implement manager view and dialog (#124)

* implement manager view and dialog

and delegate tooltips to views

* add up-to-date check to manager view

+ tweak to avoid hard-coded column index

* make get_tooltip public and more robust

* improve test coverage

found a tiny bug in the process!

* use reload module to patch thread_worker

so it's picked up by coverage

* Improve docstring

Co-authored-by: Igor Tatarnikov <[email protected]>

---------

Co-authored-by: Igor Tatarnikov <[email protected]>

brainrender_napari/data_models/atlas_table_model.py

@@ -1,27 +1,30 @@
 from bg_atlasapi.list_atlases import (
     get_all_atlases_lastversions,
     get_atlases_lastversions,
-    get_downloaded_atlases,
     get_local_atlas_version,
 )
 from qtpy.QtCore import QAbstractTableModel, QModelIndex, Qt
+from qtpy.QtWidgets import QTableView
 
-from brainrender_napari.utils.load_user_data import (
-    read_atlas_metadata_from_file,
-)
+from brainrender_napari.utils.formatting import format_atlas_name
 
 
 class AtlasTableModel(QAbstractTableModel):
     """A table data model for atlases."""
 
-    def __init__(self):
+    def __init__(self, view_type: QTableView):
         super().__init__()
         self.column_headers = [
             "Raw name",
             "Atlas",
             "Local version",
             "Latest version",
         ]
+        assert hasattr(
+            view_type, "get_tooltip_text"
+        ), "Views for this model must implement"
+        "a `classmethod` called `get_tooltip_text`"
+        self.view_type = view_type
         self.refresh_data()
 
     def refresh_data(self) -> None:
@@ -33,30 +36,24 @@ def refresh_data(self) -> None:
                 data.append(
                     [
                         name,
-                        self._format_name(name),
+                        format_atlas_name(name),
                         get_local_atlas_version(name),
                         latest_version,
                     ]
                 )
             else:
                 data.append(
-                    [name, self._format_name(name), "n/a", latest_version]
+                    [name, format_atlas_name(name), "n/a", latest_version]
                 )
 
         self._data = data
 
-    def _format_name(self, name: str) -> str:
-        formatted_name = name.split("_")
-        formatted_name[0] = formatted_name[0].capitalize()
-        formatted_name[-1] = f"({formatted_name[-1].split('um')[0]} \u03BCm)"
-        return " ".join([formatted for formatted in formatted_name])
-
     def data(self, index: QModelIndex, role=Qt.DisplayRole):
         if role == Qt.DisplayRole:
             return self._data[index.row()][index.column()]
         if role == Qt.ToolTipRole:
             hovered_atlas_name = self._data[index.row()][0]
-            return AtlasTableModel._get_tooltip_text(hovered_atlas_name)
+            return self.view_type.get_tooltip_text(hovered_atlas_name)
 
     def rowCount(self, index: QModelIndex = QModelIndex()):
         return len(self._data)
@@ -76,21 +73,3 @@ def headerData(
                 raise ValueError("Unexpected horizontal header value.")
         else:
             return super().headerData(section, orientation, role)
-
-    @classmethod
-    def _get_tooltip_text(cls, atlas_name: str):
-        """Returns the atlas metadata as a formatted string,
-        as well as instructions on how to interact with the atlas."""
-        if atlas_name in get_downloaded_atlases():
-            metadata = read_atlas_metadata_from_file(atlas_name)
-            metadata_as_string = ""
-            for key, value in metadata.items():
-                metadata_as_string += f"{key}:\t{value}\n"
-
-            tooltip_text = f"{atlas_name} (double-click to add to viewer)\
-            \n{metadata_as_string}"
-        elif atlas_name in get_all_atlases_lastversions().keys():
-            tooltip_text = f"{atlas_name} (double-click to download)"
-        else:
-            raise ValueError("Tooltip text called with invalid atlas name.")
-        return tooltip_text

brainrender_napari/utils/formatting.py

@@ -0,0 +1,12 @@
+from bg_atlasapi.list_atlases import get_all_atlases_lastversions
+
+
+def format_atlas_name(name: str) -> str:
+    """Format an atlas name nicely.
+    Assumes input in the form of atlas_name_in_snake_case_RESOLUTIONum,
+    e.g. allen_mouse_100um"""
+    assert name in get_all_atlases_lastversions().keys(), "invalid atlas name!"
+    formatted_name = name.split("_")
+    formatted_name[0] = formatted_name[0].capitalize()
+    formatted_name[-1] = f"({formatted_name[-1].split('um')[0]} \u03BCm)"
+    return " ".join([formatted for formatted in formatted_name])

brainrender_napari/widgets/atlas_download_dialog.py → brainrender_napari/widgets/atlas_manager_dialog.py

