Update based on suggestions

NeurodataWithoutBorders · Sep 26, 2023 · 973ab33 · 973ab33
1 parent 1f85f8e
commit 973ab33
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Showing 20 changed files with 44 additions and 42 deletions.
diff --git a/paths.config.json b/paths.config.json
@@ -3,7 +3,7 @@
     "subfolders": {
         "progress": ["pipelines"],
         "conversions": ["conversions"],
-        "stubs": ["stubs"],
+        "preview": ["preview"],
         "tutorial": ["tutorial"]
     }
 }
diff --git a/pyflask/app.py b/pyflask/app.py
@@ -84,8 +84,8 @@ def send_conversions(path):
     return send_from_directory(CONVERSION_SAVE_FOLDER_PATH, path)
 
 
-@app.route("/stubs/<path:path>")
-def send_stubs(path):
+@app.route("/preview/<path:path>")
+def send_preview(path):
     return send_from_directory(STUB_SAVE_FOLDER_PATH, path)
 
 

diff --git a/pyflask/manageNeuroconv/info/urls.py b/pyflask/manageNeuroconv/info/urls.py
@@ -20,7 +20,7 @@ def resource_path(relative_path):
 )  # 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)
-STUB_SAVE_FOLDER_PATH = Path(Path.home(), data["root"], *data["subfolders"]["stubs"])
+STUB_SAVE_FOLDER_PATH = Path(Path.home(), data["root"], *data["subfolders"]["preview"])
 CONVERSION_SAVE_FOLDER_PATH = Path(Path.home(), data["root"], *data["subfolders"]["conversions"])
 TUTORIAL_SAVE_FOLDER_PATH = Path(Path.home(), data["root"], *data["subfolders"]["tutorial"])
 

diff --git a/schemas/json/project/globals.json b/schemas/json/project/globals.json
@@ -6,10 +6,10 @@
             "description": "Provide a custom output location for your NWB files. Will default to ~/NWB_GUIDE/conversions"
         },
 
-        "stub_output_folder": {
+        "preview_output_folder": {
             "type": "string",
             "format": "directory",
-            "description": "Provide a custom output location for your NWB stub files. Will default to ~/NWB_GUIDE/stubs"
+            "description": "Provide a custom output location for your NWB stub files. Will default to ~/NWB_GUIDE/preview. These files are expected to much smaller than the conversion files (only ~MB in scale)."
         }
     }
 }
diff --git a/src/renderer/src/dependencies/simple.js b/src/renderer/src/dependencies/simple.js
@@ -12,8 +12,8 @@ export const homeDirectory = app?.getPath("home") ?? "";
 export const appDirectory = homeDirectory ? joinPath(homeDirectory, paths.root) : "";
 export const guidedProgressFilePath = homeDirectory ? joinPath(appDirectory, ...paths.subfolders.progress) : "";
 
-export const stubSaveFolderPath = homeDirectory
-    ? joinPath(homeDirectory, paths["root"], ...paths.subfolders.stubs)
+export const previewSaveFolderPath = homeDirectory
+    ? joinPath(homeDirectory, paths["root"], ...paths.subfolders.preview)
     : "";
 export const conversionSaveFolderPath = homeDirectory
     ? joinPath(homeDirectory, paths["root"], ...paths.subfolders.conversions)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
@@ -4,9 +4,7 @@ import {
     guidedProgressFilePath,
     reloadPageToHome,
     isStorybook,
-    appDirectory,
-    stubSaveFolderPath,
-    conversionSaveFolderPath,
+    appDirectory
 } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
 import { joinPath, runOnLoad } from "../globals.js";

diff --git a/src/renderer/src/progress/operations.js b/src/renderer/src/progress/operations.js
@@ -1,5 +1,5 @@
 import { joinPath } from "../globals";
-import { conversionSaveFolderPath, guidedProgressFilePath, stubSaveFolderPath } from "../dependencies/simple";
+import { conversionSaveFolderPath, guidedProgressFilePath, previewSaveFolderPath } from "../dependencies/simple";
 import { fs } from "../electron";
 
 export const remove = (name) => {
@@ -11,8 +11,8 @@ export const remove = (name) => {
     else localStorage.removeItem(progressFilePathToDelete);
 
     if (fs) {
-        // delete default stub location
-        fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
+        // delete default preview location
+        fs.rmSync(joinPath(previewSaveFolderPath, name), { recursive: true, force: true });
 
