Merge branch 'master' into update-1508-33

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 64.5.28
+current_version = 64.5.30
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "64.5.28"
+__version__ = "64.5.30"

cg/exc.py

@@ -298,10 +298,6 @@ class OrderNotFoundError(CgError):
     """Exception raised when an order is not found."""
 
 
-class OrderExistsError(CgError):
-    """Exception raised when cases and samples are added to a pre-existing order."""
-
-
 class OrderMismatchError(CgError):
     """Exception raised when cases expected to belong to the same order are not part of the same order."""
 

cg/meta/orders/api.py

@@ -12,9 +12,7 @@
 from cg.apps.lims import LimsAPI
 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 (
-    OrderSubmitterRegistry,
-)
+from cg.services.orders.submitters.order_submitter_registry import OrderSubmitterRegistry
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -43,18 +41,8 @@ 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 = 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
-            )
-        else:
-            self.ticket_handler.connect_to_ticket(
-                order=order_in,
-                user_name=user_name,
-                project=project,
-                ticket_number=ticket_number,
-            )
+        ticket_number = self.ticket_handler.create_ticket(
+            order=order_in, user_name=user_name, user_mail=user_mail, project=project
+        )
         order_in.ticket = ticket_number
         return submit_handler.submit_order(order_in=order_in)

cg/meta/orders/ticket_handler.py

@@ -1,11 +1,10 @@
 import logging
-import re
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from typing import Any
 
 from cg.clients.freshdesk.freshdesk_client import FreshdeskClient
-from cg.clients.freshdesk.models import ReplyCreate, TicketCreate, TicketResponse
+from cg.clients.freshdesk.models import TicketCreate, TicketResponse
 from cg.models.orders.order import OrderIn
 from cg.models.orders.samples import Of1508Sample
 from cg.store.models import Customer, Sample
@@ -25,18 +24,6 @@ def __init__(self, db: Store, client: FreshdeskClient, system_email_id: int, env
         self.system_email_id: int = system_email_id
         self.env: str = env
 
-    @staticmethod
-    def parse_ticket_number(name: str) -> str | None:
-        """Try to parse a ticket number from a string"""
-        # detect manual ticket assignment
-        ticket_match = re.fullmatch(r"#(\d{6,10})", name)
-        if ticket_match:
-            ticket_id = ticket_match.group(1)
-            LOG.info(f"{ticket_id}: detected ticket in order name")
-            return ticket_id
-        LOG.info(f"Could not detected ticket number in name {name}")
-        return None
-
     def create_ticket(
         self, order: OrderIn, user_name: str, user_mail: str, project: str
     ) -> int | None:
@@ -105,13 +92,6 @@ def create_xml_sample_list(self, order: OrderIn, user_name: str) -> str:
     def create_new_ticket_header(message: str, order: OrderIn, project: str) -> str:
         return f"New order with {len(order.samples)} {project} samples:" + message
 
-    @staticmethod
-    def add_existing_ticket_header(message: str, order: OrderIn, project: str) -> str:
-        return (
-            f"A new order with {len(order.samples)} {project} samples has been connected to this ticket:"
-            + message
-        )
-
     def add_sample_name_to_message(self, message: str, sample_name: str) -> str:
         message += f"{self.NEW_LINE}{sample_name}"
         return message
@@ -188,27 +168,3 @@ def replace_empty_string_with_none(cls, obj: Any) -> Any:
                 else:
                     obj[key] = cls.replace_empty_string_with_none(item)
         return obj
-
-    def connect_to_ticket(
-        self, order: OrderIn, user_name: str, project: str, ticket_number: str
-    ) -> None:
-        """Appends a new order message to the ticket selected by the customer"""
-        LOG.info(f"Connecting order to ticket {ticket_number}")
-
-        message: str = self.add_existing_ticket_header(
-            message=self.create_xml_sample_list(order=order, user_name=user_name),
-            order=order,
-            project=project,
-        )
-
-        with TemporaryDirectory() as temp_dir:
-            attachments: Path = self.create_attachment_file(order=order, temp_dir=temp_dir)
-
-            reply = ReplyCreate(ticket_number=ticket_number, body=message)
-
-            self.client.reply_to_ticket(
-                reply=reply,
-                attachments=[attachments],
-            )
-
-            LOG.info(f"Connected order to ticket {ticket_number} in Freshdesk")

