Source code for datalad_container.containers_add

"""Add a container environment to a dataset"""

__docformat__ = 'restructuredtext'

import re
import logging
import os
import os.path as op
import sys
from shutil import copyfile
from simplejson import loads

from datalad.cmd import WitlessRunner
from datalad.interface.base import Interface
from datalad.interface.base import build_doc
from import Parameter
from datalad.distribution.dataset import datasetmethod, EnsureDataset
from datalad.distribution.dataset import require_dataset
from datalad.interface.utils import eval_results
from import EnsureStr
from import EnsureNone
from import InsufficientArgumentsError
from datalad.interface.results import get_status_dict

from .definitions import definitions

lgr = logging.getLogger("datalad.containers.containers_add")

# The DataLad special remote has built-in support for Singularity Hub URLs. Let
# it handle shub:// URLs if it's available.
    import datalad.downloaders.shub
except ImportError:
    lgr.debug("DataLad's shub downloader not found. "
              "Custom handling for shub:// will be used")

def _resolve_img_url(url):
    """Takes a URL and tries to resolve it to an actual download
    URL that `annex addurl` can handle"""
    if not _HAS_SHUB_DOWNLOADER and url.startswith('shub://'):
        # TODO: Remove this handling once the minimum DataLad version is at
        # least 0.14.
        lgr.debug('Query singularity-hub for image download URL')
        import requests
        req = requests.get(
        shub_info = loads(req.text)
        url = shub_info['image']
    return url

def _guess_call_fmt(ds, name, url):
    """Helper to guess a container exec setup based on
    - a name (to be able to look up more config
    - a plain url to make inference based on the source location

    Should return `None` is no guess can be made.
    if url is None:
        return None
    elif url.startswith('shub://') or url.startswith('docker://'):
        return 'singularity exec {img} {cmd}'
    elif url.startswith('dhub://'):
        return op.basename(sys.executable) + ' -m datalad_container.adapters.docker run {img} {cmd}'

def _ensure_datalad_remote(repo):
    """Initialize and enable datalad special remote if it isn't already."""
    dl_remote = None
    for info in repo.get_special_remotes().values():
        if info.get("externaltype") == "datalad":
            dl_remote = info["name"]

    if not dl_remote:
        from datalad.consts import DATALAD_SPECIAL_REMOTE
        from datalad.customremotes.base import init_datalad_remote

        init_datalad_remote(repo, DATALAD_SPECIAL_REMOTE, autoenable=True)
    elif repo.is_special_annex_remote(dl_remote, check_if_known=False):
        lgr.debug("datalad special remote '%s' is already enabled",
        lgr.debug("datalad special remote '%s' found. Enabling",

