cg 76.0.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

cg/server/admin.py

@@ -12,6 +12,7 @@ from wtforms.form import Form
 
 from cg.constants.constants import NG_UL_SUFFIX, CaseActions, DataDelivery, Workflow
 from cg.models.orders.constants import OrderType
+from cg.server.app_config import app_config
 from cg.server.ext import applications_service, db, sample_service
 from cg.server.utils import MultiCheckboxField
 from cg.store.models import Application
@@ -111,12 +112,6 @@ def view_pacbio_sample_sequencing_metrics_link(unused1, unused2, model, unused3)
     )
 
 
-def is_external_application(unused1, unused2, model, unused3):
-    """column formatter to open this view"""
-    del unused1, unused2, unused3
-    return model.application_version.application.is_external if model.application_version else ""
-
-
 def view_order_types(unused1, unused2, model, unused3):
     del unused1, unused2, unused3
     order_type_list = "<br>".join(model.order_types)
@@ -197,6 +192,44 @@ def view_customer_link(unused1, unused2, model, unused3):
     return markup
 
 
+def view_ticket_link(unused1, unused2, model, attribute_name):
+    """Column formatter used to add hyperlink to ticket ID, if applicable."""
+    del unused1, unused2
+
+    # Ticket attribute called differently from models, infer attribute name from args
+    ticket_attr = getattr(model, attribute_name)
+    ticket_str = str(ticket_attr).strip()
+
+    # Freshdesk ticket IDs have >=7 digits
+    if len(ticket_str) >= 7:
+        ticket_link = f"{app_config.freshdesk_url}/a/tickets/{ticket_str}"
+        ticket_markup = Markup(f"<a href='{ticket_link}'>{ticket_str}</a>")
+        return ticket_markup
+    else:
+        return ticket_str
+
+
+def view_tickets_links(unused1, unused2, model, unused3):
+    """Column formatter used to add hyperlinks to comma-separated ticket IDs, if applicable. Assumes attribute name 'tickets'."""
+    del unused1, unused2, unused3
+
+    tickets_list = str(model.tickets).strip().split(sep=",")
+
+    tickets_markups = []
+    for ticket in tickets_list:
+        ticket_str = str(ticket).strip()
+
+        # Freshdesk ticket IDs have >=7 digits
+        if len(ticket_str) >= 7:
+            ticket_link = f"{app_config.freshdesk_url}/a/tickets/{ticket_str}"
+            ticket_markup = Markup(f"<a href='{ticket_link}'>{ticket_str}</a>")
+            tickets_markups.append(ticket_markup)
+        else:
+            tickets_markups.append(ticket_str)
+
+    return Markup(", ".join(tickets_markups))
+
+
 class ApplicationView(BaseView):
     """Admin view for Model.Application"""
 
@@ -207,6 +240,8 @@ class ApplicationView(BaseView):
         "is_accredited",
         "target_reads",
         "percent_reads_guaranteed",
+        "target_hifi_yield",
+        "percent_hifi_yield_guaranteed",
         "comment",
         "prep_category",
         "sequencing_depth",
@@ -267,10 +302,11 @@ class ApplicationView(BaseView):
     def on_model_change(self, form: Form, model: Application, is_created: bool):
         """Override to persist entries to the OrderTypeApplication table."""
         super(ApplicationView, self).on_model_change(form=form, model=model, is_created=is_created)
-        order_types: list[OrderType] = form["suitable_order_types"].data
-        applications_service.update_application_order_types(
-            application=model, order_types=order_types
-        )
+        if "suitable_order_types" in form.data:
+            order_types: list[OrderType] = form["suitable_order_types"].data
+            applications_service.update_application_order_types(
+                application=model, order_types=order_types
+            )
 
     def edit_form(self, obj=None):
         """Override to prefill the order types according to the current Application entry."""
@@ -435,6 +471,7 @@ class CaseView(BaseView):
         "customer": view_customer_link,
         "internal_id": view_case_sample_link,
         "priority": view_priority,
+        "tickets": view_tickets_links,
     }
     column_searchable_list = [
         "internal_id",
@@ -650,7 +687,10 @@ class OrderView(BaseView):
 
