bfabric-web-apps 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

bfabric_web_apps/__init__.py

@@ -1,25 +1,34 @@
+import os
+
 # Export objects and classes
 from bfabric_web_apps.objects import BfabricInterface, Logger
 
 # Export components
-from .utils.components import *
+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.app_config import load_config
 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
 
-HOST = '0.0.0.0'
-PORT = 8050
-DEV = False 
-CONFIG_FILE_PATH = "~/.bfabricpy.yml"
+from .utils import defaults
+
+from bfabric_web_apps.utils.resource_utilities import create_workunit, create_resource
+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__ = [
@@ -28,9 +37,64 @@ __all__ = [
     "components",
     "get_static_layout",
     "create_app",
-    "load_config",
     "process_url_and_token",
     "submit_bug_report",
     'get_logger',
-    'get_power_user_wrapper'
+    'get_power_user_wrapper',
+    'HOST',
+    'PORT', 
+    'DEV',
+    'CONFIG_FILE_PATH',
+    'DEVELOPER_EMAIL_ADDRESS',
+    'BUG_REPORT_EMAIL_ADDRESS',
+    'create_app_in_bfabric',
+    'create_workunit',
+    'create_resource'
 ]
+
+
+
+'''
+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

@@ -1,25 +1,38 @@
 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):
+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.
+
+    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.
+
+    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
+
             dbc.Container(
                 children=[
-                    # Banner
+                    # Banner Section
                     dbc.Row(
                         dbc.Col(
                             html.Div(
                                 className="banner",
                                 children=[
+                                    # Title
                                     html.Div(
                                         children=[
                                             html.P(
@@ -35,30 +48,70 @@ def get_static_layout(base_title = None, main_content = None, documentation_cont
                                             )
                                         ],
                                         style={"background-color": "#000000", "border-radius": "10px"}
-                                    )
+                                    ),
+                                ],
+                                style={"position": "relative", "padding": "10px"}
+                            ),
+                        ),
+                    ),
+
+                    # 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
+                                }
                             ),
                         ),
                     ),
-                    # Page Title
+
+                    # Bug Report Alerts (Restored)
                     dbc.Row(
                         dbc.Col(
                             [
-                                html.Div(
-                                    children=[
-                                        html.P(
-                                            id="page-title",
-                                            children=[str(" ")],
-                                            style={"font-size": "40px", "margin-left": "20px", "margin-top": "10px"}
-                                        )
-                                    ],
-                                    style={
-                                        "margin-top": "0px",
-                                        "min-height": "80px",
-                                        "height": "6vh",
-                                        "border-bottom": "2px solid #d4d7d9"
-                                    }
-                                ),
                                 dbc.Alert(
                                     "Your bug report has been submitted. Thanks for helping us improve!",
                                     id="alert-fade-bug-success",
@@ -86,7 +139,8 @@ def get_static_layout(base_title = None, main_content = None, documentation_cont
                             ]           
                         )
                     ),
-                    # Tabs
+
+                    # Tabs Section
                     dbc.Tabs(
                         [
                             dbc.Tab(main_content, label="Main", tab_id="main"),
@@ -167,8 +221,8 @@ def get_report_bug_tab():
                             [
                                 "Please use the form below to report a bug. If you have any questions, please email the developer at ",
                                 html.A(
-                                    "griffin@gwcustom.com",
-                                    href="mailto:griffin@gwcustom.com",
+                                    bfabric_web_apps.DEVELOPER_EMAIL_ADDRESS,
+                                    href=f"mailto:{bfabric_web_apps.DEVELOPER_EMAIL_ADDRESS}",
                                 ),
                             ]
                         ),

bfabric_web_apps/objects/BfabricInterface.py

@@ -5,10 +5,10 @@ import datetime
 import bfabric
 from bfabric import BfabricAuth
 from bfabric import BfabricClientConfig
-from dash import html
-import dash_bootstrap_components as dbc
-from bfabric_web_apps.objects.Logger import Logger
+from bfabric_web_apps.utils.get_logger import get_logger
 import os
+import bfabric_web_apps
+
 
