Merge branch 'main' into ephys-metadata-v2

NeurodataWithoutBorders · Mar 12, 2024 · 94ae7d7 · 94ae7d7
2 parents 3e5a1be + 3d994b7
commit 94ae7d7
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Showing 18 changed files with 194 additions and 67 deletions.
diff --git a/environments/environment-MAC.yml b/environments/environment-MAC.yml
@@ -11,6 +11,7 @@ dependencies:
   - jsonschema = 4.18.0  # installs jsonschema-specifications
   - pip
   - pip:
+      - scipy<1.12.0 # Fix needed for scipy._lib._testutils
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2

diff --git a/package.json b/package.json
@@ -20,8 +20,6 @@
     "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask && npm run build:electron:linux",
     "build:flask": "python -m PyInstaller nwb-guide.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all dandi --collect-all keyrings --collect-all unittest --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all hdmf_zarr --collect-all ndx_dandi_icephys --collect-all sklearn --collect-all ci_info ./pyflask/app.py",
-    "build:flask:spec": "npm run build:flask:spec:base && python prepare_pyinstaller_spec.py",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
diff --git a/schemas/json/generated/BlackrockRecordingInterface.json b/schemas/json/generated/BlackrockRecordingInterface.json
@@ -8,8 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string",
-                    "description": "Path to Blackrock file."
+                    "description": "Path to Blackrock file.",
+                    "type": "string"
                 },
                 "nsx_override": {
                     "format": "file",

diff --git a/schemas/json/generated/BlackrockSortingInterface.json b/schemas/json/generated/BlackrockSortingInterface.json
@@ -8,13 +8,15 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string",
-                    "description": "Path to Blackrock file."
+                    "description": "Path to Blackrock file.",
+                    "type": "string"
                 },
                 "sampling_frequency": {
+                    "description": "The sampling frequency for the sorting extractor. When the signal data is available (.ncs) those files will be",
                     "type": "number"
                 },
                 "verbose": {
+                    "description": "Enables verbosity",
                     "type": "boolean",
                     "default": true
                 }

diff --git a/schemas/json/generated/CellExplorerRecordingInterface.json b/schemas/json/generated/CellExplorerRecordingInterface.json
@@ -0,0 +1,35 @@
+{
+    "required": [],
+    "properties": {
+        "CellExplorerRecordingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "description": "The folder where the session data is located. It should contain a\n`{folder.name}.session.mat` file and the binary files `{folder.name}.dat`\nor `{folder.name}.lfp` for the LFP interface.",
+                    "type": "string"
+                },
+                "verbose": {
+                    "description": "Whether to output verbose text.",
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/schemas/json/generated/FicTracDataInterface.json b/schemas/json/generated/FicTracDataInterface.json
@@ -10,6 +10,13 @@
                     "format": "file",
                     "type": "string"
                 },
+                "radius": {
+                    "type": "number"
+                },
+                "configuration_file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
                 "verbose": {
                     "type": "boolean",
                     "default": true

diff --git a/schemas/json/generated/OpenEphysRecordingInterface.json b/schemas/json/generated/OpenEphysRecordingInterface.json
@@ -13,6 +13,9 @@
                 "stream_name": {
                     "type": "string"
                 },
+                "block_index": {
+                    "type": "number"
+                },
                 "verbose": {
                     "type": "boolean",
                     "default": true

diff --git a/schemas/json/generated/PhySortingInterface.json b/schemas/json/generated/PhySortingInterface.json
@@ -11,7 +11,10 @@
                     "type": "string"
                 },
                 "exclude_cluster_groups": {
-                    "type": "array"
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    }
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/schemas/json/generated/Spike2RecordingInterface.json b/schemas/json/generated/Spike2RecordingInterface.json
@@ -8,8 +8,8 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string",
-                    "description": "Path to CED data file."
+                    "description": "Path to CED data file.",
+                    "type": "string"
                 },
                 "verbose": {
                     "type": "boolean",

diff --git a/schemas/json/generated/SpikeGLXConverterPipe.json b/schemas/json/generated/SpikeGLXConverterPipe.json
@@ -8,10 +8,11 @@
             "properties": {
                 "folder_path": {
                     "format": "directory",
-                    "type": "string",
-                    "description": "Path to the folder containing SpikeGLX streams."
+                    "description": "Path to the folder containing SpikeGLX streams.",
+                    "type": "string"
                 },
                 "verbose": {
+                    "description": "Whether to output verbose text.",
                     "type": "boolean",
                     "default": false
                 }

diff --git a/schemas/json/generated/SpikeGLXNIDQInterface.json b/schemas/json/generated/SpikeGLXNIDQInterface.json
@@ -8,14 +8,16 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string",
-                    "description": "Path to SpikeGLX .nidq file."
+                    "description": "Path to SpikeGLX .nidq file.",
+                    "type": "string"
                 },
                 "verbose": {
+                    "description": "Whether to output verbose text.",
                     "type": "boolean",
                     "default": true
                 },
                 "load_sync_channel": {
+                    "description": "Whether to load the last channel in the stream, which is typically used for synchronization.\nIf True, then the probe is not loaded.",
                     "type": "boolean",
                     "default": false
                 },

