debugging

src/pyflask/apis/_dandi.py

@@ -2,9 +2,9 @@
 
 from typing import List, Tuple, Union
 
-import flask.restx
+import flask_restx
 
-from ..utils import catch_exception_and_abort, server_error_responses
+from .utils import catch_exception_and_abort, server_error_responses
 
 dandi_api = flask_restx.Namespace(
     name="dandi", description="Request various static listings from the DANDI Python API."
@@ -14,7 +14,7 @@
 @dandi_api.route(rule="/get-recommended-species")
 class SupportedSpecies(flask_restx.Resource):
 
-    @neurosift_api.doc(
+    @dandi_api.doc(
         description="Request the list of currently supported species (by Latin Binomial name) for DANDI. Note that any "
         "explicit NCBI taxonomy link is also supported.",
         responses=server_error_responses(codes=[200, 500]),

src/pyflask/apis/_neurosift.py

@@ -4,9 +4,9 @@
 from typing import Union
 
 import flask
-import flask.restx
+import flask_restx
 
-from ..utils import (
+from .utils import (
     abort_if_not_nwb_file,
     catch_exception_and_abort,
     server_error_responses,

src/pyflask/apis/_system.py

@@ -2,9 +2,9 @@
 
 from typing import Dict, Union
 
-import flask.restx
+import flask_restx
 
-from ..utils import catch_exception_and_abort, server_error_responses
+from .utils import catch_exception_and_abort, server_error_responses
 
 system_api = flask_restx.Namespace(name="system", description="Request various system specific information.")
 

src/pyflask/apis/data.py

@@ -4,7 +4,8 @@
 
 from flask_restx import Namespace, Resource, reqparse
 from manageNeuroconv import generate_dataset, generate_test_data
-from utils import catch_exception_and_abort, server_error_responses
+
+from .utils import catch_exception_and_abort, server_error_responses
 
 data_api = Namespace(name="data", description="API route for dataset generation in the NWB GUIDE.")
 

src/pyflask/app.py

@@ -7,11 +7,8 @@
 from datetime import datetime
 from logging import DEBUG, Formatter
 from logging.handlers import RotatingFileHandler
-from os.path import isabs
 from pathlib import Path
 from signal import SIGINT
-from typing import Union
-from urllib.parse import unquote
 
 # https://stackoverflow.com/questions/32672596/pyinstaller-loads-script-multiple-times#comment103216434_32677108
 multiprocessing.freeze_support()
@@ -25,16 +22,11 @@
     startup_api,
     system_api,
 )
-from flask import Flask, Response, send_file, send_from_directory
+from apis.utils import catch_exception_and_abort, server_error_responses
+from flask import Flask
 from flask_cors import CORS
 from flask_restx import Api, Resource
-from manageNeuroconv.info import (
-    CONVERSION_SAVE_FOLDER_PATH,
-    GUIDE_ROOT_FOLDER,
-    STUB_SAVE_FOLDER_PATH,
-    resource_path,
-)
-from utils import catch_exception_and_abort, server_error_responses
+from manageNeuroconv.info import GUIDE_ROOT_FOLDER, get_project_root_path
 
 all_apis = [data_api, neuroconv_api, startup_api, neurosift_api, dandi_api, system_api]
 
@@ -51,8 +43,8 @@
 LOG_FILE_PATH = Path(LOG_FOLDER) / f"{timestamp}.log"
 
 # Fetch version from package.json
-package_json_file_path = resource_path("package.json")
-with open(file=package_json_file_path) as fp:
+package_json_file_path = get_project_root_path() / "package.json"
+with open(file=package_json_file_path, mode="r") as fp:
     package_json = json.load(fp=fp)
 
