vars-localize 0.1.0__tar.gz

vars_localize-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+# build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
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+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
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+/site
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+.idea/
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+# Project specific
+cache/
+requirements.lock
+requirements-dev.lock

vars_localize-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: vars-localize
+Version: 0.1.0
+Summary: Tool for creating localization with VARS.
+Author-email: Kevin Barnard <kbarnard@mbari.org>
+Requires-Python: >=3.8
+Requires-Dist: pyqt6>=6.7.1
+Requires-Dist: qdarkstyle>=3.2.3
+Requires-Dist: requests>=2.32.3
+Description-Content-Type: text/markdown
+
+# vars-localize
+Tool for creating localizations within the VARS database.
+
+Author: Kevin Barnard ([kbarnard@mbari.org](mailto:kbarnard@mbari.org))
+
+## :hammer: Installation
+
+> [!NOTE]
+> VARS Localize requires Python 3.8 or later.
+
+To install VARS Localize, run:
+```bash
+pip install vars-localize
+```
+
+## :rocket: Usage
+
+To start the application, run:
+```bash
+vars-localize [-u URL]
+```
+
+Once the application launches, log in with your VARS username and password.
+
+Search for a concept in the bar at the top left of the application, then select a concept from the list of results to populate a tree of imaged moments in the pane below. 
+Select an observation from the children in the subtree of the imaged moment, and draw a bounding box around the observed concept by clicking and dragging.
+
+You can double-click on any localization to edit its properties in a dialog.
+Additionally, a localization can be resized by dragging the square corners of its bounding box.
+
+## Credits
+
+VARS Localize is made with [PyQt6](https://pypi.org/project/PyQt6/).
+
+---
+
+Copyright &copy; 2019 [Monterey Bay Aquarium Research Institute](https://www.mbari.org/)

vars_localize-0.1.0/README.md

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+# vars-localize
+Tool for creating localizations within the VARS database.
+
+Author: Kevin Barnard ([kbarnard@mbari.org](mailto:kbarnard@mbari.org))
+
+## :hammer: Installation
+
+> [!NOTE]
+> VARS Localize requires Python 3.8 or later.
+
+To install VARS Localize, run:
+```bash
+pip install vars-localize
+```
+
+## :rocket: Usage
+
+To start the application, run:
+```bash
+vars-localize [-u URL]
+```
+
+Once the application launches, log in with your VARS username and password.
+
+Search for a concept in the bar at the top left of the application, then select a concept from the list of results to populate a tree of imaged moments in the pane below. 
+Select an observation from the children in the subtree of the imaged moment, and draw a bounding box around the observed concept by clicking and dragging.
+
+You can double-click on any localization to edit its properties in a dialog.
+Additionally, a localization can be resized by dragging the square corners of its bounding box.
+
+## Credits
+
+VARS Localize is made with [PyQt6](https://pypi.org/project/PyQt6/).
+
+---
+
+Copyright © 2019 [Monterey Bay Aquarium Research Institute](https://www.mbari.org/)

vars_localize-0.1.0/pyproject.toml

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+[project]
+name = "vars-localize"
+version = "0.1.0"
+description = "Tool for creating localization with VARS."
+authors = [
+    { name = "Kevin Barnard", email = "kbarnard@mbari.org" }
+]
+dependencies = [
+    "pyqt6>=6.7.1",
+    "requests>=2.32.3",
+    "qdarkstyle>=3.2.3",
+]
+readme = "README.md"
+requires-python = ">= 3.8"
+
+[project.scripts]
+vars-localize = "vars_localize.__main__:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.rye]
+managed = true
+dev-dependencies = []
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/vars_localize"]

vars_localize-0.1.0/src/vars_localize/__main__.py

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+"""
+Main entry point for the VARS Localize application.
+"""
+
+import argparse
+import sys
+
+from PyQt6.QtWidgets import QApplication
+
+from vars_localize.ui.AppWindow import AppWindow
+from vars_localize.util.endpoints import DEFAULT_M3_URL
+
+
+def main():
+    """
+    Main entry point for the VARS Localize application.
+    """
+    parser = argparse.ArgumentParser(description="VARS Localize")
+    parser.add_argument(
+        "-u", "--url", type=str, default=DEFAULT_M3_URL, help="URL of M3 server"
+    )
+    args = parser.parse_args()
+
+    app = QApplication(sys.argv)
+
+    window = AppWindow(args.url)
+    window.show()
+
+    exit_code = app.exec()
+    sys.exit(exit_code)
+
+
+if __name__ == "__main__":
+    main()

