Merge pull request #326 from NeurodataWithoutBorders/preview-inspecto…

…r-results

Preview Inspector Results

pyflask/apis/neuroconv.py

@@ -122,6 +122,78 @@ def post(self):
                 neuroconv_api.abort(500, str(e))
 
 
+@neuroconv_api.route("/inspect_file")
+class InspectNWBFile(Resource):
+    @neuroconv_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            import json
+            from nwbinspector import inspect_nwbfile
+            from nwbinspector.nwbinspector import InspectorOutputJSONEncoder
+
+            return json.loads(
+                json.dumps(
+                    list(
+                        inspect_nwbfile(
+                            ignore=[
+                                "check_description",
+                                "check_data_orientation",
+                            ],  # TODO: remove when metadata control is exposed
+                            **neuroconv_api.payload,
+                        )
+                    ),
+                    cls=InspectorOutputJSONEncoder,
+                )
+            )
+
+        except Exception as e:
+            if notBadRequestException(e):
+                neuroconv_api.abort(500, str(e))
+
+
+@neuroconv_api.route("/inspect_folder")
+class InspectNWBFolder(Resource):
+    @neuroconv_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            import json
+            from nwbinspector import inspect_all
+            from nwbinspector.nwbinspector import InspectorOutputJSONEncoder
+
+            messages = list(
+                inspect_all(
+                    n_jobs=-2,  # uses number of CPU - 1
+                    ignore=[
+                        "check_description",
+                        "check_data_orientation",
+                    ],  # TODO: remove when metadata control is exposed
+                    **neuroconv_api.payload,
+                )
+            )
+
+            return json.loads(json.dumps(messages, cls=InspectorOutputJSONEncoder))
+
+        except Exception as e:
+            if notBadRequestException(e):
+                neuroconv_api.abort(500, str(e))
+
+
+@neuroconv_api.route("/html")
+class NWBToHTML(Resource):
+    @neuroconv_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})
+    def post(self):
+        try:
+            from pynwb import NWBHDF5IO
+
+            with NWBHDF5IO(neuroconv_api.payload.nwbfile_path, mode="r") as io:
+                html = io.read()._repr_html_()
+            return html
+
+        except Exception as e:
+            if notBadRequestException(e):
+                neuroconv_api.abort(500, str(e))
+
+
 @neuroconv_api.route("/generate_dataset")
 class GenerateDataset(Resource):
     @neuroconv_api.doc(responses={200: "Success", 400: "Bad Request", 500: "Internal server error"})

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -327,7 +327,7 @@ def update_conversion_progress(**kwargs):
         if not default_output_directory.exists():
             os.symlink(resolved_output_directory, default_output_directory)
 
-    return str(resolved_output_path)
+    return dict(file=str(resolved_output_path))
 
 
 def upload_to_dandi(

src/renderer/src/index.ts

@@ -50,7 +50,7 @@ async function isOffline() {
   await Swal.fire({
     title: "No Internet Connection",
     icon: "warning",
-    text: "It appears that your computer is not connected to the internet. You may continue, but you will not be able to use features of NWB GUIDE related to uploading data to DANDI.",
+    text: "You may continue, but certain features (e.g. uploading data to DANDI, viewing data on Neurosift, etc.) will be unavailable.",
     heightAuto: false,
     backdrop: "rgba(0,0,0, 0.4)",
     confirmButtonText: "I understand",
@@ -87,7 +87,7 @@ async function checkInternetConnection() {
     window.addEventListener('online', isOnline);
     window.addEventListener('offline', isOffline);
 
-    let hasInternet = navigator.onLine
+    const hasInternet = navigator.onLine
     if (hasInternet) isOnline()
     else await isOffline()
 

src/renderer/src/stories/InstanceManager.js

@@ -132,13 +132,20 @@ export class InstanceManager extends LitElement {
         this.instances = props.instances ?? {};
         this.header = props.header;
         this.instanceType = props.instanceType ?? "Instance";
-        if (props.renderInstance) this.renderInstance = props.renderInstance;
         if (props.onAdded) this.onAdded = props.onAdded;
         if (props.onRemoved) this.onRemoved = props.onRemoved;
         this.controls = props.controls ?? [];
     }
 
-    renderInstance = (_, value) => value.content ?? value;
+    #dynamicInstances = {};
+
+    getInstanceContent = ({ id, metadata }) => {
+        const content = metadata.content ?? metadata;
+        if (typeof content === "function") {
+            this.#dynamicInstances[id] = content;
+            return "";
+        } else return content;
+    };
 
     updateState = (id, state) => {
         const item = this.#items.find((i) => i.id === id);
@@ -211,6 +218,8 @@ export class InstanceManager extends LitElement {
                 el.removeAttribute("selected");
                 this.shadowRoot.querySelector(`div[data-instance="${instance}"]`).setAttribute("hidden", "");
             });
+
+        this.#onSelected();
     };
 
