databases.py 25.1 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 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>] [--docker] [<name>]...
  %(prog)s databases view [--exclude=<output>] [--uid=<uid>] [--db-root=<path>] [--docker] <set_name>
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  %(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
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import logging
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logger = logging.getLogger(__name__)
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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


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#----------------------------------------------------------


def load_database_sets(configuration, database_name):
    # Process the name of the database
    parts = database_name.split('/')

    if len(parts) == 2:
      db_name         = os.path.join(*parts[:2])
      protocol_filter = None
      set_filter      = None

    elif len(parts) == 3:
      db_name         = os.path.join(*parts[:2])
      protocol_filter = parts[2]
      set_filter      = None

    elif len(parts) == 4:
      db_name         = os.path.join(*parts[:2])
      protocol_filter = parts[2]
      set_filter      = parts[3]

    else:
      logger.error("Database specification should have the format " \
                   "`<database>/<version>/[<protocol>/[<set>]]', the value you " \
                   "passed (%s) is not valid", (dataset_name))
      return (None, None)


    # Load the dataformat
    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 (None, None, None)


    # Filter the protocols
    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' - " \
                     "choose one of `%s'", db_name, protocol_filter,
                     ', '.join(protocols))

        return (None, None, None)

      protocols = [protocol_filter]


    # Filter the sets
    loaded_sets = []

    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 " \
                       "set `%s' - choose one of `%s'", db_name, protocol_name,
                       set_filter, ', '.join(sets))
          return (None, None, None)

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

      loaded_sets.extend([ (protocol_name, set_name, database.set(protocol_name, set_name))
                          for set_name in sets ])

    return (db_name, database, loaded_sets)


#----------------------------------------------------------


def start_db_container(host, db_name, protocol_name, set_name, database, db_set,
                       excluded_outputs=None, uid=None, db_root=None):

    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

    input_list = inputs.InputList()

    input_group = inputs.InputGroup(set_name, restricted_access=False)
    input_list.add(input_group)

    db_configuration = {
        'inputs': {},
        'channel': set_name,
    }

    if uid is not None:
        db_configuration['datasets_uid'] = uid

    if db_root is not None:
        db_configuration['datasets_root_path'] = db_root

    for output_name, dataformat_name in db_set['outputs'].items():
        if (excluded_outputs is not None) and (output_name in excluded_outputs):
            continue

        input = inputs.RemoteInput(output_name, database.dataformats[dataformat_name], db_socket)
        input_group.add(input)

        db_configuration['inputs'][output_name] = dict(
           database=db_name,
           protocol=protocol_name,
           set=set_name,
           output=output_name,
           channel=set_name
        )

    db_tempdir = utils.temporary_directory()

    with open(os.path.join(db_tempdir, 'configuration.json'), 'wb') as f:
        simplejson.dump(db_configuration, f, indent=4)

    tmp_prefix = os.path.join(db_tempdir, 'prefix')
    if not os.path.exists(tmp_prefix):
        os.makedirs(tmp_prefix)

    database.export(tmp_prefix)

    if db_root is None:
        json_path = os.path.join(tmp_prefix, 'databases', db_name + '.json')

        with open(json_path, 'r') as f:
            db_data = simplejson.load(f)

        database_path = db_data['root_folder']
        db_data['root_folder'] = os.path.join('/databases', db_name)

        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' " \
                           "- available environments are %s" % (
                               db_name,
                               ", ".join(host.db_environments.keys())))

    # 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))
    else:
        databases_container.add_volume(db_configuration['datasets_root_path'],
                                       db_configuration['datasets_root_path'])

    # Start the container
    host.start(databases_container)

    return (databases_container, db_socket, zmq_context, input_list)


#----------------------------------------------------------


def load_db_view(db_name, protocol_name, set_name, database, excluded_outputs=None):

    try:
        view = database.view(protocol_name, set_name)
        view.prepare_outputs()
        view.setup()
    except Exception:
        logger.error("Failed to setup the database set `%s/%s/%s'", db_name, protocol_name,
                     set_name)
        import traceback
        for e in traceback.format_exc().split('\n'):
            logger.error('  %s', e)
        return (None, None)

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    if excluded_outputs is None:
        excluded_outputs = []

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

    return (view, input_group)