     column_default_sort = ("order_date", True)
     column_editable_list = ["is_open"]
-    column_formatters = {"customer": view_customer_link}
+    column_formatters = {
+        "customer": view_customer_link,
+        "ticket_id": view_ticket_link,
+    }
     column_searchable_list = ["id", "ticket_id"]
     column_display_pk = True
     create_modal = True
@@ -691,10 +731,36 @@ class PoolView(BaseView):
 class SampleView(BaseView):
     """Admin view for Model.Sample"""
 
-    column_exclude_list = [
-        "age_at_sampling",
-        "_phenotype_groups",
-        "_phenotype_terms",
+    column_list = [
+        "application_version",
+        "customer",
+        "organism",
+        "invoice",
+        "is_cancelled",
+        "capture_kit",
+        "comment",
+        "control",
+        "created_at",
+        "delivered_at",
+        "downsampled_to",
+        "from_sample",
+        "internal_id",
+        "is_tumour",
+        "loqusdb_id",
+        "name",
+        "no_invoice",
+        "order",
+        "ordered_at",
+        "original_ticket",
+        "prepared_at",
+        "priority",
+        "reads",
+        "hifi_yield",
+        "last_sequenced_at",
+        "received_at",
+        "reference_genome",
+        "sex",
+        "subject_id",
     ]
     column_default_sort = ("created_at", True)
     column_editable_list = [
@@ -714,9 +780,9 @@ class SampleView(BaseView):
     column_formatters = {
         "application_version": view_application_link_via_application_version,
         "customer": view_customer_link,
-        "is_external": is_external_application,
         "internal_id": view_case_sample_link,
         "invoice": InvoiceView.view_invoice_link,
+        "original_ticket": view_ticket_link,
         "priority": view_priority,
     }
     column_searchable_list = [
@@ -834,12 +900,12 @@ class IlluminaSampleSequencingMetricsView(BaseView):
     column_searchable_list = ["sample.internal_id", "instrument_run.device.internal_id"]
 
 
-class PacbioSmrtCellView(BaseView):
+class PacbioSmrtCellMetricsView(BaseView):
     """Admin view for Model.PacbioSMRTCell"""
 
     column_list = (
         "internal_id",
-        "run_name",
+        "sequencing_run.run_name",
         "movie_name",
         "well",
         "plate",
@@ -863,8 +929,9 @@ class PacbioSmrtCellView(BaseView):
         "internal_id": view_pacbio_sample_sequencing_metrics_link,
         "model": view_smrt_cell_model,
     }
+    column_labels = {"sequencing_run.run_name": "Run Name"}
     column_default_sort = ("completed_at", True)
-    column_searchable_list = ["device.internal_id", "run_name", "movie_name"]
+    column_searchable_list = ["device.internal_id", "movie_name", "sequencing_run.run_name"]
     column_sortable_list = [
         ("internal_id", "device.internal_id"),
         "started_at",
@@ -880,7 +947,7 @@ class PacbioSmrtCellView(BaseView):
                 "<a href='%s'>%s</a>"
                 % (
                     url_for(
-                        "pacbiosequencingrun.index_view",
+                        "pacbiosmrtcellmetrics.index_view",
                         search=model.instrument_run.device.internal_id,
                     ),
                     model.instrument_run.device.internal_id,
@@ -892,16 +959,30 @@ class PacbioSmrtCellView(BaseView):
 
