Add mip rna messages (#3902) (patch)

### Added

- crud functions to retrieve dna cases related to an case.
- Logic for generation of delivery messages for mip-rna.

cg/constants/__init__.py

@@ -6,6 +6,7 @@
     CAPTUREKIT_OPTIONS,
     CONTAINER_OPTIONS,
     DEFAULT_CAPTURE_KIT,
+    DNA_WORKFLOWS_WITH_SCOUT_UPLOAD,
     STATUS_OPTIONS,
     DataDelivery,
     FileExtensions,

cg/constants/constants.py

@@ -140,6 +140,13 @@ class Workflow(StrEnum):
     TOMTE: str = "tomte"
 
 
+DNA_WORKFLOWS_WITH_SCOUT_UPLOAD: list[Workflow] = [
+    Workflow.MIP_DNA,
+    Workflow.BALSAMIC,
+    Workflow.BALSAMIC_UMI,
+]
+
+
 class FileFormat(StrEnum):
     CSV: str = "csv"
     FASTQ: str = "fastq"

cg/constants/sequencing.py

@@ -72,3 +72,10 @@ class SeqLibraryPrepCategory(StrEnum):
     WHOLE_EXOME_SEQUENCING: str = "wes"
     WHOLE_GENOME_SEQUENCING: str = "wgs"
     WHOLE_TRANSCRIPTOME_SEQUENCING: str = "wts"
+
+
+DNA_PREP_CATEGORIES: list[SeqLibraryPrepCategory] = [
+    SeqLibraryPrepCategory.WHOLE_GENOME_SEQUENCING,
+    SeqLibraryPrepCategory.TARGETED_GENOME_SEQUENCING,
+    SeqLibraryPrepCategory.WHOLE_EXOME_SEQUENCING,
+]

cg/server/endpoints/cases.py

@@ -1,7 +1,9 @@
 import logging
 from http import HTTPStatus
+
 from flask import Blueprint, abort, g, jsonify, request
-from cg.exc import CaseNotFoundError, OrderMismatchError
+
+from cg.exc import CaseNotFoundError, CgDataError, OrderMismatchError
 from cg.server.dto.delivery_message.delivery_message_request import DeliveryMessageRequest
 from cg.server.dto.delivery_message.delivery_message_response import DeliveryMessageResponse
 from cg.server.endpoints.utils import before_request
@@ -62,7 +64,7 @@ def get_cases_delivery_message():
             delivery_message_request
         )
         return jsonify(response.model_dump()), HTTPStatus.OK
-    except (CaseNotFoundError, OrderMismatchError) as error:
+    except (CaseNotFoundError, OrderMismatchError, CgDataError) as error:
         return jsonify({"error": str(error)}), HTTPStatus.BAD_REQUEST
 
 
@@ -74,7 +76,7 @@ def get_case_delivery_message(case_id: str):
             delivery_message_request
         )
         return jsonify(response.model_dump()), HTTPStatus.OK
-    except CaseNotFoundError as error:
+    except (CaseNotFoundError, CgDataError) as error:
         return jsonify({"error": str(error)}), HTTPStatus.BAD_REQUEST
 
 

cg/services/delivery_message/delivery_message_service.py

@@ -1,9 +1,7 @@
 from cg.apps.tb import TrailblazerAPI
 from cg.apps.tb.models import TrailblazerAnalysis
 from cg.exc import OrderNotDeliverableError
-from cg.server.dto.delivery_message.delivery_message_request import (
-    DeliveryMessageRequest,
-)
+from cg.server.dto.delivery_message.delivery_message_request import DeliveryMessageRequest
 from cg.server.dto.delivery_message.delivery_message_response import (
     DeliveryMessageOrderResponse,
     DeliveryMessageResponse,
@@ -54,5 +52,5 @@ def _get_validated_analyses(
     def _get_delivery_message(self, case_ids: set[str]) -> str:
         cases: list[Case] = self.store.get_cases_by_internal_ids(case_ids)
         validate_cases(cases=cases, case_ids=case_ids)
-        message: str = get_message(cases)
+        message: str = get_message(cases=cases, store=self.store)
         return message

