[Refactor Flask II] Break up top-level

src/electron/renderer/src/server/globals.ts

@@ -56,7 +56,7 @@ export const activateServer = () => {
 export const serverGlobals = {
     species: new Promise((res, rej) => {
       onServerOpen(() => {
-        fetch(new URL("get-recommended-species", baseUrl))
+        fetch(new URL("/dandi/get-recommended-species", baseUrl))
           .then((res) => res.json())
           .then((species) => {
             res(species)
@@ -67,7 +67,7 @@ export const serverGlobals = {
     }),
     cpus: new Promise((res, rej) => {
       onServerOpen(() => {
-        fetch(new URL("cpus", baseUrl))
+        fetch(new URL("/system/cpus", baseUrl))
           .then((res) => res.json())
           .then((cpus) => {
             res(cpus)

src/electron/renderer/src/stories/pages/preview/PreviewPage.js

@@ -18,7 +18,12 @@ export class PreviewPage extends Page {
 
     updatePath = async (path) => {
         if (path) {
-            const result = await fetch(`${baseUrl}/files/${path}`, { method: "POST" }).then((res) => res.text());
+            // Enable access to the explicit file path
+            const result = await fetch(`${baseUrl}/files/${path}`, {
+                method: "POST",
+            }).then((res) => res.text());
+
+            // Set Neurosift to access the returned URL
             if (result) this.neurosift.url = result;
         } else this.neurosift.url = undefined;
     };

src/electron/renderer/src/stories/preview/NWBFilePreview.js

@@ -56,7 +56,10 @@ class NWBPreviewInstance extends LitElement {
         const isOnline = navigator.onLine;
 
         return isOnline
-            ? new Neurosift({ url: getURLFromFilePath(this.file, this.project), fullscreen: false })
+            ? new Neurosift({
+                  url: getURLFromFilePath(this.file, this.project),
+                  fullscreen: false,
+              })
             : until(
                   (async () => {
                       const htmlRep = await run("html", { nwbfile_path: this.file }, { swal: false });

src/electron/renderer/src/stories/preview/Neurosift.js

@@ -80,7 +80,9 @@ export class Neurosift extends LitElement {
     render() {
         return this.url
             ? html` <div class="loader-container">
-                      ${new Loader({ message: `Loading Neurosift view...<br/><small>${this.url}</small>` })}
+                      ${new Loader({
+                          message: `Loading Neurosift view...<br/><small>${this.url}</small>`,
+                      })}
                   </div>
                   ${this.fullscreen ? new FullScreenToggle({ target: this }) : ""}
                   <iframe

src/pyflask/app.py

@@ -1,5 +1,6 @@
 """The primary Flask server for the Python backend."""
 
+import collections
 import json
 import multiprocessing
 import sys
@@ -10,13 +11,12 @@
 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()
 
-
-from apis import data_api, neuroconv_api, startup_api
 from flask import Flask, request, send_file, send_from_directory
 from flask_cors import CORS
 from flask_restx import Api, Resource
@@ -27,12 +27,22 @@
     is_packaged,
     resource_path,
 )
+from namespaces import (
+    dandi_namespace,
+    data_namespace,
+    neuroconv_namespace,
+    neurosift_namespace,
+    startup_namespace,
+    system_namespace,
+)
 
-app = Flask(__name__)
+neurosift_file_registry = collections.defaultdict(bool)
+
+flask_app = Flask(__name__)
 
 # Always enable CORS to allow distinct processes to handle frontend vs. backend
-CORS(app)
-app.config["CORS_HEADERS"] = "Content-Type"
+CORS(flask_app)
+flask_app.config["CORS_HEADERS"] = "Content-Type"
 
 # Create logger configuration
 LOG_FOLDER = Path(GUIDE_ROOT_FOLDER, "logs")
@@ -50,63 +60,39 @@
     title="NWB GUIDE API",
     description="The REST API for the NWB GUIDE provided by the Python Flask Server.",
 )
-api.add_namespace(startup_api)
-api.add_namespace(neuroconv_api)
-api.add_namespace(data_api)
-api.init_app(app)
+api.add_namespace(startup_namespace)
+api.add_namespace(neuroconv_namespace)
+api.add_namespace(data_namespace)
+api.add_namespace(system_namespace)
+api.add_namespace(dandi_namespace)
+# api.add_namespace(neurosift_namespace)  # TODO: enable later
+api.init_app(flask_app)
 
-registered = {}
 
+@flask_app.route("/preview/<path:file_path>")
+def send_preview(file_path):
+    return send_from_directory(directory=STUB_SAVE_FOLDER_PATH, path=file_path)
 
-@app.route("/files")
-def get_all_files():
-    return list(registered.keys())
 
+@flask_app.route("/files/<path:file_path>", methods=["GET", "POST"])
+def handle_file_request(file_path) -> Union[str, None]:
+    if ".nwb" not in file_path:
+        raise ValueError("This endpoint must be called on an NWB file!")
 
