Merge pull request #65 from sanger/dpl-952-remaining-fixes

DPL-952: Remaining Fixes
sanger · Feb 15, 2024 · 0c040f5 · 0c040f5
2 parents d7e226f + d6c81b1
commit 0c040f5
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Showing 7 changed files with 42 additions and 72 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -138,7 +138,7 @@ def valid_sample():
         "countryOfOrigin": "United Kingdom",
         "genomeSize": "14",
         "accessionNumber": "EE1234",
-        "sampleCollectionDateUtc": datetime.now(),
+        "sampleCollectionDateUtc": datetime.utcnow(),
         "costCode": "S1234",
         "shearedFemtoFragmentSize": "8",
         "postSPRIConcentration": "9",
@@ -147,7 +147,7 @@ def valid_sample():
         "finalNanoDrop230": "200",
         "finalNanoDrop": "150",
         "shearingAndQCComments": "",
-        "dateSubmittedUTC": datetime.now(),
+        "dateSubmittedUTC": datetime.utcnow(),
         "priorityLevel": "Medium",
     }
 
@@ -171,15 +171,15 @@ def invalid_sample():
         "genomeSize": "14",
         "accessionNumber": "EE1234",
         "costCode": 1234,
-        "sampleCollectionDateUtc": datetime.now(),
+        "sampleCollectionDateUtc": datetime.utcnow(),
         "shearedFemtoFragmentSize": "8",
         "postSPRIConcentration": "9",
         "postSPRIVolume": "10",
         "finalNanoDrop280": 200,
         "finalNanoDrop230": 200,
         "finalNanoDrop": "150",
         "shearingAndQCComments": "",
-        "dateSubmittedUTC": datetime.now(),
+        "dateSubmittedUTC": datetime.utcnow(),
         "priorityLevel": "Medium",
     }
 

diff --git a/tests/data/examples_create_labware_messages.py b/tests/data/examples_create_labware_messages.py
@@ -3,7 +3,7 @@
 
 TEST_CREATE_LABWARE_MSG_OBJECT: dict[str, Any] = {
     "messageUuid": "b01aa0ad-7b19-4f94-87e9-70d74fb8783c".encode(),
-    "messageCreateDateUtc": datetime.now(),
+    "messageCreateDateUtc": datetime.utcnow(),
     "labware": {
         "labwareType": "Plate12x8",
         "barcode": "BARCODE001",
@@ -24,7 +24,7 @@
                 "countryOfOrigin": "United Kingdom",
                 "genomeSize": "14",
                 "accessionNumber": "EE3383",
-                "sampleCollectionDateUtc": datetime.now(),
+                "sampleCollectionDateUtc": datetime.utcnow(),
                 "costCode": "S1234",
                 "shearedFemtoFragmentSize": "5",
                 "postSPRIConcentration": "10",
@@ -33,7 +33,7 @@
                 "finalNanoDrop230": "6",
                 "finalNanoDrop": "7",
                 "shearingAndQCComments": "Comments",
-                "dateSubmittedUTC": datetime.now(),
+                "dateSubmittedUTC": datetime.utcnow(),
                 "priorityLevel": "Medium",
             },
             {
@@ -52,7 +52,7 @@
                 "countryOfOrigin": "United Kingdom",
                 "genomeSize": "14",
                 "accessionNumber": "EE3383",
-                "sampleCollectionDateUtc": datetime.now(),
+                "sampleCollectionDateUtc": datetime.utcnow(),
                 "costCode": "S1234",
                 "shearedFemtoFragmentSize": "5",
                 "postSPRIConcentration": "10",
@@ -61,7 +61,7 @@
                 "finalNanoDrop230": "6",
                 "finalNanoDrop": "7",
                 "shearingAndQCComments": "Comments",
-                "dateSubmittedUTC": datetime.now(),
+                "dateSubmittedUTC": datetime.utcnow(),
                 "priorityLevel": "Medium",
             },
         ],
@@ -71,7 +71,7 @@
 