     #isCategory(value) {
@@ -258,6 +267,13 @@ export class InstanceManager extends LitElement {
     #onSelected = () => {
         const selected = this.shadowRoot.querySelector("#selectedName");
         selected.innerText = this.#selected;
+
+        const dynamic = this.#dynamicInstances[this.#selected];
+        if (typeof dynamic === "function") {
+            this.shadowRoot
+                .querySelector(`div[data-instance="${this.#selected}"]`)
+                .append((this.#dynamicInstances[this.#selected] = dynamic()));
+        }
     };
 
     #render(toRender = this.instances, path = []) {
@@ -293,7 +309,7 @@ export class InstanceManager extends LitElement {
 
         const list = html`
             ${Object.entries(instances).map(([key, info], i) => {
-                if (info instanceof HTMLElement) info = { content: info };
+                if (info instanceof HTMLElement || typeof info === "function") info = { content: info };
                 const listItemInfo = {
                     id: key,
                     label: key.split("/").pop(),
@@ -399,7 +415,7 @@ export class InstanceManager extends LitElement {
                 </div>
                 <div id="content">
                     <div class="controls">
-                        <span id="selectedName">${this.#selected}</span>
+                        <span id="selectedName"></span>
                         <div>
                             ${this.controls.map((o) => {
                                 return html`<nwb-button
@@ -422,7 +438,7 @@ export class InstanceManager extends LitElement {
                         ${this.#items.map((item, i) => {
                             return html`
                                 <div data-instance="${item.id}" ?hidden=${this.#selected !== item.id}>
-                                    ${this.renderInstance(item.id, item.metadata)}
+                                    ${this.getInstanceContent(item)}
                                 </div>
                             `;
                         })}

src/renderer/src/stories/JSONSchemaForm.js

@@ -8,6 +8,7 @@ import { merge } from "./pages/utils";
 import { resolveProperties } from "./pages/guided-mode/data/utils";
 
 import { JSONSchemaInput } from "./JSONSchemaInput";
+import { InspectorListItem } from "./preview/inspector/InspectorList";
 
 const componentCSS = `
 
@@ -29,30 +30,6 @@ const componentCSS = `
       background: rgb(255, 229, 228) !important;
     }
 
-    .errors {
-      color: #9d0b0b;
-    }
-
-    .errors > * {
-      padding: 25px;
-      background: #f8d7da;
-      border: 1px solid #f5c2c7;
-      border-radius: 4px;
-      margin: 0 0 1em;
-    }
-
-    .warnings {
-      color: #856404;
-    }
-
-    .warnings > * {
-      padding: 25px;
-      background: #fff3cd;
-      border: 1px solid #ffeeba;
-      border-radius: 4px;
-      margin: 0 0 1em;
-    }
-
     .guided--form-label {
       display: block;
       width: 100%;
@@ -277,9 +254,8 @@ export class JSONSchemaForm extends LitElement {
     #addMessage = (name, message, type) => {
         if (Array.isArray(name)) name = name.join("-"); // Convert array to string
         const container = this.shadowRoot.querySelector(`#${name} .${type}`);
-        const p = document.createElement("p");
-        p.innerText = message;
-        container.appendChild(p);
+        const item = new InspectorListItem(message);
+        container.appendChild(item);
     };
 
     #clearMessages = (fullPath, type) => {
@@ -625,7 +601,7 @@ export class JSONSchemaForm extends LitElement {
         this.checkStatus();
 
         // Show aggregated errors and warnings (if any)
-        warnings.forEach((info) => this.#addMessage(fullPath, info.message, "warnings"));
+        warnings.forEach((info) => this.#addMessage(fullPath, info, "warnings"));
 
         const isFunction = typeof valid === "function";
 
@@ -658,7 +634,7 @@ export class JSONSchemaForm extends LitElement {
                 [...path, name]
             );
 
-            errors.forEach((info) => this.#addMessage(fullPath, info.message, "errors"));
+            errors.forEach((info) => this.#addMessage(fullPath, info, "errors"));
             // element.title = errors.map((info) => info.message).join("\n"); // Set all errors to show on hover
 
             return false;

src/renderer/src/stories/List.stories.js

@@ -6,9 +6,11 @@ export default {
 
 const Template = (args) => new List(args);
 
+const generateString = () => Math.floor(Math.random() * Date.now()).toString(36);
+
 export const Default = Template.bind({});
 Default.args = {
-    items: [{ value: "test" }],
+    items: [{ value: "test" }, { value: Array.from({ length: 1000 }).map(generateString).join("") }],
 };
 
 export const WithKeys = Template.bind({});