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biolink / biolink-model-toolkit

A collection of useful python functions for looking up information and working with the Biolink Model
https://biolink.github.io/biolink-model-toolkit/
BSD 3-Clause "New" or "Revised" License
20 stars 11 forks source link

deployment of bmt on IRTB environments means pystow can't store cache files in default directory #113

Closed sierra-moxon closed 1 year ago

sierra-moxon commented 1 year ago

From Eric D in Translator:

from reasoner_validator import TRAPIResponseValidator File "/usr/local/lib/python3.9/dist-packages/reasoner_validator/init.py", line 3, in from reasoner_validator.biolink import ( File "/usr/local/lib/python3.9/dist-packages/reasoner_validator/biolink/init.py", line 11, in from bmt import Toolkit File "/usr/local/lib/python3.9/dist-packages/bmt/init.py", line 1, in from bmt.toolkit import Toolkit File "/usr/local/lib/python3.9/dist-packages/bmt/toolkit.py", line 6, in from oaklib.implementations import UbergraphImplementation File "/usr/local/lib/python3.9/dist-packages/oaklib/init.py", line 9, in from oaklib.selector import get_implementation_from_shorthand # noqa:F401 File "/usr/local/lib/python3.9/dist-packages/oaklib/selector.py", line 8, in from oaklib.implementations import GildaImplementation File "/usr/local/lib/python3.9/dist-packages/oaklib/implementations/init.py", line 5, in from oaklib.implementations.funowl.funowl_implementation import FunOwlImplementation File "/usr/local/lib/python3.9/dist-packages/oaklib/implementations/funowl/funowl_implementation.py", line 28, in from oaklib.interfaces.patcher_interface import PatcherInterface File "/usr/local/lib/python3.9/dist-packages/oaklib/interfaces/patcher_interface.py", line 21, in from oaklib.utilities.kgcl_utilities import generate_change_id File "/usr/local/lib/python3.9/dist-packages/oaklib/utilities/kgcl_utilities.py", line 11, in import kgcl_schema.grammar.parser as kgcl_parser File "/usr/local/lib/python3.9/dist-packages/kgcl_schema/grammar/parser.py", line 9, in from bioregistry import parse_iri, get_preferred_prefix, curie_to_str File "/usr/local/lib/python3.9/dist-packages/bioregistry/init.py", line 5, in from .collection_api import get_collection, get_context # noqa:F401 File "/usr/local/lib/python3.9/dist-packages/bioregistry/collection_api.py", line 7, in from .resource_manager import manager File "/usr/local/lib/python3.9/dist-packages/bioregistry/resource_manager.py", line 27, in from .constants import ( File "/usr/local/lib/python3.9/dist-packages/bioregistry/constants.py", line 84, in URI_PARSING.mkdir(exist_ok=True, parents=True) File "/usr/lib/python3.9/pathlib.py", line 1327, in mkdir self.parent.mkdir(parents=True, exist_ok=True) File "/usr/lib/python3.9/pathlib.py", line 1327, in mkdir self.parent.mkdir(parents=True, exist_ok=True) File "/usr/lib/python3.9/pathlib.py", line 1323, in mkdir self._accessor.mkdir(self, mode) PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.9/exports'

sierra-moxon commented 1 year ago

see: https://github.com/INCATools/kgcl/pull/24 https://github.com/INCATools/ontology-access-kit/pull/468