 
 class PacbioSampleRunMetricsView(BaseView):
+    column_filters = [
+        "instrument_run.plate",
+        "instrument_run.sequencing_run.run_name",
+    ]
+    column_formatters = {
+        "smrt_cell": PacbioSmrtCellMetricsView.view_smrt_cell_link,
+        "sample": SampleView.view_sample_link,
+    }
+    column_labels = {
+        "instrument_run.plate": "Plate",
+        "instrument_run.sequencing_run.run_name": "Run Name",
+    }
     column_list = [
         "smrt_cell",
         "sample",
+        "instrument_run.sequencing_run.run_name",
+        "instrument_run.plate",
         "hifi_reads",
         "hifi_yield",
         "hifi_mean_read_length",
         "hifi_median_read_quality",
     ]
-    column_formatters = {
-        "smrt_cell": PacbioSmrtCellView.view_smrt_cell_link,
-        "sample": SampleView.view_sample_link,
-    }
-    column_searchable_list = ["sample.internal_id", "instrument_run.device.internal_id"]
+    column_searchable_list = [
+        "sample.internal_id",
+        "instrument_run.device.internal_id",
+        "instrument_run.sequencing_run.run_name",
+    ]

cg/server/app.py

@@ -19,7 +19,12 @@ from cg.server.endpoints.sequencing_metrics.illumina_sequencing_metrics import F
 from cg.server.endpoints.sequencing_metrics.pacbio_sequencing_metrics import (
     PACBIO_SAMPLE_SEQUENCING_METRICS_BLUEPRINT,
 )
-from cg.server.endpoints.sequencing_run.pacbio_sequencing_run import PACBIO_SEQUENCING_RUN_BLUEPRINT
+from cg.server.endpoints.sequencing_run.pacbio_sequencing_run import (
+    PACBIO_SEQUENCING_RUNS_BLUEPRINT,
+)
+from cg.server.endpoints.sequencing_run.pacbio_smrt_cell_metrics import (
+    PACBIO_SMRT_CELL_METRICS_BLUEPRINT,
+)
 from cg.server.endpoints.users import USERS_BLUEPRINT
 from cg.store.database import get_scoped_session_registry
 from cg.store.models import (
@@ -39,7 +44,7 @@ from cg.store.models import (
     Order,
     Organism,
     PacbioSampleSequencingMetrics,
-    PacbioSequencingRun,
+    PacbioSMRTCellMetrics,
     Panel,
     Pool,
     Sample,
@@ -107,7 +112,8 @@ def _register_blueprints(app: Flask):
     app.register_blueprint(ANALYSES_BLUEPRINT)
     app.register_blueprint(USERS_BLUEPRINT)
     app.register_blueprint(PACBIO_SAMPLE_SEQUENCING_METRICS_BLUEPRINT)
-    app.register_blueprint(PACBIO_SEQUENCING_RUN_BLUEPRINT)
+    app.register_blueprint(PACBIO_SEQUENCING_RUNS_BLUEPRINT)
+    app.register_blueprint(PACBIO_SMRT_CELL_METRICS_BLUEPRINT)
     app.register_blueprint(INDEX_SEQUENCES_BLUEPRINT)
     _register_admin_views()
 
@@ -119,6 +125,7 @@ def _register_blueprints(app: Flask):
     ext.csrf.exempt(FLOW_CELLS_BLUEPRINT)
     ext.csrf.exempt(ANALYSES_BLUEPRINT)
     ext.csrf.exempt(USERS_BLUEPRINT)
+    ext.csrf.exempt(PACBIO_SEQUENCING_RUNS_BLUEPRINT)
 
     @app.route("/")
     def index():
@@ -158,7 +165,11 @@ def _register_admin_views():
     ext.admin.add_view(
         admin.IlluminaSampleSequencingMetricsView(IlluminaSampleSequencingMetrics, ext.db.session)
     )
-    ext.admin.add_view(admin.PacbioSmrtCellView(PacbioSequencingRun, ext.db.session))
+    ext.admin.add_view(
+        admin.PacbioSmrtCellMetricsView(
+            PacbioSMRTCellMetrics, ext.db.session, "Pacbio SMRT Cell Metrics"
+        )
+    )
     ext.admin.add_view(
         admin.PacbioSampleRunMetricsView(PacbioSampleSequencingMetrics, ext.db.session)
     )

cg/server/endpoints/sequencing_run/dtos.py

@@ -3,7 +3,7 @@ from datetime import datetime
 from pydantic import BaseModel
 
 
-class PacbioSequencingRunDTO(BaseModel):
+class PacbioSmrtCellMetricsDTO(BaseModel):
     barcoded_hifi_mean_read_length: int
     barcoded_hifi_reads: int
     barcoded_hifi_reads_percentage: float
@@ -24,5 +24,23 @@ class PacbioSequencingRunDTO(BaseModel):
     well: str
 
