bfabric-web-apps 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

bfabric_web_apps/__init__.py

@@ -16,11 +16,15 @@ 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.callbacks import (
+    process_url_and_token, 
+    submit_bug_report,
+    populate_workunit_details
+)
 
 from .utils import defaults
 
-from bfabric_web_apps.utils.resource_utilities import create_workunit, create_resource
+from bfabric_web_apps.utils.resource_utilities import create_workunit, create_resource, create_workunits, create_resources
 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
@@ -49,52 +53,8 @@ __all__ = [
     'BUG_REPORT_EMAIL_ADDRESS',
     'create_app_in_bfabric',
     'create_workunit',
-    'create_resource'
+    'create_resource',
+    'create_workunits',
+    'create_resources',
+    'populate_workunit_details',
 ]
-
-
-
-'''
-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

@@ -144,8 +144,9 @@ def get_static_layout(base_title=None, main_content=None, documentation_content=
                     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"),
+                            dbc.Tab(dcc.Loading(get_documentation_tab(documentation_content)), label="Documentation", tab_id="documentation"),
+                            dbc.Tab(dcc.Loading(get_workunits_tab()), label="Workunits", tab_id="workunits"),
+                            dbc.Tab(dcc.Loading(get_report_bug_tab()), label="Report a Bug", tab_id="report-bug"),
                         ],
                         id="tabs",
                         active_tab="main",
@@ -250,6 +251,54 @@ def get_report_bug_tab():
                         "margin-left": "2vw",
                         "font-size": "20px",
                         "padding-right": "40px",
+                        "overflow-y": "scroll",
+                        "max-height": "65vh",
+                    },
+                ),
+                width=9,
+            ),
+        ],
+        style={"margin-top": "0px", "min-height": "40vh"},
+    )
+
+
+def get_workunits_tab():
+    """
+    Returns the content for the Workunits tab with the upgraded layout.
+    """
+    return dbc.Row(
+        id="page-content-workunits",
+        children=[
+            dbc.Col(
+                html.Div(
+                    id="sidebar_workunits",
+                    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-workunits-children",
+                    children=[
+                        html.H2("Workunits"),
+                        html.Div(id="refresh-workunits", children=[]),
+                        html.Div(
+                            id="workunits-content"
+                        )
+                    ],
+                    style={
+                        "margin-top": "2vh",
+                        "margin-left": "2vw",
+                        "font-size": "20px",
+                        "padding-right": "40px",
+                        "overflow-y": "scroll",
+                        "max-height": "65vh",
                     },
                 ),
                 width=9,

bfabric_web_apps/objects/BfabricInterface.py

@@ -9,12 +9,9 @@ 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="
 HOST = "fgcz-bfabric.uzh.ch"
 
-
 class BfabricInterface( Bfabric ):
     _instance = None  # Singleton instance
     _wrapper = None   # Shared wrapper instance
@@ -50,8 +47,7 @@ class BfabricInterface( Bfabric ):
         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):
         """
@@ -96,8 +92,6 @@ 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'],
@@ -267,7 +261,7 @@ class BfabricInterface( Bfabric ):
 
         # 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"),
@@ -312,10 +306,9 @@ class BfabricInterface( Bfabric ):
         os.system(mail)
 
         return True
+    
 
-
-
-
+    
 # Create a globally accessible instance
 bfabric_interface = BfabricInterface()
 

bfabric_web_apps/utils/callbacks.py

@@ -1,5 +1,5 @@
 from dash import Input, Output, State, html, dcc
-from bfabric_web_apps.objects.BfabricInterface import BfabricInterface
+from bfabric_web_apps.objects.BfabricInterface import bfabric_interface
 import json
 import dash_bootstrap_components as dbc
 from datetime import datetime as dt
@@ -28,7 +28,6 @@ def process_url_and_token(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:
@@ -88,7 +87,6 @@ def process_url_and_token(url_params):
         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.
@@ -103,7 +101,7 @@ def submit_bug_report(n_clicks, bug_description, token, entity_data):
         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
@@ -168,3 +166,66 @@ def submit_bug_report(n_clicks, bug_description, token, entity_data):
 
