bfabric-web-apps 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

bfabric_web_apps/__init__.py

@@ -20,6 +20,7 @@ from .utils.callbacks import process_url_and_token, submit_bug_report
 
 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
@@ -46,7 +47,9 @@ __all__ = [
     'CONFIG_FILE_PATH',
     'DEVELOPER_EMAIL_ADDRESS',
     'BUG_REPORT_EMAIL_ADDRESS',
-    'create_app_in_bfabric'
+    'create_app_in_bfabric',
+    'create_workunit',
+    'create_resource'
 ]
 
 

bfabric_web_apps/objects/BfabricInterface.py

@@ -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)
         
 
@@ -133,7 +164,7 @@ class BfabricInterface( Bfabric ):
         if not token_data:
             return json.dumps({})
         
-        wrapper = self.token_response_to_bfabric(token_data)
+        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)
@@ -209,7 +240,7 @@ class BfabricInterface( Bfabric ):
         L = get_logger(token_data)
         
         # Get API wrapper
-        wrapper = self.token_response_to_bfabric(token_data)  # Same as entity_data
+        wrapper = self.get_wrapper()
         if not wrapper:
             print("Failed to get Bfabric API wrapper")
             return json.dumps({})
@@ -234,9 +265,11 @@ class BfabricInterface( Bfabric ):
             )
             return json.dumps({})
 
-        # Extract Name and Description
+        # 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")
         })
@@ -283,3 +316,7 @@ class BfabricInterface( Bfabric ):
 
 
 
+# Create a globally accessible instance
+bfabric_interface = BfabricInterface()
+
+

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-0.1.2.dist-info → bfabric_web_apps-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bfabric-web-apps
-Version: 0.1.2
+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-0.1.2.dist-info → bfabric_web_apps-0.1.3.dist-info}/RECORD

@@ -1,6 +1,6 @@
-bfabric_web_apps/__init__.py,sha256=zZvM0CQPkiu0y9xOZos-d2hK-h6erc8K_nov7vD1bdE,2362
+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=nRdU_cYLW2_xp2x1cvP9b30gQ5blavbOz66B-Hi6UZQ,8980
+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
@@ -9,7 +9,8 @@ bfabric_web_apps/utils/create_app_in_bfabric.py,sha256=eVk3cQDXxW-yo9b9n_zzGO6kL
 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-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/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,,