 
 VALIDATION_URL = "https://fgcz-bfabric.uzh.ch/bfabric/rest/token/validate?token="
@@ -16,6 +16,8 @@ HOST = "fgcz-bfabric.uzh.ch"
 
 
 class BfabricInterface( Bfabric ):
+    _instance = None  # Singleton instance
+    _wrapper = None   # Shared wrapper instance
     """
     A class to interface with the Bfabric API, providing methods to validate tokens,
     retrieve data, and send bug reports.
@@ -27,6 +29,30 @@ class BfabricInterface( Bfabric ):
         """
         pass
 
+    def __new__(cls, *args, **kwargs):
+        """Ensure only one instance exists (Singleton Pattern)."""
+        if cls._instance is None:
+            cls._instance = super(BfabricInterface, cls).__new__(cls)
+        return cls._instance
+    
+    def _initialize_wrapper(self, token_data):
+        """Internal method to initialize the Bfabric wrapper after token validation."""
+        if not token_data:
+            raise ValueError("Token data is required to initialize the wrapper.")
+
+        # Create and store the wrapper
+        if self._wrapper is None:
+            self._wrapper = self.token_response_to_bfabric(token_data)
+
+
+    def get_wrapper(self):
+        """Return the existing wrapper or raise an error if not initialized."""
+        if self._wrapper is None:
+            raise RuntimeError("Bfabric wrapper is not initialized. Token validation must run first.")
+        return self._wrapper
+
+
+
     def token_to_data(self, token):
         """
         Validates the given token and retrieves its associated data.
@@ -70,6 +96,8 @@ class BfabricInterface( Bfabric ):
             
             environment_dict = {"Production":"https://fgcz-bfabric.uzh.ch/bfabric","Test":"https://fgcz-bfabric-test.uzh.ch/bfabric"}
             
+            print('userinfo', userinfo)
+
             token_data = dict(
                 environment = userinfo['environment'],
                 user_data = userinfo['user'],
@@ -83,6 +111,9 @@ class BfabricInterface( Bfabric ):
                 jobId = userinfo['jobId']
             )
 
+            # Initialize the wrapper right after validating the token
+            self._initialize_wrapper(token_data)
+
             return json.dumps(token_data)
         
 
@@ -110,7 +141,6 @@ class BfabricInterface( Bfabric ):
     
 
     def entity_data(self, token_data: dict) -> str: 
-
         """
         Retrieves entity data associated with the provided token.
 
@@ -119,7 +149,7 @@ class BfabricInterface( Bfabric ):
 
         Returns:
             str: A JSON string containing entity data.
-            None: If the retrieval fails.
+            {}: If the retrieval fails or token_data is invalid.
         """
 
         entity_class_map = {
@@ -132,24 +162,18 @@ class BfabricInterface( Bfabric ):
         }
 
         if not token_data:
-            return None
-
-        wrapper = self.token_response_to_bfabric(token_data)
+            return json.dumps({})
+        
+        wrapper = self.get_wrapper()
         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")
-
+        environment = token_data.get("environment", "None")
 
         if wrapper and entity_class and endpoint and entity_id and jobId:
-
-            L = Logger(
-                jobid = jobId,
-                username= username,
-                environment= environment
-            ) 
+            L = get_logger(token_data)
             
             # Log the read operation directly using Logger L
             entity_data_dict = L.logthis(
@@ -157,9 +181,10 @@ class BfabricInterface( Bfabric ):
                 endpoint=endpoint,
                 obj={"id": entity_id},
                 max_results=None,
-                params = None,
-                flush_logs = True
+                params=None,
+                flush_logs=True
             )[0]
+
             
             if entity_data_dict:
                 json_data = json.dumps({
@@ -171,18 +196,86 @@ class BfabricInterface( Bfabric ):
                 return json_data
             else:
                 L.log_operation(
-                    operation= "entity_data",
-                    message= "Entity data retrieval failed or returned None.",
+                    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 None
+                return json.dumps({})
             