cg/services/delivery_message/messages/__init__.py

@@ -1,11 +1,25 @@
-from cg.services.delivery_message.messages.analysis_scout_message import AnalysisScoutMessage
+from cg.services.delivery_message.messages.analysis_scout_message import (
+    AnalysisScoutMessage,
+)
 from cg.services.delivery_message.messages.covid_message import CovidMessage
-from cg.services.delivery_message.messages.fastq_message import FastqMessage
-from cg.services.delivery_message.messages.fastq_scout_message import FastqScoutMessage
 from cg.services.delivery_message.messages.fastq_analysis_scout_message import (
     FastqAnalysisScoutMessage,
 )
-from cg.services.delivery_message.messages.microsalt_mwr_message import MicrosaltMwrMessage
-from cg.services.delivery_message.messages.microsalt_mwx_message import MicrosaltMwxMessage
+from cg.services.delivery_message.messages.fastq_message import FastqMessage
+from cg.services.delivery_message.messages.fastq_scout_message import FastqScoutMessage
+from cg.services.delivery_message.messages.microsalt_mwr_message import (
+    MicrosaltMwrMessage,
+)
+from cg.services.delivery_message.messages.microsalt_mwx_message import (
+    MicrosaltMwxMessage,
+)
 from cg.services.delivery_message.messages.scout_message import ScoutMessage
 from cg.services.delivery_message.messages.statina_message import StatinaMessage
+from cg.services.delivery_message.messages.rna_delivery_message import (
+    RNAScoutStrategy,
+    RNAFastqStrategy,
+    RNAAnalysisStrategy,
+    RNAFastqAnalysisStrategy,
+    RNAUploadMessageStrategy,
+    RNADeliveryMessage,
+)

cg/services/delivery_message/messages/rna_delivery_message.py

@@ -0,0 +1,81 @@
+from abc import abstractmethod, ABC
+
+from cg.services.delivery_message.messages.utils import (
+    get_scout_links_row_separated,
+    get_caesar_delivery_path,
+)
+from cg.store.models import Case
+
+
+class RNAUploadMessageStrategy(ABC):
+    """Abstract base class for delivery message strategies."""
+
+    @abstractmethod
+    def get_file_upload_message(self, delivery_path: str) -> str:
+        """Generate the file upload message part."""
+        pass
+
+
+class RNAAnalysisStrategy(RNAUploadMessageStrategy):
+    def get_file_upload_message(self, delivery_path: str) -> str:
+        return (
+            f"The analysis files are currently being uploaded to your inbox on Caesar:\n\n"
+            f"{delivery_path}"
+        )
+
+
+class RNAFastqAnalysisStrategy(RNAUploadMessageStrategy):
+    def get_file_upload_message(self, delivery_path: str) -> str:
+        return (
+            f"The fastq and analysis files are currently being uploaded to your inbox on Caesar:\n\n"
+            f"{delivery_path}"
+        )
+
+
+class RNAFastqStrategy(RNAUploadMessageStrategy):
+    def get_file_upload_message(self, delivery_path: str) -> str:
+        return (
+            f"The fastq files are currently being uploaded to your inbox on Caesar:\n\n"
+            f"{delivery_path}"
+        )
+
+
+class RNAScoutStrategy(RNAUploadMessageStrategy):
+    def get_file_upload_message(self, delivery_path: str) -> str:
+        return ""  # No file upload message needed for this case.
+
+
+class RNADeliveryMessage:
+    def __init__(self, store, strategy: RNAUploadMessageStrategy):
+        self.store = store
+        self.strategy = strategy
+
+    def create_message(self, cases: list[Case]) -> str:
+        if len(cases) == 1:
+            return self._get_case_message(cases[0])
+        return self._get_cases_message(cases)
+
+    def _get_case_message(self, case: Case) -> str:
+        related_uploaded_dna_cases = self.store.get_uploaded_related_dna_cases(rna_case=case)
+        scout_links = get_scout_links_row_separated(cases=related_uploaded_dna_cases)
+        delivery_path = get_caesar_delivery_path(case)
+        file_upload_message = self.strategy.get_file_upload_message(delivery_path)
+        return (
+            f"Hello,\n\n"
+            f"The analysis for case {case.name} has been uploaded to the corresponding DNA case(s) on Scout at:\n\n"
+            f"{scout_links}\n\n"
+            f"{file_upload_message}"
+        )
+
+    def _get_cases_message(self, cases: list[Case]) -> str:
+        message = "Hello,\n\n"
+        for case in cases:
+            related_uploaded_dna_cases = self.store.get_uploaded_related_dna_cases(rna_case=case)
+            scout_links = get_scout_links_row_separated(cases=related_uploaded_dna_cases)
+            message += (
+                f"The analysis for case {case.name} has been uploaded to the corresponding DNA case(s) on Scout at:\n\n"
+                f"{scout_links}\n\n"
+            )
+        delivery_path = get_caesar_delivery_path(cases[0])
+        file_upload_message = self.strategy.get_file_upload_message(delivery_path)
+        return message + file_upload_message

