bfabric-web-apps 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

bfabric_web_apps/__init__.py

@@ -1,6 +1,97 @@
-from objects import (
-    BfabricInterface,
-    Logger
-)
+import os
 
-from layouts.layouts import *
+# Export objects and classes
+from bfabric_web_apps.objects import BfabricInterface, Logger
+
+# Export components
+from .utils import components
+
+# Export layouts
+from .layouts.layouts import get_static_layout
+
+# Export app initialization utilities
+from .utils.app_init import create_app
+from .utils.get_logger import get_logger
+from .utils.get_power_user_wrapper import get_power_user_wrapper
+from .utils.create_app_in_bfabric import create_app_in_bfabric
+
+# Export callbacks
+from .utils.callbacks import process_url_and_token, submit_bug_report
+
+from .utils import defaults
+
+HOST = os.getenv("HOST", defaults.HOST)
+PORT = int(os.getenv("PORT", defaults.PORT))  # Convert to int since env variables are strings
+DEV = os.getenv("DEV", str(defaults.DEV)).lower() in ["true", "1", "yes"]  # Convert to bool
+CONFIG_FILE_PATH = os.getenv("CONFIG_FILE_PATH", defaults.CONFIG_FILE_PATH)
+
+DEVELOPER_EMAIL_ADDRESS = os.getenv("DEVELOPER_EMAIL_ADDRESS", defaults.DEVELOPER_EMAIL_ADDRESS)
+BUG_REPORT_EMAIL_ADDRESS = os.getenv("BUG_REPORT_EMAIL_ADDRESS", defaults.BUG_REPORT_EMAIL_ADDRESS)
+
+
+# Define __all__ for controlled imports
+__all__ = [
+    "BfabricInterface",
+    "Logger",
+    "components",
+    "get_static_layout",
+    "create_app",
+    "process_url_and_token",
+    "submit_bug_report",
+    'get_logger',
+    'get_power_user_wrapper',
+    'HOST',
+    'PORT', 
+    'DEV',
+    'CONFIG_FILE_PATH',
+    'DEVELOPER_EMAIL_ADDRESS',
+    'BUG_REPORT_EMAIL_ADDRESS',
+    'create_app_in_bfabric'
+]
+
+
+
+'''
+import os
+from .utils import defaults
+
+# Private variable for CONFIG_FILE_PATH
+_CONFIG_FILE_PATH = os.getenv("CONFIG_FILE_PATH", defaults.CONFIG_FILE_PATH)
+
+def set_config_file_path(path):
+    """
+    Setter for the CONFIG_FILE_PATH variable.
+    """
+    global _CONFIG_FILE_PATH
+    if not isinstance(path, str):
+        raise ValueError("CONFIG_FILE_PATH must be a string.")
+    _CONFIG_FILE_PATH = path
+
+def get_config_file_path():
+    """
+    Getter for the CONFIG_FILE_PATH variable.
+    """
+    return _CONFIG_FILE_PATH
+
+# Expose CONFIG_FILE_PATH as a read-only property
+class Config:
+    @property
+    def CONFIG_FILE_PATH(self):
+        return get_config_file_path()
+
+config = Config()
+
+'''
+
+
+
+'''
+from bfabric import config
+
+config.CONFIG_FILE_PATH
+'''
+
+'''
+from bfabric import set_config_file_path
+set_config_file_path("new/path/to/config.json")
+'''

bfabric_web_apps/layouts/layouts.py

@@ -1,13 +1,259 @@
+from dash import html, dcc
+import dash_bootstrap_components as dbc
+import bfabric_web_apps
 
+def get_static_layout(base_title=None, main_content=None, documentation_content=None):
+    """
+    Returns a layout with static tabs for Main, Documentation, and Report a Bug.
+    The main content is customizable, while the other tabs are generic.
 
-def get_empty_layout(): 
+    Args:
+        base_title (str): The main title to be displayed in the banner.
+        main_content (html.Div): Content to be displayed in the "Main" tab.
+        documentation_content (html.Div): Content for the "Documentation" tab.
 
-    pass 
+    Returns:
+        html.Div: The complete static layout of the web app.
+    """
+    return html.Div(
+        children=[
+            dcc.Location(id='url', refresh=False),
+            dcc.Store(id='token', storage_type='session'),
+            dcc.Store(id='entity', storage_type='session'),
+            dcc.Store(id='app_data', storage_type='session'),
+            dcc.Store(id='token_data', storage_type='session'),
+            dcc.Store(id='dynamic-link-store', storage_type='session'),  # Store for dynamic job link
 
-def get_layout_with_sidebar(): 
-    
-    pass 
+            dbc.Container(
+                children=[
+                    # Banner Section
+                    dbc.Row(
+                        dbc.Col(
+                            html.Div(
+                                className="banner",
+                                children=[
+                                    # Title
+                                    html.Div(
+                                        children=[
+                                            html.P(
+                                                base_title,
+                                                style={
+                                                    'color': '#ffffff',
+                                                    'margin-top': '15px',
+                                                    'height': '80px',
+                                                    'width': '100%',
+                                                    'font-size': '40px',
+                                                    'margin-left': '20px'
+                                                }
+                                            )
+                                        ],
+                                        style={"background-color": "#000000", "border-radius": "10px"}
+                                    ),
+                                ],
+                                style={"position": "relative", "padding": "10px"}
+                            ),
+                        ),
+                    ),
 