     return False, False
 
+
+def populate_workunit_details(token_data):
+
+    """
+    Function to populate workunit data for the current app instance.
+
+    Args: 
+        token_data (dict): Token metadata.
+
+    Returns:
+        html.Div: A div containing the populated workunit data.
+    """
+
+    environment_urls = {
+        "Test": "https://fgcz-bfabric-test.uzh.ch/bfabric/workunit/show.html?id=",
+        "Prod": "https://fgcz-bfabric.uzh.ch/bfabric/workunit/show.html?id="
+    }
+
+    if token_data:
+
+        jobId = token_data.get('jobId', None)
+        print("jobId", jobId)
+        
+        job = bfabric_interface.get_wrapper().read("job", {"id": jobId})[0]
+        workunits = job.get("workunit", [])
+
+        if workunits:
+            wus = bfabric_interface.get_wrapper().read(
+                "workunit", 
+                {"id": [wu["id"] for wu in workunits]}
+            )
+        else:
+            return html.Div(
+                [
+                    html.P("No workunits found for the current job.")
+                ]
+            )
+
+        wu_cards = []
+
+        for wu in wus: 
+            print(wu)
+            wu_card = html.A(
+                dbc.Card([
+                    dbc.CardHeader(html.B(f"Workunit {wu['id']}")),
+                    dbc.CardBody([
+                        html.P(f"Name: {wu.get('name', 'n/a')}"),
+                        html.P(f"Description: {wu.get('description', 'n/a')}"),
+                        html.P(f"Num Resources: {len(wu.get('resource', []))}"),
+                        html.P(f"Created: {wu.get('created', 'n/a')}"),
+                        html.P(f"Status: {wu.get('status', 'n/a')}")
+                    ])
+                ], style={"width": "400px", "margin":"10px"}),
+                href=environment_urls[token_data.get("environment", "Test")] + str(wu["id"]),
+                target="_blank",
+                style={"text-decoration": "none"}
+            )
+
+            wu_cards.append(wu_card)
+
+        return dbc.Container(wu_cards, style={"display": "flex", "flex-wrap": "wrap"})
+    else:
+        return html.Div()

bfabric_web_apps/utils/resource_utilities.py

@@ -4,64 +4,94 @@ 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):
+def create_workunit(token_data, application_name, application_description, application_id, container_id):
     """
-    Create a new workunit in B-Fabric for each container ID.
+    Create a single workunit in B-Fabric.
 
     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.
+        container_id (int): Container ID (Order ID).
     
     Returns:
-        list: List of created workunit IDs.
+        int: Created workunit ID or None if creation fails.
     """
     L = get_logger(token_data)
     wrapper = bfabric_interface.get_wrapper()
-    workunit_ids = []
 
-    # Ensure container_ids is a list
+    workunit_data = {
+        "name": f"{application_name} - Order {container_id}",
+        "description": f"{application_description} for Order {container_id}",
+        "applicationid": int(application_id),
+        "containerid": container_id, 
+    }
+
+    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}")
+
+        # First we get the existing workunit_ids for the current job object: 
+        pre_existing_workunit_ids = [elt.get("id") for elt in wrapper.read("job", {"id": token_data.get("jobId")})[0].get("workunit", [])]
+        
+        # Now we associate the job object with the workunits 
+        job = L.logthis(
+            api_call=L.power_user_wrapper.save,
+            endpoint="job",
+            obj={"id": token_data.get("jobId"), "workunitid": [workunit_id] + pre_existing_workunit_ids},
+            params=None,
+            flush_logs=True
+        )
+        return 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 None
+
+
+def create_workunits(token_data, application_name, application_description, application_id, container_ids):
+    """
+    Create multiple workunits in B-Fabric.
+
+    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.
+    """
     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)
+        container_ids = [container_ids]  # Ensure it's a list
 
