dsa-helpers 0.4.dev0__tar.gz → 0.4.dev2__tar.gz

{dsa_helpers-0.4.dev0/dsa_helpers.egg-info → dsa_helpers-0.4.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.4.dev0
+Version: 0.4.dev2
 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>

{dsa_helpers-0.4.dev0 → dsa_helpers-0.4.dev2}/dsa_helpers/dash/header.py

@@ -1,24 +1,37 @@
 from dash import html, dcc
 import dash_bootstrap_components as dbc
-from . import header_callbacks
+from .header_callbacks import get_callbacks
 
 
-def get_header(title: str = "App", config: dict | None = None) -> html.Div:
+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:
-        title (str): The title of the application.
-        config (dict): The configuration of the component.
-
-            backgroundColor
-            titleColor
-            fontColor
+        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"),
@@ -28,7 +41,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                         "Login or email", style={"margin": 5, "fontWeight": "bold"}
                     ),
                     dbc.Input(
-                        id="login",
+                        id=f"{store_id}=login",
                         type="text",
                         placeholder="Enter login",
                         style={"margin": 5},
@@ -38,7 +51,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                         style={"margin": 5, "marginTop": 15, "fontWeight": "bold"},
                     ),
                     dbc.Input(
-                        id="password",
+                        id=f"{store_id}=password",
                         type="password",
                         placeholder="Enter password",
                         style={"margin": 5},
@@ -46,7 +59,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                     html.Div(
                         "Login failed.",
                         hidden=True,
-                        id="login-failed",
+                        id=f"{store_id}=login-failed",
                         style={"color": "red", "fontWeight": "bold", "margin": 10},
                     ),
                 ],
@@ -57,7 +70,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                         dbc.Col(
                             dbc.Button(
                                 "Close",
-                                id="close-login-modal",
+                                id=f"{store_id}=close-login-modal",
                                 className="me-1",
                                 color="light",
                             )
@@ -65,7 +78,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                         dbc.Col(
                             dbc.Button(
                                 "Login",
-                                id="log-in-btn",
+                                id=f"{store_id}=log-in-btn",
                                 className="me-1",
                                 color="primary",
                             )
@@ -75,7 +88,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
             ),
         ],
         is_open=False,
-        id="login-modal",
+        id=f"{store_id}=login-modal",
     )
 
     logout_modal = dbc.Modal(
@@ -84,7 +97,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                 [
                     dbc.Button(
                         "Log out",
-                        id="logout-btn",
+                        id=f"{store_id}=logout-btn",
                         color="danger",
                         className="me-1",
                     ),
@@ -92,12 +105,9 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
             )
         ],
         is_open=False,
-        id="logout-modal",
+        id=f"{store_id}=logout-modal",
     )
 
-    if config is None:
-        config = {}
-
     return html.Div(
         [
             dbc.Row(
@@ -116,7 +126,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
                     dbc.Col(
                         dbc.Button(
                             "Log in",
-                            id="login-btn",
+                            id=f"{store_id}=login-btn",
                             color=config.get("backgroundColor", "#012169"),
                             style={
                                 "color": config.get("fontColor", "#f2a900"),
@@ -132,7 +142,7 @@ def get_header(title: str = "App", config: dict | None = None) -> html.Div:
             ),
             login_modal,
             logout_modal,
-            dcc.Store(id="user-store", storage_type="local", data={}),
+            dcc.Store(id=store_id, storage_type="local", data={}),
         ],
         style={
             "backgroundColor": config.get("backgroundColor", "#012169"),

dsa_helpers-0.4.dev2/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

{dsa_helpers-0.4.dev0 → dsa_helpers-0.4.dev2}/dsa_helpers/mongo_utils.py

@@ -13,7 +13,7 @@ def get_mongo_client(
     username: str | None = None,
     password: str | None = None,
     port: int | None = None,
-) -> pymongo.MongoClient:
+):
     """Get a mongo client by providing the key parts of the URL. By default
     when the parameters are not passed, it sets them to default values first
     by looking at key environment variables. If the environment variables are
@@ -36,7 +36,7 @@ def get_mongo_client(
             missing it will default to 27017.
 
     Returns:
-        pymongo.MongoClient: The mongo client.
+        The mongo client.
 