cg/services/delivery_message/messages/utils.py

@@ -13,6 +13,11 @@ def get_scout_link(case: Case) -> str:
     return f"https://scout.scilifelab.se/{customer_id}/{case_name}"
 
 
+def get_scout_links_row_separated(cases: list[Case]) -> str:
+    scout_links: list[str] = [get_scout_link(case) for case in cases]
+    return "\n".join(scout_links)
+
+
 def get_pangolin_delivery_path(case: Case) -> str:
     customer_id: str = case.customer.internal_id
     return f"/home/{customer_id}/inbox/wwLab_automatisk_hamtning"

cg/services/delivery_message/utils.py

@@ -1,9 +1,5 @@
 from cg.constants.constants import DataDelivery, MicrosaltAppTags, Workflow
-from cg.exc import (
-    CaseNotFoundError,
-    DeliveryMessageNotSupportedError,
-    OrderMismatchError,
-)
+from cg.exc import CaseNotFoundError, OrderMismatchError
 from cg.services.delivery_message.messages import (
     AnalysisScoutMessage,
     CovidMessage,
@@ -17,47 +13,76 @@
 from cg.services.delivery_message.messages.analysis_message import AnalysisMessage
 from cg.services.delivery_message.messages.bam_message import BamMessage
 from cg.services.delivery_message.messages.delivery_message import DeliveryMessage
-from cg.services.delivery_message.messages.fastq_analysis_message import (
-    FastqAnalysisMessage,
-)
-from cg.services.delivery_message.messages.microsalt_mwx_message import (
-    MicrosaltMwxMessage,
+from cg.services.delivery_message.messages.fastq_analysis_message import FastqAnalysisMessage
+from cg.services.delivery_message.messages.microsalt_mwx_message import MicrosaltMwxMessage
+from cg.services.delivery_message.messages.rna_delivery_message import (
+    RNAScoutStrategy,
+    RNAFastqStrategy,
+    RNAAnalysisStrategy,
+    RNAFastqAnalysisStrategy,
+    RNAUploadMessageStrategy,
+    RNADeliveryMessage,
 )
 from cg.store.models import Case, Sample
+from cg.store.store import Store
+
+MESSAGE_MAP = {
+    DataDelivery.ANALYSIS_FILES: AnalysisMessage,
+    DataDelivery.FASTQ: FastqMessage,
+    DataDelivery.SCOUT: ScoutMessage,
+    DataDelivery.FASTQ_SCOUT: FastqScoutMessage,
+    DataDelivery.FASTQ_ANALYSIS: FastqAnalysisMessage,
+    DataDelivery.ANALYSIS_SCOUT: AnalysisScoutMessage,
+    DataDelivery.FASTQ_ANALYSIS_SCOUT: FastqAnalysisScoutMessage,
+    DataDelivery.STATINA: StatinaMessage,
+    DataDelivery.BAM: BamMessage,
+}
 
