Fix merge coflict

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 64.5.29
+current_version = 67.0.9
 commit = True
 tag = True
 tag_name = v{new_version}

.github/workflows/tests_and_coverage.yml

@@ -24,16 +24,8 @@ jobs:
         with:
           virtualenvs-create: false
 
-      - name: Cache dependencies
-        uses: actions/cache@v4
-        id: cache
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }}
-
       - name: Install Dependencies
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction
+        run: poetry install --no-interaction --all-extras
 
       - name: Test with Pytest & Coveralls
         run: |

Dockerfile

@@ -23,14 +23,16 @@ ENV TRAILBLAZER_SERVICE_ACCOUNT_AUTH_FILE="auth_file"
 
 
 WORKDIR /home/src/app
-COPY pyproject.toml poetry.lock gunicorn.conf.py ./
+COPY pyproject.toml poetry.lock gunicorn.conf.py README.md ./
 
 RUN pip install --no-cache-dir poetry \
     && poetry config virtualenvs.create false \
-    && poetry install --no-interaction --no-ansi
+    && poetry install --no-interaction --no-ansi --no-root
 
 COPY cg ./cg
 
+RUN poetry install --no-interaction --no-ansi
+
 CMD gunicorn \
     --config gunicorn.conf.py \
     cg.server.auto:app

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "64.5.29"
+__version__ = "67.0.9"

cg/apps/hermes/hermes_api.py

@@ -18,6 +18,7 @@ def __init__(self, config: dict):
         self.process = Process(
             binary=config["hermes"]["binary_path"],
         )
+        self.container_path: str = config["hermes"]["container_path"]
         self.container_mount_volume = config["hermes"]["container_mount_volume"]
 
     def convert_deliverables(
@@ -33,7 +34,7 @@ def convert_deliverables(
             "run",
             "--bind",
             self.container_mount_volume,
-            "/home/proj/stage/singularity_containers/hermes_latest.sif",
+            self.container_path,
             "convert",
             "deliverables",
             "--workflow",

cg/apps/housekeeper/hk.py

@@ -7,11 +7,7 @@
 
 from housekeeper.include import checksum as hk_checksum
 from housekeeper.include import include_version
-from housekeeper.store.database import (
-    create_all_tables,
-    drop_all_tables,
-    initialize_database,
-)
+from housekeeper.store.database import create_all_tables, drop_all_tables, initialize_database
 from housekeeper.store.models import Archive, Bundle, File, Tag, Version
 from housekeeper.store.store import Store
 from sqlalchemy.orm import Query
@@ -27,17 +23,13 @@
 
 
 class HousekeeperAPI:
-    """API to decouple cg code from Housekeeper"""
+    """API to decouple cg code from Housekeeper."""
 
     def __init__(self, config: dict) -> None:
         initialize_database(config["housekeeper"]["database"])
         self._store = Store(config["housekeeper"]["root"])
         self.root_dir: str = config["housekeeper"]["root"]
 
-    def __getattr__(self, name):
-        LOG.warning(f"Called undefined {name} on {self.__class__.__name__}, please wrap")
-        return getattr(self._store, name)
-
     def new_bundle(self, name: str, created_at: datetime = None) -> Bundle:
         """Create a new file bundle."""
         return self._store.new_bundle(name, created_at)

cg/apps/lims/api.py

@@ -555,3 +555,11 @@ def _get_negative_controls_from_list(samples: list[Sample]) -> list[Sample]:
             ):
                 negative_controls.append(sample)
         return negative_controls
+
+    def get_sample_region_and_lab_code(self, sample_id: str) -> str:
+        """Return the region code and lab code for a sample formatted as a prefix string."""
+        region_code: str = self.get_sample_attribute(lims_id=sample_id, key="region_code").split(
+            " "
+        )[0]
+        lab_code: str = self.get_sample_attribute(lims_id=sample_id, key="lab_code").split(" ")[0]
+        return f"{region_code}_{lab_code}_"

cg/apps/orderform/excel_orderform_parser.py

@@ -12,8 +12,8 @@
 from cg.constants import DataDelivery
 from cg.constants.orderforms import Orderform
 from cg.exc import OrderFormError
+from cg.models.orders.constants import OrderType
 from cg.models.orders.excel_sample import ExcelSample
-from cg.models.orders.order import OrderType
 
