diff options
| -rw-r--r-- | gn3/authentication.py | 4 | ||||
| -rw-r--r-- | gn3/case_attributes.py | 22 | ||||
| -rw-r--r-- | gn3/commands.py | 2 | ||||
| -rw-r--r-- | gn3/computations/gemma.py | 5 |
4 files changed, 19 insertions, 14 deletions
diff --git a/gn3/authentication.py b/gn3/authentication.py index d0b35bc..bb717dd 100644 --- a/gn3/authentication.py +++ b/gn3/authentication.py @@ -144,8 +144,8 @@ def get_user_info_by_key(key: str, value: str, def create_group(conn: Redis, group_name: Optional[str], - admin_user_uids: List = None, - member_user_uids: List = None) -> Optional[Dict]: + admin_user_uids: Optional[List] = None, + member_user_uids: Optional[List] = None) -> Optional[Dict]: """Create a group given the group name, members and admins of that group.""" if admin_user_uids is None: admin_user_uids = [] diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py index c32e762..d973b8e 100644 --- a/gn3/case_attributes.py +++ b/gn3/case_attributes.py @@ -4,6 +4,7 @@ import csv import json import uuid import tempfile +from typing import Union from enum import Enum, auto from pathlib import Path from functools import reduce @@ -59,7 +60,9 @@ class CAJSONEncoder(json.JSONEncoder): return str(obj) return json.JSONEncoder.default(self, obj) -def required_access(inbredset_id: int, access_levels: tuple[str, ...]) -> bool: +def required_access( + inbredset_id: int, access_levels: tuple[str, ...]) -> Union[ + bool, tuple[str, ...]]: """Check whether the user has the appropriate access""" def __species_id__(conn): with conn.cursor() as cursor: @@ -330,7 +333,8 @@ def __apply_modifications__( cattr: new[cattr] } for cattr in cattrs if new[cattr] != orig[cattr]) - new_rows = reduce(__retrieve_changes__, modifications_diff, tuple()) + new_rows: tuple[dict, ...] = reduce( + __retrieve_changes__, modifications_diff, tuple()) strain_names = tuple({row["Strain"] for row in new_rows}) cursor.execute("SELECT Id AS StrainId, Name AS StrainName FROM Strain " f"WHERE Name IN ({', '.join(['%s'] * len(strain_names))})", @@ -454,7 +458,7 @@ def edit_case_attributes(inbredset_id: int) -> Response: required_access(inbredset_id, ("system:inbredset:edit-case-attribute",)) user = the_token.user - fieldnames = (["Strain"] + sorted( + fieldnames = tuple(["Strain"] + sorted( attr["Name"] for attr in __case_attribute_labels_by_inbred_set__(conn, inbredset_id))) try: @@ -471,9 +475,9 @@ def edit_case_attributes(inbredset_id: int) -> Response: conn, inbredset_id), __inbredset_strains__(conn, inbredset_id)), __process_edit_data__( - fieldnames, request.json["edit-data"])) + fieldnames, request.json["edit-data"])) # type: ignore[index] }, - Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR)) + Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR)) except NoDiffError as _nde: msg = "There were no changes to make from submitted data." response = jsonify({ @@ -502,11 +506,11 @@ def edit_case_attributes(inbredset_id: int) -> Response: @caseattr.route("/<int:inbredset_id>/diff/list", methods=["GET"]) def list_diffs(inbredset_id: int) -> Response: """List any changes that have not been approved/rejected.""" - Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR).mkdir( + Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR).mkdir( parents=True, exist_ok=True) def __generate_diff_files__(diffs): - diff_dir = Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR) + diff_dir = Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR) review_files = set(afile.name for afile in diff_dir.iterdir() if ("-rejected" not in afile.name and "-approved" not in afile.name)) @@ -553,7 +557,7 @@ def list_diffs(inbredset_id: int) -> Response: @caseattr.route("/approve/<path:filename>", methods=["POST"]) def approve_case_attributes_diff(filename: str) -> Response: """Approve the changes to the case attributes in the diff.""" - diff_dir = Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR) + diff_dir = Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR) diff_filename = Path(diff_dir, filename) the_diff = __load_diff__(diff_filename) with database_connection(current_app.config["SQL_URI"]) as conn: @@ -566,7 +570,7 @@ def approve_case_attributes_diff(filename: str) -> Response: @caseattr.route("/reject/<path:filename>", methods=["POST"]) def reject_case_attributes_diff(filename: str) -> Response: """Reject the changes to the case attributes in the diff.""" - diff_dir = Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR) + diff_dir = Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR) diff_filename = Path(diff_dir, filename) the_diff = __load_diff__(diff_filename) with database_connection(current_app.config["SQL_URI"]) as conn: diff --git a/gn3/commands.py b/gn3/commands.py index a90e895..b873d4d 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -148,7 +148,7 @@ def run_sample_corr_cmd(method, this_trait_data, target_dataset_data): return correlation_results -def run_cmd(cmd: str, success_codes: Tuple = (0,), env: str = None) -> Dict: +def run_cmd(cmd: str, success_codes: Tuple = (0,), env: Optional[str] = None) -> Dict: """Run CMD and return the CMD's status code and output as a dict""" parsed_cmd = json.loads(cmd) parsed_env = (json.loads(env) if env is not None else None) diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 8036a7b..7f09b0a 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -5,6 +5,7 @@ from base64 import b64encode from hashlib import md5 from typing import Dict from typing import List +from typing import Optional from typing import ValuesView from gn3.commands import compose_gemma_cmd from gn3.fs_helpers import get_hash_of_files @@ -53,8 +54,8 @@ def generate_gemma_cmd(gemma_cmd: str, output_dir: str, token: str, gemma_kwargs: Dict, - gemma_wrapper_kwargs: Dict = None, - chromosomes: str = None) -> Dict: + gemma_wrapper_kwargs: Optional[Dict] = None, + chromosomes: Optional[str] = None) -> Dict: """Compute k values""" _hash = get_hash_of_files( [v for k, v in gemma_kwargs.items() if k in ["g", "p", "a", "c"]]) |