#----------------------------------------------------------


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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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#----------------------------------------------------------
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def index_outputs(configuration, names, uid=None, db_root=None, docker=False):
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    names = common.make_up_local_list(configuration.path, 'database', names)
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    retcode = 0
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    if docker:
      host = dock.Host(raise_on_errors=False)
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    for database_name in names:
      logger.info("Indexing database %s...", database_name)
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      (db_name, database, sets) = load_database_sets(configuration, database_name)
      if database is None:
          retcode += 1
          continue
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      for protocol_name, set_name, db_set in sets:
        if not docker:
            (view, input_group) = load_db_view(db_name, protocol_name, set_name, database)
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            if view is None:
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                retcode += 1
                continue
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        else:
            (databases_container, db_socket, zmq_context, input_list) = \
                start_db_container(
                    host, db_name, protocol_name, set_name, database, db_set,
                    uid=uid, db_root=db_root
                )
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            input_group = input_list.group(set_name)
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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)
          index_filename = os.path.join(configuration.cache,
                                        toPath(index_hash, '.index'))
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          index_filenames.append(index_filename)
          previous_data_indices.append(None)

          logger.info("Indexing database `%s', protocol `%s', set `%s', " \
                      "output `%s' -> `%s'", db_name, protocol_name, set_name,
                      output_name, index_filename)

          if os.path.exists(index_filename):
            logger.extra("Overwriting existing index file `%s'",
                         index_filename)
            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,
                                       toPath(index_hash, '.lock'))
          with open(lock_filename, 'a'):
              os.utime(lock_filename, None)

        try:
          while input_group.hasMoreData():
            input_group.next()

            for i, (input, index_filename, previous_data_index) in \
                    enumerate(zip(input_group, index_filenames,
                                  previous_data_indices)):

              with open(index_filename, 'at') as indexfile:
                if input.data_index != previous_data_index:
                  indexfile.write("%d %d\n" % (input.data_index,
                                               input.data_index_end)
                  )
                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 docker:
          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
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#----------------------------------------------------------
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def list_index_files(configuration, names):
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    names = common.make_up_local_list(configuration.path, 'database', names)
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    retcode = 0
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    for database_name in names:
        logger.info("Listing database %s indexes...", database_name)
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        (db_name, database, sets) = load_database_sets(configuration, database_name)
        if database is None:
            retcode += 1
            continue
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        for protocol_name, set_name, db_set in sets:
            for output_name in db_set['outputs'].keys():
                index_hash = database.hash_output(protocol_name, set_name, output_name)
                index_filename = os.path.join(configuration.cache,
                                              toPath(index_hash, '.index'))
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                basename = os.path.splitext(index_filename)[0]
                for g in glob.glob(basename + '.*'):
                    logger.info(g)
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    return retcode
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#----------------------------------------------------------
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def delete_index_files(configuration, names):
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    names = common.make_up_local_list(configuration.path, 'database', names)
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    retcode = 0
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    for database_name in names:
        logger.info("Deleting database %s indexes...", database_name)
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        (db_name, database, sets) = load_database_sets(configuration, database_name)
        if database is None:
            retcode += 1
            continue
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        for protocol_name, set_name, db_set in sets:
            for output_name in db_set['outputs'].keys():
                index_hash = database.hash_output(protocol_name, set_name, output_name)
                index_filename = os.path.join(configuration.cache,
                                              toPath(index_hash, '.index'))
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                basename = os.path.splitext(index_filename)[0]
                for g in glob.glob(basename + '.*'):
                    logger.info("removing `%s'...", g)
                    os.unlink(g)
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                common.recursive_rmdir_if_empty(os.path.dirname(basename),
                                                configuration.cache)
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    return retcode
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#----------------------------------------------------------
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def checksum_index_files(configuration, names):
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    names = common.make_up_local_list(configuration.path, 'database', names)
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    retcode = 0
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    for database_name in names:
        logger.info("Checksumming database %s indexes...", database_name)
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        (db_name, database, sets) = load_database_sets(configuration, database_name)
        if database is None:
            retcode += 1
            continue
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        for protocol_name, set_name, db_set in sets:
            for output_name in db_set['outputs'].keys():
                index_hash = database.hash_output(protocol_name, set_name, output_name)
                index_filename = os.path.join(configuration.cache,
                                              toPath(index_hash, '.index'))
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                assert load_data_index(configuration.cache, toPath(index_hash, '.index'))
                logger.info("index for `%s' can be loaded and checksumed",
                            index_filename)
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    return retcode
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#----------------------------------------------------------
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def view_outputs(configuration, dataset_name, excluded_outputs=None, uid=None,
                 db_root=None, docker=False):
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    def data_to_json(data, indent):
        value = common.stringify(data.as_dict())
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        value = simplejson.dumps(value, indent=4, cls=NumpyJSONEncoder) \
            .replace('"BEAT_LIST_DELIMITER[', '[') \
            .replace(']BEAT_LIST_DELIMITER"', ']') \
            .replace('"...",', '...') \
            .replace('"BEAT_LIST_SIZE(', '(') \
            .replace(')BEAT_LIST_SIZE"', ')')
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        return ('\n' + ' ' * indent).join(value.split('\n'))
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    # Load the infos about the database set
    (db_name, database, sets) = load_database_sets(configuration, dataset_name)
    if (database is None) or (len(sets) != 1):
        return 1
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    (protocol_name, set_name, db_set) = sets[0]

