databases.py 20.6 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 databases list [--remote]
  %(prog)s databases check [<name>]...
  %(prog)s databases pull [--force] [<name>]...
  %(prog)s databases push [--force] [--dry-run] [<name>]...
  %(prog)s databases diff <name>
  %(prog)s databases status
  %(prog)s databases version <name>
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  %(prog)s databases index [--list | --delete | --checksum] [--uid=<uid>] [--db-root=<path>] [<name>]...
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  %(prog)s databases view [--exclude=<output>] <set_name>
  %(prog)s databases --help


Arguments:
  <name>           Database name formated as "<database>/<version>"
  <set_name>       Set formatted as "<database>/<version>/<protocol>/<set>"


Commands:
  list      Lists all the databases available on the platform
  check     Checks a local database for validity
  pull      Downloads the specified databases from the server
  push      Uploads databases to the server (must provide a valid admin token)
  diff      Shows changes between the local database and the remote version
  status    Shows (editing) status for all available databases
  version   Creates a new version of an existing database
  index     Indexes all outputs (of all sets) of a database.
  view      View the data of the specified dataset.


Options:
  --help              Display this screen
  --remote            Only acts on the remote copy of the database
  --exclude=<output>  When viewing, excludes this output
  --list              List index files matching output if they exist
  --delete            Delete index files matching output if they exist (also,
                      recursively deletes empty directories)
  --checksum          Checksums index files


Examples:

  To list all existing databases on your local prefix:

    $ %(prog)s db list

  To view the contents of a specific set

    $ %(prog)s db view simple/1/protocol/set

  To index the contents of a database

    $ %(prog)s db index simple/1

  To index the contents of a protocol on a database

    $ %(prog)s db index simple/1/double

  To index the contents of a set in a protocol on a database

    $ %(prog)s db index simple/1/double/double
"""

import os
import glob
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import zmq.green as zmq

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import logging
logger = logging.getLogger()

import simplejson

from beat.core.hash import hash, toPath, hashFileContents
from beat.core.utils import NumpyJSONEncoder
from beat.core.database import Database
from beat.core.dataformat import DataFormat
from beat.core.data import load_data_index
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from beat.core import dock
from beat.core import inputs
from beat.core import utils
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from . import common


def pull(webapi, prefix, names, force, indentation, format_cache):
  """Copies databases (and required 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

    names (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.

    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.


  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

  status, names = common.pull(webapi, prefix, 'database', names,
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                              ['declaration', 'code', 'description'], force, indentation)
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  # see what dataformats one needs to pull
  indent = indentation * ' '

  dataformats = []
  for name in names:
    obj = Database(prefix, name)
    dataformats.extend(obj.dataformats.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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  return status + df_status


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def index_output(configuration, names, ls, delete, checksum, uid, db_root):
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  names = common.make_up_local_list(configuration.path, 'database', names)

  retcode = 0

  for database_name in names:

    parts = database_name.split('/')

    if len(parts) == 2:
      db_name         = os.path.join(*parts[:2])
      protocol_filter = None
      set_filter      = None
      if ls:
        logger.info("Listing database %s indexes...", database_name)
      elif delete:
        logger.info("Deleting database %s indexes...", database_name)
      elif checksum:
        logger.info("Checksumming database %s indexes...", database_name)
      else:
        logger.info("Indexing database %s...", database_name)

    elif len(parts) == 3:
      db_name         = os.path.join(*parts[:2])
      protocol_filter = parts[2]
      set_filter      = None
      if ls:
        logger.info("Listing database protocol %s indexes...", database_name)
      elif delete:
        logger.info("Deleting database protocol %s indexes...", database_name)
      elif checksum:
        logger.info("Checksumming database protocol %s indexes...",
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                    database_name)
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      else:
        logger.info("Indexing database protocol %s...", database_name)

    elif len(parts) == 4:
      db_name         = os.path.join(*parts[:2])
      protocol_filter = parts[2]
      set_filter      = parts[3]
      if ls:
        logger.info("Listing database set %s indexes...", database_name)
      elif delete:
        logger.info("Deleting database set %s indexes...", database_name)
      elif checksum:
        logger.info("Checksumming database set %s indexes...", database_name)
      else:
        logger.info("Indexing database set %s...", database_name)

    else:
      logger.error("Database specification should have the format " \
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                   "`<database>/<version>/[<protocol>/[<set>]]', the value you " \
                   "passed (%s) is not valid", (dataset_name))
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      retcode += 1
      continue

    dataformat_cache = {}
    database = Database(configuration.path, db_name, dataformat_cache)
    if not database.valid:
      logger.error("Failed to load the database `%s':", db_name)
      for e in database.errors: logger.error('  * %s', e)
      retcode += 1
      continue

    protocols = database.protocol_names

    if protocol_filter is not None:

      if protocol_filter not in protocols:
        logger.error("The database `%s' does not have the protocol `%s' - " \
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                     "choose one of `%s'", db_name, protocol_filter,
                     ', '.join(protocols))
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        retcode += 1
        continue

      protocols = [protocol_filter]

