Merge pull request #731 from NeurodataWithoutBorders/user-tests-updat…

…e-posttutorial

04/03/24 User Test Updates

docs/tutorials/dataset.rst

@@ -9,15 +9,15 @@ To get you started as quickly as possible, we’ve created a way to generate thi
 
   The **Phy** data format stores spike sorting results.
 
-Navigate to the **Settings** page using the main sidebar. Then press the **Generate** button in the top-right corner to initiate the dataset creation.
+Navigate to the **Settings** page using the button at the bottom of the main sidebar. Then press the **Generate** button in the top-right corner to initiate the dataset creation.
 
 .. figure:: ../assets/tutorials/dataset-creation.png
   :align: center
   :alt: Dataset Creation Screen
 
   Press the Generate button on the Settings page to create the dataset.
 
-The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory and include a ``data`` folder with the original data as well as a ``dataset`` folder that duplicates this ``data`` across multiple subjects and sessions.
+The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory, where ``~`` is the home directory of your system. This includes a ``data`` folder with the original data as well as a ``dataset`` folder that duplicates this ``data`` across multiple subjects and sessions.
 
 .. code-block:: bash
 

docs/tutorials/index.rst

@@ -1,12 +1,15 @@
 Tutorials
 =======================================
 The NWB Graphical User Interface for Data Entry (GUIDE) is a desktop tool for converting neurophysiological data
-to the Neurodata Without Borders (NWB) format and uploading to the DANDI Archive. In these tutorials, we detail this
-process from initial setup to final upload.
+to the Neurodata Without Borders (NWB) format and uploading to the DANDI Archive.
+
+In these tutorials, you'll follow along on a :doc:`local installation of the GUIDE </installation>` as we detail the conversion process from initial setup to final upload.
 
 Before you begin these tutorials, **you'll need to generate the tutorial dataset** using the instructions on the Dataset page.
 
 
+
+
 .. toctree::
    :maxdepth: 2
 

docs/tutorials/multiple_sessions.rst

@@ -3,6 +3,8 @@ Managing Multiple Sessions
 
 Now, let’s say that you’ve already run some of your experiments and now you want to convert them all at the same time. This is where a multi-session workflow will come in handy.
 
+Begin a new conversion on the **Convert** page and provide a name for your pipeline.
+
 Workflow Configuration
 ----------------------
 
@@ -12,7 +14,9 @@ On the Workflow page, confirm that this pipeline will be run on multiple session
   :align: center
   :alt: Workflow page with multiple sessions and locate data selected
 
-Complete the first section of the GUIDE as normal until you reach a new **Locate Data** page after the Data Formats page.
+Data Formats
+------------
+As before, specify **SpikeGLX Recording** and **Phy Sorting** as the data formats for this conversion.
 
 Locate Data
 -----------
@@ -91,6 +95,7 @@ We should also indicate the ``sex`` of each subject since this is a requirement
 
     You’ll be able to specify Global Metadata on the Source Data and File Metadata pages as well.
 
+Advance to the next page when you have entered subject metadata for all subjects.
 
 Source Data Information
 -----------------------

docs/tutorials/single_session.rst

@@ -83,16 +83,17 @@ Data Entry
 
 Source Data Information
 ^^^^^^^^^^^^^^^^^^^^^^^
-On this page, specify the relevant **.bin** (Spikeglx) file and **phy** folder so that the GUIDE can find this source data to complete the conversion.
+On this page, specify the **.ap.bin** (SpikeGLX) file and **phy** folder so that the GUIDE can find this source data to complete the conversion.
 
-As discussed in the :doc:`Dataset Generation </tutorials/dataset>` tutorial, these can be found in the ``~/NWB_GUIDE/test-data/data`` directory.
+As discussed in the :doc:`Dataset Generation </tutorials/dataset>` tutorial, these can be found in the ``~/NWB_GUIDE/test-data/data`` directory, where **~** is the home directory of your system.
 
 You can either click the file selector to navigate to the file or drag-and-drop into the GUIDE from your file navigator.
 
 .. figure:: ../assets/tutorials/single/sourcedata-page-specified.png
   :align: center
   :alt: Source Data page with source locations specified
 
+Advance to the next page to extract metadata from the source data.
 
 Session Metadata
 ^^^^^^^^^^^^^^^^
@@ -104,6 +105,7 @@ The Session Start Time in the **General Metadata** section is already specified
   :align: center
   :alt: Metadata page with invalid Subject information
 
+While the **General Metadata** section is complete, take some time to fill out additional information such as the **Institutional Info** box and the **Experimenter** field.
 
 However, we still need to add the Subject information—as noted by the red accents around that item. Let’s say that our subject is a male mouse with an age of P25W, which represents 25 weeks old.
 
@@ -137,7 +139,7 @@ The Inspector Report page allows you to validate the preview file against the la
   :align: center
   :alt: NWB Inspector report
 
-
+Advance to the next page when you are satisfied with the Inspector Report.
 