-def get_layout_without_sidebar(): 
-    
-    pass
+                    # Page Title Section + View Logs Button (Aligned Right)
+                    dbc.Row(
+                        dbc.Col(
+                            html.Div(
+                                children=[
+                                    # Page Title (Aligned Left)
+                                    html.P(
+                                        id="page-title",
+                                        children=[str(" ")],
+                                        style={"font-size": "40px", "margin-left": "20px", "margin-top": "10px"}
+                                    ),
+
+                                    # View Logs Button (Aligned Right)
+                                    html.Div(
+                                        children=[
+                                            html.A(
+                                                dbc.Button(
+                                                    "View Logs",
+                                                    id="dynamic-link-button",
+                                                    color="secondary",  # Greyish color
+                                                    style={
+                                                        "font-size": "18px",
+                                                        "padding": "10px 20px",
+                                                        "border-radius": "8px"
+                                                    }
+                                                ),
+                                                id="dynamic-link",
+                                                href="#",  # Will be dynamically set in the callback
+                                                target="_blank"
+                                            )
+                                        ],
+                                        style={
+                                            "position": "absolute",
+                                            "right": "20px",
+                                            "top": "10px",  # Aligns with title
+                                        }
+                                    ),
+                                ],
+                                style={
+                                    "position": "relative",  # Ensures absolute positioning works
+                                    "margin-top": "0px",
+                                    "min-height": "80px",
+                                    "height": "6vh",
+                                    "border-bottom": "2px solid #d4d7d9",
+                                    "display": "flex",
+                                    "align-items": "center",
+                                    "justify-content": "space-between",  # Title left, button right
+                                    "padding-right": "20px"  # Space between button & right edge
+                                }
+                            ),
+                        ),
+                    ),
+
+                    # Bug Report Alerts (Restored)
+                    dbc.Row(
+                        dbc.Col(
+                            [
+                                dbc.Alert(
+                                    "Your bug report has been submitted. Thanks for helping us improve!",
+                                    id="alert-fade-bug-success",
+                                    dismissable=True,
+                                    is_open=False,
+                                    color="info",
+                                    style={
+                                        "max-width": "50vw",
+                                        "margin-left": "10px",
+                                        "margin-top": "10px",
+                                    }
+                                ),
+                                dbc.Alert(
+                                    "Failed to submit bug report! Please email the developers directly at the email below!",
+                                    id="alert-fade-bug-fail",
+                                    dismissable=True,
+                                    is_open=False,
+                                    color="danger",
+                                    style={
+                                        "max-width": "50vw",
+                                        "margin-left": "10px",
+                                        "margin-top": "10px",
+                                    }
+                                ),
+                            ]           
+                        )
+                    ),
+
+                    # Tabs Section
+                    dbc.Tabs(
+                        [
+                            dbc.Tab(main_content, label="Main", tab_id="main"),
+                            dbc.Tab(get_documentation_tab(documentation_content), label="Documentation", tab_id="documentation"),
+                            dbc.Tab(get_report_bug_tab(), label="Report a Bug", tab_id="report-bug"),
+                        ],
+                        id="tabs",
+                        active_tab="main",
+                    ),
+                ],
+                fluid=True,
+                style={"width": "100vw"}
+            )
+        ],
+        style={"width": "100vw", "overflow-x": "hidden", "overflow-y": "scroll"}
+    )
+
+
+def get_documentation_tab(documentation_content):
+    """
+    Returns the content for the Documentation tab with the upgraded layout.
+    """
+    return dbc.Row(
+        id="page-content-docs",
+        children=[
+            dbc.Col(
+                html.Div(
+                    id="sidebar_docs",
+                    children=[],
+                    style={
+                        "border-right": "2px solid #d4d7d9",
+                        "height": "100%",
+                        "padding": "20px",
+                        "font-size": "20px",
+                    },
+                ),
+                width=3,
+            ),
+            dbc.Col(
+                html.Div(
+                    id="page-content-docs-children",
+                    children= documentation_content,
+                    style={"margin-top":"2vh", "margin-left":"2vw", "font-size":"20px", "padding-right":"40px", "overflow-y": "scroll", "max-height": "60vh"},
+                ),
+                width=9,
+            ),
+        ],
+        style={"margin-top": "0px", "min-height": "40vh"},
+    )
+
+
+def get_report_bug_tab():
+    """
+    Returns the content for the Report a Bug tab with the upgraded layout.
+    """
+    return dbc.Row(
+        id="page-content-bug-report",
+        children=[
+            dbc.Col(
+                html.Div(
+                    id="sidebar_bug_report",
+                    children=[],  # Optional: Add sidebar content here if needed
+                    style={
+                        "border-right": "2px solid #d4d7d9",
+                        "height": "100%",
+                        "padding": "20px",
+                        "font-size": "20px",
+                    },
+                ),
+                width=3,
+            ),
+            dbc.Col(
+                html.Div(
+                    id="page-content-bug-report-children",
+                    children=[
+                        html.H2("Report a Bug"),
+                        html.P(
+                            [
+                                "Please use the form below to report a bug. If you have any questions, please email the developer at ",
+                                html.A(
+                                    bfabric_web_apps.DEVELOPER_EMAIL_ADDRESS,
+                                    href=f"mailto:{bfabric_web_apps.DEVELOPER_EMAIL_ADDRESS}",
+                                ),
+                            ]
+                        ),
+                        html.Br(),
+                        html.H4("Session Details: "),
+                        html.Br(),
+                        html.P(id="session-details", children="No Active Session"),
+                        html.Br(),
+                        html.H4("Bug Description"),
+                        dbc.Textarea(
+                            id="bug-description",
+                            placeholder="Please describe the bug you encountered here.",
+                            style={"width": "100%"},
+                        ),
+                        html.Br(),
+                        dbc.Button(
+                            "Submit Bug Report",
+                            id="submit-bug-report",
+                            n_clicks=0,
+                            style={"margin-bottom": "60px"},
+                        ),   
+                    ],
+                    style={
+                        "margin-top": "2vh",
+                        "margin-left": "2vw",
+                        "font-size": "20px",
+                        "padding-right": "40px",
+                    },
+                ),
+                width=9,
+            ),
+        ],
+        style={"margin-top": "0px", "min-height": "40vh"},
+    )