         else:
             print("Invalid input or entity information")
-            return None
+            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.get_wrapper()
+        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 App ID, Name, and Description
+        app_info = app_data_dict[0]  # First (and only) result
+        print('app_info', app_info)
+        json_data = json.dumps({
+            "id": app_info.get("id", "Unknown"),
+            "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):
         """
@@ -207,7 +300,7 @@ class BfabricInterface( Bfabric ):
         """
 
         mail = f"""
-            echo "{mail_string}" | mail -s "Bug Report" gwtools@fgcz.system
+            echo "{mail_string}" | mail -s "Bug Report" {bfabric_web_apps.BUG_REPORT_EMAIL_ADDRESS}
         """
 
         print("MAIL STRING:")
@@ -220,3 +313,10 @@ class BfabricInterface( Bfabric ):
 
         return True
 
+
+
+
+# Create a globally accessible instance
+bfabric_interface = BfabricInterface()
+
+

bfabric_web_apps/objects/Logger.py

@@ -4,9 +4,8 @@ from typing import List
 from bfabric import Bfabric
 from datetime import datetime as dt
 import base64
-from ..utils.app_config import load_config
+import bfabric_web_apps
 
-CONFIG_FILE_PATH = load_config()["CONFIG_FILE_PATH"]
 
 class Logger:
     """
@@ -23,6 +22,7 @@ class Logger:
         """
         self.jobid = jobid
         self.username = username
+        self.config_file_path = bfabric_web_apps.CONFIG_FILE_PATH
         self.power_user_wrapper = self._get_power_user_wrapper(environment)
         self.logs = []
 
@@ -37,7 +37,7 @@ class Logger:
             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

bfabric_web_apps/utils/callbacks.py

@@ -2,25 +2,30 @@ 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 bfabric_web_apps.objects.Logger import Logger
 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.
-        base_title (str): The base title of the page.
 
     Returns:
-        tuple: A tuple containing token data, entity data, and the page content.
-               (token, token_data, entity_data, page_content, page_title)
+        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, base_title, None
+        return None, None, None, None, base_title, None, None
 
     token = "".join(url_params.split('token=')[1:])
     bfabric_interface = BfabricInterface()
@@ -28,43 +33,60 @@ def process_url_and_token(url_params):
 
     if tdata_raw:
         if tdata_raw == "EXPIRED":
-            return None, None, None, base_title, None
+            return None, None, None, None, base_title, None, None
         else:
             tdata = json.loads(tdata_raw)
     else:
-        return None, None, None, base_title, None
+        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['entityClass_data']} - {entity_data['name']} "
-            f"({tdata['environment']} System)"
+            f"{tdata.get('entityClass_data', 'Unknown')} - {entity_data.get('name', 'Unknown')} "
+            f"({tdata.get('environment', 'Unknown')} System)"
         ) if tdata else "Bfabric App Interface"
 
-        if not entity_data:
-            return token, tdata, None, page_title, None
-        else:
-            session_details = [
+        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['name'],
+                html.B("Entity Name: "), entity_data.get('name', 'Unknown'),
+                html.Br(),
+                html.B("Entity Class: "), tdata.get('entityClass_data', 'Unknown'),
                 html.Br(),
-                html.B("Entity Class: "), tdata['entityClass_data'],
+                html.B("Environment: "), tdata.get('environment', 'Unknown'),
                 html.Br(),
-                html.B("Environment: "), tdata['environment'],
+                html.B("Entity ID: "), tdata.get('entity_id_data', 'Unknown'),
                 html.Br(),
-                html.B("Entity ID: "), tdata['entity_id_data'],
+                html.B("Job ID: "), job_id if job_id else "Unknown",
                 html.Br(),
-                html.B("User Name: "), tdata['user_data'],
+                html.B("User Name: "), tdata.get('user_data', 'Unknown'),
                 html.Br(),
-                html.B("Session Expires: "), tdata['token_expires'],
+                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, page_title, session_details
+
+        return token, tdata, entity_data, app_data, page_title, session_details, job_link
     else:
-        return None, None, None, base_title, None
+        return None, None, None, None, base_title, None, None
+
 