diff --git a/schemas/json/generated/SpikeGLXRecordingInterface.json b/schemas/json/generated/SpikeGLXRecordingInterface.json
@@ -8,10 +8,11 @@
             "properties": {
                 "file_path": {
                     "format": "file",
-                    "type": "string",
-                    "description": "Path to SpikeGLX ap.bin or lf.bin file."
+                    "description": "Path to SpikeGLX ap.bin or lf.bin file.",
+                    "type": "string"
                 },
                 "verbose": {
+                    "description": "Whether to output verbose text.",
                     "type": "boolean",
                     "default": true
                 },

diff --git a/schemas/json/generated/Suite2pSegmentationInterface.json b/schemas/json/generated/Suite2pSegmentationInterface.json
@@ -10,17 +10,25 @@
                     "format": "directory",
                     "type": "string"
                 },
-                "combined": {
-                    "type": "boolean",
-                    "default": false
+                "channel_name": {
+                    "type": "string"
                 },
-                "plane_no": {
-                    "type": "number",
-                    "default": 0
+                "plane_name": {
+                    "type": "string"
+                },
+                "plane_segmentation_name": {
+                    "type": "string"
                 },
                 "verbose": {
                     "type": "boolean",
                     "default": true
+                },
+                "combined": {
+                    "type": "boolean",
+                    "default": false
+                },
+                "plane_no": {
+                    "type": "number"
                 }
             },
             "type": "object",

diff --git a/schemas/json/generated/TdtRecordingInterface.json b/schemas/json/generated/TdtRecordingInterface.json
@@ -0,0 +1,41 @@
+{
+    "required": [],
+    "properties": {
+        "TdtRecordingInterface": {
+            "required": [
+                "folder_path",
+                "gain"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "gain": {
+                    "type": "number"
+                },
+                "stream_id": {
+                    "type": "string",
+                    "default": "0"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "es_key": {
+                    "type": "string",
+                    "default": "ElectricalSeries"
+                }
+            },
+            "type": "object",
+            "additionalProperties": false
+        }
+    },
+    "type": "object",
+    "additionalProperties": false,
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "source.schema.json",
+    "title": "Source data schema",
+    "description": "Schema for the source data, files and directories",
+    "version": "0.1.0"
+}
diff --git a/schemas/source-data.schema.ts b/schemas/source-data.schema.ts
@@ -8,6 +8,7 @@ export default function preprocessSourceDataSchema (schema) {
             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,
                     })

diff --git a/src/renderer/src/stories/JSONSchemaInput.js b/src/renderer/src/stories/JSONSchemaInput.js
@@ -14,6 +14,9 @@ import { JSONSchemaForm, getIgnore } from "./JSONSchemaForm";
 import { Search } from "./Search";
 import tippy from "tippy.js";
 import { merge } from "./pages/utils";
+import { InspectorListItem } from "./preview/inspector/InspectorList";
+
+const isDevelopment = !!import.meta.env;
 
 const dateTimeRegex = /(\d{4})-(\d{2})-(\d{2})T(\d{2}):(\d{2})/;
 
@@ -504,6 +507,27 @@ export class JSONSchemaInput extends LitElement {
     required = false;
     validateOnChange = true;
 
+    // Print the default value of the schema if not caught
+    onUncaughtSchema = (schema) => {
+        // In development, show uncaught schemas
+        if (!isDevelopment) {
+            if (this.form) {
+                const inputContainer = this.form.shadowRoot.querySelector(`#${this.path.slice(-1)[0]}`);
+                inputContainer.style.display = "none";
+            }
+        }
+
+        if (schema.default) return `<pre>${JSON.stringify(schema.default, null, 2)}</pre>`;
+
+        const error = new InspectorListItem({
+            message:
+                "<h3 style='margin: 0'>Internal GUIDE Error</h3><span>Cannot render this property because of a misformatted schema.</span>",
+        });
+        error.style.width = "100%";
+
+        return error;
+    };
+
     constructor(props) {
         super();
         Object.assign(this, props);
@@ -872,7 +896,16 @@ export class JSONSchemaInput extends LitElement {
             if (isArray) {
                 const hasItemsRef = "items" in schema && "$ref" in schema.items;
                 if (!("items" in schema)) schema.items = {};
-                if (!("type" in schema.items) && !hasItemsRef) schema.items.type = this.#getType(this.value?.[0]);
+                if (!("type" in schema.items) && !hasItemsRef) {
+                    // Guess the type of the first item
+                    if (this.value) {
+                        const itemToCheck = this.value[0];
+                        schema.items.type = itemToCheck ? this.#getType(itemToCheck) : "string";
+                    }
+
+                    // If no value, handle uncaught schema
+                    else return this.onUncaughtSchema(schema);
+                }
             }
 
             const itemSchema = this.form?.getSchema ? this.form.getSchema("items", schema) : schema["items"];
@@ -1138,8 +1171,7 @@ export class JSONSchemaInput extends LitElement {
             }
         }
 
-        // Print out the immutable default value
-        return html`<pre>${schema.default ? JSON.stringify(schema.default, null, 2) : "No default value"}</pre>`;
+        return this.onUncaughtSchema(schema);
     }
 }