@@ -8,16 +8,16 @@
 )
 
 
-class AtlasDownloadDialog(QDialog):
-    """A modal dialog to ask users to confirm they'd like to download
+class AtlasManagerDialog(QDialog):
+    """A modal dialog to ask users to confirm they'd like to download/update
     the selected atlas, and warn them that it may be slow.
     """
 
-    def __init__(self, atlas_name):
+    def __init__(self, atlas_name: str, action: str) -> None:
         if atlas_name in get_all_atlases_lastversions().keys():
             super().__init__()
 
-            self.setWindowTitle(f"Download {atlas_name} Atlas")
+            self.setWindowTitle(f"{action} {atlas_name} Atlas")
             self.setModal(True)
 
             self.label = QLabel("Are you sure?\n(It may take a while)")
@@ -36,5 +36,6 @@ def __init__(self, atlas_name):
             self.setLayout(layout)
         else:
             raise ValueError(
-                "Download Dialog constructor called with invalid atlas name."
+                "Atlas manager dialog constructor"
+                "called with invalid atlas name."
             )

brainrender_napari/widgets/atlas_manager_view.py

@@ -0,0 +1,118 @@
+"""The purpose of this file is to provide interactive table view to download
+and update atlases. Users interacting with the table can request to
+* download an atlas (double-click on row of a not-yet downloaded atlas)
+* update an atlas (double-click on row of outdated local atlas)
+They can also hover over an up-to-date local atlas and see that
+it's up to date.
+
+It is designed to be agnostic from the viewer framework by emitting signals
+that any interested observers can connect to.
+"""
+
+from typing import Callable
+
+from bg_atlasapi.list_atlases import (
+    get_all_atlases_lastversions,
+    get_atlases_lastversions,
+    get_downloaded_atlases,
+)
+from bg_atlasapi.update_atlases import install_atlas, update_atlas
+from napari.qt import thread_worker
+from qtpy.QtCore import Signal
+from qtpy.QtWidgets import QTableView, QWidget
+
+from brainrender_napari.data_models.atlas_table_model import AtlasTableModel
+from brainrender_napari.utils.formatting import format_atlas_name
+from brainrender_napari.widgets.atlas_manager_dialog import AtlasManagerDialog
+
+
+class AtlasManagerView(QTableView):
+    download_atlas_confirmed = Signal(str)
+    update_atlas_confirmed = Signal(str)
+
+    def __init__(self, parent: QWidget = None):
+        """Initialises an atlas table view with latest atlas versions.
+
+        Also responsible for appearance, behaviour on selection, and
+        setting up signal-slot connections.
+        """
+        super().__init__(parent)
+
+        self.setModel(AtlasTableModel(AtlasManagerView))
+        self.setEnabled(True)
+        self.verticalHeader().hide()
+        self.resizeColumnsToContents()
+
+        self.setSelectionBehavior(QTableView.SelectionBehavior.SelectRows)
+        self.setSelectionMode(QTableView.SelectionMode.SingleSelection)
+
+        self.doubleClicked.connect(self._on_row_double_clicked)
+        self.hideColumn(
+            self.model().column_headers.index("Raw name")
+        )  # hide raw name
+
+    def _on_row_double_clicked(self):
+        atlas_name = self.selected_atlas_name()
+        if atlas_name in get_downloaded_atlases():
+            up_to_date = get_atlases_lastversions()[atlas_name]["updated"]
+            if not up_to_date:
+                update_dialog = AtlasManagerDialog(atlas_name, "Update")
+                update_dialog.ok_button.clicked.connect(
+                    self._on_update_atlas_confirmed
+                )
+                update_dialog.exec()
+        else:
+            download_dialog = AtlasManagerDialog(atlas_name, "Download")
+            download_dialog.ok_button.clicked.connect(
+                self._on_download_atlas_confirmed
+            )
+            download_dialog.exec()
+
+    def _on_download_atlas_confirmed(self):
+        """Downloads the currently selected atlas and signals this."""
+        atlas_name = self.selected_atlas_name()
+        worker = self._apply_in_thread(install_atlas, atlas_name)
+        worker.returned.connect(self.download_atlas_confirmed.emit)
+        worker.start()
+
+    def _on_update_atlas_confirmed(self):
+        """Updates the currently selected atlas and signals this."""
+        atlas_name = self.selected_atlas_name()
+        worker = self._apply_in_thread(update_atlas, atlas_name)
+        worker.returned.connect(self.update_atlas_confirmed.emit)
+        worker.start()
+
+    def selected_atlas_name(self) -> str:
+        """A single place to get a valid selected atlas name."""
+        selected_index = self.selectionModel().currentIndex()
+        assert selected_index.isValid()
+        selected_atlas_name_index = selected_index.siblingAtColumn(0)
+        selected_atlas_name = self.model().data(selected_atlas_name_index)
+        return selected_atlas_name
+
+    @thread_worker
+    def _apply_in_thread(self, apply: Callable, atlas_name: str):
+        """Calls `apply` on the given atlas in a separate thread."""
+        apply(atlas_name)
+        self.model().refresh_data()
+        return atlas_name
+
+    @classmethod
+    def get_tooltip_text(cls, atlas_name: str):
+        """Returns the atlas name as a formatted string,
+        as well as instructions on how to interact with the atlas."""
+        if atlas_name in get_downloaded_atlases():
+            is_up_to_date = get_atlases_lastversions()[atlas_name]["updated"]
+            if is_up_to_date:
+                tooltip_text = f"{format_atlas_name(atlas_name)} is up-to-date"
+            else:  # needs updating
+                tooltip_text = (
+                    f"{format_atlas_name(atlas_name)} (double-click to update)"
+                )
+        elif atlas_name in get_all_atlases_lastversions().keys():
+            tooltip_text = (
+                f"{format_atlas_name(atlas_name)} (double-click to download)"
+            )
+        else:
+            raise ValueError("Tooltip text called with invalid atlas name.")
+        return tooltip_text

