Merge pull request #48 from sanger/develop

Develop to master

.release-version

@@ -1 +1 @@
-0.2.0
+0.3.0

schemas/create-labware/1-create-labware.avsc

@@ -109,6 +109,43 @@
                   {
                     "name": "accessionNumber", "type": "string",
                     "doc": "Accession number for publication in ENA/EBI"
+                  },
+                  {
+                    "name": "shearedFemtoFragmentSize", "type": "string",
+                    "doc": "Sheared Femto Fragment Size (bp)"
+                  },
+                  {
+                    "name": "postSPRIConcentration", "type": "string",
+                    "doc": "Post SPRI Concentration (ng/ul)"
+                  },
+                  {
+                    "name": "postSPRIVolume", "type": "string",
+                    "doc": "Post SPRI Volume (ul)"
+                  },
+                  {
+                    "name": "finalNanoDrop280", "type": "string",
+                    "doc": "Final NanoDrop 260/280"
+                  },
+                  {
+                    "name": "finalNanoDrop230", "type": "string",
+                    "doc": "Final NanoDrop 260/230"
+                  },
+                  {
+                    "name": "finalNanoDrop", "type": "string",
+                    "doc": "Final NanoDrop ng/ul"
+                  },
+                  {
+                    "name": "shearingAndQCComments", "type": "string",
+                    "doc": "Shearing & QC comments"
+                  },
+                  {
+                    "name": "dateSubmittedUTC",
+                    "doc": "Date submitted in UTC format.",
+                    "type": { "type": "long", "logicalType": "timestamp-millis" }
+                  },
+                  {
+                    "name": "priorityLevel", "type": "string",
+                    "doc": "Priority level (if High or Medium)"
                   }
                 ]
               }

tests/conftest.py

@@ -1,16 +1,15 @@
-import pytest
 import logging
 import logging.config
-from tol_lab_share.helpers import get_config
-from lab_share_lib.processing.rabbit_message import RabbitMessage
-from lab_share_lib.constants import (
-    RABBITMQ_HEADER_KEY_SUBJECT,
-    RABBITMQ_HEADER_KEY_VERSION,
-)
 from datetime import datetime
+from unittest.mock import MagicMock
+
+import pytest
 from data.examples_create_labware_messages import TEST_CREATE_LABWARE_MSG_OBJECT, TEST_INVALID_CREATE_LABWARE_MSG_OBJECT
+from lab_share_lib.constants import RABBITMQ_HEADER_KEY_SUBJECT, RABBITMQ_HEADER_KEY_VERSION
+from lab_share_lib.processing.rabbit_message import RabbitMessage
 
-from unittest.mock import MagicMock
+from tol_lab_share.helpers import get_config
+from tol_lab_share.messages.output_feedback_message import OutputFeedbackMessage
 
 CONFIG = get_config("tol_lab_share.config.test")
 logging.config.dictConfig(CONFIG.LOGGING)
@@ -78,6 +77,28 @@ def traction_success_creation_response():
     }
 
 
+@pytest.fixture()
+def traction_qc_success_response():
+    return {
+        "data": {
+            "id": "10",
+            "type": "qc_receptions",
+            "links": {"self": "http://localhost:3000/v1/qc_receptions/10"},
+            "attributes": {"source": "tol-lab-share.tol"},
+        }
+    }
+
+
+@pytest.fixture()
+def valid_feedback_message():
+    instance = OutputFeedbackMessage()
+    instance.count_of_total_samples = 0
+    instance.count_of_valid_samples = 0
+    instance.source_message_uuid = b"b01aa0ad-7b19-4f94-87e9-70d74fb8783c"
+    instance.operation_was_error_free = True
+    return instance
+
+
 @pytest.fixture
 def taxonomy_record():
     return {
@@ -119,6 +140,15 @@ def valid_sample():
         "accessionNumber": "EE1234",
         "sampleCollectionDateUtc": datetime.now(),
         "costCode": "S1234",
+        "shearedFemtoFragmentSize": "8",
+        "postSPRIConcentration": "9",
+        "postSPRIVolume": "10",
+        "finalNanoDrop280": "200",
+        "finalNanoDrop230": "200",
+        "finalNanoDrop": "150",
+        "shearingAndQCComments": "",
+        "dateSubmittedUTC": datetime.now(),
+        "priorityLevel": "Medium",
     }
 
 
@@ -142,6 +172,15 @@ def invalid_sample():
         "accessionNumber": "EE1234",
         "costCode": 1234,
         "sampleCollectionDateUtc": datetime.now(),
+        "shearedFemtoFragmentSize": "8",
+        "postSPRIConcentration": "9",
+        "postSPRIVolume": "10",
+        "finalNanoDrop280": 200,
+        "finalNanoDrop230": 200,
+        "finalNanoDrop": "150",
+        "shearingAndQCComments": "",
+        "dateSubmittedUTC": datetime.now(),
+        "priorityLevel": "Medium",
     }
 
