comparison venv/lib/python2.7/site-packages/planemo/shed/interface.py @ 0:d67268158946 draft

planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b

0:d67268158946

""" Interface over bioblend and direct access to ToolShed
API via requests.
"""
import json
from planemo.io import untar_to
from planemo.bioblend import (
    toolshed,
    ensure_module,
)

REPOSITORY_DOWNLOAD_TEMPLATE = (
    "%srepository/download?repository_id=%s"
    "&changeset_revision=default&file_type=gz"
)


def tool_shed_instance(url, key, email, password):
    ensure_module(toolshed)
    tsi = toolshed.ToolShedInstance(
        url=url,
        key=key,
        email=email,
        password=password
    )
    return tsi


def find_repository(tsi, owner, name):
    """ Find repository information for given owner and repository
    name.
    """
    repos = tsi.repositories.get_repositories()

    def matches(r):
        return r["owner"] == owner and r["name"] == name

    matching_repos = list(filter(matches, repos))
    if not matching_repos:
        return None
    else:
        return matching_repos[0]


def latest_installable_revision(tsi, repository_id):
    info = tsi.repositories.show_repository(repository_id)
    owner = info["owner"]
    name = info["name"]
    revisions = tsi.repositories.get_ordered_installable_revisions(
        name, owner
    )
    if len(revisions) == 0:
        msg = "Failed to find installable revisions for [{0}, {1}].".format(
            owner,
            name,
        )
        raise Exception(msg)
    else:
        return revisions[-1]


def username(tsi):
    """ Fetch current username from shed given API key/auth.
    """
    user = _user(tsi)
    return user["username"]


def api_exception_to_message(e):
    """ Convert API exception to human digestable error message - parsing
    out the shed generate message if possible.
    """
    message = str(e)
    if hasattr(e, "read"):
        message = e.read()
        try:
            # Galaxy passes nice JSON messages as their errors, which bioblend
            # blindly returns. Attempt to parse those.
            upstream_error = json.loads(message)
            message = upstream_error['err_msg']
        except Exception:
            pass
    return message


def find_category_ids(tsi, categories):
    """ Translate human readable category names into their associated IDs.
    """
    category_list = tsi.repositories.get_categories()

    category_ids = []
    for cat in categories:
        matching_cats = [x for x in category_list if x['name'] == cat]
        if not matching_cats:
            message = "Failed to find category %s" % cat
            raise Exception(message)
        category_ids.append(matching_cats[0]['id'])
    return category_ids


def download_tar(tsi, repo_id, destination, to_directory):
    base_url = tsi.base_url
    if not base_url.endswith("/"):
        base_url += "/"
    download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
    if to_directory:
        untar_args = "-xzf - -C %s --strip-components 1" % destination
    else:
        untar_args = None
    untar_to(download_url, destination, untar_args)


def _user(tsi):
    """ Fetch user information from the ToolShed API for given
    key.
    """
    # TODO: this should be done with an actual bioblend method,
    # see https://github.com/galaxyproject/bioblend/issues/130.
    response = tsi.make_get_request(tsi.url + "/users")
    return response.json()[0]