bfabric_web_apps/objects/BfabricInterface.py

@@ -1,16 +1,285 @@
-from bfabric import Bfabric 
+from bfabric import Bfabric
+import requests
+import json
+import datetime
+import bfabric
+from bfabric import BfabricAuth
+from bfabric import BfabricClientConfig
+from bfabric_web_apps.utils.get_logger import get_logger
+import os
+import bfabric_web_apps
 
-class BfabricInterface( Bfabric ): 
 
-    def __init__(): 
-        pass
 
-    def token_to_data(self, token): 
-        pass
+VALIDATION_URL = "https://fgcz-bfabric.uzh.ch/bfabric/rest/token/validate?token="
+HOST = "fgcz-bfabric.uzh.ch"
 
-    def token_response_to_bfabric(self, token_response): 
-        pass
 
-    def entity_data(self, entity): 
+class BfabricInterface( Bfabric ):
+    """
+    A class to interface with the Bfabric API, providing methods to validate tokens,
+    retrieve data, and send bug reports.
+    """
+
+    def __init__(self):
+        """
+        Initializes an instance of BfabricInterface.
+        """
         pass
 
+    def token_to_data(self, token):
+        """
+        Validates the given token and retrieves its associated data.
+
+        Args:
+            token (str): The token to validate.
+
+        Returns:
+            str: A JSON string containing token data if valid.
+            str: "EXPIRED" if the token is expired.
+            None: If the token is invalid or validation fails.
+        """
+
+        if not token:
+            return None
+
+        validation_url = VALIDATION_URL + token
+        res = requests.get(validation_url, headers={"Host": HOST})
+        
+        if res.status_code != 200:
+            res = requests.get(validation_url)
+        
+            if res.status_code != 200:
+                return None
+        try:
+            master_data = json.loads(res.text)
+        except:
+            return None
+        
+        if True: 
+
+            userinfo = json.loads(res.text)
+            expiry_time = userinfo['expiryDateTime']
+            current_time = datetime.datetime.now()
+            five_minutes_later = current_time + datetime.timedelta(minutes=5)
+
+            # Comparing the parsed expiry time with the five minutes later time
+
+            if not five_minutes_later <= datetime.datetime.strptime(expiry_time, "%Y-%m-%d %H:%M:%S"):
+                return "EXPIRED"
+            
+            environment_dict = {"Production":"https://fgcz-bfabric.uzh.ch/bfabric","Test":"https://fgcz-bfabric-test.uzh.ch/bfabric"}
+            
+            token_data = dict(
+                environment = userinfo['environment'],
+                user_data = userinfo['user'],
+                token_expires = expiry_time,
+                entity_id_data = userinfo['entityId'],
+                entityClass_data = userinfo['entityClassName'],
+                webbase_data = environment_dict.get(userinfo['environment'], None),
+                application_params_data = {},
+                application_data = str(userinfo['applicationId']),
+                userWsPassword = userinfo['userWsPassword'],
+                jobId = userinfo['jobId']
+            )
+
+            return json.dumps(token_data)
+        
+
+
+    def token_response_to_bfabric(self, token_response):
+
+        """
+        Converts token response data into a Bfabric object for further interactions.
+
+        Args:
+            token_response (dict): The token response data.
+
+        Returns:
+            Bfabric: An authenticated Bfabric instance.
+        """
+
+        bfabric_auth = BfabricAuth(login=token_response.get('user_data'), password=token_response.get('userWsPassword'))
+        bfabric_client_config = BfabricClientConfig(base_url=token_response.get('webbase_data')) 
+
+        bfabric_wrapper = bfabric.Bfabric(config=bfabric_client_config, auth=bfabric_auth)
+
+        return bfabric_wrapper
+    
+
+    
+
+    def entity_data(self, token_data: dict) -> str: 
+        """
+        Retrieves entity data associated with the provided token.
+
+        Args:
+            token_data (dict): The token data.
+
+        Returns:
+            str: A JSON string containing entity data.
+            {}: If the retrieval fails or token_data is invalid.
+        """
+
+        entity_class_map = {
+            "Run": "run",
+            "Sample": "sample",
+            "Project": "container",
+            "Order": "container",
+            "Container": "container",
+            "Plate": "plate"
+        }
+
+        if not token_data:
+            return json.dumps({})
+        
+        wrapper = self.token_response_to_bfabric(token_data)
+        entity_class = token_data.get('entityClass_data', None)
+        endpoint = entity_class_map.get(entity_class, None)
+        entity_id = token_data.get('entity_id_data', None)
