~~[Refactor Flask III] 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

@@ -1,12 +1,13 @@
 import { LitElement, css, html } from "lit";
 import { InspectorList } from "./inspector/InspectorList";
-import { Neurosift, getURLFromFilePath } from "./Neurosift";
+import { Neurosift } from "./Neurosift";
 import { unsafeHTML } from "lit/directives/unsafe-html.js";
 import { run } from "../pages/guided-mode/options/utils";
 import { until } from "lit/directives/until.js";
 import { InstanceManager } from "../InstanceManager";
 import { path } from "../../electron";
 import { FullScreenToggle } from "../FullScreenToggle";
+import { baseUrl } from "../../server/globals";
 
 export function getSharedPath(array) {
     array = array.map((str) => str.replace(/\\/g, "/")); // Convert to Mac-style path
@@ -55,15 +56,26 @@ class NWBPreviewInstance extends LitElement {
     render() {
         const isOnline = navigator.onLine;
 
-        return isOnline
-            ? new Neurosift({ url: getURLFromFilePath(this.file, this.project), fullscreen: false })
-            : until(
-                  (async () => {
-                      const htmlRep = await run("html", { nwbfile_path: this.file }, { swal: false });
-                      return unsafeHTML(htmlRep);
-                  })(),
-                  html`<small>Loading HTML representation...</small>`
-              );
+        if (!isOnline)
+            return until(
+                (async () => {
+                    const htmlRep = await run("html", { nwbfile_path: this.file }, { swal: false });
+                    return unsafeHTML(htmlRep);
+                })(),
+                html`<small>Loading HTML representation...</small>`
+            );
+
+        const neurosift = new Neurosift({ fullscreen: false });
+
+        // Enable access to the explicit file path
+        fetch(`${baseUrl}/files/${this.file}`, { method: "POST" })
+            .then((res) => res.text())
+            .then((result) => {
+                // Set Neurosift to access the returned URL
+                if (result) neurosift.url = result;
+            });
+
+        return neurosift;
     }
 }
 

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

@@ -2,12 +2,6 @@ import { LitElement, css, html } from "lit";
 
 import { Loader } from "../Loader";
 import { FullScreenToggle } from "../FullScreenToggle";
-import { baseUrl } from "../../server/globals";
-
-export function getURLFromFilePath(file, projectName) {
-    const regexp = new RegExp(`.+(${projectName}.+)`);
-    return `${baseUrl}/preview/${file.match(regexp)[1]}`;
-}
 
 export class Neurosift extends LitElement {
     static get styles() {
@@ -80,7 +74,9 @@ 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/apis/__init__.py

@@ -1,3 +1,15 @@
+from .dandi import dandi_api
 from .data import data_api
 from .neuroconv import neuroconv_api
+from .neurosift import neurosift_api
 from .startup import startup_api
+from .system import system_api
+
+__all__ = [
+    "neurosift_api",
+    "dandi_api",
+    "system_api",
+    "data_api",
+    "neuroconv_api",
+    "startup_api",
+]

src/pyflask/apis/dandi.py

@@ -0,0 +1,26 @@
+"""An API for handling requests to the DANDI Python API."""
+
+from typing import List, Tuple, Union
+
+import flask_restx
+
+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."
+)
+
+
+@dandi_api.route(rule="/get-recommended-species")
+class SupportedSpecies(flask_restx.Resource):
+
+    @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]),
+    )
+    @catch_exception_and_abort(api=dandi_api, code=500)
+    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

@@ -2,17 +2,16 @@
 
 import traceback
 
-from apis.utils import catch_exception_and_abort
 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_api = Namespace(name="data", description="API route for dataset generation in the NWB GUIDE.")
 
 
 @data_api.errorhandler(Exception)
 def exception_handler(error):
     exceptiondata = traceback.format_exception(type(error), error, error.__traceback__)
-    return {"message": exceptiondata[-1], "traceback": "".join(exceptiondata)}
+    return {"message": exceptiondata[-1], "traceback": "".join(exceptiondata)}, 500
 
 
 generate_test_data_parser = reqparse.RequestParser()
@@ -22,13 +21,17 @@ def exception_handler(error):
 @data_api.route("/generate")
 @data_api.expect(generate_test_data_parser)
 class GeneratetestData(Resource):
-    @data_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
 
-    # @catch_exception_and_abort(api=data_api, code=500)
+    @data_api.doc(
+        description="Generate example ecephys data using SpikeInterface.",
+    )
+    def post(self):
+        arguments = generate_test_data_parser.parse_args()
+
+    @data_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
     def post(self):
         arguments = generate_test_data_parser.parse_args()
 
-        raise NotImplementedError("test")
         generate_test_data(output_path=arguments["output_path"])
 
 
@@ -40,10 +43,8 @@ def post(self):
 @data_api.route("/generate/dataset")
 @data_api.expect(generate_test_data_parser)
 class GenerateDataset(Resource):
-    @data_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
-    @catch_exception_and_abort(api=data_api, code=500)
+
     def post(self):
         arguments = generate_test_dataset_parser.parse_args()
 
-        raise NotImplementedError("test2")
         return generate_dataset(input_path=arguments["input_path"], output_path=arguments["output_path"])

src/pyflask/apis/neuroconv.py

@@ -1,6 +1,7 @@
 """API endpoint definitions for interacting with NeuroConv."""
 