 # Initialize top-level API and set namespaces
@@ -89,21 +81,14 @@ def post(self):
         selected_logger(message)
 
 
-@flask_app.route("/cpus")
-def get_cpu_count():
-    from psutil import cpu_count
-
-    physical = cpu_count(logical=False)
-    logical = cpu_count()
-
-    return dict(physical=physical, logical=logical)
-
-
 @flask_api.route("/server_shutdown", endpoint="shutdown")
-@neurosift_api.doc(
-    description="Handle adding and fetching NWB files from the global file registry.",
-)
+@flask_api.doc(description="Close the Flask server.")
 class Shutdown(Resource):
+
+    @flask_api.doc(
+        description="To trigger a shutdown, set a GET request to this endpoint. It will not return a response.",
+        responses=server_error_responses(codes=[200, 500]),
+    )
     def get(self) -> None:
         werkzeug_shutdown_function = flask.request.environ.get("werkzeug.server.shutdown")
         flask_api.logger.info("Shutting down server...")

src/pyflask/manageNeuroconv/info/__init__.py

@@ -3,5 +3,6 @@
     CONVERSION_SAVE_FOLDER_PATH,
     GUIDE_ROOT_FOLDER,
     STUB_SAVE_FOLDER_PATH,
-    resource_path,
+    get_project_root_path,
+    get_source_base_path,
 )

src/pyflask/manageNeuroconv/info/urls.py

@@ -1,36 +1,50 @@
 import json
 import os
+import pathlib
 import sys
-from pathlib import Path
 
 
-def resource_path(relative_path):
-    """Get absolute path to resource, works for dev and for PyInstaller"""
-    try:
+def get_source_base_path() -> pathlib.Path:
+    """Get absolute path of a relative resource to the app; works for both dev mode and for PyInstaller."""
+    # Production: PyInstaller creates a temp folder and stores path in _MEIPASS
+    if hasattr(sys, "_MEIPASS"):
         # PyInstaller creates a temp folder and stores path in _MEIPASS
-        base_path = sys._MEIPASS
-    except Exception:
-        base_path = Path(__file__).parent.parent.parent.parent
+        base_path = pathlib.Path(sys._MEIPASS)
 
-    return Path(base_path) / relative_path
+    # Dev mode: base is the root of the `src` directory for the project
+    else:
+        base_path = pathlib.Path(__file__).parent.parent.parent.parent
+
+    return base_path
+
+
+def get_project_root_path() -> pathlib.Path:
+    """Get absolute path of a relative resource to the app; works for both dev mode and for PyInstaller."""
+    # Production: PyInstaller creates a temp folder and stores path in _MEIPASS
+    if hasattr(sys, "_MEIPASS"):
+        # PyInstaller creates a temp folder and stores path in _MEIPASS
+        base_path = pathlib.Path(sys._MEIPASS).parent
+
+    # Dev mode: base is the root of the `src` directory for the project
+    else:
+        base_path = pathlib.Path(__file__).parent.parent.parent.parent.parent
+
+    return base_path
 
 
 is_test_environment = os.environ.get("VITEST")
 
-path_config = resource_path(
-    "paths.config.json"
-)  # NOTE: Must have pyflask for running the GUIDE as a whole, but errors for just the server
-f = path_config.open()
-data = json.load(f)
-GUIDE_ROOT_FOLDER = Path(Path.home(), data["root"])
+
+path_config_file_path = get_source_base_path() / "paths.config.json"
+with open(file=path_config_file_path, mode="r") as fp:
+    path_config = json.load(fp=fp)
+GUIDE_ROOT_FOLDER = pathlib.Path.home() / path_config["root"]
 
 if is_test_environment:
     GUIDE_ROOT_FOLDER = GUIDE_ROOT_FOLDER / ".test"
 
-STUB_SAVE_FOLDER_PATH = Path(GUIDE_ROOT_FOLDER, *data["subfolders"]["preview"])
-CONVERSION_SAVE_FOLDER_PATH = Path(GUIDE_ROOT_FOLDER, *data["subfolders"]["conversions"])
-
-f.close()
+STUB_SAVE_FOLDER_PATH = pathlib.Path(GUIDE_ROOT_FOLDER, *path_config["subfolders"]["preview"])
+CONVERSION_SAVE_FOLDER_PATH = pathlib.Path(GUIDE_ROOT_FOLDER, *path_config["subfolders"]["conversions"])
 
 # Create all nested home folders
 STUB_SAVE_FOLDER_PATH.mkdir(exist_ok=True, parents=True)