 
-class PacbioSequencingRunsResponse(BaseModel):
-    runs: list[PacbioSequencingRunDTO]
+class PacbioSmrtCellMetricsResponse(BaseModel):
+    runs: list[PacbioSmrtCellMetricsDTO]
+
+
+class PacbioSequencingRunDTO(BaseModel):
+    id: int
+    run_name: str
+    comment: str
+    processed: bool
+
+
+class PacbioSequencingRunResponse(BaseModel):
+    pacbio_sequencing_runs: list[PacbioSequencingRunDTO]
+    total_count: int
+
+
+class PacbioSequencingRunUpdateRequest(BaseModel):
+    id: int
+    comment: str | None = None
+    processed: bool | None = None

cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py

@@ -1,20 +1,39 @@
-from flask import Blueprint, jsonify
+from http import HTTPStatus
+
+from flask import Blueprint, Response, jsonify, request
+from pydantic import ValidationError
 
 from cg.server.endpoints.error_handler import handle_missing_entries
-from cg.server.endpoints.sequencing_run.dtos import PacbioSequencingRunsResponse
+from cg.server.endpoints.sequencing_run.dtos import (
+    PacbioSequencingRunResponse,
+    PacbioSequencingRunUpdateRequest,
+)
 from cg.server.endpoints.utils import before_request
 from cg.server.ext import pacbio_sequencing_runs_service
 
-PACBIO_SEQUENCING_RUN_BLUEPRINT = Blueprint(
-    "pacbio_sequencing_run", __name__, url_prefix="/api/v1/pacbio_sequencing_run"
+PACBIO_SEQUENCING_RUNS_BLUEPRINT = Blueprint(
+    "pacbio_sequencing_runs", __name__, url_prefix="/api/v1/"
 )
-PACBIO_SEQUENCING_RUN_BLUEPRINT.before_request(before_request)
+PACBIO_SEQUENCING_RUNS_BLUEPRINT.before_request(before_request)
 
 
-@PACBIO_SEQUENCING_RUN_BLUEPRINT.route("/<run_name>", methods=["GET"])
+@PACBIO_SEQUENCING_RUNS_BLUEPRINT.route("/pacbio_sequencing_runs", methods=["GET"])
 @handle_missing_entries
-def get_sequencing_runs(run_name: str):
-    response: PacbioSequencingRunsResponse = (
-        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
+def get_sequencing_runs():
+    page: int = int(request.args.get("page", "0"))
+    page_size: int = int(request.args.get("pageSize", "0"))
+    sequencing_runs: PacbioSequencingRunResponse = (
+        pacbio_sequencing_runs_service.get_sequencing_runs(page=page, page_size=page_size)
     )
-    return jsonify(response.model_dump())
+    return jsonify(sequencing_runs.model_dump())
+
+
+@PACBIO_SEQUENCING_RUNS_BLUEPRINT.route("/pacbio_sequencing_runs/<id>", methods=["PATCH"])
+@handle_missing_entries
+def update_sequencing_run(id: str):
+    try:
+        update_request = PacbioSequencingRunUpdateRequest(id=id, **request.json)
+    except ValidationError:
+        return Response(status=HTTPStatus.UNPROCESSABLE_ENTITY)
+    pacbio_sequencing_runs_service.update_sequencing_run(update_request=update_request)
+    return Response(status=HTTPStatus.NO_CONTENT)

cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py

@@ -0,0 +1,20 @@
+from flask import Blueprint, jsonify
+
+from cg.server.endpoints.error_handler import handle_missing_entries
+from cg.server.endpoints.sequencing_run.dtos import PacbioSmrtCellMetricsResponse
+from cg.server.endpoints.utils import before_request
+from cg.server.ext import pacbio_sequencing_runs_service
+
+PACBIO_SMRT_CELL_METRICS_BLUEPRINT = Blueprint(
+    "pacbio_smrt_cell_metrics", __name__, url_prefix="/api/v1/pacbio_smrt_cell_metrics"
+)
+PACBIO_SMRT_CELL_METRICS_BLUEPRINT.before_request(before_request)
+
+
+@PACBIO_SMRT_CELL_METRICS_BLUEPRINT.route("/<run_name>", methods=["GET"])
+@handle_missing_entries
+def get_smrt_cell_metrics(run_name: str):
+    response: PacbioSmrtCellMetricsResponse = (
+        pacbio_sequencing_runs_service.get_sequencing_runs_by_name(run_name)
+    )
+    return jsonify(response.model_dump())

cg/services/analysis_starter/{service.py → analysis_starter.py}

@@ -1,8 +1,10 @@
 import logging
 from subprocess import CalledProcessError
 
+from requests import HTTPError
+
 from cg.constants import Workflow
-from cg.exc import AnalysisNotReadyError
+from cg.exc import AnalysisNotReadyError, SeqeraError
 from cg.services.analysis_starter.configurator.abstract_model import CaseConfig
 from cg.services.analysis_starter.configurator.configurator import Configurator
 from cg.services.analysis_starter.input_fetcher.input_fetcher import InputFetcher
@@ -51,20 +53,20 @@ class AnalysisStarter:
         LOG.info(f"Starting case {case_id}")
         self.tracker.ensure_analysis_not_ongoing(case_id)
         self.input_fetcher.ensure_files_are_ready(case_id)
-        parameters: CaseConfig = self.configurator.configure(case_id=case_id, **flags)
-        self._run_and_track(case_id=case_id, parameters=parameters)
+        case_config: CaseConfig = self.configurator.configure(case_id=case_id, **flags)
+        self._run_and_track(case_id=case_id, case_config=case_config)
 
     def run(self, case_id: str, **flags) -> None:
         """Run a case using an assumed existing configuration."""
         self.tracker.ensure_analysis_not_ongoing(case_id)
-        parameters: CaseConfig = self.configurator.get_config(case_id=case_id, **flags)
-        self._run_and_track(case_id=case_id, parameters=parameters)
+        case_config: CaseConfig = self.configurator.get_config(case_id=case_id, **flags)
+        self._run_and_track(case_id=case_id, case_config=case_config)
 
-    def _run_and_track(self, case_id: str, parameters: CaseConfig):
+    def _run_and_track(self, case_id: str, case_config: CaseConfig):
         self.tracker.set_case_as_running(case_id)
         try:
-            tower_workflow_id: str | None = self.submitter.submit(parameters)
-            self.tracker.track(case_config=parameters, tower_workflow_id=tower_workflow_id)
-        except CalledProcessError as exception:
+            submitted_case_config: CaseConfig = self.submitter.submit(case_config)
+            self.tracker.track(case_config=submitted_case_config)
+        except (CalledProcessError, HTTPError, SeqeraError) as exception:
             self.tracker.set_case_as_not_running(case_id)
             raise exception

cg/services/analysis_starter/configurator/abstract_model.py

@@ -6,3 +6,11 @@ from cg.constants import Workflow
 class CaseConfig(BaseModel):
     case_id: str
     workflow: Workflow
+
+    def get_session_id(self) -> str | None:
+        # This will be set by the NextflowCaseConfig
+        return None
+
+    def get_workflow_id(self) -> str | None:
+        # This will be set by the NextflowCaseConfig
+        return None

cg/services/analysis_starter/configurator/configurator.py

@@ -20,7 +20,7 @@ class Configurator(ABC):
     @staticmethod
     def _set_flags(config: SpecificCaseConfig, **flags) -> SpecificCaseConfig:
         curated_flags: dict = {key: value for key, value in flags.items() if value is not None}
-        return config.model_copy(update=curated_flags)
+        return config.model_validate(config.model_dump(by_alias=True) | curated_flags)
 