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    if not (ls or delete or checksum): #we're indexing
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      host = dock.Host(raise_on_errors=False)
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    for protocol_name in protocols:

      sets = database.set_names(protocol_name)

      if set_filter is not None:
        if set_filter not in sets:
          logger.error("The database/protocol `%s/%s' does not have the " \
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                       "set `%s' - choose one of `%s'", db_name, protocol_name,
                       set_filter, ', '.join(sets))
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          retcode += 1
          continue

        sets = [z for z in sets if z == set_filter]

      for set_name in sets:

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        db_set = database.set(protocol_name, set_name)
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        if not (ls or delete or checksum): #we're indexing
          zmq_context = zmq.Context()
          db_socket = zmq_context.socket(zmq.PAIR)
          db_address = 'tcp://' + host.ip
          port = db_socket.bind_to_random_port(db_address)
          db_address += ':%d' % port
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          input_list = inputs.InputList()
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          input_group = inputs.InputGroup(set_name, restricted_access=False)
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          input_list.add(input_group)
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          db_configuration = {
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            'inputs': {},
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            'channel': set_name,
          }
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          if uid is not None:
            db_configuration['datasets_uid'] = uid
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          if db_root is not None:
            db_configuration['datasets_root_path'] = db_root
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          for output_name, dataformat_name in db_set['outputs'].items():
            input = inputs.RemoteInput(output_name, database.dataformats[dataformat_name], db_socket)
            input_group.add(input)
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            db_configuration['inputs'][output_name] = dict(
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              database=db_name,
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              protocol=protocol_name,
              set=set_name,
              output=output_name,
              channel=set_name
            )
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          db_tempdir = utils.temporary_directory()
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          with open(os.path.join(db_tempdir, 'configuration.json'), 'wb') as f:
            simplejson.dump(db_configuration, f, indent=4)
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          tmp_prefix = os.path.join(db_tempdir, 'prefix')
          if not os.path.exists(tmp_prefix):
            os.makedirs(tmp_prefix)
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          database.export(tmp_prefix)
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          if db_root is None:
            json_path = os.path.join(tmp_prefix, 'databases', db_name + '.json')
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            with open(json_path, 'r') as f:
              db_data = simplejson.load(f)
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            database_path = db_data['root_folder']
            db_data['root_folder'] = os.path.join('/databases', db_name)
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            with open(json_path, 'w') as f:
              simplejson.dump(db_data, f, indent=4)

          try:
            db_envkey = host.db2docker([db_name])
          except:
            raise RuntimeError("No environment found for the database `%s' " \
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                               "- available environments are %s" % (
                                   db_name,
                                   ", ".join(host.db_environments.keys())))
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          # Creation of the container
          # Note: we only support one databases image loaded at the same time
          db_cmd = [
            'databases_provider',
            db_address,
            os.path.join('/tmp', os.path.basename(db_tempdir))
          ]

          databases_container = host.create_container(db_envkey, db_cmd)
          databases_container.copy_path(db_tempdir, '/tmp')

          # Specify the volumes to mount inside the container
          if not db_configuration.has_key('datasets_root_path'):
              databases_container.add_volume(database_path, os.path.join('/databases', db_name))
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          else:
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              databases_container.add_volume(db_configuration['datasets_root_path'],
                                             db_configuration['datasets_root_path'])

          # Start the container
          host.start(databases_container)
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        index_filenames = []
        previous_data_indices = []

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        for output_name in db_set['outputs'].keys():
          index_hash = database.hash_output(protocol_name, set_name, output_name)
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          index_filename = os.path.join(configuration.cache,
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                                        toPath(index_hash, '.index'))
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          if ls:
            basename = os.path.splitext(index_filename)[0]
            for g in glob.glob(basename + '.*'): logger.info(g)

          elif delete:

            basename = os.path.splitext(index_filename)[0]
            for g in glob.glob(basename + '.*'):
              logger.info("removing `%s'...", g)
              os.unlink(g)
            common.recursive_rmdir_if_empty(os.path.dirname(basename),
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                                            configuration.cache)
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          elif checksum:
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            assert load_data_index(configuration.cache, toPath(index_hash, '.index'))
            logger.info("index for `%s' can be loaded and checksumed",
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                        index_filename)
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          else:

            index_filenames.append(index_filename)
            previous_data_indices.append(None)

            logger.info("Indexing database `%s', protocol `%s', set `%s', " \
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                        "output `%s' -> `%s'", db_name, protocol_name, set_name,
                        output_name, index_filename)
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            if os.path.exists(index_filename):
              logger.extra("Overwriting existing index file `%s'",
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                           index_filename)
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              os.remove(index_filename)

            index_dir = os.path.dirname(index_filename)
            if not os.path.exists(index_dir):
              logger.extra("Creating directory `%s'", index_dir)
              os.makedirs(index_dir)

