Merge pull request #20 from KitwareMedical/plug-action-buttons

Plug action buttons

Author: Justineantoine

CONTRIBUTING.rst

@@ -1,4 +1,4 @@
-# Contributing to GirderEGGAnnotator
+# Contributing to GirderEEGAnnotator
 
 1. Clone the repository using ``git clone``
 2. Install the dev dependencies in your
@@ -17,7 +17,7 @@ pip install -e ."[dev]"
 
 ## Commit messages
 
-GirderEGGAnnotator follows trame\'s commit message convention to be compatible with
+GirderEEGAnnotator follows trame\'s commit message convention to be compatible with
 its CI features including the auto semantic release.
 
 ## Tips

girdereegannotator/app/app_logic.py

@@ -4,7 +4,7 @@
 from girdereegannotator.utils.base_logic import BaseLogic
 
 from ..authentication import AuthenticationLogic
-from ..eeg_annotator import EGGAnnotatorLogic
+from ..eeg_annotator import EEGAnnotatorLogic
 from ..portal import PortalLogic
 from .app_ui import AnnotatorAppState, AnnotatorAppUI
 from .components.navigation_card import NavigationWindow
@@ -15,7 +15,7 @@ def __init__(self, server: Server):
         super().__init__(server, AnnotatorAppState)
 
         self._portal_logic = PortalLogic(self.server)
-        self._eeg_annotator_logic = EGGAnnotatorLogic(self.server)
+        self._eeg_annotator_logic = EEGAnnotatorLogic(self.server)
         self._auth_logic = AuthenticationLogic(server)
 
         self._eeg_annotator_logic.next_clicked.connect(self._portal_logic.select_next_eeg)

girdereegannotator/app/app_ui.py

@@ -8,14 +8,14 @@
 from girdereegannotator.utils.base_ui import BaseUI
 
 from ..authentication import AuthenticationUI
-from ..eeg_annotator import EGGAnnotatorUI
+from ..eeg_annotator import EEGAnnotatorUI
 from ..portal import PortalUI
 from .components.navigation_card import NavigationCard, NavigationState
 
 
 @dataclass
 class AnnotatorAppState:
-    app_name: str = "GirderEGGAnnotator"
+    app_name: str = "GirderEEGAnnotator"
     nav_state: NavigationState = field(default_factory=NavigationState)
 
 
@@ -50,12 +50,13 @@ def __init__(self, server: Server):
 
             client.Style(
                 "html { overflow-y: hidden; } "
-                ".annotation-actions { width: 130px; height: 100%; display: flex; align-items: center; justify-content: space-around }"
-                ".annotation-input { width: 450px; height: 100%; display: flex; align-items: center; }"
+                ".annotation-actions { height: 100%; display: flex; align-items: center; justify-content: space-around }"
+                ".annotation-input { height: 100%; display: flex; align-items: center; flex-grow: 1 }"
                 ".annotation-input__menu .v-field { background-color: inherit; }"
                 ".annotation-input__menu .v-field__input:has(.v-select__selection) { padding: 0; }"
                 ".annotation-input__menu { height: 100%; display: flex; flex-grow: 1; }"
                 ".annotation-list .annotation-list-item:hover { background-color: color-mix(in srgb, rgb(var(--v-theme-surface)) 95%, rgb(var(--v-theme-primary))); }"
+                ".annotation-tool { height: 100%; display: flex; align-items: center; width: 600px; }"
                 ".annotator { height: 100%; }"
                 ".annotator-tool { height: 100%; display: flex; flex-direction: column; }"
                 ".annotator-tool__content { height: 40px; padding-left: 8px; padding-right: 8px; display: flex; align-items: center; border-radius: 24px; background-color: rgb(var(--v-theme-surface-variant)); }"
@@ -91,6 +92,7 @@ def __init__(self, server: Server):
                 ".nav-bar { height: 65px; }"
                 ".nav-content { height: calc(100% - 65px); padding: 0px; }"
                 ".nav-window { height: 100%; }"
+                ".nav-window-group { height: 100%; overflow: unset; }"
                 ".portal { padding-left: 20px; padding-right: 20px; padding-bottom: 10px; height: 100%;}"
                 ".portal-toolbar { display: flex; flex-grow: 1; align-items: center; justify-content: end; height: 100%; }"
                 ".remote-controlled-area:focus-visible { outline: none !important; }"
@@ -109,6 +111,7 @@ def __init__(self, server: Server):
                 ".viewer__content { height: calc(100% - 5px); }"
                 ".viewer__error { height: calc(100% - 5px); }"
                 ".viewer__load { height: 5px; }"
+                ".viewer-status { padding: 6px; width: 36px; height: 36px; }"
             )
             with self.bar:
                 self.auth_ui = AuthenticationUI()
@@ -123,7 +126,7 @@ def __init__(self, server: Server):
                 self.portal_ui.build_toolbar()
 
             with self.navigation.annotator:
-                self.eeg_annotator_ui = EGGAnnotatorUI()
+                self.eeg_annotator_ui = EEGAnnotatorUI()
 
             with self.navigation.annotator_toolbar:
                 self.eeg_annotator_ui.build_toolbar()

girdereegannotator/app/components/navigation_card.py

@@ -41,7 +41,7 @@ def __init__(self, nav_state: TypedState[NavigationState], **kwargs):
 
