["config"], key)
     if value is None:
         # Exit the command line with ClickException in case of errors.
-        raise click.ClickException(
-            "The requested key `{}' does not exist".format(key))
+        raise click.ClickException("The requested key `{}' does not exist".format(key))
     click.echo(value)
 
 
 @config.command()
-@click.argument('args', nargs=-1)
-@click.option('--local/--not-local', default=False, help='Save values on the '
-              'local configuration file (.beatrc) instead of using the global '
-              'file (~/.beatrc)')
+@click.argument("args", nargs=-1)
+@click.option(
+    "--local/--not-local",
+    default=False,
+    help="Save values on the "
+    "local configuration file (.beatrc) instead of using the global "
+    "file (~/.beatrc)",
+)
 @click.pass_context
 def set(ctx, args, local):
     """Sets the value for a key.
@@ -260,10 +252,10 @@ def set(ctx, args, local):
     """
 
     if len(args) % 2 != 0:
-        raise click.BadParameter('You must provide pair(s) of key/value')
+        raise click.BadParameter("You must provide pair(s) of key/value")
 
     try:
         for idx in range(0, len(args), 2):
-            ctx.meta['config'].set(args[idx], args[idx + 1], local)
+            ctx.meta["config"].set(args[idx], args[idx + 1], local)
     except Exception:
         raise click.ClickException("Failed to change the configuration.")

beat/cmdline/databases.py

@@ -34,31 +34,30 @@
 ###################################################################################
 
 
-import os
-import click
 import glob
-import random
-import zmq
 import logging
+import os
+import random
+
+import click
 import simplejson
+import zmq
 
-from beat.core.hash import toPath
-from beat.core.hash import hashDataset
-from beat.core.utils import NumpyJSONEncoder
-from beat.core.database import Database
-from beat.core.data import RemoteDataSource
 from beat.core import dock
 from beat.core import inputs
 from beat.core import utils
+from beat.core.data import RemoteDataSource
+from beat.core.database import Database
+from beat.core.hash import hashDataset
+from beat.core.hash import toPath
+from beat.core.utils import NumpyJSONEncoder
 
-from . import common
 from . import commands
-
-from .decorators import raise_on_error
+from . import common
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
-
+from .decorators import raise_on_error
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/dataformats.py

@@ -35,17 +35,17 @@
 
 
 import logging
+
 import click
 
 from beat.core import dataformat
 
-from . import common
 from . import commands
-
-from .decorators import raise_on_error
+from . import common
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
+from .decorators import raise_on_error
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/decorators.py

@@ -34,9 +34,11 @@
 
 
 import logging
-import click
 
 from functools import wraps
+
+import click
+
 from .log import set_verbosity_level
 
 # This needs to be beat so that logger is configured for all beat packages.

beat/cmdline/environments.py

@@ -34,17 +34,16 @@
 ###################################################################################
 
 
-import click
 import logging
+
+import click
 import simplejson as json
 
 from beat.core.dock import Host
 
 from . import common
-
 from .click_helper import AliasedGroup
 
-
 logger = logging.getLogger(__name__)
 
 

beat/cmdline/libraries.py

@@ -74,18 +74,17 @@ Options:
 """
 
 import logging
+
 import click
 
 from beat.core import library
 
-from . import common
 from . import commands
-
-from .decorators import raise_on_error
+from . import common
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
-
+from .decorators import raise_on_error
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/log.py

@@ -5,6 +5,7 @@
 
 import logging
 
+
 def set_verbosity_level(logger, level):
     """Sets the log level for the given logger.
 
@@ -30,7 +31,7 @@ def set_verbosity_level(logger, level):
         0: logging.ERROR,
         1: logging.WARNING,
         2: logging.INFO,
-        3: logging.DEBUG
+        3: logging.DEBUG,
     }[level]
 
     # set this log level to the logger with the specified name

beat/cmdline/plotterparameters.py

@@ -36,13 +36,12 @@
 
 import click
 
-from . import common
 from . import commands
-
-from .decorators import raise_on_error
+from . import common
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
+from .decorators import raise_on_error
 
 
 def pull_impl(webapi, prefix, names, force, indentation, format_cache):

beat/cmdline/plotters.py

@@ -34,31 +34,30 @@
 ###################################################################################
 
 
+import collections
 import io
+import logging
 import os
 import sys
+
 import click
-import logging
 import simplejson
-import collections
 
 from PIL import Image
 
-from beat.core import plotter
 from beat.core import dataformat
+from beat.core import plotter
 from beat.core.plotterparameter import Storage as PPStorage
 
-from . import common
 from . import commands
-
-from .dataformats import pull_impl as dataformats_pull
-from .plotterparameters import pull_impl as plotterparameters_pull
-from .libraries import pull_impl as libraries_pull
-from .decorators import raise_on_error
+from . import common
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
-
+from .dataformats import pull_impl as dataformats_pull
+from .decorators import raise_on_error
+from .libraries import pull_impl as libraries_pull
+from .plotterparameters import pull_impl as plotterparameters_pull
 
 logger = logging.getLogger(__name__)
 

beat/cmdline/protocoltemplates.py

@@ -34,16 +34,15 @@
 ###################################################################################
 
 
-import click
 import logging
 
-from . import commands
+import click
 
+from . import commands
 from .click_helper import AliasedGroup
 from .click_helper import AssetCommand
 from .click_helper import AssetInfo
 
-
 logger = logging.getLogger(__name__)
 
 

beat/cmdline/scripts/__init__.py

 #!/usr/bin/env python
 # vim: set fileencoding=utf-8 :
-

beat/cmdline/scripts/main_cli.py

@@ -2,12 +2,15 @@
 """
 
 import logging
-import pkg_resources
+
 import click
+import pkg_resources
+
 from click_plugins import with_plugins
+
 from ..click_helper import AliasedGroup
-from ..decorators import verbosity_option
 from ..config import Configuration
+from ..decorators import verbosity_option
 
 # defines our own logging level for extra information to be printed
 logging.EXTRA = 15

beat/cmdline/status.py

@@ -51,10 +51,10 @@ from .decorators import raise_on_error
 @raise_on_error
 def status(ctx):
     """Shows the working folder status for different objects"""
-    path = ctx.meta['config'].path
-    with common.make_webapi(ctx.meta['config']) as webapi:
-        retval = common.status(webapi, path, 'dataformat')[0]
-        retval += common.status(webapi, path, 'algorithm')[0]
-        retval += common.status(webapi, path, 'toolchain')[0]