         // delete default conversion location
         fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });

diff --git a/src/renderer/src/stories/Main.js b/src/renderer/src/stories/Main.js
@@ -4,6 +4,8 @@ import { GuidedFooter } from "./pages/guided-mode/GuidedFooter";
 import { GuidedCapsules } from "./pages/guided-mode/GuidedCapsules.js";
 import { GuidedHeader } from "./pages/guided-mode/GuidedHeader.js";
 
+import { unsafeHTML } from "lit/directives/unsafe-html.js";
+
 const componentCSS = `
     :host {
         display: grid;
@@ -147,7 +149,7 @@ export class Main extends LitElement {
                               >
                                   <div style="white-space: nowrap; overflow: hidden; text-overflow: ellipsis;">
                                       <h1 class="title" style="margin: 0; padding: 0;">${title}</h1>
-                                      <small style="color: gray;">${subtitle}</small>
+                                      <small style="color: gray;">${unsafeHTML(subtitle)}</small>
                                   </div>
                                   <div style="padding-left: 25px">${controls}</div>
                               </div>

diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
@@ -151,7 +151,7 @@ export class Page extends LitElement {
             const { subject, session, globalState = this.info.globalState } = info;
             const file = `sub-${subject}/sub-${subject}_ses-${session}.nwb`;
 
-            const { conversion_output_folder, stub_output_folder, name } = globalState.project;
+            const { conversion_output_folder, preview_output_folder, name } = globalState.project;
 
             // Resolve the correct session info from all of the metadata for this conversion
             const sessionInfo = {
@@ -161,7 +161,7 @@ export class Page extends LitElement {
 
             const result = await runConversion(
                 {
-                    output_folder: conversionOptions.stub_test ? stub_output_folder : conversion_output_folder,
+                    output_folder: conversionOptions.stub_test ? preview_output_folder : conversion_output_folder,
                     project_name: name,
                     nwbfile_path: file,
                     overwrite: true, // We assume override is true because the native NWB file dialog will not allow the user to select an existing file (unless they approve the overwrite)

diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedSourceData.js
@@ -20,7 +20,7 @@ export class GuidedSourceDataPage extends ManagedPage {
     };
 
     header = {
-        subtitle: "Essential information about the source files for this conversion",
+        subtitle: "Specify the file and folder locations on your local system for each interface, as well as any additional details that might be required",
     };
 
     footer = {

diff --git a/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js b/src/renderer/src/stories/pages/guided-mode/data/GuidedStructure.js
@@ -30,7 +30,7 @@ export class GuidedStructurePage extends Page {
     }
 
     header = {
-        subtitle: "Required interfaces for this conversion",
+        subtitle: "Select all interfaces which apply to this experiment",
     };
 
     search = new Search({

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedInspectorPage.js
@@ -33,7 +33,7 @@ export class GuidedInspectorPage extends Page {
     }
 
     header = {
-        subtitle: () => `${getStubArray(this.info.globalState.preview.stubs).length} Files`,
+        subtitle: `The NWB Inspector has scanned your files for adherence to <a target="_blank" href="https://nwbinspector.readthedocs.io/en/dev/best_practices/best_practices_index.html">best practices</a>`,
         controls: () =>
             html`<nwb-button
                 size="small"

diff --git a/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js b/src/renderer/src/stories/pages/guided-mode/options/GuidedStubPreview.js
@@ -19,7 +19,7 @@ export class GuidedStubPreviewPage extends Page {
     }
 
     header = {
-        subtitle: () => `${getStubArray(this.info.globalState.preview.stubs).length} Files`,
+        subtitle: `Preview file contents on truncated files using the Neurosift application`,
         controls: () =>
             html`<nwb-button
                 size="small"

diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
@@ -29,7 +29,7 @@ export class GuidedNewDatasetPage extends Page {
     #nameNotification;
 
     header = {
-        subtitle: "Essential metadata for pipeline creation",
+        subtitle: "Enter a name for this pipeline and specify the base folders to save all outputs to",
     };
 