 
 def submit_bug_report(n_clicks, bug_description, token, entity_data):
@@ -100,11 +122,7 @@ def submit_bug_report(n_clicks, bug_description, token, entity_data):
     # Initialize the logger only if token_data is available
     L = None
     if token_data:
-        L = Logger(
-            jobid=jobId,
-            username=username,
-            environment=environment
-        )
+        L = get_logger(token_data)
 
     if n_clicks:
         # Log the operation only if the logger is initialized

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

@@ -10,5 +10,5 @@ def get_logger(token_data):
     return Logger(
         jobid=jobId,
         username=username,
-        environment=environment
+        environment=environment,
     )

bfabric_web_apps/utils/get_power_user_wrapper.py

@@ -1,8 +1,6 @@
 import os
 from bfabric import Bfabric
-from .app_config import load_config
-
-CONFIG_FILE_PATH = load_config()["CONFIG_FILE_PATH"]
+import bfabric_web_apps
 
 def get_power_user_wrapper(token_data):
     """
@@ -13,7 +11,7 @@ def get_power_user_wrapper(token_data):
     determined by the `CONFIG_FILE_PATH` from the application's configuration.
 
     Args:
-        token_data (dict): A dictionary containing token information. 
+        token_data (dict): A dictionary containing token information
             The key "environment" is used to determine the environment 
             (default is "None" if not specified).
 
@@ -24,6 +22,6 @@ def get_power_user_wrapper(token_data):
     environment = token_data.get("environment", "None")
 
     return  Bfabric.from_config(
-            config_path = os.path.expanduser(CONFIG_FILE_PATH),
+            config_path = os.path.expanduser(bfabric_web_apps.CONFIG_FILE_PATH),
             config_env = environment.upper()
     )