     @abstractmethod
     def _ensure_required_config_files_exist(self, **kwargs) -> None:

cg/services/analysis_starter/configurator/extensions/nallo.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+
+from cg.constants.scout import ScoutExportFileName
+from cg.services.analysis_starter.configurator.extensions.pipeline_extension import (
+    PipelineExtension,
+)
+from cg.services.analysis_starter.configurator.file_creators.gene_panel import GenePanelFileCreator
+
+
+class NalloExtension(PipelineExtension):
+    def __init__(self, gene_panel_file_creator: GenePanelFileCreator):
+        self.gene_panel_file_creator = gene_panel_file_creator
+
+    def configure(self, case_id: str, case_run_directory: Path) -> None:
+        self.gene_panel_file_creator.create(
+            case_id=case_id,
+            file_path=self._get_gene_panel_file_path(case_run_directory),
+            double_hashtag_filtering=True,
+        )
+
+    def do_required_files_exist(self, case_run_directory: Path) -> bool:
+        gene_panel_file_path: Path = self._get_gene_panel_file_path(case_run_directory)
+        return gene_panel_file_path.is_file()
+
+    @staticmethod
+    def _get_gene_panel_file_path(case_run_directory: Path) -> Path:
+        return case_run_directory.joinpath(ScoutExportFileName.PANELS_TSV)

cg/services/analysis_starter/configurator/extensions/{abstract.py → pipeline_extension.py}

@@ -7,5 +7,5 @@ class PipelineExtension:
         can be used."""
         pass
 
-    def do_required_files_exist(self, **kwargs) -> bool:
+    def do_required_files_exist(self, case_run_directory: Path) -> bool:
         return True

cg/services/analysis_starter/configurator/extensions/raredisease.py

@@ -1,7 +1,9 @@
 from os.path import isfile
 from pathlib import Path
 
-from cg.services.analysis_starter.configurator.extensions.abstract import PipelineExtension
+from cg.services.analysis_starter.configurator.extensions.pipeline_extension import (
+    PipelineExtension,
+)
 from cg.services.analysis_starter.configurator.file_creators.gene_panel import GenePanelFileCreator
 from cg.services.analysis_starter.configurator.file_creators.managed_variants import (
     ManagedVariantsFileCreator,

cg/services/analysis_starter/configurator/extensions/tomte_extension.py

@@ -0,0 +1,28 @@
+from os.path import isfile
+from pathlib import Path
+
+from cg.constants.scout import ScoutExportFileName
+from cg.services.analysis_starter.configurator.extensions.pipeline_extension import (
+    PipelineExtension,
+)
+from cg.services.analysis_starter.configurator.file_creators.gene_panel import GenePanelFileCreator
+
+
+class TomteExtension(PipelineExtension):
+    def __init__(self, gene_panel_file_creator: GenePanelFileCreator):
+        self.gene_panel_file_creator = gene_panel_file_creator
+
+    def configure(self, case_id: str, case_run_directory: Path) -> None:
+        self.gene_panel_file_creator.create(
+            case_id=case_id,
+            file_path=self._get_gene_panel_file_path(case_run_directory),
+            double_hashtag_filtering=False,
+        )
+
+    def do_required_files_exist(self, case_run_directory: Path) -> bool:
+        gene_panel_file_path: Path = self._get_gene_panel_file_path(case_run_directory)
+        return isfile(gene_panel_file_path)
+
+    @staticmethod
+    def _get_gene_panel_file_path(case_run_directory: Path) -> Path:
+        return case_run_directory.joinpath(ScoutExportFileName.PANELS)