Merge pull request #422 from NeurodataWithoutBorders/anomalous-linux-…

…branch

Add instructions to run on unsupported Linux machines

README.md

@@ -37,11 +37,15 @@ Run the `setup.exe` file and follow all instructions.
 
 Run the `.dmg` file and follow all instructions to move the file into your Applications folder.
 
-### Ubuntu - Graphical Interface
+### Ubuntu
+
+> **Note:** If you're running the `.AppImage` and the app window clears to a white screen within a few seconds of starting, you will need to follow the [Developer Instructions](#developer-installation) on the [linux-fix](https://github.com/neurodatawithoutborders/nwb-guide/tree/linux-fix) branch of the NWB GUIDE.
+
+#### Graphical Interface
 
 Right-click the `.AppImage` file, navigate to `permissions`, and check any box which mentions 'run as executable'.
 
-### Ubuntu - CLI
+#### Ubuntu - CLI
 
 From the terminal, simply type
 
@@ -57,6 +61,7 @@ Where you are using version `X.Y.Z`; then execute by calling
 
 
 
+
 ## Developer Installation
 
 Start by cloning the repository

pyflask/manageNeuroconv/info/urls.py

@@ -29,6 +29,5 @@ def resource_path(relative_path):
 
 # Create all nested home folders
 STUB_SAVE_FOLDER_PATH.mkdir(exist_ok=True, parents=True)
-CONVERSION_SAVE_FOLDER_PATH.mkdir(exist_ok=True, parents=True) 
+CONVERSION_SAVE_FOLDER_PATH.mkdir(exist_ok=True, parents=True)
 TUTORIAL_SAVE_FOLDER_PATH.mkdir(exist_ok=True, parents=True)
-

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -460,7 +460,6 @@ def upload_to_dandi(
 ):
     from neuroconv.tools.data_transfers import automatic_dandi_upload
 
-
     # CONVERSION_SAVE_FOLDER_PATH.mkdir(exist_ok=True, parents=True)  # Ensure base directory exists
 
     os.environ["DANDI_API_KEY"] = api_key  # Update API Key

src/preload/preload.js

@@ -1,13 +1,12 @@
-
-const electron = require('electron')
+const electron = require("electron");
 
 // Expose ipcRenderer
 if (process.contextIsolated) {
     try {
-      electron.contextBridge.exposeInMainWorld('electron', electron)
+        electron.contextBridge.exposeInMainWorld("electron", electron);
     } catch (error) {
-      console.error(error)
+        console.error(error);
     }
-  } else {
-    globalThis.electron = electron
-  }
+} else {
+    globalThis.electron = electron;
+}

src/renderer/src/stories/InstanceManager.js

@@ -224,11 +224,9 @@ export class InstanceManager extends LitElement {
 
         setTimeout(() => {
             Object.entries(this.#info).forEach(([id, { status }]) => {
-                if (status) this.updateState(id, status) 
-            })
-        }) // NOTE: Why is this not possible without waiting?
-
-
+                if (status) this.updateState(id, status);
+            });
+        }); // NOTE: Why is this not possible without waiting?
     };
 
     #isCategory(value) {
@@ -272,7 +270,7 @@ export class InstanceManager extends LitElement {
         });
     }
 
-    #ids = {}
+    #ids = {};
     #accordions = {};
 
     #onSelected = () => {
@@ -359,10 +357,9 @@ export class InstanceManager extends LitElement {
 
         return list;
     }
-
 
     render() {
-        this.#info = {}
+        this.#info = {};
         this.#items = [];
 
         const instances = this.#render();

src/renderer/src/stories/Table.js

@@ -65,15 +65,15 @@ export class Table extends LitElement {
         onUpdate,
         validateEmptyCells,
         onStatusChange,
-        contextMenu
+        contextMenu,
     } = {}) {
         super();
         this.schema = schema ?? {};
         this.data = data ?? [];
         this.keyColumn = keyColumn;
         this.template = template ?? {};
         this.validateEmptyCells = validateEmptyCells ?? true;
-        this.contextMenu = contextMenu ?? {}
+        this.contextMenu = contextMenu ?? {};
 
         if (onUpdate) this.onUpdate = onUpdate;
         if (validateOnChange) this.validateOnChange = validateOnChange;
@@ -288,25 +288,25 @@ export class Table extends LitElement {
         let contextMenu = ["row_below", "remove_row"];
         if (this.schema.additionalProperties) contextMenu.push("col_right", "remove_col");
 