-@app.route("/files/<path:path>", methods=["GET", "POST"])
-def handle_file_request(path):
     if request.method == "GET":
-        if registered[path]:
-            path = unquote(path)
-            if not isabs(path):
-                path = f"/{path}"
-            return send_file(path)
+        if neurosift_file_registry[file_path] is True:
+            file_path = unquote(file_path)
+            if not isabs(file_path):
+                file_path = f"/{file_path}"
+
+            return send_file(path_or_file=file_path)
         else:
             app.abort(404, "Resource is not accessible.")
 
     else:
-        if ".nwb" in path:
-            registered[path] = True
-            return request.base_url
-        else:
-            app.abort(400, str("Path does not point to an NWB file."))
-
-
-@app.route("/conversions/<path:path>")
-def send_conversions(path):
-    return send_from_directory(CONVERSION_SAVE_FOLDER_PATH, path)
-
-
-@app.route("/preview/<path:path>")
-def send_preview(path):
-    return send_from_directory(STUB_SAVE_FOLDER_PATH, path)
-
-
-@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)
-
-
-@app.route("/get-recommended-species")
-def get_species():
-    from dandi.metadata.util import species_map
+        neurosift_file_registry[file_path] = True
 
-    return species_map
+        return request.base_url
 
 
 @api.route("/log")
@@ -154,13 +140,13 @@ def get(self):
         )
         log_handler.setFormatter(log_formatter)
 
-        app.logger.addHandler(log_handler)
-        app.logger.setLevel(DEBUG)
+        flask_app.logger.addHandler(log_handler)
+        flask_app.logger.setLevel(DEBUG)
 
-        app.logger.info(f"Logging to {LOG_FILE_PATH}")
+        flask_app.logger.info(f"Logging to {LOG_FILE_PATH}")
 
         # Run the server
         api.logger.info(f"Starting server on port {port}")
-        app.run(host="127.0.0.1", port=port)
+        flask_app.run(host="127.0.0.1", port=port)
     else:
         raise Exception("No port provided for the NWB GUIDE backend.")

src/pyflask/namespaces/__init__.py

@@ -0,0 +1,6 @@
+from .dandi import dandi_namespace
+from .data import data_namespace
+from .neuroconv import neuroconv_namespace
+from .neurosift import neurosift_namespace
+from .startup import startup_namespace
+from .system import system_namespace

src/pyflask/namespaces/dandi.py

@@ -0,0 +1,24 @@
+"""An API for handling requests to the DANDI Python API."""
+
+from typing import List, Tuple, Union
+
+import flask_restx
+
+dandi_namespace = flask_restx.Namespace(
+    name="dandi", description="Request various static listings from the DANDI Python API."
+)
+
+
+@dandi_namespace.route("/get-recommended-species")
+class SupportedSpecies(flask_restx.Resource):
+
+    @dandi_namespace.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."
+        ),
+    )
+    def get(self) -> Union[List[Tuple[List[str], str, str, str]], None]:
+        from dandi.metadata.util import species_map
+
+        return species_map

src/pyflask/apis/data.py → src/pyflask/namespaces/data.py

@@ -5,10 +5,10 @@
 from flask_restx import Namespace, Resource, reqparse
 from manageNeuroconv import generate_dataset, generate_test_data
 
-data_api = Namespace("data", description="API route for dataset generation in the NWB GUIDE.")
+data_namespace = Namespace("data", description="API route for dataset generation in the NWB GUIDE.")
 
 
-@data_api.errorhandler(Exception)
+@data_namespace.errorhandler(Exception)
 def exception_handler(error):
     exceptiondata = traceback.format_exception(type(error), error, error.__traceback__)
     return {"message": exceptiondata[-1], "traceback": "".join(exceptiondata)}
@@ -18,16 +18,16 @@ def exception_handler(error):
 generate_test_data_parser.add_argument("output_path", type=str, required=True)
 
 
-@data_api.route("/generate")
-@data_api.expect(generate_test_data_parser)
+@data_namespace.route("/generate")
+@data_namespace.expect(generate_test_data_parser)
 class GeneratetestData(Resource):
-    @data_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    @data_namespace.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         try:
             arguments = generate_test_data_parser.parse_args()
             generate_test_data(output_path=arguments["output_path"])
         except Exception as exception:
-            data_api.abort(500, str(exception))
+            data_namespace.abort(500, str(exception))
             raise exception
 
 
@@ -36,14 +36,14 @@ def post(self):
 generate_test_dataset_parser.add_argument("input_path", type=str, required=True)
 
 
-@data_api.route("/generate/dataset")
-@data_api.expect(generate_test_data_parser)
+@data_namespace.route("/generate/dataset")
+@data_namespace.expect(generate_test_data_parser)
 class GenerateDataset(Resource):
-    @data_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    @data_namespace.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         try:
             arguments = generate_test_dataset_parser.parse_args()
             return generate_dataset(input_path=arguments["input_path"], output_path=arguments["output_path"])
 
         except Exception as exception:
-            data_api.abort(500, str(exception))
+            data_namespace.abort(500, str(exception))