algorithms.py 13.1 KB
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#!/usr/bin/env python
# vim: set fileencoding=utf-8 :

###############################################################################
#                                                                             #
# Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/           #
# Contact: beat.support@idiap.ch                                              #
#                                                                             #
# This file is part of the beat.cmdline module of the BEAT platform.          #
#                                                                             #
# Commercial License Usage                                                    #
# Licensees holding valid commercial BEAT licenses may use this file in       #
# accordance with the terms contained in a written agreement between you      #
# and Idiap. For further information contact tto@idiap.ch                     #
#                                                                             #
# Alternatively, this file may be used under the terms of the GNU Affero      #
# Public License version 3 as published by the Free Software and appearing    #
# in the file LICENSE.AGPL included in the packaging of this file.            #
# The BEAT platform is distributed in the hope that it will be useful, but    #
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  #
# or FITNESS FOR A PARTICULAR PURPOSE.                                        #
#                                                                             #
# You should have received a copy of the GNU Affero Public License along      #
# with the BEAT platform. If not, see http://www.gnu.org/licenses/.           #
#                                                                             #
###############################################################################


"""Usage:
  %(prog)s algorithms list [--remote]
  %(prog)s algorithms check [<name>]...
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  %(prog)s algorithms path [<name>]...
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  %(prog)s algorithms pull [--force] [<name>]...
  %(prog)s algorithms push [--force] [--dry-run] [<name>]...
  %(prog)s algorithms diff <name>
  %(prog)s algorithms status
  %(prog)s algorithms create <name>...
  %(prog)s algorithms version <name>
  %(prog)s algorithms fork <src> <dst>
  %(prog)s algorithms rm [--remote] <name>...
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  %(prog)s algorithms execute <instructions>
  %(prog)s algorithms execute --examples
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  %(prog)s algorithms --help


Commands:
  list      Lists all the algorithms available on the platform
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  path      Displays local path of algorithm files
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  check     Checks a local algorithm for validity
  pull      Downloads the specified algorithms from the server
  push      Uploads algorithms to the server
  diff      Shows changes between the local algorithm and the remote version
  status    Shows (editing) status for all available algorithms
  create    Creates a new local algorithm
  version   Creates a new version of an existing algorithm
  fork      Forks a local algorithm
  rm        Deletes a local algorithm (unless --remote is specified)
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  execute   Execute an algorithm following instructions in a JSON file
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Options:
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  --force     Performs operation regardless of conflicts
  --dry-run   Doesn't really perform the task, just comments what would do
  --remote    Only acts on the remote copy of the algorithm
  --examples  Display some example JSON instruction files
  --help      Display this screen


Arguments for 'execute':
  <instructions>  JSON file containing the instructions
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Examples:

  To list all algorithms available locally:

    $ %(prog)s al list

  To list all algorithms available at the platform:

    $ %(prog)s al list --remote

"""

import logging
logger = logging.getLogger(__name__)

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import os
import sys
import docopt
import simplejson as json

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from . import common

from beat.core import algorithm
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from beat.core.execution import DockerExecutor
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from beat.core.dock import Host
from beat.core import hash

from beat.backend.python.database import Storage as DatabaseStorage
from beat.backend.python.algorithm import Storage as AlgorithmStorage

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def pull(webapi, prefix, names, force, indentation, format_cache, lib_cache):
  """Copies algorithms (and required libraries/dataformats) from the server.

  Parameters:

    webapi (object): An instance of our WebAPI class, prepared to access the
      BEAT server of interest

    prefix (str): A string representing the root of the path in which the user
      objects are stored

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    names (:py:class:`list`): A list of strings, each representing the unique
      relative path of the objects to retrieve or a list of usernames from
      which to retrieve objects. If the list is empty, then we pull all
      available objects of a given type. If no user is set, then pull all
      public objects of a given type.
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    force (bool): If set to ``True``, then overwrites local changes with the
      remotely retrieved copies.

    indentation (int): The indentation level, useful if this function is called
      recursively while downloading different object types. This is normally
      set to ``0`` (zero).

    format_cache (dict): A dictionary containing all dataformats already
      downloaded.

    lib_cache (dict): A dictionary containing all libraries already
      downloaded.


