From f2a06be181683dfa5a32c93f5831cbb6bd42698d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 23 Jan 2025 16:23:27 +0100 Subject: [PATCH 1/6] fix typo (#4151) | patch ### Fixed - Typo in paths for raredisease --- .../raredisease_bundle_filenames.yaml | 50 +++++++++---------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/cg/resources/raredisease_bundle_filenames.yaml b/cg/resources/raredisease_bundle_filenames.yaml index 971d5f6d31..21ca8587c4 100644 --- a/cg/resources/raredisease_bundle_filenames.yaml +++ b/cg/resources/raredisease_bundle_filenames.yaml @@ -798,151 +798,151 @@ tag: regions - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_1.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_1.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_2.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_2.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_3.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_3.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_4.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_4.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_5.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_5.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_6.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_6.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_7.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_7.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_8.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_8.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_9.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_9.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_10.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_10.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_11.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_11.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_12.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_12.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_13.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_13.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_14.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_14.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_15.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_15.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_16.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_16.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_17.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_17.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_18.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_18.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_19.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_19.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_20.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_20.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_21.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_21.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_22.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_22.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_X.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_X.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_Y.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_Y.png path_index: ~ step: chromograph_upd tag: sites - format: png id: SAMPLEID - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_M.png + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_M.png path_index: ~ step: chromograph_upd tag: sites From 8cec5df47e9e3f73dbae520e5b25a1652e4637c7 Mon Sep 17 00:00:00 2001 From: Clinical Genomics Bot Date: Thu, 23 Jan 2025 15:23:56 +0000 Subject: [PATCH 2/6] =?UTF-8?q?Bump=20version:=2067.0.2=20=E2=86=92=2067.0?= =?UTF-8?q?.3=20[skip=20ci]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- cg/__init__.py | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 5eb49ea1a6..de1944f325 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 67.0.2 +current_version = 67.0.3 commit = True tag = True tag_name = v{new_version} diff --git a/cg/__init__.py b/cg/__init__.py index 2d7cf32248..91a7e716b8 100644 --- a/cg/__init__.py +++ b/cg/__init__.py @@ -1,2 +1,2 @@ __title__ = "cg" -__version__ = "67.0.2" +__version__ = "67.0.3" diff --git a/pyproject.toml b/pyproject.toml index 77db412be4..014eabf8c2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [project] name = "cg" -version = "67.0.2" +version = "67.0.3" description = "Clinical Genomics command center" readme = {file = "README.md", content-type = "text/markdown"} homepage = "https://github.com/Clinical-Genomics/cg" From ad7320200e46227ce5bfe4a351e809bdc1849521 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Isak=20Ohlsson=20=C3=85ngnell?