+        jobId = token_data.get('jobId', None)
+        username = token_data.get("user_data", "None")
+        environment = token_data.get("environment", "None")
+
+        if wrapper and entity_class and endpoint and entity_id and jobId:
+            L = get_logger(token_data)
+            
+            # Log the read operation directly using Logger L
+            entity_data_dict = L.logthis(
+                api_call=wrapper.read,
+                endpoint=endpoint,
+                obj={"id": entity_id},
+                max_results=None,
+                params=None,
+                flush_logs=True
+            )[0]
+
+            
+            if entity_data_dict:
+                json_data = json.dumps({
+                    "name": entity_data_dict.get("name", ""),
+                    "createdby": entity_data_dict.get("createdby"),
+                    "created": entity_data_dict.get("created"),
+                    "modified": entity_data_dict.get("modified"),
+                })
+                return json_data
+            else:
+                L.log_operation(
+                    operation="entity_data",
+                    message="Entity data retrieval failed or returned None.",
+                    params=None,
+                    flush_logs=True
+                )
+                print("entity_data_dict is empty or None")
+                return json.dumps({})
+            
+        else:
+            print("Invalid input or entity information")
+            return json.dumps({})
+        
+
+    def app_data(self, token_data: dict) -> str:
+        """
+        Retrieves application data (App Name and Description) associated with the provided token.
+
+        Args:
+            token_data (dict): The token data.
+
+        Returns:
+            str: A JSON string containing application data.
+            {}: If retrieval fails or token_data is invalid.
+        """
+
+        if not token_data:
+            return json.dumps({})  # Return empty JSON if no token data
+
+        # Extract App ID from token
+        app_data_raw = token_data.get("application_data", None)
+        
+        try:
+            app_id = int(app_data_raw)
+        except:
+            print("Invalid application_data format in token_data")
+            return json.dumps({})  # Return empty JSON if app_id is invalid
+
+        # Define API endpoint
+        endpoint = "application"
+        
+        # Initialize Logger
+        L = get_logger(token_data)
+        
+        # Get API wrapper
+        wrapper = self.token_response_to_bfabric(token_data)  # Same as entity_data
+        if not wrapper:
+            print("Failed to get Bfabric API wrapper")
+            return json.dumps({})
+
+        # Make API Call
+        app_data_dict = L.logthis(
+            api_call=wrapper.read,
+            endpoint=endpoint,
+            obj={"id": app_id},  # Query using the App ID
+            max_results=None,
+            params=None,
+            flush_logs=True
+        )
+
+        # If API call fails, return empty JSON
+        if not app_data_dict or len(app_data_dict) == 0:
+            L.log_operation(
+                operation="app_data",
+                message=f"Failed to retrieve application data for App ID {app_id}",
+                params=None,
+                flush_logs=True
+            )
+            return json.dumps({})
+
+        # Extract Name and Description
+        app_info = app_data_dict[0]  # First (and only) result
+        json_data = json.dumps({
+            "name": app_info.get("name", "Unknown"),
+            "description": app_info.get("description", "No description available")
+        })
+
+        return json_data
+     
+    
+    def send_bug_report(self, token_data = None, entity_data = None, description = None):
+        """
+        Sends a bug report via email.
+
+        Args:
+            token_data (dict): Token data to include in the report.
+            entity_data (dict): Entity data to include in the report.
+            description (str): A description of the bug.
+
+        Returns:
+            bool: True if the report is sent successfully, False otherwise.
+        """
+
+        mail_string = f"""
+        BUG REPORT FROM QC-UPLOADER
+            \n\n
+            token_data: {token_data} \n\n 
+            entity_data: {entity_data} \n\n
+            description: {description} \n\n
+            sent_at: {datetime.datetime.now()} \n\n
+        """
+
+        mail = f"""
+            echo "{mail_string}" | mail -s "Bug Report" {bfabric_web_apps.BUG_REPORT_EMAIL_ADDRESS}
+        """
+
+        print("MAIL STRING:")
+        print(mail_string)
+
+        print("MAIL:")
+        print(mail)
+
+        os.system(mail)
+
+        return True
+
+
+
+