[docs]@build_doc # all commands must be derived from Interface class ContainersAdd(Interface): # first docstring line is used a short description in the cmdline help # the rest is put in the verbose help and manpage """Add a container to a dataset """ # parameters of the command, must be exhaustive _params_ = dict( dataset=Parameter( args=("-d", "--dataset"), doc="""specify the dataset to add the container to. If no dataset is given, an attempt is made to identify the dataset based on the current working directory""", constraints=EnsureDataset() | EnsureNone() ), name=Parameter( args=("name",), doc="""The name to register the container under. This also determines the default location of the container image within the dataset.""", metavar="NAME", constraints=EnsureStr(), ), url=Parameter( args=("-u", "--url"), doc="""A URL (or local path) to get the container image from. If the URL scheme is one recognized by Singularity ('shub://' or 'docker://'), a command format string for Singularity-based execution will be auto-configured when [CMD: --call-fmt CMD][PY: call_fmt PY] is not specified. For Docker-based container execution with the URL scheme 'dhub://', the rest of the URL will be interpreted as the argument to 'docker pull', the image will be saved to a location specified by `name`, and the call format will be auto-configured to run docker, unless overwritten.""", metavar="URL", constraints=EnsureStr() | EnsureNone(), ), # TODO: The "prepared command stuff should ultimately go somewhere else # (probably datalad-run). But first figure out, how exactly to address # container datasets call_fmt=Parameter( args=("--call-fmt",), doc="""Command format string indicating how to execute a command in this container, e.g. "singularity exec {img} {cmd}". Where '{img}' is a placeholder for the path to the container image and '{cmd}' is replaced with the desired command. Additional placeholders: '{img_dspath}' is relative path to the dataset containing the image. """, metavar="FORMAT", constraints=EnsureStr() | EnsureNone(), ), image=Parameter( args=("-i", "--image"), doc="""Relative path of the container image within the dataset. If not given, a default location will be determined using the `name` argument.""", metavar="IMAGE", constraints=EnsureStr() | EnsureNone(), ), update=Parameter( args=("--update",), action="store_true", doc="""Update the existing container for `name`. If no other options are specified, URL will be set to 'updateurl', if configured. If a container with `name` does not already exist, this option is ignored.""" ) ) @staticmethod @datasetmethod(name='containers_add') @eval_results def __call__(name, url=None, dataset=None, call_fmt=None, image=None, update=False): if not name: raise InsufficientArgumentsError("`name` argument is required") ds = require_dataset(dataset, check_installed=True, purpose='add container') runner = WitlessRunner() # prevent madness in the config file if not re.match(r'^[0-9a-zA-Z-]+$', name): raise ValueError( "Container names can only contain alphanumeric characters " "and '-', got: '{}'".format(name)) cfgbasevar = "datalad.containers.{}".format(name) if cfgbasevar + ".image" in ds.config: if not update: yield get_status_dict( action="containers_add", ds=ds, logger=lgr, status="impossible", message=("Container named %r already exists. " "Use --update to reconfigure.", name)) return if not (url or image or call_fmt): # No updated values were provided. See if an update url is # configured (currently relevant only for Singularity Hub). url = ds.config.get(cfgbasevar + ".updateurl") if not url: yield get_status_dict( action="containers_add", ds=ds, logger=lgr, status="impossible", message="No values to update specified") return call_fmt = call_fmt or ds.config.get(cfgbasevar + ".cmdexec") image = image or ds.config.get(cfgbasevar + ".image") if not image: loc_cfg_var = "datalad.containers.location" # TODO: We should provide an entry point (or sth similar) for extensions # to get config definitions into the ConfigManager. In other words an # easy way to extend definitions in datalad's container_loc = \ ds.config.obtain( loc_cfg_var, where=definitions[loc_cfg_var]['destination'], # if not False it would actually modify the # dataset config file -- undesirable store=False, default=definitions[loc_cfg_var]['default'], dialog_type=definitions[loc_cfg_var]['ui'][0], valtype=definitions[loc_cfg_var]['type'], **definitions[loc_cfg_var]['ui'][1] ) image = op.join(ds.path, container_loc, name, 'image') else: image = op.join(ds.path, image) result = get_status_dict( action="containers_add", path=image, type="file", logger=lgr, ) if call_fmt is None: # maybe built in knowledge can help call_fmt = _guess_call_fmt(ds, name, url) # collect bits for a final and single save() call to_save = [] imgurl = url was_updated = False if url: if update and op.lexists(image): was_updated = True # XXX: check=False is used to avoid dropping the image. It # should use drop=False if remove() gets such an option (see # DataLad's gh-2673). for r in ds.remove(image, save=False, check=False, return_type="generator"): yield r imgurl = _resolve_img_url(url) lgr.debug('Attempt to obtain container image from: %s', imgurl) if url.startswith("dhub://"): from .adapters import docker docker_image = url[len("dhub://"):] lgr.debug( "Running 'docker pull %s and saving image to %s", docker_image, image)["docker", "pull", docker_image]), image) elif url.startswith("docker://"): image_dir, image_basename = op.split(image) if not image_basename: raise ValueError("No basename in path {}".format(image)) if image_dir and not op.exists(image_dir): os.makedirs(image_dir)"Building Singularity image for %s " "(this may take some time)", url)["singularity", "build", image_basename, url], cwd=image_dir or None) elif op.exists(url):"Copying local file %s to %s", url, image) image_dir = op.dirname(image) if image_dir and not op.exists(image_dir): os.makedirs(image_dir) copyfile(url, image) else: if _HAS_SHUB_DOWNLOADER and url.startswith('shub://'): _ensure_datalad_remote(ds.repo) try: ds.repo.add_url_to_file(image, imgurl) except Exception as e: result["status"] = "error" result["message"] = str(e) yield result # TODO do we have to take care of making the image executable # if --call_fmt is not provided? to_save.append(image) # continue despite a remote access failure, the following config # setting will enable running the command again with just the name # given to ease a re-run if not op.lexists(image): result["status"] = "error" result["message"] = ('no image at %s', image) yield result return # store configs if imgurl != url: # store originally given URL, as it resolves to something # different and maybe can be used to update the container # at a later point in time ds.config.set("{}.updateurl".format(cfgbasevar), url) # force store the image, and prevent multiple entries ds.config.set( "{}.image".format(cfgbasevar), op.relpath(image, start=ds.path), force=True) if call_fmt: ds.config.set( "{}.cmdexec".format(cfgbasevar), call_fmt, force=True) # store changes to_save.append(op.join(".datalad", "config")) for r in path=to_save, message="[DATALAD] {do} containerized environment '{name}'".format( do="Update" if was_updated else "Configure", name=name)): yield r result["status"] = "ok" yield result