algorithms.py 14.3 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/.           #
#                                                                             #
###############################################################################

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import click
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import logging
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import os
import sys
import docopt
import simplejson as json

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from . import common

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from .click_helper import AliasedGroup
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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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logger = logging.getLogger(__name__)
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def pull_impl(webapi, prefix, names, force, indentation, format_cache, lib_cache):
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  """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).

  """

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  from .dataformats import pull_impl as dataformats_pull
  from .libraries import pull_impl as libraries_pull
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  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_impl(prefix, cache, instructions_file):
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  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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@click.group(cls=AliasedGroup)
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@click.pass_context
def algorithms(ctx):
    """Configuration and manipulation of algorithms"""
    pass

@algorithms.command()
@click.option('--remote', help='Only acts on the remote copy of the algorithm',
              is_flag=True)
@click.pass_context
def list(ctx, remote):
  '''Lists all the algorithms available on the platform

  Example:
    $ beat algorithms list --remote
  '''
  if remote:
    with common.make_webapi(ctx.meta['config']) as webapi:
      return common.display_remote_list(webapi, 'algorithm')
  else:
    return common.display_local_list(ctx.meta['config'].path, 'algorithm')

@algorithms.command()
@click.argument('names', nargs=-1)
@click.pass_context
def path(ctx, names):
  '''Displays local path of algorithm files
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  Example:
    $ beat algorithms path xxx
  '''
  return common.display_local_path(ctx.meta['config'].path, 'algorithm', names)


@algorithms.command()
@click.argument('name', nargs=1)
@click.pass_context
def edit(ctx, name):
  '''Edit local algorithm file
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  Example:
    $ beat algorithms edit xxx
  '''
  return common.edit_local_file(ctx.meta['config'].path,
                                ctx.meta['config'].editor, 'algorithm',
                                name)
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@algorithms.command()
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@click.argument('name', nargs=-1)
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@click.pass_context
def check(ctx, name):
  '''Checks a local algorithm for validity
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  Example:
    $ beat algorithms check xxx
  '''
  return common.check(ctx.meta['config'].path, 'algorithm', name)
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@algorithms.command()
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@click.argument('name', nargs=-1)
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@click.option('--force', help='Performs operation regardless of conflicts',
              is_flag=True)
@click.pass_context
def pull(ctx, name, force):
  '''Downloads the specified algorithms from the server
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  Example:
    $ beat algorithms pull --force yyy
  '''
  with common.make_webapi(ctx.meta['config']) as webapi:
    return pull_impl(webapi, ctx.meta['config'].path, name, force, 0, {}, {})
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@algorithms.command()
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@click.argument('name', nargs=-1)
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@click.option('--force', help='Performs operation regardless of conflicts',
              is_flag=True)
@click.option('--dry-run', help="Doesn't really perform the task, just "
              "comments what would do", is_flag=True)
@click.pass_context
def push(ctx, name, force, dry_run):
  '''Uploads algorithms to the server
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  Example:
    $ beat algorithms push --dry-run yyy
  '''
  with common.make_webapi(ctx.meta['config']) as webapi:
    return common.push(webapi, ctx.meta['config'].path, 'algorithm',
                       name, ['name', 'declaration', 'code', 'description'],
                       {}, force, dry_run, 0)
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@algorithms.command()
@click.argument('name', nargs=1)
@click.pass_context
def diff(ctx, name):
  '''Shows changes between the local algorithm and the remote version

  Example:
    $ beat algorithms diff xxx
  '''
  with common.make_webapi(ctx.meta['config']) as webapi:
    return common.diff(webapi, ctx.meta['config'].path, 'algorithm',
                       name, ['declaration', 'code', 'description'])



@algorithms.command()
@click.pass_context
def status(ctx):
  '''Shows (editing) status for all available algorithms

  Example:
    $ beat algorithms status
  '''
  with common.make_webapi(ctx.meta['config']) as webapi:
    return common.status(webapi, ctx.meta['config'].path, 'algorithm')[0]



@algorithms.command()
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@click.argument('name', nargs=-1)
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@click.pass_context
def create(ctx, name):
  '''Creates a new local algorithm

  Example:
    $ beat algorithms create xxx
  '''
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  return common.create(ctx.meta['config'].path, 'algorithm', name)
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@algorithms.command()
@click.argument('name', nargs=1)
@click.pass_context
def version(ctx, name):
  '''Creates a new version of an existing algorithm

  Example:
    $ beat algorithms version xxx
  '''
  return common.new_version(ctx.meta['config'].path, 'algorithm', name)



@algorithms.command()
@click.argument('src', nargs=1)
@click.argument('dst', nargs=1)
@click.pass_context
def fork(ctx, src, dst):
  '''Forks a local algorithm

  Example:
      $ beat algorithms fork xxx yyy
  '''
  return common.fork(ctx.meta['config'].path, 'algorithm', src, dst)



@algorithms.command()
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@click.argument('name', nargs=-1)
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@click.option('--remote', help='Only acts on the remote copy of the algorithm',
              is_flag=True)
@click.pass_context
def rm(ctx, name, remote):
  '''Deletes a local algorithm (unless --remote is specified)

  Example:
      $ beat algorithms rm xxx
  '''
  if remote:
    with common.make_webapi(ctx.meta['config']) as webapi:
      return common.delete_remote(webapi, 'algorithm', name)
  else:
    return common.delete_local(ctx.meta['config'].path, 'algorithm', name)



@algorithms.command()
@click.argument('instructions', nargs=-1)
@click.option('--example', help='Display some example JSON instruction files',
              is_flag=True)
@click.pass_context
def execute(ctx, instructions, example):
  '''Execute an algorithm following instructions in a JSON file

  Example:
    $ beat algorithms execute <instructions>
    $ beat algorithms execute --examples
  '''
  if example:
    print_examples()
    return 0

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  return execute_impl(ctx.meta['config'].path, ctx.meta['config'].cache,
                      instructions)