 TEST_INVALID_CREATE_LABWARE_MSG_OBJECT: dict[str, Any] = {
     "messageUuid": "b01aa0ad7b19-4f94-87e9-70d74fb8783c".encode(),
-    "messageCreateDateUtc": datetime.now(),
+    "messageCreateDateUtc": datetime.utcnow(),
     "labware": {
         "labwareType": "Plate12x8",
         "barcode": "BARCODE001",
@@ -92,7 +92,7 @@
                 "countryOfOrigin": "United Kingdom",
                 "genomeSize": "14",
                 "accessionNumber": "EE3383",
-                "sampleCollectionDateUtc": datetime.now(),
+                "sampleCollectionDateUtc": datetime.utcnow(),
                 "costCode": "S1234",
                 "shearedFemtoFragmentSize": "5",
                 "postSPRIConcentration": "10",
@@ -101,7 +101,7 @@
                 "finalNanoDrop230": "6",
                 "finalNanoDrop": 7,
                 "shearingAndQCComments": "Comments",
-                "dateSubmittedUTC": datetime.now(),
+                "dateSubmittedUTC": datetime.utcnow(),
                 "priorityLevel": "Medium",
             },
             {
@@ -120,7 +120,7 @@
                 "countryOfOrigin": "United Kingdom",
                 "genomeSize": "14",
                 "accessionNumber": "EE3383",
-                "sampleCollectionDateUtc": datetime.now(),
+                "sampleCollectionDateUtc": datetime.utcnow(),
                 "costCode": "S1234",
                 "shearedFemtoFragmentSize": "5",
                 "postSPRIConcentration": "10",
@@ -129,7 +129,7 @@
                 "finalNanoDrop230": "6",
                 "finalNanoDrop": "7",
                 "shearingAndQCComments": "Comments",
-                "dateSubmittedUTC": datetime.now(),
+                "dateSubmittedUTC": datetime.utcnow(),
                 "priorityLevel": "Medium",
             },
         ],

diff --git a/tests/message_properties/definitions/test_message_property.py b/tests/message_properties/definitions/test_message_property.py
@@ -134,7 +134,7 @@ def test_message_property_check_is_date_utc():
     instance = MessageProperty(Input(None))
     assert instance.check_is_date_utc() is False
 
-    instance = MessageProperty(Input(datetime.now()))
+    instance = MessageProperty(Input(datetime.utcnow()))
     assert instance.check_is_date_utc() is True
 
     instance = MessageProperty(Input({}))

diff --git a/tests/messages/test_output_traction_message.py b/tests/messages/test_output_traction_message.py
@@ -37,7 +37,7 @@ def test_output_traction_message_can_validate():
 
 
 def test_output_traction_message_can_generate_payload_for_plates():
-    my_date = datetime.now()
+    my_date = datetime.utcnow()
     instance = OutputTractionMessage()
 
     request = instance.create_request()
@@ -144,7 +144,7 @@ def test_output_traction_message_can_generate_payload_for_plates():
 
 
 def test_output_traction_message_can_generate_payload_for_multiple_plates():
-    my_date = datetime.now()
+    my_date = datetime.utcnow()
     instance = OutputTractionMessage()
 
     # Mix the order of the requests to ensure the grouping for plates works.
@@ -348,7 +348,7 @@ def test_output_traction_message_can_generate_payload_for_multiple_plates():
 
 
 def test_output_traction_message_can_generate_payload_for_ont_library_types():
-    my_date = datetime.now()
+    my_date = datetime.utcnow()
     instance = OutputTractionMessage()
 
     request = instance.create_request()
@@ -457,7 +457,7 @@ def test_output_traction_message_can_generate_payload_for_ont_library_types():
 
 
 def test_output_traction_message_can_generate_payload_for_tubes():
-    my_date = datetime.now()
+    my_date = datetime.utcnow()
     instance = OutputTractionMessage()
 
     request = instance.create_request()
@@ -558,7 +558,7 @@ def test_output_traction_message_can_generate_payload_for_tubes():
 
 
 def test_output_traction_message_can_generate_payload_for_mix_of_plate_and_tubes():
-    my_date = datetime.now()
+    my_date = datetime.utcnow()
     instance = OutputTractionMessage()
 
     request = instance.create_request()

diff --git a/tests/messages/test_traction_qc_message.py b/tests/messages/test_traction_qc_message.py
@@ -9,18 +9,9 @@
 logger = logging.getLogger(__name__)
 