bfabric_web_apps/objects/Logger.py

@@ -1,47 +1,80 @@
 import os
 import pickle
+from typing import List
 from bfabric import Bfabric
 from datetime import datetime as dt
 import base64
-
-try:
-    from PARAMS import CONFIG_FILE_PATH
-except ImportError:
-    CONFIG_FILE_PATH = "~/.bfabricpy.yml"
+import bfabric_web_apps
 
 
 class Logger:
     """
     A Logger class to manage and batch API call logs locally and flush them to the backend when needed.
     """
-    def __init__(self, jobid: int, username: str):
+    def __init__(self, jobid: int, username: str, environment: str):
+        """
+        Initializes the Logger with a job ID, username, and environment.
+
+        Args:
+            jobid (int): The ID of the current job.
+            username (str): The name of the user performing the operations.
+            environment (str): The environment (e.g., Production, Test).
+        """
         self.jobid = jobid
         self.username = username
-        self.power_user_wrapper = self._get_power_user_wrapper()
+        self.config_file_path = bfabric_web_apps.CONFIG_FILE_PATH
+        self.power_user_wrapper = self._get_power_user_wrapper(environment)
         self.logs = []
 
-    def _get_power_user_wrapper(self) -> Bfabric:
+    def _get_power_user_wrapper(self, environment) -> Bfabric:
         """
         Initializes a B-Fabric wrapper using the power user's credentials.
+
+        Args:
+            environment (str): The environment in which to initialize the wrapper.
+
+        Returns:
+            Bfabric: An authenticated Bfabric instance.
         """
         power_user_wrapper = Bfabric.from_config(
-            config_path=os.path.expanduser(CONFIG_FILE_PATH)
+            config_path = os.path.expanduser(self.config_file_path),
+            config_env = environment.upper()
         )
         return power_user_wrapper
 
     def to_pickle(self):
+        """
+        Serializes the Logger object and encodes it as a base64 string.
+
+        Returns:
+            dict: A dictionary containing the base64-encoded pickle string.
+        """
         # Pickle the object and then encode it as a base64 string
         return {"data": base64.b64encode(pickle.dumps(self)).decode('utf-8')}
 
     @classmethod 
     def from_pickle(cls, pickle_object):
+        """
+        Deserializes a Logger object from a base64-encoded pickle string.
+
+        Args:
+            pickle_object (dict): A dictionary containing the base64-encoded pickle string.
+
+        Returns:
+            Logger: The deserialized Logger object.
+        """
         # Decode the base64 string back to bytes and then unpickle
         return pickle.loads(base64.b64decode(pickle_object.get("data").encode('utf-8')))
 
     def log_operation(self, operation: str, message: str, params = None, flush_logs: bool = True):
         """
-        Log an operation either locally (if flush_logs=False) or flush to the backend.
-        Creates well-structured, readable log entries.
+        Logs an operation locally or flushes it to the backend.
+
+        Args:
+            operation (str): The name of the operation being logged.
+            message (str): A detailed message about the operation.
+            params (dict, optional): Additional parameters to log. Defaults to None.
+            flush_logs (bool, optional): Whether to immediately flush the logs to the backend. Defaults to True.
         """
         # Define the timestamp format
         timestamp = dt.now().strftime('%Y-%m-%d %H:%M:%S')
@@ -83,7 +116,17 @@ class Logger:
 
     def logthis(self, api_call: callable, *args, params=None , flush_logs: bool = True, **kwargs) -> any:
         """
-        Generic logging function to wrap any API call using a Logger instance.
+        Wraps an API call with logging functionality.
+
+        Args:
+            api_call (callable): The API call to be logged and executed.
+            *args: Positional arguments to pass to the API call.
+            params (dict, optional): Additional parameters to log. Defaults to None.
+            flush_logs (bool, optional): Whether to flush logs immediately. Defaults to True.
+            **kwargs: Keyword arguments to pass to the API call.
+
+        Returns:
+            any: The result of the API call.
         """
         # Construct a message describing the API call
         call_args = ', '.join([repr(arg) for arg in args])

bfabric_web_apps/utils/app_init.py

@@ -0,0 +1,11 @@
+from dash import Dash
+import dash_bootstrap_components as dbc
+
+def create_app():
+    """Initialize and return a Dash app instance with suppressed callback exceptions."""
+    return Dash(
+        __name__,
+        suppress_callback_exceptions=True,  # Allow dynamic callbacks
+        external_stylesheets=[dbc.themes.BOOTSTRAP],
+        meta_tags=[{"name": "viewport", "content": "width=device-width, initial-scale=1.0"}],
+    )

