Merge branch 'main' into FicTracDataInterface

NeurodataWithoutBorders · Oct 17, 2023 · 0da12f2 · 0da12f2
2 parents 3c30770 + c84139e
commit 0da12f2
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Showing 42 changed files with 576 additions and 331 deletions.
diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
@@ -75,7 +75,7 @@ This will automatically add the new page to the sidebar. The page itself can be
         constructor(...args) {
             super(...args);
 
-            console.log(this.info.globalState) // This will print the global state that is currently being passed between subpages (i.e. within guided mode)
+            console.log(this.info.globalState) // This will print the global state that is currently being passed between subpages
         }
 
         render() {

diff --git a/guideGlobalMetadata.json b/guideGlobalMetadata.json
@@ -15,6 +15,8 @@
         "KiloSortSortingInterface",
         "Spike2RecordingInterface",
         "BrukerTiffSinglePlaneImagingInterface",
+        "ExtractSegmentationInterface",
+        "CnmfeSegmentationInterface",
         "BrukerTiffMultiPlaneImagingInterface",
         "MicroManagerTiffImagingInterface",
         "ScanImageImagingInterface",
@@ -27,6 +29,10 @@
         "PlexonRecordingInterface",
         "PlexonSortingInterface",
         "AxonaRecordingInterface",
+        "NeuralynxRecordingInterface",
+        "AlphaOmegaRecordingInterface",
+        "DeepLabCutInterface",
+        "SLEAPInterface",
         "FicTracDataInterface"
     ]
 }
diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py
@@ -341,11 +341,7 @@ def convert_to_nwb(info: dict) -> str:
     resolved_output_path = resolved_output_directory / nwbfile_path
 
     # Remove symlink placed at the default_output_directory if this will hold real data
-    if (
-        not run_stub_test
-        and resolved_output_directory == default_output_directory
-        and default_output_directory.is_symlink()
-    ):
+    if resolved_output_directory == default_output_directory and default_output_directory.is_symlink():
         default_output_directory.unlink()
 
     resolved_output_path.parent.mkdir(exist_ok=True, parents=True)  # Ensure all parent directories exist
@@ -401,7 +397,7 @@ def update_conversion_progress(**kwargs):
     )
 
     # Create a symlink between the fake data and custom data
-    if not run_stub_test and not resolved_output_directory == default_output_directory:
+    if not resolved_output_directory == default_output_directory:
         if default_output_directory.exists():
             # If default default_output_directory is not a symlink, delete all contents and create a symlink there
             if not default_output_directory.is_symlink():

diff --git a/schemas/json/dandi/global.json b/schemas/json/dandi/global.json
@@ -14,7 +14,7 @@
                     "description": "From the <a href='https://gui-staging.dandiarchive.org' target='_blank'>staging (testing) server</a>"
                 }
             },
-            "required": ["main_api_key", "staging_api_key"]
+            "required": ["main_api_key"]
         }
     }
 }
diff --git a/schemas/json/generated/AlphaOmegaRecordingInterface.json b/schemas/json/generated/AlphaOmegaRecordingInterface.json
@@ -0,0 +1,33 @@
+{
+    "required": [],
+    "properties": {
+        "AlphaOmegaRecordingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "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/json/generated/CnmfeSegmentationInterface.json b/schemas/json/generated/CnmfeSegmentationInterface.json
@@ -0,0 +1,29 @@
+{
+    "required": [],
+    "properties": {
+        "CnmfeSegmentationInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "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/DeepLabCutInterface.json b/schemas/json/generated/DeepLabCutInterface.json
@@ -0,0 +1,38 @@
+{
+    "required": [],
+    "properties": {
+        "DeepLabCutInterface": {
+            "required": [
+                "file_path",
+                "config_file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "config_file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "subject_name": {
+                    "type": "string",
+                    "default": "ind1"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "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/ExtractSegmentationInterface.json b/schemas/json/generated/ExtractSegmentationInterface.json
@@ -0,0 +1,36 @@
+{
+    "required": [],
+    "properties": {
+        "ExtractSegmentationInterface": {
+            "required": [
+                "file_path",
+                "sampling_frequency"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "sampling_frequency": {
+                    "type": "number"
+                },
+                "output_struct_name": {
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                }
+            },
+            "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/NeuralynxRecordingInterface.json b/schemas/json/generated/NeuralynxRecordingInterface.json
@@ -0,0 +1,36 @@
+{
+    "required": [],
+    "properties": {
+        "NeuralynxRecordingInterface": {
+            "required": [
+                "folder_path"
+            ],
+            "properties": {
+                "folder_path": {
+                    "format": "directory",
+                    "type": "string"
+                },
+                "stream_name": {
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": false
+                },
+                "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/SLEAPInterface.json b/schemas/json/generated/SLEAPInterface.json
@@ -0,0 +1,36 @@
+{
+    "required": [],
+    "properties": {
+        "SLEAPInterface": {
+            "required": [
+                "file_path"
+            ],
+            "properties": {
+                "file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "video_file_path": {
+                    "format": "file",
+                    "type": "string"
+                },
+                "verbose": {
+                    "type": "boolean",
+                    "default": true
+                },
+                "frames_per_second": {
+                    "type": "number"
+                }
+            },
+            "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/src/renderer/assets/css/global.css b/src/renderer/assets/css/global.css
@@ -10,7 +10,7 @@
 