    if excluded_outputs is not None:
        excluded_outputs = map(lambda x: x.strip(), excluded_outputs.split(','))
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    # Setup the view so the outputs can be used
    if not docker:
        (view, input_group) = load_db_view(db_name, protocol_name, set_name, database,
                                           excluded_outputs=excluded_outputs)
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        if view is None:
            return 1
    else:
        host = dock.Host(raise_on_errors=False)

        (databases_container, db_socket, zmq_context, input_list) = \
            start_db_container(
                host, db_name, protocol_name, set_name, database, db_set,
                excluded_outputs=excluded_outputs, uid=uid, db_root=db_root
            )
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        input_group = input_list.group(set_name)
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    # Display the data
    try:
        previous_start = -1
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        while input_group.hasMoreData():
            input_group.next()
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            start = input_group.data_index
            end = input_group.data_index_end
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            if start != previous_start:
                print(80 * '-')
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                print 'FROM %d TO %d' % (start, end)
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                whole_inputs = [ input for input in input_group
                                       if (input.data_index == start) and \
                                          (input.data_index_end == end) ]
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                for input in whole_inputs:
                    label = ' - ' + str(input.name) + ': '
                    print label + data_to_json(input.data, len(label))
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                previous_start = start
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            selected_inputs = [ input for input in input_group
                                   if (input.data_index == input_group.first_data_index) and \
                                      ((input.data_index != start) or \
                                       (input.data_index_end != end)) ]
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            grouped_inputs = {}
            for input in selected_inputs:
                key = (input.data_index, input.data_index_end)
                if not grouped_inputs.has_key(key):
                    grouped_inputs[key] = []
                grouped_inputs[key].append(input)
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            sorted_keys = grouped_inputs.keys()
            sorted_keys.sort()

            for key in sorted_keys:
                print
                print '  FROM %d TO %d' % key

                for input in grouped_inputs[key]:
                    label = '   - ' + str(input.name) + ': '
                    print label + data_to_json(input.data, len(label))
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    except Exception as e:
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        logger.error("Failed to retrieve the next data: %s", e)
        return 1

    return 0
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#----------------------------------------------------------
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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, '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']:
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      return view_outputs(args['config'], args['<set_name>'], args['--exclude'],
                          uid=int(args['--uid']) if args['--uid'] is not None else None,
                          db_root=args['--db-root'], docker=args['--docker'])
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    else:
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      return view_outputs(args['config'], args['<set_name>'],
                          uid=int(args['--uid']) if args['--uid'] is not None else None,
                          db_root=args['--db-root'], docker=args['--docker'])
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  elif args['index']:
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    if args['--list']:
        return list_index_files(args['config'], args['<name>'])
    elif args['--delete']:
        return delete_index_files(args['config'], args['<name>'])
    elif args['--checksum']:
        return checksum_index_files(args['config'], args['<name>'])
    else:
        return index_outputs(args['config'], args['<name>'],
                             uid=int(args['--uid']) if args['--uid'] is not None else None,
                             db_root=args['--db-root'], docker=args['--docker'])
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  # Should not happen
  logger.error("unrecognized `databases' subcommand")
  return 1