bfabric_web_apps/utils/callbacks.py

@@ -0,0 +1,170 @@
+from dash import Input, Output, State, html, dcc
+from bfabric_web_apps.objects.BfabricInterface import BfabricInterface
+import json
+import dash_bootstrap_components as dbc
+from datetime import datetime as dt
+from bfabric_web_apps.utils.get_logger import get_logger
+
+def process_url_and_token(url_params):
+    """
+    Processes URL parameters to extract the token, validates it, and retrieves the corresponding data.
+    Additionally, it constructs a dynamic job link based on the environment and job ID.
+
+    Args:
+        url_params (str): The URL parameters containing the token.
+
+    Returns:
+        tuple: A tuple containing:
+               - token (str): Authentication token.
+               - token_data (dict): Token metadata.
+               - entity_data (dict): Retrieved entity information.
+               - page_title (str): Title for the page header.
+               - session_details (list): HTML-formatted session details.
+               - job_link (str): Dynamically generated link to the job page.
+    """
+    base_title = " "
+
+    if not url_params:
+        return None, None, None, None, base_title, None, None
+
+    token = "".join(url_params.split('token=')[1:])
+    bfabric_interface = BfabricInterface()
+    tdata_raw = bfabric_interface.token_to_data(token)
+
+    if tdata_raw:
+        if tdata_raw == "EXPIRED":
+            return None, None, None, None, base_title, None, None
+        else:
+            tdata = json.loads(tdata_raw)
+    else:
+        return None, None, None, None, base_title, None, None
+
+    if tdata:
+        entity_data_json = bfabric_interface.entity_data(tdata)
+        app_data_json = bfabric_interface.app_data(tdata)
+        entity_data = json.loads(entity_data_json)
+        app_data = json.loads(app_data_json)
+        page_title = (
+            f"{tdata.get('entityClass_data', 'Unknown')} - {entity_data.get('name', 'Unknown')} "
+            f"({tdata.get('environment', 'Unknown')} System)"
+        ) if tdata else "Bfabric App Interface"
+
+        environment = tdata.get("environment", "").strip().lower()  # 'test' or 'prod'
+        job_id = tdata.get("jobId", None)  # Extract job ID
+
+        job_link = None
+        if job_id:
+            if "test" in environment:
+                job_link = f"https://fgcz-bfabric-test.uzh.ch/bfabric/job/show.html?id={job_id}&tab=details"
+            else:
+                job_link = f"https://fgcz-bfabric.uzh.ch/bfabric/job/show.html?id={job_id}&tab=details"
+
+        session_details = [
+            html.P([
+                html.B("Entity Name: "), entity_data.get('name', 'Unknown'),
+                html.Br(),
+                html.B("Entity Class: "), tdata.get('entityClass_data', 'Unknown'),
+                html.Br(),
+                html.B("Environment: "), tdata.get('environment', 'Unknown'),
+                html.Br(),
+                html.B("Entity ID: "), tdata.get('entity_id_data', 'Unknown'),
+                html.Br(),
+                html.B("Job ID: "), job_id if job_id else "Unknown",
+                html.Br(),
+                html.B("User Name: "), tdata.get('user_data', 'Unknown'),
+                html.Br(),
+                html.B("Session Expires: "), tdata.get('token_expires', 'Unknown'),
+                html.Br(),
+                html.B("App Name: "), app_data.get("name", "Unknown"),
+                html.Br(),
+                html.B("App Description: "), app_data.get("description", "No description available"),
+                html.Br(),
+                html.B("Current Time: "), str(dt.now().strftime("%Y-%m-%d %H:%M:%S"))
+            ])
+        ]
+
+        return token, tdata, entity_data, app_data, page_title, session_details, job_link
+    else:
+        return None, None, None, None, base_title, None, None
+
+
+
+def submit_bug_report(n_clicks, bug_description, token, entity_data):
+    """
+    Submits a bug report based on user input, token, and entity data.
+
+    Args:
+        n_clicks (int): The number of times the submit button has been clicked.
+        bug_description (str): The description of the bug provided by the user.
+        token (str): The authentication token.
+        entity_data (dict): The data related to the current entity.
+
+    Returns:
+        tuple: A tuple containing two boolean values indicating success and failure status of the submission.
+               (is_open_success, is_open_failure)
+    """
+    bfabric_interface = BfabricInterface()
+    print("submit bug report", token)
+
+    # Parse token data if token is provided, otherwise set it to an empty dictionary
+    if token:
+        token_data = json.loads(bfabric_interface.token_to_data(token))
+    else:
+        token_data = {}
+
+    print(token_data)
+
+    # Extract logging-related information from token_data, with defaults for missing values
+    jobId = token_data.get('jobId', None)
+    username = token_data.get("user_data", "None")
+    environment = token_data.get("environment", "None")
+
+    # Initialize the logger only if token_data is available
+    L = None
+    if token_data:
+        L = get_logger(token_data)
+
+    if n_clicks:
+        # Log the operation only if the logger is initialized
+        if L:
+            L.log_operation(
+                "bug report",
+                "Initiating bug report submission process.",
+                params=None,
+                flush_logs=False,
+            )
+        try:
+            sending_result = bfabric_interface.send_bug_report(
+                token_data, entity_data, bug_description
+            )
+
+            if sending_result:
+                if L:
+                    L.log_operation(
+                        "bug report",
+                        f"Bug report successfully submitted. | DESCRIPTION: {bug_description}",
+                        params=None,
+                        flush_logs=True,
+                    )
+                return True, False
+            else:
+                if L:
+                    L.log_operation(
+                        "bug report",
+                        "Failed to submit bug report!",
+                        params=None,
+                        flush_logs=True,
+                    )
+                return False, True
+        except Exception as e:
+            if L:
+                L.log_operation(
+                    "bug report",
+                    f"Failed to submit bug report! Error: {str(e)}",
+                    params=None,
+                    flush_logs=True,
+                )
+            return False, True
+
+    return False, False
+