  Returns:

    int: Indicating the exit status of the command, to be reported back to the
      calling process. This value should be zero if everything works OK,
      otherwise, different than zero (POSIX compliance).

  """

  from .dataformats import pull as dataformats_pull
  from .libraries import pull as libraries_pull

  status, names = common.pull(webapi, prefix, 'algorithm', names,
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                              ['declaration', 'code', 'description'], force, indentation)
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  if status != 0: return status

  # see what dataformats one needs to pull
  indent = indentation * ' '

  dataformats = []
  libraries = []
  for name in names:
    obj = algorithm.Algorithm(prefix, name)
    dataformats.extend(obj.dataformats.keys())
    libraries.extend(obj.libraries.keys())

  # downloads any formats to which we depend on
  df_status = dataformats_pull(webapi, prefix, dataformats, force,
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                               indentation + 2, format_cache)
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  lib_status = libraries_pull(webapi, prefix, libraries, force,
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                              indentation + 2, lib_cache)
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  return status + df_status + lib_status


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def print_examples():
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    print("""
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To feed data from a database to an algorithm:
=============================================

{
    "algorithm": "<username>/<algorithm>/<version>",
    "channel": "main",
    "inputs": {
        "<input_name>": {
            "database": "<database>/<version>",
            "protocol": "<protocol>",
            "set": "<set>",
            "output": "<output_name>",
            "channel": "main"
        }
    },
    "outputs": {
        "<output_name>": {
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          "channel": "main"
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        }
    },
    "parameters": {
      "<parameter_name>": <value>
    },
    "environment": {
        "name": "<environment_name>",
        "version": "<environment_version>"
    }
}


To feed data from a file in the cache:
======================================

{
    "algorithm": "<username>/<algorithm>/<version>",
    "channel": "main",
    "inputs": {
        "<input_name>": {
            "hash": "<hash>",
            "channel": "main"
        }
    },
    "outputs": {
        "<output_name>": {
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          "channel": "main"
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        }
    },
    "parameters": {
      "<parameter_name>": <value>
    },
    "environment": {
        "name": "<environment_name>",
        "version": "<environment_version>"
    }
}


To execute an analyzer:
=======================

{
    "algorithm": "<username>/<algorithm>/<version>",
    "channel": "main",
    "inputs": {
        "<input_name>": {
            "hash": "<hash>",
            "channel": "main"
        }
    },
    "parameters": {
      "<parameter_name>": <value>
    },
    "environment": {
        "name": "<environment_name>",
        "version": "<environment_version>"
    }
}
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""")
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def execute(prefix, cache, instructions_file):
  try:
    # Load the JSON configuration
    if not os.path.exists(instructions_file):
      raise IOError("JSON instructions file `%s' not found" % instructions_file)

    with open(instructions_file, 'r') as f:
      configuration = json.load(f)

    # Add missing configuration fields
    configuration['queue'] = 'unused'
    configuration['nb_slots'] = 1

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    if 'parameters' not in configuration:
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      configuration['parameters'] = {}

    for name, cfg in configuration['inputs'].items():
      cfg['endpoint'] = name
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      suffix = ''
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      if 'database' in cfg:   # Connected to a database output
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        cfg['hash'] = hash.hashDataset(cfg['database'], cfg['protocol'], cfg['set'])
        suffix = '.db'

      cfg['path'] = hash.toPath(cfg['hash'], suffix=suffix)
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    algo = AlgorithmStorage(prefix, configuration['algorithm'])

