comparison env/lib/python3.9/site-packages/bioblend/galaxy/objects/galaxy_instance.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

0:4f3585e2f14b

"""
A representation of a Galaxy instance based on oo wrappers.
"""

import time

import bioblend
import bioblend.galaxy
from bioblend.galaxy.datasets import TERMINAL_STATES
from . import client


def _get_error_info(hda):
    msg = hda.id
    try:
        msg += ' (%s): ' % hda.name
        msg += hda.wrapped['misc_info']
    except Exception:  # avoid 'error while generating an error report'
        msg += ': error'
    return msg


class GalaxyInstance:
    """
    A representation of an instance of Galaxy, identified by a URL and
    a user's API key.

    :type url: str
    :param url: a FQDN or IP for a given instance of Galaxy. For example:
      ``http://127.0.0.1:8080``

    :type api_key: str
    :param api_key: user's API key for the given instance of Galaxy, obtained
      from the Galaxy web UI.

    This is actually a factory class which instantiates the entity-specific
    clients.

    Example: get a list of all histories for a user with API key 'foo'::

      from bioblend.galaxy.objects import *
      gi = GalaxyInstance('http://127.0.0.1:8080', 'foo')
      histories = gi.histories.list()
    """
    def __init__(self, url, api_key=None, email=None, password=None, verify=True):
        self.gi = bioblend.galaxy.GalaxyInstance(url, api_key, email, password, verify)
        self.log = bioblend.log
        self.histories = client.ObjHistoryClient(self)
        self.libraries = client.ObjLibraryClient(self)
        self.workflows = client.ObjWorkflowClient(self)
        self.tools = client.ObjToolClient(self)
        self.jobs = client.ObjJobClient(self)

    def _wait_datasets(self, datasets, polling_interval, break_on_error=True):
        """
        Wait for datasets to come out of the pending states.

        :type datasets: :class:`~collections.Iterable` of
          :class:`~.wrappers.Dataset`
        :param datasets: datasets

        :type polling_interval: float
        :param polling_interval: polling interval in seconds

        :type break_on_error: bool
        :param break_on_error: if ``True``, raise a RuntimeError exception as
          soon as at least one of the datasets is in the 'error' state.

        .. warning::

          This is a blocking operation that can take a very long time.
          Also, note that this method does not return anything;
          however, each input dataset is refreshed (possibly multiple
          times) during the execution.
        """
        def poll(ds_list):
            pending = []
            for ds in ds_list:
                ds.refresh()
                if break_on_error and ds.state == 'error':
                    raise RuntimeError(_get_error_info(ds))
                if not ds.state:
                    self.log.warning("Dataset %s has an empty state", ds.id)
                elif ds.state not in TERMINAL_STATES:
                    self.log.info("Dataset {0.id} is in non-terminal state {0.state}".format(ds))
                    pending.append(ds)
            return pending

        self.log.info('Waiting for datasets')
        while datasets:
            datasets = poll(datasets)
            time.sleep(polling_interval)