             with (
                 v3.VCardText(classes="nav-content"),
-                v3.VWindow(v_model=(nav_state.name.window,), classes="fill-height", style="overflow: unset;"),
+                v3.VWindow(v_model=(nav_state.name.window,), classes="nav-window-group"),
             ):
                 self.portal = v3.VWindowItem(classes="nav-window", value=(NavigationWindow.PORTAL.value,))
                 self.annotator = v3.VWindowItem(

girdereegannotator/database/girder/girder_bids_handler.py

@@ -10,6 +10,7 @@
 
 from ..models import (
     AnnotationsFile,
+    AnnotationStatus,
     Asset,
     Dataset,
     EEGFile,
@@ -162,6 +163,7 @@ def _find_annotations_files(
                 _id=annotations_file["_id"],
                 name=annotations_file["name"],
                 author=self._get_user_from_id(annotations_file["creatorId"]),
+                status=AnnotationStatus(annotations_file["bids_metadata"].get("status", AnnotationStatus.IN_PROGRESS)),
             )
             for annotations_file in eeg_annotations_files
         ]
@@ -178,6 +180,12 @@ def upload_annotations_file(
         )
         return AnnotationsFile(_id=file._id, name=file.name, author=author)
 
+    def update_annotation_status(self, annotations_file: AnnotationsFile) -> AnnotationsFile:
+        self.girder_client.put(
+            path=f"{self.resource.file}/{annotations_file._id}/metadata",
+            parameters={"metadata": json.dumps({"status": annotations_file.status.value})},
+        )
+
     def download_file(self, file: EEGFile, path: Path, refresh: bool = False) -> Asset:
         asset = self._load_asset_from_file(file)
         if not path.exists() or refresh:

girdereegannotator/database/girder/girder_database.py

@@ -158,6 +158,8 @@ def download_eeg_files(
         if annotations_file is None:
             annotations_asset_name = self.bids_handler.get_next_annotations_file_name(eeg_fileset)
             annotations_asset_path = Path(download_dir) / annotations_asset_name
+            if annotations_asset_path.exists():
+                annotations_asset_path.unlink()
             annotations_asset_path.touch()
             annotations_asset = Asset(annotations_asset_name, str(annotations_asset_path))
 
@@ -175,3 +177,19 @@ def upload_annotations_file(self, eeg_fileset: EEGFileset, annotations_asset: As
             raise DatabaseError(
                 f"Could not upload annotations file {annotations_asset.name} to {eeg_fileset.name}: {handle_database_error(e)}"
             ) from e
+
+    def update_annotations_file_status(self, annotations_file: AnnotationsFile) -> None:
+        try:
+            self.bids_handler.update_annotation_status(annotations_file)
+        except GirderHTTPError as e:
+            raise DatabaseError(
+                f"Could not update annotations file ({annotations_file.name}) status to {annotations_file.status.value}: {handle_database_error(e)}"
+            ) from e
+
+    def delete_annotations_file(self, annotations_file: AnnotationsFile) -> None:
+        try:
+            self.girder_client.delete(f"item/{annotations_file._id}")
+        except GirderHTTPError as e:
+            raise DatabaseError(
+                f"Could not delete annotations file ({annotations_file.name}): {handle_database_error(e)}"
+            ) from e

girdereegannotator/database/interface_database.py

@@ -45,6 +45,14 @@ def download_eeg_files(
     def upload_annotations_file(self, eeg_fileset: EEGFileset, eeg_annotations_asset: Asset) -> AnnotationsFile:
         pass
 
+    @abstractmethod
+    def update_annotations_file_status(self, annotations_file: AnnotationsFile) -> None:
+        pass
+
+    @abstractmethod
+    def delete_annotations_file(self, annotations_file: AnnotationsFile) -> None:
+        pass
+
 
 def register_interface(interface: DatabaseInterface, controller: Controller) -> None:
     """Register all interface methods in the controller"""

girdereegannotator/database/models.py

@@ -57,6 +57,7 @@ class EEGFile(Model): ...
 
 
 class AnnotationStatus(Enum):
+    UNDEFINED = auto()
     IN_PROGRESS = auto()
     IN_REVIEW = auto()
     DONE = auto()

girdereegannotator/eeg_annotator/__init__.py

@@ -1,4 +1,4 @@
-from .eeg_annotator_logic import EGGAnnotatorLogic
-from .eeg_annotator_ui import EGGAnnotatorUI
+from .eeg_annotator_logic import EEGAnnotatorLogic
+from .eeg_annotator_ui import EEGAnnotatorUI
 
-__all__ = ["EGGAnnotatorLogic", "EGGAnnotatorUI"]
+__all__ = ["EEGAnnotatorLogic", "EEGAnnotatorUI"]

girdereegannotator/eeg_annotator/components/__init__.py

@@ -1,18 +1,18 @@
-from .annotation_actions import AnnotateActions, NoAction, ReadonlyAction, ReviewActions
+from .annotation_actions import AnnotateActions, ReviewActions
 from .annotation_input import AnnotationInput
 from .fileset_input import FilesetInput
 from .rca_view import RCAView, RCAViewError, RCAViewMode
 from .shortcuts_panel import ShortcutsPanel
+from .viewer_status import ViewerStatus
 
 __all__ = [
     "AnnotateActions",
     "AnnotationInput",
     "FilesetInput",
-    "NoAction",
     "RCAView",
     "RCAViewError",
     "RCAViewMode",
-    "ReadonlyAction",
     "ReviewActions",
     "ShortcutsPanel",
+    "ViewerStatus",
 ]