bfabric_web_apps/utils/resource_utilities.py

@@ -0,0 +1,218 @@
+from bfabric_web_apps.utils.get_logger import get_logger
+from bfabric_web_apps.objects.BfabricInterface import bfabric_interface
+from bfabric_web_apps.utils.get_power_user_wrapper import get_power_user_wrapper
+from bfabric_scripts.bfabric_upload_resource import bfabric_upload_resource
+from pathlib import Path
+
+def create_workunit(token_data, application_name, application_description, application_id, container_ids):
+    """
+    Create a new workunit in B-Fabric for each container ID.
+
+    Args:
+        token_data (dict): Authentication token data.
+        application_name (str): Name of the application.
+        application_description (str): Description of the application.
+        application_id (int): Application ID.
+        container_ids (list): List of container IDs.
+    
+    Returns:
+        list: List of created workunit IDs.
+    """
+    L = get_logger(token_data)
+    wrapper = bfabric_interface.get_wrapper()
+    workunit_ids = []
+
+    # Ensure container_ids is a list
+    if not isinstance(container_ids, list):
+        container_ids = [container_ids]  # Convert to list if single value
+
+    for container_id in container_ids:
+        workunit_data = {
+            "name": f"{application_name} - Order {container_id}",
+            "description": f"{application_description} for Order {container_id}",
+            "applicationid": int(application_id),
+            "containerid": container_id,  # Assigning order ID dynamically
+        }
+
+        try:
+            workunit_response = L.logthis(
+                api_call=wrapper.save,
+                endpoint="workunit",
+                obj=workunit_data,
+                params=None,
+                flush_logs=True
+            )
+            workunit_id = workunit_response[0].get("id")
+            print(f"Created Workunit ID: {workunit_id} for Order ID: {container_id}")
+            workunit_ids.append(workunit_id)
+
+        except Exception as e:
+            L.log_operation(
+                "Error",
+                f"Failed to create workunit for Order {container_id}: {e}",
+                params=None,
+                flush_logs=True,
+            )
+            print(f"Failed to create workunit for Order {container_id}: {e}")
+
+    return workunit_ids  # Returning a list of all created workunits
+
+
+def create_resource(token_data, workunit_id, gz_file_path):
+    """
+    Upload a .gz resource to an existing B-Fabric workunit.
+    
+    Args:
+        token_data (dict): Authentication token data.
+        workunit_id (int): ID of the workunit to associate the resource with.
+        gz_file_path (str): Full path to the .gz file to upload.
+    
+    Returns:
+        int: Resource ID if successful, None otherwise.
+    """
+    L = get_logger(token_data)
+    wrapper = get_power_user_wrapper(token_data)
+
+    try:
+        file_path = Path(gz_file_path)
+
+        # Use the proper upload function
+        print("test", wrapper, file_path, workunit_id)
+        result = bfabric_upload_resource(wrapper, file_path, workunit_id)
+
+        if result:
+            print(f"Resource uploaded: {file_path.name}")
+            L.log_operation(
+                "upload_resource",
+                f"Resource uploaded successfully: {file_path.name}",
+                params=None,
+                flush_logs=True,
+            )
+            return result
+        else:
+            raise ValueError(f"Failed to upload resource: {file_path.name}")
+
+    except Exception as e:
+        L.log_operation(
+            "error",
+            f"Failed to upload resource: {e}",
+            params=None,
+            flush_logs=True,
+        )
+        print(f"Failed to upload resource: {e}")
+        return None
+
+
+
+'''
+
+
+
+    # Upload a resource to the created workunit
+    resource_name = "example_resource.txt"
+    resource_content = b"This is an example resource content."
+
+    try:
+        resource_response = bfabric.upload_resource(
+            resource_name=resource_name,
+            content=resource_content,
+            workunit_id=workunit_id
+        )
+        print(f"Resource '{resource_name}' uploaded successfully.")
+    except Exception as e:
+        print(f"Failed to upload resource: {e}")
+        exit(1)
+
+        
+
+
+
+
+
+
+
+import subprocess
+from zeep import Client
+import os
+from bfabric_web_apps.utils.get_logger import get_logger
+
+BFABRIC_WORKUNIT_WSDL = "https://fgcz-bfabric-test.uzh.ch:443/bfabric/workunit?wsdl"
+BFABRIC_RESOURCE_WSDL = "https://fgcz-bfabric-test.uzh.ch:443/bfabric/resource?wsdl"
+
+def run_pipeline_and_register_in_bfabric(run_name: str, output_dir: str):
+    """
+    Startet die Nextflow-Pipeline und speichert die Ergebnisse in B-Fabric.
+    
+    :param run_name: Name des Sequenzierungslaufs
+    :param output_dir: Verzeichnis, in dem die FASTQ-Dateien gespeichert werden
+    """
+    print(f"[INFO] Starte Nextflow-Pipeline für {run_name}...")
+    
+    # Nextflow Pipeline starten
+    process = subprocess.run([
+        "nextflow", "run", "nf-core/bclconvert", 
+        "-profile", "docker", 
+        "--outdir", output_dir,
+        "-resume"
+    ], capture_output=True, text=True)
+    
+    if process.returncode != 0:
+        print(f"[ERROR] Nextflow Pipeline fehlgeschlagen: {process.stderr}")
+        return False
+    
+    print(f"[INFO] Pipeline abgeschlossen. Ergebnisse werden registriert...")
+    
+    # Workunit in B-Fabric anlegen
+    workunit_id = create_bfabric_workunit(run_name)
+    
+    # Falls Workunit erfolgreich erstellt, dann Ressourcen speichern
+    if workunit_id:
+        register_fastq_files_in_bfabric(output_dir, workunit_id)
+    else:
+        print("[ERROR] Konnte Workunit nicht in B-Fabric registrieren!")
+    
+    return True
+
+def create_bfabric_workunit(run_name: str):
+    """Erstellt eine Workunit in B-Fabric."""
+    try:
+        client = Client(BFABRIC_WORKUNIT_WSDL)
+        workunit_data = {
+            "name": run_name,
+            "description": "Illumina BCL zu FASTQ Konvertierung",
+            "status": "Completed"
+        }
+        L = get_logger({})
+        response = L.logthis(
+            api_call=client.service.createWorkunit,
+            obj=workunit_data
+        )[0]
+        print(f"[INFO] Workunit erstellt mit ID: {response}")
+        return response
+    except Exception as e:
+        print(f"[ERROR] Fehler beim Erstellen der Workunit: {e}")
+        return None
+
+def register_fastq_files_in_bfabric(output_dir: str, workunit_id: int):
+    """Registriert alle FASTQ-Dateien aus dem Output-Verzeichnis in B-Fabric."""
+    try:
+        client = Client(BFABRIC_RESOURCE_WSDL)
+        L = get_logger({})
+        for file_name in os.listdir(output_dir):
+            if file_name.endswith(".fastq.gz"):
+                file_path = os.path.join(output_dir, file_name)
+                resource_data = {
+                    "name": file_name,
+                    "description": "Erzeugt von nf-core/bclconvert",
+                    "path": file_path,
+                    "type": "FASTQ",
+                    "workunitId": workunit_id
+                }
+                response = L.logthis(
+                    api_call=client.service.createResource,
+                    obj=resource_data
+                )[0]
+                print(f"[INFO] Ressource gespeichert mit ID: {response}")
+    except Exception as e:
+        print(f"[ERROR] Fehler beim Registrieren der Ressourcen: {e}")
+'''