 
-class FreezeDate(datetime):
-    @classmethod
-    def now(cls):
-        return cls(2023, 7, 11, 12, 29, 11, 564246)
-
-
-datetime = FreezeDate  # type: ignore
-
-
 class TestTractionQcMessage:
     @pytest.fixture()
-    def valid_traction_qc_message(self):
+    def valid_traction_qc_message(self, freezer):
         traction_qc_message = TractionQcMessage()
 
         request = traction_qc_message.create_request()
@@ -33,7 +24,7 @@ def valid_traction_qc_message(self):
         request.final_nano_drop_230 = "230"
         request.final_nano_drop = "200"
         request.shearing_qc_comments = "Comments"
-        request.date_submitted_utc = datetime.now().timestamp() * 1000
+        request.date_submitted_utc = datetime.utcnow().timestamp() * 1000
 
         request = traction_qc_message.create_request()
         request.sanger_sample_id = "sanger_sample_id_DDD2"
@@ -45,7 +36,7 @@ def valid_traction_qc_message(self):
         request.final_nano_drop_230 = "130"
         request.final_nano_drop = "100"
         request.shearing_qc_comments = ""
-        request.date_submitted_utc = datetime.now().timestamp() * 1000
+        request.date_submitted_utc = datetime.utcnow().timestamp() * 1000
 
         return traction_qc_message
 
@@ -66,7 +57,7 @@ def test_validate_traction_qc_message(self, valid_traction_qc_message, invalid_t
         assert not invalid_traction_qc_message.validate()
         assert valid_traction_qc_message.validate()
 
-    def test_can_generate_correct_payload(self, valid_traction_qc_message):
+    def test_can_generate_correct_payload(self, valid_traction_qc_message, freezer):
         payload = valid_traction_qc_message.payload()
 
         expected_payload = {
@@ -81,7 +72,7 @@ def test_can_generate_correct_payload(self, valid_traction_qc_message):
                             "post_spri_volume": "20",
                             "sheared_femto_fragment_size": "5",
                             "shearing_qc_comments": "Comments",
-                            "date_submitted": datetime.now().timestamp() * 1000,
+                            "date_submitted": datetime.utcnow().timestamp() * 1000,
                             "labware_barcode": "FD20706500",
                             "sample_external_id": "sanger_sample_id_DDD",
                         },
@@ -92,7 +83,7 @@ def test_can_generate_correct_payload(self, valid_traction_qc_message):
                             "post_spri_concentration": "10",
                             "post_spri_volume": "30",
                             "sheared_femto_fragment_size": "9",
-                            "date_submitted": datetime.now().timestamp() * 1000,
+                            "date_submitted": datetime.utcnow().timestamp() * 1000,
                             "labware_barcode": "FD20706501",
                             "sample_external_id": "sanger_sample_id_DDD2",
                         },

diff --git a/tol_lab_share/message_properties/definitions/labware_type.py b/tol_lab_share/message_properties/definitions/labware_type.py
@@ -1,3 +1,4 @@
+import string
 from .message_property import MessageProperty
 from tol_lab_share import error_codes
 import logging
@@ -31,39 +32,17 @@ def check_labware_type(self):
             self.trigger_error(error_codes.ERROR_6_LABWARE_TYPE, text=f"input: {self._input.value}")
         return result
 