 Conversion Preview
 ^^^^^^^^^^^^^^^^^^

src/renderer/src/pages.js

@@ -2,7 +2,6 @@ import { GettingStartedPage } from "./stories/pages/getting-started/GettingStart
 import { DocumentationPage } from "./stories/pages/documentation/Documentation";
 import { ContactPage } from "./stories/pages/contact-us/Contact";
 import { GuidedHomePage } from "./stories/pages/guided-mode/GuidedHome";
-import { GuidedStartPage } from "./stories/pages/guided-mode/GuidedStart";
 import { GuidedNewDatasetPage } from "./stories/pages/guided-mode/setup/GuidedNewDatasetInfo";
 import { GuidedStructurePage } from "./stories/pages/guided-mode/data/GuidedStructure";
 import { sections } from "./stories/pages/globals";
@@ -85,10 +84,6 @@ const pages = {
         label: "Convert",
         icon: guidedIcon,
         pages: {
-            start: new GuidedStartPage({
-                label: "Start",
-            }),
-
             details: new GuidedNewDatasetPage({
                 title: "Project Setup",
                 label: "Project details",

src/renderer/src/stories/pages/guided-mode/data/GuidedPathExpansion.js

@@ -265,6 +265,7 @@ export class GuidedPathExpansionPage extends Page {
     workflow = {
         subject_id: {},
         session_id: {},
+        base_directory: {},
         locate_data: {
             skip: () => {
                 this.#initialize();
@@ -432,9 +433,15 @@ export class GuidedPathExpansionPage extends Page {
         // Require properties for all sources
         const generatedSchema = { type: "object", properties: {}, additionalProperties: false };
         const controls = {};
+
+        const baseDirectory = this.workflow.base_directory.value;
+        const globals = (structureState.globals = {});
+
         for (let key in this.info.globalState.interfaces) {
             generatedSchema.properties[key] = { type: "object", ...pathExpansionSchema };
 
+            if (baseDirectory) globals[key] = { base_directory: baseDirectory };
+
             controls[key] = {
                 format_string_path: [
                     new Button({
@@ -450,8 +457,6 @@ export class GuidedPathExpansionPage extends Page {
         }
         structureState.schema = generatedSchema;
 
-        // this.optional.requestUpdate();
-
         const form = (this.form = new JSONSchemaForm({
             ...structureState,
             onThrow,

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

@@ -43,6 +43,18 @@ const questions = {
         },
         default: false,
     },
+
+    base_directory: {
+        type: "string",
+        format: "directory",
+        title: "Where is your data located?",
+        description:
+            "A single directory where all data is contained. Can override for specific data formats.<br><small>Leave blank if unknown</small>",
+        dependencies: {
+            locate_data: {},
+        },
+    },
+
     upload_to_dandi: {
         type: "boolean",
         title: "Would you like to upload your data to DANDI?",
@@ -81,6 +93,7 @@ const projectWorkflowSchema = {
         return acc;
     }, {}),
     order: Object.keys(questions),
+    additionalProperties: false,
 };
 
 // ----------------------------------------------------------------------

tests/e2e/workflow.ts

@@ -88,11 +88,6 @@ export default async function runWorkflow(name, workflow, identifier) {
 
   test('Create new pipeline by specifying a name', async () => {
 
-    // Advance to instructions page
-    await toNextPage('start')
-
-    await takeScreenshot(join(identifier, 'intro-page'), 500)
-
     // Advance to general information page
     await toNextPage('details')
 
@@ -209,26 +204,27 @@ export default async function runWorkflow(name, workflow, identifier) {
         baseInput.updateData(basePath)
       })
 
-      dashboard.main.querySelector('main > section').scrollTop = 200 // Scroll down to see all interfaces
-
     },
       testInterfaceInfo,
       testDatasetPath
     )
 
     await takeScreenshot(join(identifier, 'pathexpansion-basepath'), 300)
 
-    const name = Object.keys(testInterfaceInfo.common)[0]
-    const interfaceId = testInterfaceInfo.common[name].id
-    const autocompleteInfo = testInterfaceInfo.multi[name].autocomplete
 
-    await evaluate(id => {
+    const interfaceId = await evaluate(() => {
       const dashboard = document.querySelector('nwb-dashboard')
       const form = dashboard.page.form
+      const id = Object.keys(form.accordions)[0]
       const formatInput = form.getFormElement([id, 'format_string_path'])
       const autocompleteButton = formatInput.controls[0]
       autocompleteButton.onClick()
-    }, interfaceId)
+      return id
+    })
+
+    // Use autocomplete on first interface
+    const name = Object.entries(testInterfaceInfo.common).find(([name, info]) => info.id === interfaceId)![0]
+    const autocompleteInfo = testInterfaceInfo.multi[name].autocomplete
 
     await takeScreenshot(join(identifier, 'pathexpansion-autocomplete-open'), 300)
 
@@ -258,16 +254,16 @@ export default async function runWorkflow(name, workflow, identifier) {
       const dashboard = document.querySelector('nwb-dashboard')
       const form = dashboard.page.form
 
+      const accordionKeys = Object.keys(form.accordions)
+
       // Fill out the path expansion information for non-autocompleted interfaces
-      Object.entries(common).slice(1).forEach(([ name, info ]) => {
-        const id = info.id
+      accordionKeys.slice(1).forEach(id => {
+        const name = Object.entries(common).find(([_, info]) => info.id === id)![0]
         const { format } = multi[name]
         const formatInput = form.getFormElement([id, 'format_string_path'])
         formatInput.updateData(format)
       })
 
-      dashboard.main.querySelector('main > section').scrollTop = 200
-
     }, testInterfaceInfo)