 LOG = logging.getLogger(__name__)
 

cg/apps/orderform/json_orderform_parser.py

@@ -1,8 +1,8 @@
 from cg.apps.orderform.orderform_parser import OrderformParser
 from cg.constants import DataDelivery, Workflow
 from cg.exc import OrderFormError
+from cg.models.orders.constants import OrderType
 from cg.models.orders.json_sample import JsonSample
-from cg.models.orders.order import OrderType
 
 
 class JsonOrderformParser(OrderformParser):

cg/apps/orderform/orderform_parser.py

@@ -7,7 +7,7 @@
 from cg.apps.orderform.utils import ORDER_TYPES_WITH_CASES
 from cg.constants import DataDelivery
 from cg.exc import OrderFormError
-from cg.models.orders.order import OrderType
+from cg.models.orders.constants import OrderType
 from cg.models.orders.orderform_schema import OrderCase, Orderform, OrderPool
 from cg.models.orders.sample_base import OrderSample
 from cg.store.models import Customer

cg/apps/tb/api.py

@@ -4,8 +4,8 @@
 import logging
 from typing import Any
 
-from google.auth import jwt
-from google.auth.crypt import RSASigner
+from google.auth.transport.requests import Request
+from google.oauth2 import service_account
 
 from cg.apps.tb.dto.create_job_request import CreateJobRequest
 from cg.apps.tb.dto.summary_response import AnalysisSummary, SummariesResponse
@@ -50,10 +50,12 @@ def __init__(self, config: dict):
 
     @property
     def auth_header(self) -> dict:
-        signer = RSASigner.from_service_account_file(self.service_account_auth_file)
-        payload = {"email": self.service_account}
-        jwt_token = jwt.encode(signer=signer, payload=payload).decode("ascii")
-        return {"Authorization": f"Bearer {jwt_token}"}
+        credentials = service_account.IDTokenCredentials.from_service_account_file(
+            filename=self.service_account_auth_file,
+            target_audience="trailblazer",
+        )
+        credentials.refresh(Request())
+        return {"Authorization": f"Bearer {credentials.token}"}
 
     def query_trailblazer(
         self, command: str, request_body: dict, method: str = APIMethods.POST

cg/cli/deliver/base.py

@@ -15,7 +15,7 @@
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
-from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
+from cg.services.deliver_files.factory import (
     DeliveryServiceFactory,
 )
 from cg.services.deliver_files.rsync.service import DeliveryRsyncService
@@ -88,8 +88,7 @@ def deliver_case(
         LOG.error(f"Could not find case with id {case_id}")
         return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-        case=case,
-        delivery_type=delivery_type,
+        case=case, delivery_type=delivery_type
     )
     delivery_service.deliver_files_for_case(
         case=case, delivery_base_path=Path(inbox), dry_run=dry_run
@@ -124,8 +123,7 @@ def deliver_ticket(
         LOG.error(f"Could not find case connected to ticket {ticket}")
         return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-        case=cases[0],
-        delivery_type=delivery_type,
+        case=cases[0], delivery_type=delivery_type
     )
     delivery_service.deliver_files_for_ticket(
         ticket_id=ticket, delivery_base_path=Path(inbox), dry_run=dry_run
@@ -172,8 +170,7 @@ def deliver_sample_raw_data(
         LOG.error(f"Could not find case with id {case_id}")
         return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-        case=case,
-        delivery_type=delivery_type,
+        case=case, delivery_type=delivery_type
     )
     delivery_service.deliver_files_for_sample(
         case=case, sample_id=sample_id, delivery_base_path=Path(inbox), dry_run=dry_run

cg/cli/deliver/utils.py

@@ -5,7 +5,7 @@
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
-from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
+from cg.services.deliver_files.factory import (
     DeliveryServiceFactory,
 )
 from cg.store.models import Analysis, Case
@@ -26,8 +26,7 @@ def deliver_raw_data_for_analyses(
         try:
             case: Case = analysis.case
             delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-                case=case,
-                delivery_type=case.data_delivery,
+                case=case, delivery_type=case.data_delivery
             )
 
             delivery_service.deliver_files_for_case(

cg/cli/upload/base.py

@@ -39,6 +39,7 @@
 from cg.meta.upload.microsalt.microsalt_upload_api import MicrosaltUploadAPI
 from cg.meta.upload.mip.mip_dna import MipDNAUploadAPI
 from cg.meta.upload.mip.mip_rna import MipRNAUploadAPI
+from cg.meta.upload.mutant.mutant import MutantUploadAPI
 from cg.meta.upload.nf_analysis import NfAnalysisUploadAPI
 from cg.meta.upload.tomte.tomte import TomteUploadAPI
 from cg.meta.upload.raredisease.raredisease import RarediseaseUploadAPI
@@ -94,6 +95,8 @@ def upload(context: click.Context, case_id: str | None, restart: bool):
             Workflow.TAXPROFILER,
         }:
             upload_api = NfAnalysisUploadAPI(config_object, case.data_analysis)
+        elif case.data_analysis == Workflow.MUTANT:
+            upload_api = MutantUploadAPI(config_object)
 
