algorithms.py 12.6 KB
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#!/usr/bin/env python
# vim: set fileencoding=utf-8 :

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###################################################################################
#                                                                                 #
# Copyright (c) 2019 Idiap Research Institute, http://www.idiap.ch/               #
# Contact: beat.support@idiap.ch                                                  #
#                                                                                 #
# Redistribution and use in source and binary forms, with or without              #
# modification, are permitted provided that the following conditions are met:     #
#                                                                                 #
# 1. Redistributions of source code must retain the above copyright notice, this  #
# list of conditions and the following disclaimer.                                #
#                                                                                 #
# 2. Redistributions in binary form must reproduce the above copyright notice,    #
# this list of conditions and the following disclaimer in the documentation       #
# and/or other materials provided with the distribution.                          #
#                                                                                 #
# 3. Neither the name of the copyright holder nor the names of its contributors   #
# may be used to endorse or promote products derived from this software without   #
# specific prior written permission.                                              #
#                                                                                 #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND #
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED   #
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE          #
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE    #
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER      #
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,   #
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE   #
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.            #
#                                                                                 #
###################################################################################

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import logging
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import os

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import click
import simplejson as json
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from beat.backend.python.algorithm import Storage as AlgorithmStorage
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from beat.core import algorithm
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from beat.core import hash
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from beat.core.dock import Host
from beat.core.execution import DockerExecutor
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from . import commands
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from . import common
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from .click_helper import AliasedGroup
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from .click_helper import AssetCommand
from .click_helper import AssetInfo
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from .decorators import raise_on_error
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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.
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    Parameters:
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      webapi (object): An instance of our WebAPI class, prepared to access the
        BEAT server of interest
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      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.
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      indentation (int): The indentation level, useful if this function is called
        recursively while downloading different object types. This is normally
        set to ``0`` (zero).
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      format_cache (dict): A dictionary containing all dataformats already
        downloaded.
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      lib_cache (dict): A dictionary containing all libraries already
        downloaded.
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    Returns:
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      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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    """
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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,
        ["declaration", "code", "description"],
        force,
        indentation,
    )
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    if status != 0:
        return status
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    # see what dataformats one needs to pull
    if indentation == 0:
        indentation = 4
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    dataformats = []
    libraries = []
    for name in names:
        obj = algorithm.Algorithm(prefix, name)
        dataformats.extend(obj.dataformats.keys())
        libraries.extend(obj.libraries.keys())
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    # downloads any formats to which we depend on
    df_status = dataformats_pull(
        webapi, prefix, dataformats, force, indentation, format_cache
    )
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    lib_status = libraries_pull(
        webapi, prefix, libraries, force, indentation, 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

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

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

            cfg["path"] = hash.toPath(cfg["hash"], suffix=suffix)

        algo = AlgorithmStorage(prefix, configuration["algorithm"])

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

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

        host = Host(raise_on_errors=False)

        executor = DockerExecutor(
            host,
            prefix,
            configuration,
            cache,
            dataformat_cache,
            database_cache,
            algorithm_cache,
        )

        if not executor.valid:
            logger.error(
                "Invalid configuration:\n  * %s" % "\n  * ".join(executor.errors)
            )
            return 1

        # Execute the algorithm
        with executor:
            result = executor.process()
            if result["status"] != 0:
                print("STDERR:")
                print(result["stderr"])

        # Display the results
        if "outputs" in configuration:  # Standard algorithm
            print("Outputs of the algorithms available at:")
            for name, cfg in configuration["outputs"].items():
                print("  - %s: %s" % (name, cfg["path"]))
        else:
            print(
                "Results of the analyzer available at: %s"
                % configuration["result"]["path"]
            )

    except Exception:
        import traceback

        logger.error(traceback.format_exc())
        return 1
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    return 0
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def get_dependencies(ctx, asset_name):
    prefix = ctx.meta["config"].path
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    alg = algorithm.Algorithm(prefix, asset_name)
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    dependencies = {}

    libraries = list(alg.libraries.keys())
    if libraries:
        dependencies["libraries"] = libraries

    dataformats = list(alg.dataformats.keys())
    if dataformats:
        dependencies["dataformats"] = dataformats

    return dependencies


class AlgorithmCommand(AssetCommand):
    asset_info = AssetInfo(
        asset_type="algorithm",
        diff_fields=["declaration", "code", "description"],
        push_fields=["name", "declaration", "code", "description"],
        get_dependencies=get_dependencies,
    )


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@click.group(cls=AliasedGroup)
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@click.pass_context
def algorithms(ctx):
    """Configuration and manipulation of algorithms"""


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CMD_LIST = [
    "list",
    "path",
    "edit",
    "check",
    "status",
    "create",
    "version",
    "fork",
    "rm",
    "diff",
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    "push",
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]

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commands.initialise_asset_commands(algorithms, CMD_LIST, AlgorithmCommand)
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@algorithms.command()
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@click.argument("name", nargs=-1)
@click.option(
    "--force", help="Performs operation regardless of conflicts", is_flag=True
)
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@click.pass_context
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@raise_on_error
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def pull(ctx, name, force):
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    """Downloads the specified algorithms from the server
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    Example:
      $ beat algorithms pull --force yyy
    """
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    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("instructions", nargs=1)
@click.option(
    "--example", help="Display some example JSON instruction files", is_flag=True
)
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@click.pass_context
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@raise_on_error
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def execute(ctx, instructions, example):
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    """Execute an algorithm following instructions in a JSON file
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    Example:
      $ beat algorithms execute <instructions>
      $ beat algorithms execute --examples
    """
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    if example:
        print_examples()
        return 0
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    return execute_impl(ctx.meta["config"].path, ctx.meta["config"].cache, instructions)