 

tests/data/examples_create_labware_messages.py

@@ -1,5 +1,5 @@
 from datetime import datetime
-from typing import Dict, Any
+from typing import Any, Dict
 
 TEST_CREATE_LABWARE_MSG_OBJECT: Dict[str, Any] = {
     "messageUuid": "b01aa0ad-7b19-4f94-87e9-70d74fb8783c".encode(),
@@ -26,6 +26,15 @@
                 "accessionNumber": "EE3383",
                 "sampleCollectionDateUtc": datetime.now(),
                 "costCode": "S1234",
+                "shearedFemtoFragmentSize": "5",
+                "postSPRIConcentration": "10",
+                "postSPRIVolume": "20",
+                "finalNanoDrop280": "5",
+                "finalNanoDrop230": "6",
+                "finalNanoDrop": "7",
+                "shearingAndQCComments": "Comments",
+                "dateSubmittedUTC": datetime.now(),
+                "priorityLevel": "Medium",
             },
             {
                 "sampleUuid": "dd490ee5-fd1d-456d-99fd-eb9d3861e0f7".encode(),
@@ -45,6 +54,15 @@
                 "accessionNumber": "EE3383",
                 "sampleCollectionDateUtc": datetime.now(),
                 "costCode": "S1234",
+                "shearedFemtoFragmentSize": "5",
+                "postSPRIConcentration": "10",
+                "postSPRIVolume": "20",
+                "finalNanoDrop280": "5",
+                "finalNanoDrop230": "6",
+                "finalNanoDrop": "7",
+                "shearingAndQCComments": "Comments",
+                "dateSubmittedUTC": datetime.now(),
+                "priorityLevel": "Medium",
             },
         ],
     },
@@ -76,6 +94,15 @@
                 "accessionNumber": "EE3383",
                 "sampleCollectionDateUtc": datetime.now(),
                 "costCode": "S1234",
+                "shearedFemtoFragmentSize": "5",
+                "postSPRIConcentration": "10",
+                "postSPRIVolume": "20",
+                "finalNanoDrop280": "5",
+                "finalNanoDrop230": "6",
+                "finalNanoDrop": 7,
+                "shearingAndQCComments": "Comments",
+                "dateSubmittedUTC": datetime.now(),
+                "priorityLevel": "Medium",
             },
             {
                 "sampleUuid": "dd490ee5-fd1d-456d-99fd-eb9d3861e0f7".encode(),
@@ -95,6 +122,15 @@
                 "accessionNumber": "EE3383",
                 "sampleCollectionDateUtc": datetime.now(),
                 "costCode": "S1234",
+                "shearedFemtoFragmentSize": "5",
+                "postSPRIConcentration": "10",
+                "postSPRIVolume": 20,
+                "finalNanoDrop280": "5",
+                "finalNanoDrop230": "6",
+                "finalNanoDrop": "7",
+                "shearingAndQCComments": "Comments",
+                "dateSubmittedUTC": datetime.now(),
+                "priorityLevel": "Medium",
             },
         ],
     },

tests/message_properties/definitions/test_country_of_origin.py

@@ -23,6 +23,6 @@ def test_CountryOfOrigin_check_CountryOfOrigin_is_valid():
     assert instance.validate() is False
     assert len(instance.errors) > 0
 
-    instance = CountryOfOrigin(Input("United Kingdom"))
+    instance = CountryOfOrigin(Input("UNITED KINGDOM"))
     assert instance.validate() is True
     assert len(instance.errors) == 0

tests/message_properties/definitions/test_labware.py

@@ -1,7 +1,8 @@
+from tol_lab_share.message_properties.definitions.input import Input
 from tol_lab_share.message_properties.definitions.labware import Labware
 from tol_lab_share.message_properties.definitions.location import Location
-from tol_lab_share.message_properties.definitions.input import Input
 from tol_lab_share.messages.output_traction_message import OutputTractionMessage
+from tol_lab_share.messages.traction_qc_message import TractionQcMessage
 
 
 def test_labware_is_valid():
@@ -114,7 +115,9 @@ def test_labware_add_to_traction_message_wells(valid_sample):
     instance.add_to_traction_message(traction_message)
 
     assert traction_message.requests(0).study_uuid == "dd490ee5-fd1d-456d-99fd-eb9d3861e014"
-    assert traction_message.requests(0).sample_name == "SamplePublicName1"
+    assert traction_message.requests(0).sample_name == "cichlid_pacbio8196429"
+    assert traction_message.requests(0).public_name == "SamplePublicName1"
+    assert traction_message.requests(0).sanger_sample_id == "cichlid_pacbio8196429"
     assert traction_message.requests(0).sample_uuid == "dd490ee5-fd1d-456d-99fd-eb9d3861e0f6"
     assert traction_message.requests(0).library_type == "Library1"
     assert traction_message.requests(0).species == "Mus musculus"
@@ -137,7 +140,9 @@ def test_labware_add_to_traction_message_tubes(valid_sample):
     instance.add_to_traction_message(traction_message)
 