{bfabric_web_apps-0.1.1.dist-info → bfabric_web_apps-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bfabric-web-apps
-Version: 0.1.1
+Version: 0.1.3
 Summary: A package containing handy boilerplate utilities for developing bfabric web-applications
 Author: Marc Zuber, Griffin White, GWC GmbH
 Requires-Python: >=3.8,<4.0

bfabric_web_apps-0.1.3.dist-info/RECORD

@@ -0,0 +1,16 @@
+bfabric_web_apps/__init__.py,sha256=xqh-kddXaV4xblnMcDA73bTuy3zn5viucueuuIx41HM,2495
+bfabric_web_apps/layouts/layouts.py,sha256=XoSLcQPcgMBhQz2VfxkUzNL23FLBXFRFvbCL2mNLfnk,11636
+bfabric_web_apps/objects/BfabricInterface.py,sha256=YC6VimARZfG2t90TK5xhQDsNzgMNljwqbCOT8Qz_Uhs,10247
+bfabric_web_apps/objects/Logger.py,sha256=62LC94xhm7YG5LUw3yH46NqvJQsAX7wnc9D4zbY16rA,5224
+bfabric_web_apps/utils/app_init.py,sha256=RCdpCXp19cF74bouYJLPe-KSETZ0Vwqtd02Ta2VXEF8,428
+bfabric_web_apps/utils/callbacks.py,sha256=PiP1ZJ-QxdrOAZ-Mt-MN-g9wJLSOoLkWkXwPq_TLqDI,6472
+bfabric_web_apps/utils/components.py,sha256=V7ECGmF2XYy5O9ciDJVH1nofJYP2a_ELQF3z3X_ADbo,844
+bfabric_web_apps/utils/create_app_in_bfabric.py,sha256=eVk3cQDXxW-yo9b9n_zzGO6kLg_SLxYbIDECyvEPJXU,2752
+bfabric_web_apps/utils/defaults.py,sha256=B82j3JEbysLEU9JDZgoDBTX7WGvW3Hn5YMZaWAcjZew,278
+bfabric_web_apps/utils/get_logger.py,sha256=0Y3SrXW93--eglS0_ZOc34NOriAt6buFPik5n0ltzRA,434
+bfabric_web_apps/utils/get_power_user_wrapper.py,sha256=T33z64XjmJ0KSlmfEmrEP8eYpbpINCVD6Xld_V7PR2g,1027
+bfabric_web_apps/utils/resource_utilities.py,sha256=AVaqIXEfmCdWZfXDt32QfkZ9ChTL8D8cm1lCHXfT4Nc,7317
+bfabric_web_apps-0.1.3.dist-info/LICENSE,sha256=k0O_i2k13i9e35aO-j7FerJafAqzzu8x0kkBs0OWF3c,1065
+bfabric_web_apps-0.1.3.dist-info/METADATA,sha256=gTd86dYPrHKfypKFPry0SKjYtydW1z17fA-tSxz8vuM,480
+bfabric_web_apps-0.1.3.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+bfabric_web_apps-0.1.3.dist-info/RECORD,,