-    def pad_number(self, number: int) -> str:
-        """Given a number, it generates a string of size 2 padded with zeros at the left representing
-        the same value. Eg: 3 would be converted to '03', while 12 would be converted to '12'.
-        Parameters:
-        number (int) value we want to convert
-        Returns:
-        str with the padded value
-        """
-        padded_number = str(number)
-        if len(padded_number) == 1:
-            padded_number = f"0{padded_number}"
-        return padded_number
-
-    def _locations_for_plate12x8_column_order(self) -> list[str]:
-        """It generates the list of all valid locations for a labware type following column
-        order. Eg: ['A01', 'B01', 'C01', .... 'H12']
-        Returns:
-        list[str] with al the valid locations
-        """
-        locations = []
-        for number in range(12):
-            for letter_ord in range(ord("A"), ord("H") + 1):
-                locations.append(f"{chr(letter_ord)}{self.pad_number(number+1)}")
-        return locations
-
     def valid_locations(self) -> list[str]:
-        """It returns the list of valid locations for the labware type. If the labware type is
-        a tube, it returns ane empty list. If it is a plate 12x8 it returns all locations in
-        column order.
+        """It returns the list of valid locations for the labware type.
+        If the labware type is a tube, it returns ane empty list.
+        If it is a plate 12x8 it returns all locations in column order. i.e. ['A01', 'B01', 'C01', .... 'H12']
+
         Returns:
-        list[str] with all the valid locations
+            list[str]: A list with all the valid locations.
         """
         if self.value == "Plate12x8":
-            return self._locations_for_plate12x8_column_order()
+            return [
+                f"{letter}{str(number).zfill(2)}" for number in range(1, 13) for letter in string.ascii_uppercase[:8]
+            ]
         else:
             return []
diff --git a/tools/demo/testing_data.py b/tools/demo/testing_data.py
@@ -20,7 +20,7 @@ def build_create_labware_96_msg(unique_id, num_msg):
     unique_id_lab = f"TOLTESTING-PLATE-{unique_id}-{num_msg}"
     return {
         "messageUuid": str(uuid4()).encode(),
-        "messageCreateDateUtc": datetime.now().timestamp() * 1000,
+        "messageCreateDateUtc": datetime.utcnow().timestamp() * 1000,
         "labware": {
             "labwareType": "Plate12x8",
             "barcode": barcode_for_unique_id("PLATE", unique_id, num_msg),
@@ -42,15 +42,15 @@ def build_create_labware_96_msg(unique_id, num_msg):
                     "genomeSize": "1",
                     "accessionNumber": "A1234",
                     "costCode": "S1234",
-                    "sampleCollectionDateUtc": datetime.now().timestamp() * 1000,
+                    "sampleCollectionDateUtc": datetime.utcnow().timestamp() * 1000,
                     "shearedFemtoFragmentSize": "5",
                     "postSPRIConcentration": "10",
                     "postSPRIVolume": "20",
                     "finalNanoDrop280": "5",
                     "finalNanoDrop230": "6",
                     "finalNanoDrop": "7",
                     "shearingAndQCComments": "Comments",
-                    "dateSubmittedUTC": datetime.now().timestamp() * 1000,
+                    "dateSubmittedUTC": datetime.utcnow().timestamp() * 1000,
                     "priorityLevel": "Medium",
                 }
                 for letter in range(ord("A"), ord("H") + 1)
@@ -64,7 +64,7 @@ def build_create_tube_msg(unique_id, num_msg):
     unique_id_lab = f"TOLTESTING-TUBE-{unique_id}-{num_msg}"
     return {
         "messageUuid": str(uuid4()).encode(),
-        "messageCreateDateUtc": datetime.now().timestamp() * 1000,
+        "messageCreateDateUtc": datetime.utcnow().timestamp() * 1000,
         "labware": {
             "labwareType": "Tube",
             "barcode": barcode_for_unique_id("TUBE", unique_id, num_msg),
@@ -86,15 +86,15 @@ def build_create_tube_msg(unique_id, num_msg):
                     "genomeSize": "1",
                     "accessionNumber": "A1234",
                     "costCode": "S1234",
-                    "sampleCollectionDateUtc": datetime.now().timestamp() * 1000,
+                    "sampleCollectionDateUtc": datetime.utcnow().timestamp() * 1000,
                     "shearedFemtoFragmentSize": "5",
                     "postSPRIConcentration": "10",
                     "postSPRIVolume": "20",
                     "finalNanoDrop280": "5",
                     "finalNanoDrop230": "6",
                     "finalNanoDrop": "7",
                     "shearingAndQCComments": "Comments",
-                    "dateSubmittedUTC": datetime.now().timestamp() * 1000,
+                    "dateSubmittedUTC": datetime.utcnow().timestamp() * 1000,
                     "priorityLevel": "Medium",
                 }
             ],
@@ -105,7 +105,7 @@ def build_create_tube_msg(unique_id, num_msg):
 def build_update_labware_msg(sample_msg):
     return {
         "messageUuid": str(uuid4()).encode(),
-        "messageCreateDateUtc": datetime.now().timestamp() * 1000,
+        "messageCreateDateUtc": datetime.utcnow().timestamp() * 1000,
         "sampleUpdates": [
             {
                 "sampleUuid": sample_msg["labware"]["samples"][3]["sampleUuid"],