-        console.log(this.contextMenu)
-        contextMenu = contextMenu.filter(k => !(this.contextMenu.ignore ?? []).includes(k))
+        console.log(this.contextMenu);
+        contextMenu = contextMenu.filter((k) => !(this.contextMenu.ignore ?? []).includes(k));
 
-        const descriptionEl = this.querySelector('#description')
+        const descriptionEl = this.querySelector("#description");
         const operations = {
             rows: [],
-            columns: []
-        }
-        
-        if (contextMenu.includes('row_below')) operations.rows.push('add')
-        if (contextMenu.includes('remove_row')) operations.rows.push('remove')
-        if (contextMenu.includes('col_right')) operations.columns.push('add')
-        if (contextMenu.includes('remove_col')) operations.columns.push('remove')
-        const operationSet = new Set(Object.values(operations).flat())
-        const operationOn = Object.keys(operations).filter(k => operations[k].length)
+            columns: [],
+        };
+
+        if (contextMenu.includes("row_below")) operations.rows.push("add");
+        if (contextMenu.includes("remove_row")) operations.rows.push("remove");
+        if (contextMenu.includes("col_right")) operations.columns.push("add");
+        if (contextMenu.includes("remove_col")) operations.columns.push("remove");
+        const operationSet = new Set(Object.values(operations).flat());
+        const operationOn = Object.keys(operations).filter((k) => operations[k].length);
 
         if (operationSet.size) {
-            const desc = `Right click to ${Array.from(operationSet).join('/')} ${operationOn.join('and')}.`
-            descriptionEl.innerText = desc
+            const desc = `Right click to ${Array.from(operationSet).join("/")} ${operationOn.join("and")}.`;
+            descriptionEl.innerText = desc;
         }
 
         const table = new Handsontable(div, {

src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js

@@ -28,8 +28,7 @@ const filter = (list, toFilter) => {
     });
 };
 
-
-const emptyMessage = 'No issues detected in these files!'
+const emptyMessage = "No issues detected in these files!";
 
 export class GuidedInspectorPage extends Page {
     constructor(...args) {
@@ -58,11 +57,11 @@ export class GuidedInspectorPage extends Page {
 
     getStatus = (list) => {
         return list.reduce((acc, o) => {
-            const res = getMessageType(o)
-            if (acc === 'error') return acc
-            else return res
-        }, 'valid') 
-    }
+            const res = getMessageType(o);
+            if (acc === "error") return acc;
+            else return res;
+        }, "valid");
+    };
 
     render() {
         const { globalState } = this.info;
@@ -80,8 +79,6 @@ export class GuidedInspectorPage extends Page {
             .flat();
         return html` ${until(
             (async () => {
-
-
                 if (fileArr.length <= 1) {
                     const items =
                         inspector ??
@@ -101,58 +98,54 @@ export class GuidedInspectorPage extends Page {
                     return truncateFilePaths(report, path);
                 })();
 
-    
                 const _instances = fileArr.map(({ subject, session, info }) => {
+                    const file_path = [`sub-${subject}`, `sub-${subject}_ses-${session}`];
+                    const filtered = removeFilePaths(filter(items, { file_path }));
 
-                    const file_path = [`sub-${subject}`, `sub-${subject}_ses-${session}`] 
-                    const filtered = removeFilePaths(filter(items, { file_path }))
-
-                    const display = () => new InspectorList({ items: filtered, emptyMessage })
-                    display.status = this.getStatus(filtered)
+                    const display = () => new InspectorList({ items: filtered, emptyMessage });
+                    display.status = this.getStatus(filtered);
 
                     return {
                         subject,
                         session,
-                        display
+                        display,
                     };
                 });
 
                 const instances = _instances.reduce((acc, { subject, session, display }) => {
-                    const subLabel = `sub-${subject}`
+                    const subLabel = `sub-${subject}`;
                     if (!acc[`sub-${subject}`]) acc[subLabel] = {};
                     acc[subLabel][`ses-${session}`] = display;
                     return acc;
                 }, {});
 
                 Object.keys(instances).forEach((subLabel) => {
-
                     const subItems = filter(items, { file_path: `${subLabel}${nodePath.sep}${subLabel}_ses-` }); // NOTE: This will not run on web-only now
                     const path = getSharedPath(subItems.map((o) => o.file_path));
-                    const filtered = truncateFilePaths(subItems, path)
+                    const filtered = truncateFilePaths(subItems, path);
 
-                    const display = () => new InspectorList({ items: filtered, emptyMessage })
-                    display.status = this.getStatus(filtered)
+                    const display = () => new InspectorList({ items: filtered, emptyMessage });
+                    display.status = this.getStatus(filtered);
 
                     instances[subLabel] = {
                         ["All Files"]: display,
                         ...instances[subLabel],
                     };
                 });
 
-                const allDisplay = () => new InspectorList({ items, emptyMessage })
-                allDisplay.status = this.getStatus(items)
+                const allDisplay = () => new InspectorList({ items, emptyMessage });
+                allDisplay.status = this.getStatus(items);
 
-                
                 const allInstances = {
                     ["All Files"]: allDisplay,
                     ...instances,
-                }
+                };
 
                 const manager = new InstanceManager({
-                    instances:allInstances
+                    instances: allInstances,
                 });
-                
-                return manager
+
+                return manager;
             })(),
             ""
         )}`;

src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js

@@ -88,7 +88,7 @@ export class GuidedSubjectsPage extends Page {
             keyColumn: "subject_id",
             validateEmptyCells: false,
             contextMenu: {
-                ignore: ['row_below']
+                ignore: ["row_below"],
             },
             onUpdate: () => {
                 this.unsavedUpdates = true;

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

@@ -20,7 +20,7 @@ export function getSharedPath(array) {
         }
     });
 
-    return shared ? path.normalize(shared.join("/")) : ''; // Convert back to OS-specific path
+    return shared ? path.normalize(shared.join("/")) : ""; // Convert back to OS-specific path
 }
 
 export function truncateFilePaths(items, basepath) {

src/renderer/src/stories/preview/inspector/InspectorList.js

@@ -42,7 +42,7 @@ export class InspectorList extends List {
     }
 
     constructor(props) {
-        const { items } = props
+        const { items } = props;
         const aggregatedItems = Object.values(aggregateMessages(items)).map((items) => {
             const aggregate = { ...items.pop() }; // Create a base object for the aggregation
             aggregate.files = [aggregate.file_path, ...items.map((o) => o.file_path)];
@@ -57,7 +57,7 @@ export class InspectorList extends List {
                 const item = new InspectorListItem(o);
                 item.style.flexGrow = "1";
                 return { content: item };
-            })
+            }),
         });
     }
 }
@@ -133,8 +133,8 @@ export class InspectorListItem extends LitElement {
     render() {
         this.type = getMessageType({
             ...this,
-            type: this.ORIGINAL_TYPE
-        })
+            type: this.ORIGINAL_TYPE,
+        });
 
         this.setAttribute("title", this.message);
 

src/renderer/src/validation/index.js

@@ -4,7 +4,7 @@ import validationSchema from "./validation";
 
 // NOTE: Only validation missing on NWBFile Metadata is check_subject_exists and check_processing_module_name
 
-export const isErrorImportance = ["PYNWB_VALIDATION", "CRITICAL", "ERROR"]
+export const isErrorImportance = ["PYNWB_VALIDATION", "CRITICAL", "ERROR"];
 export function getMessageType(item) {
     return item.type ?? (isErrorImportance.includes(item.importance) ? "error" : "warning");
 }