= <40887124+islean@users.noreply.github.com> Date: Mon, 27 Jan 2025 09:42:45 +0100 Subject: [PATCH 3/6] Fix order messages (#4147) (patch) ### Fixed - New lines for every sample - Use sample priority name to avoid ints --- cg/services/orders/submitter/ticket_handler.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cg/services/orders/submitter/ticket_handler.py b/cg/services/orders/submitter/ticket_handler.py index 54ff979156..d6907a41da 100644 --- a/cg/services/orders/submitter/ticket_handler.py +++ b/cg/services/orders/submitter/ticket_handler.py @@ -119,14 +119,12 @@ def add_sample_case_name_to_message(message: str, case_name: str | None) -> str: def add_existing_sample_info_to_message( self, message: str, customer_id: str, internal_id: str, case_name: str ) -> str: - existing_sample: Sample = self.status_db.get_sample_by_internal_id(internal_id=internal_id) sample_customer = "" if existing_sample.customer_id != customer_id: sample_customer = " from " + existing_sample.customer.internal_id - - message += f"{existing_sample.name}, application: {existing_sample.application_version.application.tag}, case: {case_name} (already existing sample{sample_customer}), priority: {existing_sample.priority}" + message += f"{existing_sample.name}, application: {existing_sample.application_version.application.tag}, case: {case_name} (already existing sample{sample_customer}), priority: {existing_sample.priority.name.lower()}" return message @staticmethod @@ -180,6 +178,7 @@ def create_case_xml_sample_list(self, order, message: str) -> str: if not case.is_new: db_case = self.status_db.get_case_by_internal_id(case.internal_id) for sample in db_case.samples: + message += self.NEW_LINE message = self.add_existing_sample_info_to_message( message=message, customer_id=sample.customer.internal_id, @@ -189,6 +188,7 @@ def create_case_xml_sample_list(self, order, message: str) -> str: else: for sample in case.samples: if not sample.is_new: + message += self.NEW_LINE message = self.add_existing_sample_info_to_message( message=message, customer_id=order.customer, From 9d76931876b0c17dcb25a25d742fe471db0efc8b Mon Sep 17 00:00:00 2001 From: Clinical Genomics Bot Date: Mon, 27 Jan 2025 08:43:14 +0000 Subject: [PATCH 4/6] =?UTF-8?q?Bump=20version:=2067.0.3=20=E2=86=92=2067.0?= =?UTF-8?q?.4=20[skip=20ci]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- cg/__init__.py | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index de1944f325..c983d93f94 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 67.0.3 +current_version = 67.0.4 commit = True tag = True tag_name = v{new_version} diff --git a/cg/__init__.py b/cg/__init__.py index 91a7e716b8..a0b124633f 100644 --- a/cg/__init__.py +++ b/cg/__init__.py @@ -1,2 +1,2 @@ __title__ = "cg" -__version__ = "67.0.3" +__version__ = "67.0.4" diff --git a/pyproject.toml b/pyproject.toml index 014eabf8c2..8928a9771f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [project] name = "cg" -version = "67.0.3" +version = "67.0.4" description = "Clinical Genomics command center" readme = {file = "README.md", content-type = "text/markdown"} homepage = "https://github.com/Clinical-Genomics/cg" From 0eb937400c3c64abbdcc8c3d68396406d0fbfc4a Mon Sep 17 00:00:00 2001 From: Sebastian Diaz Date: Mon, 27 Jan 2025 09:57:45 +0100 Subject: [PATCH 5/6] Fix tests from improve order flow (#4152)(patch) Fix some tests set to fail in the main branch and adds a test for the case when skipping reception control is set to true. --- .../lims_service/test_order_lims_service.py | 101 ++++++++++-------- 1 file changed, 57 insertions(+), 44 deletions(-) diff --git a/tests/services/orders/lims_service/test_order_lims_service.py b/tests/services/orders/lims_service/test_order_lims_service.py index af30e418f4..70765098b1 100644 --- a/tests/services/orders/lims_service/test_order_lims_service.py +++ b/tests/services/orders/lims_service/test_order_lims_service.py @@ -1,5 +1,3 @@ -import pytest - from cg.constants import Workflow from cg.models.lims.sample import LimsSample from cg.services.orders.lims_service.service import OrderLimsService @@ -12,17 +10,17 @@ from cg.services.orders.validation.workflows.rml.models.order import RmlOrder -def test_to_lims_mip(mip_dna_order_to_submit): +def test_to_lims_mip(mip_dna_order: MipDnaOrder): # GIVEN a scout order for a trio - order_data = MipDnaOrder.model_validate(mip_dna_order_to_submit) + # WHEN