     assert traction_message.requests(0).study_uuid == "dd490ee5-fd1d-456d-99fd-eb9d3861e014"
-    assert traction_message.requests(0).sample_name == "SamplePublicName1"
+    assert traction_message.requests(0).sample_name == "cichlid_pacbio8196429"
+    assert traction_message.requests(0).sanger_sample_id == "cichlid_pacbio8196429"
+    assert traction_message.requests(0).public_name == "SamplePublicName1"
     assert traction_message.requests(0).sample_uuid == "dd490ee5-fd1d-456d-99fd-eb9d3861e0f6"
     assert traction_message.requests(0).library_type == "Library1"
     assert traction_message.requests(0).species == "Mus musculus"
@@ -159,3 +164,30 @@ def test_labware_add_to_traction_message_uses_unpadded_location(valid_sample):
     traction_message = OutputTractionMessage()
     instance.add_to_traction_message(traction_message)
     assert traction_message.requests(0).container_location == "B1"
+
+
+def test_add_to_traction_qc_message(valid_sample):
+    data = {
+        "labwareType": "Plate12x8",
+        "labwareUuid": "dd490ee5-fd1d-456d-99fd-eb9d3861e0f9".encode(),
+        "barcode": "BARCODE001",
+        "samples": [valid_sample],
+    }
+    instance = Labware(Input(data))
+    assert instance.validate()
+
+    traction_message = OutputTractionMessage()
+    instance.add_to_traction_message(traction_message)
+
+    traction_qc_message = TractionQcMessage()
+    instance.add_to_traction_qc_message(traction_qc_message)
+
+    assert traction_qc_message.requests(0).supplier_sample_name == "SampleSupplied1"
+    assert traction_qc_message.requests(0).container_barcode == "BARCODE001"
+    assert traction_qc_message.requests(0).sheared_femto_fragment_size == "8"
+    assert traction_qc_message.requests(0).post_spri_concentration == "9"
+    assert traction_qc_message.requests(0).post_spri_volume == "10"
+    assert traction_qc_message.requests(0).final_nano_drop_280 == "200"
+    assert traction_qc_message.requests(0).final_nano_drop_230 == "200"
+    assert traction_qc_message.requests(0).final_nano_drop == "150"
+    assert traction_qc_message.requests(0).shearing_qc_comments == ""

tests/message_properties/definitions/test_sample.py

@@ -1,8 +1,8 @@
-from tol_lab_share.message_properties.definitions.sample import Sample
-from tol_lab_share.message_properties.definitions.labware_type import LabwareType
-from tol_lab_share.message_properties.definitions.labware import Labware
-from tol_lab_share.message_properties.definitions.input import Input
 from tol_lab_share import error_codes
+from tol_lab_share.message_properties.definitions.input import Input
+from tol_lab_share.message_properties.definitions.labware import Labware
+from tol_lab_share.message_properties.definitions.labware_type import LabwareType
+from tol_lab_share.message_properties.definitions.sample import Sample
 
 
 def build_sample(sample_data):
@@ -39,17 +39,18 @@ def test_sample_is_invalid(invalid_sample):
 
     instance = build_sample(invalid_sample)
     assert instance.validate() is False
+
     check_presence_error(instance.errors, error_codes.ERROR_1_UUID_NOT_BINARY, "study_uuid")
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "study_uuid")
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "common_name")
-    check_presence_error(instance.errors, error_codes.ERROR_20_INPUT_IS_NOT_VALID_FLOAT_STRING, "concentration")
-    check_presence_error(instance.errors, error_codes.ERROR_20_INPUT_IS_NOT_VALID_FLOAT_STRING, "volume")
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "country_of_origin")
     check_presence_error(instance.errors, error_codes.ERROR_4_NOT_VALID_COUNTRY_INSDC, "country_of_origin")
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "donor_id")
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "library_type")
     check_presence_error(instance.errors, error_codes.ERROR_7_INVALID_LOCATION, "location")
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "sanger_sample_id")
-    check_presence_error(instance.errors, error_codes.ERROR_9_INVALID_INPUT, "scientific_name")
+
     check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "cost_code")
+    check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "final_nano_drop_280")
+    check_presence_error(instance.errors, error_codes.ERROR_2_NOT_STRING, "final_nano_drop_230")
     assert len(instance.errors) == 13

tests/messages/test_input_create_labware_message.py

@@ -16,7 +16,7 @@ def test_input_create_labware_message_can_validate_when_valid(valid_create_labwa
 def test_input_create_labware_message_can_validate_when_invalid(invalid_create_labware_message):
     instance = InputCreateLabwareMessage(invalid_create_labware_message)
     assert instance.validate() is False
-    assert len(instance.errors) == 9
+    assert len(instance.errors) == 5
 
 
 def test_input_create_labware_message_can_add_to_feedback_message_if_invalid(invalid_create_labware_message):