bfabric_web_apps/utils/app_config.py

@@ -1,27 +0,0 @@
-import os
-import importlib.util
-
-def load_config(params_path="./PARAMS.py"):
-    """Load configuration for the Dash app."""
-    if os.path.exists(params_path):
-        try:
-            # Dynamically import the PARAMS module
-            spec = importlib.util.spec_from_file_location("PARAMS", params_path)
-            params_module = importlib.util.module_from_spec(spec)
-            spec.loader.exec_module(params_module)
-            
-            # Retrieve values with defaults
-            PORT = getattr(params_module, "PORT", 8050)
-            HOST = getattr(params_module, "HOST", "localhost")
-            DEV = getattr(params_module, "DEV", True)
-            CONFIG_FILE_PATH = getattr(params_module, "CONFIG_FILE_PATH", "~/.bfabricpy.yml")
-        except ImportError:
-            # Fallback to default values in case of import errors
-            PORT, HOST, DEV = 8050, 'localhost', True
-            CONFIG_FILE_PATH = "~/.bfabricpy.yml"
-    else:
-        # Fallback to default values if PARAMS.py is not found
-        PORT, HOST, DEV = 8050, 'localhost', True
-        CONFIG_FILE_PATH = "~/.bfabricpy.yml"
-
-    return {"PORT": PORT, "HOST": HOST, "DEV": DEV, "CONFIG_FILE_PATH": CONFIG_FILE_PATH}

bfabric_web_apps-0.1.1.dist-info/RECORD

@@ -1,14 +0,0 @@
-bfabric_web_apps/__init__.py,sha256=XDzAg0boEE3nj3RXGB85YbVc0KgEeRNOcQfrSkJoV-0,880
-bfabric_web_apps/layouts/layouts.py,sha256=oQHfT65PdoFU5js8JkEJqFhxfgNjwU0GRvD1xbkfYD4,8758
-bfabric_web_apps/objects/BfabricInterface.py,sha256=pHse1UgC_XFD-PsYqOs0Ho3xTRMDRCvtRgsILVYy-0k,6919
-bfabric_web_apps/objects/Logger.py,sha256=ikMJJZYDPhJZEmgCY63_htGmPvXv1ItSmfb_xiFFZMQ,5225
-bfabric_web_apps/utils/app_config.py,sha256=u7lz8sonf9CSkJsVK0nhTzIls227FksGCOb_SzYE_fE,1204
-bfabric_web_apps/utils/app_init.py,sha256=RCdpCXp19cF74bouYJLPe-KSETZ0Vwqtd02Ta2VXEF8,428
-bfabric_web_apps/utils/callbacks.py,sha256=OlNelwAJUKsEtnaJ4OuTdrgyu9PhEgm4uqCde4NNKHA,5270
-bfabric_web_apps/utils/components.py,sha256=V7ECGmF2XYy5O9ciDJVH1nofJYP2a_ELQF3z3X_ADbo,844
-bfabric_web_apps/utils/get_logger.py,sha256=_cn0en-itaGEeeCDtws-nw2ubd36w2xc6VfDNoBMFu4,433
-bfabric_web_apps/utils/get_power_user_wrapper.py,sha256=ZUrv-xNLEXtMVeFEpAwmPbPFUmcAxu3hITIuPY2dhF8,1078
-bfabric_web_apps-0.1.1.dist-info/LICENSE,sha256=k0O_i2k13i9e35aO-j7FerJafAqzzu8x0kkBs0OWF3c,1065
-bfabric_web_apps-0.1.1.dist-info/METADATA,sha256=R1zgL1bVK18CV4uPQc1vUABgBnOn6us0YBbcC6yqy0g,480
-bfabric_web_apps-0.1.1.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-bfabric_web_apps-0.1.1.dist-info/RECORD,,