 /*  Notfy */
 .notyf__toast {
-    max-width: clamp(300px, 40vw, min-content) !important;
+    max-width: 40vw !important;
 }
 
 .notyf__message {

diff --git a/src/renderer/assets/css/guided.css b/src/renderer/assets/css/guided.css
@@ -27,7 +27,6 @@
     width: 100%;
     height: 100%;
     border-radius: 5px;
-    margin-top: 15px;
 }
 
 .guided--nav-bar-dropdown {
@@ -434,14 +433,6 @@
     margin: 6px;
 }
 
-.guided--main-tab,
-.guided--parent-tab {
-    height: 100%;
-    width: 100%;
-    display: flex;
-    flex-direction: column;
-}
-
 .guided--page,
 .guided--panel {
     width: 100%;
@@ -900,9 +891,10 @@ h1.guided--text-sub-step {
     background-color: var(--color-border);
     border: none;
     display: inline-block;
-    cursor: pointer;
     border-radius: 16px;
+    cursor: pointer;
 }
+
 .guided--capsule.active {
     background-color: var(--color-light-green);
 }
@@ -922,7 +914,6 @@ h1.guided--text-sub-step {
     background-color: #d5eaff;
     border: none;
     display: inline-block;
-    cursor: pointer;
     transform: skewx(-25deg);
 }
 .guided--capsule-sub-page.active {
@@ -1196,7 +1187,6 @@ h1.guided--text-sub-step {
     margin-bottom: 15px;
     border-bottom: 5px solid #b80d49;
     width: 100%;
-    margin-top: -0.5rem !important;
 }
 
 .guided--button-tab-container {

diff --git a/src/renderer/assets/css/main.css b/src/renderer/assets/css/main.css
@@ -1471,43 +1471,12 @@ details[open] > summary::before {
     box-shadow: var(--tw-ring-offset-shadow, 0 0 #0000), var(--tw-ring-shadow, 0 0 #0000), var(--tw-shadow);
 }
 
-.getting-started-overview {
-    padding-left: 0 !important;
-    padding-right: 0 !important;
-    height: 100%;
-    text-align: center;
-    display: flex;
-    flex-direction: column;
-    /* display: grid;
-  grid-template-rows: 68% 14% 15%; */
-}
-
-.getting-started-header {
-    width: auto;
-    height: 18rem;
+.standalone-section {
+    width: 100%;
     display: flex;
     flex-direction: column;
-    justify-content: center;
-    margin: 0 auto;
-    margin-top: 3rem;
     align-items: center;
-    margin-bottom: 0rem;
-}
-
-.front-page_logo {
-    margin-top: 0.5rem;
-    display: flex;
-    align-items: center;
-    flex-direction: row;
-    width: 63rem;
-    flex-direction: column;
-    justify-content: center;
-}
-
-.header-text {
-    font-size: 18px;
-    margin-top: 1rem;
-    font-weight: bold;
+    margin-bottom: 20px;
 }
 
 .overview-card-layout {