dsa-helpers 0.3.dev0__tar.gz → 0.4__tar.gz

{dsa_helpers-0.3.dev0 → dsa_helpers-0.4}/.gitignore

@@ -5,4 +5,7 @@ pyenv/
 # Do not push the version file.
 dsa_utils/_version.py
 
-*.pyc
+*.pyc
+*.egg-info
+dist/
+.env

dsa_helpers-0.4/PKG-INFO

@@ -0,0 +1,50 @@
+Metadata-Version: 2.1
+Name: dsa_helpers
+Version: 0.4
+Summary: Utility functions for working with the DSA girder client.
+Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
+Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
+Project-URL: Repository, https://github.com/Gutman-Lab/dsa-python-utils
+Keywords: dsa,girder,girder_client
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: girder-client
+Requires-Dist: numpy
+Requires-Dist: setuptools
+Requires-Dist: opencv-python
+Requires-Dist: pandas
+Requires-Dist: pymongo
+Requires-Dist: pillow
+Requires-Dist: dash
+Requires-Dist: dash_bootstrap_components
+Requires-Dist: shapely
+Requires-Dist: geopandas
+Requires-Dist: torch
+Requires-Dist: datasets
+Requires-Dist: transformers
+Requires-Dist: torchvision
+
+# Digital Slide Archive (DSA) Helpers
+Digital Slide Archive Python utility library.
+
+This library is available for installation through [Python Package Index (PyPI)](https://pypi.org/).
+
+This library was tested using Python version 3.11.8 and uses the dependencies described in requirements.txt.
+
+This Python PyPI package is found [here](https://pypi.org/project/dsa-helpers/).
+
+## Instructions for Development
+1. Install requirements for building and distributing package:
+```
+$ python3 -m pip install --upgrade build  # for building package
+$ python3 -m pip install --upgrade twine  # for uploading to PyPI
+```
+2. When ready to build:
+    - Modify "pyproject.toml" file, change the "version" key to a different value than a version already pushed.
+    - Run ```$ python3 -m build```. This will create a dist directory and put your new wheel and tar distribution files there.
+3. To install locally for development: ```$ pip3 install dist/dsa_helpers-*.whl```, choosing the wheel version you want to test.
+4. Upload to PyPI using twine: ```python3 -m twine upload --repository pypi dist/*```
+    * You can specify specific files to upload, the line above pushes everything in dist directory.

dsa_helpers-0.4/README.md

@@ -0,0 +1,21 @@
+# Digital Slide Archive (DSA) Helpers
+Digital Slide Archive Python utility library.
+
+This library is available for installation through [Python Package Index (PyPI)](https://pypi.org/).
+
+This library was tested using Python version 3.11.8 and uses the dependencies described in requirements.txt.
+
+This Python PyPI package is found [here](https://pypi.org/project/dsa-helpers/).
+
+## Instructions for Development
+1. Install requirements for building and distributing package:
+```
+$ python3 -m pip install --upgrade build  # for building package
+$ python3 -m pip install --upgrade twine  # for uploading to PyPI
+```
+2. When ready to build:
+    - Modify "pyproject.toml" file, change the "version" key to a different value than a version already pushed.
+    - Run ```$ python3 -m build```. This will create a dist directory and put your new wheel and tar distribution files there.
+3. To install locally for development: ```$ pip3 install dist/dsa_helpers-*.whl```, choosing the wheel version you want to test.
+4. Upload to PyPI using twine: ```python3 -m twine upload --repository pypi dist/*```
+    * You can specify specific files to upload, the line above pushes everything in dist directory.

dsa_helpers-0.4/app.py

@@ -0,0 +1,14 @@
+# A test application.
+from dash import Dash, html
+import dash_bootstrap_components as dbc
+from dsa_helpers.dash.header import get_header
+import os
+
+os.environ["DSA_API_URL"] = "https://megabrain.neurology.emory.edu/api/v1"
+
+app = Dash(__name__, external_stylesheets=[dbc.themes.BOOTSTRAP])
+
+app.layout = html.Div([get_header("Test")])
+
+if __name__ == "__main__":
+    app.run_server(debug=True)

{dsa_helpers-0.3.dev0 → dsa_helpers-0.4}/dsa_helpers/__init__.py

@@ -1,7 +1,8 @@
 # Shadow imports.
-from .login import login
 from .imread import imread
 from .imwrite import imwrite
 
 # Modules that should be available.
-from . import girder_utils, image_utils
+# from . import girder_utils, image_utils, dash
+
+__all__ = ["girder_utils", "image_utils", "dash", "ml"]

dsa_helpers-0.4/dsa_helpers/dash/__init__.py

@@ -0,0 +1 @@
+from . import header

dsa_helpers-0.4/dsa_helpers/dash/header.py

@@ -0,0 +1,151 @@
+from dash import html, dcc
+import dash_bootstrap_components as dbc
+from .header_callbacks import get_callbacks
+
+
+def get_header(
+    dsa_api_url: str,
+    title: str = "App",
+    store_id: str = "user-store",
+    config: dict | None = None,
+) -> html.Div:
+    """Get the Dash html component that contains the header of the application
+    with login capabilities.
+
+    Args:
+        dsa_api_url (str): The URL of the DSA API.
+        title (str, optional): The title of the application. Defaults to "App".
+        config (dict, optional): The configuration of the component. Defaults to None.
+            If None the default configuration is:
+            {
+                "backgroundColor": "#012169",
+                "titleColor": "#d9d9d6",
+                "fontColor": "#f2a900",
+            }
+
+    Returns:
+        html.Div: The header component.
+
+    """
+    if config is None:
+        config = {}
+
+    get_callbacks(dsa_api_url, store_id)
+
+    login_modal = dbc.Modal(
+        [
+            dbc.ModalHeader("Log in"),
+            dbc.ModalBody(
+                [
+                    html.Div(
+                        "Login or email", style={"margin": 5, "fontWeight": "bold"}
+                    ),
+                    dbc.Input(
+                        id=f"{store_id}=login",
+                        type="text",
+                        placeholder="Enter login",
+                        style={"margin": 5},
+                    ),
+                    html.Div(
+                        "Password",
+                        style={"margin": 5, "marginTop": 15, "fontWeight": "bold"},
+                    ),
+                    dbc.Input(
+                        id=f"{store_id}=password",
+                        type="password",
+                        placeholder="Enter password",
+                        style={"margin": 5},
+                    ),
+                    html.Div(
+                        "Login failed.",
+                        hidden=True,
+                        id=f"{store_id}=login-failed",
+                        style={"color": "red", "fontWeight": "bold", "margin": 10},
+                    ),
+                ],
+            ),
+            dbc.ModalFooter(
+                dbc.Row(
+                    [
+                        dbc.Col(
+                            dbc.Button(
+                                "Close",
+                                id=f"{store_id}=close-login-modal",
+                                className="me-1",
+                                color="light",
+                            )
+                        ),
+                        dbc.Col(
+                            dbc.Button(
+                                "Login",
+                                id=f"{store_id}=log-in-btn",
+                                className="me-1",
+                                color="primary",
+                            )
+                        ),
+                    ],
+                )
+            ),
+        ],
+        is_open=False,
+        id=f"{store_id}=login-modal",
+    )
+
+    logout_modal = dbc.Modal(
+        [
+            dbc.ModalFooter(
+                [
+                    dbc.Button(
+                        "Log out",
+                        id=f"{store_id}=logout-btn",
+                        color="danger",
+                        className="me-1",
+                    ),
+                ]
+            )
+        ],
+        is_open=False,
+        id=f"{store_id}=logout-modal",
+    )
+
+    return html.Div(
+        [
+            dbc.Row(
+                [
+                    dbc.Col(
+                        html.H1(
+                            title,
+                            style={
+                                "fontWeight": "bold",
+                                "color": config.get("titleColor", "#d9d9d6"),
+                                "marginLeft": 5,
+                            },
+                        ),
+                        width="auto",
+                    ),
+                    dbc.Col(
+                        dbc.Button(
+                            "Log in",
+                            id=f"{store_id}=login-btn",
+                            color=config.get("backgroundColor", "#012169"),
+                            style={
+                                "color": config.get("fontColor", "#f2a900"),
+                                "fontSize": "1.2rem",
+                            },
+                            className="me-1",
+                        ),
+                        width="auto",
+                    ),
+                ],
+                justify="between",
+                align="center",
+            ),
+            login_modal,
+            logout_modal,
+            dcc.Store(id=store_id, storage_type="local", data={}),
+        ],
+        style={
+            "backgroundColor": config.get("backgroundColor", "#012169"),
+            "padding": 5,
+        },
+    )

