Source code for planemo.shed.interface

"""Interface over bioblend and direct access to ToolShed API via requests."""

import json

from bioblend.toolshed import ToolShedInstance
from galaxy.util import unicodify

from import untar_to

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

[docs]def tool_shed_instance(url, key, email, password): return ToolShedInstance(url=url, key=key, email=email, password=password)
[docs]def find_repository(tsi, owner, name): """Find repository information for given owner and repository name. """ repos = tsi.repositories.get_repositories(owner=owner, name=name) 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]
[docs]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 = f"Failed to find installable revisions for [{owner}, {name}]." raise Exception(msg) else: return revisions[-1]
[docs]def username(tsi): """Fetch current username from shed given API key/auth.""" user = _user(tsi) return user["username"]
[docs]def api_exception_to_message(e): """Convert API exception to human digestable error message - parsing out the shed generate message if possible. """ message = unicodify(e) if hasattr(e, "read"): message = 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
[docs]def find_category_ids(tsi, categories): """Translate human readable category names into their associated IDs.""" category_list = tsi.categories.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
[docs]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: tar_args = ["-xzf", "-", "--strip-components=1"] untar_to(download_url, tar_args=tar_args, dest_dir=destination) else: untar_to(download_url, path=destination)
def _user(tsi): """Fetch user information from the ToolShed API for given key. """ # TODO: this should be done with an actual bioblend method, # see response = tsi.make_get_request(tsi.url + "/users") return response.json()[0]