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    if 'outputs' in  configuration:   # Standard algorithm
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      for name, cfg in configuration['outputs'].items():
          cfg['endpoint'] = name
          cfg['hash'] = hash.hashBlockOutput(
              'block',
              configuration['algorithm'],
              algo.hash(),
              configuration['parameters'],
              configuration['environment'],
              dict([(k, v['hash']) for k, v in configuration['inputs'].items()]),
              name,
          )
          cfg['path'] = hash.toPath(cfg['hash'], '')

    else:   # Analyzer
      configuration['result'] = {}
      configuration['result']['hash'] = hash.hashAnalyzer(
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          'block',
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              configuration['algorithm'],
              algo.hash(),
              configuration['parameters'],
              configuration['environment'],
              dict([(k, v['hash']) for k, v in configuration['inputs'].items()]),
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      )
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      configuration['result']['path'] = hash.toPath(configuration['result']['hash'], '')

    # Sets up the execution
    dataformat_cache = {}
    database_cache = {}
    algorithm_cache = {}

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    host = Host(raise_on_errors=False)
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    executor = DockerExecutor(host, prefix, configuration, cache, dataformat_cache,
                              database_cache, algorithm_cache)
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    if not executor.valid:
      logger.error('Invalid configuration:\n  * %s' % '\n  * '.join(executor.errors))
      return 1

    # Execute the algorithm
    with executor:
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      result = executor.process()
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      if result['status'] != 0:
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          print('STDERR:')
          print(result['stderr'])
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    # Display the results
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    if 'outputs' in configuration:   # Standard algorithm
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      print('Outputs of the algorithms available at:')
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      for name, cfg in configuration['outputs'].items():
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        print('  - %s: %s' % (name, cfg['path']))
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    else:
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      print('Results of the analyzer available at: %s' % configuration['result']['path'])
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  except Exception as e:
    import traceback
    logger.error(traceback.format_exc())
    return 1

  return 0



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def process(args):

  if args['list']:
    if args['--remote']:
      with common.make_webapi(args['config']) as webapi:
        return common.display_remote_list(webapi, 'algorithm')
    else:
      return common.display_local_list(args['config'].path, 'algorithm')

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  elif args['path']:
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    return common.display_local_path(args['config'].path, 'algorithm', args['<name>'])

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  elif args['check']:
    return common.check(args['config'].path, 'algorithm', args['<name>'])

  elif args['pull']:
    with common.make_webapi(args['config']) as webapi:
      return pull(webapi, args['config'].path, args['<name>'],
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                  args['--force'], 0, {}, {})
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  elif args['push']:
    with common.make_webapi(args['config']) as webapi:
      return common.push(webapi, args['config'].path, 'algorithm',
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                         args['<name>'], ['name', 'declaration', 'code', 'description'],
                         {}, args['--force'], args['--dry-run'], 0)
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  elif args['diff']:
    with common.make_webapi(args['config']) as webapi:
      return common.diff(webapi, args['config'].path, 'algorithm',
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                         args['<name>'][0], ['declaration', 'code', 'description'])
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  elif args['status']:
    with common.make_webapi(args['config']) as webapi:
      return common.status(webapi, args['config'].path, 'algorithm')[0]

  elif args['create']:
    return common.create(args['config'].path, 'algorithm', args['<name>'])

  elif args['version']:
    return common.new_version(args['config'].path, 'algorithm',
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                              args['<name>'][0])
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  elif args['fork']:
    return common.fork(args['config'].path, 'algorithm',
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                       args['<src>'], args['<dst>'])
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  elif args['execute']:
    if args['--examples']:
      print_examples()
      return 0

    return execute(args['config'].path, args['config'].cache, args['<instructions>'])

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  elif args['rm']:
    if args['--remote']:
      with common.make_webapi(args['config']) as webapi:
        return common.delete_remote(webapi, 'algorithm', args['<name>'])
    else:
      return common.delete_local(args['config'].path, 'algorithm',
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                                 args['<name>'])
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  # Should not happen
  logger.error("unrecognized `algorithms' subcommand")
  return 1