         context.obj.meta_apis["upload_api"] = upload_api
         upload_api.upload(ctx=context, case=case, restart=restart)

cg/cli/upload/fohm.py

@@ -41,7 +41,11 @@ def aggregate_delivery(
     context: CGConfig, cases: list, dry_run: bool = False, datestr: str | None = None
 ):
     """Re-aggregates delivery files for FOHM and saves them to default working directory."""
-    fohm_api = FOHMUploadAPI(config=context, dry_run=dry_run, datestr=datestr)
+    fohm_api = FOHMUploadAPI(
+        config=context,
+        dry_run=dry_run,
+        datestr=datestr,
+    )
     try:
         fohm_api.aggregate_delivery(cases)
     except (ValidationError, TypeError) as error:
@@ -57,7 +61,11 @@ def create_komplettering(
     context: CGConfig, cases: list, dry_run: bool = False, datestr: str | None = None
 ):
     """Re-aggregates komplettering files for FOHM and saves them to default working directory."""
-    fohm_api = FOHMUploadAPI(config=context, dry_run=dry_run, datestr=datestr)
+    fohm_api = FOHMUploadAPI(
+        config=context,
+        dry_run=dry_run,
+        datestr=datestr,
+    )
     try:
         fohm_api.create_and_write_complementary_report(cases)
     except ValidationError as error:
@@ -73,7 +81,11 @@ def preprocess_all(
     context: CGConfig, cases: list, dry_run: bool = False, datestr: str | None = None
 ):
     """Create all FOHM upload files, upload to GISAID, sync SFTP and mail reports for all provided cases."""
-    fohm_api = FOHMUploadAPI(config=context, dry_run=dry_run, datestr=datestr)
+    fohm_api = FOHMUploadAPI(
+        config=context,
+        dry_run=dry_run,
+        datestr=datestr,
+    )
     gisaid_api = GisaidAPI(config=context)
     cases = list(cases)
     upload_cases = []
@@ -105,7 +117,11 @@ def preprocess_all(
 @click.pass_obj
 def upload_rawdata(context: CGConfig, dry_run: bool = False, datestr: str | None = None):
     """Deliver files in daily upload directory via sftp."""
-    fohm_api = FOHMUploadAPI(config=context, dry_run=dry_run, datestr=datestr)
+    fohm_api = FOHMUploadAPI(
+        config=context,
+        dry_run=dry_run,
+        datestr=datestr,
+    )
     fohm_api.sync_files_sftp()
 
 
@@ -115,5 +131,9 @@ def upload_rawdata(context: CGConfig, dry_run: bool = False, datestr: str | None
 @click.pass_obj
 def send_reports(context: CGConfig, dry_run: bool = False, datestr: str | None = None):
     """Send all komplettering reports found in the current daily directory to target recipients."""
-    fohm_api = FOHMUploadAPI(config=context, dry_run=dry_run, datestr=datestr)
+    fohm_api = FOHMUploadAPI(
+        config=context,
+        dry_run=dry_run,
+        datestr=datestr,
+    )
     fohm_api.send_mail_reports()

cg/cli/workflow/base.py

@@ -14,6 +14,7 @@
 from cg.cli.workflow.mip_dna.base import mip_dna
 from cg.cli.workflow.mip_rna.base import mip_rna
 from cg.cli.workflow.mutant.base import mutant
+from cg.cli.workflow.nallo.base import nallo
 from cg.cli.workflow.raredisease.base import raredisease
 from cg.cli.workflow.rnafusion.base import rnafusion
 from cg.cli.workflow.taxprofiler.base import taxprofiler
@@ -27,16 +28,17 @@ def workflow():
 
 workflow.add_command(balsamic)
 workflow.add_command(balsamic_qc)
-workflow.add_command(balsamic_umi)
 workflow.add_command(balsamic_pon)
+workflow.add_command(balsamic_umi)
+workflow.add_command(fluffy)
+workflow.add_command(jasen)
 workflow.add_command(microsalt)
 workflow.add_command(mip_dna)
 workflow.add_command(mip_rna)
-workflow.add_command(fluffy)
-workflow.add_command(jasen)
 workflow.add_command(mutant)
+workflow.add_command(nallo)
 workflow.add_command(raredisease)
+workflow.add_command(raw_data)
 workflow.add_command(rnafusion)
 workflow.add_command(taxprofiler)
 workflow.add_command(tomte)
-workflow.add_command(raw_data)