     """
     if username is None:
@@ -67,7 +67,7 @@ def chunks(lst: list, n=500):
 
 
 def add_many_to_collection(
-    mongo_collection: pymongo.collection.Collection,
+    mongo_collection,
     items: dict | list,
     key: str = "_id",
 ) -> dict[str | dict]:
@@ -75,7 +75,7 @@ def add_many_to_collection(
     user key.
 
     Args:
-        mongo_collection (pymongo.collection.Collection): The mongo collection to add to.
+        mongo_collection: The mongo collection to add to.
         items (dict | list): The items to add to the collection.
         key (str): The key to use to identify the items.
 
@@ -100,13 +100,11 @@ def add_many_to_collection(
     return items
 
 
-def get_img_from_db(
-    mongo_db: pymongo.database.Database, img_id: str
-) -> Union[np.ndarray, None]:
+def get_img_from_db(mongo_db, img_id: str) -> Union[np.ndarray, None]:
     """Get an image from the database by its location id.
 
     Args:
-        mongo_db (pymongo.database.Database): The mongo database.
+        mongo_db: The mongo database.
         img_loc (str): The image id in mongo.
 
     Returns:
@@ -131,13 +129,13 @@ def get_img_from_db(
 
 
 def add_img_to_db(
-    mongo_db: pymongo.database.Database,
+    mongo_db,
     img: Image.Image | np.ndarray,
 ) -> str:
     """Add an image to the database.
 
     Args:
-        mongo_db (pymongo.database.Database): The mongo database.
+        mongo_db: The mongo database.
         img (np.ndarray or PIL.Image.Image): The image.
 
     Returns:

{dsa_helpers-0.4.dev0 → dsa_helpers-0.4.dev2/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dsa_helpers
-Version: 0.4.dev0
+Version: 0.4.dev2
 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>

{dsa_helpers-0.4.dev0 → dsa_helpers-0.4.dev2}/pyproject.toml

@@ -31,7 +31,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v0.4dev0"
+version = "v0.4dev2"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"

dsa_helpers-0.4.dev2/tests/test.ipynb

@@ -0,0 +1,79 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Test Python Package Build"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import all modules.\n",
+    "from dsa_helpers import *"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Authenticate girder client."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "gc = girder_utils.login(\"\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Get DSA items recursively"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Get items from a folder.\n",
+    "items = girder_utils.get_items(gc, \"\")\n",
+    "print(f\"Got {len(items)} items from folder.\")\n",
+    "\n",
+    "items = girder_utils.get_items(gc, \"\")\n",
+    "print(f\"Got {len(items)} items from collection.\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "env",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

dsa_helpers-0.4.dev0/dsa_helpers/dash/header_callbacks.py

@@ -1,98 +0,0 @@
-# Callbacks for the header component.
-from dash import callback, Output, Input, State, no_update
-from girder_client import GirderClient
-from os import getenv
-
-
-@callback(Output("login-btn", "children"), Input("user-store", "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("login-modal", "is_open", allow_duplicate=True),
-        Output("logout-modal", "is_open", allow_duplicate=True),
-    ],
-    [Input("login-btn", "n_clicks"), State("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("user-store", "data"),
-        Output("login-failed", "hidden", allow_duplicate=True),
-        Output("login-modal", "is_open", allow_duplicate=True),
-        Output("login", "value", allow_duplicate=True),
-        Output("password", "value", allow_duplicate=True),
-    ],
-    [
-        Input("log-in-btn", "n_clicks"),
-        State("login", "value"),
-        State("password", "value"),
-    ],
-    prevent_initial_call=True,
-)
-def login(n_clicks, login, password):
-    # Try to login.
-    gc = GirderClient(apiUrl=getenv("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("login-modal", "is_open", allow_duplicate=True),
-        Output("login", "value", allow_duplicate=True),
-        Output("password", "value", allow_duplicate=True),
-        Output("login-failed", "hidden", allow_duplicate=True),
-    ],
-    Input("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("user-store", "data", allow_duplicate=True),
-        Output("logout-modal", "is_open", allow_duplicate=True),
-    ],
-    Input("logout-btn", "n_clicks"),
-    prevent_initial_call=True,
-)
-def logout(n_clicks):
-    if n_clicks:
-        return {}, False
-
-    return no_update, False