bfabric_web_apps/utils/components.py

@@ -0,0 +1,22 @@
+from dash import html
+
+DEVELOPER_EMAIL = "gwhite@fgcz.ethz.ch"
+
+expired = [
+    html.P("Your session has expired. Please log into bfabric to continue:"),
+    html.A('Login to Bfabric', href='https://fgcz-bfabric.uzh.ch/bfabric/')
+]
+
+no_entity = [
+    html.P("There was an error fetching the data for your entity. Please try accessing the applicaiton again from bfabric:"),
+    html.A('Login to Bfabric', href='https://fgcz-bfabric.uzh.ch/bfabric/')
+]
+
+dev = [html.P("This page is under development. Please check back later."),html.Br(),html.A("email the developer for more details",href="mailto:"+DEVELOPER_EMAIL)]
+
+auth = [html.Div(id="auth-div")]
+
+no_auth = [
+    html.P("You are not currently logged into an active session. Please log into bfabric to continue:"),
+    html.A('Login to Bfabric', href='https://fgcz-bfabric.uzh.ch/bfabric/')
+]

bfabric_web_apps/utils/create_app_in_bfabric.py

@@ -0,0 +1,86 @@
+from bfabric import Bfabric
+
+def get_user_input():
+    """Prompt user for necessary inputs."""
+    
+    systems = {"TEST": "TEST", "PROD": "PRODUCTION"}
+
+    technologies = {
+        "TEST": {
+            "1": "Genomics / Transcriptomics",
+            "2": "Proteomics",
+            "4": "Metabolomics / Biophysics",
+            "6": "General",
+            "10": "New Tech"
+        },
+        "PRODUCTION": {
+            "1": "Genomics / Transcriptomics",
+            "2": "Proteomics",
+            "4": "Metabolomics / Biophysics",
+            "6": "General",
+            "10": "Bioinformatics"
+        }
+    }
+
+    # Get system input
+    system = input("In which system do you want to create the app? (Type 'TEST' for the test system or 'PROD' for the production system): ").strip().upper()
+    
+    while system not in systems:
+        print("Invalid input! Please enter 'TEST' or 'PROD'.")
+        system = input("Enter system (TEST/PROD): ").strip().upper()
+
+    selected_system = systems[system]  # Map input to full system name
+
+    # Display technology options based on selected system
+    print("\nAvailable Technologies:")
+    for key, value in technologies[selected_system].items():
+        print(f"{key}: {value}")
+
+    # Get technology ID from user
+    technologyid = input("\nEnter the number corresponding to your chosen application type: ").strip()
+    
+    while technologyid not in technologies[selected_system]:
+        print("Invalid technology ID! Please select a valid number from the list.")
+        technologyid = input("Enter a valid technology ID: ").strip()
+
+    # Get remaining inputs
+    name = input("Enter app name: ")
+    weburl = input("Enter web URL: ")
+    description = input("Enter description: ")
+
+    return {
+        "system": selected_system,
+        "name": name,
+        "weburl": weburl,
+        "type": "WebApp",
+        "technologyid": technologyid,
+        "supervisorid": "2446",
+        "enabled": True,
+        "valid": True,
+        "hidden": False,
+        "description": description
+    }
+
+def create_app_in_bfabric():
+    """Create an app in B-Fabric using user inputs."""
+    # Get user input for parameters
+    user_input = get_user_input()
+
+    # Determine configuration environment based on user input
+    config_env = user_input.pop("system")
+
+    # Initialize Bfabric instance
+    bfabric = Bfabric.from_config(config_env=config_env)
+
+    # Set endpoint for app creation
+    endpoint = "application"
+
+    # Make API call to save the app
+    try:
+        result = bfabric.save(endpoint=endpoint, obj=user_input)
+        print("App created successfully:", result)
+    except Exception as e:
+        print("Failed to create app:", str(e))
+
+if __name__ == "__main__":
+    create_app_in_bfabric()