-        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}")
+    workunit_ids = [
+        create_workunit(token_data, application_name, application_description, application_id, container_id)
+        for container_id in container_ids
+    ]
 
-    return workunit_ids  # Returning a list of all created workunits
+    return [wu_id for wu_id in workunit_ids if wu_id is not None]  # Filter out None values
 
 
 def create_resource(token_data, workunit_id, gz_file_path):
     """
-    Upload a .gz resource to an existing B-Fabric workunit.
-    
+    Upload a single .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.
@@ -76,8 +106,8 @@ def create_resource(token_data, workunit_id, gz_file_path):
     try:
         file_path = Path(gz_file_path)
 
-        # Use the proper upload function
-        print("test", wrapper, file_path, workunit_id)
+        # Upload the resource
+        print("Uploading:", file_path, "to workunit:", workunit_id)
         result = bfabric_upload_resource(wrapper, file_path, workunit_id)
 
         if result:
@@ -103,116 +133,24 @@ def create_resource(token_data, workunit_id, gz_file_path):
         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):
+def create_resources(token_data, workunit_id, gz_file_paths):
     """
-    Startet die Nextflow-Pipeline und speichert die Ergebnisse in B-Fabric.
+    Upload multiple .gz resources to an existing B-Fabric workunit.
+
+    Args:
+        token_data (dict): Authentication token data.
+        workunit_id (int): ID of the workunit to associate the resources with.
+        gz_file_paths (list): List of full paths to .gz files to upload.
     
-    :param run_name: Name des Sequenzierungslaufs
-    :param output_dir: Verzeichnis, in dem die FASTQ-Dateien gespeichert werden
+    Returns:
+        list: List of successfully uploaded resource IDs.
     """
-    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
+    if not isinstance(gz_file_paths, list):
+        gz_file_paths = [gz_file_paths]  # Ensure it's a list
 
-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
+    resource_ids = [
+        create_resource(token_data, workunit_id, gz_file_path)
+        for gz_file_path in gz_file_paths
+    ]
 
-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}")
-'''
+    return [res_id for res_id in resource_ids if res_id is not None]  # Filter out None values

{bfabric_web_apps-0.1.3.dist-info → bfabric_web_apps-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bfabric-web-apps
-Version: 0.1.3
+Version: 0.1.4
 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-0.1.4.dist-info/RECORD

@@ -0,0 +1,16 @@
+bfabric_web_apps/__init__.py,sha256=jU5o22wl7kXHNJVCH6aqW0llZLfxeQssCIeX1OerQfI,1790
+bfabric_web_apps/layouts/layouts.py,sha256=fmv_QTJeAmiOxreAwx14QojzyRV_8RHu1c4sCPN5r5U,13382
+bfabric_web_apps/objects/BfabricInterface.py,sha256=wmcL9JuSC0QEopgImvkZxmtCIS7izt6bwb6y_ch0zus,10178
+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=XbRMK2sL55twtR6IWGAf5B1m2fnMTOpkhyR55-76nes,8444
+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=q0gC_Lr5GQlMBU0_gLm48zjq3XlXbT4QArqzJcmxrTo,5476
+bfabric_web_apps-0.1.4.dist-info/LICENSE,sha256=k0O_i2k13i9e35aO-j7FerJafAqzzu8x0kkBs0OWF3c,1065
+bfabric_web_apps-0.1.4.dist-info/METADATA,sha256=5TKRMRQB4an34gV7b4_hValbQEvuLvOmJpB9DsKBFR4,480
+bfabric_web_apps-0.1.4.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+bfabric_web_apps-0.1.4.dist-info/RECORD,,

bfabric_web_apps-0.1.3.dist-info/RECORD

@@ -1,16 +0,0 @@
-bfabric_web_apps/__init__.py,sha256=xqh-kddXaV4xblnMcDA73bTuy3zn5viucueuuIx41HM,2495
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