Merge branch 'main' into improve-subject-interaction-with-results

NeurodataWithoutBorders · Mar 13, 2024 · feb915f · feb915f
2 parents ae598c4 + 7c918cd
commit feb915f
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Showing 21 changed files with 365 additions and 232 deletions.
diff --git a/docs/conf_extlinks.py b/docs/conf_extlinks.py
@@ -1,6 +1,6 @@
 # Use this for mapping to external links
 extlinks = {
-    "linux-fix": ("https://github.com/neurodatawithoutborders/nwb-guide/tree/linux-fix/%s", "%s"),
+    "linux-latest": ("https://github.com/neurodatawithoutborders/nwb-guide/tree/linux-latest/%s", "%s"),
     "releases": ("https://github.com/NeurodataWithoutBorders/nwb-guide/releases/%s", "%s"),
     "pynwb-docs": ("https://pynwb.readthedocs.io/en/stable/%s", "%s"),
     "matnwb-src": ("https://github.com/NeurodataWithoutBorders/matnwb/%s", "%s"),

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -23,9 +23,9 @@ Download `NWB-GUIDE-arm64.dmg <https://github.com/NeurodataWithoutBorders/nwb-gu
 Linux
 -----
 
-Please clone the :linux-fix:`linux-fix <>` branch of the NWB GUIDE and follow the :ref:`Developer Installation instructions<developer_installation>` after the "Clone the Repo" step.
+Please clone the :linux-latest:`linux-latest <>` branch of the NWB GUIDE and follow the :ref:`Developer Installation instructions<developer_installation>` after the "Clone the Repo" step.
 
 .. code-block:: bash
 
-   git clone --branch linux-fix https://github.com/NeurodataWithoutBorders/nwb-guide
+   git clone --branch linux-latest https://github.com/NeurodataWithoutBorders/nwb-guide
    cd nwb-guide
diff --git a/package.json b/package.json
@@ -26,8 +26,8 @@
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s -vv",
-    "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
-    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait3s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
+    "wait5s": "node -e \"setTimeout(() => process.exit(0),5000)\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait5s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",

diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -617,9 +617,9 @@ def upload_multiple_filesystem_objects_to_dandi(**kwargs):
     innerKwargs = {**kwargs}
     del innerKwargs["filesystem_paths"]
     innerKwargs["nwb_folder_path"] = tmp_folder_path
-    result = upload_folder_to_dandi(**innerKwargs)
+    results = upload_folder_to_dandi(**innerKwargs)
     rmtree(tmp_folder_path)
-    return result
+    return results
 
 
 def upload_folder_to_dandi(

diff --git a/schemas/dandi-upload.schema.ts b/schemas/dandi-upload.schema.ts
@@ -100,7 +100,7 @@ export const addDandiset = async (info) => {
     const enumLabels = `${id} — ${latestVersionInfo.name}`
 
     const isDraft = latestVersionInfo.version === 'draft'
-    const enumCategories = (isDraft ? 'Drafts — ' : '') + (staging ? 'Staging' : 'Main')
+    const enumCategories = (isDraft ? 'Unpublished' : '') + (staging ? ' - Staging' : '')
 
     const fullInfo = await info.getInfo({ version: latestVersionInfo.version });
 

diff --git a/schemas/json/dandi/create.json b/schemas/json/dandi/create.json
@@ -14,6 +14,7 @@
         },
 
         "embargo_status": {
+            "title": "Would you like to embargo this Dandiset?",
             "type": "boolean",
             "description": "Embargoed Dandisets are hidden from public access until a specific time period has elapsed. Uploading data to the DANDI archive under embargo requires a relevant NIH award number, and the data will be automatically published when the embargo period expires.",
             "default": false
@@ -36,15 +37,29 @@
 