bfabric_web_apps/utils/defaults.py

@@ -0,0 +1,11 @@
+# defaults.py
+CONFIG_FILE_PATH = "~/.bfabricpy.yml"
+
+# Default values for application settings
+HOST = "0.0.0.0"
+PORT = 8050
+DEV = False
+
+# Developer and bug report email addresses
+DEVELOPER_EMAIL_ADDRESS = "griffin@gwcustom.com"
+BUG_REPORT_EMAIL_ADDRESS = "gwtools@fgcz.system"

bfabric_web_apps/utils/get_logger.py

@@ -0,0 +1,14 @@
+from bfabric_web_apps.objects.Logger import Logger
+
+def get_logger(token_data):
+
+    """ Extract logging-related information from token_data, with defaults for missing values """
+    jobId = token_data.get('jobId', None)
+    username = token_data.get("user_data", "None")
+    environment = token_data.get("environment", "None")
+
+    return Logger(
+        jobid=jobId,
+        username=username,
+        environment=environment,
+    )

bfabric_web_apps/utils/get_power_user_wrapper.py

@@ -0,0 +1,27 @@
+import os
+from bfabric import Bfabric
+import bfabric_web_apps
+
+def get_power_user_wrapper(token_data):
+    """
+    Initializes and returns a Bfabric power user instance configured for a specific environment.
+
+    This function retrieves the environment information from the provided `token_data` 
+    and uses it to initialize a Bfabric instance. The configuration file path is 
+    determined by the `CONFIG_FILE_PATH` from the application's configuration.
+
+    Args:
+        token_data (dict): A dictionary containing token information
+            The key "environment" is used to determine the environment 
+            (default is "None" if not specified).
+
+    Returns:
+        Bfabric: A Bfabric instance initialized with the configuration 
+        corresponding to the specified environment.
+    """
+    environment = token_data.get("environment", "None")
+
+    return  Bfabric.from_config(
+            config_path = os.path.expanduser(bfabric_web_apps.CONFIG_FILE_PATH),
+            config_env = environment.upper()
+    )

bfabric_web_apps-0.1.2.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 GWC GmbH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{bfabric_web_apps-0.1.0.dist-info → bfabric_web_apps-0.1.2.dist-info}/METADATA

@@ -1,10 +1,11 @@
 Metadata-Version: 2.1
 Name: bfabric-web-apps
-Version: 0.1.0
+Version: 0.1.2
 Summary: A package containing handy boilerplate utilities for developing bfabric web-applications
-Author: Mark Zuber, Griffin White, GWC GmbH
+Author: Marc Zuber, Griffin White, GWC GmbH
 Requires-Python: >=3.8,<4.0
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11

bfabric_web_apps-0.1.2.dist-info/RECORD

@@ -0,0 +1,15 @@
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+bfabric_web_apps/utils/callbacks.py,sha256=PiP1ZJ-QxdrOAZ-Mt-MN-g9wJLSOoLkWkXwPq_TLqDI,6472
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+bfabric_web_apps/utils/defaults.py,sha256=B82j3JEbysLEU9JDZgoDBTX7WGvW3Hn5YMZaWAcjZew,278
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+bfabric_web_apps-0.1.2.dist-info/LICENSE,sha256=k0O_i2k13i9e35aO-j7FerJafAqzzu8x0kkBs0OWF3c,1065
+bfabric_web_apps-0.1.2.dist-info/METADATA,sha256=tvvoNH4-tMyPbWJdoe_pVgC_cDzQpDzdGtqd49vt9QI,480
+bfabric_web_apps-0.1.2.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+bfabric_web_apps-0.1.2.dist-info/RECORD,,

{bfabric_web_apps-0.1.0.dist-info → bfabric_web_apps-0.1.2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry 1.0.7
+Generator: poetry-core 1.7.0
 Root-Is-Purelib: true
 Tag: py3-none-any

bfabric_web_apps-0.1.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-bfabric_web_apps/__init__.py,sha256=6IFMcIq8biYvtMafM-gELPRBq19k5kHRlEYmRTsXlYI,87
-bfabric_web_apps/layouts/layouts.py,sha256=6b5_wk2fk1ZLyWhhhKfz2EnsSdZtlPx8aR-pMfPC1t0,135
-bfabric_web_apps/objects/BfabricInterface.py,sha256=IU1D1Q6ZdAR0oo64Fpcru9LWVj-3Ydmlti6Vy_-VSj4,275
-bfabric_web_apps/objects/Logger.py,sha256=Sikkqfbkp7NGqEkFZ4cHKtjGX1Bu9Y8sf1PWDLOOjco,3467
-bfabric_web_apps/objects/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bfabric_web_apps-0.1.0.dist-info/WHEEL,sha256=y3eDiaFVSNTPbgzfNn0nYn5tEn1cX6WrdetDlQM4xWw,83
-bfabric_web_apps-0.1.0.dist-info/METADATA,sha256=9GcQM9qWxhYBDHgmq0r0Gu9mAmvvn0Lxy0YJrfFCiPc,429
-bfabric_web_apps-0.1.0.dist-info/RECORD,,