cg/server/endpoints/orders.py

@@ -17,7 +17,6 @@
 from cg.constants.constants import FileFormat
 from cg.exc import (
     OrderError,
-    OrderExistsError,
     OrderFormError,
     OrderNotDeliverableError,
     OrderNotFoundError,
@@ -27,9 +26,7 @@
 from cg.meta.orders import OrdersAPI
 from cg.models.orders.order import OrderIn, OrderType
 from cg.models.orders.orderform_schema import Orderform
-from cg.server.dto.delivery_message.delivery_message_response import (
-    DeliveryMessageResponse,
-)
+from cg.server.dto.delivery_message.delivery_message_response import DeliveryMessageResponse
 from cg.server.dto.orders.order_delivery_update_request import OrderOpenUpdateRequest
 from cg.server.dto.orders.order_patch_request import OrderOpenPatch
 from cg.server.dto.orders.orders_request import OrdersRequest
@@ -170,9 +167,6 @@ def submit_order(order_type):
         )
         project = OrderType(order_type)
         order_in = OrderIn.parse_obj(request_json, project=project)
-        existing_ticket: str | None = ticket_handler.parse_ticket_number(order_in.name)
-        if existing_ticket and order_service.store.get_order_by_ticket_id(existing_ticket):
-            raise OrderExistsError(f"Order with ticket id {existing_ticket} already exists.")
 
         result: dict = api.submit(
             project=project,
@@ -183,7 +177,6 @@ def submit_order(order_type):
 
     except (  # user misbehaviour
         OrderError,
-        OrderExistsError,
         OrderFormError,
         ValidationError,
         ValueError,

cg/services/orders/validate_order_services/validate_microbial_order.py

@@ -1,7 +1,7 @@
 from cg.exc import OrderError
 from cg.models.orders.constants import OrderType
 from cg.models.orders.order import OrderIn
-from cg.models.orders.samples import SarsCov2Sample
+from cg.models.orders.samples import MicrobialFastqSample, SarsCov2Sample
 from cg.services.orders.submitters.order_submitter import ValidateOrderService
 from cg.store.models import Customer
 from cg.store.store import Store
@@ -15,18 +15,25 @@ def __init__(self, status_db: Store):
     def validate_order(self, order: OrderIn) -> None:
         if order.order_type == OrderType.SARS_COV_2:
             self._validate_sample_names_are_available(
-                samples=order.samples, customer_id=order.customer
+                samples=order.samples, customer_id=order.customer, is_sars_cov_2=True
+            )
+        elif order.order_type == OrderType.MICROBIAL_FASTQ:
+            self._validate_sample_names_are_available(
+                samples=order.samples, customer_id=order.customer, is_sars_cov_2=False
             )
 
     def _validate_sample_names_are_available(
-        self, samples: list[SarsCov2Sample], customer_id: str
+        self,
+        samples: list[SarsCov2Sample] | list[MicrobialFastqSample],
+        customer_id: str,
+        is_sars_cov_2: bool,
     ) -> None:
         """Validate names of all samples are not already in use."""
         customer: Customer = self.status_db.get_customer_by_internal_id(
             customer_internal_id=customer_id
         )
         for sample in samples:
-            if sample.control:
+            if is_sars_cov_2 and sample.control:
                 continue
             if self.status_db.get_sample_by_customer_and_name(
                 customer_entry_id=[customer.id], sample_name=sample.name

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "64.5.28"
+version = "64.5.30"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/meta/orders/test_ticket_handler.py

@@ -1,17 +1,6 @@
 from cg.meta.orders.ticket_handler import TicketHandler
 
 
-def test_parse_ticket_number(ticket_id: str):
-    # GIVEN a string with a ticket number
-    order_name = f"#{ticket_id}"
-
-    # WHEN parsing the string
-    result = TicketHandler.parse_ticket_number(order_name)
-
-    # THEN assert that the correct string was parsed
-    assert result == ticket_id
-
-
 def test_add_user_name_message(ticket_handler: TicketHandler):
     # GIVEN a message string
     message = ""