         "license": {
             "type": "array",
+            "description": "Provide a set of licenses for this Dandiset. Review the individual licenses and select the one that best fits your needs.",
             "items": {
                 "type": "string",
+                "enumLinks": {
+                    "spdx:CC0-1.0": "https://creativecommons.org/public-domain/cc0/",
+                    "spdx:CC-BY-4.0": "https://creativecommons.org/licenses/by/4.0/deed.en"
+                },
+                "enumKeywords": {
+                    "spdx:CC0-1.0": ["No Rights Reserved"],
+                    "spdx:CC-BY-4.0": ["Attribution 4.0 International"]
+                },
+                "enumLabels": {
+                    "spdx:CC0-1.0": "CC0 1.0",
+                    "spdx:CC-BY-4.0": "CC BY 4.0"
+                },
                 "enum": [
                     "spdx:CC0-1.0",
                     "spdx:CC-BY-4.0"
                 ]
             },
+            "maxItems": 1,
             "uniqueItems": true,
-            "description": "Licenses associated with the item. <br><small><b>Note:</b> DANDI only supports a subset of <a href='https://creativecommons.org' target='_blank'>Creative Commons Licenses</a> applicable to datasets</small>"
+            "strict": true
         },
 
         "nih_award_number": {

diff --git a/schemas/source-data.schema.ts b/schemas/source-data.schema.ts
@@ -5,14 +5,12 @@ export default function preprocessSourceDataSchema (schema) {
     // Abstract across different interfaces
     Object.entries(schema.properties ?? {}).forEach(([key, schema]: [string, any]) => {
 
-            if (key === 'VideoInterface' || key === 'AudioInterface') {
-                if (schema.properties.file_paths) {
-                    Object.assign(schema.properties.file_paths, {
-                        items: { type: 'string' },
-                        description: '<b>Only one file supported at this time.</b> Multiple file support coming soon.',
-                        maxItems: 1,
-                    })
-                }
+            if (schema.properties.file_paths) {
+                Object.assign(schema.properties.file_paths, {
+                    items: { type: 'string' },
+                    description: '<b>Only one file supported at this time.</b> Multiple file support coming soon.',
+                    maxItems: 1,
+                })
             }
 
             // Do not show steps

diff --git a/src/renderer/assets/css/nativize.css b/src/renderer/assets/css/nativize.css
@@ -5,7 +5,6 @@
 
 html {
     font-family: sans-serif;
-    -webkit-user-select: none; /* disable selection */
     -webkit-user-drag: none; /* disable dragging */
     cursor: default; /* use default cursor */
 }

diff --git a/src/renderer/src/stories/DandiResults.js b/src/renderer/src/stories/DandiResults.js
@@ -91,12 +91,15 @@ export class DandiResults extends LitElement {
                     <ol class="publication"></ol>
 
                     ${this.files
-                        ? html` <h3 style="padding: 0;">Files Uploaded</h3>
+                        ? html` <h3 style="padding: 0;">Updated DANDI Assets</h3>
                               <ol>
                                   ${Object.values(this.files)
                                       .map((item) => Object.values(item))
                                       .flat()
-                                      .map(({ file }) => html`<li>${file}</li>`)}
+                                      .map(({ file }) => {
+                                          const truncated = file.split(this.id)[1].slice(1);
+                                          return html`<li>${truncated}</li>`;
+                                      })}
                               </ol>`
                         : ""}
                     <hr />

diff --git a/src/renderer/src/stories/JSONSchemaForm.js b/src/renderer/src/stories/JSONSchemaForm.js
@@ -121,10 +121,11 @@ const componentCSS = `
     }
 
     .link {
-      margin-top: 20px;
+      margin: 20px 0px;
       border: 1px solid black;
       border-radius: 4px;
       position: relative;
+
     }
 
     .link > div {
@@ -869,11 +870,12 @@ export class JSONSchemaForm extends LitElement {
 
         const value = parent[name];
 
-        const skipValidation = !this.validateEmptyValues && value === undefined;
+        const skipValidation = this.validateEmptyValues === null && value === undefined;
+
         const validateArgs = input.pattern || skipValidation ? [] : [value, schema];
 
+        // Run validation functions
         const jsonSchemaErrors = validateArgs.length === 2 ? this.validateSchema(...validateArgs, name) : [];
-
         const valid = skipValidation ? true : await this.validateOnChange(name, parent, pathToValidate, value);
 
         if (valid === null) return null; // Skip validation / data change if the value is null