vars_localize-0.1.0/src/vars_localize/assets/__init__.py

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+"""
+Helpers for dealing with assets.
+"""
+
+from pathlib import Path
+from typing import Union
+
+
+ASSETS_DIR = Path(__file__).parent.resolve()
+
+
+def get_asset_path(rel_path: Union[str, Path]) -> Path:
+    """
+    Get the absolute path to an asset.
+
+    Args:
+        rel_path (Union[str, Path]): The relative path to the asset.
+
+    Returns:
+        Path: The absolute path to the asset.
+
+    Raises:
+        ValueError: If rel_path is an absolute path.
+    """
+    rel_path = Path(rel_path)
+    if rel_path.is_absolute():
+        raise ValueError("rel_path must be a relative path.")
+    return ASSETS_DIR / rel_path

vars_localize-0.1.0/src/vars_localize/ui/AppWindow.py

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+"""
+Main application window.
+"""
+
+from datetime import datetime
+
+from PyQt6.QtCore import Qt
+from PyQt6.QtGui import QCloseEvent, QIcon, QAction
+from PyQt6.QtWidgets import QMainWindow, QWidget, QHBoxLayout, QMessageBox, QInputDialog
+
+from vars_localize.ui.EntryTree import EntryTreeItem
+from vars_localize.ui.LoginDialog import LoginDialog
+from vars_localize.ui.DisplayPanel import DisplayPanel
+from vars_localize.ui.SearchPanel import SearchPanel
+from vars_localize.util.m3 import (
+    check_connection,
+    get_all_users,
+    get_annotations_by_video_refernce,
+    get_imaged_moments_by_image_reference,
+)
+from vars_localize.util.utils import log, split_comma_list
+
+
+class AppWindow(QMainWindow):
+    def __init__(self, m3_url: str, parent=None):
+        super(AppWindow, self).__init__(parent)
+        self._m3_url = m3_url.rstrip("/")
+
+        self.setWindowTitle("VARS Localize")
+
+        log(f"Checking connection to M3 at {self._m3_url}...")
+        if not check_connection(self._m3_url):
+            log(
+                "You are not connected to M3. Check your internet connection and/or VPN.",
+                level=2,
+            )
+            QMessageBox.critical(
+                self,
+                "No connection to M3",
+                "You are not connected to M3. Check your internet connection and/or VPN.",
+            )
+            exit(1)
+        log("Connected.")
+
+        self.observer = None
+        self.observer_role = None
+        self.admin_mode = False
+
+        login_ok = self.login()
+        if not login_ok:
+            log("You must log in to use this tool.", level=2)
+            exit(1)
+
+        self.central_container = QWidget()
+        self.central_container.setLayout(QHBoxLayout())
+
+        self.search_panel = SearchPanel(parent=self)
+        self.addDockWidget(Qt.DockWidgetArea.LeftDockWidgetArea, self.search_panel)
+
+        self.display_panel = DisplayPanel(parent=self)
+        self.central_container.layout().addWidget(self.display_panel)
+
+        self.setCentralWidget(self.central_container)
+
+        # Add admin menu if available to user
+        if self.observer_role in ("Maint", "Admin"):
+            self.add_admin_menu()
+
+        self.add_search_menu()
+        self.add_video_menu()
+
+        self.display_panel.image_view.observer = self.observer
+        self.display_panel.image_view.select_next = self.search_panel.select_next
+        self.display_panel.image_view.select_prev = self.search_panel.select_prev
+
+        self.search_panel.observer = self.observer
+
+    def load_entry(self, current: EntryTreeItem, previous: EntryTreeItem):
+        """
+        Load the current entry into the display panel
+        :param current: Current selected entry
+        :param previous: Previously selected entry
+        :return: None
+        """
+        if current and current.metadata:
+            self.display_panel.load_entry(current)
+
+    def login(self):
+        """
+        Prompt for observer login
+        :return: None
+        """
+        login_dialog = LoginDialog(parent=self)
+        login_dialog._login_form._username_line_edit.setFocus()
+        ok = login_dialog.exec()
+
+        if ok:
+            # Get the username/password from the dialog
+            username, password = login_dialog.credentials
+
+            # Set up the M3 configuration, returning False if login fails
+            if not self.configure_m3(username, password):
+                return False
+
+            all_valid_users = get_all_users()
+            users_dict = {
+                user_data["username"]: user_data for user_data in all_valid_users
+            }
+
+            # Set the observer and role
+            self.observer = username
+            self.observer_role = users_dict[username]["role"]
+        else:  # Login cancel, return failure
+            return False
+
+        return True  # Return success
+
+    def configure_m3(self, username, password) -> bool:
+        """
+        Configure endpoints and set up Annosaurus auth
+        """
+        from vars_localize.util.endpoints import configure as configure_endpoints
+        from vars_localize.util.m3 import configure_anno_session
+
+        try:
+            configure_endpoints(self._m3_url, username, password)
+        except Exception as e:
+            log("Login failed.", level=2)
+            log(e, level=2)
+            return False
+
+        configure_anno_session()
+
+        return True
+
+    def add_admin_menu(self):
+        """
+        Add the admin menu for observation modification/deletion
+        """
+        main_menu = self.menuBar()
+        options_menu = main_menu.addMenu("&Options")
+
+        admin_mode_action = QAction("Admin Mode", options_menu, checkable=True)