 
-def get_message(cases: list[Case]) -> str:
-    message_strategy: DeliveryMessage = get_message_strategy(cases[0])
+RNA_STRATEGY_MAP: dict[DataDelivery, type[RNAUploadMessageStrategy]] = {
+    # Only returns a message strategy if there is a scout delivery for the case.
+    DataDelivery.SCOUT: RNAScoutStrategy,
+    DataDelivery.FASTQ_SCOUT: RNAFastqStrategy,
+    DataDelivery.ANALYSIS_SCOUT: RNAAnalysisStrategy,
+    DataDelivery.FASTQ_ANALYSIS_SCOUT: RNAFastqAnalysisStrategy,
+}
+
+
+def get_message(cases: list[Case], store: Store) -> str:
+    message_strategy: DeliveryMessage = get_message_strategy(cases[0], store)
     return message_strategy.create_message(cases)
 
 
-def get_message_strategy(case: Case) -> DeliveryMessage:
+def get_message_strategy(case: Case, store: Store) -> DeliveryMessage:
     if case.data_analysis == Workflow.MICROSALT:
         return get_microsalt_message_strategy(case)
 
     if case.data_analysis == Workflow.MUTANT:
         return CovidMessage()
 
+    if case.data_analysis == Workflow.MIP_RNA:
+        return get_rna_message_strategy_from_data_delivery(case=case, store=store)
+
     message_strategy: DeliveryMessage = get_message_strategy_from_data_delivery(case)
     return message_strategy
 
 
 def get_message_strategy_from_data_delivery(case: Case) -> DeliveryMessage:
-    message_strategy: DeliveryMessage = message_map[case.data_delivery]()
+    message_strategy: DeliveryMessage = MESSAGE_MAP[case.data_delivery]()
     return message_strategy
 
 
-message_map = {
-    DataDelivery.ANALYSIS_FILES: AnalysisMessage,
-    DataDelivery.FASTQ: FastqMessage,
-    DataDelivery.SCOUT: ScoutMessage,
-    DataDelivery.FASTQ_SCOUT: FastqScoutMessage,
-    DataDelivery.FASTQ_ANALYSIS: FastqAnalysisMessage,
-    DataDelivery.ANALYSIS_SCOUT: AnalysisScoutMessage,
-    DataDelivery.FASTQ_ANALYSIS_SCOUT: FastqAnalysisScoutMessage,
-    DataDelivery.STATINA: StatinaMessage,
-    DataDelivery.BAM: BamMessage,
-}
+def get_rna_message_strategy_from_data_delivery(
+    case: Case, store: Store
+) -> DeliveryMessage | RNADeliveryMessage:
+    """Get the RNA delivery message strategy based on the data delivery type.
+    If a scout delivery is required it will use the RNADeliveryMessage class that links RNA to DNA cases.
+    Otherwise it used the conventional delivery message strategy.
+    """
+    message_strategy = RNA_STRATEGY_MAP[case.data_delivery]
+    if message_strategy:
+        return RNADeliveryMessage(store=store, strategy=message_strategy())
+    return MESSAGE_MAP[case.data_delivery]()
 
 
 def get_microsalt_message_strategy(case: Case) -> DeliveryMessage:
@@ -100,11 +125,6 @@ def validate_cases(cases: list[Case], case_ids: list[str]) -> None:
         raise CaseNotFoundError("Internal id not found in the database")
     if not is_matching_order(cases):
         raise OrderMismatchError("Cases do not belong to the same order")
-    cases_with_mip_rna: list[Case] = [
-        case for case in cases if case.data_analysis == Workflow.MIP_RNA
-    ]
-    if cases_with_mip_rna:
-        raise DeliveryMessageNotSupportedError("Workflow is not supported.")
 
 
 def is_matching_order(cases: list[Case]) -> bool: