Merge branch 'master' into patch_taxprofiler_versions

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 62.2.1
+current_version = 62.2.5
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "62.2.1"
+__version__ = "62.2.5"

cg/apps/invoice/render.py

@@ -1,8 +1,11 @@
 import datetime as dt
+from pathlib import Path
 
 from openpyxl import Workbook, load_workbook
 from openpyxl.styles import Border, Font, PatternFill, Side
-from pkg_resources import resource_filename
+
+from cg.constants import FileExtensions
+from cg.utils.files import get_project_root_dir
 
 
 def render_xlsx(data: dict) -> Workbook:
@@ -34,11 +37,17 @@ def render_xlsx(data: dict) -> Workbook:
             }]
         }
     """
-    pkg_dir = __name__.rpartition(".")[0]
+    project_root_dir = get_project_root_dir()
     sample_type = "pool" if data["pooled_samples"] else "sample"
     costcenter = data["cost_center"]
-    template_path = resource_filename(pkg_dir, f"templates/{costcenter}_{sample_type}_invoice.xlsx")
-    workbook = load_workbook(template_path)
+    template_path = Path(
+        project_root_dir,
+        "apps",
+        "invoice",
+        "templates",
+        f"{costcenter}_{sample_type}_invoice{FileExtensions.XLSX}",
+    )
+    workbook = load_workbook(template_path.as_posix())
     if data["pooled_samples"]:
         worksheet = workbook["Bilaga Prover"]
         worksheet["C1"] = costcenter.upper()

cg/cli/post_process/post_process.py

@@ -35,5 +35,4 @@ def post_process_sequencing_run(context: CGConfig, run_name: str, dry_run: bool)
     post_processing_service.post_process(run_name=run_name, dry_run=dry_run)
 
 
-post_process_group: click.Group
 post_process_group.add_command(post_process_sequencing_run)

cg/clients/freshdesk/freshdesk_client.py

@@ -1,19 +1,13 @@
-import logging
 from http import HTTPStatus
+from pathlib import Path
 
-from pydantic import ValidationError
-from requests import RequestException, Response, Session
+from requests import Session
 from requests.adapters import HTTPAdapter
 from urllib3 import Retry
 
 from cg.clients.freshdesk.constants import EndPoints
-from cg.clients.freshdesk.exceptions import (
-    FreshdeskAPIException,
-    FreshdeskModelException,
-)
-from cg.clients.freshdesk.models import TicketCreate, TicketResponse
-
-LOG = logging.getLogger(__name__)
+from cg.clients.freshdesk.models import ReplyCreate, TicketCreate, TicketResponse
+from cg.clients.freshdesk.utils import handle_client_errors, prepare_attachments
 
 
 class FreshdeskClient:
@@ -24,33 +18,23 @@ def __init__(self, base_url: str, api_key: str):
         self.api_key = api_key
         self.session = self._get_session()
 
-    def create_ticket(self, ticket: TicketCreate) -> TicketResponse:
-        """Create a ticket."""
-        LOG.debug(ticket.model_dump_json())
-        try:
-            response: Response = self.session.post(
-                url=self._url(EndPoints.TICKETS),
-                json=ticket.model_dump(exclude_none=True),
-            )
-            response.raise_for_status()
-            return TicketResponse.model_validate(response.json())
-        except RequestException as error:
-            LOG.error(f"Could not create ticket: {error}")
-            raise FreshdeskAPIException(error) from error
-        except ValidationError as error:
-            LOG.error(f"Response from Freshdesk does not fit model: {TicketResponse}.\n{error}")
-            raise FreshdeskModelException(error) from error
+    @handle_client_errors
+    def create_ticket(self, ticket: TicketCreate, attachments: list[Path] = None) -> TicketResponse:
+        """Create a ticket with multipart form data."""
+        multipart_data = ticket.to_multipart_data()
+        files = prepare_attachments(attachments) if attachments else None
 
-    def _url(self, endpoint: str) -> str:
-        """Get the full URL for the endpoint."""
-        return f"{self.base_url}{endpoint}"
+        response = self.session.post(
+            url=f"{self.base_url}{EndPoints.TICKETS}", data=multipart_data, files=files
+        )
+        response.raise_for_status()
+        return TicketResponse.model_validate(response.json())
 
+    @handle_client_errors
     def _get_session(self) -> Session:
-        """Configures and sets a session to be used for requests."""
         session = Session()
-        self._configure_retries(session)
         session.auth = (self.api_key, "X")
-        session.headers.update({"Content-Type": "application/json"})
+        self._configure_retries(session)
         return session
 
     @staticmethod
@@ -69,3 +53,14 @@ def _configure_retries(session: Session) -> None:
         )
         adapter = HTTPAdapter(max_retries=retry_strategy)
         session.mount("https://", adapter)
+
+    @handle_client_errors
+    def reply_to_ticket(self, reply: ReplyCreate, attachments: list[Path] = None) -> None:
+        """Send a reply to an existing ticket in Freshdesk."""
+        url = f"{self.base_url}{EndPoints.TICKETS}/{reply.ticket_number}/reply"
+
+        files = prepare_attachments(attachments) if attachments else None
+        multipart_data = reply.to_multipart_data()
+
+        response = self.session.post(url=url, data=multipart_data, files=files)
+        response.raise_for_status()

cg/clients/freshdesk/models.py

@@ -1,36 +1,61 @@
-from datetime import datetime
+from typing import Tuple, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, EmailStr, Field
 
 from cg.clients.freshdesk.constants import Priority, Source, Status
 
 
 class TicketCreate(BaseModel):
     """Freshdesk ticket."""
 
-    attachments: list[dict[str, str]] = []
-    email: str
+    attachments: list[str | bytes] = Field(default_factory=list)
+    email: EmailStr
     email_config_id: int | None = None
+    description: str
     name: str
     priority: int = Priority.LOW
     source: int = Source.EMAIL
     status: int = Status.OPEN
     subject: str
     tags: list[str] = []
     type: str | None = None
+    custom_fields: dict[str, str | int | float | None] = Field(default_factory=dict)
+
+    def to_multipart_data(self) -> list[Tuple[str, str | int | bytes]]:
+        """Custom converter to multipart form data."""
+        multipart_data = []
+
+        for field, value in self.model_dump(exclude_none=True).items():
+            if isinstance(value, list):
+                multipart_data.extend([(f"{field}[]", v) for v in value])
+            elif isinstance(value, dict):
+                multipart_data.extend([(f"{field}[{k}]", v) for k, v in value.items()])
+            else:
+                multipart_data.append((field, value))
+
+        return multipart_data
 
 
 class TicketResponse(BaseModel):
-    """Freshdesk ticket response."""
+    """Response from Freshdesk"""
 
-    attachments: list[dict[str, str]] = []
-    created_at: datetime | None = None
-    email: str
     id: int
-    name: str | None = None
-    priority: int
-    source: int
-    status: int
+    description: str
     subject: str
-    tags: list[str] = []
-    type: str | None = None
+    to_emails: list[str] | None = None
+    status: int
+    priority: int
+
+
+class ReplyCreate(BaseModel):
+    """Reply to a ticket."""
+
+    ticket_number: str
+    body: str
+
+    def to_multipart_data(self) -> list[Tuple[str, Union[str, int, bytes]]]:
+        """Custom converter to multipart form data."""
+        multipart_data = [
+            ("body", self.body),
+        ]
+        return multipart_data

cg/clients/freshdesk/utils.py

@@ -0,0 +1,86 @@
+import logging
+from functools import wraps
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+from pydantic import ValidationError
+from requests import ConnectionError, HTTPError
+from requests.exceptions import MissingSchema
+
+from cg.clients.freshdesk.exceptions import (
+    FreshdeskAPIException,
+    FreshdeskModelException,
+)
+from cg.constants.constants import FileFormat
+from cg.io.controller import WriteFile
+
+LOG = logging.getLogger(__name__)
+
+
+def extract_error_detail(error):
+    """Extract detailed error information from HTTPError."""
+    if error.response is not None:
+        try:
+            return error.response.json()
+        except ValueError:
+            return error.response.text
+    return None
+
+
+def log_and_raise(exception_class, message, error):
+    """Log the error and raise the appropriate exception."""
+    LOG.error(message)
+    raise exception_class(error) from error
+
+
+def handle_client_errors(func):
+    """Decorator to handle and log errors in Freshdesk client methods."""
+
+    @wraps(func)
+    def wrapper(*args, **kwargs):
+        try:
+            return func(*args, **kwargs)
+        except HTTPError as error:
+            error_detail = extract_error_detail(error)
+            log_and_raise(
+                FreshdeskAPIException,
+                f"Failed request to Freshdesk: {error} - Status code: "
+                f"{error.response.status_code if error.response else 'N/A'}, Details: {error_detail}",
+                error,
+            )
+        except (MissingSchema, ConnectionError) as error:
+            log_and_raise(FreshdeskAPIException, f"Request to Freshdesk failed: {error}", error)
+        except ValidationError as error:
+            log_and_raise(
+                FreshdeskModelException, f"Invalid response from Freshdesk: {error}", error
+            )
+        except ValueError as error:
+            log_and_raise(FreshdeskAPIException, f"Operation failed: {error}", error)
+        except Exception as error:
+            log_and_raise(
+                FreshdeskAPIException, f"Unexpected error in Freshdesk client: {error}", error
+            )
+
+    return wrapper
+
+
+def prepare_attachments(attachments: list[Path]) -> list[tuple[str, tuple[str, bytes]]]:
+    """Prepare the attachments for a request."""
+    return [
+        ("attachments[]", (attachment.name, open(attachment, "rb"))) for attachment in attachments
+    ]
+
+
+def create_temp_attachment_file(content: dict, file_name: Path) -> TemporaryDirectory:
+    """Create a file-based attachment."""
+    if content and file_name:
+        directory = TemporaryDirectory()
+        WriteFile.write_file_from_content(
+            content=content,
+            file_format=FileFormat.JSON,
+            file_path=Path(directory.name, "order.json"),
+        )
+        return directory
+    else:
+        LOG.error("Content or file path is None. Cannot create file attachment.")
+        raise ValueError("Both content and file path must be provided and cannot be None")

cg/constants/constants.py

@@ -223,6 +223,7 @@ class FileExtensions(StrEnum):
     TSV: str = ".tsv"
     TXT: str = ".txt"
     VCF: str = ".vcf"
+    XLSX: str = ".xlsx"
     XML: str = ".xml"
     YAML: str = ".yaml"
 

cg/constants/report.py

@@ -1,15 +1,17 @@
 """Delivery report constants."""
 
-from importlib.resources import files
 from pathlib import Path
 
 from cg.constants import DataDelivery
 from cg.constants.constants import CancerAnalysisType, FileExtensions, Workflow
 from cg.constants.subject import Sex
+from cg.utils.files import get_project_root_dir
+
+project_root_dir: Path = get_project_root_dir()
 
 DELIVERY_REPORT_FILE_NAME: str = f"delivery-report{FileExtensions.HTML}"
 SWEDAC_LOGO_PATH = Path(
-    files("cg"), "meta", "report", "templates", "static", "images", "SWEDAC_logo.png"
+    project_root_dir, "meta", "report", "templates", "static", "images", "SWEDAC_logo.png"
 )
 
 BALSAMIC_REPORT_ACCREDITED_PANELS: list[str] = ["gmsmyeloid"]

cg/meta/orders/api.py

@@ -10,7 +10,6 @@
 import logging
 
 from cg.apps.lims import LimsAPI
-from cg.apps.osticket import OsTicket
 from cg.meta.orders.ticket_handler import TicketHandler
 from cg.models.orders.order import OrderIn, OrderType
 from cg.services.orders.submitters.order_submitter_registry import (
@@ -28,13 +27,13 @@ def __init__(
         self,
         lims: LimsAPI,
         status: Store,
-        osticket: OsTicket,
+        ticket_handler: TicketHandler,
         submitter_registry: OrderSubmitterRegistry,
     ):
         super().__init__()
         self.lims = lims
         self.status = status
-        self.ticket_handler: TicketHandler = TicketHandler(osticket_api=osticket, status_db=status)
+        self.ticket_handler = ticket_handler
         self.submitter_registry = submitter_registry
 
     def submit(self, project: OrderType, order_in: OrderIn, user_name: str, user_mail: str) -> dict:
@@ -45,7 +44,7 @@ def submit(self, project: OrderType, order_in: OrderIn, user_name: str, user_mai
         submit_handler = self.submitter_registry.get_order_submitter(project)
         submit_handler.order_validation_service.validate_order(order_in)
         # detect manual ticket assignment
-        ticket_number: str | None = TicketHandler.parse_ticket_number(order_in.name)
+        ticket_number: str | None = self.ticket_handler.parse_ticket_number(order_in.name)
         if not ticket_number:
             ticket_number = self.ticket_handler.create_ticket(
                 order=order_in, user_name=user_name, user_mail=user_mail, project=project
@@ -54,7 +53,6 @@ def submit(self, project: OrderType, order_in: OrderIn, user_name: str, user_mai
             self.ticket_handler.connect_to_ticket(
                 order=order_in,
                 user_name=user_name,
-                user_mail=user_mail,
                 project=project,
                 ticket_number=ticket_number,
             )