+
+        def set_admin_mode(val):
+            if val:
+                QMessageBox.warning(
+                    self,
+                    "Entering Admin Mode",
+                    "WARNING: You are now entering administrator mode. This mode allows modification and deletion of observations within VARS.",
+                )
+            self.admin_mode = val
+
+        admin_mode_action.toggled.connect(set_admin_mode)
+        options_menu.addAction(admin_mode_action)
+
+    def add_search_menu(self):
+        """
+        Add the Go menu for non-concept searches
+        """
+        main_menu = self.menuBar()
+        search_menu = main_menu.addMenu("&Search")
+
+        def search_imaged_moment():
+            imaged_moment_uuid_list, ok = QInputDialog.getText(
+                self,
+                "Imaged Moment UUID Search",
+                "Imaged Moment UUID (or comma-separated list)",
+            )
+            if ok:
+                imaged_moment_uuids = split_comma_list(imaged_moment_uuid_list)
+                imaged_moment_uuids = list(
+                    set(imaged_moment_uuids)
+                )  # Ensure no duplicates
+
+                # Set the UUIDs and load the first page
+                self.search_panel.set_uuids(imaged_moment_uuids)
+                self.search_panel.load_page()
+
+        search_imaged_moment_action = QAction("Imaged Moment UUID", search_menu)
+        search_imaged_moment_action.triggered.connect(search_imaged_moment)
+        search_menu.addAction(search_imaged_moment_action)
+
+        def search_image_reference():
+            image_reference_uuid_list, ok = QInputDialog.getText(
+                self,
+                "Image Reference UUID Search",
+                "Image Reference UUID (or comma-separated list)",
+            )
+            if ok:
+                all_image_reference_uuids = split_comma_list(image_reference_uuid_list)
+                imaged_moment_uuids = []
+                for image_reference_uuid in all_image_reference_uuids:
+                    res = get_imaged_moments_by_image_reference(image_reference_uuid)
+                    if res:
+                        imaged_moment_uuids.extend(
+                            [item["imaged_moment_uuid"] for item in res]
+                        )
+                imaged_moment_uuids = list(
+                    set(imaged_moment_uuids)
+                )  # Ensure no duplicates
+
+                # Set the UUIDs and load the first page
+                self.search_panel.set_uuids(imaged_moment_uuids)
+                self.search_panel.load_page()
+
+        search_image_reference_action = QAction("Image Reference UUID", search_menu)
+        search_image_reference_action.triggered.connect(search_image_reference)
+        search_menu.addAction(search_image_reference_action)
+
+        def search_video_reference():
+            video_reference_uuid, ok = QInputDialog.getText(
+                self, "Video Reference UUID Search", "Video Reference UUID"
+            )
+            if ok:
+                res = get_annotations_by_video_refernce(video_reference_uuid)
+                if res:
+                    timestamp_uuid_tuples = set()
+                    for item in res:
+                        timestamp = datetime.now()
+                        if "recorded_timestamp" in item:
+                            try:
+                                timestamp = datetime.strptime(
+                                    item["recorded_timestamp"], "%Y-%m-%dT%H:%M:%S.%fZ"
+                                )
+                            except ValueError:
+                                timestamp = datetime.strptime(
+                                    item["recorded_timestamp"], "%Y-%m-%dT%H:%M:%SZ"
+                                )
+
+                        timestamp_uuid_tuples.add(
+                            (timestamp, item["imaged_moment_uuid"])
+                        )
+
+                    # Sort by timestamp, then UUID
+                    timestamp_uuid_tuples = sorted(timestamp_uuid_tuples)
+                    imaged_moment_uuids = [item[1] for item in timestamp_uuid_tuples]
+
+                    # Set the UUIDs and load the first page
+                    self.search_panel.set_uuids(imaged_moment_uuids)
+                    self.search_panel.load_page()
+                else:
+                    # No results, warning dialog
+                    QMessageBox.warning(
+                        self,
+                        "No Results",
+                        "No results found for video reference UUID: {}".format(
+                            video_reference_uuid
+                        ),
+                    )
+
+        search_video_reference_action = QAction("Video Reference UUID", search_menu)
+        search_video_reference_action.triggered.connect(search_video_reference)
+        search_menu.addAction(search_video_reference_action)
+
+    def add_video_menu(self):
+        """
+        Add the Video menu for video-level operations
+        """
+        main_menu = self.menuBar()
+        video_menu = main_menu.addMenu("&Video")
+
+        def open_video():
+            self.search_panel.open_video()
+
+        open_video_action = QAction("Open Video", video_menu)
+        open_video_action.triggered.connect(open_video)
+        video_menu.addAction(open_video_action)
+
+    def closeEvent(self, a0: QCloseEvent) -> None:
+        """
+        Detect window close and tear down components
+        :param a0: Close event
+        :return: None
+        """
+        self.deleteLater()