dsa_helpers-0.4/dsa_helpers/dash/header_callbacks.py

@@ -0,0 +1,99 @@
+# Callbacks for the header component.
+from dash import callback, Output, Input, State, no_update
+from girder_client import GirderClient
+
+
+def get_callbacks(dsa_api_url: str, store_id: str):
+    """Setup the callbacks to the DSA API url of interest and the proper store id."""
+
+    @callback(Output(f"{store_id}=login-btn", "children"), Input(store_id, "data"))
+    def check_user_store(data):
+        # Check if the user store has user info or if no one is logged in.
+        return data["user"] if len(data) else "Log in"
+
+    @callback(
+        [
+            Output(f"{store_id}=login-modal", "is_open", allow_duplicate=True),
+            Output(f"{store_id}=logout-modal", "is_open", allow_duplicate=True),
+        ],
+        [
+            Input(f"{store_id}=login-btn", "n_clicks"),
+            State(f"{store_id}=login-btn", "children"),
+        ],
+        prevent_initial_call=True,
+    )
+    def open_login_modal(n_clicks, children):
+        # Open login / logout modal.
+        if n_clicks:
+            if children == "Log in":
+                return True, False
+            else:
+                return False, True
+
+        return False, False
+
+    @callback(
+        [
+            Output(store_id, "data"),
+            Output(f"{store_id}=login-failed", "hidden", allow_duplicate=True),
+            Output(f"{store_id}=login-modal", "is_open", allow_duplicate=True),
+            Output(f"{store_id}=login", "value", allow_duplicate=True),
+            Output(f"{store_id}=password", "value", allow_duplicate=True),
+        ],
+        [
+            Input(f"{store_id}=log-in-btn", "n_clicks"),
+            State(f"{store_id}=login", "value"),
+            State(f"{store_id}=password", "value"),
+        ],
+        prevent_initial_call=True,
+    )
+    def login(n_clicks, login, password):
+        # Try to login.
+        gc = GirderClient(apiUrl=dsa_api_url)
+
+        try:
+            _ = gc.authenticate(username=login, password=password)
+
+            response = gc.get("token/session")
+
+            user = gc.get("user/me")["login"]
+
+            return {"user": user, "token": response["token"]}, True, False, "", ""
+        except:
+            return (
+                {},
+                False,
+                True,
+                no_update,
+                no_update,
+            )
+
+    @callback(
+        [
+            Output(f"{store_id}=login-modal", "is_open", allow_duplicate=True),
+            Output(f"{store_id}=login", "value", allow_duplicate=True),
+            Output(f"{store_id}=password", "value", allow_duplicate=True),
+            Output(f"{store_id}=login-failed", "hidden", allow_duplicate=True),
+        ],
+        Input(f"{store_id}=close-login-modal", "n_clicks"),
+        prevent_initial_call=True,
+    )
+    def close_login_modal(n_clicks):
+        if n_clicks:
+            return False, "", "", True
+
+        return False, "", "", True
+
+    @callback(
+        [
+            Output(store_id, "data", allow_duplicate=True),
+            Output(f"{store_id}=logout-modal", "is_open", allow_duplicate=True),
+        ],
+        Input(f"{store_id}=logout-btn", "n_clicks"),
+        prevent_initial_call=True,
+    )
+    def logout(n_clicks):
+        if n_clicks:
+            return {}, False
+
+        return no_update, False