diff options
| -rw-r--r-- | gn3/api/gemma.py | 1 | ||||
| -rw-r--r-- | gn3/api/metadata_api/wiki.py | 2 | ||||
| -rw-r--r-- | gn3/api/rqtl.py | 1 | ||||
| -rw-r--r-- | gn3/app.py | 1 | ||||
| -rw-r--r-- | gn3/computations/gemma.py | 4 | ||||
| -rw-r--r-- | gn3/computations/rqtl.py | 2 | ||||
| -rw-r--r-- | gn3/debug.py | 4 | ||||
| -rw-r--r-- | gn3/fs_helpers.py | 15 |
8 files changed, 16 insertions, 14 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index 2dd53ea..abe772c 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -12,7 +12,6 @@ from gn3.commands import run_cmd from gn3.fs_helpers import cache_ipfs_file from gn3.fs_helpers import jsonfile_to_dict, assert_paths_exist from gn3.computations.gemma import generate_gemma_cmd -from gn3.computations.gemma import assert_paths_exist gemma = Blueprint("gemma", __name__) diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py index 9ea0d53..6436f3d 100644 --- a/gn3/api/metadata_api/wiki.py +++ b/gn3/api/metadata_api/wiki.py @@ -5,7 +5,6 @@ from typing import Any, Dict from flask import Blueprint, request, jsonify, current_app, make_response from gn3 import db_utils from gn3.db import wiki -from gn3.db.rdf import query_frame_and_compact from gn3.db.rdf.wiki import (get_wiki_entries_by_symbol, get_comment_history) @@ -121,6 +120,7 @@ def get_species(): @wiki_blueprint.route("/<int:comment_id>/history", methods=["GET"]) def get_history(comment_id): + """Fetch all of a given comment's history given it's comment id""" status_code = 200 response = get_comment_history(comment_id=comment_id, sparql_uri=current_app.config["SPARQL_ENDPOINT"]) diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 68299d4..c2d988a 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -6,7 +6,6 @@ from flask import current_app from flask import jsonify from flask import request -from gn3.debug import __pk__ from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \ process_rqtl_pairscan, process_perm_output from gn3.fs_helpers import assert_paths_exist, get_tmpdir diff --git a/gn3/app.py b/gn3/app.py index d7fcbea..c8f0c5a 100644 --- a/gn3/app.py +++ b/gn3/app.py @@ -28,7 +28,6 @@ from gn3.api.sampledata import sampledata from gn3.api.llm import gnqa from gn3.auth import oauth2 from gn3.case_attributes import caseattr -from gn3.fs_helpers import get_tmpdir def create_app(config: Union[Dict, str, None] = None) -> Flask: diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 577d8e8..6c53ecc 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -1,14 +1,12 @@ """Procedures related gemma computations""" -import errno import os from base64 import b64encode from hashlib import md5 from typing import Optional, Dict from typing import List -from typing import ValuesView from gn3.commands import compose_gemma_cmd -from gn3.fs_helpers import get_hash_of_files, assert_paths_exist +from gn3.fs_helpers import get_hash_of_files def generate_hash_of_string(unhashed_str: str) -> str: diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 0b8c23d..16f1398 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -1,7 +1,5 @@ """Procedures related to R/qtl computations""" import os -import sys -import logging from bisect import bisect from typing import Dict, List, Tuple, Union diff --git a/gn3/debug.py b/gn3/debug.py index 945e237..8b67a92 100644 --- a/gn3/debug.py +++ b/gn3/debug.py @@ -4,13 +4,17 @@ from flask import current_app __this_module_name__ = __name__ + +# pylint: disable=invalid-name def getLogger(): + """Return a logger""" return ( logging.getLogger(__this_module_name__) if not bool(current_app) else current_app.logger) def __pk__(*args): + """Format log entry""" value = args[-1] title_vals = " => ".join(args[0:-1]) logger = getLogger() diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py index 1b226bc..2ce381e 100644 --- a/gn3/fs_helpers.py +++ b/gn3/fs_helpers.py @@ -16,14 +16,20 @@ from werkzeug.utils import secure_filename from flask import current_app def get_tmpdir() -> str: - """Get the temp directory from the FLASK tmpdir setting. If it is not set, set it to /tmp. Note - that the app should check for environment settings to initialize its TMPDIR. + """Get the temp directory from the FLASK tmpdir setting. If it is + not set, set it to /tmp. Note that the app should check for + environment settings to initialize its TMPDIR. + """ tmpdir = current_app.config.get("TMPDIR") if not tmpdir: tmpdir = "/tmp" if not os.path.isdir(tmpdir): - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), f"TMPDIR {tmpdir} is not a valid directory") + raise FileNotFoundError( + errno.ENOENT, + os.strerror(errno.ENOENT), + f"TMPDIR {tmpdir} is not a valid directory" + ) return tmpdir @@ -32,8 +38,7 @@ def assert_path_exists(path: str, throw_error: bool = True) -> bool: if not os.path.isfile(path): if throw_error: raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path) - else: - return False + return False return True def assert_paths_exist(paths: ValuesView, throw_error: bool = True) -> bool: |