brainrender_napari/widgets/atlas_viewer_view.py

@@ -15,6 +15,7 @@
 from qtpy.QtWidgets import QMenu, QTableView, QWidget
 
 from brainrender_napari.data_models.atlas_table_model import AtlasTableModel
+from brainrender_napari.utils.formatting import format_atlas_name
 from brainrender_napari.utils.load_user_data import (
     read_atlas_metadata_from_file,
 )
@@ -34,7 +35,7 @@ def __init__(self, parent: QWidget = None):
         """
         super().__init__(parent)
 
-        self.setModel(AtlasTableModel())
+        self.setModel(AtlasTableModel(AtlasViewerView))
 
         self.setEnabled(True)
         self.verticalHeader().hide()
@@ -102,3 +103,19 @@ def _on_row_double_clicked(self) -> None:
     def _on_current_changed(self) -> None:
         """Emits a signal with the newly selected atlas name"""
         self.selected_atlas_changed.emit(self.selected_atlas_name())
+
+    @classmethod
+    def get_tooltip_text(cls, atlas_name: str):
+        """Returns the atlas metadata as a formatted string,
+        as well as instructions on how to interact with the atlas."""
+        if atlas_name in get_downloaded_atlases():
+            metadata = read_atlas_metadata_from_file(atlas_name)
+            metadata_as_string = ""
+            for key, value in metadata.items():
+                metadata_as_string += f"{key}:\t{value}\n"
+            tooltip_text = f"{format_atlas_name(atlas_name)}\
+                (double-click to add to viewer)\
+                \n{metadata_as_string}"
+        else:
+            raise ValueError("Tooltip text called with invalid atlas name.")
+        return tooltip_text

tests/conftest.py

@@ -1,8 +1,9 @@
 import os
+import shutil
 from pathlib import Path
 
 import pytest
-from bg_atlasapi import BrainGlobeAtlas, config
+from bg_atlasapi import BrainGlobeAtlas, config, list_atlases
 from qtpy.QtCore import Qt
 
 
@@ -88,3 +89,28 @@ def inner_double_click_on_view(view, index):
         )
 
     return inner_double_click_on_view
+
+
+@pytest.fixture
+def mock_newer_atlas_version_available():
+    current_version_path = Path.home() / ".brainglobe/example_mouse_100um_v1.2"
+    older_version_path = Path.home() / ".brainglobe/example_mouse_100um_v1.1"
+    assert current_version_path.exists() and not older_version_path.exists()
+
+    current_version_path.rename(older_version_path)
+    assert older_version_path.exists() and not current_version_path.exists()
+    assert (
+        list_atlases.get_atlases_lastversions()["example_mouse_100um"][
+            "latest_version"
+        ]
+        == "1.2"
+    )
+    assert list_atlases.get_local_atlas_version("example_mouse_100um") == "1.1"
+
+    yield  # run test with outdated version
+
+    # cleanup: ensure version is up-to-date again
+    if older_version_path.exists():
+        shutil.rmtree(path=older_version_path)
+        _ = BrainGlobeAtlas("example_mouse_100um")
+    assert current_version_path.exists() and not older_version_path.exists()