            # Create empty lock file to indicate that this cache file *must*
            # not be cleaned
            lock_filename = os.path.join(configuration.cache,
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                                         toPath(index_hash, '.lock'))
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            with open(lock_filename, 'a'): os.utime(lock_filename, None)

        if not (ls or delete or checksum): #we're indexing
          try:

            while input_group.hasMoreData():

              input_group.next()

              for i, (input, index_filename, previous_data_index) in \
                      enumerate(zip(input_group, index_filenames,
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                                    previous_data_indices)):
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                with open(index_filename, 'at') as indexfile:
                  if input.data_index != previous_data_index:
                    indexfile.write("%d %d\n" % (
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                        input.data_index,
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                      input.data_index_end,
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                    )
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                    )
                  previous_data_indices[i] = input.data_index

                # creates the checksums for all indexes
                chksum = hashFileContents(index_filename)
                with open(index_filename + '.checksum', 'wt') as f:
                  f.write(chksum)

          except Exception as e:
            logger.critical("Failed to retrieve the next data: %s", e)
            retcode += 1
            continue

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        if not (ls or delete or checksum): #we're indexing
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          host.kill(databases_container)
          host.wait(databases_container)
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          db_socket.setsockopt(zmq.LINGER, 0)
          db_socket.close()
          zmq_context.term()
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  return retcode


def view_output(configuration, dataset_name, excluded_outputs=''):

  parts = dataset_name.split('/')

  if len(parts) == 4:
    db_name       = os.path.join(*parts[:2])
    protocol_name = parts[2]
    set_name      = parts[3]
  else:
    logger.error("Database view specification should have the format " \
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                 "`<database>/<version>/<protocol>/<set>', the value you " \
                 "passed (%s) is not valid", dataset_name)
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    return 1

  excluded_outputs = map(lambda x: x.strip(), excluded_outputs.split(','))

  dataformat_cache = {}
  database = Database(configuration.path, db_name, dataformat_cache)
  if not database.valid:
    logger.error("Failed to load the database `%s':", db_name)
    for e in database.errors: logger.error('  * %s', e)
    return 1

  if protocol_name not in database.protocol_names:
    logger.error("Unknown protocol `%s' for database `%s'. Valid protocols " \
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                 "are `%s'", protocol_name, db_name,
                 ', '.join(database.protocol_names))
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    return 1

  if set_name not in database.set_names(protocol_name):
    set_names = database.set_names(protocol_name)
    logger.error("Unknown set `%s' for database `%s' and protocol `%s'. " \
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                 "Valid set names for this protocol are `%s'", set_name, db_name,
                 protocol_name, ', '.join(set_names))
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    return 1

  view = database.view(protocol_name, set_name)

  try:
    view.prepare_outputs()
    view.setup()
  except Exception:
    logger.error("Failed to setup the set `%s/%s/%s'", db_name, protocol_name,
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                 set_name)
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    import traceback
    for e in traceback.format_exc().split('\n'): logger.error('  %s', e)
    return 1

  # Setup the inputs
  input_group = view.input_group(exclude_outputs=excluded_outputs)

  # Display the data
  while input_group.hasMoreData():

    try:
      input_group.next()
    except Exception as e:
      logger.error("Failed to retrieve the next data: %s", e)
      return 1

    logger.extra(80 * '-')

    for input in input_group:
      header = str(input.name)
      if input.data_index == input.data_index_end:
        header += '[%d]' % input.data_index
      else:
        header += '[%d:%d]' % (input.data_index, input.data_index_end)
      header += ": "

      json_data = input.data.as_dict()
      for name, value in json_data.items():
        json_data[name] = common.stringify(value)
        json_data_ = simplejson.dumps(json_data[name], indent=2,
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                                      cls=NumpyJSONEncoder).\
            replace('"BEAT_LIST_DELIMITER[', '[')\
            .replace(']BEAT_LIST_DELIMITER"', ']')\
            .replace('"...",', '...')\
            .replace('"BEAT_LIST_SIZE(', '(')\
            .replace(')BEAT_LIST_SIZE"', ')')
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        print(header + json_data_)

  return 0


def process(args):

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

  elif args['check']:
    return common.check(args['config'].path, 'database', 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, 'database',
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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, 'database',
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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, 'database')[0]

  elif args['version']:
    return common.new_version(args['config'].path, 'database',
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                              args['<name>'][0])
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  elif args['view']:
    if args['--exclude']:
      return view_output(args['config'], args['<set_name>'], args['--exclude'])
    else:
      return view_output(args['config'], args['<set_name>'])

  elif args['index']:
    return index_output(args['config'], args['<name>'], args['--list'],
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                        args['--delete'], args['--checksum'],
                        int(args['--uid']) if args['--uid'] is not None else None,
                        args['--db-root'])
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  # Should not happen
  logger.error("unrecognized `databases' subcommand")
  return 1