     footer = {
@@ -97,7 +97,7 @@ export class GuidedNewDatasetPage extends Page {
 
         pages.forEach((page) => {
             page.header = {
-                subtitle: `Uniform ${page.info.label} metadata across all sessions`,
+                subtitle: `Enter any ${page.info.label}-level metadata that can serve as the common default across each experiment session`,
             };
             this.addPage(page.info.label, page);
         });

diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedSubjects.js
@@ -13,7 +13,7 @@ export class GuidedSubjectsPage extends Page {
     }
 
     header = {
-        subtitle: "Uniform metadata for the subjects included in this conversion",
+        subtitle: "Enter all metadata known about each experiment subject",
     };
 
     beforeSave = () => {

diff --git a/src/renderer/src/stories/pages/inspect/InspectPage.js b/src/renderer/src/stories/pages/inspect/InspectPage.js
@@ -14,6 +14,7 @@ export class InspectPage extends Page {
         super(...args);
     }
 
+
     showReport = async (value) => {
         if (!value) {
             const message = "Please provide a folder to inspect.";

diff --git a/src/renderer/src/stories/pages/preview/PreviewPage.js b/src/renderer/src/stories/pages/preview/PreviewPage.js
@@ -6,6 +6,7 @@ import { Neurosift } from "../../preview/Neurosift.js";
 import { baseUrl } from "../../../globals.js";
 
 export class PreviewPage extends Page {
+
     constructor(...args) {
         super(...args);
     }

diff --git a/src/renderer/src/stories/preview/Neurosift.js b/src/renderer/src/stories/preview/Neurosift.js
@@ -5,7 +5,7 @@ import { Loader } from "../Loader";
 
 export function getURLFromFilePath(file, projectName) {
     const regexp = new RegExp(`.+(${projectName}.+)`);
-    return `${baseUrl}/stubs/${file.match(regexp)[1]}`;
+    return `${baseUrl}/preview/${file.match(regexp)[1]}`;
 }
 
 export class Neurosift extends LitElement {

diff --git a/src/renderer/src/stories/preview/inspector/test.json b/src/renderer/src/stories/preview/inspector/test.json
@@ -7,7 +7,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
     },
     {
         "message": "Experiment description is missing.",
@@ -17,7 +17,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
     },
     {
         "message": "Metadata /general/institution is missing.",
@@ -27,7 +27,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
     },
     {
         "message": "Metadata /general/keywords is missing.",
@@ -37,7 +37,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-070623.nwb"
     },
     {
         "message": "Experimenter is missing.",
@@ -47,7 +47,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
     },
     {
         "message": "Experiment description is missing.",
@@ -57,7 +57,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
     },
     {
         "message": "Metadata /general/institution is missing.",
@@ -67,7 +67,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
     },
     {
         "message": "Metadata /general/keywords is missing.",
@@ -77,7 +77,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-070623.nwb"
     },
     {
         "message": "Experimenter is missing.",
@@ -87,7 +87,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
     },
     {
         "message": "Experiment description is missing.",
@@ -97,7 +97,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
     },
     {
         "message": "Metadata /general/institution is missing.",
@@ -107,7 +107,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
     },
     {
         "message": "Metadata /general/keywords is missing.",
@@ -117,7 +117,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse2/sub-mouse2_ses-060623.nwb"
     },
     {
         "message": "Experimenter is missing.",
@@ -127,7 +127,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
     },
     {
         "message": "Experiment description is missing.",
@@ -137,7 +137,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
     },
     {
         "message": "Metadata /general/institution is missing.",
@@ -147,7 +147,7 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
     },
     {
         "message": "Metadata /general/keywords is missing.",
@@ -157,6 +157,6 @@
         "object_type": "NWBFile",
         "object_name": "root",
         "location": "/",
-        "file_path": "/Users/garrettflynn/NWB_GUIDE/stubs/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
+        "file_path": "/Users/garrettflynn/NWB_GUIDE/preview/NWB GUIDE Tutorial Data/sub-mouse1/sub-mouse1_ses-060623.nwb"
     }
 ]
diff --git a/src/renderer/src/validation/validation.json b/src/renderer/src/validation/validation.json
@@ -3,7 +3,7 @@
 
     "name": false,
     "conversion_output_folder": false,
-    "stub_output_folder": false,
+    "preview_output_folder": false,
 
     "NWBFile": {
         "identifier": false,