parsing the order to format for LIMS import - new_samples = [sample for _, _, sample in order_data.enumerated_new_samples] + new_samples = [sample for _, _, sample in mip_dna_order.enumerated_new_samples] samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="cust003", samples=new_samples, workflow=Workflow.MIP_DNA, - delivery_type=order_data.delivery_type, - skip_reception_control=order_data.skip_reception_control, + delivery_type=mip_dna_order.delivery_type, + skip_reception_control=mip_dna_order.skip_reception_control, ) # THEN it should list all samples @@ -35,7 +33,7 @@ def test_to_lims_mip(mip_dna_order_to_submit): container_names = {sample.container_name for sample in samples if sample.container_name} assert container_names == {"MipPlate"} - # ... and pick out relevant UDFs + # THEN it should pick out relevant UDFs first_sample: LimsSample = samples[0] assert first_sample.well_position == "A:1" assert first_sample.udfs.priority == "standard" @@ -48,40 +46,39 @@ def test_to_lims_mip(mip_dna_order_to_submit): assert isinstance(samples[1].udfs.comment, str) -def test_to_lims_fastq(fastq_order_to_submit): +def test_to_lims_fastq(fastq_order: FastqOrder): # GIVEN a fastq order for two samples; normal vs. tumour - order_data = FastqOrder.model_validate(fastq_order_to_submit) # WHEN parsing the order to format for LIMS samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="dummyCust", - samples=order_data.samples, + samples=fastq_order.samples, workflow=Workflow.RAW_DATA, - delivery_type=order_data.delivery_type, - skip_reception_control=order_data.skip_reception_control, + delivery_type=fastq_order.delivery_type, + skip_reception_control=fastq_order.skip_reception_control, ) - # THEN should "work" + # THEN two samples should be parsed, one normal and one tumour assert len(samples) == 2 normal_sample = samples[0] tumour_sample = samples[1] - # ... and pick out relevant UDF values + + # THEN it should pick out relevant UDFs assert normal_sample.udfs.tumour is False assert tumour_sample.udfs.tumour is True assert normal_sample.udfs.volume == "54" -@pytest.mark.xfail(reason="RML sample container validation not working") -def test_to_lims_rml(rml_order_to_submit: dict): +def test_to_lims_rml(rml_order: RmlOrder): # GIVEN a rml order for four samples - order_data = RmlOrder.model_validate(rml_order_to_submit) # WHEN parsing for LIMS samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="cust000", - samples=order_data.samples, + samples=rml_order.samples, workflow=Workflow.RAW_DATA, - delivery_type=order_data.delivery_type, + delivery_type=rml_order.delivery_type, + skip_reception_control=rml_order.skip_reception_control, ) # THEN it should have found the same number of samples @@ -97,17 +94,16 @@ def test_to_lims_rml(rml_order_to_submit: dict): assert first_sample.udfs.well_position_rml == "A:1" -@pytest.mark.xfail(reason="Fluffy sample container validation not working") -def test_to_lims_fluffy(fluffy_order_to_submit: dict): +def test_to_lims_fluffy(fluffy_order: FluffyOrder): # GIVEN a Fluffy order for four samples - order_data = FluffyOrder.model_validate(fluffy_order_to_submit) # WHEN parsing for LIMS samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="cust000", - samples=order_data.samples, + samples=fluffy_order.samples, workflow=Workflow.FLUFFY, - delivery_type=order_data.delivery_type, + delivery_type=fluffy_order.delivery_type, + skip_reception_control=fluffy_order.skip_reception_control, ) # THEN it should have found the same number of samples @@ -123,22 +119,22 @@ def test_to_lims_fluffy(fluffy_order_to_submit: dict): assert first_sample.udfs.well_position_rml == "A:1" -def test_to_lims_microbial(microbial_order_to_submit: dict): +def test_to_lims_microbial(microsalt_order: MicrosaltOrder): # GIVEN a microbial order for three samples - order_data = MicrosaltOrder.model_validate(microbial_order_to_submit) # WHEN parsing for LIMS samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="cust000", - samples=order_data.samples, + samples=microsalt_order.samples, workflow=Workflow.MICROSALT, - delivery_type=order_data.delivery_type, - skip_reception_control=order_data.skip_reception_control, + delivery_type=microsalt_order.delivery_type, + skip_reception_control=microsalt_order.skip_reception_control, ) - # THEN it should "work" + # THEN 5 samples should be parsed assert len(samples) == 5 - # ... and pick out relevant UDFs + + # THEN it should pick out relevant UDFs first_sample = samples[0].dict() assert first_sample["udfs"]["priority"] == "research" assert first_sample["udfs"]["organism"] == "C. jejuni" @@ -161,7 +157,8 @@ def test_to_lims_sarscov2(mutant_order: MutantOrder): # THEN it should have found the same number of samples assert len(samples) == 6 - # ... and pick out relevant UDFs + + # THEN it should pick out relevant UDFs first_sample = samples[0].dict() assert first_sample["udfs"]["collection_date"] == "2021-05-05" assert first_sample["udfs"]["extraction_method"] == "MagNaPure 96" @@ -178,27 +175,26 @@ def test_to_lims_sarscov2(mutant_order: MutantOrder): assert first_sample["udfs"]["volume"] == "20" -def test_to_lims_balsamic(balsamic_order_to_submit: dict): +def test_to_lims_balsamic(balsamic_order: BalsamicOrder): # GIVEN a cancer order for a sample - order_data = BalsamicOrder.model_validate(balsamic_order_to_submit) - new_samples = [sample for _, _, sample in order_data.enumerated_new_samples] + new_samples = [sample for _, _, sample in balsamic_order.enumerated_new_samples] # WHEN parsing the order to format for LIMS import samples: list[LimsSample] = OrderLimsService._build_lims_sample( customer="cust000", samples=new_samples, workflow=Workflow.BALSAMIC, - delivery_type=order_data.delivery_type, - skip_reception_control=order_data.skip_reception_control, + delivery_type=balsamic_order.delivery_type, + skip_reception_control=balsamic_order.skip_reception_control, ) - # THEN it should list all samples + # THEN it should list all samples assert len(samples) == 1 - # ... and determine the container, container name, and well position + # THEN it should determine the container, container name, and well position container_names = {sample.container_name for sample in samples if sample.container_name} - # ... and pick out relevant UDFs + # THEN it should pick out relevant UDFs first_sample = samples[0].dict() assert first_sample["name"] == "BalsamicSample" assert {sample.container for sample in samples} == set(["96 well plate"]) @@ -209,15 +205,32 @@ def test_to_lims_balsamic(balsamic_order_to_submit: dict): assert first_sample["udfs"]["source"] == "cytology (FFPE)" assert first_sample["udfs"]["volume"] == "42" assert first_sample["udfs"]["priority"] == "standard" - assert container_names == set(["BalsamicPlate"]) assert first_sample["well_position"] == "A:1" assert first_sample["udfs"]["tumour"] is True assert first_sample["udfs"]["capture_kit"] == "GMCKsolid" assert first_sample["udfs"]["tumour_purity"] == "13" - assert first_sample["udfs"]["formalin_fixation_time"] == "15" assert first_sample["udfs"]["post_formalin_fixation_time"] == "3" assert first_sample["udfs"]["tissue_block_size"] == "large" - assert first_sample["udfs"]["comment"] == "This is a sample comment" + + +def test_order_with_skip_reception_control(balsamic_order: BalsamicOrder): + """Test that an order set to skip reception control can be parsed correctly by LIMS.""" + # GIVEN a Balsamic order with one case and one sample set to skip reception control + balsamic_order.skip_reception_control = True + + # WHEN parsing the order to format for LIMS import + new_samples = [sample for _, _, sample in balsamic_order.enumerated_new_samples] + samples: list[LimsSample] = OrderLimsService._build_lims_sample( + customer="cust000", + samples=new_samples, + workflow=Workflow.BALSAMIC, + delivery_type=balsamic_order.delivery_type, + skip_reception_control=balsamic_order.skip_reception_control, + ) + + # THEN the parsed samples should have the skip reception control flag set + first_sample = samples[0].dict() + assert first_sample["udfs"]["skip_reception_control"] is True From e7621a7ca6c2ac34bbcb3d83d72276ab4c1e6b54 Mon Sep 17 00:00:00 2001 From: Clinical Genomics Bot Date: Mon, 27 Jan 2025 08:58:19 +0000 Subject: [PATCH 6/6] =?UTF-8?q?Bump=20version:=2067.0.4=20=E2=86=92=2067.0?= =?UTF-8?q?.5=20[skip=20ci]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- cg/__init__.py | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index c983d93f94..2871b01f7c 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 67.0.4 +current_version = 67.0.5 commit = True tag = True tag_name = v{new_version} diff --git a/cg/__init__.py b/cg/__init__.py index a0b124633f..fec30ebd0b 100644 --- a/cg/__init__.py +++ b/cg/__init__.py @@ -1,2 +1,2 @@ __title__ = "cg" -__version__ = "67.0.4" +__version__ = "67.0.5" diff --git a/pyproject.toml b/pyproject.toml index 8928a9771f..ab380588b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [project] name = "cg" -version = "67.0.4" +version = "67.0.5" description = "Clinical Genomics command center" readme = {file = "README.md", content-type = "text/markdown"} homepage = "https://github.com/Clinical-Genomics/cg"