 import traceback
+from typing import Dict
 
 from flask import Response, request
 from flask_restx import Namespace, Resource, reqparse
@@ -24,16 +25,18 @@
 )
 from manageNeuroconv.info import announcer
 
-neuroconv_api = Namespace("neuroconv", description="Neuroconv neuroconv_api for the NWB GUIDE.")
+neuroconv_api = Namespace(name="neuroconv", description="Neuroconv neuroconv_api for the NWB GUIDE.")
 
 parser = reqparse.RequestParser()
-parser.add_argument("interfaces", type=str, action="split", help="Interfaces cannot be converted")
+parser.add_argument("interfaces", type=str, action="split", help="Interfaces cannot be converted.")
 
 
 @neuroconv_api.errorhandler(Exception)
-def exception_handler(error):
-    exceptiondata = traceback.format_exception(type(error), error, error.__traceback__)
-    return {"message": exceptiondata[-1], "traceback": "".join(exceptiondata)}
+def exception_handler(error: Exception) -> Dict[str, str]:
+    full_traceback = traceback.format_exception(type(error), error, error.__traceback__)
+    message = full_traceback[-1]
+    remaining_traceback = "".join(full_traceback[:-1])
+    return {"message": message, "traceback": remaining_traceback}
 
 
 @neuroconv_api.route("/")

src/pyflask/apis/neurosift.py

@@ -0,0 +1,68 @@
+"""An API for handling file system communication with the standalone Neurosift preview page."""
+
+import collections
+from typing import Union
+
+import flask
+import flask_restx
+
+from .utils import (
+    abort_if_not_nwb_file,
+    catch_exception_and_abort,
+    server_error_responses,
+)
+
+neurosift_api = flask_restx.Namespace(
+    name="neurosift", description="Handle file system communication with the " "standalone Neurosift preview page."
+)
+
+# A global in-memory registry of NWB files - much faster than asking if file is in a global list
+# Keys are NWB files; values are booleans indicating if the base URL has been exposed for that file
+neurosift_file_registry = collections.defaultdict(bool)
+
+
+@neurosift_api.route(rule="/files/<path:file_path>")
+@neurosift_api.doc(
+    description="Handle adding and fetching NWB files from the global file registry.",
+)
+class NeurosiftFileManager(flask_restx.Resource):
+
+    @neurosift_api.doc(
+        description="If the file path has been added to the registry (and therefore sent its base "
+        "URL), return the absolute file path. This is implicitly called by Neurosift.",
+        responses=server_error_responses(codes=[200, 400, 500]),
+    )
+    @catch_exception_and_abort(api=neurosift_api, code=500)
+    def get(self, file_path: str) -> Union[flask.Response, None]:
+        abort_if_not_nwb_file(file_path=file_path, api=neurosift_api)
+        if neurosift_file_registry[file_path]:
+            code = 404
+            base_message = server_error_responses(codes=[code])[code]
+            message = f"{base_message}: The base URL has not been exposed for this NWB file."
+            api.abort(code=code, message=message)
+
+            return
+
+        # Decode any URL encoding applied to the file path
+        parsed_file_path = unquote(file_path)
+
+        # Check if the file path is relative
+        is_file_relative = not isabs(parsed_file_path)
+        if is_file_relative:
+            parsed_file_path = f"/{parsed_file_path}"
+
+        return flask.send_file(path_or_file=parsed_file_path)
+
+    @neurosift_api.doc(
+        description="Add the file to a global in-memory registry (refreshes on App restart) and return "
+        "the base URL of the newly "
+        "added file",
+        responses=server_error_responses(codes=[200, 400, 500]),
+    )
+    @catch_exception_and_abort(api=neurosift_api, code=500)
+    def post(self, file_path: str) -> Union[str, None]:
+        abort_if_not_nwb_file(file_path=file_path, api=neurosift_api)
+
+        neurosift_file_registry[file_path] = True
+
+        return request.base_url

src/pyflask/apis/startup.py

@@ -2,7 +2,7 @@
 
 from flask_restx import Namespace, Resource
 
-startup_api = Namespace("startup", description="API for startup commands related to the NWB GUIDE.")
+startup_api = Namespace(name="startup", description="API for startup commands related to the NWB GUIDE.")
 
 parser = startup_api.parser()
 parser.add_argument(

src/pyflask/apis/system.py

@@ -0,0 +1,26 @@
+"""An API for handling general system information."""
+
+from typing import Dict, Union
+
+import flask_restx
+
+from .utils import catch_exception_and_abort, server_error_responses
+
+system_api = flask_restx.Namespace(name="system", description="Request various system specific information.")
+
+
+@system_api.route("/cpus")
+class SupportedSpecies(flask_restx.Resource):
+
+    @system_api.doc(
+        description="Request the number of physical and logical cores on the system.",
+        responses=server_error_responses(codes=[200, 500]),
+    )
+    @catch_exception_and_abort(api=system_api, code=500)
+    def get(self) -> Union[Dict[str, int], None]:
+        from psutil import cpu_count
+
+        physical = cpu_count(logical=False)
+        logical = cpu_count()
+
+        return dict(physical=physical, logical=logical)